diff --git a/.github/CODE_OF_CONDUCT.md b/.github/CODE_OF_CONDUCT.md deleted file mode 100644 index da272db..0000000 --- a/.github/CODE_OF_CONDUCT.md +++ /dev/null @@ -1,28 +0,0 @@ -## Code Of Conduct -Like the technical community as a whole, the Overture.bio team and community is made up of a mixture of professionals and volunteers from all over the world, working on every aspect of the mission - including mentorship, teaching, and connecting people. - -Diversity is one of our huge strengths, but it can also lead to communication issues and unhappiness. To that end, we have a few ground rules that we ask people to adhere to. This code applies equally to founders, mentors and those seeking help and guidance. - -This isn’t an exhaustive list of things that you can’t do. Rather, take it in the spirit in which it’s intended - a guide to make it easier to enrich all of us and the technical communities in which we participate. - -This code of conduct applies to all spaces managed by the Overture.bio team. This includes mailing lists, github issue tracker, Slack, and any other forums created by the project team which the community uses for communication. In addition, violations of this code outside these spaces may affect a person's ability to participate within them. - -If you believe someone is violating the code of conduct, we ask that you report it by emailing contact@overture.bio. - -- Be friendly and patient. -- Be welcoming. We strive to be a community that welcomes and supports people of all backgrounds and identities. This includes, but is not limited to members of any race, ethnicity, culture, national origin, colour, immigration status, social and economic class, educational level, sex, sexual orientation, gender identity and expression, age, size, family status, political belief, religion, and mental and physical ability. -- Be considerate. Your work will be used by other people, and you in turn will depend on the work of others. Any decision you take will affect users and colleagues, and you should take those consequences into account when making decisions. Remember that we're a world-wide community, so you might not be communicating in someone else's primary language. -- Be respectful. Not all of us will agree all the time, but disagreement is no excuse for poor behaviour and poor manners. We might all experience some frustration now and then, but we cannot allow that frustration to turn into a personal attack. It’s important to remember that a community where people feel uncomfortable or threatened is not a productive one. Members of the Django community should be respectful when dealing with other members as well as with people outside the Django community. -- Be careful in the words that you choose. We are a community of professionals, and we conduct ourselves professionally. Be kind to others. Do not insult or put down other participants. Harassment and other exclusionary behaviour aren't acceptable. This includes, but is not limited to: - - Violent threats or language directed against another person. - - Discriminatory jokes and language. - - Posting sexually explicit or violent material. - - Posting (or threatening to post) other people's personally identifying information ("doxing"). - - Personal insults, especially those using racist or sexist terms. - - Unwelcome sexual attention. - - Advocating for, or encouraging, any of the above behaviour. - - Repeated harassment of others. In general, if someone asks you to stop, then stop. -- When we disagree, try to understand why. Disagreements, both social and technical, happen all the time and Overture.bio is no exception. It is important that we resolve disagreements and differing views constructively. Remember that we’re different. The strength of Overture.bio comes from its varied community, people from a wide range of backgrounds. Different people have different perspectives on issues. Being unable to understand why someone holds a viewpoint doesn’t mean that they’re wrong. Don’t forget that it is human to err and blaming each other doesn’t get us anywhere. Instead, focus on helping to resolve issues and learning from mistakes. - -Original text courtesy of the [Speak Up! project](http://web.archive.org/web/20141109123859/http://speakup.io/coc.html). - diff --git a/.github/ISSUE_TEMPLATE/security.md b/.github/ISSUE_TEMPLATE/security.md deleted file mode 100644 index 237ea31..0000000 --- a/.github/ISSUE_TEMPLATE/security.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -name: Security Upgrade -about: Request a security upgrade for an application dependency. -title: "Security Upgrade" -labels: 'major' -assignees: 'rosibaj' - ---- -A needed scurity upgrade has been indiated: - - diff --git a/.github/ReadmeTemplate/Documentation-Style-Guide.md b/.github/ReadmeTemplate/Documentation-Style-Guide.md deleted file mode 100644 index ddc5149..0000000 --- a/.github/ReadmeTemplate/Documentation-Style-Guide.md +++ /dev/null @@ -1,172 +0,0 @@ -# :book: Documentation Guidelines - -**Estimated Reading Time:** 5 minutes - ---- - -Thanks for taking an interest in our documentation. This guide outlines principles and best practices for writing clear and consistent Overture documentation. See our contribution guide for information on how to submit changes. Join our slack channel if you have any unanswered questions, comments, or suggestions. We're here and happy to chat. - -## Audience - -Overture has two primary audiences: - -**Software Engineers**: They install, customize and configure Overture components within their software stack. - -**Bioinformaticians & Data Scientists**: They use Overtures CLI tools and GUIs to interact with the data. - -## Voice & Tone - -Our writing should consistently convey a friendly, informative and empathetic personality. - -We want to ensure that our documentation gets written in the right tone. Different contexts will necessitate different approaches. Tutorials typically require a more enthusiastic and instructive tone, while warnings require a more serious and pressing tone. To help know if your tone matches the content, ask yourself, "What is the reader likely feeling when presented with this content? Why are they here?" From your answer, adjust your language with the appropriate tone. - -## Language & Grammar - -Practice best judgment. These are non-prescriptive guidelines, and there will always be exceptions. - -### Language - -We use Canadian English (en-CA) as our standard language for all written and verbal communication. - -### Use an Active Voice - -The active voice is concise and more accessible for readers to comprehend. Active voice is naturally used in conversation and therefore, readers understand and engage more with writing in the active voice. - -| 👎 Disengaging| 👍 Engaging| -|---|---| -|The developer environment has been set up successfully.|We have successfully set up the developer environment.| -|The necessary tools and dependencies are being installed.|We are installing the necessary tools and dependencies.| - -### Put Conditional Clauses First - -Put conditional clauses up front in sentences. With conditional clauses upfront, readers can skim or skip information they do not require. If done consistently, this saves significant time reading irrelevant information. - -| 👎 Slow | 👍 Skimmable | -|---|---| -|See How to Use the Score Client for more information | For more information, see How to Use the Score Client.| -| Set the analysis state to published, this will enable the analysis to be indexed| To index the analysis, set the analysis state to published | - -### Write Accessibly - -Take note of how you describe software behaviours or user actions. Each reader will have a unique background and familiarity with the content, so avoid using language that assumes knowledge. - -| 👎 Sets expectations that can lead to frustration| 👍 No assumptions, made reader friendly| -|---|---| -|Start by *simply* entering the following command|Start by entering the following command| -|To *easily* interact with our API see the Song Swagger UI| To interact with our API see the Song Swagger UI| - -Whenever possible, also include descriptive links to prerequisite or contextual material. Our services benefit a variety of people and data; therefore, experience levels and fields of expertise can vary significantly from user to user. - -## Formatting & Punctuation - -### Markdown - -Documentation is written using GitHub-flavoured markdown within `.md` files. For information on basic syntax, see this [ cheatsheet](https://github.com/adam-p/markdown-here/wiki/Markdown-Cheatsheet) or for more in-depth information, check out the official [Github-flavored Markdown info page](https://docs.github.com/en/get-started/writing-on-github). - -If you draft `.md` files within VS code, we have found the following [Markdown Preview Github Styling](https://marketplace.visualstudio.com/items?itemName=bierner.markdown-preview-github-styles) extension helpful. - -### Using Code Blocks - -To wrap code within a code block, use ``` before and after the sample code. - -For example: - -``` -Here is a code block -``` - -When appropriate, include the language immediately following the first ``` - -Example(s): - -```bash -# this is a bash terminal -cd desktop -``` - -```json -// this is a JSON file - -{ - "name": "variant_calling", - "schema": { - "type": "object", - "required": [ - "experiment", - "donor_clinical_data" - ] - } -} -``` - -### Headers - -To appropriately capitalize words in a title or heading, follow these guidelines: - -- Capitalize the first word of a title or subtitle, even if it is a little word like "The" or "A." -- Capitalize the first word after a colon and dash (ex., "Self-Report" instead of "Self-report"). -- Capitalize words of four letters or more (e.g., "With," "Between," and "From"). -- Except for the above rules, lowercase minor words that are three letters or fewer in a title or subtitle. - -### Numbered lists vs bulleted points - -- **numbered lists** for sequential items -- **bulleted points** for all other lists - -### Commas - -Use an Oxford comma for a list of three or more items. - -| Can lead to confusion | Clearer separatation | -|---|---| -|I had eggs, toast and orange juice for breakfast.|I had eggs, toast, and orange juice for breakfast.| - -### UI/Navigation Elements - -When referencing UI elements, have them in **Bold** - -1. Click **Documentation** > **Get Started**. -2. Select **Pre-Configuration Setup**. - -## Organization - -### Modular Documentation - -With modular documentation, we organize our writing into modules, which writers combine into assemblies. Assemblies can include other assemblies. However, modules cannot contain other modules. - -Three types of modules exist: - -|Module|Description| -|---|---| -|Concept Module|A concept module is an "understand" module. Concept modules give the user descriptions and explanations needed to understand and use a product.| -|Procedure Module|Procedure modules explain how to do something. A procedure module contains numbered, step-by-step instructions to help the user accomplish a single task.| -|Reference Module|Reference modules provide data that users might want to look up but do not need to remember.| - -### User Stories - -We combine modules into assemblies that are based on user stories. User stories are specific use cases which a user coming to our documentation may be interested in fulfilling. Modular documentation allows us to reuse modules within various assemblies to fulfill multiple current and future user stories. - -Our team is continually documenting user stories. If you have a use case that still needs to be documented, feel free to contact us on our [slack channel](http://slack.overture.bio/) or send us an email at [contact@overture.bio]( - -For more information on modular documentation, see [Red Hats Modular Documentation Reference Guide](https://redhat-documentation.github.io/modular-docs/) - -### Headers - -Use level 1 headers at the top of the page and divide your document using the lower level headers for subsections. - -Try and use headers wisely, with too many headers it can make the document difficult to navigate. Too little can lead to a disordered page and reduces the readers' ability to scan the document. - -## Images & Diagrams - -Images and diagrams can be valuable, but they can take lots of time and require maintenance. When using images or diagrams, consider how beneficial the visualization will be and how frequently you need to update it. - -### Creating Diagrams - -We use Mermaid to create our diagrams. For more information, see the official [GitHub Docs on creating Mermaid diagrams](https://docs.github.com/en/get-started/writing-on-github/working-with-advanced-formatting/creating-diagrams). - - -## Attributions - -- Based off the [Pachyderm Documentation Style Guide](https://docs.pachyderm.com/latest/contributing/docs-style-guide/) - -- For information on Modular documentation, see [Red Hats Modular Documentation Reference Guide](https://redhat-documentation.github.io/modular-docs/) \ No newline at end of file diff --git a/.github/ReadmeTemplate/ReadmeTemplate.md b/.github/ReadmeTemplate/ReadmeTemplate.md deleted file mode 100644 index d62a27d..0000000 --- a/.github/ReadmeTemplate/ReadmeTemplate.md +++ /dev/null @@ -1,92 +0,0 @@ -# Name of component - Caveman description (Two to five keywords) - -[](http://slack.overture.bio) -[](https://github.com/overture-stack/ego/blob/develop/LICENSE) -[](code_of_conduct.md) - -
-component-logo -
- -*What is the problem. What does this component do to solve it. Are there any related components (JS client, UI, etc.) *~3-5 sentences* - - - - - - -
- -> ->
-> ->
-> -> *x is a core component within the [Overture](https://www.overture.bio/) research software ecosystem. Overture is a toolkit of modular software components made to build into scalable genomics data management systems. See our [related products](#related-products) for more information on what Overture can offer.* -> -> - - -Alternative - -> ->
-> ->
-> -> *X is part of [Overture](https://www.overture.bio/) an ecosystem of open source and modular software components made to build into scalable genomics data management systems. See our [related products](#related-products) for more information on what Overture can offer.

* -> -> - - - -****Info and logos should line up from view of Repo*** - -## Technical Specifications - -- Point form -- Linking where neccessary - -## Documentation - -***update link URLS*** - -- Developer documentation, including instructions for running x from source can be found in the [Wiki](https://github.com/overture-stack/score/wiki) :construction: -- For user documentation, including installation, configuration and usage guides, see the Overture websites [Score documentation page](https://www.overture.bio/documentation/score/) - -## Setting up the developer environment (Quick Start, Setup, etc.) - -Use ```code snippets``` when requried - -```bash -# Bash if applicable -``` - -## Support & Contributions - -- Filing an [issue](https://github.com/overture-stack/ego/issues) -- Making a [contribution](CONTRIBUTING.md) -- Connect with us on [Slack](http://slack.overture.bio) -- Add or Upvote a [feature request](https://github.com/overture-stack/ego/issues?q=is%3Aopen+is%3Aissue+label%3Anew-feature+sort%3Areactions-%2B1-desc) - -## Related Software - -
- Overture overview -
- -All our core microservices are included in the Overture **Data Management System** (DMS). Built from our core collection of microservices, the DMS offers turnkey installation, configuration, and deployment of Overture software. For more information on the DMS, read our [DMS documentation](https://www.overture.bio/documentation/dms/). - -See the links below for information on our other research software tools: - -
- -|Software|Description| -|---|---| -|[Ego](https://www.overture.bio/products/ego/)|An authorization and user management service| -|[Ego UI](https://www.overture.bio/products/ego-ui/)|A UI for managing Ego authentication and authorization services| -|[Score](https://www.overture.bio/products/score/)| Transfer data to and from any cloud-based storage system| -|[Song](https://www.overture.bio/products/song/)|Catalog and manage metadata associated to file data spread across cloud storage systems| -|[Maestro](https://www.overture.bio/products/maestro/)|Organizing your distributed data into a centralized Elasticsearch index| -|[Arranger](https://www.overture.bio/products/arranger/)|A search API with reusable UI components that build into configurable and functional data portals| -|[DMS-UI](https://github.com/overture-stack/dms-ui)|A simple web browser UI that integrates Ego and Arranger| diff --git a/CODEOWNERS.txt b/CODEOWNERS.txt new file mode 100644 index 0000000..a558ae9 --- /dev/null +++ b/CODEOWNERS.txt @@ -0,0 +1,81 @@ +# If we choose to use the codeowners functionality update the file as a .md then uncomment and update the following: + + + + + \ No newline at end of file diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md index bf374a1..b98ba47 100644 --- a/CODE_OF_CONDUCT.md +++ b/CODE_OF_CONDUCT.md @@ -1,28 +1,132 @@ -## Code Of Conduct -Like the technical community as a whole, the Overture.bio team and community is made up of a mixture of professionals and volunteers from all over the world, working on every aspect of the mission - including mentorship, teaching, and connecting people. - -Diversity is one of our huge strengths, but it can also lead to communication issues and unhappiness. To that end, we have a few ground rules that we ask people to adhere to. This code applies equally to founders, mentors and those seeking help and guidance. - -This isn’t an exhaustive list of things that you can’t do. Rather, take it in the spirit in which it’s intended - a guide to make it easier to enrich all of us and the technical communities in which we participate. - -This code of conduct applies to all spaces managed by the Overture.bio team. This includes mailing lists, github issue tracker, Slack, and any other forums created by the project team which the community uses for communication. In addition, violations of this code outside these spaces may affect a person's ability to participate within them. - -If you believe someone is violating the code of conduct, we ask that you report it by emailing contact@overture.bio. - -- Be friendly and patient. -- Be welcoming. We strive to be a community that welcomes and supports people of all backgrounds and identities. This includes, but is not limited to members of any race, ethnicity, culture, national origin, colour, immigration status, social and economic class, educational level, sex, sexual orientation, gender identity and expression, age, size, family status, political belief, religion, and mental and physical ability. -- Be considerate. Your work will be used by other people, and you in turn will depend on the work of others. Any decision you take will affect users and colleagues, and you should take those consequences into account when making decisions. Remember that we're a world-wide community, so you might not be communicating in someone else's primary language. -- Be respectful. Not all of us will agree all the time, but disagreement is no excuse for poor behaviour and poor manners. We might all experience some frustration now and then, but we cannot allow that frustration to turn into a personal attack. It’s important to remember that a community where people feel uncomfortable or threatened is not a productive one. Members of the Overture community should be respectful when dealing with other members as well as with people outside the Overture community. -- Be careful in the words that you choose. We are a community of professionals, and we conduct ourselves professionally. Be kind to others. Do not insult or put down other participants. Harassment and other exclusionary behaviour aren't acceptable. This includes, but is not limited to: - - Violent threats or language directed against another person. - - Discriminatory jokes and language. - - Posting sexually explicit or violent material. - - Posting (or threatening to post) other people's personally identifying information ("doxing"). - - Personal insults, especially those using racist or sexist terms. - - Unwelcome sexual attention. - - Advocating for, or encouraging, any of the above behaviour. - - Repeated harassment of others. In general, if someone asks you to stop, then stop. -- When we disagree, try to understand why. Disagreements, both social and technical, happen all the time and Overture.bio is no exception. It is important that we resolve disagreements and differing views constructively. Remember that we’re different. The strength of Overture.bio comes from its varied community, people from a wide range of backgrounds. Different people have different perspectives on issues. Being unable to understand why someone holds a viewpoint doesn’t mean that they’re wrong. Don’t forget that it is human to err and blaming each other doesn’t get us anywhere. Instead, focus on helping to resolve issues and learning from mistakes. - -Original text courtesy of the [Speak Up! project](http://web.archive.org/web/20141109123859/http://speakup.io/coc.html). +# Code of Conduct +## Our Pledge + +We as members, contributors, and leaders pledge to make participation in our +community a harassment-free experience for everyone, regardless of age, body +size, visible or invisible disability, ethnicity, sex characteristics, gender +identity and expression, level of experience, education, socio-economic status, +nationality, personal appearance, caste, color, religion, or sexual +identity and orientation. + +We pledge to act and interact in ways that contribute to an open, welcoming, +diverse, inclusive, and healthy community. + +## Our Standards + +Examples of behavior that contributes to a positive environment for our +community include: + +* Demonstrating empathy and kindness toward other people +* Being respectful of differing opinions, viewpoints, and experiences +* Giving and gracefully accepting constructive feedback +* Accepting responsibility and apologizing to those affected by our mistakes, + and learning from the experience +* Focusing on what is best not just for us as individuals, but for the overall + community + +Examples of unacceptable behavior include: + +* The use of sexualized language or imagery, and sexual attention or advances of + any kind +* Trolling, insulting or derogatory comments, and personal or political attacks +* Public or private harassment +* Publishing others' private information, such as a physical or email address, + without their explicit permission +* Other conduct which could reasonably be considered inappropriate in a + professional setting + +## Enforcement Responsibilities + +Community leaders are responsible for clarifying and enforcing our standards of +acceptable behavior and will take appropriate and fair corrective action in +response to any behavior that they deem inappropriate, threatening, offensive, +or harmful. + +Community leaders have the right and responsibility to remove, edit, or reject +comments, commits, code, wiki edits, issues, and other contributions that are +not aligned to this Code of Conduct, and will communicate reasons for moderation +decisions when appropriate. + +## Scope + +This Code of Conduct applies within all community spaces, and also applies when +an individual is officially representing the community in public spaces. +Examples of representing our community include using an official email address, +posting via an official social media account, or acting as an appointed +representative at an online or offline event. + +## Enforcement + +Instances of abusive, harassing, or otherwise unacceptable behavior may be +reported to the community leaders responsible for enforcement at +[this email](contact@overture.bio). +All complaints will be reviewed and investigated promptly and fairly. + +All community leaders are obligated to respect the privacy and security of the +reporter of any incident. + +## Enforcement Guidelines + +Community leaders will follow these Community Impact Guidelines in determining +the consequences for any action they deem in violation of this Code of Conduct: + +### 1. Correction + +**Community Impact**: Use of inappropriate language or other behavior deemed +unprofessional or unwelcome in the community. + +**Consequence**: A private, written warning from community leaders, providing +clarity around the nature of the violation and an explanation of why the +behavior was inappropriate. A public apology may be requested. + +### 2. Warning + +**Community Impact**: A violation through a single incident or series of +actions. + +**Consequence**: A warning with consequences for continued behavior. No +interaction with the people involved, including unsolicited interaction with +those enforcing the Code of Conduct, for a specified period of time. This +includes avoiding interactions in community spaces as well as external channels +like social media. Violating these terms may lead to a temporary or permanent +ban. + +### 3. Temporary Ban + +**Community Impact**: A serious violation of community standards, including +sustained inappropriate behavior. + +**Consequence**: A temporary ban from any sort of interaction or public +communication with the community for a specified period of time. No public or +private interaction with the people involved, including unsolicited interaction +with those enforcing the Code of Conduct, is allowed during this period. +Violating these terms may lead to a permanent ban. + +### 4. Permanent Ban + +**Community Impact**: Demonstrating a pattern of violation of community +standards, including sustained inappropriate behavior, harassment of an +individual, or aggression toward or disparagement of classes of individuals. + +**Consequence**: A permanent ban from any sort of public interaction within the +community. + +## Attribution + +This Code of Conduct is adapted from the [Contributor Covenant][homepage], +version 2.1, available at +[https://www.contributor-covenant.org/version/2/1/code_of_conduct.html][v2.1]. + +Community Impact Guidelines were inspired by +[Mozilla's code of conduct enforcement ladder][Mozilla CoC]. + +For answers to common questions about this code of conduct, see the FAQ at +[https://www.contributor-covenant.org/faq][FAQ]. Translations are available at +[https://www.contributor-covenant.org/translations][translations]. + +[homepage]: https://www.contributor-covenant.org +[v2.1]: https://www.contributor-covenant.org/version/2/1/code_of_conduct.html +[Mozilla CoC]: https://github.com/mozilla/diversity +[FAQ]: https://www.contributor-covenant.org/faq +[translations]: https://www.contributor-covenant.org/translations \ No newline at end of file diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 4918ce9..4af1c59 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -1,38 +1,102 @@ -# Contributing to Overture Stack - -Overture-stack is an open source project focusing on advancing genomic science through data management and visualizations. We love to see contributions from our community, so please let us know how we can improve or help us by putting up some code that we will help review. - -## Bug Reports -If you think you have found a bug, we want to know! First, search our issues list on GitHub in case a similar issue has already been opened and add your comments or experience to that issue. If you think you have a new bug, please: -- Submit a ticket with the `bug` template. -- Add the label `user-submitted`. -- Provide a repo with a minimal reproducible setup (if possible). -- Describe in as much detail, with steps, how to reproduce the bug. -- Include screenshots or specific commands in the bug report if applicable. -- Provide as much information as you can (e.g. context, os, browser). Anything helps when debugging. -- Provide an example of what you think the expected behaviour should be. - -The better your bug submission, that faster we will get to fixing it! - -## Feature Requests -Have a feature you would love to see? Submit a ticket with the `Feature Request` template which describes the feature you would like to see, why you need it, and how it should work. -- Add the label `user-submitted`. -- Describe in as much detail as you can the feature request. -- Include example usage or why it would be of benefit to users. - -# Contributing Code -1. You will need to fork the repository and clone it to your local machine. See [github help page](https://help.github.com/articles/fork-a-repo) for help. -1. Develop your changes, with tests included. -1. Run the test suite to make sure that nothing is broken. -1. Submit a Pull Request against the `develop` branch of the repository. -1. Add [Overture-stack/Reviewers](https://github.com/orgs/overture-stack/teams/reviewers) as a the reviewer for your PR. -1. Wait for one of our reviewers to get back to you about your PR. Any questions/comments or requests for changes will be completed through the PR request. - -## Testing -1. Test databases via test containers - no in-memory DB or OS specific services -1. Tests should have no dependencies on any external services (ie. production micro-service) -1. Tests DO NOT clear their data between runs, meaning that no test should rely on or expect a clean DB when running - +# Contributing to Overture + +We appreciate your interest in contributing to the Overture project. We are the Genome Informatics Software Engineering team from Ontario Institute for Cancer Research. At OICR we develop new software, databases and other necessary components to store, organize and compute over the large and complex datasets being generated by our cancer research programs. Embodying OICR's values of collaboration and community, we are firm believers in open-source and open-science. As such we strongly believe in the collective power of expertise and shared resources. ## Code of Conduct -Please respect our [Code of Conduct](https://github.com/overture-stack/.github/blob/master/CODE_OF_CONDUCT.md) in all interactions, including ticket submission and pull request conversations. + +By participating in this project, you are expected to abide by our [Code of Conduct](https://docs.overture.bio/community/code-of-conduct). Please take the time to read it carefully before contributing. + +## Get Involved + +**Getting Started:** Our primary platform for community support, feature requests, and general discussions is GitHub Discussions. This allows us to keep all conversations in one place and make them easily searchable for future reference. + +**Community Support:** Our primary platform for community support, feature requests, and general discussions is [GitHub Discussions](https://github.com/overture-stack/docs/discussions). This allows us to keep all conversations in one place and make them easily searchable for future reference. + +- **Getting Help:** If you need assistance with Overture, please create a [new discussion in our support category](https://github.com/overture-stack/docs/discussions/categories/support). + - Before creating a new discussion, please search existing discussions to see if your question has already been answered. +- **Feature Requests & Proposals:** We love hearing your ideas for improving Overture! Before making a feature request, please check our [**feature roadmap**](https://github.com/orgs/overture-stack/projects/11/views/1) to see if your idea is already planned. + - If your idea isn't on the roadmap, feel free to [**submit a feature request**](https://github.com/overture-stack/docs/discussions/categories/ideas) by creating a new discussion in our Ideas category +- **Report a Potential Bug:** We use GitHub Issues primarily for tracking confirmed bugs and ticketing development tasks. If you come across a potential bug or issue, please first post it to our [**GitHub support discussion forum**](https://github.com/overture-stack/docs/discussions/categories/support). + - This allows us to confirm the issue and gather more information if needed. If we determine that further development is required, we will create and tag you into a GitHub Issue from your discussion post. + +## Our Development Process + +We use GitHub issues and pull requests for communication related to code changes. + +### Branch Organization + +We use the following standard branches: + +- `main` is for stable production code +- `develop` is the integration branch for new features +- `feature/` for feature branches +- `release/v` for release branches +- `hotfix/` for hotfix branches + +## Pull Requests + +### Submitting a Pull Request + +We welcome and encourage pull requests from the community. To submit a pull request, please follow these steps: + +1. **Fork the Repository**: Fork the Overture repository on GitHub. +2. **Clone Your Fork**: Clone your forked repository to your local machine. +3. **Create a New Branch**: Create a new branch for your changes. Use lowercase and hyphens (e.g., `feature/user-authentication`). Include ticket/issue numbers when applicable (e.g., `feature/PROJ-123-user-authentication`). +4. **Make Your Changes**: Implement your changes and commit them to your branch. Write clear, concise commit messages in present tense (e.g., "Add feature" not "Added feature"). Reference issue numbers in commits when applicable. +5. **Push Your Changes**: Push your changes to your forked repository. +6. **Submit a Pull Request**: Open a pull request against the main repository. + +### Best Practices + +1. **Keep PRs as small as possible:** Focus on one feature or bug fix per pull request. Break large changes into smaller, more manageable pieces making it easier for reviewers to understand and approve your changes. + +2. **Use descriptive titles:** Start with a verb (e.g., "Add", "Fix", "Update", "Refactor"), briefly summarize the main purpose of the PR and include the issue number if applicable (e.g., "Fix user authentication bug (#123)"). + +3. **Describe how you tested it:** Explain the testing process you followed and mention any new automated tests you've added. + +4. **Provide a clear description:** Explain the purpose of your changes and list the main modifications you've made. Mention any potential side effects or areas that might need extra attention. + +5. **Link related issues:** Reference any related issues or pull requests. Use GitHub keywords to automatically link issues (e.g., "Closes #123", "Fixes #456"). +6. **Keep the PR's branch up-to-date:** Regularly rebase your branch on the latest main branch and resolve any merge conflicts promptly. + +7. **Respond to feedback:** Be open to suggestions and willing to make changes. Address all comments from reviewers. If you disagree with a suggestion, explain your reasoning politely. + +8. **Include documentation updates:** If your changes affect user-facing features, update or create and issue detailing the relevant changes need to the documentation. Where appropriate include inline comments for complex code sections. + +10. **Be patient:** Reviewers will likely be unable to respond immediately. However, feel free to follow up politely if you haven't received feedback after a reasonable time. + +### Using Draft Pull Requests + +Draft Pull Requests are an excellent way to document work in progress and facilitate early feedback. Use them to: + +- Organize your thoughts and process +- Share early work and ideas with the team +- Get feedback on implementation approaches before finalizing code +- Track progress on long-running features + +Guidelines for Draft Pull Requests: + +1. **Creation**: + - Open a pull request and select "Create draft pull request" + - Clearly mark the title with [WIP] or [DRAFT] prefix +2. **Description**: + - Outline the current state of the work + - List planned tasks or improvements + - Highlight areas where feedback is specifically needed +3. **Updates**: + - Regularly update the description or provide comments following commits with progress notes +- Use task lists (using `- [ ]` in Markdown) to track completion of sub-tasks +4. **Collaboration**: + - Encourage early feedback and discussion + - Use the pull request comments for design discussions +5. **Finalization**: + - Complete all planned work and address feedback + - Update tests and documentation + - Click "Ready for review" to move out of draft state + +### Merging a Pull Request + +- Ensure all CI checks pass +- Obtain the required number of approvals +- Use the project's specified merge strategy (Typically squash and merge) +- Delete the source branch after merging if no longer needed diff --git a/FUNDING.yml b/FUNDING.yml new file mode 100644 index 0000000..d4dcade --- /dev/null +++ b/FUNDING.yml @@ -0,0 +1,19 @@ +# If used uncomment and update the following: + +# #################################################################################### +# # Used to define funding options for your project or organization on GitHub. +# # It's part of GitHub's Sponsors feature, +# # which allows open source developers and organizations to receive financial support for their work. +# #################################################################################### + +# # These are supported funding model platforms +# github: # Replace with up to 4 GitHub Sponsors-enabled usernames e.g., [user1, user2] +# patreon: # Replace with a single Patreon username +# open_collective: # Replace with a single Open Collective username +# ko_fi: # Replace with a single Ko-fi username +# tidelift: # Replace with a single Tidelift platform-name/package-name e.g., npm/babel +# community_bridge: # Replace with a single Community Bridge project-name e.g., cloud-foundry +# liberapay: # Replace with a single Liberapay username +# issuehunt: # Replace with a single IssueHunt username +# otechie: # Replace with a single Otechie username +# custom: # Replace with up to 4 custom sponsorship URLs e.g., ['link1', 'link2'] diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/ISSUE_TEMPLATE/bug_report.md similarity index 100% rename from .github/ISSUE_TEMPLATE/bug_report.md rename to ISSUE_TEMPLATE/bug_report.md diff --git a/ISSUE_TEMPLATE/custom_template.md b/ISSUE_TEMPLATE/custom_template.md new file mode 100644 index 0000000..8b13789 --- /dev/null +++ b/ISSUE_TEMPLATE/custom_template.md @@ -0,0 +1 @@ + diff --git a/.github/ISSUE_TEMPLATE/Feature_Requests.md b/ISSUE_TEMPLATE/feature_requests.md similarity index 73% rename from .github/ISSUE_TEMPLATE/Feature_Requests.md rename to ISSUE_TEMPLATE/feature_requests.md index d5343a6..5f684a6 100644 --- a/.github/ISSUE_TEMPLATE/Feature_Requests.md +++ b/ISSUE_TEMPLATE/feature_requests.md @@ -1,8 +1,12 @@ --- -name: Requests -about: Overture Request +name: Community Requests +title: "Request - " +labels: Community Request + --- + + ## Summary of request Please summarize clearly and concisely what you would like. diff --git a/Licensing/LICENSE b/Licensing/LICENSE new file mode 100644 index 0000000..921896b --- /dev/null +++ b/Licensing/LICENSE @@ -0,0 +1,202 @@ + + Apache License + Version 2.0, January 2004 + http://www.apache.org/licenses/ + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. Definitions. + + "License" shall mean the terms and conditions for use, reproduction, + and distribution as defined by Sections 1 through 9 of this document. + + "Licensor" shall mean the copyright owner or entity authorized by + the copyright owner that is granting the License. + + "Legal Entity" shall mean the union of the acting entity and all + other entities that control, are controlled by, or are under common + control with that entity. For the purposes of this definition, + "control" means (i) the power, direct or indirect, to cause the + direction or management of such entity, whether by contract or + otherwise, or (ii) ownership of fifty percent (50%) or more of the + outstanding shares, or (iii) beneficial ownership of such entity. + + "You" (or "Your") shall mean an individual or Legal Entity + exercising permissions granted by this License. + + "Source" form shall mean the preferred form for making modifications, + including but not limited to software source code, documentation + source, and configuration files. + + "Object" form shall mean any form resulting from mechanical + transformation or translation of a Source form, including but + not limited to compiled object code, generated documentation, + and conversions to other media types. + + "Work" shall mean the work of authorship, whether in Source or + Object form, made available under the License, as indicated by a + copyright notice that is included in or attached to the work + (an example is provided in the Appendix below). + + "Derivative Works" shall mean any work, whether in Source or Object + form, that is based on (or derived from) the Work and for which the + editorial revisions, annotations, elaborations, or other modifications + represent, as a whole, an original work of authorship. For the purposes + of this License, Derivative Works shall not include works that remain + separable from, or merely link (or bind by name) to the interfaces of, + the Work and Derivative Works thereof. + + "Contribution" shall mean any work of authorship, including + the original version of the Work and any modifications or additions + to that Work or Derivative Works thereof, that is intentionally + submitted to Licensor for inclusion in the Work by the copyright owner + or by an individual or Legal Entity authorized to submit on behalf of + the copyright owner. For the purposes of this definition, "submitted" + means any form of electronic, verbal, or written communication sent + to the Licensor or its representatives, including but not limited to + communication on electronic mailing lists, source code control systems, + and issue tracking systems that are managed by, or on behalf of, the + Licensor for the purpose of discussing and improving the Work, but + excluding communication that is conspicuously marked or otherwise + designated in writing by the copyright owner as "Not a Contribution." + + "Contributor" shall mean Licensor and any individual or Legal Entity + on behalf of whom a Contribution has been received by Licensor and + subsequently incorporated within the Work. + + 2. Grant of Copyright License. Subject to the terms and conditions of + this License, each Contributor hereby grants to You a perpetual, + worldwide, non-exclusive, no-charge, royalty-free, irrevocable + copyright license to reproduce, prepare Derivative Works of, + publicly display, publicly perform, sublicense, and distribute the + Work and such Derivative Works in Source or Object form. + + 3. Grant of Patent License. Subject to the terms and conditions of + this License, each Contributor hereby grants to You a perpetual, + worldwide, non-exclusive, no-charge, royalty-free, irrevocable + (except as stated in this section) patent license to make, have made, + use, offer to sell, sell, import, and otherwise transfer the Work, + where such license applies only to those patent claims licensable + by such Contributor that are necessarily infringed by their + Contribution(s) alone or by combination of their Contribution(s) + with the Work to which such Contribution(s) was submitted. If You + institute patent litigation against any entity (including a + cross-claim or counterclaim in a lawsuit) alleging that the Work + or a Contribution incorporated within the Work constitutes direct + or contributory patent infringement, then any patent licenses + granted to You under this License for that Work shall terminate + as of the date such litigation is filed. + + 4. Redistribution. You may reproduce and distribute copies of the + Work or Derivative Works thereof in any medium, with or without + modifications, and in Source or Object form, provided that You + meet the following conditions: + + (a) You must give any other recipients of the Work or + Derivative Works a copy of this License; and + + (b) You must cause any modified files to carry prominent notices + stating that You changed the files; and + + (c) You must retain, in the Source form of any Derivative Works + that You distribute, all copyright, patent, trademark, and + attribution notices from the Source form of the Work, + excluding those notices that do not pertain to any part of + the Derivative Works; and + + (d) If the Work includes a "NOTICE" text file as part of its + distribution, then any Derivative Works that You distribute must + include a readable copy of the attribution notices contained + within such NOTICE file, excluding those notices that do not + pertain to any part of the Derivative Works, in at least one + of the following places: within a NOTICE text file distributed + as part of the Derivative Works; within the Source form or + documentation, if provided along with the Derivative Works; or, + within a display generated by the Derivative Works, if and + wherever such third-party notices normally appear. The contents + of the NOTICE file are for informational purposes only and + do not modify the License. You may add Your own attribution + notices within Derivative Works that You distribute, alongside + or as an addendum to the NOTICE text from the Work, provided + that such additional attribution notices cannot be construed + as modifying the License. + + You may add Your own copyright statement to Your modifications and + may provide additional or different license terms and conditions + for use, reproduction, or distribution of Your modifications, or + for any such Derivative Works as a whole, provided Your use, + reproduction, and distribution of the Work otherwise complies with + the conditions stated in this License. + + 5. Submission of Contributions. Unless You explicitly state otherwise, + any Contribution intentionally submitted for inclusion in the Work + by You to the Licensor shall be under the terms and conditions of + this License, without any additional terms or conditions. + Notwithstanding the above, nothing herein shall supersede or modify + the terms of any separate license agreement you may have executed + with Licensor regarding such Contributions. + + 6. Trademarks. This License does not grant permission to use the trade + names, trademarks, service marks, or product names of the Licensor, + except as required for reasonable and customary use in describing the + origin of the Work and reproducing the content of the NOTICE file. + + 7. Disclaimer of Warranty. Unless required by applicable law or + agreed to in writing, Licensor provides the Work (and each + Contributor provides its Contributions) on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or + implied, including, without limitation, any warranties or conditions + of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A + PARTICULAR PURPOSE. You are solely responsible for determining the + appropriateness of using or redistributing the Work and assume any + risks associated with Your exercise of permissions under this License. + + 8. Limitation of Liability. In no event and under no legal theory, + whether in tort (including negligence), contract, or otherwise, + unless required by applicable law (such as deliberate and grossly + negligent acts) or agreed to in writing, shall any Contributor be + liable to You for damages, including any direct, indirect, special, + incidental, or consequential damages of any character arising as a + result of this License or out of the use or inability to use the + Work (including but not limited to damages for loss of goodwill, + work stoppage, computer failure or malfunction, or any and all + other commercial damages or losses), even if such Contributor + has been advised of the possibility of such damages. + + 9. Accepting Warranty or Additional Liability. While redistributing + the Work or Derivative Works thereof, You may choose to offer, + and charge a fee for, acceptance of support, warranty, indemnity, + or other liability obligations and/or rights consistent with this + License. However, in accepting such obligations, You may act only + on Your own behalf and on Your sole responsibility, not on behalf + of any other Contributor, and only if You agree to indemnify, + defend, and hold each Contributor harmless for any liability + incurred by, or claims asserted against, such Contributor by reason + of your accepting any such warranty or additional liability. + + END OF TERMS AND CONDITIONS + + APPENDIX: How to apply the Apache License to your work. + + To apply the Apache License to your work, attach the following + boilerplate notice, with the fields enclosed by brackets "[]" + replaced with your own identifying information. (Don't include + the brackets!) The text should be enclosed in the appropriate + comment syntax for the file format. We also recommend that a + file or class name and description of purpose be included on the + same "printed page" as the copyright notice for easier + identification within third-party archives. + + Copyright 2025 Ontario Institute for Cancer Research + + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. + You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + + Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. \ No newline at end of file diff --git a/Licensing/NOTICE b/Licensing/NOTICE new file mode 100644 index 0000000..0da3642 --- /dev/null +++ b/Licensing/NOTICE @@ -0,0 +1,15 @@ +[Project Name] +Copyright 2025 Ontario Instituite for Cancer Research + +This product includes software developed at the: +Ontario Instituite for Cancer Research (https://oicr.on.ca/) + +------------------------------------------------------------------------ +Third Party Content: + +[List any third-party software, its copyright notice, and license if applicable] +Example: +The XYZ Library (http://xyz-library.com) +Copyright (c) [Year] [Copyright Owner] +Licensed under Apache License 2.0 +------------------------------------------------------------------------ \ No newline at end of file diff --git a/Licensing/requirements.md b/Licensing/requirements.md new file mode 100644 index 0000000..76fc786 --- /dev/null +++ b/Licensing/requirements.md @@ -0,0 +1,136 @@ +# Apache 2.0 Licensing Requirements + +This guide outlines the requirements for ensuring your repository properly adheres to Apache 2.0 licensing standards. + +## Required Files + +### 1. LICENSE File +- Must be placed in the root directory +- Must contain the complete Apache 2.0 license text +- Must be named `LICENSE` (uppercase, no file extension) +- Must not be modified from the original Apache 2.0 text + +### 2. NOTICE File +- Must be placed in the root directory +- Must be named `NOTICE` (uppercase, no file extension) +- Must include: + - Copyright statements + - Your organization name + - Any required attributions for third-party software + - Any additional notices required by your organization + +## Source Code Requirements + +### License Headers +All source code files must include the Apache 2.0 license header with appropriate comment syntax: + +#### Docker Files (`Dockerfile`, `docker-compose.yml`) +```yaml +# Copyright 2025 Ontario Institute for Cancer Research +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +``` + +#### Other Source Files (`.js`, `.java`, `.cpp`, etc.) +```java +/* + Copyright 2025 Ontario Institute for Cancer Research + + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. + You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + + Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. +*/ +``` + +#### Python Files (`.py`) +```python +""" + Copyright 2025 Ontario Institute for Cancer Research + + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. + You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + + Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. +""" +``` + +## Files to Exclude +Do NOT add license headers to: + +1. Configuration Files: + - `.env` + - `.gitignore` + - `.editorconfig` + - `requirements.txt` + - `package.json` + - `poetry.lock` + - `Pipfile`/`Pipfile.lock` + +2. Data Files: + - `.json` + - `.csv` + - `.xml` data files + +3. Documentation: + - `README.md` + - `CHANGELOG.md` + - `CONTRIBUTING.md` + +4. Generated Files: + - Auto-generated code + - Build outputs + - Log files + +## Automation Tools + +We provide a script (`add-headers.js`) to automatically add license headers to your source files. To use it: + +1. Copy the script to your project root +2. Run: `node add-headers.js` + +The script will: +- Add appropriate license headers to all relevant files +- Skip already licensed files +- Use the correct comment syntax for each file type +- Skip excluded files and directories + +## Checklist for Compliance + +- [ ] LICENSE file in root directory +- [ ] NOTICE file in root directory +- [ ] License headers in all source code files +- [ ] Headers use correct comment syntax for each language +- [ ] Third-party attributions listed in NOTICE file +- [ ] Configuration and data files excluded +- [ ] Copyright year and organization name updated + +## Additional Resources + +- [Apache License 2.0 Full Text](http://www.apache.org/licenses/LICENSE-2.0) +- [Apache License Policy](https://www.apache.org/legal/resolve.html) +- [How to Apply Apache License](https://www.apache.org/foundation/license-faq.html) \ No newline at end of file diff --git a/PULL_REQUEST_TEMPLATE.md b/PULL_REQUEST_TEMPLATE.md new file mode 100644 index 0000000..b07bcab --- /dev/null +++ b/PULL_REQUEST_TEMPLATE.md @@ -0,0 +1,41 @@ +# Pull Request + +## Description + +Please include a summary of the change and which issue or ticket is being addressed, if any. You may also include relevant motivation and context, as well as list any dependencies that are required for this change. + +Fixes # (issue) + +## Type of change + +Please choose only the relevant options and remove the others. + +- [ ] Bug fix (non-breaking change which fixes an issue) +- [ ] New feature (non-breaking change which adds functionality) +- [ ] Breaking change (fix or feature that would cause existing functionality to not work as expected) +- [ ] This change requires a documentation update + +## How Has This Been Tested? + +Please describe the tests that you ran to verify your changes. Provide instructions so we can reproduce. Please also list any relevant details for your test configuration. + +- [ ] Test A +- [ ] Test B + +## Checklist: + +You do not need to fullfill all requirements of this checklist, select all that apply: + +- [ ] My code follows the style guidelines of this project +- [ ] I have performed a self-review of my own code +- [ ] I have commented my code, particularly in hard-to-understand areas +- [ ] I have made corresponding changes to the documentation +- [ ] My changes generate no new warnings +- [ ] I have added tests that prove my fix is effective or that my feature works +- [ ] New and existing unit tests pass locally with my changes +- [ ] Any dependent changes have been merged and published in downstream modules +- [ ] I have checked my code and corrected any misspellings + +## Additional context + +Add any other context or screenshots about the pull request here. \ No newline at end of file diff --git a/README.md b/README.md index 3bc5727..fff6119 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,32 @@ -# Github Templates +# .github -This repo hosts a few templates to be applied across all repos in this organisation. -It also holds the organisation's profile, which is public to everyone. +This repository contains organization-wide GitHub configurations and community health files for the Overture project. These files serve as default community health files for all Overture repositories that don't have their own specific versions. + +## Repository Structure + +The repository is organized with the following structure: + +``` +. +├── ISSUE_TEMPLATE/ +│ ├── bug_report.md +│ ├── feature_request.md +│ └── custom_template.md +├── workflows/ +├── profile/ +├── Standards/ +├── CODE_OF_CONDUCT.md +├── CONTRIBUTING.md +├── CODEOWNERS +├── FUNDING.yml +├── PULL_REQUEST_TEMPLATE.md +├── README.md +└── ROADMAP.md +``` + +- `ISSUE_TEMPLATE/`: Contains templates for different types of issues. +- `workflows/`: Can hold GitHub Actions workflow files for CI/CD. +- `profile/`: Contains the files used for the organization landing page readme found on https://github.com/overture-stack. +- `Standards/`: Includes organizational documentation standards and guidelines. +- All Root-level files are community health files and GitHub-specific templates. + - These will serve as default files for all Overture repositories that don't have their own versions. \ No newline at end of file diff --git a/ROADMAP.MD b/ROADMAP.MD index f56be8f..96cec85 100644 --- a/ROADMAP.MD +++ b/ROADMAP.MD @@ -21,49 +21,4 @@ a feature request](https://github.com/overture-stack/roadmap/issues/new?assignee | **Ontology-based validation** | Update existing Lectern validation to support validation of values against an ontology, e.g., the field “disease” must have a value from the MONDO disease hierarchy. | | **Participant portal** | A GA4GH compliant electronic system to support participant enrollment in new studies, collecting their demographic information and data consent, enabling dynamic consent. | | **Phenopacket export** | Provide a GA4GH Phenopackets formatted export of our data. | -| **Song base schema model** | Remove some of the cancer-specific constraints in our Song's base schema model to support additional datatypes natively. | - -## How to Contribute - -We appreciate your interest in contributing to Overture! Please take the time to -read and follow these guidelines before submitting your contributions. - -### Issues and Feature Requests - -Before opening a new issue or feature request, please check if a similar one -already exists. If so, please add a comment to the existing issue instead of -creating a new one. When submitting an issue or feature request, please include -a detailed description of the problem or feature you would like to see, along -with any relevant code, error messages, or screenshots. This will help us better -understand the issue and respond more efficiently. - -### Pull Requests - -We welcome and encourage pull requests from the community. To submit a pull -request, please follow these steps: - -1. **Fork the Repository**: Fork the score repository on GitHub. -2. **Clone Your Fork**: Clone your forked repository to your local machine. -3. **Create a New Branch**: Create a new branch for your changes. -4. **Make Your Changes**: Implement your changes and commit them to your branch. -5. **Push Your Changes**: Push your changes to your forked repository. -6. **Submit a Pull Request**: Open a pull request against the main repository. - -Please ensure your code adheres to the following guidelines before submission: - -- The code should be well-documented and readable. -- The code should be tested. -- Include a clear description of the changes made and the reason for the changes - in the pull request. -- If contributing to any of the features on our development roadmap, please - label your pull appropriately - -We use GitHub issues and pull requests for communication-related to code -changes. For general discussion, feel free to join our -[Slack channel](https://overture-bio.slack.com/join/shared_invite/zt-21tdumtdh-9fP1TFeLepK4~Lc377rOYw#/shared-invite/email). - -By participating in this project, you are expected to abide by the -[Code of Conduct](https://github.com/overture-stack/SCORE/blob/readme-update/code_of_conduct.md). - -Thank you for contributing to Overture-Stack! - +| **Song base schema model** | Remove some of the cancer-specific constraints in our Song's base schema model to support additional datatypes natively. | diff --git a/profile/Overture-logo.png b/profile/Overture-logo.png deleted file mode 100644 index 6bf407c..0000000 Binary files a/profile/Overture-logo.png and /dev/null differ diff --git a/profile/Overture_logo.png b/profile/Overture_logo.png new file mode 100755 index 0000000..d612af0 Binary files /dev/null and b/profile/Overture_logo.png differ diff --git a/profile/README.md b/profile/README.md index 930eabf..13afe8f 100644 --- a/profile/README.md +++ b/profile/README.md @@ -1,42 +1,22 @@ -# Build, Deploy, Discover +
+ overture-logo -
-overture-logo -
- -**Overture** is a collection of open-source software used to overcome significant -obstacles in storing, managing, and sharing genome-scale datasets. Overture is -developed and maintained by the Software Engineering team at the Ontario -Institute for Cancer Research (OICR). Our vision is to help research, -healthcare, and patient communities collaborate and advance genomic research by -providing cutting-edge open source software solutions. +

Open-source genomics data platforms

- -- **Genome informatics first:** You can use our solutions for anything, but here - at Overture we focus on Genome Informatics. With rapidly expanding datasets at - the heart, we build data platforms to gather, organize, and share genomic data - in distributed cloud environments. - -- **Swappable:** There is no such thing as perfection. Our tools are implemented - to be interchangeable from the get-go. You can pick-and-choose from our - software stack and simply use the components that best match your use case. +We build software that enables researchers and the public to access, manage and study large amounts of genomics data. -- **An open world:** We are strong believers in open-source software, open - science, and open communication. Don’t hesitate to follow our teams activities - on GitHub, or contact us from our Slack channel. +Central to our work is Overture, our suite of open-source & freely available modular software microservices. Each service has been generalized with narrow responsibilities that combine to form powerful data platforms where researchers can organize, share and explore their genomics data. -- **Closing the loop:** Our team has established a strong foundation in building - software solutions for genomic projects, from data generation and submission - all the way to dissemination and analysis, leading to a deep understanding of - the genomic data lifecycle. The Overture stack contains a wide array of - components for cloud infrastructure, data shepherding, and analysis. +By sharing these tools we aim to promote the growth and development of reliable genomic data management systems quickly, flexibly, and at multiple scales. -As an open-source project, we are continuously refining our software and are -**[open to contributions](https://github.com/overture-stack/.github/blob/master/CONTRIBUTING.md)** and **[feedback](https://github.com/overture-stack/roadmap/issues/new?assignees=&labels=&projects=&template=Feature_Requests.md)** from -the community. We invite you to check out our -**[development goals](https://github.com/overture-stack/.github/blob/master/ROADMAP.MD)**, and if you wish to contact us -remotely, **[our Slack channel](https://join.slack.com/t/overture-bio/shared_invite/zt-21tdumtdh-9fP1TFeLepK4~Lc377rOYw)**, like our software, will always be open and -available. +
+ Demo Portal +
\ No newline at end of file diff --git a/profile/overview.webp b/profile/overview.webp deleted file mode 100644 index 39b763c..0000000 Binary files a/profile/overview.webp and /dev/null differ diff --git a/profile/portal-services.webp b/profile/portal-services.webp new file mode 100644 index 0000000..2bd113c Binary files /dev/null and b/profile/portal-services.webp differ diff --git a/profile/portalOverview2.0.webp b/profile/portalOverview2.0.webp deleted file mode 100644 index a233cd2..0000000 Binary files a/profile/portalOverview2.0.webp and /dev/null differ diff --git a/standards/01-github.md b/standards/01-github.md new file mode 100644 index 0000000..babcd4a --- /dev/null +++ b/standards/01-github.md @@ -0,0 +1,94 @@ +# Documenting Projects + +Several documentation standards should be met at the level of the organization or project, as opposed to software repos and inline code. + +- The following organization documents, templates, and community health files should be included within a dedicated `.github` repository of the organization. +- This special repository acts as a centralized location for default community health files and templates for the entire organization. Files placed here will apply to all repositories within the organization that don't have their own specific versions of these files. + +## .GitHub Repository Structure + +Here is an overview of the [Overture-Stack .github repository](https://github.com/overture-stack/.github): + +``` +. +├── ISSUE_TEMPLATE/ +│ ├── bug_report.md +│ ├── feature_request.md +│ └── custom_template.md +├── workflows/ +├── profile/ +├── Standards/ +├── CODE_OF_CONDUCT.md +├── CONTRIBUTING.md +├── CODEOWNERS +├── FUNDING.yml +├── PULL_REQUEST_TEMPLATE.md +├── README.md +└── ROADMAP.md +``` + +### ISSUE_TEMPLATE/ + +This directory contains templates for creating new issues in the repository. It helps standardize the information provided when reporting bugs, requesting features, or submitting other types of issues. + +[View ISSUE_TEMPLATE Directory](https://github.com/overture-stack/.github/tree/master/.github/ISSUE_TEMPLATE) + +### workflows/ + +The workflows directory typically contains GitHub Actions workflow files. These YAML files define automated processes for CI/CD, testing, or other repository management tasks. + +[View Workflows Directory](https://github.com/overture-stack/.github/tree/master/.github/workflows) + +### profile/ + +This directory is used to customize the organization's GitHub profile. It often contains a README.md file that is displayed on the organization's master page. + +[View Profile Directory](https://github.com/overture-stack/.github/tree/master/profile) + +### Standards/ + +This directory likely contains documents outlining coding standards, best practices, and other guidelines specific to the Overture-Stack organization. + +[View Standards Directory](https://github.com/overture-stack/.github/tree/master/Standards) + +### CODE_OF_CONDUCT.md + +This file outlines the expected behavior and values for all contributors and participants in the project, fostering a positive and inclusive community. + +[View Code of Conduct](https://github.com/overture-stack/.github/blob/master/CODE_OF_CONDUCT.md) + +### CONTRIBUTING.md + +The CONTRIBUTING.md file provides guidelines for how to contribute to the project, including information on submitting pull requests, reporting issues, and coding standards. + +[View Contributing Guidelines](https://github.com/overture-stack/.github/blob/master/CONTRIBUTING.md) + +### CODEOWNERS + +This file defines individuals or teams responsible for code in the repository. It's used to automatically request reviews from the relevant people when a pull request changes certain files. + +[View CODEOWNERS File](https://github.com/overture-stack/.github/blob/master/CODEOWNERS) + +### FUNDING.yml + +The FUNDING.yml file is used to provide information about how people can financially support the project, such as through GitHub Sponsors or other platforms. + +[View Funding Information](https://github.com/overture-stack/.github/blob/master/FUNDING.yml) + +### PULL_REQUEST_TEMPLATE.md + +This template is automatically loaded when creating a new pull request, guiding contributors to provide necessary information about their changes. + +[View PR Template](https://github.com/overture-stack/.github/blob/master/PULL_REQUEST_TEMPLATE.md) + +### README.md + +The master README file for the .github repository, likely containing an overview of its purpose and contents. + +[View README](https://github.com/overture-stack/.github/blob/master/README.md) + +### ROADMAP.md + +This file outlines the future plans and direction for the project or organization, helping contributors understand long-term goals and upcoming features. + +[View Roadmap](https://github.com/overture-stack/.github/blob/master/ROADMAP.md) \ No newline at end of file diff --git a/standards/02-Software/01-Readme.md b/standards/02-Software/01-Readme.md new file mode 100644 index 0000000..d6a6647 --- /dev/null +++ b/standards/02-Software/01-Readme.md @@ -0,0 +1,102 @@ +# ReadMe + +All Overture repositories have a `README.md` file stored in the root directory of the project. + +
+ Click here for our templated readme.md +`````` +# repoName + +What does this component do? Are there any related components (JS client, UI, etc.)? *Keep it to ~3-5 sentences* + +
+ +> +>
+> +>
+> +> *{Component Name} is part of [Overture](https://www.overture.bio/), a collection of open-source software microservices used to create platforms for researchers to organize and share genomics data.* +> +> + +## Repository Structure + +The repository is organized with the following directory structure: + +``` +. +├── apps/ +│ └── server +└── packages/ + ├── client + ├── common + ├── dictionary + └── validation +``` + +The modules in the monorepo are organized into two categories: + +- __apps/__ - Standalone processes meant to be run. These are published to [ghcr.io](https://ghcr.io) as container images. +- __packages/__ - Reusable packages shared between applications and other packages. Packages are published to [NPM](https://npmjs.com). +- __scripts__ - Utility scripts for use within this repo. + + +## Documentation + +Technical resources for those working with or contributing to the project are available from our official documentation site, the following content can also be read and updated within the `/docs` folder of this repository. + +- **[Component Name Overview](link)** +- [**Setting up the Development Enviornment**](link) +- [**Common Usage Docs**](link) + +## Development Environment + +- [PNPM](https://pnpm.io/) Project manager +- [Node.js](https://nodejs.org/en) Runtime environment (v20 or higher) +- [VS Code](https://code.visualstudio.com/) As recommended code editor. Plugins recommended: ESLint, Prettier - Code formatter, Mocha Test Explorer, Monorepo Workspace + +## Support & Contributions + +- For support, feature requests, and bug reports, please see our [Support Guide](https://docs.overture.bio/community/support). + +- For detailed information on how to contribute to this project, please see our [Contributing Guide](https://docs.overture.bio/docs/contribution). + +## Related Software + +The Overture Platform includes the following Overture Components: + +
+ +|Software|Description| +|---|---| +|[Score](https://github.com/overture-stack/score/)| Transfer data to and from any cloud-based storage system | +|[Song](https://github.com/overture-stack/song/)| Catalog and manage metadata associated to file data spread across cloud storage systems | +|[Maestro](https://github.com/overture-stack/maestro/)| Organizing your distributed data into a centralized Elasticsearch index | +|[Arranger](https://github.com/overture-stack/arranger/)| A search API with reusable search UI components | +|[Stage](https://github.com/overture-stack/stage)| A React-based web portal scaffolding | +|[Lyric](https://github.com/overture-stack/lyric)| A model-agnostic, tabular data submission system | +|[Lectern](https://github.com/overture-stack/lectern)| Schema Manager, designed to validate, store, and manage collections of data dictionaries. | + +If you'd like to get started using our platform [check out our quickstart guides](https://docs.overture.bio/guides/getting-started) + +## Funding Acknowledgement + +Overture is supported by grant #U24CA253529 from the National Cancer Institute at the US National Institutes of Health, and additional funding from Genome Canada, the Canada Foundation for Innovation, the Canadian Institutes of Health Research, Canarie, and the Ontario Institute for Cancer Research. +`````` + +
+ +This standardized README template is broken down as follows: + +1. **Project Overview**: High-level summary of what the project does, its relationship to the broader Overture platform, and any relevant software components or related projects. + +2. **Repository Structure**: An explanation of the repository's structure, using a diagram to illustrate the organization of directories and files (see https://tree.nathanfriend.io/). + +3. **Local Development**: Information on development tools, system dependencies, setup instructions, and links to relevant information not suitable for the conciseness of a readme but needed for local development. + +4. **Documentation**: Links our more detailed developer docs, platform guides, and other resources to help users understand how to work with and configure the software. + +5. **Support & Contribution**: Encourages users to get involved by reporting issues, making contributions, and connecting on our discussion board. + +6. **Related Software**: A table about related Overture components and their descriptions. diff --git a/standards/02-Software/02-Docs/01-overview.md b/standards/02-Software/02-Docs/01-overview.md new file mode 100644 index 0000000..062c102 --- /dev/null +++ b/standards/02-Software/02-Docs/01-overview.md @@ -0,0 +1,94 @@ +# Overview + +Brief description of the softwares main function and purpose. + +## System Architecture + +Explanation of the system's architecture + +![System Architecture Diagram](./images/platform.svg 'System Architecture Diagram') + +As part of the larger System Name, Software Name is typically used with additional integrations, including: + +- **Integration 1:** Brief description of integration 1 +- **Integration 2:** Brief description of integration 2 + +## Key Features + +- **Feature 1:** Description of feature 1 +- **Feature 2:** Description of feature 2 +- **Feature 3:** Description of feature 3 +- **Feature 4:** Description of feature 4 + +## Repository Structure + +``` +. +├── directory +├── directory/ +│ └── subDirectory/ +└── directory +``` + +:::tip + +To help produce these codeblocks use this resource: https://tree.nathanfriend.io/ + +::: + + +Click here to view the [software name repository on GitHub](https://github.com/organization/repo-name) + +- `directory`: Explanation of directory +- `directory`: Explanation of directory +- `directory`: Explanation of directory + +
+ Click here for a copy of the markdown used for this page +`````` +# Overview + +Brief description of the softwares main function and purpose + +## System Architecture + +Explanation of the system's architecture + +[!System Architecture Diagram](./images/platform.svg 'System Architecture Diagram') + +As part of the larger System Name, Software Name is typically used with additional integrations, including: + +- **Integration 1:** Brief description of integration 1 +- **Integration 2:** Brief description of integration 2 + +## Key Features + +- **Feature 1:** Description of feature 1 +- **Feature 2:** Description of feature 2 +- **Feature 3:** Description of feature 3 +- **Feature 4:** Description of feature 4 + +## Repository Structure + +``` +. +├── directory +├── directory/ +│ └── subDirectory/ +└── directory +``` + +:::tip + +To help produce these codeblocks use this resource: https://tree.nathanfriend.io/ + +::: + + +Click here to view the [Software Name repository on GitHub](https://github.com/organization/repo-name) + +- `directory`: Explanation of directory +- `directory`: Explanation of directory +- `directory`: Explanation of directory +`````` +
\ No newline at end of file diff --git a/standards/02-Software/02-Docs/02-Docs.mdx b/standards/02-Software/02-Docs/02-Docs.mdx new file mode 100644 index 0000000..71aaac4 --- /dev/null +++ b/standards/02-Software/02-Docs/02-Docs.mdx @@ -0,0 +1,24 @@ +# `/docs` + +The following pages describe the minimum standard of developer documentation required within the `/docs` folder of an Overture project: + + ``` + . + └── docs/ + ├── 01-overview.md + ├── 02-setup.md + ├── 03-usage.md + ├── 04-deployment.md + └── 05-contributing.md + ``` + +:::tip + +The codeblock above was made using the following resource: https://tree.nathanfriend.io/ + +::: + + +Examples and markdown templates for each page can be found on the following pages. + + diff --git a/standards/02-Software/02-Docs/02-setups/01-maven.md b/standards/02-Software/02-Docs/02-setups/01-maven.md new file mode 100644 index 0000000..2e49486 --- /dev/null +++ b/standards/02-Software/02-Docs/02-setups/01-maven.md @@ -0,0 +1,145 @@ +# Maven Setup + +For Java-based Overture services + +## Prerequisites + +Before you begin, ensure you have the following installed on your system: +- JDK version (e.g., JDK11) +- Docker (version X or higher) +- [Any other project-specific prerequisites] + +## Developer Setup + +This guide will walk you through setting up a complete development environment for [Software Name], including its complementary services. + +### Setting up supporting services + +We'll use Conductor to spin up [Software Name]'s complementary services. + +1. Clone the Conductor repository and move into its directory: + + ```bash + git clone [orchestration-tool-repo-url] + cd [orchestration-tool-directory] + ``` + +2. Run the appropriate start command for your operating system: + + | Operating System | Command | + |------------------|-----------------| + | Unix/macOS | `[unix-command]`| + | Windows | `[windows-command]` | + + +
+ **Click here for a detailed breakdown** + + This command will set up all complementary services for [Software Name] development as follows: + + ![Dev Environment](../images/platform.svg '[Software Name] Dev Environment') + + | Service | Port | Description | Purpose in [Software Name] Development | + |---------|------|-------------|----------------------------------------| + | [Service 1] | [Port] | [Description] | [Purpose] | + | [Service 2] | [Port] | [Description] | [Purpose] | + | [Service 3] | [Port] | [Description] | [Purpose] | + + - Ensure all ports are free on your system before starting the environment. + - You may need to adjust the ports in the configuration file if you have conflicts with existing services. + + For more information, see our Conductor documentation + +
+ +### Running the Development Server + +1. Clone [Software Name] and move into its directory: + + ```bash + git clone [project-repo-url] + cd [project-directory] + ``` + +2. Build the application locally: + + ```bash + ./mvnw clean install -DskipTests + ``` + +
+ **Click here for an explanation of the command above** + + - `./mvnw`: This is the Maven wrapper script, which ensures you're using the correct version of Maven. + - `clean`: This removes any previously compiled files. + - `install`: This compiles the project, runs tests, and installs the package into your local Maven repository. + - `-DskipTests`: This flag skips running tests during the build process to speed things up. + +
+ + :::tip + Ensure you are running the correct JDK version. To check, you can run `java --version`. You should see something similar to the following: + ```bash + [Expected Java version output] + ``` + ::: + +3. Start the [Software Name] Server: + + ```bash + [command-to-start-server] + ``` + :::info + + If you are looking to configure [Software Name] for your specific environment, **the server configuration file can be found here**. A summary of the available Spring profiles is provided below: + +
+ **Click here for a summary of the server spring profiles** + + **[Software Name] Profiles** + | Profile | Description | + |---------|-------------| + | `[profile1]` | [Description] | + | `[profile2]` | [Description] | + | `[profile3]` | [Description] | + +
+ + ::: + +### Verification + +After installing and configuring [Software Name], verify that the system is functioning correctly: + +1. **Check Server Health** + ```bash + [health-check-command] + ``` + - Expected result: [Expected result] + - Troubleshooting: + - [Troubleshooting step 1] + - [Troubleshooting step 2] + +2. **Check the API Documentation** + - Navigate to `[api-docs-url]` in a web browser + - Expected result: [Expected result] + - Troubleshooting: + - [Troubleshooting step 1] + - [Troubleshooting step 2] + +3. **Test [Key API Endpoint]** + - Using API Documentation UI: + 1. [Step 1] + 2. [Step 2] + 3. [Step 3] + - Alternatively, use curl: + ```bash + [curl-command] + ``` + - Expected result: [Expected result] + +For further assistance, open an issue on GitHub. + +:::warning +This guide is meant to demonstrate the configuration and usage of [Software Name] for development purposes and is not intended for production. If you ignore this warning and use this in any public or production environment, please remember to use appropriate Spring profiles and security measures. +::: \ No newline at end of file diff --git a/standards/02-Software/02-Docs/02-setups/02-Setups.mdx b/standards/02-Software/02-Docs/02-setups/02-Setups.mdx new file mode 100644 index 0000000..8e8b4fd --- /dev/null +++ b/standards/02-Software/02-Docs/02-setups/02-Setups.mdx @@ -0,0 +1,10 @@ +# Setups + +Setup instructions vary depending on the technical specifications of each Overture service. This section provides templates for common application setups used across our projects. + +## Available Setup Guides + +Choose the appropriate template based on your project's requirements: + + + diff --git a/standards/02-Software/02-Docs/02-setups/02-node.md b/standards/02-Software/02-Docs/02-setups/02-node.md new file mode 100644 index 0000000..c7817e0 --- /dev/null +++ b/standards/02-Software/02-Docs/02-setups/02-node.md @@ -0,0 +1,142 @@ +# Node Setup + +For JavaScript or TypeScript based Overture services + +# Setup + +## Prerequisites + +Before you begin, ensure you have the following installed on your system: + +- [Prerequisite 1] (version X or higher) +- [Prerequisite 2] (version Y or higher) +- [Prerequisite 3] (version Z or higher) + +## Developer Setup + +This guide will walk you through setting up a complete development environment for [Service Name], including its complementary services. + +### Setting up supporting services + +We'll use Conductor to spin up [Service Name]'s complementary services. + +1. Clone the Conductor repository and move into its directory: + + ```bash + git clone [repository-url] + cd [repository-directory] + ``` + +2. Run the appropriate start command for your operating system: + + | Operating System | Command | + | ---------------- | ------------------- | + | Unix/macOS | `[unix-command]` | + | Windows | `[windows-command]` | + +
+ **Click here for a detailed breakdown** + + This command will set up all complementary services for [Service Name] development as follows: + + ![Dev Environment Diagram](../images/platform.svg '[Service Name] Dev Environment') + + | Service | Port | Description | Purpose in [Service Name] Development | + | --------------- | ------ | ------------------------------ | ------------------------------------ | + | [Service 1] | [Port] | [Brief description] | [Purpose in development] | + | [Service 2] | [Port] | [Brief description] | [Purpose in development] | + | [Service 3] | [Port] | [Brief description] | [Purpose in development] | + + - Ensure all ports are free on your system before starting the environment. + - You may need to adjust the ports in the configuration file if you have conflicts with existing services. + + For more information on configuring and using these services, see our Conductor documentation + +
+ +In the next steps, we will run a [Service Name] development server against these supporting services. + +### Running the Development Server + +1. Clone [Service Name] and move into its directory: + + ```bash + git clone [service-repository-url] + cd [service-directory] + ``` + +2. Configure environment variables: + + ```bash + mv [example-env-file] .env + ``` + + :::info + + This `.env` file is preconfigured as follows for the [Service Name] environment: + + ```env + # Variables subtitle + KEY1=value + + # Variables subtitle + KEY2=value + ``` + +
+ **Click here for an explanation of [Service Name] environment variables** + + - **Variable Subtitle** + - `KEY1`: Definition + + - **Variable Subtitle** + - `KEY2`: Definition + + +
+ +3. Install the required dependencies: + + ```bash + npm ci + ``` + + :::tip + [Any relevant tips or version requirements] + ::: + +4. Start the [Service Name] development server: + + ```bash + [start-server-command] + ``` + +### Verification + +After installation and configuration, verify that [Service Name] is functioning correctly: + +1. **Check the [Service Name] UI** + + - Navigate to `[service-url]` in a web browser. + - Expected result: [Description of expected result] + - Troubleshooting: + - [Troubleshooting step 1] + - [Troubleshooting step 2] + +2. **Test [Key Functionality 1]** + + - [Steps to test functionality] + - Expected result: [Description of expected result] + - Troubleshooting: + - [Troubleshooting step 1] + - [Troubleshooting step 2] + +3. **Test [Key Functionality 2]** + - [Steps to test functionality] + - Expected result: [Description of expected result] + +For further assistance, open an issue on GitHub. + +:::warning +This guide is meant for development purposes and is not intended for production use. If you use this in any public or production environment, please implement appropriate security measures and configure your environment variables accordingly. +::: \ No newline at end of file diff --git a/standards/02-Software/02-Docs/03-Usage.md b/standards/02-Software/02-Docs/03-Usage.md new file mode 100644 index 0000000..4119d2d --- /dev/null +++ b/standards/02-Software/02-Docs/03-Usage.md @@ -0,0 +1,154 @@ +# Usage + +Covers common usage of the software, allowing developers to see how the software can be used and tested. + +This is a template. Customize each section with specific details relevant to your project. For a multi-page structure, each main section could be a separate Markdown file, with a main page serving as an index with links to the individual pages. + +
+ Click here for a copy of the markdown used for this page +`````` + +# Usage Guide + +## API Usage + +### Authentication + +Explain how to authenticate with the API: + +- How to obtain API keys or tokens +- How to include authentication in requests +- Token expiration and renewal process + +Example: + +``` +Authorization: Bearer +``` + +### Endpoints Overview + +Provide a high-level overview of available API endpoints + +### Request/Response Examples + +Provide detailed examples for common API operations: + +#### common API operation 1 + +Request: +``` +``` + +Response: +``` +``` + +## Client Usage + +### Installation +Provide step-by-step installation instructions + +### Configuration +Explain how to configure the client + +### Basic Operations +Demonstrate how to perform basic operations using the client + +### Advanced Features +Describe any advanced features or usage patterns: + +- Batch operations +- Webhooks integration +- Data streaming + +## Command Reference + +### CLI Commands +List and explain available CLI commands, these can be organized into subheadings or tables if appropriate: + +- `yourapp init`: Initialize the application +- `yourapp user list`: List all users + +## Troubleshooting +List common issues and their solutions: + +1. **Issue**: Unable to authenticate + **Solution**: Verify your API key and ensure it hasn't expired + +2. **Issue**: Receiving timeout errors + **Solution**: Check your network connection and increase the client timeout setting +`````` + +
+ +# Usage Guide + +## API Usage + +### Authentication + +Explain how to authenticate with the API: + +- How to obtain API keys or tokens +- How to include authentication in requests +- Token expiration and renewal process + +Example: + +``` +Authorization: Bearer +``` + +### Endpoints Overview + +Provide a high-level overview of available API endpoints + +### Request/Response Examples + +Provide detailed examples for common API operations: + +#### common API operation 1 + +Request: +``` +``` + +Response: +``` +``` + +## Client Usage + +### Installation +Provide step-by-step installation instructions + +### Configuration +Explain how to configure the client + +### Basic Operations +Demonstrate how to perform basic operations using the client + +### Advanced Features +Describe any advanced features or usage patterns: + +- Batch operations +- Webhooks integration +- Data streaming + +## Command Reference + +### CLI Commands +List and explain available CLI commands, these can be organized into subheadings or tables if appropriate: + +- `yourapp init`: Initialize the application +- `yourapp user list`: List all users + +## Troubleshooting +List common issues and their solutions: + +1. **Issue**: Unable to authenticate + **Solution**: Verify your API key and ensure it hasn't expired + +2. **Issue**: Receiving timeout errors + **Solution**: Check your network connection and increase the client timeout setting diff --git a/standards/02-Software/02-Docs/04-Deployment.md b/standards/02-Software/02-Docs/04-Deployment.md new file mode 100644 index 0000000..2f980ba --- /dev/null +++ b/standards/02-Software/02-Docs/04-Deployment.md @@ -0,0 +1,216 @@ + +# Deployment (WIP) + +Covers deployment environments, processes, and configuration management. + +
+ Click here for a copy of the markdown used for this page +`````` + +# Deployment + +## Table of Contents +1. [Introduction](#introduction) +2. [Deployment Environments](#deployment-environments) +3. [Prerequisites](#prerequisites) +4. [Deployment Process](#deployment-process) +5. [Configuration Management](#configuration-management) +6. [Database Migrations](#database-migrations) +7. [Continuous Deployment](#continuous-deployment) +8. [Monitoring and Logging](#monitoring-and-logging) +9. [Rollback Procedures](#rollback-procedures) +10. [Security Considerations](#security-considerations) +11. [Troubleshooting](#troubleshooting) +12. [Maintenance and Updates](#maintenance-and-updates) + +## Introduction +Provide an overview of the deployment process and what this guide covers. + +## Deployment Environments +Describe the different environments used in your deployment pipeline (e.g., development, staging, production). + +### Development +- [Description of development environment] +- [How to deploy to development] + +### Staging +- [Description of staging environment] +- [How to deploy to staging] + +### Production +- [Description of production environment] +- [How to deploy to production] + +## Prerequisites +List all prerequisites for deploying the application: +- Required software and tools +- Access permissions +- Environment-specific requirements + +## Deployment Process +Detailed step-by-step guide for deploying the application: + +1. [Step 1] +2. [Step 2] +3. [Step 3] +... + +## Configuration Management +Explain how configuration is managed across different environments: +- Environment variables +- Configuration files +- Secrets management + +## Database Migrations +If applicable, describe the process for handling database migrations during deployment: +- How to run migrations +- Rollback procedures for failed migrations + +## Continuous Deployment +If using CD, describe the process: +- CI/CD pipeline overview +- Automated deployment triggers +- Manual intervention points + +## Monitoring and Logging +Explain how to monitor the application post-deployment: +- Logging systems +- Monitoring tools +- Key metrics to watch + +## Rollback Procedures +Detailed steps for rolling back a deployment if issues occur: +1. [Rollback Step 1] +2. [Rollback Step 2] +3. [Rollback Step 3] +... + +## Security Considerations +Outline security measures and best practices for deployment: +- SSL/TLS configuration +- Firewall settings +- Access control + +## Troubleshooting +List common deployment issues and their solutions: + +### [Issue 1] +- Symptoms +- Possible causes +- Resolution steps + +### [Issue 2] +- Symptoms +- Possible causes +- Resolution steps + +## Maintenance and Updates +Describe procedures for maintaining and updating the deployed application: +- Scheduled maintenance +- Applying security patches +- Updating dependencies +`````` +
+ +# Deployment + +## Table of Contents +1. [Introduction](#introduction) +2. [Deployment Environments](#deployment-environments) +3. [Prerequisites](#prerequisites) +4. [Deployment Process](#deployment-process) +5. [Configuration Management](#configuration-management) +6. [Database Migrations](#database-migrations) +7. [Continuous Deployment](#continuous-deployment) +8. [Monitoring and Logging](#monitoring-and-logging) +9. [Rollback Procedures](#rollback-procedures) +10. [Security Considerations](#security-considerations) +11. [Troubleshooting](#troubleshooting) +12. [Maintenance and Updates](#maintenance-and-updates) + +## Introduction +Provide an overview of the deployment process and what this guide covers. + +## Deployment Environments +Describe the different environments used in your deployment pipeline (e.g., development, staging, production). + +### Development +- [Description of development environment] +- [How to deploy to development] + +### Staging +- [Description of staging environment] +- [How to deploy to staging] + +### Production +- [Description of production environment] +- [How to deploy to production] + +## Prerequisites +List all prerequisites for deploying the application: +- Required software and tools +- Access permissions +- Environment-specific requirements + +## Deployment Process +Detailed step-by-step guide for deploying the application: + +1. [Step 1] +2. [Step 2] +3. [Step 3] +... + +## Configuration Management +Explain how configuration is managed across different environments: +- Environment variables +- Configuration files +- Secrets management + +## Database Migrations +If applicable, describe the process for handling database migrations during deployment: +- How to run migrations +- Rollback procedures for failed migrations + +## Continuous Deployment +If using CD, describe the process: +- CI/CD pipeline overview +- Automated deployment triggers +- Manual intervention points + +## Monitoring and Logging +Explain how to monitor the application post-deployment: +- Logging systems +- Monitoring tools +- Key metrics to watch + +## Rollback Procedures +Detailed steps for rolling back a deployment if issues occur: +1. [Rollback Step 1] +2. [Rollback Step 2] +3. [Rollback Step 3] +... + +## Security Considerations +Outline security measures and best practices for deployment: +- SSL/TLS configuration +- Firewall settings +- Access control + +## Troubleshooting +List common deployment issues and their solutions: + +### [Issue 1] +- Symptoms +- Possible causes +- Resolution steps + +### [Issue 2] +- Symptoms +- Possible causes +- Resolution steps + +## Maintenance and Updates +Describe procedures for maintaining and updating the deployed application: +- Scheduled maintenance +- Applying security patches +- Updating dependencies \ No newline at end of file diff --git a/standards/02-Software/02-Docs/images/platform.svg b/standards/02-Software/02-Docs/images/platform.svg new file mode 100644 index 0000000..9544fee --- /dev/null +++ b/standards/02-Software/02-Docs/images/platform.svg @@ -0,0 +1 @@ +
e
e
Search & Exploration
Search & Exploration
Arranger Configs
Define the structure and formatting of your data
Arranger Configs...


Index Mapping
Define the structure of your index

Index Mapping...
Event Processing
Message queuing of publication events for triggering downstream data indexing 
Event Processing...
Data Management & Storage
Data Management & Storagez

Song Schema
Define input fields with rules, logic and syntax

Song Schema...

Object Storage Providers
Score is compatible with any S3 compliant object storage provider

Object Storage Providers...
Authorization & Authentication
Authorization & Authentication

Overture API Key Provider
Extends Keyloak's functionality to support API authentication

Overture API Key Provider...Text is not SVG - cannot display \ No newline at end of file diff --git a/standards/02-Software/02-software.mdx b/standards/02-Software/02-software.mdx new file mode 100644 index 0000000..8f60764 --- /dev/null +++ b/standards/02-Software/02-software.mdx @@ -0,0 +1,206 @@ +# Documenting Software + +The following pages define the minimum standard of developer documentation required within an Overture project, which include: + +1. A **`Readme.md`** file. +2. A **`/docs`** folder with the following basic structure: + + ``` + . + └── docs/ + ├── 01-Overview/ + │ └── 01-Overview.md + ├── 02-Setup.md + └── 03-Guides/ + ├── 01-Usage.md + ├── 02-Development.md + └── 03-Deployment.md + ``` + + :::tip + + To ensure your folders and files are ordered correctly in the sidebar use the numbered naming convention seen above. + + ::: + +3. A **`CONTRIBUTING.md`** file +4. A **`code_of_conduct`** file +5. A **`license.md`** file + +## Markdown formatting + +When adding and editing markdown files within the project repository there are a few considerations to be made to ensure your files get rendered correctly by docusaurus: + +- The top level heading (ex. # Top Title) will be used by docusaurus for the sidebar label + +- Docusaurus supports codeblocks, [tabs](https://docusaurus.io/docs/markdown-features/tabs), [dropdowns](https://docusaurus.io/docs/markdown-features#details) and [admonitions](https://docusaurus.io/docs/markdown-features/admonitions). + + + :::tip Using Codeblocks + + - Always reference the language being used + - When appropriate use the following syntax to reference the source: + - `markdown title="website/docs/04-standards/03-guides.md"` + + + ```markdown title="website/docs/04-standards/03-guides.md" + # The title value renders out the code block with the path provided + ``` + ::: + +- Include callouts for important information using these styles: + + :::tip + **Helpful Tips** + Provide additional insights or shortcuts + ::: + + :::caution + **Important Notes** + Highlight crucial considerations or potential pitfalls + ::: + + :::info + **Additional Context** + Provide supplementary information that adds value + ::: + +- If your page shares the same name as a folder, you can use the DocsCardList component to automatically display card-style links to all files contained within that folder: + + + +- Use dropdowns to condense the page and hide optional or supplemental content + +
+ **Click here for the markdown code used to write the above examples** + + `````` + ## Markdown formatting + + When adding and editing markdown files within the project repository there are a few considerations to be made to ensure your files get rendered correctly by docusaurus: + + - The top level heading (ex. # Top Title) will be used by docusaurus for the sidebar label + + - Docusaurus supports codeblocks, [tabs](https://docusaurus.io/docs/markdown-features/tabs), [dropdowns](https://docusaurus.io/docs/markdown-features#details) and [admonitions](https://docusaurus.io/docs/markdown-features/admonitions). + + + :::tip Using Codeblocks + + - Always reference the language being used + - When appropriate use the following syntax to reference the source: + - `markdown title="website/docs/04-standards/03-guides.md"` + + + ```markdown title="website/docs/04-standards/03-guides.md" + # The title value renders out the code block with the path provided + ``` + ::: + + - Include callouts for important information using these styles: + + :::tip + **Helpful Tips** + Provide additional insights or shortcuts + ::: + + :::caution + **Important Notes** + Highlight crucial considerations or potential pitfalls + ::: + + :::info + **Additional Context** + Provide supplementary information that adds value + ::: + + - If your page shares the same name as a folder, you can use the DocsCardList component to automatically display card-style links to all files contained within that folder. This creates a dropdown-style navigation menu. + + + +
+ **Click here for the markdown code used for the above examples** + [The content seen in this dropdown would go in here] +
+ + `````` + +
+ +## Images & Diagrams + +Images and diagrams can be valuable, but they can take lots of time and require maintenance. When using images or diagrams, consider how beneficial the visualization will be and how frequently you need to update it. + +- Both Docusaurus and GitHub supports [rendering of Mermaid](https://docusaurus.io/docs/markdown-features/diagrams), feel free to use this for any diagrams. For more information, see the official [GitHub Docs on creating Mermaid diagrams](https://docs.github.com/en/get-started/writing-on-github/working-with-advanced-formatting/creating-diagrams). + +## Writing Guidelines + +### Language + +We use Canadian English (en-CA) as our standard language for all written and verbal communication. + +#### Use an Active Voice + +The active voice is concise and more accessible for readers to comprehend. Active voice is naturally used in conversation and therefore, readers understand and engage more with writing in the active voice. + +| 👎 Disengaging | 👍 Engaging | +|---|---| +|The developer environment has been set up successfully.|We have successfully set up the developer environment.| +|The necessary tools and dependencies are being installed.|We are installing the necessary tools and dependencies.| + +#### Put Conditional Clauses First + +Put conditional clauses up front in sentences. With conditional clauses upfront, readers can skim or skip information they do not require. If done consistently, this saves significant time reading irrelevant information. + +| 👎 Slow | 👍 Skimmable | +|---|---| +|See How to Use the Score Client for more information | For more information, see How to Use the Score Client.| +| Set the analysis state to published, this will enable the analysis to be indexed| To index the analysis, set the analysis state to published | + +#### Write Accessibly + +Take note of how you describe software behaviours or user actions. Each reader will have a unique background and familiarity with the content, so avoid using language that assumes knowledge. + +| 👎 Sets expectations that can lead to frustration | 👍 No assumptions, made reader friendly | +|---|---| +|Start by *simply* entering the following command|Start by entering the following command| +|To *easily* interact with our API see the Song Swagger UI| To interact with our API see the Song Swagger UI| + +Whenever possible, also include descriptive links to prerequisite or contextual material. Our services benefit a variety of people and data; therefore, experience levels and fields of expertise can vary significantly from user to user. + +### Formatting & Punctuation + +#### Headers + +Use level 1 headers at the top of the page and divide your document using the lower level headers for subsections. + +- Capitalize the first word of a title or subtitle, even if it is a little word like "The" or "A." +- Capitalize the first word after a colon and dash (ex., "Self-Report" instead of "Self-report"). +- Capitalize words of four letters or more (e.g., "With," "Between," and "From"). +- Except for the above rules, lowercase minor words that are three letters or fewer in a title or subtitle. + +#### Numbered lists vs bulleted points + +- Numbered lists for sequential items +- Bulleted points for all other lists + +#### Commas + +Use an Oxford comma for a list of three or more items. + +| Can lead to confusion | Clearer separatation | +|---|---| +|I had eggs, toast and orange juice for breakfast.|I had eggs, toast, and orange juice for breakfast.| + +### UI/Navigation Elements + +When referencing UI elements, have them in **Bold** + +1. Click **Documentation** > **Get Started**. +2. Select **Pre-Configuration Setup**. + + + + + + + diff --git a/standards/02-Software/04-Conduct.md b/standards/02-Software/04-Conduct.md new file mode 100644 index 0000000..042e79a --- /dev/null +++ b/standards/02-Software/04-Conduct.md @@ -0,0 +1,147 @@ +# Code of Conduct + +All Overture repositories have a `code_of_conduct.md` file stored in the root directory of the project. + +The code of conduct establishes a pledge to make the community a harassment-free, open, welcoming, diverse, and inclusive environment. It outlines standards of behavior, including examples of positive and unacceptable conduct. Incident reporting and enforcement guidelines are provided, ranging from private warnings to permanent bans. + +The `code_of_conduct.md` copy available below and is sourced and adapted from the [Contributor Covenant website](https://www.contributor-covenant.org/version/2/1/code_of_conduct/) +
+ Click here for a copy of our code of conduct + + + +``` +# Code of Conduct + +## Our Pledge + +We as members, contributors, and leaders pledge to make participation in our +community a harassment-free experience for everyone, regardless of age, body +size, visible or invisible disability, ethnicity, sex characteristics, gender +identity and expression, level of experience, education, socio-economic status, +nationality, personal appearance, caste, color, religion, or sexual +identity and orientation. + +We pledge to act and interact in ways that contribute to an open, welcoming, +diverse, inclusive, and healthy community. + +## Our Standards + +Examples of behavior that contributes to a positive environment for our +community include: + +* Demonstrating empathy and kindness toward other people +* Being respectful of differing opinions, viewpoints, and experiences +* Giving and gracefully accepting constructive feedback +* Accepting responsibility and apologizing to those affected by our mistakes, + and learning from the experience +* Focusing on what is best not just for us as individuals, but for the overall + community + +Examples of unacceptable behavior include: + +* The use of sexualized language or imagery, and sexual attention or advances of + any kind +* Trolling, insulting or derogatory comments, and personal or political attacks +* Public or private harassment +* Publishing others' private information, such as a physical or email address, + without their explicit permission +* Other conduct which could reasonably be considered inappropriate in a + professional setting + +## Enforcement Responsibilities + +Community leaders are responsible for clarifying and enforcing our standards of +acceptable behavior and will take appropriate and fair corrective action in +response to any behavior that they deem inappropriate, threatening, offensive, +or harmful. + +Community leaders have the right and responsibility to remove, edit, or reject +comments, commits, code, wiki edits, issues, and other contributions that are +not aligned to this Code of Conduct, and will communicate reasons for moderation +decisions when appropriate. + +## Scope + +This Code of Conduct applies within all community spaces, and also applies when +an individual is officially representing the community in public spaces. +Examples of representing our community include using an official email address, +posting via an official social media account, or acting as an appointed +representative at an online or offline event. + +## Enforcement + +Instances of abusive, harassing, or otherwise unacceptable behavior may be +reported to the community leaders responsible for enforcement at +[this email](contact@overture.bio). +All complaints will be reviewed and investigated promptly and fairly. + +All community leaders are obligated to respect the privacy and security of the +reporter of any incident. + +## Enforcement Guidelines + +Community leaders will follow these Community Impact Guidelines in determining +the consequences for any action they deem in violation of this Code of Conduct: + +### 1. Correction + +**Community Impact**: Use of inappropriate language or other behavior deemed +unprofessional or unwelcome in the community. + +**Consequence**: A private, written warning from community leaders, providing +clarity around the nature of the violation and an explanation of why the +behavior was inappropriate. A public apology may be requested. + +### 2. Warning + +**Community Impact**: A violation through a single incident or series of +actions. + +**Consequence**: A warning with consequences for continued behavior. No +interaction with the people involved, including unsolicited interaction with +those enforcing the Code of Conduct, for a specified period of time. This +includes avoiding interactions in community spaces as well as external channels +like social media. Violating these terms may lead to a temporary or permanent +ban. + +### 3. Temporary Ban + +**Community Impact**: A serious violation of community standards, including +sustained inappropriate behavior. + +**Consequence**: A temporary ban from any sort of interaction or public +communication with the community for a specified period of time. No public or +private interaction with the people involved, including unsolicited interaction +with those enforcing the Code of Conduct, is allowed during this period. +Violating these terms may lead to a permanent ban. + +### 4. Permanent Ban + +**Community Impact**: Demonstrating a pattern of violation of community +standards, including sustained inappropriate behavior, harassment of an +individual, or aggression toward or disparagement of classes of individuals. + +**Consequence**: A permanent ban from any sort of public interaction within the +community. + +## Attribution + +This Code of Conduct is adapted from the [Contributor Covenant][homepage], +version 2.1, available at +[https://www.contributor-covenant.org/version/2/1/code_of_conduct.html][v2.1]. + +Community Impact Guidelines were inspired by +[Mozilla's code of conduct enforcement ladder][Mozilla CoC]. + +For answers to common questions about this code of conduct, see the FAQ at +[https://www.contributor-covenant.org/faq][FAQ]. Translations are available at +[https://www.contributor-covenant.org/translations][translations]. + +[homepage]: https://www.contributor-covenant.org +[v2.1]: https://www.contributor-covenant.org/version/2/1/code_of_conduct.html +[Mozilla CoC]: https://github.com/mozilla/diversity +[FAQ]: https://www.contributor-covenant.org/faq +[translations]: https://www.contributor-covenant.org/translations +``` +
\ No newline at end of file diff --git a/standards/02-Software/05-Contribute.md b/standards/02-Software/05-Contribute.md new file mode 100644 index 0000000..6c4900b --- /dev/null +++ b/standards/02-Software/05-Contribute.md @@ -0,0 +1,226 @@ +# Contribution + +All Overture project repositories contain a `CONTRIBUTING.md` saved in the root directory. This file outlines the guidelines and expectations for contributing to the Overture project. + +Ensure all links correctly resolve and names and content are updated based on your project needs. Use the `CONTRIBUTING.md` copy here to get you started: + +
+ Click here for a copy of our contributing.md + +`````` +--- +sidebar_label: Contribution +--- + +# Contributing to Overture + +We appreciate your interest in contributing to the Overture project. We are the Genome Informatics Software Engineering team from Ontario Institute for Cancer Research. At OICR we develop new software, databases and other necessary components to store, organize and compute over the large and complex datasets being generated by our cancer research programs. Embodying OICR's values of collaboration and community, we are firm believers in open-source and open-science. As such we strongly believe in the collective power of expertise and shared resources. + +## Code of Conduct + +By participating in this project, you are expected to abide by our [Code of Conduct](https://docs.overture.bio/community/code-of-conduct). Please take the time to read it carefully before contributing. + +## Get Involved + +**Getting Started:** Our primary platform for community support, feature requests, and general discussions is GitHub Discussions. This allows us to keep all conversations in one place and make them easily searchable for future reference. + + +**Community Support:** Our primary platform for community support, feature requests, and general discussions is [GitHub Discussions](https://github.com/overture-stack/docs/discussions). This allows us to keep all conversations in one place and make them easily searchable for future reference. + +- **Getting Help:** If you need assistance with Overture, please create a [new discussion in our support category](https://github.com/overture-stack/docs/discussions/categories/support). + - Before creating a new discussion, please search existing discussions to see if your question has already been answered. +- **Feature Requests & Proposals:** We love hearing your ideas for improving Overture! Before making a feature request, please check our [**feature roadmap**](https://github.com/orgs/overture-stack/projects/11/views/1) to see if your idea is already planned. + - If your idea isn't on the roadmap, feel free to [**submit a feature request**](https://github.com/overture-stack/docs/discussions/categories/ideas) by creating a new discussion in our Ideas category +- **Report a Potential Bug:** We use GitHub Issues primarily for tracking confirmed bugs and ticketing development tasks. If you come across a potential bug or issue, please first post it to our [**GitHub support discussion forum**](https://github.com/overture-stack/docs/discussions/categories/support). + - This allows us to confirm the issue and gather more information if needed. If we determine that further development is required, we will create and tag you into a GitHub Issue from your discussion post. + +## Our Development Process + +We use GitHub issues and pull requests for communication related to code changes. + +### Branch Organization + +We use the following standard branches: + +- `main` is for stable production code +- `develop` is the integration branch for new features +- `feature/` for feature branches +- `release/v` for release branches +- `hotfix/` for hotfix branches + +## Pull Requests + +### Submitting a Pull Request + +We welcome and encourage pull requests from the community. To submit a pull request, please follow these steps: + +1. **Fork the Repository**: Fork the Overture repository on GitHub. +2. **Clone Your Fork**: Clone your forked repository to your local machine. +3. **Create a New Branch**: Create a new branch for your changes. Use lowercase and hyphens (e.g., `feature/user-authentication`). Include ticket/issue numbers when applicable (e.g., `feature/PROJ-123-user-authentication`). +4. **Make Your Changes**: Implement your changes and commit them to your branch. Write clear, concise commit messages in present tense (e.g., "Add feature" not "Added feature"). Reference issue numbers in commits when applicable. +5. **Push Your Changes**: Push your changes to your forked repository. +6. **Submit a Pull Request**: Open a pull request against the main repository. + +### Best Practices + +1. **Keep PRs as small as possible:** Focus on one feature or bug fix per pull request. Break large changes into smaller, more manageable pieces making it easier for reviewers to understand and approve your changes. + +2. **Use descriptive titles:** Start with a verb (e.g., "Add", "Fix", "Update", "Refactor"), briefly summarize the main purpose of the PR and include the issue number if applicable (e.g., "Fix user authentication bug (#123)"). + +3. **Describe how you tested it:** Explain the testing process you followed and mention any new automated tests you've added. + +4. **Provide a clear description:** Explain the purpose of your changes and list the main modifications you've made. Mention any potential side effects or areas that might need extra attention. + +5. **Link related issues:** Reference any related issues or pull requests. Use GitHub keywords to automatically link issues (e.g., "Closes #123", "Fixes #456"). +6. **Keep the PR's branch up-to-date:** Regularly rebase your branch on the latest main branch and resolve any merge conflicts promptly. + +7. **Respond to feedback:** Be open to suggestions and willing to make changes. Address all comments from reviewers. If you disagree with a suggestion, explain your reasoning politely. + +8. **Include documentation updates:** If your changes affect user-facing features, update or create and issue detailing the relevant changes need to the documentation. Where appropriate include inline comments for complex code sections. + +10. **Be patient:** Reviewers will likely be unable to respond immediately. However, feel free to follow up politely if you haven't received feedback after a reasonable time. + +### Using Draft Pull Requests + +Draft Pull Requests are an excellent way to document work in progress and facilitate early feedback. Use them to: + +- Organize your thoughts and process +- Share early work and ideas with the team +- Get feedback on implementation approaches before finalizing code +- Track progress on long-running features + +Guidelines for Draft Pull Requests: + +1. **Creation**: + - Open a pull request and select "Create draft pull request" + - Clearly mark the title with [WIP] or [DRAFT] prefix +2. **Description**: + - Outline the current state of the work + - List planned tasks or improvements + - Highlight areas where feedback is specifically needed +3. **Updates**: + - Regularly update the description or provide comments following commits with progress notes +- Use task lists (using `- [ ]` in Markdown) to track completion of sub-tasks +4. **Collaboration**: + - Encourage early feedback and discussion + - Use the pull request comments for design discussions +5. **Finalization**: + - Complete all planned work and address feedback + - Update tests and documentation + - Click "Ready for review" to move out of draft state + +### Merging a Pull Request + +- Ensure all CI checks pass +- Obtain the required number of approvals +- Use the project's specified merge strategy (Typically squash and merge) +- Delete the source branch after merging if no longer needed + +`````` +
+ +# Contributing to Overture + +We appreciate your interest in contributing to the Overture project. We are the Genome Informatics Software Engineering team from Ontario Institute for Cancer Research. At OICR we develop new software, databases and other necessary components to store, organize and compute over the large and complex datasets being generated by our cancer research programs. Embodying OICR's values of collaboration and community, we are firm believers in open-source and open-science. As such we strongly believe in the collective power of expertise and shared resources. + +## Code of Conduct + +By participating in this project, you are expected to abide by our [Code of Conduct](https://docs.overture.bio/community/code-of-conduct). Please take the time to read it carefully before contributing. + +## Get Involved + +**Getting Started:** Our primary platform for community support, feature requests, and general discussions is GitHub Discussions. This allows us to keep all conversations in one place and make them easily searchable for future reference. + + +**Community Support:** Our primary platform for community support, feature requests, and general discussions is [GitHub Discussions](https://github.com/overture-stack/docs/discussions). This allows us to keep all conversations in one place and make them easily searchable for future reference. + +- **Getting Help:** If you need assistance with Overture, please create a [new discussion in our support category](https://github.com/overture-stack/docs/discussions/categories/support). + - Before creating a new discussion, please search existing discussions to see if your question has already been answered. +- **Feature Requests & Proposals:** We love hearing your ideas for improving Overture! Before making a feature request, please check our [**feature roadmap**](https://github.com/orgs/overture-stack/projects/11/views/1) to see if your idea is already planned. + - If your idea isn't on the roadmap, feel free to [**submit a feature request**](https://github.com/overture-stack/docs/discussions/categories/ideas) by creating a new discussion in our Ideas category +- **Report a Potential Bug:** We use GitHub Issues primarily for tracking confirmed bugs and ticketing development tasks. If you come across a potential bug or issue, please first post it to our [**GitHub support discussion forum**](https://github.com/overture-stack/docs/discussions/categories/support). + - This allows us to confirm the issue and gather more information if needed. If we determine that further development is required, we will create and tag you into a GitHub Issue from your discussion post. + +## Our Development Process + +We use GitHub issues and pull requests for communication related to code changes. + +### Branch Organization + +We use the following standard branches: + +- `main` is for stable production code +- `develop` is the integration branch for new features +- `feature/` for feature branches +- `release/v` for release branches +- `hotfix/` for hotfix branches + +## Pull Requests + +### Submitting a Pull Request + +We welcome and encourage pull requests from the community. To submit a pull request, please follow these steps: + +1. **Fork the Repository**: Fork the Overture repository on GitHub. +2. **Clone Your Fork**: Clone your forked repository to your local machine. +3. **Create a New Branch**: Create a new branch for your changes. Use lowercase and hyphens (e.g., `feature/user-authentication`). Include ticket/issue numbers when applicable (e.g., `feature/PROJ-123-user-authentication`). +4. **Make Your Changes**: Implement your changes and commit them to your branch. Write clear, concise commit messages in present tense (e.g., "Add feature" not "Added feature"). Reference issue numbers in commits when applicable. +5. **Push Your Changes**: Push your changes to your forked repository. +6. **Submit a Pull Request**: Open a pull request against the main repository. + +### Best Practices + +1. **Keep PRs as small as possible:** Focus on one feature or bug fix per pull request. Break large changes into smaller, more manageable pieces making it easier for reviewers to understand and approve your changes. + +2. **Use descriptive titles:** Start with a verb (e.g., "Add", "Fix", "Update", "Refactor"), briefly summarize the main purpose of the PR and include the issue number if applicable (e.g., "Fix user authentication bug (#123)"). + +3. **Describe how you tested it:** Explain the testing process you followed and mention any new automated tests you've added. + +4. **Provide a clear description:** Explain the purpose of your changes and list the main modifications you've made. Mention any potential side effects or areas that might need extra attention. + +5. **Link related issues:** Reference any related issues or pull requests. Use GitHub keywords to automatically link issues (e.g., "Closes #123", "Fixes #456"). +6. **Keep the PR's branch up-to-date:** Regularly rebase your branch on the latest main branch and resolve any merge conflicts promptly. + +7. **Respond to feedback:** Be open to suggestions and willing to make changes. Address all comments from reviewers. If you disagree with a suggestion, explain your reasoning politely. + +8. **Include documentation updates:** If your changes affect user-facing features, update or create and issue detailing the relevant changes need to the documentation. Where appropriate include inline comments for complex code sections. + +10. **Be patient:** Reviewers will likely be unable to respond immediately. However, feel free to follow up politely if you haven't received feedback after a reasonable time. + +### Using Draft Pull Requests + +Draft Pull Requests are an excellent way to document work in progress and facilitate early feedback. Use them to: + +- Organize your thoughts and process +- Share early work and ideas with the team +- Get feedback on implementation approaches before finalizing code +- Track progress on long-running features + +Guidelines for Draft Pull Requests: + +1. **Creation**: + - Open a pull request and select "Create draft pull request" + - Clearly mark the title with [WIP] or [DRAFT] prefix +2. **Description**: + - Outline the current state of the work + - List planned tasks or improvements + - Highlight areas where feedback is specifically needed +3. **Updates**: + - Regularly update the description or provide comments following commits with progress notes +- Use task lists (using `- [ ]` in Markdown) to track completion of sub-tasks +4. **Collaboration**: + - Encourage early feedback and discussion + - Use the pull request comments for design discussions +5. **Finalization**: + - Complete all planned work and address feedback + - Update tests and documentation + - Click "Ready for review" to move out of draft state + +### Merging a Pull Request + +- Ensure all CI checks pass +- Obtain the required number of approvals +- Use the project's specified merge strategy (Typically squash and merge) +- Delete the source branch after merging if no longer needed + + diff --git a/standards/02-Software/05-license.md b/standards/02-Software/05-license.md new file mode 100644 index 0000000..fca83fe --- /dev/null +++ b/standards/02-Software/05-license.md @@ -0,0 +1,698 @@ +--- +sidebar_label: License +--- + +# `license.md` + +The `licence.md` file is available below and sourced from [GNUs Official website](https://www.gnu.org/licenses/agpl-3.0.en.html). + + +All Overture projects use the the GNU Affero General Public License (AGPL) Version 3. What does this mean? + +- **Copyleft License**: AGPL is a copyleft license, which means that derivative works must be released under the same or a compatible license. + +- **Attribution**: Users must retain copyright notices and provide attribution to the original work. + +- **Network Use**: If the program is modified and run over a network, the modified source code must be made available. + +- **Patent License**: The license grants a patent license to contributors, protecting downstream users from patent infringement claims. + +- **Disclaimer of Warranty**: The software is provided "as is" without warranty. + +- **Limitation of Liability**: Contributors are not liable for damages resulting from use of the software. + +- **Term and Termination**: The license remains in effect unless violated, at which point rights are automatically terminated. + +- **Future Versions**: Users may choose to follow the terms of a later version of the AGPL license. + + +This text is stored at the root of every Overture repository in a file titled `license.md`. + +It may be tempting to include a URL that refers to the license but we cannot be sure that the URL will be valid in perpetuity. The only way to make sure that people who have copies of our software will continue to be able to see the license, despite all the changes that will happen, is to include a copy of the license in the repository. + +
+ Click here for a copy of our License +``` +# GNU AFFERO GENERAL PUBLIC LICENSE + +Version 3, 19 November 2007 + +Copyright (C) 2007 Free Software Foundation, Inc. +https://fsf.org/ + +Everyone is permitted to copy and distribute verbatim copies of this +license document, but changing it is not allowed. + +## Preamble + +The GNU Affero General Public License is a free, copyleft license for +software and other kinds of works, specifically designed to ensure +cooperation with the community in the case of network server software. + +The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. By contrast, +our General Public Licenses are intended to guarantee your freedom to +share and change all versions of a program--to make sure it remains +free software for all its users. + +When we speak of free software, we are referring to freedom, not +price. Our General Public Licenses are designed to make sure that you +have the freedom to distribute copies of free software (and charge for +them if you wish), that you receive source code or can get it if you +want it, that you can change the software or use pieces of it in new +free programs, and that you know you can do these things. + +Developers that use our General Public Licenses protect your rights +with two steps: (1) assert copyright on the software, and (2) offer +you this License which gives you legal permission to copy, distribute +and/or modify the software. + +A secondary benefit of defending all users' freedom is that +improvements made in alternate versions of the program, if they +receive widespread use, become available for other developers to +incorporate. Many developers of free software are heartened and +encouraged by the resulting cooperation. However, in the case of +software used on network servers, this result may fail to come about. +The GNU General Public License permits making a modified version and +letting the public access it on a server without ever releasing its +source code to the public. + +The GNU Affero General Public License is designed specifically to +ensure that, in such cases, the modified source code becomes available +to the community. It requires the operator of a network server to +provide the source code of the modified version running there to the +users of that server. Therefore, public use of a modified version, on +a publicly accessible server, gives the public access to the source +code of the modified version. + +An older license, called the Affero General Public License and +published by Affero, was designed to accomplish similar goals. This is +a different license, not a version of the Affero GPL, but Affero has +released a new version of the Affero GPL which permits relicensing +under this license. + +The precise terms and conditions for copying, distribution and +modification follow. + +## TERMS AND CONDITIONS + +### 0. Definitions. + +"This License" refers to version 3 of the GNU Affero General Public +License. + +"Copyright" also means copyright-like laws that apply to other kinds +of works, such as semiconductor masks. + +"The Program" refers to any copyrightable work licensed under this +License. Each licensee is addressed as "you". "Licensees" and +"recipients" may be individuals or organizations. + +To "modify" a work means to copy from or adapt all or part of the work +in a fashion requiring copyright permission, other than the making of +an exact copy. 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Protecting Users' Legal Rights From Anti-Circumvention Law. + +No covered work shall be deemed part of an effective technological +measure under any applicable law fulfilling obligations under article +11 of the WIPO copyright treaty adopted on 20 December 1996, or +similar laws prohibiting or restricting circumvention of such +measures. + +When you convey a covered work, you waive any legal power to forbid +circumvention of technological measures to the extent such +circumvention is effected by exercising rights under this License with +respect to the covered work, and you disclaim any intention to limit +operation or modification of the work as a means of enforcing, against +the work's users, your or third parties' legal rights to forbid +circumvention of technological measures. + +### 4. 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Additional Terms. + +"Additional permissions" are terms that supplement the terms of this +License by making exceptions from one or more of its conditions. +Additional permissions that are applicable to the entire Program shall +be treated as though they were included in this License, to the extent +that they are valid under applicable law. If additional permissions +apply only to part of the Program, that part may be used separately +under those permissions, but the entire Program remains governed by +this License without regard to the additional permissions. + +When you convey a copy of a covered work, you may at your option +remove any additional permissions from that copy, or from any part of +it. (Additional permissions may be written to require their own +removal in certain cases when you modify the work.) You may place +additional permissions on material, added by you to a covered work, +for which you have or can give appropriate copyright permission. + +Notwithstanding any other provision of this License, for material you +add to a covered work, you may (if authorized by the copyright holders +of that material) supplement the terms of this License with terms: + +- a) Disclaiming warranty or limiting liability differently from the + terms of sections 15 and 16 of this License; or +- b) Requiring preservation of specified reasonable legal notices or + author attributions in that material or in the Appropriate Legal + Notices displayed by works containing it; or +- c) Prohibiting misrepresentation of the origin of that material, + or requiring that modified versions of such material be marked in + reasonable ways as different from the original version; or +- d) Limiting the use for publicity purposes of names of licensors + or authors of the material; or +- e) Declining to grant rights under trademark law for use of some + trade names, trademarks, or service marks; or +- f) Requiring indemnification of licensors and authors of that + material by anyone who conveys the material (or modified versions + of it) with contractual assumptions of liability to the recipient, + for any liability that these contractual assumptions directly + impose on those licensors and authors. + +All other non-permissive additional terms are considered "further +restrictions" within the meaning of section 10. If the Program as you +received it, or any part of it, contains a notice stating that it is +governed by this License along with a term that is a further +restriction, you may remove that term. If a license document contains +a further restriction but permits relicensing or conveying under this +License, you may add to a covered work material governed by the terms +of that license document, provided that the further restriction does +not survive such relicensing or conveying. + +If you add terms to a covered work in accord with this section, you +must place, in the relevant source files, a statement of the +additional terms that apply to those files, or a notice indicating +where to find the applicable terms. + +Additional terms, permissive or non-permissive, may be stated in the +form of a separately written license, or stated as exceptions; the +above requirements apply either way. + +### 8. Termination. + +You may not propagate or modify a covered work except as expressly +provided under this License. Any attempt otherwise to propagate or +modify it is void, and will automatically terminate your rights under +this License (including any patent licenses granted under the third +paragraph of section 11). + +However, if you cease all violation of this License, then your license +from a particular copyright holder is reinstated (a) provisionally, +unless and until the copyright holder explicitly and finally +terminates your license, and (b) permanently, if the copyright holder +fails to notify you of the violation by some reasonable means prior to +60 days after the cessation. + +Moreover, your license from a particular copyright holder is +reinstated permanently if the copyright holder notifies you of the +violation by some reasonable means, this is the first time you have +received notice of violation of this License (for any work) from that +copyright holder, and you cure the violation prior to 30 days after +your receipt of the notice. + +Termination of your rights under this section does not terminate the +licenses of parties who have received copies or rights from you under +this License. If your rights have been terminated and not permanently +reinstated, you do not qualify to receive new licenses for the same +material under section 10. + +### 9. Acceptance Not Required for Having Copies. + +You are not required to accept this License in order to receive or run +a copy of the Program. Ancillary propagation of a covered work +occurring solely as a consequence of using peer-to-peer transmission +to receive a copy likewise does not require acceptance. However, +nothing other than this License grants you permission to propagate or +modify any covered work. These actions infringe copyright if you do +not accept this License. Therefore, by modifying or propagating a +covered work, you indicate your acceptance of this License to do so. + +### 10. Automatic Licensing of Downstream Recipients. + +Each time you convey a covered work, the recipient automatically +receives a license from the original licensors, to run, modify and +propagate that work, subject to this License. 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For example, you may +not impose a license fee, royalty, or other charge for exercise of +rights granted under this License, and you may not initiate litigation +(including a cross-claim or counterclaim in a lawsuit) alleging that +any patent claim is infringed by making, using, selling, offering for +sale, or importing the Program or any portion of it. + +### 11. Patents. + +A "contributor" is a copyright holder who authorizes use under this +License of the Program or a work on which the Program is based. The +work thus licensed is called the contributor's "contributor version". + +A contributor's "essential patent claims" are all patent claims owned +or controlled by the contributor, whether already acquired or +hereafter acquired, that would be infringed by some manner, permitted +by this License, of making, using, or selling its contributor version, +but do not include claims that would be infringed only as a +consequence of further modification of the contributor version. For +purposes of this definition, "control" includes the right to grant +patent sublicenses in a manner consistent with the requirements of +this License. + +Each contributor grants you a non-exclusive, worldwide, royalty-free +patent license under the contributor's essential patent claims, to +make, use, sell, offer for sale, import and otherwise run, modify and +propagate the contents of its contributor version. + +In the following three paragraphs, a "patent license" is any express +agreement or commitment, however denominated, not to enforce a patent +(such as an express permission to practice a patent or covenant not to +sue for patent infringement). To "grant" such a patent license to a +party means to make such an agreement or commitment not to enforce a +patent against the party. + +If you convey a covered work, knowingly relying on a patent license, +and the Corresponding Source of the work is not available for anyone +to copy, free of charge and under the terms of this License, through a +publicly available network server or other readily accessible means, +then you must either (1) cause the Corresponding Source to be so +available, or (2) arrange to deprive yourself of the benefit of the +patent license for this particular work, or (3) arrange, in a manner +consistent with the requirements of this License, to extend the patent +license to downstream recipients. "Knowingly relying" means you have +actual knowledge that, but for the patent license, your conveying the +covered work in a country, or your recipient's use of the covered work +in a country, would infringe one or more identifiable patents in that +country that you have reason to believe are valid. + +If, pursuant to or in connection with a single transaction or +arrangement, you convey, or propagate by procuring conveyance of, a +covered work, and grant a patent license to some of the parties +receiving the covered work authorizing them to use, propagate, modify +or convey a specific copy of the covered work, then the patent license +you grant is automatically extended to all recipients of the covered +work and works based on it. + +A patent license is "discriminatory" if it does not include within the +scope of its coverage, prohibits the exercise of, or is conditioned on +the non-exercise of one or more of the rights that are specifically +granted under this License. You may not convey a covered work if you +are a party to an arrangement with a third party that is in the +business of distributing software, under which you make payment to the +third party based on the extent of your activity of conveying the +work, and under which the third party grants, to any of the parties +who would receive the covered work from you, a discriminatory patent +license (a) in connection with copies of the covered work conveyed by +you (or copies made from those copies), or (b) primarily for and in +connection with specific products or compilations that contain the +covered work, unless you entered into that arrangement, or that patent +license was granted, prior to 28 March 2007. + +Nothing in this License shall be construed as excluding or limiting +any implied license or other defenses to infringement that may +otherwise be available to you under applicable patent law. + +### 12. No Surrender of Others' Freedom. + +If conditions are imposed on you (whether by court order, agreement or +otherwise) that contradict the conditions of this License, they do not +excuse you from the conditions of this License. If you cannot convey a +covered work so as to satisfy simultaneously your obligations under +this License and any other pertinent obligations, then as a +consequence you may not convey it at all. For example, if you agree to +terms that obligate you to collect a royalty for further conveying +from those to whom you convey the Program, the only way you could +satisfy both those terms and this License would be to refrain entirely +from conveying the Program. + +### 13. Remote Network Interaction; Use with the GNU General Public License. + +Notwithstanding any other provision of this License, if you modify the +Program, your modified version must prominently offer all users +interacting with it remotely through a computer network (if your +version supports such interaction) an opportunity to receive the +Corresponding Source of your version by providing access to the +Corresponding Source from a network server at no charge, through some +standard or customary means of facilitating copying of software. This +Corresponding Source shall include the Corresponding Source for any +work covered by version 3 of the GNU General Public License that is +incorporated pursuant to the following paragraph. + +Notwithstanding any other provision of this License, you have +permission to link or combine any covered work with a work licensed +under version 3 of the GNU General Public License into a single +combined work, and to convey the resulting work. The terms of this +License will continue to apply to the part which is the covered work, +but the work with which it is combined will remain governed by version +3 of the GNU General Public License. + +### 14. Revised Versions of this License. + +The Free Software Foundation may publish revised and/or new versions +of the GNU Affero General Public License from time to time. Such new +versions will be similar in spirit to the present version, but may +differ in detail to address new problems or concerns. + +Each version is given a distinguishing version number. If the Program +specifies that a certain numbered version of the GNU Affero General +Public License "or any later version" applies to it, you have the +option of following the terms and conditions either of that numbered +version or of any later version published by the Free Software +Foundation. If the Program does not specify a version number of the +GNU Affero General Public License, you may choose any version ever +published by the Free Software Foundation. + +If the Program specifies that a proxy can decide which future versions +of the GNU Affero General Public License can be used, that proxy's +public statement of acceptance of a version permanently authorizes you +to choose that version for the Program. + +Later license versions may give you additional or different +permissions. However, no additional obligations are imposed on any +author or copyright holder as a result of your choosing to follow a +later version. + +### 15. Disclaimer of Warranty. + +THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY +APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT +HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT +WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT +LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR +A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND +PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE +DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR +CORRECTION. + +### 16. Limitation of Liability. + +IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING +WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR +CONVEYS THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, +INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES +ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT +NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR +LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM +TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER +PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. + +### 17. Interpretation of Sections 15 and 16. + +If the disclaimer of warranty and limitation of liability provided +above cannot be given local legal effect according to their terms, +reviewing courts shall apply local law that most closely approximates +an absolute waiver of all civil liability in connection with the +Program, unless a warranty or assumption of liability accompanies a +copy of the Program in return for a fee. + +END OF TERMS AND CONDITIONS + +## How to Apply These Terms to Your New Programs + +If you develop a new program, and you want it to be of the greatest +possible use to the public, the best way to achieve this is to make it +free software which everyone can redistribute and change under these +terms. + +To do so, attach the following notices to the program. It is safest to +attach them to the start of each source file to most effectively state +the exclusion of warranty; and each file should have at least the +"copyright" line and a pointer to where the full notice is found. + + one line to give the program's name and a brief idea of what it does. + Copyright (C) year name of author + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as + published by the Free Software Foundation, either version 3 of the + License, or (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see https://www.gnu.org/licenses/. + +Also add information on how to contact you by electronic and paper +mail. + +If your software can interact with users remotely through a computer +network, you should also make sure that it provides a way for users to +get its source. For example, if your program is a web application, its +interface could display a "Source" link that leads users to an archive +of the code. There are many ways you could offer source, and different +solutions will be better for different programs; see section 13 for +the specific requirements. + +You should also get your employer (if you work as a programmer) or +school, if any, to sign a "copyright disclaimer" for the program, if +necessary. For more information on this, and how to apply and follow +the GNU AGPL, see https://www.gnu.org/licenses/. +``` + +
\ No newline at end of file diff --git a/standards/03-guides.md b/standards/03-guides.md new file mode 100644 index 0000000..a1315df --- /dev/null +++ b/standards/03-guides.md @@ -0,0 +1,199 @@ +# Creating Guides + +## Overview Section + +### Purpose & Prerequisites + +**This guide is for** [target audience] who need to [primary goal/task]. By the end of this guide you will [specific learning outcomes/deliverables]. + +**You will need:** +- [Required software/tools with versions] +- [Required access/permissions] +- [Required background knowledge] +- [Time estimate if applicable] + +### Background Information + +[2-3 sentences providing essential context and background information that readers need to understand the guide] + +### Visual Overview (Optional) + +[If applicable, include a diagram or visual representation of the end goal/architecture] + +## Getting Started + +Clear step-by-step instructions for an initial prerequisites setup (i.e. Using the Quickstart) + +## Structuring of Primary Steps + +1. **Introduction:** Provide a brief overview of what this step accomplishes and why it's necessary + +2. **Implementation:** Stepwise instructions on what to do. + + :::tip Using Codeblocks + + - Always reference the language being used + - When appropriate use the following syntax to reference the source: + - `markdown title="website/docs/04-standards/03-guides.md"` + + + ```markdown title="website/docs/04-standards/03-guides.md" + # The title value renders out the code block with the path provided + ``` + + ::: + +3. **Validation** How can we verify the implementation was successful. What is the expected output? What common errors can occur and what is the relevant solution? + +## Best Practices + +### Markdown Elements + +- The top level heading (ex. # Top Title) will be used by docusaurus for the sidebar label + +- Docusaurus supports codeblocks, [tabs](https://docusaurus.io/docs/markdown-features/tabs), [dropdowns](https://docusaurus.io/docs/markdown-features#details) and [admonitions](https://docusaurus.io/docs/markdown-features/admonitions). + + :::tip Using Codeblocks + + - Always reference the language being used + - When appropriate use the following syntax to reference the source: + - `markdown title="website/docs/04-standards/03-guides.md"` + + + ```markdown title="website/docs/04-standards/03-guides.md" + # The title value renders out the code block with the path provided + ``` + ::: + +- Include callouts for important information using these styles: + + :::tip + **Helpful Tips** + Provide additional insights or shortcuts + ::: + + :::caution + **Important Notes** + Highlight crucial considerations or potential pitfalls + ::: + + :::info + **Additional Context** + Provide supplementary information that adds value + ::: + +- If your page shares the same name as a folder, you can use the DocsCardList component to automatically display card-style links to all files contained within that folder: + + + +- Use dropdowns to condense the page and hide optional or supplemental content + +
+ **Click here for the markdown code used to write the above examples** + + `````` + + ## Markdown formatting + + When adding and editing markdown files within the project repository there are a few considerations to be made to ensure your files get rendered correctly by docusaurus: + + - The top level heading (ex. # Top Title) will be used by docusaurus for the sidebar label + + - Docusaurus supports codeblocks, [tabs](https://docusaurus.io/docs/markdown-features/tabs), [dropdowns](https://docusaurus.io/docs/markdown-features#details) and [admonitions](https://docusaurus.io/docs/markdown-features/admonitions). + + + :::tip Using Codeblocks + + - Always reference the language being used + - When appropriate use the following syntax to reference the source: + - `markdown title="website/docs/04-standards/03-guides.md"` + + + ```markdown title="website/docs/04-standards/03-guides.md" + # The title value renders out the code block with the path provided + ``` + ::: + + - Include callouts for important information using these styles: + + :::tip + **Helpful Tips** + Provide additional insights or shortcuts + ::: + + :::caution + **Important Notes** + Highlight crucial considerations or potential pitfalls + ::: + + :::info + **Additional Context** + Provide supplementary information that adds value + ::: + + - If your page shares the same name as a folder, you can use the DocsCardList component to automatically display card-style links to all files contained within that folder. This creates a dropdown-style navigation menu. + + + +
+ **Click here for the markdown code used for the above examples** + [The content seen in this dropdown would go in here] +
+ + `````` + +
+ +Add support callouts at key points in your guide, especially before complex procedures, after steps where users commonly encounter issues and when introducing advanced concepts: + + :::info Need Help? + Having trouble? Connect with us through our [community support channels](https://docs.overture.bio/community/support). + ::: + +### Writing Style + +1. **Voice & Style:** + - Use active voice: "Run the command" vs "The command should be run" + - Start instructions with verbs: "Install the package" vs "The package should be installed" + - Keep paragraphs focused on one topic. + +2. **Structure** + - Break complex procedures into smaller steps + - Scaffold concepts appropriately (basic → advanced) + - Include validation steps when appropriate + - Provide troubleshooting guidance for complex steps when appropriate + - Use numbered lists for sequential steps + - Use bullet points for related but non-sequential items + +3. **Include Context** + - Explain the "why" behind important steps + - Provide relevant background information + - Link to related documentation + +### Visual Elements +- Use Screenshots When Helpful, keep images current and provide alt text for accessibility + +## Quality Checklist + +Before publishing, ensure your guide: + +- [ ] Clearly states its purpose and audience +- [ ] Lists all prerequisites +- [ ] Includes necessary background information +- [ ] Provides step-by-step instructions +- [ ] Shows example code and expected outputs +- [ ] Includes troubleshooting guidance +- [ ] Has been tested end-to-end +- [ ] Clear headings +- [ ] Uses consistent formatting +- [ ] Proper code highlighting +- [ ] Includes relevant visuals +- [ ] Links to related documentation are valid and relevant + +## Wrapping Up + +Conclude your guide with a clear call to action: + +:::info Next Steps +List specific, actionable next steps, link to related guides or documentation or suggest common use cases to explore +::: \ No newline at end of file diff --git a/standards/04-Standards.mdx b/standards/04-Standards.mdx new file mode 100644 index 0000000..977812d --- /dev/null +++ b/standards/04-Standards.mdx @@ -0,0 +1,14 @@ +--- +sidebar_postion: 9999 +--- + +# Standards + +The following pages are an aggregate of fundamental principles and established precedents that constitute the formal basis of our Overture documentation and developement practices. + + + + + + + diff --git a/standards/04-community.md b/standards/04-community.md new file mode 100644 index 0000000..10225cf --- /dev/null +++ b/standards/04-community.md @@ -0,0 +1,431 @@ +# Community Resources + +## Suport Page + +A guide for users seeking assistance, reporting issues, or requesting features. This page outlines the primary channels for community support and details how to effectively engage with the project's support system through GitHub Discussions and Issues. + +
+**Click here for our templated support page** + +`````` +# Support + +We take pride in our software and are passionate about helping others use them. If you are looking for help or collaboration, here is how you can get in touch. + +## GitHub Discussions + +Our primary platform for community support, feature requests, and general discussions is GitHub Discussions. This allows us to keep all conversations in one place and make them easily searchable for future reference. + +### Getting Help + +- [**Create a Support Discussion**](https://github.com/overture-stack/docs/discussions/categories/support) + - If you need assistance with Overture, please create a new discussion in our support category. + - Before creating a new discussion, please search existing discussions to see if your question has already been answered. + +### Feature Requests + +We love hearing your ideas for improving Overture! Before making a feature request, please check our current roadmap to see if your idea is already planned: + +- [**Overture feature roadmap](https://github.com/orgs/overture-stack/projects/11/views/1) + +If your idea isn't on the roadmap, feel free to create a new discussion in our Ideas category: + +- [**Submit a Feature Request**](https://github.com/overture-stack/docs/discussions/categories/ideas) + +## GitHub Issues + +We use GitHub Issues primarily for tracking confirmed bugs and ticketing development tasks. + +### Reporting Bugs + +If you come across a potential bug or issue, please post it as a GitHub support discussion first: + +- [**Report a Potential Bug**](https://github.com/overture-stack/docs/discussions/categories/support) + +This allows us to confirm the issue and gather more information if needed. If we determine that further development is required, we will create a GitHub Issue from your discussion post. + +## Staying Informed + +### Release Announcements + +- [**Release Announcements**](https://github.com/overture-stack/docs/discussions/categories/announcements) + - To stay up-to-date with the latest Overture releases and updates, keep an eye on our Announcements category in our GitHub Discussions. + +## Community Guidelines + +When participating in our community, please adhere to the following guidelines: + +1. Be respectful and inclusive of all community members. +2. Provide as much relevant information as possible when asking for help. +3. Use clear and descriptive titles for your discussions and issues. +4. Search existing discussions before creating a new one to avoid duplicates. +5. Follow the GitHub Community Guidelines and abide by our [code of conduct](https://docs.overture.bio/community/code-of-conduct). + +`````` + +
+ +## Team Page + +A showcase of the project's core team members, contributors, and acknowledgments. This page helps users connect with the people behind the project and recognizes those who have made significant contributions to its development. + +
+**Click here for our templated support page** + +`````` +## Team Page + +
+**Click here for our templated team page** + +# Team + +[Introduce your team, your expertise and your mission] + +## Authors + +
+
+
+
+ + + +
+

Team Memeber

+
+
+
+
+ + +## Honorary Mentions + +- **Name**: [Acknowledgement] +- **Name**: [Acknowledgement] +- **Name**: [Acknowledgement] +- **Name**: [Acknowledgement] + +`````` + +
+ +## Funding Page + +A transparent overview of the financial support and organizations that make the project possible. This page acknowledges funding sources, grants, and additional support while providing information about project sustainability and institutional backing. + +
+**Click here for our templated funding page** + +`````` +# Funding + +We gratefully acknowledge the financial support that has made this project possible. Our work has been funded by the following organizations and grants: + +### [Funding Source] + +Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. + + - Grant Number: [#U24CA253529] + - Project Title: "Project Title" + - Funding Period: [YYYY-YYYY] + +### [Funding Source] + +Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. + + - Grant Number: [XXX-XXXX] + - Project Title: "Project Title" + - Funding Period: [YYYY-YYYY] + + +### [Funding Source] + +Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. + + - Grant Number: [XXX-XXXX] + - Project Title: "Project Title" + - Funding Period: [YYYY-YYYY] + +## Additional Support + +We also thank the following organizations for their contributions: + +- [Supporting Organization 1] - [Type of Support] +- [Supporting Organization 2] - [Type of Support] +- [Supporting Organization 3] - [Type of Support] + +For more information about our funding or to discuss potential collaborations, please email us at contact@overture.bio. + +**Last updated:** mm-dd-yy +`````` + +
+ + +## Code of Conduct Page + +A clear set of guidelines establishing community behavior standards and expectations. This document ensures a respectful, inclusive, and harassment-free environment for all community members while outlining enforcement procedures for maintaining these standards. + +
+**Click here for our code of conduct page** + +`````` +# Code of Conduct + +We as members, contributors, and leaders pledge to make participation in our +community a harassment-free experience for everyone, regardless of age, body +size, visible or invisible disability, ethnicity, sex characteristics, gender +identity and expression, level of experience, education, socio-economic status, +nationality, personal appearance, caste, color, religion, or sexual +identity and orientation. + +We pledge to act and interact in ways that contribute to an open, welcoming, +diverse, inclusive, and healthy community. + +## Our Standards + +Examples of behavior that contributes to a positive environment for our +community include: + +* Demonstrating empathy and kindness toward other people +* Being respectful of differing opinions, viewpoints, and experiences +* Giving and gracefully accepting constructive feedback +* Accepting responsibility and apologizing to those affected by our mistakes, + and learning from the experience +* Focusing on what is best not just for us as individuals, but for the overall + community + +Examples of unacceptable behavior include: + +* The use of sexualized language or imagery, and sexual attention or advances of + any kind +* Trolling, insulting or derogatory comments, and personal or political attacks +* Public or private harassment +* Publishing others' private information, such as a physical or email address, + without their explicit permission +* Other conduct which could reasonably be considered inappropriate in a + professional setting + +## Enforcement Responsibilities + +Community leaders are responsible for clarifying and enforcing our standards of +acceptable behavior and will take appropriate and fair corrective action in +response to any behavior that they deem inappropriate, threatening, offensive, +or harmful. + +Community leaders have the right and responsibility to remove, edit, or reject +comments, commits, code, wiki edits, issues, and other contributions that are +not aligned to this Code of Conduct, and will communicate reasons for moderation +decisions when appropriate. + +## Scope + +This Code of Conduct applies within all community spaces, and also applies when +an individual is officially representing the community in public spaces. +Examples of representing our community include using an official email address, +posting via an official social media account, or acting as an appointed +representative at an online or offline event. + +## Enforcement + +Instances of abusive, harassing, or otherwise unacceptable behavior may be +reported to the community leaders responsible for enforcement at +[this email](contact@overture.bio). +All complaints will be reviewed and investigated promptly and fairly. + +All community leaders are obligated to respect the privacy and security of the +reporter of any incident. + +## Enforcement Guidelines + +Community leaders will follow these Community Impact Guidelines in determining +the consequences for any action they deem in violation of this Code of Conduct: + +### 1. Correction + +**Community Impact**: Use of inappropriate language or other behavior deemed +unprofessional or unwelcome in the community. + +**Consequence**: A private, written warning from community leaders, providing +clarity around the nature of the violation and an explanation of why the +behavior was inappropriate. A public apology may be requested. + +### 2. Warning + +**Community Impact**: A violation through a single incident or series of +actions. + +**Consequence**: A warning with consequences for continued behavior. No +interaction with the people involved, including unsolicited interaction with +those enforcing the Code of Conduct, for a specified period of time. This +includes avoiding interactions in community spaces as well as external channels +like social media. Violating these terms may lead to a temporary or permanent +ban. + +### 3. Temporary Ban + +**Community Impact**: A serious violation of community standards, including +sustained inappropriate behavior. + +**Consequence**: A temporary ban from any sort of interaction or public +communication with the community for a specified period of time. No public or +private interaction with the people involved, including unsolicited interaction +with those enforcing the Code of Conduct, is allowed during this period. +Violating these terms may lead to a permanent ban. + +### 4. Permanent Ban + +**Community Impact**: Demonstrating a pattern of violation of community +standards, including sustained inappropriate behavior, harassment of an +individual, or aggression toward or disparagement of classes of individuals. + +**Consequence**: A permanent ban from any sort of public interaction within the +community. + +## Attribution + +This Code of Conduct is adapted from the [Contributor Covenant][homepage], +version 2.1, available at +[https://www.contributor-covenant.org/version/2/1/code_of_conduct.html][v2.1]. + +Community Impact Guidelines were inspired by +[Mozilla's code of conduct enforcement ladder][Mozilla CoC]. + +For answers to common questions about this code of conduct, see the FAQ at +[https://www.contributor-covenant.org/faq][FAQ]. Translations are available at +[https://www.contributor-covenant.org/translations][translations]. + +[homepage]: https://www.contributor-covenant.org +[v2.1]: https://www.contributor-covenant.org/version/2/1/code_of_conduct.html +[Mozilla CoC]: https://github.com/mozilla/diversity +[FAQ]: https://www.contributor-covenant.org/faq +[translations]: https://www.contributor-covenant.org/translations + +`````` + +
+ +## Contribution Page + +A detailed guide for potential contributors, outlining how to participate in the project's development. This page provides step-by-step instructions for submitting code changes, best practices for pull requests, and explains the development workflow to help new contributors get started effectively. + +
+**Click here for our code of conduct page** + +`````` +--- +sidebar_label: Contribution +--- + +# Contributing to Overture + +We appreciate your interest in contributing to the Overture project. We are the Genome Informatics Software Engineering team from Ontario Institute for Cancer Research. At OICR we develop new software, databases and other necessary components to store, organize and compute over the large and complex datasets being generated by our cancer research programs. Embodying OICR's values of collaboration and community, we are firm believers in open-source and open-science. As such we strongly believe in the collective power of expertise and shared resources. + +## Code of Conduct + +By participating in this project, you are expected to abide by our [Code of Conduct](https://docs.overture.bio/community/code-of-conduct). Please take the time to read it carefully before contributing. + +## Get Involved + +**Getting Started:** Our primary platform for community support, feature requests, and general discussions is GitHub Discussions. This allows us to keep all conversations in one place and make them easily searchable for future reference. + + +**Community Support:** Our primary platform for community support, feature requests, and general discussions is [GitHub Discussions](https://github.com/overture-stack/docs/discussions). This allows us to keep all conversations in one place and make them easily searchable for future reference. + +- **Getting Help:** If you need assistance with Overture, please create a [new discussion in our support category](https://github.com/overture-stack/docs/discussions/categories/support). + - Before creating a new discussion, please search existing discussions to see if your question has already been answered. +- **Feature Requests & Proposals:** We love hearing your ideas for improving Overture! Before making a feature request, please check our [**feature roadmap**](https://github.com/orgs/overture-stack/projects/11/views/1) to see if your idea is already planned. + - If your idea isn't on the roadmap, feel free to [**submit a feature request**](https://github.com/overture-stack/docs/discussions/categories/ideas) by creating a new discussion in our Ideas category +- **Report a Potential Bug:** We use GitHub Issues primarily for tracking confirmed bugs and ticketing development tasks. If you come across a potential bug or issue, please first post it to our [**GitHub support discussion forum**](https://github.com/overture-stack/docs/discussions/categories/support). + - This allows us to confirm the issue and gather more information if needed. If we determine that further development is required, we will create and tag you into a GitHub Issue from your discussion post. + +## Our Development Process + +We use GitHub issues and pull requests for communication related to code changes. + +### Branch Organization + +We use the following standard branches: + +- `main` is for stable production code +- `develop` is the integration branch for new features +- `feature/` for feature branches +- `release/v` for release branches +- `hotfix/` for hotfix branches + +## Pull Requests + +### Submitting a Pull Request + +We welcome and encourage pull requests from the community. To submit a pull request, please follow these steps: + +1. **Fork the Repository**: Fork the Overture repository on GitHub. +2. **Clone Your Fork**: Clone your forked repository to your local machine. +3. **Create a New Branch**: Create a new branch for your changes. Use lowercase and hyphens (e.g., `feature/user-authentication`). Include ticket/issue numbers when applicable (e.g., `feature/PROJ-123-user-authentication`). +4. **Make Your Changes**: Implement your changes and commit them to your branch. Write clear, concise commit messages in present tense (e.g., "Add feature" not "Added feature"). Reference issue numbers in commits when applicable. +5. **Push Your Changes**: Push your changes to your forked repository. +6. **Submit a Pull Request**: Open a pull request against the main repository. + +### Best Practices + +1. **Keep PRs as small as possible:** Focus on one feature or bug fix per pull request. Break large changes into smaller, more manageable pieces making it easier for reviewers to understand and approve your changes. + +2. **Use descriptive titles:** Start with a verb (e.g., "Add", "Fix", "Update", "Refactor"), briefly summarize the main purpose of the PR and include the issue number if applicable (e.g., "Fix user authentication bug (#123)"). + +3. **Describe how you tested it:** Explain the testing process you followed and mention any new automated tests you've added. + +4. **Provide a clear description:** Explain the purpose of your changes and list the main modifications you've made. Mention any potential side effects or areas that might need extra attention. + +5. **Link related issues:** Reference any related issues or pull requests. Use GitHub keywords to automatically link issues (e.g., "Closes #123", "Fixes #456"). +6. **Keep the PR's branch up-to-date:** Regularly rebase your branch on the latest main branch and resolve any merge conflicts promptly. + +7. **Respond to feedback:** Be open to suggestions and willing to make changes. Address all comments from reviewers. If you disagree with a suggestion, explain your reasoning politely. + +8. **Include documentation updates:** If your changes affect user-facing features, update or create and issue detailing the relevant changes need to the documentation. Where appropriate include inline comments for complex code sections. + +10. **Be patient:** Reviewers will likely be unable to respond immediately. However, feel free to follow up politely if you haven't received feedback after a reasonable time. + +### Using Draft Pull Requests + +Draft Pull Requests are an excellent way to document work in progress and facilitate early feedback. Use them to: + +- Organize your thoughts and process +- Share early work and ideas with the team +- Get feedback on implementation approaches before finalizing code +- Track progress on long-running features + +Guidelines for Draft Pull Requests: + +1. **Creation**: + - Open a pull request and select "Create draft pull request" + - Clearly mark the title with [WIP] or [DRAFT] prefix +2. **Description**: + - Outline the current state of the work + - List planned tasks or improvements + - Highlight areas where feedback is specifically needed +3. **Updates**: + - Regularly update the description or provide comments following commits with progress notes +- Use task lists (using `- [ ]` in Markdown) to track completion of sub-tasks +4. **Collaboration**: + - Encourage early feedback and discussion + - Use the pull request comments for design discussions +5. **Finalization**: + - Complete all planned work and address feedback + - Update tests and documentation + - Click "Ready for review" to move out of draft state + +### Merging a Pull Request + +- Ensure all CI checks pass +- Obtain the required number of approvals +- Use the project's specified merge strategy (Typically squash and merge) +- Delete the source branch after merging if no longer needed + +`````` + +
+