Replace pylint + autopep8 with ruff (#1300)

Author: sbryngelson

CLAUDE.md

@@ -41,7 +41,7 @@ All commands run from the repo root via `./mfc.sh`.
 # Verification (pre-commit CI checks)
 ./mfc.sh precheck -j 8                     # Run all 5 lint checks (same as CI gate)
 ./mfc.sh format -j 8                       # Auto-format Fortran (.fpp/.f90) + Python
-./mfc.sh lint                              # Pylint + Python unit tests
+./mfc.sh lint                              # Ruff lint + Python unit tests
 ./mfc.sh spelling                          # Spell check
 
 # Module loading (HPC clusters only — must use `source`)

benchmarks/5eq_rk3_weno3_hllc/case.py

@@ -6,9 +6,9 @@
 # - weno_order : 3
 # - riemann_solver : 2
 
+import argparse
 import json
 import math
-import argparse
 
 parser = argparse.ArgumentParser(prog="Benchmarking Case 1", description="This MFC case was created for the purposes of benchmarking MFC.", formatter_class=argparse.ArgumentDefaultsHelpFormatter)
 

benchmarks/hypo_hll/case.py

@@ -4,9 +4,9 @@
 # - hypoelasticity : T
 # - riemann_solver : 1
 
+import argparse
 import json
 import math
-import argparse
 
 parser = argparse.ArgumentParser(prog="Benchmarkin Case 3", description="This MFC case was created for the purposes of benchmarking MFC.", formatter_class=argparse.ArgumentDefaultsHelpFormatter)
 

benchmarks/ibm/case.py

@@ -3,9 +3,9 @@
 # Additional Benchmarked Features
 # - ibm : T
 
+import argparse
 import json
 import math
-import argparse
 
 parser = argparse.ArgumentParser(prog="Benchmarking Case 4", description="This MFC case was created for the purposes of benchmarking MFC.", formatter_class=argparse.ArgumentDefaultsHelpFormatter)
 

benchmarks/igr/case.py

@@ -5,9 +5,9 @@
 # - viscous : T
 # - igr_order : 5
 
+import argparse
 import json
 import math
-import argparse
 
 parser = argparse.ArgumentParser(prog="Benchmarking Case 5", description="This MFC case was created for the purposes of benchmarking MFC.", formatter_class=argparse.ArgumentDefaultsHelpFormatter)
 

benchmarks/viscous_weno5_sgb_acoustic/case.py

@@ -8,9 +8,9 @@
 # - bubble_model : 3
 # - acoustic_source : T
 
+import argparse
 import json
 import math
-import argparse
 
 parser = argparse.ArgumentParser(prog="Benchmarking Case 2", description="This MFC case was created for the purposes of benchmarking MFC.", formatter_class=argparse.ArgumentDefaultsHelpFormatter)
 

docs/documentation/contributing.md

@@ -715,14 +715,15 @@ Every push to a PR triggers CI. Understanding the pipeline helps you fix failure
 
 ### Lint Gate (runs first, blocks all other jobs)
 
-All four checks must pass before any builds start:
+All five checks must pass before any builds start:
 
 1. **Formatting** — `./mfc.sh format` (auto-handled by pre-commit hook)
 2. **Spelling** — `./mfc.sh spelling`
-3. **Toolchain lint** — `./mfc.sh lint` (Python code quality)
+3. **Toolchain lint** — `./mfc.sh lint` (ruff + Python unit tests)
 4. **Source lint** — checks for:
    - Raw `!$acc` or `!$omp` directives (must use Fypp GPU macros)
    - Double-precision intrinsics (`dsqrt`, `dexp`, `dble`, etc.)
+5. **Doc references** — validates documentation cross-references
 
 ### Build and Test Matrix
 

examples/0D_bubblecollapse_adap/case.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
-import math
 import json
+import math
 
 # FLUID PROPERTIES
 # Water

examples/1D_bubblescreen/case.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
-import math
 import json
+import math
 
 # FLUID PROPERTIES
 R_uni = 8314.0  # [J/kmol/K]
@@ -53,7 +53,6 @@
 u0 = math.sqrt(p0 / rho0)  # [m/s]
 t0 = x0 / u0  # [s]
 
-#
 cfl = 0.1
 Nx = 100
 Ldomain = 20.0e-03

examples/1D_convergence/case.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
-import math
-import json
 import argparse
+import json
+import math
 
 # Parsing command line arguments
 parser = argparse.ArgumentParser(description="Generate JSON case configuration for two-fluid convergence simulation.")
@@ -67,10 +67,10 @@
             "patch_icpp(1)%length_x": 1.0,
             "patch_icpp(1)%vel(1)": 1.0,
             "patch_icpp(1)%pres": 1.0,
-            "patch_icpp(1)%alpha_rho(1)": f"0.5 - 0.5*sin(2*pi*x)",
-            "patch_icpp(1)%alpha(1)": f"0.5 - 0.5*sin(2*pi*x)",
-            "patch_icpp(1)%alpha_rho(2)": f"0.5 + 0.5*sin(2*pi*x)",
-            "patch_icpp(1)%alpha(2)": f"0.5 + 0.5*sin(2*pi*x)",
+            "patch_icpp(1)%alpha_rho(1)": "0.5 - 0.5*sin(2*pi*x)",
+            "patch_icpp(1)%alpha(1)": "0.5 - 0.5*sin(2*pi*x)",
+            "patch_icpp(1)%alpha_rho(2)": "0.5 + 0.5*sin(2*pi*x)",
+            "patch_icpp(1)%alpha(2)": "0.5 + 0.5*sin(2*pi*x)",
             # Fluids Physical Parameters
             "fluid_pp(1)%gamma": 1.0e00 / (1.4 - 1.0e00),
             "fluid_pp(1)%pi_inf": 0.0,