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chore: Ensure we're always using named indexes to access the internal data structure #784

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Merged
krlmlr merged 14 commits into from
Apr 21, 2023
Merged

chore: Ensure we're always using named indexes to access the internal data structure #784

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fc89fcb
igraph_t_idx_max
krlmlr Apr 18, 2023
34fdeb5
igraph_t_idx_env
krlmlr Apr 18, 2023
714842e
add `igraph_t_idx_attr`
Antonov548 Apr 19, 2023
0cac024
add `igraph_t_idx_attr`
Antonov548 Apr 19, 2023
9a6d686
add `igraph_t_idx_os`
Antonov548 Apr 19, 2023
f615f75
skip test with old data type
Antonov548 Apr 19, 2023
c2c601e
add `igraph_t_idx_ii`
Antonov548 Apr 20, 2023
cd7a664
add `igraph_t_idx_oi`
Antonov548 Apr 20, 2023
b02d24f
add `igraph_t_idx_to`
Antonov548 Apr 20, 2023
48bcef5
add `igraph_t_idx_from`
Antonov548 Apr 20, 2023
57daed6
add `igraph_t_idx_directed`
Antonov548 Apr 20, 2023
6222e73
add `igraph_t_idx_n`
Antonov548 Apr 20, 2023
bc599c9
update index list
Antonov548 Apr 20, 2023
cda21d5
unskip tests
Antonov548 Apr 20, 2023
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2 changes: 1 addition & 1 deletion R/glet.R
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Original file line number Diff line number Diff line change
Expand Up @@ -94,7 +94,7 @@ graphlet_basis <- function(graph, weights = NULL) {

## Drop all attributes, we don't want to deal with them, TODO
graph2 <- graph
graph2[[9]] <- list(c(1, 0, 1), list(), list(), list())
graph2[[igraph_t_idx_attr]] <- list(c(1, 0, 1), list(), list(), list())
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@Antonov548 Antonov548 Apr 19, 2023

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@krlmlr I think it should be replaced with some Call of C function. Should it be in this pull request?

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@krlmlr krlmlr Apr 19, 2023

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I agree. Yes, please.

I wonder why the tests fail in CI/CD. Can you please try reverting the change to the .svg file?

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@krlmlr krlmlr Apr 19, 2023

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It seems slightly better to have all .Call() calls in separate R functions. So, this can be a call to a function whose only purpose is to .Call() a C function.

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@Antonov548 Antonov548 Apr 19, 2023 •
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I wonder why the tests fail in CI/CD. Can you please try reverting the change to the .svg file?

There is one failing test which is related to update old graph. I think it should be fixed after all properties will be fine. For now I just ignored it locally.

CC: test-old-data-type.R

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@krlmlr krlmlr Apr 19, 2023

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You can use skip() to officially skip the test for now, I had used that in this PR too.


on.exit(.Call(R_igraph_finalizer))
## Function call
Expand Down
1 change: 1 addition & 0 deletions R/idx.R
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,7 @@ igraph_t_idx_os <- 7L
igraph_t_idx_is <- 8L
igraph_t_idx_attr <- 9L
igraph_t_idx_env <- 10L
igraph_t_idx_max <- 11L

# Indexes into unclass(g)[[igraph_t_idx_attr]]
igraph_attr_idx_unknown <- 1L # integer of length 3, for what purpose?
Expand Down
139 changes: 78 additions & 61 deletions src/rinterface_extra.c
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Expand Up @@ -121,6 +121,19 @@ SEXP R_igraph_0ormatrix_to_SEXP(const igraph_matrix_t *m);
SEXP R_igraph_vector_to_SEXPp1(const igraph_vector_t *v);
SEXP R_igraph_arpack_options_to_SEXP(const igraph_arpack_options_t *opt);

enum igraph_t_idx {
igraph_t_idx_n = 0,
igraph_t_idx_directed = 1,
igraph_t_idx_from = 2,
igraph_t_idx_to = 3,
igraph_t_idx_oi = 4,
igraph_t_idx_ii = 5,
igraph_t_idx_os = 6,
igraph_t_idx_is = 7,
igraph_t_idx_attr = 8,
igraph_t_idx_env = 9,
igraph_t_idx_max = 10,
};

SEXP R_igraph_i_lang7(SEXP s, SEXP t, SEXP u, SEXP v, SEXP w, SEXP x, SEXP y)
{
Expand Down Expand Up @@ -253,7 +266,7 @@ SEXP R_igraph_handle_safe_eval_result(SEXP result) {

SEXP R_igraph_get_attr_mode(SEXP graph, SEXP pwhich) {
int which=INTEGER(pwhich)[0]-1;
SEXP obj=VECTOR_ELT(VECTOR_ELT(graph, 8), which);
SEXP obj=VECTOR_ELT(VECTOR_ELT(graph, igraph_t_idx_attr), which);
int i, len=GET_LENGTH(obj);
SEXP result;

Expand Down Expand Up @@ -2844,39 +2857,39 @@ SEXP R_igraph_to_SEXP(const igraph_t *graph) {
long int no_of_nodes=igraph_vcount(graph);
long int no_of_edges=igraph_ecount(graph);

PROTECT(result=NEW_LIST(10));
SET_VECTOR_ELT(result, 0, NEW_NUMERIC(1));
SET_VECTOR_ELT(result, 1, NEW_LOGICAL(1));
SET_VECTOR_ELT(result, 2, NEW_NUMERIC(no_of_edges));
SET_VECTOR_ELT(result, 3, NEW_NUMERIC(no_of_edges));
SET_VECTOR_ELT(result, 4, NEW_NUMERIC(no_of_edges));
SET_VECTOR_ELT(result, 5, NEW_NUMERIC(no_of_edges));
SET_VECTOR_ELT(result, 6, NEW_NUMERIC(no_of_nodes+1));
SET_VECTOR_ELT(result, 7, NEW_NUMERIC(no_of_nodes+1));

REAL(VECTOR_ELT(result, 0))[0]=no_of_nodes;
LOGICAL(VECTOR_ELT(result, 1))[0]=graph->directed;
memcpy(REAL(VECTOR_ELT(result, 2)), graph->from.stor_begin,
PROTECT(result=NEW_LIST(igraph_t_idx_max));
SET_VECTOR_ELT(result, igraph_t_idx_n, NEW_NUMERIC(1));
SET_VECTOR_ELT(result, igraph_t_idx_directed, NEW_LOGICAL(1));
SET_VECTOR_ELT(result, igraph_t_idx_from, NEW_NUMERIC(no_of_edges));
SET_VECTOR_ELT(result, igraph_t_idx_to, NEW_NUMERIC(no_of_edges));
SET_VECTOR_ELT(result, igraph_t_idx_oi, NEW_NUMERIC(no_of_edges));
SET_VECTOR_ELT(result, igraph_t_idx_ii, NEW_NUMERIC(no_of_edges));
SET_VECTOR_ELT(result, igraph_t_idx_os, NEW_NUMERIC(no_of_nodes+1));
SET_VECTOR_ELT(result, igraph_t_idx_is, NEW_NUMERIC(no_of_nodes+1));

REAL(VECTOR_ELT(result, igraph_t_idx_n))[0]=no_of_nodes;
LOGICAL(VECTOR_ELT(result, igraph_t_idx_directed))[0]=graph->directed;
memcpy(REAL(VECTOR_ELT(result, igraph_t_idx_from)), graph->from.stor_begin,
sizeof(igraph_real_t)*(size_t) no_of_edges);
memcpy(REAL(VECTOR_ELT(result, 3)), graph->to.stor_begin,
memcpy(REAL(VECTOR_ELT(result, igraph_t_idx_to)), graph->to.stor_begin,
sizeof(igraph_real_t)*(size_t) no_of_edges);
memcpy(REAL(VECTOR_ELT(result, 4)), graph->oi.stor_begin,
memcpy(REAL(VECTOR_ELT(result, igraph_t_idx_oi)), graph->oi.stor_begin,
sizeof(igraph_real_t)*(size_t) no_of_edges);
memcpy(REAL(VECTOR_ELT(result, 5)), graph->ii.stor_begin,
memcpy(REAL(VECTOR_ELT(result, igraph_t_idx_ii)), graph->ii.stor_begin,
sizeof(igraph_real_t)*(size_t) no_of_edges);
memcpy(REAL(VECTOR_ELT(result, 6)), graph->os.stor_begin,
memcpy(REAL(VECTOR_ELT(result, igraph_t_idx_os)), graph->os.stor_begin,
sizeof(igraph_real_t)*(size_t) (no_of_nodes+1));
memcpy(REAL(VECTOR_ELT(result, 7)), graph->is.stor_begin,
memcpy(REAL(VECTOR_ELT(result, igraph_t_idx_is)), graph->is.stor_begin,
sizeof(igraph_real_t)*(size_t) (no_of_nodes+1));

SET_CLASS(result, Rf_ScalarString(Rf_mkChar("igraph")));

/* Attributes */
SET_VECTOR_ELT(result, 8, graph->attr);
SET_VECTOR_ELT(result, igraph_t_idx_attr, graph->attr);
REAL(VECTOR_ELT(graph->attr, 0))[0] += 1;

/* Environment for vertex/edge seqs */
SET_VECTOR_ELT(result, 9, R_NilValue);
SET_VECTOR_ELT(result, igraph_t_idx_env, R_NilValue);
R_igraph_add_env(result);

UNPROTECT(1);
Expand Down Expand Up @@ -3479,44 +3492,44 @@ int R_igraph_SEXP_to_array3_copy(SEXP rval, igraph_array3_t *a) {

int R_SEXP_to_igraph(SEXP graph, igraph_t *res) {

res->n=(igraph_integer_t) REAL(VECTOR_ELT(graph, 0))[0];
res->directed=LOGICAL(VECTOR_ELT(graph, 1))[0];
R_SEXP_to_vector(VECTOR_ELT(graph, 2), &res->from);
R_SEXP_to_vector(VECTOR_ELT(graph, 3), &res->to);
R_SEXP_to_vector(VECTOR_ELT(graph, 4), &res->oi);
R_SEXP_to_vector(VECTOR_ELT(graph, 5), &res->ii);
R_SEXP_to_vector(VECTOR_ELT(graph, 6), &res->os);
R_SEXP_to_vector(VECTOR_ELT(graph, 7), &res->is);
res->n=(igraph_integer_t) REAL(VECTOR_ELT(graph, igraph_t_idx_n))[0];
res->directed=LOGICAL(VECTOR_ELT(graph, igraph_t_idx_directed))[0];
R_SEXP_to_vector(VECTOR_ELT(graph, igraph_t_idx_from), &res->from);
R_SEXP_to_vector(VECTOR_ELT(graph, igraph_t_idx_to), &res->to);
R_SEXP_to_vector(VECTOR_ELT(graph, igraph_t_idx_oi), &res->oi);
R_SEXP_to_vector(VECTOR_ELT(graph, igraph_t_idx_ii), &res->ii);
R_SEXP_to_vector(VECTOR_ELT(graph, igraph_t_idx_os), &res->os);
R_SEXP_to_vector(VECTOR_ELT(graph, igraph_t_idx_is), &res->is);

/* attributes */
REAL(VECTOR_ELT(VECTOR_ELT(graph, 8), 0))[0] = 1; /* R objects refcount */
REAL(VECTOR_ELT(VECTOR_ELT(graph, 8), 0))[1] = 0; /* igraph_t objects */
res->attr=VECTOR_ELT(graph, 8);
REAL(VECTOR_ELT(VECTOR_ELT(graph, igraph_t_idx_attr), 0))[0] = 1; /* R objects refcount */
REAL(VECTOR_ELT(VECTOR_ELT(graph, igraph_t_idx_attr), 0))[1] = 0; /* igraph_t objects */
res->attr=VECTOR_ELT(graph, igraph_t_idx_attr);

return 0;
}

int R_SEXP_to_igraph_copy(SEXP graph, igraph_t *res) {

res->n=(igraph_integer_t) REAL(VECTOR_ELT(graph, 0))[0];
res->directed=LOGICAL(VECTOR_ELT(graph, 1))[0];
igraph_vector_init_copy(&res->from, REAL(VECTOR_ELT(graph, 2)),
GET_LENGTH(VECTOR_ELT(graph, 2)));
igraph_vector_init_copy(&res->to, REAL(VECTOR_ELT(graph, 3)),
GET_LENGTH(VECTOR_ELT(graph, 3)));
igraph_vector_init_copy(&res->oi, REAL(VECTOR_ELT(graph, 4)),
GET_LENGTH(VECTOR_ELT(graph, 4)));
igraph_vector_init_copy(&res->ii, REAL(VECTOR_ELT(graph, 5)),
GET_LENGTH(VECTOR_ELT(graph, 5)));
igraph_vector_init_copy(&res->os, REAL(VECTOR_ELT(graph, 6)),
GET_LENGTH(VECTOR_ELT(graph, 6)));
igraph_vector_init_copy(&res->is, REAL(VECTOR_ELT(graph, 7)),
GET_LENGTH(VECTOR_ELT(graph, 7)));
res->n=(igraph_integer_t) REAL(VECTOR_ELT(graph, igraph_t_idx_n))[0];
res->directed=LOGICAL(VECTOR_ELT(graph, igraph_t_idx_directed))[0];
igraph_vector_init_copy(&res->from, REAL(VECTOR_ELT(graph, igraph_t_idx_from)),
GET_LENGTH(VECTOR_ELT(graph, igraph_t_idx_from)));
igraph_vector_init_copy(&res->to, REAL(VECTOR_ELT(graph, igraph_t_idx_to)),
GET_LENGTH(VECTOR_ELT(graph, igraph_t_idx_to)));
igraph_vector_init_copy(&res->oi, REAL(VECTOR_ELT(graph, igraph_t_idx_oi)),
GET_LENGTH(VECTOR_ELT(graph, igraph_t_idx_oi)));
igraph_vector_init_copy(&res->ii, REAL(VECTOR_ELT(graph, igraph_t_idx_ii)),
GET_LENGTH(VECTOR_ELT(graph, igraph_t_idx_ii)));
igraph_vector_init_copy(&res->os, REAL(VECTOR_ELT(graph, igraph_t_idx_os)),
GET_LENGTH(VECTOR_ELT(graph, igraph_t_idx_os)));
igraph_vector_init_copy(&res->is, REAL(VECTOR_ELT(graph, igraph_t_idx_is)),
GET_LENGTH(VECTOR_ELT(graph, igraph_t_idx_is)));

/* attributes */
REAL(VECTOR_ELT(VECTOR_ELT(graph, 8), 0))[0] = 1; /* R objects */
REAL(VECTOR_ELT(VECTOR_ELT(graph, 8), 0))[1] = 1; /* igraph_t objects */
R_PreserveObject(res->attr=VECTOR_ELT(graph, 8));
REAL(VECTOR_ELT(VECTOR_ELT(graph, igraph_t_idx_attr), 0))[0] = 1; /* R objects */
REAL(VECTOR_ELT(VECTOR_ELT(graph, igraph_t_idx_attr), 0))[1] = 1; /* igraph_t objects */
R_PreserveObject(res->attr=VECTOR_ELT(graph, igraph_t_idx_attr));

return 0;
}
Expand Down Expand Up @@ -9700,7 +9713,7 @@ SEXP R_igraph_weak_ref_run_finalizer(SEXP ref) {

SEXP R_igraph_identical_graphs(SEXP g1, SEXP g2, SEXP attrs) {
int i;
int n = LOGICAL(attrs)[0] ? 9 : 8;
int n = LOGICAL(attrs)[0] ? igraph_t_idx_attr + 1 : igraph_t_idx_attr;
for (i = 0; i < n; i++) {
if (!R_compute_identical(VECTOR_ELT(g1, i), VECTOR_ELT(g2, i), 0)) {
return Rf_ScalarLogical(0);
Expand All @@ -9709,9 +9722,13 @@ SEXP R_igraph_identical_graphs(SEXP g1, SEXP g2, SEXP attrs) {
return Rf_ScalarLogical(1);
}

SEXP R_igraph_graph_env(SEXP graph) {
return VECTOR_ELT(graph, igraph_t_idx_env);
}

SEXP R_igraph_graph_version(SEXP graph) {
if (GET_LENGTH(graph) == 10 && Rf_isEnvironment(VECTOR_ELT(graph, 9))) {
SEXP ver = Rf_findVar(Rf_install(R_IGRAPH_VERSION_VAR), VECTOR_ELT(graph, 9));
if (GET_LENGTH(graph) == igraph_t_idx_max && Rf_isEnvironment(R_igraph_graph_env(graph))) {
SEXP ver = Rf_findVar(Rf_install(R_IGRAPH_VERSION_VAR), R_igraph_graph_env(graph));
if (ver != R_UnboundValue) {
return ver;
} else {
Expand All @@ -9732,11 +9749,11 @@ SEXP R_igraph_add_version_to_env(SEXP graph) {
uuid_unparse_lower(my_id, my_id_chr);
SEXP l1 = PROTECT(Rf_install("myid"));
SEXP l2 = PROTECT(Rf_mkString(my_id_chr));
Rf_defineVar(l1, l2, VECTOR_ELT(graph, 9));
Rf_defineVar(l1, l2, R_igraph_graph_env(graph));
UNPROTECT(2);
l1 = PROTECT(Rf_install(R_IGRAPH_VERSION_VAR));
l2 = PROTECT(Rf_mkString(R_IGRAPH_TYPE_VERSION));
Rf_defineVar(l1, l2, VECTOR_ELT(graph, 9));
Rf_defineVar(l1, l2, R_igraph_graph_env(graph));
UNPROTECT(2);

UNPROTECT(1);
Expand All @@ -9750,33 +9767,33 @@ SEXP R_igraph_add_env(SEXP graph) {
char my_id_chr[40];
int px = 0;

if (GET_LENGTH(graph) != 10) {
PROTECT(result = NEW_LIST(10)); px++;
for (i = 0; i < 9; i++) {
if (GET_LENGTH(graph) <= igraph_t_idx_env) {
PROTECT(result = NEW_LIST(igraph_t_idx_max)); px++;
for (i = 0; i < igraph_t_idx_env; i++) {
SET_VECTOR_ELT(result, i, Rf_duplicate(VECTOR_ELT(graph, i)));
}
SET_ATTRIB(result, Rf_duplicate(ATTRIB(graph)));
SET_CLASS(result, Rf_duplicate(GET_CLASS(graph)));
}

SET_VECTOR_ELT(result, 9, Rf_allocSExp(ENVSXP));
SET_VECTOR_ELT(result, igraph_t_idx_env, Rf_allocSExp(ENVSXP));

uuid_generate(my_id);
uuid_unparse_lower(my_id, my_id_chr);

SEXP l1 = PROTECT(Rf_install("myid")); px++;
SEXP l2 = PROTECT(Rf_mkString(my_id_chr)); px++;
Rf_defineVar(l1, l2, VECTOR_ELT(result, 9));
Rf_defineVar(l1, l2, R_igraph_graph_env(result));

l1 = PROTECT(Rf_install(R_IGRAPH_VERSION_VAR)); px++;
l2 = PROTECT(Rf_mkString(R_IGRAPH_TYPE_VERSION)); px++;
Rf_defineVar(l1, l2, VECTOR_ELT(result, 9));
Rf_defineVar(l1, l2, R_igraph_graph_env(result));

UNPROTECT(px);

return result;
}

SEXP R_igraph_get_graph_id(SEXP graph) {
return Rf_findVar(Rf_install("myid"), VECTOR_ELT(graph, 9));
return Rf_findVar(Rf_install("myid"), R_igraph_graph_env(graph));
}