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Add dense pair support in the API #57

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merged 20 commits into from
Jan 14, 2025
Merged

Add dense pair support in the API #57

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2d05089
Add cstring equivalents for BPTree methods
sfiligoi Jan 7, 2025
df1bc03
Add load_bptree_opaque and one_off_wtree
sfiligoi Jan 5, 2025
55449df
Add one_off_matrix_v2_T to reduce code replication
sfiligoi Jan 6, 2025
864c19c
Add one_off_matrix_v2t and add test in capi
sfiligoi Jan 6, 2025
11645a0
Rename load_bptree_opaque to read_bptree_opaque, load_bptree_opaque n…
sfiligoi Jan 7, 2025
2a895f0
Change opaque_bptree_t struct and add get_bptree_opaque_els
sfiligoi Jan 7, 2025
dbaedf4
Pass by reference, not by value
sfiligoi Jan 7, 2025
211e0da
Add one_dense_pair_v2t, which required addind a dense option to biom_…
sfiligoi Jan 8, 2025
9c3fc99
Add pair test
sfiligoi Jan 10, 2025
b65a192
Add docstring to one_dense_pair_v2t
sfiligoi Jan 10, 2025
f1916ae
Add convert_bptree_opaque and one_dense_pair_v2
sfiligoi Jan 10, 2025
bd2603d
Add test_bptree_constructor_inmem and test_biom_constructor_from_dense
sfiligoi Jan 10, 2025
90ca67e
Add capi_inmem_test.c
sfiligoi Jan 10, 2025
b63cc3f
Add test_bptree_constructor_simple_cpp
sfiligoi Jan 10, 2025
a3f7531
Exercise old API, too
sfiligoi Jan 10, 2025
bcbdd94
Add dynlib selectors for the new functions
sfiligoi Jan 10, 2025
365151f
Fix typo
sfiligoi Jan 10, 2025
656c68a
Run capi_inmem_test in the CI
sfiligoi Jan 10, 2025
8165bb1
Fix tab vs space issue
sfiligoi Jan 14, 2025
48cbb11
Fix typo
sfiligoi Jan 14, 2025
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1 change: 1 addition & 0 deletions .github/workflows/main.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -94,6 +94,7 @@ jobs:
popd
pushd test
./capi_test 1
./capi_inmem_test 1
# explicitly check that we do not have hdf5 dependencies
if [[ "$(uname -s)" == "Linux" ]];
then
Expand Down
96 changes: 96 additions & 0 deletions combined/libssu.c
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Original file line number Diff line number Diff line change
Expand Up @@ -106,6 +106,12 @@ static void (*dl_destroy_mat_full_fp32)(mat_full_fp32_t**) = NULL;
static void (*dl_destroy_partial_mat)(partial_mat_t**) = NULL;
static void (*dl_destroy_partial_dyn_mat)(partial_dyn_mat_t**) = NULL;
static void (*dl_destroy_results_vec)(r_vec**) = NULL;
static void (*dl_destroy_bptree_opaque)(opaque_bptree_t**) = NULL;

static IOStatus (*dl_read_bptree_opaque)(const char*, opaque_bptree_t**) = NULL;
static void (*dl_load_bptree_opaque)(const char*, opaque_bptree_t**) = NULL;
static void (*dl_convert_bptree_opaque)(const support_bptree_t*, opaque_bptree_t**) = NULL;
static int (*dl_get_bptree_opaque_els)(opaque_bptree_t*) = NULL;

void destroy_mat(mat_t** result) {
if (dl_destroy_mat==NULL) ssu_load("destroy_mat", (void **) &dl_destroy_mat);
Expand Down Expand Up @@ -143,9 +149,41 @@ void destroy_results_vec(r_vec** result) {
(*dl_destroy_results_vec)(result);
}

void destroy_bptree_opaque(opaque_bptree_t** tree_data) {
if (dl_destroy_bptree_opaque==NULL) ssu_load("destroy_bptree_opaque", (void **) &dl_destroy_bptree_opaque);
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This is cool


(*dl_destroy_bptree_opaque)(tree_data);
}

IOStatus read_bptree_opaque(const char* tree_filename, opaque_bptree_t** tree_data) {
if (dl_read_bptree_opaque==NULL) ssu_load("read_bptree_opaque", (void **) &dl_read_bptree_opaque);

return (*dl_read_bptree_opaque)(tree_filename,tree_data);
}

void load_bptree_opaque(const char* newick, opaque_bptree_t** tree_data) {
if (dl_load_bptree_opaque==NULL) ssu_load("load_bptree_opaque", (void **) &dl_load_bptree_opaque);

(*dl_load_bptree_opaque)(newick,tree_data);
}

void convert_bptree_opaque(const support_bptree_t* in_tree, opaque_bptree_t** tree_data) {
if (dl_convert_bptree_opaque==NULL) ssu_load("convert_bptree_opaque", (void **) &dl_convert_bptree_opaque);

(*dl_convert_bptree_opaque)(in_tree,tree_data);
}

int get_bptree_opaque_els(opaque_bptree_t* tree_data) {
if (dl_get_bptree_opaque_els==NULL) ssu_load("get_bptree_opaque_els", (void **) &dl_get_bptree_opaque_els);

return (*dl_get_bptree_opaque_els)(tree_data);
}

/*********************************************************************/

static ComputeStatus (*dl_one_off)(const char*, const char*, const char*, bool, double, bool, unsigned int, mat_t**) = NULL;
static ComputeStatus (*dl_one_off_wtree)(const char*, const opaque_bptree_t*, const char*, bool, double, bool, unsigned int, mat_t**) = NULL;

ComputeStatus one_off(const char* biom_filename, const char* tree_filename,
const char* unifrac_method, bool variance_adjust, double alpha,
bool bypass_tips, unsigned int n_substeps, mat_t** result) {
Expand All @@ -154,6 +192,14 @@ ComputeStatus one_off(const char* biom_filename, const char* tree_filename,
return (*dl_one_off)(biom_filename, tree_filename, unifrac_method, variance_adjust, alpha, bypass_tips, n_substeps, result);
}

ComputeStatus one_off_wtree(const char* biom_filename, const opaque_bptree_t* tree_data,
const char* unifrac_method, bool variance_adjust, double alpha,
bool bypass_tips, unsigned int n_substeps, mat_t** result) {
if (dl_one_off_wtree==NULL) ssu_load("one_off_wtree", (void **) &dl_one_off_wtree);

return (*dl_one_off_wtree)(biom_filename, tree_data, unifrac_method, variance_adjust, alpha, bypass_tips, n_substeps, result);
}

/*********************************************************************/

static ComputeStatus (*dl_one_off_matrix_inmem_v2)(const support_biom_t *, const support_bptree_t *, const char*, bool, double,
Expand Down Expand Up @@ -207,10 +253,14 @@ ComputeStatus one_off_inmem_fp32(const support_biom_t *table_data, const support

static ComputeStatus (*dl_one_off_matrix_v2)(const char*, const char*, const char*, bool, double,
bool, unsigned int, unsigned int, bool, const char *, mat_full_fp64_t**) = NULL;
static ComputeStatus (*dl_one_off_matrix_v2t)(const char*, const opaque_bptree_t*, const char*, bool, double,
bool, unsigned int, unsigned int, bool, const char *, mat_full_fp64_t**) = NULL;
static ComputeStatus (*dl_one_off_matrix)(const char*, const char*, const char*, bool, double,
bool, unsigned int, const char *, mat_full_fp64_t**) = NULL;
static ComputeStatus (*dl_one_off_matrix_fp32_v2)(const char*, const char*, const char*, bool, double,
bool, unsigned int, unsigned int, bool, const char *, mat_full_fp32_t**) = NULL;
static ComputeStatus (*dl_one_off_matrix_fp32_v2t)(const char*, const opaque_bptree_t*, const char*, bool, double,
bool, unsigned int, unsigned int, bool, const char *, mat_full_fp32_t**) = NULL;
static ComputeStatus (*dl_one_off_matrix_fp32)(const char*, const char*, const char*, bool, double,
bool, unsigned int, const char *, mat_full_fp32_t**) = NULL;

Expand All @@ -225,6 +275,17 @@ ComputeStatus one_off_matrix_v2(const char* biom_filename, const char* tree_file
bypass_tips, n_substeps, subsample_depth, subsample_with_replacement, mmap_dir, result);
}

ComputeStatus one_off_matrix_v2t(const char* biom_filename, const opaque_bptree_t* tree_data,
const char* unifrac_method, bool variance_adjust, double alpha,
bool bypass_tips, unsigned int n_substeps,
unsigned int subsample_depth, bool subsample_with_replacement, const char *mmap_dir,
mat_full_fp64_t** result) {
if (dl_one_off_matrix_v2t==NULL) ssu_load("one_off_matrix_v2t", (void **) &dl_one_off_matrix_v2t);

return (*dl_one_off_matrix_v2t)(biom_filename, tree_data, unifrac_method, variance_adjust, alpha,
bypass_tips, n_substeps, subsample_depth, subsample_with_replacement, mmap_dir, result);
}

ComputeStatus one_off_matrix(const char* biom_filename, const char* tree_filename,
const char* unifrac_method, bool variance_adjust, double alpha,
bool bypass_tips, unsigned int n_substeps,
Expand All @@ -247,6 +308,17 @@ ComputeStatus one_off_matrix_fp32_v2(const char* biom_filename, const char* tree
bypass_tips, n_substeps, subsample_depth, subsample_with_replacement, mmap_dir, result);
}

ComputeStatus one_off_matrix_fp32_v2t(const char* biom_filename, const opaque_bptree_t* tree_data,
const char* unifrac_method, bool variance_adjust, double alpha,
bool bypass_tips, unsigned int n_substeps,
unsigned int subsample_depth, bool subsample_with_replacement, const char *mmap_dir,
mat_full_fp32_t** result) {
if (dl_one_off_matrix_fp32_v2t==NULL) ssu_load("one_off_matrix_fp32_v2t", (void **) &dl_one_off_matrix_fp32_v2t);

return (*dl_one_off_matrix_fp32_v2t)(biom_filename, tree_data, unifrac_method, variance_adjust, alpha,
bypass_tips, n_substeps, subsample_depth, subsample_with_replacement, mmap_dir, result);
}

ComputeStatus one_off_matrix_fp32(const char* biom_filename, const char* tree_filename,
const char* unifrac_method, bool variance_adjust, double alpha,
bool bypass_tips, unsigned int n_substeps,
Expand Down Expand Up @@ -413,3 +485,27 @@ IOStatus write_mat_from_matrix_hdf5_fp32(const char* filename, mat_full_fp32_t*
}


/*********************************************************************/

static ComputeStatus (*dl_one_dense_pair_v2t)(unsigned int, const char **, const double*,const double*,const opaque_bptree_t*,const char*, bool, double,bool, double*) = NULL;
static ComputeStatus (*dl_one_dense_pair_v2)(unsigned int, const char **, const double*,const double*,const support_bptree_t*,const char*, bool, double,bool, double*) = NULL;

ComputeStatus one_dense_pair_v2t(unsigned int n_obs, const char ** obs_ids, const double* sample1, const double* sample2,
const opaque_bptree_t* tree_data,
const char* unifrac_method, bool variance_adjust, double alpha,
bool bypass_tips, double* result) {
if (dl_one_dense_pair_v2t==NULL) ssu_load("one_dense_pair_v2t", (void **) &dl_one_dense_pair_v2t);

return (*dl_one_dense_pair_v2t)(n_obs,obs_ids,sample1,sample2,tree_data,unifrac_method,variance_adjust,alpha,bypass_tips,result);
}

ComputeStatus one_dense_pair_v2(unsigned int n_obs, const char ** obs_ids, const double* sample1, const double* sample2,
const support_bptree_t* tree_data,
const char* unifrac_method, bool variance_adjust, double alpha,
bool bypass_tips, double* result) {
if (dl_one_dense_pair_v2==NULL) ssu_load("one_dense_pair_v2", (void **) &dl_one_dense_pair_v2);

return (*dl_one_dense_pair_v2)(n_obs,obs_ids,sample1,sample2,tree_data,unifrac_method,variance_adjust,alpha,bypass_tips,result);
}


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