Skip to content

Do not use kastore memory for columns. #530

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
jeromekelleher merged 2 commits into from
Apr 16, 2020
Merged

Do not use kastore memory for columns. #530

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
a4a7220
Do not use kastore memory for columns.
jeromekelleher Apr 11, 2020
e63b9ae
Split file format tests to new file.
jeromekelleher Apr 14, 2020
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 2 additions & 0 deletions .circleci/config.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -109,6 +109,7 @@ jobs:
gcov -pb tskit@sta/tskit_convert.c.gcno ../c/tskit/convert.c
gcov -pb tskit@sta/tskit_stats.c.gcno ../c/tskit/stats.c
gcov -pb tskit@sta/tskit_haplotype_matching.c.gcno ../c/tskit/haplotype_matching.c
gcov -pb tskit@sta/tskit_file_format.c.gcno ../c/tskit/file_format.c
cd ..
codecov -X gcov -F c_tests

Expand All @@ -122,6 +123,7 @@ jobs:
valgrind --leak-check=full --error-exitcode=1 ./build-gcc/test_convert
valgrind --leak-check=full --error-exitcode=1 ./build-gcc/test_stats
valgrind --leak-check=full --error-exitcode=1 ./build-gcc/test_haplotype_matching
valgrind --leak-check=full --error-exitcode=1 ./build-gcc/test_file_format
valgrind --leak-check=full --error-exitcode=1 ./build-gcc/test_minimal_cpp

- run:
Expand Down
3 changes: 3 additions & 0 deletions c/CHANGELOG.rst
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -48,6 +48,9 @@ In development.
- Tables with metadata now have an optional `metadata_schema` field that can contain
arbitary bytes. (:user:`benjeffery`, :pr:`493`)

- Tables loaded from a file can now be edited in the same way as any other
table collection (:user:`jeromekelleher`, :issue:`536`, :pr:`530`.


**Deprecated**

Expand Down
68 changes: 36 additions & 32 deletions c/meson.build
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -15,95 +15,99 @@ extra_c_args = [
'-fshort-enums', '-fno-common']

lib_sources = [
'tskit/core.c', 'tskit/tables.c', 'tskit/trees.c',
'tskit/core.c', 'tskit/tables.c', 'tskit/trees.c',
'tskit/genotypes.c', 'tskit/stats.c', 'tskit/convert.c', 'tskit/haplotype_matching.c']
lib_headers = [
'tskit/core.h', 'tskit/tables.h', 'tskit/trees.h',
'tskit/core.h', 'tskit/tables.h', 'tskit/trees.h',
'tskit/genotypes.h', 'tskit/stats.h', 'tskit/convert.h', 'tskit/haplotype_matching.h']

# Subprojects use the static library for simplicity.
inc = include_directories(['.', 'tskit'])
tskit_lib = static_library('tskit',
tskit_lib = static_library('tskit',
sources: lib_sources, dependencies: lib_deps)
tskit_dep = declare_dependency(include_directories:inc, link_with: tskit_lib)

if not meson.is_subproject()

# Shared library install target.
shared_library('tskit',
shared_library('tskit',
sources: lib_sources, dependencies: lib_deps, c_args: extra_c_args, install: true)
install_headers('tskit.h')
install_headers(lib_headers, subdir: 'tskit')
install_headers(lib_headers, subdir: 'tskit')

cunit_dep = dependency('cunit')
# We don't specify extra C args here as CUnit won't pass the checks.
test_lib = static_library('testlib',
test_lib = static_library('testlib',
sources: ['tests/testlib.c'], dependencies: [cunit_dep, kastore_dep, tskit_dep])

test_core = executable('test_core',
sources: ['tests/test_core.c'],
test_core = executable('test_core',
sources: ['tests/test_core.c'],
link_with: [tskit_lib, test_lib], c_args: extra_c_args, dependencies: kastore_dep)
test('core', test_core)

test_tables = executable('test_tables',
sources: ['tests/test_tables.c'],
test_tables = executable('test_tables',
sources: ['tests/test_tables.c'],
link_with: [tskit_lib, test_lib], c_args: extra_c_args, dependencies: kastore_dep)
test('tables', test_tables)

test_trees = executable('test_trees',
sources: ['tests/test_trees.c'],
test_trees = executable('test_trees',
sources: ['tests/test_trees.c'],
link_with: [tskit_lib, test_lib], c_args: extra_c_args, dependencies: kastore_dep)
test('trees', test_trees)

test_genotypes = executable('test_genotypes',
sources: ['tests/test_genotypes.c'],
test_genotypes = executable('test_genotypes',
sources: ['tests/test_genotypes.c'],
link_with: [tskit_lib, test_lib], c_args: extra_c_args, dependencies: kastore_dep)
test('genotypes', test_genotypes)

test_convert = executable('test_convert',
sources: ['tests/test_convert.c'],
test_convert = executable('test_convert',
sources: ['tests/test_convert.c'],
link_with: [tskit_lib, test_lib], c_args: extra_c_args, dependencies: kastore_dep)
test('convert', test_convert)
test_stats = executable('test_stats',
sources: ['tests/test_stats.c'],

test_stats = executable('test_stats',
sources: ['tests/test_stats.c'],
link_with: [tskit_lib, test_lib], c_args: extra_c_args, dependencies: kastore_dep)
test('stats', test_stats)

test_haplotype_matching = executable('test_haplotype_matching',
sources: ['tests/test_haplotype_matching.c'],
test_haplotype_matching = executable('test_haplotype_matching',
sources: ['tests/test_haplotype_matching.c'],
link_with: [tskit_lib, test_lib], c_args: extra_c_args, dependencies: kastore_dep)
test('haplotype_matching', test_haplotype_matching)

test_minimal_cpp = executable('test_minimal_cpp',
test_file_format = executable('test_file_format',
sources: ['tests/test_file_format.c'],
link_with: [tskit_lib, test_lib], c_args: extra_c_args, dependencies: kastore_dep)
test('file_format', test_file_format)

test_minimal_cpp = executable('test_minimal_cpp',
sources: ['tests/test_minimal_cpp.cpp'], link_with: [tskit_lib],
dependencies: kastore_dep)
test('minimal_cpp', test_minimal_cpp)

# The development CLI. Don't use extra C args because argtable code won't pass
executable('dev-cli',
sources: ['dev-tools/dev-cli.c', 'dev-tools/argtable3.c'],
executable('dev-cli',
sources: ['dev-tools/dev-cli.c', 'dev-tools/argtable3.c'],
link_with: [tskit_lib], c_args:['-Dlint'], dependencies: kastore_dep)

# Example programs.
executable('api_structure',
# Example programs.
executable('api_structure',
sources: ['examples/api_structure.c'], link_with: [tskit_lib], dependencies: lib_deps)
executable('error_handling',
executable('error_handling',
sources: ['examples/error_handling.c'], link_with: [tskit_lib], dependencies: lib_deps)
executable('tree_iteration',
executable('tree_iteration',
sources: ['examples/tree_iteration.c'], link_with: [tskit_lib], dependencies: lib_deps)
executable('tree_traversal',
executable('tree_traversal',
sources: ['examples/tree_traversal.c'], link_with: [tskit_lib], dependencies: lib_deps)

gsl_dep = dependency('gsl', required: false)
if gsl_dep.found()
executable('haploid_wright_fisher',
executable('haploid_wright_fisher',
sources: ['examples/haploid_wright_fisher.c'], link_with: [tskit_lib],
dependencies: [gsl_dep, lib_deps])
endif
endif

# TMP: until we've ported all the tests, keep this compilable.
# gsl_dep = dependency('gsl')
# executable('old_tests', sources: ['tests/old_tests.c'], link_with: tskit_lib,
# dependencies: [cunit_dep, gsl_dep])
# executable('old_tests', sources: ['tests/old_tests.c'], link_with: tskit_lib, # dependencies: [cunit_dep, gsl_dep])
Loading