From 839dd668713ec16b646d3bd9c9eb6f37d7c12e35 Mon Sep 17 00:00:00 2001 From: Sean Bryan Date: Wed, 20 Mar 2024 15:57:02 +1100 Subject: [PATCH 1/2] Switch to src layout --- setup.cfg | 17 ++++++++++++++++- {benchcab => src/benchcab}/__init__.py | 0 {benchcab => src/benchcab}/benchcab.py | 0 {benchcab => src/benchcab}/cli.py | 0 {benchcab => src/benchcab}/comparison.py | 0 {benchcab => src/benchcab}/config.py | 0 .../benchcab}/data/config-schema.yml | 0 .../benchcab}/data/pbs_jobscript.j2 | 0 .../benchcab}/data/test/config-basic.yml | 0 .../benchcab}/data/test/config-invalid.yml | 0 .../benchcab}/data/test/config-optional.yml | 0 .../benchcab}/data/test/integration.sh | 0 .../data/test/pbs_jobscript_default.sh | 0 .../data/test/pbs_jobscript_skip_bitwise.sh | 0 .../data/test/pbs_jobscript_verbose.sh | 0 .../benchcab}/data/test/template.j2 | 0 .../benchcab}/environment_modules.py | 0 {benchcab => src/benchcab}/fluxsite.py | 0 {benchcab => src/benchcab}/internal.py | 0 {benchcab => src/benchcab}/main.py | 0 {benchcab => src/benchcab}/model.py | 0 {benchcab => src/benchcab}/spatial.py | 0 {benchcab => src/benchcab}/utils/__init__.py | 0 {benchcab => src/benchcab}/utils/dict.py | 0 {benchcab => src/benchcab}/utils/fs.py | 0 {benchcab => src/benchcab}/utils/namelist.py | 0 {benchcab => src/benchcab}/utils/pbs.py | 0 {benchcab => src/benchcab}/utils/repo.py | 0 {benchcab => src/benchcab}/utils/subprocess.py | 0 {benchcab => src/benchcab}/workdir.py | 0 30 files changed, 16 insertions(+), 1 deletion(-) rename {benchcab => src/benchcab}/__init__.py (100%) rename {benchcab => src/benchcab}/benchcab.py (100%) rename {benchcab => src/benchcab}/cli.py (100%) rename {benchcab => src/benchcab}/comparison.py (100%) rename {benchcab => src/benchcab}/config.py (100%) rename {benchcab => src/benchcab}/data/config-schema.yml (100%) rename {benchcab => src/benchcab}/data/pbs_jobscript.j2 (100%) rename {benchcab => src/benchcab}/data/test/config-basic.yml (100%) rename {benchcab => src/benchcab}/data/test/config-invalid.yml (100%) rename {benchcab => src/benchcab}/data/test/config-optional.yml (100%) rename {benchcab => src/benchcab}/data/test/integration.sh (100%) rename {benchcab => src/benchcab}/data/test/pbs_jobscript_default.sh (100%) rename {benchcab => src/benchcab}/data/test/pbs_jobscript_skip_bitwise.sh (100%) rename {benchcab => src/benchcab}/data/test/pbs_jobscript_verbose.sh (100%) rename {benchcab => src/benchcab}/data/test/template.j2 (100%) rename {benchcab => src/benchcab}/environment_modules.py (100%) rename {benchcab => src/benchcab}/fluxsite.py (100%) rename {benchcab => src/benchcab}/internal.py (100%) rename {benchcab => src/benchcab}/main.py (100%) rename {benchcab => src/benchcab}/model.py (100%) rename {benchcab => src/benchcab}/spatial.py (100%) rename {benchcab => src/benchcab}/utils/__init__.py (100%) rename {benchcab => src/benchcab}/utils/dict.py (100%) rename {benchcab => src/benchcab}/utils/fs.py (100%) rename {benchcab => src/benchcab}/utils/namelist.py (100%) rename {benchcab => src/benchcab}/utils/pbs.py (100%) rename {benchcab => src/benchcab}/utils/repo.py (100%) rename {benchcab => src/benchcab}/utils/subprocess.py (100%) rename {benchcab => src/benchcab}/workdir.py (100%) diff --git a/setup.cfg b/setup.cfg index 1f7d9990..b2a4e504 100644 --- a/setup.cfg +++ b/setup.cfg @@ -16,7 +16,22 @@ console_scripts = benchcab=benchcab.main:main [tool:pytest] -addopts = --doctest-modules --doctest-glob='*.rst' --ignore setup.py --ignore conftest.py --ignore docs/conf.py +testpaths = tests +addopts = + --doctest-modules + --doctest-glob='*.rst' + --ignore setup.py + --ignore conftest.py + --ignore docs/conf.py + --import-mode=importlib + +[options] +package_dir= + =src +packages=find: + +[options.packages.find] +where=src [options.package_data] benchcab = diff --git a/benchcab/__init__.py b/src/benchcab/__init__.py similarity index 100% rename from benchcab/__init__.py rename to src/benchcab/__init__.py diff --git a/benchcab/benchcab.py b/src/benchcab/benchcab.py similarity index 100% rename from benchcab/benchcab.py rename to src/benchcab/benchcab.py diff --git a/benchcab/cli.py b/src/benchcab/cli.py similarity index 100% rename from benchcab/cli.py rename to src/benchcab/cli.py diff --git a/benchcab/comparison.py b/src/benchcab/comparison.py similarity index 100% rename from benchcab/comparison.py rename to src/benchcab/comparison.py diff --git a/benchcab/config.py b/src/benchcab/config.py similarity index 100% rename from benchcab/config.py rename to src/benchcab/config.py diff --git a/benchcab/data/config-schema.yml b/src/benchcab/data/config-schema.yml similarity index 100% rename from benchcab/data/config-schema.yml rename to src/benchcab/data/config-schema.yml diff --git a/benchcab/data/pbs_jobscript.j2 b/src/benchcab/data/pbs_jobscript.j2 similarity index 100% rename from benchcab/data/pbs_jobscript.j2 rename to src/benchcab/data/pbs_jobscript.j2 diff --git a/benchcab/data/test/config-basic.yml b/src/benchcab/data/test/config-basic.yml similarity index 100% rename from benchcab/data/test/config-basic.yml rename to src/benchcab/data/test/config-basic.yml diff --git a/benchcab/data/test/config-invalid.yml b/src/benchcab/data/test/config-invalid.yml similarity index 100% rename from benchcab/data/test/config-invalid.yml rename to src/benchcab/data/test/config-invalid.yml diff --git a/benchcab/data/test/config-optional.yml b/src/benchcab/data/test/config-optional.yml similarity index 100% rename from benchcab/data/test/config-optional.yml rename to src/benchcab/data/test/config-optional.yml diff --git a/benchcab/data/test/integration.sh b/src/benchcab/data/test/integration.sh similarity index 100% rename from benchcab/data/test/integration.sh rename to src/benchcab/data/test/integration.sh diff --git a/benchcab/data/test/pbs_jobscript_default.sh b/src/benchcab/data/test/pbs_jobscript_default.sh similarity index 100% rename from benchcab/data/test/pbs_jobscript_default.sh rename to src/benchcab/data/test/pbs_jobscript_default.sh diff --git a/benchcab/data/test/pbs_jobscript_skip_bitwise.sh b/src/benchcab/data/test/pbs_jobscript_skip_bitwise.sh similarity index 100% rename from benchcab/data/test/pbs_jobscript_skip_bitwise.sh rename to src/benchcab/data/test/pbs_jobscript_skip_bitwise.sh diff --git a/benchcab/data/test/pbs_jobscript_verbose.sh b/src/benchcab/data/test/pbs_jobscript_verbose.sh similarity index 100% rename from benchcab/data/test/pbs_jobscript_verbose.sh rename to src/benchcab/data/test/pbs_jobscript_verbose.sh diff --git a/benchcab/data/test/template.j2 b/src/benchcab/data/test/template.j2 similarity index 100% rename from benchcab/data/test/template.j2 rename to src/benchcab/data/test/template.j2 diff --git a/benchcab/environment_modules.py b/src/benchcab/environment_modules.py similarity index 100% rename from benchcab/environment_modules.py rename to src/benchcab/environment_modules.py diff --git a/benchcab/fluxsite.py b/src/benchcab/fluxsite.py similarity index 100% rename from benchcab/fluxsite.py rename to src/benchcab/fluxsite.py diff --git a/benchcab/internal.py b/src/benchcab/internal.py similarity index 100% rename from benchcab/internal.py rename to src/benchcab/internal.py diff --git a/benchcab/main.py b/src/benchcab/main.py similarity index 100% rename from benchcab/main.py rename to src/benchcab/main.py diff --git a/benchcab/model.py b/src/benchcab/model.py similarity index 100% rename from benchcab/model.py rename to src/benchcab/model.py diff --git a/benchcab/spatial.py b/src/benchcab/spatial.py similarity index 100% rename from benchcab/spatial.py rename to src/benchcab/spatial.py diff --git a/benchcab/utils/__init__.py b/src/benchcab/utils/__init__.py similarity index 100% rename from benchcab/utils/__init__.py rename to src/benchcab/utils/__init__.py diff --git a/benchcab/utils/dict.py b/src/benchcab/utils/dict.py similarity index 100% rename from benchcab/utils/dict.py rename to src/benchcab/utils/dict.py diff --git a/benchcab/utils/fs.py b/src/benchcab/utils/fs.py similarity index 100% rename from benchcab/utils/fs.py rename to src/benchcab/utils/fs.py diff --git a/benchcab/utils/namelist.py b/src/benchcab/utils/namelist.py similarity index 100% rename from benchcab/utils/namelist.py rename to src/benchcab/utils/namelist.py diff --git a/benchcab/utils/pbs.py b/src/benchcab/utils/pbs.py similarity index 100% rename from benchcab/utils/pbs.py rename to src/benchcab/utils/pbs.py diff --git a/benchcab/utils/repo.py b/src/benchcab/utils/repo.py similarity index 100% rename from benchcab/utils/repo.py rename to src/benchcab/utils/repo.py diff --git a/benchcab/utils/subprocess.py b/src/benchcab/utils/subprocess.py similarity index 100% rename from benchcab/utils/subprocess.py rename to src/benchcab/utils/subprocess.py diff --git a/benchcab/workdir.py b/src/benchcab/workdir.py similarity index 100% rename from benchcab/workdir.py rename to src/benchcab/workdir.py From 59910edec4b8fdc76344747620d6e0c43ca1da97 Mon Sep 17 00:00:00 2001 From: Sean Bryan Date: Thu, 21 Mar 2024 13:56:59 +1100 Subject: [PATCH 2/2] Fix code coverage generation in CI workflow --- .github/workflows/ci.yaml | 5 +++++ setup.cfg | 3 +++ 2 files changed, 8 insertions(+) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index e6384dc5..826cb5c3 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -31,6 +31,11 @@ jobs: - name: Test with pytest run: | conda install pytest-cov + pytest + - name: Generate coverage reports + run: | + conda remove --force benchcab + pip install -e . pytest --cov=./ --cov-report=xml - name: Upload coverage reports to Codecov uses: codecov/codecov-action@v3 diff --git a/setup.cfg b/setup.cfg index b2a4e504..8adf2f01 100644 --- a/setup.cfg +++ b/setup.cfg @@ -25,6 +25,9 @@ addopts = --ignore docs/conf.py --import-mode=importlib +[coverage:report] +include = src/* + [options] package_dir= =src