Merge pull request #271 from CABLE-LSM/270-switch-to-src-layout

Switch to src layout
CABLE-LSM · Mar 21, 2024 · ef0dc85 · ef0dc85
2 parents f19781b + 59910ed
commit ef0dc85
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Showing 31 changed files with 24 additions and 1 deletion.
diff --git 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
@@ -16,7 +16,25 @@ 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
+
+[coverage:report]
+include = src/*
+
+[options]
+package_dir=
+    =src
+packages=find:
+
+[options.packages.find]
+where=src
 
 [options.package_data]
 benchcab =

diff --git a/benchcab/__init__.py → src/benchcab/__init__.py b/benchcab/__init__.py → src/benchcab/__init__.py
diff --git a/benchcab/benchcab.py → src/benchcab/benchcab.py b/benchcab/benchcab.py → src/benchcab/benchcab.py
diff --git a/benchcab/cli.py → src/benchcab/cli.py b/benchcab/cli.py → src/benchcab/cli.py
diff --git a/benchcab/comparison.py → src/benchcab/comparison.py b/benchcab/comparison.py → src/benchcab/comparison.py
diff --git a/benchcab/config.py → src/benchcab/config.py b/benchcab/config.py → src/benchcab/config.py
diff --git a/benchcab/data/config-schema.yml → src/benchcab/data/config-schema.yml b/benchcab/data/config-schema.yml → src/benchcab/data/config-schema.yml
diff --git a/benchcab/data/pbs_jobscript.j2 → src/benchcab/data/pbs_jobscript.j2 b/benchcab/data/pbs_jobscript.j2 → src/benchcab/data/pbs_jobscript.j2
diff --git a/benchcab/data/test/config-basic.yml → src/benchcab/data/test/config-basic.yml b/benchcab/data/test/config-basic.yml → src/benchcab/data/test/config-basic.yml
diff --git a/benchcab/data/test/config-invalid.yml → src/benchcab/data/test/config-invalid.yml b/benchcab/data/test/config-invalid.yml → src/benchcab/data/test/config-invalid.yml
diff --git a/benchcab/data/test/config-optional.yml → src/benchcab/data/test/config-optional.yml b/benchcab/data/test/config-optional.yml → src/benchcab/data/test/config-optional.yml
diff --git a/benchcab/data/test/integration.sh → src/benchcab/data/test/integration.sh b/benchcab/data/test/integration.sh → src/benchcab/data/test/integration.sh
diff --git a/benchcab/data/test/pbs_jobscript_default.sh → ...nchcab/data/test/pbs_jobscript_default.sh b/benchcab/data/test/pbs_jobscript_default.sh → ...nchcab/data/test/pbs_jobscript_default.sh
diff --git a/...b/data/test/pbs_jobscript_skip_bitwise.sh → ...b/data/test/pbs_jobscript_skip_bitwise.sh b/...b/data/test/pbs_jobscript_skip_bitwise.sh → ...b/data/test/pbs_jobscript_skip_bitwise.sh
diff --git a/benchcab/data/test/pbs_jobscript_verbose.sh → ...nchcab/data/test/pbs_jobscript_verbose.sh b/benchcab/data/test/pbs_jobscript_verbose.sh → ...nchcab/data/test/pbs_jobscript_verbose.sh
diff --git a/benchcab/data/test/template.j2 → src/benchcab/data/test/template.j2 b/benchcab/data/test/template.j2 → src/benchcab/data/test/template.j2
diff --git a/benchcab/environment_modules.py → src/benchcab/environment_modules.py b/benchcab/environment_modules.py → src/benchcab/environment_modules.py
diff --git a/benchcab/fluxsite.py → src/benchcab/fluxsite.py b/benchcab/fluxsite.py → src/benchcab/fluxsite.py
diff --git a/benchcab/internal.py → src/benchcab/internal.py b/benchcab/internal.py → src/benchcab/internal.py
diff --git a/benchcab/main.py → src/benchcab/main.py b/benchcab/main.py → src/benchcab/main.py
diff --git a/benchcab/model.py → src/benchcab/model.py b/benchcab/model.py → src/benchcab/model.py
diff --git a/benchcab/spatial.py → src/benchcab/spatial.py b/benchcab/spatial.py → src/benchcab/spatial.py
diff --git a/benchcab/utils/__init__.py → src/benchcab/utils/__init__.py b/benchcab/utils/__init__.py → src/benchcab/utils/__init__.py
diff --git a/benchcab/utils/dict.py → src/benchcab/utils/dict.py b/benchcab/utils/dict.py → src/benchcab/utils/dict.py
diff --git a/benchcab/utils/fs.py → src/benchcab/utils/fs.py b/benchcab/utils/fs.py → src/benchcab/utils/fs.py
diff --git a/benchcab/utils/namelist.py → src/benchcab/utils/namelist.py b/benchcab/utils/namelist.py → src/benchcab/utils/namelist.py
diff --git a/benchcab/utils/pbs.py → src/benchcab/utils/pbs.py b/benchcab/utils/pbs.py → src/benchcab/utils/pbs.py
diff --git a/benchcab/utils/repo.py → src/benchcab/utils/repo.py b/benchcab/utils/repo.py → src/benchcab/utils/repo.py
diff --git a/benchcab/utils/subprocess.py → src/benchcab/utils/subprocess.py b/benchcab/utils/subprocess.py → src/benchcab/utils/subprocess.py
diff --git a/benchcab/workdir.py → src/benchcab/workdir.py b/benchcab/workdir.py → src/benchcab/workdir.py