Fix toolkit tests (#227)

* Ensure 0.11.0 RC version of toolkit is installed * Possible fix to finish #191 * Try to ensure bash args thing is passed through * Naive unit refactor * Work through tests * Update CI matrix * Use mamba for development * Debug, add boilerplate .gitignore * Fix syntax * make sure the package didn't get installed before we install it * Do not install Espaloma * Fix some unit registries in tests * install espaloma, but remove openmmforcefields * add back in espaloma * switch to micromamba * Explicitly move ffxml sources into entry point * Remove symlinking * Add boilerplate `.gitignore` * Update package installation in CI * Fix finding Amber files in test * Soft import whatever units module is used by the toolkit * Switch to micromamba for setting up conda environment Add boilerplate `.gitignore` file Do not pull from non-standard labels Install instead of update Try to figure out why if: {{ false }} still triggers Syntax? Tinker Bring in (full) mamba Bash thing everywhere Bring down old toolkit Do not present un-loadable ff14SB port as available More pins * Fix YAML syntax * Use pip * More fixes * No particles * Fix unit serialization * Fix Atom.element calls * Update some tests * Clean up un-used imports * Fix more tests * Fix more tests * Exclude Python 3.10 on macOS * Skip ff14SB being treated as a small molecule * Fix test * Track duration of longest 20 tests * Update action versions * Try to fix exclusions in CI matrix * Fix pathing in Amber conversion * Run `pyupgrade --py38-plus` * Try directly uploading coverage report * Fix syntax * Add back some tests * Debug * Drop `pytest-xdist` arg * Fiddle with path * Just try to get stuff passing * Try uploading again * Switch back to codecov * Simply coverage reporting * Allow 0 coverage * Simplify coverage arguments * Add `__init__.py` in `/tests/` submodule https://stackoverflow.com/a/60579142 * Add `__init__.py` in `/tests/` submodule https://stackoverflow.com/a/60579142 * Simplify coverage arguments * Add back durations argument * Apply suggestions from code review * only upload report if it is not scheduled Co-authored-by: Matthew W. Thompson <mattwthompson@protonmail.com>
openmm · Sep 15, 2022 · 35496e5 · 35496e5
1 parent e7f2fe3
commit 35496e5
Show file tree

Hide file tree

Showing 103 changed files with 47,811 additions and 47,311 deletions.
diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
@@ -27,12 +27,15 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, macOS-latest]
+        os: [ubuntu-latest, macos-latest]
         python-version: ["3.8", "3.9", "3.10"]
         latest-openff-toolkit: [true, false]
+        exclude:
+          - python-version: "3.10"
+            os: macos-latest
 
     steps:
-    - uses: actions/checkout@v3.0.2
+    - uses: actions/checkout@v3
 
     - name: Setup Conda Environment
       uses: mamba-org/provision-with-micromamba@main
@@ -52,25 +55,29 @@ jobs:
     - name: "Install latest openff-toolkit"
       if: ${{ matrix.latest-openff-toolkit == true }}
       run: |
-        # Until #225 is complete, we should not assume compatibility with new API
-        micromamba install "openff-toolkit =0.10.6" -c conda-forge -y
+        micromamba update -y -c conda-forge "openff-toolkit >=0.11.0"
 
     - name: Install Package
       run: |
-        # Can't use 'develop' mode because we remove symlinks after install is complete
-        python setup.py install
+        pip list
+        micromamba list
+        micromamba remove --force openmmforcefields
+        python -m pip install .
 
     - name: Conda Environment Information
       run: |
-        conda info
-        conda list
+        micromamba info
+        micromamba list
+        python -c "from openmmforcefields import __version__, __file__; print(__version__, __file__)"
 
     - name: Test Installed Package
       run: |
-        pytest -v -x -s --log-cli-level $LOGLEVEL --cov=openmmforcefields openmmforcefields/tests/test_amber_import.py
-        pytest -v -x -s --log-cli-level $LOGLEVEL --cov=openmmforcefields openmmforcefields/tests/test_template_generators.py
-        pytest -v -x -s --log-cli-level $LOGLEVEL --cov=openmmforcefields openmmforcefields/tests/test_system_generator.py
+        pytest -v -x --log-cli-level $LOGLEVEL $COV_ARGS --durations=20 \
+          openmmforcefields/tests/test_amber_import.py \
+          openmmforcefields/tests/test_template_generators.py \
+          openmmforcefields/tests/test_system_generator.py
       env:
+        COV_ARGS: --cov=openmmforcefields --cov-config=setup.cfg --cov-append --cov-report=xml
         LOGLEVEL: "INFO"
         KMP_DUPLICATE_LIB_OK: "True"
 
@@ -93,11 +100,11 @@ jobs:
 
       working-directory: ./charmm
 
-    - name: CodeCov
+    - name: Upload coverage report to CodeCov
+      uses: codecov/codecov-action@v3.1.0
       if: ${{ github.repository == 'openmm/openmmforcefields'
               && github.event != 'schedule' }}
-      uses: codecov/codecov-action@v3.1.0
       with:
+        token: ${{ secrets.CODECOV_TOKEN }}
         file: ./coverage.xml
-        flags: unittests
-        name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}
+        fail_ci_if_error: true
diff --git a/.gitignore b/.gitignore
@@ -53,7 +53,10 @@ coverage.xml
 
 # Django stuff:
 *.log
-local_settings.py
+
+# Sphinx documentation
+docs/_build/
+docs/api/generated
 
 # Flask stuff:
 instance/
@@ -62,12 +65,13 @@ instance/
 # Scrapy stuff:
 .scrapy
 
-# Sphinx documentation
-docs/_build/
-
 # PyBuilder
 target/
 
+# PyCharm
+*.idea/vcs.xml
+
+# Jupyter
 # Jupyter Notebook
 .ipynb_checkpoints
 
@@ -108,5 +112,11 @@ ENV/
 # In-tree generated files
 */_version.py
 
-# OS X extra files
+# macOS
 *.DS_Store
+
+# Caches
+openmmforcefields/data/perses_jacs_systems/*/cache.json
+
+# Test molecules
+testsystem-bace*