complete quality checks

.github/workflows/alpha-release-ci-actions.yaml

@@ -0,0 +1,10 @@
+name: Alpha release CI Actions
+
+on:
+  push:
+    tags:
+      - '*.*.*'
+
+jobs:
+  publish-package:
+    uses: ./.github/workflows/publish-package.yaml

.github/workflows/dev-ci-actions.yaml

@@ -0,0 +1,11 @@
+name: Dev CI Actions
+
+on:
+  pull_request:
+
+jobs:
+  quality-checks:
+    uses: ./.github/workflows/quality-typing-checks.yaml
+  test-run-pinned:
+    uses: ./.github/workflows/pinned-tests.yaml
+    needs: [quality-checks]

.github/workflows/main-ci-actions.yaml

@@ -0,0 +1,12 @@
+name: Dev CI Actions
+
+on:
+  branch:
+    - main
+
+jobs:
+  quality-checks:
+    uses: ./.github/workflows/quality-typing-checks.yaml
+  test-run-pinned:
+    uses: ./.github/workflows/pinned-tests.yaml
+    needs: [quality-checks]

.github/workflows/pinned-tests.yaml

@@ -0,0 +1,30 @@
+name: Pinned Tests
+
+on:
+  workflow_call:
+
+jobs:
+  tests-pinned:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.11"]
+
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: 'pip'
+      - name: Run pinned tests
+        run: |
+          pip install nox
+          nox -s tests_run_pinned-${{ matrix.python-version }}
+      - name: Test Summary
+        uses: test-summary/action@v2
+        with:
+          paths: "test-reports/${{ matrix.python-version }}/.junitxml.*.xml"
+          show: "fail"
+        if: always()

.github/workflows/publish-package.yaml

@@ -0,0 +1,24 @@
+name: Publish package
+
+on:
+  workflow_call:
+
+jobs:
+  publish-package:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.11'
+          cache: 'pip'
+      - name: Build package
+        run: |
+          pip install nox
+          nox -s dist_build-3.11
+      - name: Deploy package
+        run: |
+          pip install twine
+          python -m twine upload --verbose -u __token__ -p ${{ secrets.EXS_PYPI_TOKEN }} dist/*

.github/workflows/quality-typing-checks.yaml

@@ -0,0 +1,43 @@
+name: Quality and Typing Checks
+
+on:
+  workflow_call:
+
+jobs:
+  quality-checks:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.11'
+          cache: 'pip'
+      - name: Linting check
+        run: |
+          pip install nox
+          nox -s linting_check-3.11
+      - name: Formatting check
+        run: |
+          pip install nox
+          nox -s formatting_check-3.11
+
+  typing-check:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.11"]
+
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: 'pip'
+      - name: Typing check
+        run: |
+          pip install nox
+          nox -s typing_check-${{ matrix.python-version }}

noxfile.py

@@ -113,6 +113,9 @@
 
 EXTRAS = list(set(EXTRAS))
 
+# skip openeye in github actions (cannot pip install)
+EXTRAS.remove("openeye")
+
 INVERTED_SUBMODULE_EXTRAS = {}
 for extra in EXTRAS:
     doctests_target_dir_core = []

pyproject.toml

@@ -56,7 +56,7 @@ dependencies = [
 [project.optional-dependencies]
 openeye = [
     'openeye-toolkits<2023.0.0; python_version == "3.8"',  # openeye 2023 not supported on python 3.8
-    'openeye-toolkits',
+    'openeye-toolkits>=2023.0.0',
 ]
 rdkit = [
     'mhfp',

tests/datasets/core/unit/io/test_save_dataset_to_store.py

@@ -129,11 +129,13 @@ def test_save_dataset_to_s3(
 @pytest.mark.parametrize(
     ("path", "format", "filesystem"),
     [
-        ("s3://my/bucket/data.parquet", "parquet", fsspec.filesystem("file")),
-        ("my/data.parquet", "parquet", fsspec.filesystem("s3")),
+        ("s3://my/bucket/data.parquet", "parquet", "file"),
+        ("my/data.parquet", "parquet", "s3"),
     ],
 )
 def test_save_dataset_with_mismatched_filesystem_raises(
+    fixture_mock_s3_client,
+    fixture_mock_s3_filesystem,
     fixture_mock_dataset,
     path,
     format,
@@ -143,7 +145,12 @@ def test_save_dataset_with_mismatched_filesystem_raises(
     local filesystem (local) raises (and vice-versa)."""
     dataset = fixture_mock_dataset
     with pytest.raises(ValueError, match="Incompatible filesystem"):
-        save_dataset_to_store(dataset, path=str(path), format=format, fs=filesystem)
+        save_dataset_to_store(
+            dataset,
+            path=str(path),
+            format=format,
+            fs=fsspec.filesystem(filesystem),
+        )
 
 
 @pytest.mark.parametrize(

tests/datasets/core/unit/test_filesystems.py

@@ -3,13 +3,19 @@
 from molflux.datasets.filesystems import S3FileSystem
 
 
-def test_s3_filesystem_is_fsspec_compliant():
+def test_s3_filesystem_is_fsspec_compliant(
+    fixture_mock_s3_client,
+    fixture_mock_s3_filesystem,
+):
     """That our custom S3FileSystem implements the fsspec protocol."""
     filesystem = S3FileSystem()
     assert isinstance(filesystem, fsspec.AbstractFileSystem)
 
 
-def test_s3_filesystem_is_registered_with_fsspec():
+def test_s3_filesystem_is_registered_with_fsspec(
+    fixture_mock_s3_client,
+    fixture_mock_s3_filesystem,
+):
     """That our custom S3FileSystem is registered as an official fsspec entrypoint.
 
     References:
@@ -19,7 +25,10 @@ def test_s3_filesystem_is_registered_with_fsspec():
     assert isinstance(filesystem, S3FileSystem)
 
 
-def test_s3_path_gets_mapped_to_our_s3_filesystem():
+def test_s3_path_gets_mapped_to_our_s3_filesystem(
+    fixture_mock_s3_client,
+    fixture_mock_s3_filesystem,
+):
     """That fsspec dispatches s3 paths to our custom S3FileSystem."""
     path = "s3://my-bucket/test"
     fs_token_paths = fsspec.get_fs_token_paths(path)