Merge pull request #35 from calpolyccg/more-ci-checks

Add more checks to CI pipeline

Author: ALescoulie

.github/workflows/CI.yaml

@@ -50,20 +50,15 @@ jobs:
         auto-update-conda: false
         auto-activate-base: false
         use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
-
-    - name: Install MDSAPT package
-      # conda setup requires this special shell
+    
+    - name: Type-check
       shell: bash -l {0}
       run: |
-        python -m pip install . --no-deps
-        conda list
+        pyright mdsapt
 
-    # TODO: possibly integrate this step with meta.yml?
     - name: Run tests
-      # conda setup requires this special shell
       shell: bash -l {0}
       run: |
-        pip install pytest-cov
         pytest -v ./mdsapt --cov=mdsapt --cov-report=xml
 
     - name: Upload CodeCov
@@ -73,6 +68,12 @@ jobs:
         flags: unittests
         name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}
 
+    - name: Install MDSAPT package
+      shell: bash -l {0}
+      run: |
+        python -m pip install . --no-deps
+        conda list
+
   package:
     name: Packaging py${{ matrix.python-version }}/${{ matrix.os }}
     runs-on: ${{ matrix.os }}
@@ -162,3 +163,23 @@ jobs:
       shell: bash -l {0}
       run: >
         python3 -c "import mdsapt"
+
+  lint-and-format:
+    # These checks are much faster and don't actually need to install any packages.
+    name: Run fast checks over code
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Install formatter and linter
+      run: |
+        pip install autopep8 pylint
+
+    - name: Lint code
+      run: |
+        pylint mdsapt
+
+    - name: Ensure formatting
+      run: |
+        autopep8 -r mdsapt --diff --exit-code

environment.yml

@@ -6,8 +6,7 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - mdanalysis>=2.0.0, <2.1
-  - nglview>=3.0.3, <3.1
+  - mdanalysis
   - numpy
   - openmm
   - pandas
@@ -17,3 +16,13 @@ dependencies:
   - pytest-cov
   - pyyaml
   - rdkit
+
+  # Optional deps
+  - nglview
+
+  # Development deps
+  - autopep8
+  - pyright # type-checking
+  - pylint
+  - pytest
+  - pytest-cov