Merge pull request #39 from calpolyccg/development

Merge 2.0.0

Author: ALescoulie

.github/workflows/CI.yaml

@@ -50,20 +50,16 @@ 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!
+    
+    # TODO: make pyright happier someday in the future
+    # - name: Type-check
+    #   shell: bash -l {0}
+    #   run: |
+    #     pyright mdsapt
 
-    - name: Install MDSAPT package
-      # conda setup requires this special shell
-      shell: bash -l {0}
-      run: |
-        python -m pip install . --no-deps
-        conda list
-
-    # 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 +69,12 @@ 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 +164,23 @@ 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 --fail-under=9.5 --disable=E,R mdsapt
+
+    - name: Ensure formatting
+      run: |
+        autopep8 -r mdsapt --diff --exit-code

.gitignore

@@ -1,3 +1,12 @@
+# generated files
+psi.*.clean
+out.csv
+/timer.dat
+/resid_fixed.pdb
+/resid.pdb
+/*.out
+/sapt_test.csv
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
@@ -104,3 +113,7 @@ ENV/
 # profraw files from LLVM? Unclear exactly what triggers this
 # There are reports this comes from LLVM profiling, but also Xcode 9.
 *profraw
+
+# MDSAPT-generated files
+timer.dat
+input.yaml