CI Updates

.github/workflows/python-package.yml

@@ -25,29 +25,43 @@ jobs:
 
   test:
     runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0} # enables conda/mamba env activation by reading bash profile
     strategy:
       fail-fast: false
       matrix:
         python-version: ["3.9", "3.10", "3.11", "3.12"]
         split: [1, 2, 3, 4, 5, 6]
 
+
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
+    - name: Check out repo
+      uses: actions/checkout@v4
+
+    - name: Set up micromamba
+      uses: mamba-org/setup-micromamba@main
+
+    - name: Create mamba environment
+      run: |
+        micromamba create -n lobpy python=${{ matrix.python-version }} --yes
+
+    - name: Install uv
+      run: micromamba run -n lobpy pip install uv
+
+    - name: Install LobsterPy and dependencies
       run: |
-        python -m pip install --upgrade pip
-        python -m pip install flake8 pytest pytest-mock pytest-split pytest-cov
-        python -m pip install types-setuptools
-        pip install .[featurizer]
+        micromamba activate lobpy
+        uv pip install --upgrade pip
+        uv pip install --editable '.[tests,featurizer]'
+
     - name: Test with pytest and coverage
       # run this locally to update tests durations
       # pytest --cov=lobsterpy --cov-append --splits 1 --group 1 --durations-path ./tests/test_data/.pytest-split-durations --store-durations
       run: |
+        micromamba activate lobpy
         pytest --cov=lobsterpy --cov-report term-missing --cov-append --splits 6 --group ${{ matrix.split }} -vv --durations-path ./tests/test_data/.pytest-split-durations
+
     - name: Upload coverage
       uses: actions/upload-artifact@v3
       with:
@@ -58,22 +72,26 @@ jobs:
       needs: test
       runs-on: ubuntu-latest
       steps:
-        - uses: actions/checkout@v3
+        - uses: actions/checkout@v4
         - name: Set up Python 3.10
           uses: actions/setup-python@v4
           with:
             python-version: '3.10'
+
         - name: Install Coverage
           run: |
            python -m pip install coverage[toml]
+
         - name: Download coverage artifacts
           continue-on-error: true
           uses: actions/download-artifact@v3
+
         - name: Run coverage
           continue-on-error: true
           run: |
             coverage combine coverage*/.coverage*
             coverage report --show-missing
+
         - name: Upload coverage reports to Codecov
           uses: codecov/[email protected]
           with:

.pre-commit-config.yaml

@@ -2,7 +2,7 @@ exclude: ^(docs|examples|tests/test_data)
 
 ci:
   autoupdate_schedule: monthly
-  skip: [mypy]
+  skip: [mypy,pyright]
   autofix_commit_msg: pre-commit auto-fixes
   autoupdate_commit_msg: pre-commit autoupdate
 
@@ -65,3 +65,7 @@ repos:
     stages: [commit, commit-msg]
     args: [--ignore-words-list, 'titel,alls,ans,nd,mater,nwo,te,hart,ontop,ist,ot,fo']
     types_or: [python, rst, markdown]
+- repo: https://github.com/RobertCraigie/pyright-python
+  rev: v1.1.372
+  hooks:
+    - id: pyright

lobsterpy/featurize/utils.py

@@ -60,7 +60,7 @@ def get_file_paths(
             if file_path.exists():
                 file_paths[file] = file_path
             else:
-                gz_file_path = Path(zpath(file_path))
+                gz_file_path = Path(zpath(str(file_path.as_posix())))
                 if gz_file_path.exists():
                     file_paths[file] = gz_file_path
                 else:
@@ -86,7 +86,7 @@ def get_structure_path(lobster_path: Path) -> Path:
         poscar_path = lobster_path / filename
         if poscar_path.exists():
             return poscar_path
-        gz_file_path = Path(zpath(poscar_path))
+        gz_file_path = Path(zpath(str(poscar_path.as_posix())))
         if gz_file_path.exists():
             return gz_file_path
 

pyproject.toml

@@ -181,3 +181,12 @@ no_implicit_optional = false
 [tool.codespell]
 ignore-words-list = "titel,alls,ans,nd,mater,nwo,te,hart,ontop,ist,ot,fo"
 check-filenames = true
+
+[tool.pyright]
+typeCheckingMode = "off"
+reportPossiblyUnboundVariable = false
+reportUnboundVariable = true
+reportMissingImports = false
+reportMissingModuleSource = false
+reportInvalidTypeForm = false
+exclude = ["**/tests"]

tests/cohp/test_describe.py

@@ -407,7 +407,7 @@ def test_warnings(self):
                 potcar_symbols=["C"],
                 bva_comp=True,
             )
-        assert "Oxidation states from BVA analyzer cannot" in str(w2[0].message)
+        assert "Oxidation states from BVA analyzer cannot" in str(w2[-1].message)
 
         calc_des2 = Description.get_calc_quality_description(calc_quality_warnings2)