Merge pull request #314 from naik-aakash/ci_updates

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/codecov-action@v4.0.1
  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)