Clean up, modernize, and release pymdgen (#22)

* Clean up, modernize, and release pymdgen (#21)

* migrate poetry to uv

* update unit test

* fix review

* set codecov token

---------

Co-authored-by: Samsul Hadi <samsulhadikediri@gmail.com>

Author: vegu

.github/workflows/tests.yml

@@ -14,36 +14,33 @@ jobs:
           path: ~/.cache/pip
           key: ${{ runner.os }}-pip
           restore-keys: ${{ runner.os }}-pip
-      - name: Install Poetry
-        uses: snok/install-poetry@v1.1.1
+      - name: Install uv
+        uses: astral-sh/setup-uv@v2
         with:
           virtualenvs-create: true
           virtualenvs-in-project: true
           # virtualenvs-path: ~/.venv
       - name: Load cached venv
-        id: cached-poetry-dependencies
+        id: cached-uv-dependencies
         uses: actions/cache@v2
         with:
           path: .venv
-          key: venv-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
+          key: venv-${{ runner.os }}-${{ hashFiles('**/uv.lock') }}
       # install dependencies if cache does not exist
       - name: Check cache and install dependencies
-        run: poetry install
-        if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
+        run: uv sync --all-extras --dev
+        if: steps.cached-uv-dependencies.outputs.cache-hit != 'true'
       - name: Run linters
         run: |
-          source .venv/bin/activate
-          flake8 .
-          black . --check
-          isort .
+          uv run pre-commit run --all-files
 
   test:
     needs: linting
     strategy:
       fail-fast: true
       matrix:
         os: [ "ubuntu-latest", "macos-latest" ]
-        python-version: [ "3.6", "3.7", "3.8", "3.9" ]
+        python-version: [ "3.8", "3.9", "3.10", "3.11", "3.12" ]
     runs-on: ${{ matrix.os }}
     steps:
       - name: Check out repository
@@ -52,28 +49,28 @@ jobs:
         uses: actions/setup-python@v2
         with:
           python-version: ${{ matrix.python-version }}
-      - name: Install Poetry
-        uses: snok/install-poetry@v1.1.1
+      - name: Install uv
+        uses: astral-sh/setup-uv@v2
         with:
           virtualenvs-create: true
           virtualenvs-in-project: true
       - name: Load cached venv
-        id: cached-poetry-dependencies
+        id: cached-uv-dependencies
         uses: actions/cache@v2
         with:
           path: .venv
-          key: venv-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
+          key: venv-${{ runner.os }}-${{ hashFiles('**/uv.lock') }}
       # install dependencies if cache does not exist
       - name: Check cache and install dependencies
-        run: poetry install
-        if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
+        run: uv sync --all-extras --dev
+        if: steps.cached-uv-dependencies.outputs.cache-hit != 'true'
       - name: Run tests
         run: |
-          poetry run pytest tests/ --cov="pymdgen" --cov-report=xml --cov-report=term-missing
-          poetry run coverage report
+          uv run tox
       # upload coverage stats
       - name: Upload coverage
         uses: codecov/codecov-action@v1
         with:
           file: ./coverage.xml
           fail_ci_if_error: true
+          token: ${{ secrets.CODECOV_TOKEN }}

.gitignore

@@ -7,3 +7,4 @@
 .coverage
 coverage.xml
 /dist
+.venv

.pre-commit-config.yaml

@@ -1,24 +1,21 @@
 fail_fast: true
 repos:
-  - repo: local
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
     hooks:
-      - id: system
-        name: isort
-        entry: poetry run isort .
-        language: system
-        pass_filenames: false
+      - id: check-yaml
+      - id: trailing-whitespace
   - repo: local
     hooks:
       - id: pyupgrade
         name: pyupgrade
-        entry: poetry run pyupgrade --py36-plus
+        entry: uv run pyupgrade --py36-plus
         language: python
         types: [python]
         pass_filenames: true
-  - repo: local
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.1.14
     hooks:
-      - id: system
-        name: Black
-        entry: poetry run black .
-        language: system
-        pass_filenames: false
+      - id: ruff
+        args: [--fix, --unsafe-fixes]
+      - id: ruff-format