fixing the pre-commit (#95)

* fixing the pre-commit

* changing names to actions.

* updating the pre-commit version.

* fixing pre-commit

* fixing some additional pre-commit

Author: mikibonacci

.github/workflows/ci.yml

@@ -9,9 +9,7 @@ jobs:
     timeout-minutes: 30
     strategy:
       matrix:
-        python-version: ["3.10"]
-        aiida-version: ["stable"]
-
+        python-version: ['3.11', '3.12', '3.13']
     services:
       postgres:
         image: postgres:10
@@ -25,45 +23,27 @@ jobs:
           --health-timeout 5s
           --health-retries 5
         ports:
-          - 5432:5432
+        - 5432:5432
       rabbitmq:
         image: rabbitmq:latest
         ports:
-          - 5672:5672
+        - 5672:5672
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
     - name: Install python dependencies
       run: |
         pip install --upgrade pip
-        pip install -e .[testing]
+        pip install -e .[run,testing]
 
     - name: Run test suite
       env:
         # show timings of tests
-        PYTEST_ADDOPTS: "--durations=0"
+        PYTEST_ADDOPTS: --durations=0
       run: pytest --cov aiida_atomistic --cov-append .
-
-  pre-commit:
-    runs-on: ubuntu-latest
-    timeout-minutes: 15
-    steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python 3.8
-      uses: actions/setup-python@v2
-      with:
-        python-version: "3.8"
-    - name: Install python dependencies
-      run: |
-        pip install --upgrade pip
-        pip install -e .[pre-commit,docs,testing]
-    - name: Run pre-commit
-      run: |
-        pre-commit install
-        pre-commit run --all-files || ( git status --short ; git diff ; exit 1 )

.github/workflows/deploy.yml

@@ -1,4 +1,4 @@
-name: aiida-atomistic GitHub Pages Deploy
+name: gh-pages-deploy
 on:
   push:
     branches: [main, develop, mkdocs]
@@ -11,7 +11,7 @@ permissions:
 
 # Allow only one concurrent deployment; do NOT cancel in-progress runs.
 concurrency:
-  group: 'pages'
+  group: pages
   cancel-in-progress: false
 
 jobs:
@@ -21,24 +21,24 @@ jobs:
       url: ${{ steps.deployment.outputs.page_url }}
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
-        with:
-          fetch-depth: 0   # required by git-revision-date-localized
-      - name: Setup Pages
-        uses: actions/configure-pages@v4
-      - uses: actions/setup-python@v5
-        with:
-          python-version: '3.11'
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install -e .[docs]
-      - name: Build MkDocs documentation
-        run: mkdocs build --site-dir ./build
-      - name: Upload artifact
-        uses: actions/upload-pages-artifact@v3
-        with:
-          path: './build'
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0     # required by git-revision-date-localized
+    - name: Setup Pages
+      uses: actions/configure-pages@v4
+    - uses: actions/setup-python@v5
+      with:
+        python-version: '3.11'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -e .[docs]
+    - name: Build MkDocs documentation
+      run: mkdocs build --site-dir ./build
+    - name: Upload artifact
+      uses: actions/upload-pages-artifact@v3
+      with:
+        path: ./build
 
   deploy:
     environment:
@@ -47,6 +47,6 @@ jobs:
     runs-on: ubuntu-latest
     needs: build
     steps:
-      - name: Deploy to GitHub Pages
-        id: deployment
-        uses: actions/deploy-pages@v4
+    - name: Deploy to GitHub Pages
+      id: deployment
+      uses: actions/deploy-pages@v4

.github/workflows/precommit.yml

@@ -0,0 +1,25 @@
+name: pre-commit
+
+on: [push, pull_request]
+
+jobs:
+
+  pre-commit:
+    runs-on: ubuntu-latest
+    timeout-minutes: 15
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.12'
+    - name: Install python dependencies
+      run: |
+        pip install --upgrade pip
+        pip install -e .[pre-commit]
+    - name: Run pre-commit
+      run: |
+        pre-commit clean
+        git add .pre-commit-config.yaml
+        pre-commit install
+        pre-commit run --all-files || ( git status --short ; git diff ; exit 1 )

.github/workflows/publish-on-pypi.yml

@@ -1,10 +1,10 @@
-name: Publish on PyPI
+name: pypi-publish
 
 on:
   push:
     tags:
       # After vMajor.Minor.Patch _anything_ is allowed (without "/") !
-      - v[0-9]+.[0-9]+.[0-9]+*
+    - v[0-9]+.[0-9]+.[0-9]+*
 
 jobs:
   publish:
@@ -30,4 +30,4 @@ jobs:
         flit publish
       env:
         FLIT_USERNAME: __token__
-        FLIT_PASSWORD:  ${{ secrets.pypi_token }}
+        FLIT_PASSWORD: ${{ secrets.pypi_token }}

.pre-commit-config.yaml

@@ -1,8 +1,46 @@
 repos:
--   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v3.2.0
-    hooks:
-    -   id: trailing-whitespace
-    -   id: end-of-file-fixer
-    -   id: check-yaml
-    -   id: check-added-large-files
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v5.0.0
+  hooks:
+  - id: check-merge-conflict
+  - id: check-added-large-files
+    exclude: uv.lock
+  - id: check-yaml
+  - id: end-of-file-fixer
+    exclude: &exclude_pre_commit_hooks >
+      (?x)^(
+        tests/.*(?<!\.py)$|
+        docs/source/.+\.aiida/repo/.+|
+        CHANGELOG.md|
+      )$
+  - id: fix-encoding-pragma
+    args: [--remove]
+  - id: mixed-line-ending
+    args: [--fix=lf]
+  - id: trailing-whitespace
+    exclude: *exclude_pre_commit_hooks
+
+- repo: https://github.com/python-jsonschema/check-jsonschema
+  rev: 0.37.0
+  hooks:
+  - id: check-github-workflows
+
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.15.4
+  hooks:
+  - id: ruff-format
+  - id: ruff
+    args: [--fix, --exit-non-zero-on-fix, --show-fixes]
+
+- repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks
+  rev: v2.16.0
+  hooks:
+  - id: pretty-format-toml
+    args: [--autofix]
+  - id: pretty-format-yaml
+    args: [--autofix]
+    exclude: >-
+      (?x)^(
+        tests/.*|
+        environment.yml|
+      )$

.readthedocs.yml

@@ -1,9 +1,9 @@
 version: 2
 
 python:
-  version: "3.8"
+  version: '3.8'
   install:
-    - method: pip
-      path: .
-      extra_requirements:
-        - docs
+  - method: pip
+    path: .
+    extra_requirements:
+    - docs

docs/how_to/creation_mutation.md

@@ -668,4 +668,3 @@ Final structure ready for calculations!
 Is alloy: False
 Total charge: -1.0
 ```
-

docs/how_to/query.md

@@ -224,7 +224,7 @@ qb.append(
 print(f"Structures with charges in ({min_charge}, {max_charge}): {len(qb.all())}")
 ```
 
-!!! tip 
+!!! tip
 **Using Statistics for Efficient Queries**
 
     Statistical properties enable efficient filtering without loading large arrays:

docs/in_depth/index.md

@@ -22,4 +22,4 @@ Comprehensive explanations of core concepts and advanced topics in `aiida-atomis
 
     [Storage Backends](storage_backends.md)
 
-</div>
+</div>

docs/in_depth/properties.md

@@ -67,7 +67,7 @@ Each `Site` object can have the following properties:
 
     - Type: `str` for pure elements, `list[str]` for alloys
     - Example: `'Cu'` or `['Cu', 'Zn']`
-  
+
 - **`position`**: Atomic coordinates in Cartesian space
 
     - Type: `np.ndarray` (shape: `(3,)`)
@@ -381,7 +381,7 @@ print(field_info.json_schema_extra)  # {'store_in': 'db'}
 
 # Properties with 'singular_form' are site properties
 field_info = StructureBaseModel.model_computed_fields['charges']
-print(field_info.json_schema_extra)  
+print(field_info.json_schema_extra)
 # {'store_in': 'repository', 'singular_form': 'charge'}
 ```
 
@@ -390,10 +390,10 @@ print(field_info.json_schema_extra)
 - **`store_in`**: Where to store the property
   - `'db'`: Database attributes (fast queries, size-limited)
   - `'repository'`: File repository (large arrays, slower queries)
-  
+
 - **`singular_form`**: Links plural computed property to singular site property
   - Example: `charges` (plural) ↔ `charge` (singular)
-  
+
 - **`statistic`**: Statistical aggregation for querying
   - `'max'`: Maximum value across all sites
   - `'min'`: Minimum value across all sites
@@ -467,4 +467,4 @@ builder.properties.sites.append({'symbol': 'Cu', 'position': [0, 0, 0]})  # OK
 # StructureData: immutable (use for storing in database)
 structure = StructureData(cell=[[3, 0, 0], [0, 3, 0], [0, 0, 3]], pbc=[True]*3, sites=[...])
 structure.properties.sites.append(...)  # Error: immutable
-```
+```