fixing the pre-commit

.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
-```
+```

docs/in_depth/storage_backends.md

@@ -27,7 +27,7 @@ class StructureBaseModel(BaseModel):
     cell: ArrayLike3x3 = Field(
         json_schema_extra={"store_in": "db"}
     )
-    
+
     # This array goes to repository
     @computed_field(json_schema_extra={"store_in": "repository", "singular_form": "position"})
     @property
@@ -176,7 +176,7 @@ def my_properties(self) -> np.ndarray:
     if all(site.my_property is None for site in self.sites):
         return None
     return np.array([
-        site.my_property if site.my_property is not None 
+        site.my_property if site.my_property is not None
         else Site.get_default_values()['my_property']
         for site in self.sites
     ])
@@ -266,4 +266,4 @@ Arrays are cached after first load to avoid repeated file I/O:
 structure = orm.load_node(pk)
 pos1 = structure.properties.positions  # Loads from .npz, caches
 pos2 = structure.properties.positions  # Returns cached (no I/O)
-```
+```

docs/index.md

@@ -60,10 +60,10 @@ If you use this plugin for your research, please cite the following work:
 
 ## Acknowledgements
 
-We acknowledge support from the [NCCR MARVEL](http://nccr-marvel.ch/) funded by the Swiss National Science Foundation and the EU Centre of Excellence ["MaX – Materials Design at the Exascale"](http://www.max-centre.eu/) (Horizon 2020 EINFRA-5, Grant No. 676598). 
+We acknowledge support from the [NCCR MARVEL](http://nccr-marvel.ch/) funded by the Swiss National Science Foundation and the EU Centre of Excellence ["MaX – Materials Design at the Exascale"](http://www.max-centre.eu/) (Horizon 2020 EINFRA-5, Grant No. 676598).
 
 ![marvel](images/MARVEL.png){ width="250" }
-![max](images/MaX.png){ width="300" } 
+![max](images/MaX.png){ width="300" }
 
 [aiida]: http://aiida.net
 [aiida-core documentation]: https://aiida.readthedocs.io/projects/aiida-core/en/latest/intro/get_started.html

docs/stylesheets/extra.css

@@ -1,3 +1,3 @@
 .md-grid {
     max-width: 1440px;
-}
+}

docs/tutorials/2_first_qe_calculation.md

@@ -8,12 +8,16 @@ This guide demonstrates how to use aiida-atomistic structures in computational w
 
 Ensure you have the necessary packages and codes installed, which you can verify by following the corresponding [installation guide](https://aiida-quantumespresso.readthedocs.io/en/stable/get_started/installation.html).
 
-:::{important}
-For now, please install these versions of the following packages:
-- aiida-core: dev/atomistic branch from https://github.com/mikibonacci/aiida-core.git
-- aiida-pseudo: dev/atomistic branch from https://github.com/mikibonacci/aiida-pseudo.git
-- aiida-quantumespresso: dev/atomistic branch from https://github.com/mikibonacci/aiida-quantumespresso.git
-:::
+!!! note "Compatible AiiDA and other plugins version with aiida-atomistic"
+
+    For now, please install these versions of the following packages:
+
+    - aiida-core: dev/atomistic branch from https://github.com/mikibonacci/aiida-core.git
+    - aiida-pseudo: dev/atomistic branch from https://github.com/mikibonacci/aiida-pseudo.git
+    - aiida-quantumespresso: dev/atomistic branch from https://github.com/mikibonacci/aiida-quantumespresso.git
+
+    You can install all of them by running `pip install .[run]`.
+
 
 If not already done, remember to install the `sssp` pseudopotentials:
 

docs/tutorials/index.md

@@ -8,7 +8,7 @@ Welcome to the aiida-atomistic tutorials! These step-by-step tutorials will get
 
     ---
 
-    **Duration**: ~5 minutes 
+    **Duration**: ~5 minutes
 
     **Level**: Beginner
 
@@ -21,8 +21,8 @@ Welcome to the aiida-atomistic tutorials! These step-by-step tutorials will get
 
     ---
 
-    **Duration**: ~10 minutes 
-    
+    **Duration**: ~10 minutes
+
     **Level**: Intermediate
 
     Use your structures in real computational workflows with Quantum ESPRESSO: