Mkdocs

.github/workflows/deploy.yml

@@ -1,25 +1,19 @@
-# This file was created automatically with `myst init --gh-pages` 🪄 💚
-
 name: aiida-atomistic GitHub Pages Deploy
 on:
   push:
-    # Runs on pushes targeting the default branch
-    branches: [main, develop]
-env:
-  # `BASE_URL` determines the website is served from, including CSS & JS assets
-  # You may need to change this to: `BASE_URL: ''`
-  BASE_URL: /${{ github.event.repository.name }}
+    branches: [main, develop, mkdocs]
 
 # Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
 permissions:
   contents: read
   pages: write
   id-token: write
-# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
-# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
+
+# Allow only one concurrent deployment; do NOT cancel in-progress runs.
 concurrency:
   group: 'pages'
   cancel-in-progress: false
+
 jobs:
   build:
     environment:
@@ -28,25 +22,24 @@ jobs:
     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@v4
+      - uses: actions/setup-python@v5
         with:
-          python-version: '3.10'
+          python-version: '3.11'
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install -e .
-          pip install -r docs/requirements.txt
-      - name: Build Sphinx documentation
-        run: |
-          make html
-        working-directory: ./docs
+          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: './docs/build/html'
-  # Deployment job
+          path: './build'
+
   deploy:
     environment:
       name: github-pages

docs/source/dev_guides/dev_adding_properties.md → docs/dev_guides/dev_adding_properties.md

@@ -2,12 +2,13 @@
 
 This guide explains how to add new properties to `StructureData` and `StructureBuilder`.
 
-:::{note}
-If you want to add a temporary/experimental property, you can add it as [custom property](../how_to/define_custom.md).
-If instead you want to contribute to this package, this is the right page!
-:::
+!!! note
+    If you want to add a temporary/experimental property, you can add it as [custom property](../how_to/define_custom.md).
+    If instead you want to contribute to this package, this is the right page!
+
 
 This guide covers two types of properties:
+
 1. **Site properties** - Properties that vary per atom (e.g., `charge`)
 2. **Global properties** - Properties that apply to the entire structure (e.g., `tot_charge`)
 
@@ -21,20 +22,20 @@ Go to the [aiida-atomistic GitHub repository](https://github.com/aiidateam/aiida
 
 ### 2. Clone Your Fork
 
-```bash
+```text
 git clone https://github.com/YOUR-USERNAME/aiida-atomistic.git
 cd aiida-atomistic
 ```
 
 ### 3. Create a Feature Branch
 
-```bash
+```text
 git checkout -b add-new-property
 ```
 
 ### 4. Install in Editable Mode
 
-```bash
+```text
 pip install -e .
 ```
 
@@ -43,16 +44,14 @@ Now you can make changes and they'll be immediately reflected in your Python env
 ### 5. Create a Pull Request
 
 Go to your fork on GitHub and click "New Pull Request". Provide a clear description of:
+
 - What property you're adding
 - Why it's useful
 - Any relevant scientific context
 - Link to related issues (if any)
 
-:::{tip}
-Before creating a PR, it's a good idea to open an issue on the main repository to discuss whether the property should be added. The maintainers can provide guidance on the best implementation approach.
-:::
-
----
+!!! tip
+    Before creating a PR, it's a good idea to open an issue on the main repository to discuss whether the property should be added. The maintainers can provide guidance on the best implementation approach.
 
 ## Adding a Site Property
 
@@ -76,43 +75,44 @@ class Site(BaseModel):
     )
 ```
 
-:::{important}
-**Why `default=None` in Field and `"default"` in `json_schema_extra`?**
+!!! note "**Why `default=None` in Field and `"default"` in `json_schema_extra`?**"
 
-We use a two-level default system:
+    We use a two-level default system:
 
-1. **Field `default=None`**: This is the Pydantic field default. Setting it to `None` means:
-   - When you create a site without specifying `property_A`, the field is truly undefined (`None`)
-   - This lets us distinguish between "property not set" vs "property set to zero"
-   - Without this, if we used `default=0.0`, every site would appear to have `property_A` defined, even when unset
+    1. **Field `default=None`**: This is the Pydantic field default. Setting it to `None` means:
 
-2. **`json_schema_extra["default"]`**: This is used when expanding arrays:
-   - When one site has `property_A=2.5` but another has `property_A=None`
-   - The array needs a concrete value for the undefined site, if the above condition is verified
-   - We use `Site.get_default_values()['property_A']` to get `0.0` as the fill value
-   - Result: `charges = [2.5, 0.0]` (not `[2.5, None]` which breaks numpy arrays)
+    - When you create a site without specifying `property_A`, the field is truly undefined (`None`)
+    - This lets us distinguish between "property not set" vs "property set to zero"
+    - Without this, if we used `default=0.0`, every site would appear to have `property_A` defined, even when unset
 
-**Example:**
-```python
-# Without property_A set
-site1 = Site(symbol="Fe", position=[0, 0, 0])
-site1.property_A  # None - we know it's undefined
+    2. **`json_schema_extra["default"]`**: This is used when expanding arrays:
 
-# With property_A set to zero
-site2 = Site(symbol="Fe", position=[0, 0, 0], property_A=0.0)
-site2.property_A  # 0.0 - explicitly set
+    - When one site has `property_A=2.5` but another has `property_A=None`
+    - The array needs a concrete value for the undefined site, if the above condition is verified
+    - We use `Site.get_default_values()['property_A']` to get `0.0` as the fill value
+    - Result: `charges = [2.5, 0.0]` (not `[2.5, None]` which breaks numpy arrays)
 
-# Array expansion uses json_schema_extra["default"]
-structure = StructureData(sites=[site1, site2])
-structure.properties.property_A_array  # [1.0, 0.0] - we populated property_A_array[0] with the json_schema_extra["default"] = 1
-```
+    **Example:**
+    ```python
+    # Without property_A set
+    site1 = Site(symbol="Fe", position=[0, 0, 0])
+    site1.property_A  # None - we know it's undefined
+
+    # With property_A set to zero
+    site2 = Site(symbol="Fe", position=[0, 0, 0], property_A=0.0)
+    site2.property_A  # 0.0 - explicitly set
+
+    # Array expansion uses json_schema_extra["default"]
+    structure = StructureData(sites=[site1, site2])
+    structure.properties.property_A_array  # [1.0, 0.0] - we populated property_A_array[0] with the json_schema_extra["default"] = 1
+    ```
 
-This pattern allows:
+    This pattern allows:
+
+    - Detecting if a property is truly set or not
+    - Creating valid numpy arrays without `None` values
+    - Distinguishing "zero" from "undefined"
 
-- Detecting if a property is truly set or not
-- Creating valid numpy arrays without `None` values
-- Distinguishing "zero" from "undefined"
-:::
 
 You can also a validation, if needed:
 
@@ -158,19 +158,18 @@ def property_A_array(self) -> t.Optional[np.ndarray]:
     ])
 ```
 
-:::{important}
-**Key Points:**
+!!! note "**Key Points**"
+
+    1. **Check for all None first**: If all sites have `property_A=None`, return `None` for the entire array. This indicates the property is truly undefined for the structure.
 
-1. **Check for all None first**: If all sites have `property_A=None`, return `None` for the entire array. This indicates the property is truly undefined for the structure.
+    2. **Use `Site.get_default_values()`**: Instead of hardcoding defaults, retrieve them from the Site field metadata:
+    ```python
+    default_value = Site.get_default_values().get('property_A', 0.0)
+    ```
+    This keeps the default value definition in one place (the Site field's `json_schema_extra`).
 
-2. **Use `Site.get_default_values()`**: Instead of hardcoding defaults, retrieve them from the Site field metadata:
-   ```python
-   default_value = Site.get_default_values().get('property_A', 0.0)
-   ```
-   This keeps the default value definition in one place (the Site field's `json_schema_extra`).
+    3. **Always include `singular_form`**: This metadata is **required** for loading structures from the database. See the metadata explanation below.
 
-3. **Always include `singular_form`**: This metadata is **required** for loading structures from the database. See the metadata explanation below.
-:::
 
 #### Step 3: storage backend decision and additional computed fields for efficient querying
 
@@ -308,6 +307,7 @@ Add the property to the documentation:
 Global properties (like temperature, pressure) follow a simpler pattern than site properties since they don't need array expansion.
 
 Key differences from site properties:
+
 - No need for `"default"` in `json_schema_extra` (no array expansion needed)
 - Only need `default=None` in Field definition
 - No need for `Site.get_default_values()` in computed fields

docs/source/dev_guides/dev_plugin_migration.md → docs/dev_guides/dev_plugin_migration.md

@@ -93,57 +93,56 @@ class MyCalculation(CalcJob):
     ]
 ```
 
-:::{important}
-**Use Plural Forms for Site Properties**
+!!! note "**Use Plural Forms for Site Properties**"
 
-When defining `supported_properties`, you must use the **plural form** for site-based properties (properties that vary per atom).
-For example:
+    When defining `supported_properties`, you must use the **plural form** for site-based properties (properties that vary per atom).
+    For example:
 
-- `'charges'` (not `'charge'`)
-- `'masses'` (not `'mass'`)
-- `'magmoms'` (not `'magmom'`)
-- `'positions'` (not `'position'`)
+    - `'charges'` (not `'charge'`)
+    - `'masses'` (not `'mass'`)
+    - `'magmoms'` (not `'magmom'`)
+    - `'positions'` (not `'position'`)
 
-Global properties (that apply to the entire structure) use their standard name:
+    Global properties (that apply to the entire structure) use their standard name:
 
-- `'cell'`
-- `'pbc'`
-- `'temperature'`
+    - `'cell'`
+    - `'pbc'`
+    - `'temperature'`
 
-**How to Find Property Names:**
+    **How to Find Property Names:**
 
-To see all available properties and their correct names:
+    To see all available properties and their correct names:
 
-```python
-from aiida_atomistic import StructureData
+    ```python
+    from aiida_atomistic import StructureData
 
-# Get all supported properties
-props = StructureData.get_supported_properties()
+    # Get all supported properties
+    props = StructureData.get_supported_properties()
 
-# Site properties (use plural forms in supported_properties)
-print(props['site'])
-# {'charge', 'mass', 'magmom', 'magnetization', 'weight', ...}
+    # Site properties (use plural forms in supported_properties)
+    print(props['site'])
+    # {'charge', 'mass', 'magmom', 'magnetization', 'weight', ...}
 
-# Global properties (use as-is in supported_properties)
-print(props['global'])
-# {'cell', 'pbc', 'tot_charge', 'temperature', ...}
+    # Global properties (use as-is in supported_properties)
+    print(props['global'])
+    # {'cell', 'pbc', 'tot_charge', 'temperature', ...}
 
-# Computed properties (arrays from site properties - use plural)
-print(props['computed'])
-# {'charges', 'masses', 'magmoms', 'positions', 'symbols', ...}
-```
+    # Computed properties (arrays from site properties - use plural)
+    print(props['computed'])
+    # {'charges', 'masses', 'magmoms', 'positions', 'symbols', ...}
+    ```
 
-**Why Plural?**
+    **Why Plural?**
 
-Site properties in the `Site` model are singular (`charge`, `mass`), but they're accessed as arrays through computed fields with plural names (`charges`, `masses`). The validation checks for the array forms since that's what your plugin actually uses:
+    Site properties in the `Site` model are singular (`charge`, `mass`), but they're accessed as arrays through computed fields with plural names (`charges`, `masses`). The validation checks for the array forms since that's what your plugin actually uses:
+
+    ```python
+    # In your plugin, you access:
+    structure.properties.charges  # Array of all charges, what you will use
+    # Not:
+    structure.properties.sites[0].charge  # Individual site charge (you don't validate this)
+    ```
 
-```python
-# In your plugin, you access:
-structure.properties.charges  # Array of all charges, what you will use
-# Not:
-structure.properties.sites[0].charge  # Individual site charge (you don't validate this)
-```
-:::
 
 #### Step 2: Add Validation Logic
 
@@ -201,13 +200,13 @@ class MyCalculation(CalcJob):
             )
 ```
 
-:::{note}
-You can also put the validation in the WorkChains using the given CalcJob, to stop prematurely instead of performing some steps and then exit only when trying to submit with the wrong structure.
-:::
+!!! tip
+    You can also put the validation in the WorkChains using the given CalcJob, to stop prematurely instead of performing some steps and then exit only when trying to submit with the wrong structure.
+
+
+!!! tip
+    Of course, you will also need to add the logic to write your input file starting from the structure properties, which before were defined in the `parameters` input `orm.Dict` (at least in the aiida-quantumespresso plugin).
 
-:::{note}
-Of course, you will also need to add the logic to write your input file starting from the structure properties, which before were defined in the `parameters` input `orm.Dict` (at least in the aiida-quantumespresso plugin).
-:::
 
 ### Real-World Example: aiida-quantumespresso
 

docs/source/dev_guides/dev_repository_storage.md → docs/dev_guides/dev_repository_storage.md

@@ -88,10 +88,10 @@ the ZIP central directory.  It does **not** decompress any other entry.
 Accessing `positions` in a file that also contains `charges`, `magmoms`, and
 `symbols` only decompresses `positions.npy`.
 
-:::{note}
-The full load (no `keys` argument) is cached on the node object after the
-first call, so repeated access to `.properties` does not re-read the file.
-:::
+!!! note
+    The full load (no `keys` argument) is cached on the node object after the
+    first call, so repeated access to `.properties` does not re-read the file.
+
 
 ---