Several improvements (#35)

* Updating deploy yaml

* modifying the base_url path

* working-directory in the deploy yaml

* fixing the get_kinds, missing tests.

* Adding tests for pymatgen and get_kinds.

* Adding the get_property_names.

* Adding docstrings, changing class Config to model_config

* Pre-commit fixings

* bugfixing t.List and ConfigDict import.

* Updating ci.yml

* Adding pydantic into deps

* Minor mods to readme

* Adding

- support for vacancies and alloys.
- tot_charge and tot_magnetization properties.
- custom properties.
- model dumping in the AiiDA db only considering the defined properties, skipping the default ones.

.github/workflows/ci.yml

@@ -9,7 +9,7 @@ jobs:
     timeout-minutes: 30
     strategy:
       matrix:
-        python-version: ["3.8"]
+        python-version: ["3.10"]
         aiida-version: ["stable"]
 
     services:
@@ -50,22 +50,6 @@ jobs:
         PYTEST_ADDOPTS: "--durations=0"
       run: pytest --cov aiida_atomistic --cov-append .
 
-  docs:
-    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 .[docs]
-    - name: Build docs
-      run: cd docs && make
-
   pre-commit:
     runs-on: ubuntu-latest
     timeout-minutes: 15

.github/workflows/deploy.yml

@@ -1,10 +1,10 @@
 # This file was created automatically with `myst init --gh-pages` 🪄 💚
 
-name: MyST GitHub Pages Deploy
+name: aiida-atomistic GitHub Pages Deploy
 on:
   push:
     # Runs on pushes targeting the default branch
-    branches: [develop]
+    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: ''`
@@ -37,10 +37,11 @@ jobs:
         run: npm install -g mystmd
       - name: Build HTML Assets
         run: myst build --html
+        working-directory: ./docs
       - name: Upload artifact
         uses: actions/upload-pages-artifact@v1
         with:
-          path: './_build/html'
+          path: './docs/_build/html'
       - name: Deploy to GitHub Pages
         id: deployment
         uses: actions/deploy-pages@v2

.pre-commit-config.yaml

@@ -0,0 +1,8 @@
+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

README.md

@@ -7,33 +7,13 @@
 
 AiiDA plugin which contains data and methods for atomistic simulations.
 
-
 ## Installation
 
 ```shell
 git clone https://github.com/aiidateam/aiida-atomistic .
 pip install ./aiida-atomistic
 verdi quicksetup  # better to set up a new profile
-verdi plugin list aiida.calculations  # should now show your calclulation plugins
-```
-
-
-## Usage
-
-Here goes a complete example of how to submit a test calculation using this plugin.
-
-A quick demo of how to submit a calculation:
-```shell
-verdi daemon start     # make sure the daemon is running
-cd examples
-./example_01.py        # run test calculation
-verdi process list -a  # check record of calculation
-```
-
-The plugin also includes verdi commands to inspect its data types:
-```shell
-verdi data atomistic list
-verdi data atomistic export <PK>
+verdi plugin list aiida.data  # should now show your data plugins
 ```
 
 ## Development
@@ -46,7 +26,6 @@ pip install -e .[pre-commit,testing]  # install extra dependencies
 pre-commit install  # install pre-commit hooks
 pytest -v  # discover and run all tests
 ```
-
 See the [developer guide](http://aiida-atomistic.readthedocs.io/en/latest/developer_guide/index.html) for more information.
 
 ## License

conftest.py

@@ -29,7 +29,7 @@ def supported_properties():
         "charge",
         "magmom",
         "kind_name",
-        "weight",
+        "weights",
     ]
 
 
@@ -48,7 +48,8 @@ def example_structure_dict():
                 "position": [0.0, 0.0, 0.0],
                 "mass": 63.546,
                 "charge": 1.0,
-                "magmom": [0,0,0],
+                "magmom": [0.0,0.0,0.0],
+                "weights": (1,)
             }
         ],
     }
@@ -117,16 +118,31 @@ def example_structure_dict_for_kinds():
         [-1.7391821518091137e-16, 2.8403, 1.7391821518091137e-16],
         [0.0, 0.0, 2.8403]],
         'sites': [{'symbol': 'Fe',
-        'weights': 55.845,
+        'mass': 55.845,
         'position': [0.0, 0.0, 0.0],
         'charge': 0.0,
         'magmom': [2.5, 0.1, 0.1],
         'kind_name': 'Fe'},
         {'symbol': 'Fe',
-        'weights': 55.845,
+        'mass': 55.845,
         'position': [1.42015, 1.42015, 1.4201500000000002],
         'charge': 0.0,
         'magmom': [2.4, 0.1, 0.1],
         'kind_name': 'Fe'}]}
 
     return structure_dict
+
+@pytest.fixture
+def example_structure_dict_alloy():
+    """
+    Return the dictionary of properties as to be used in the standards tests.
+    """
+    structure_dict ={
+        'pbc': [True, True, True],
+        'cell': [[0.0, 1.8, 1.8], [1.8, 0.0, 1.8], [1.8, 1.8, 0.0]],
+        'sites': [{'symbol': 'CuAl',
+        'position': [0.0, 0.0, 0.0],
+        'weights': (0.5,0.5)
+        }],}
+
+    return structure_dict

docs/.gitignore

@@ -1,2 +1,2 @@
 # MyST build outputs
-/_build/
+/_build/