Allowing 3.11 python version (#107)

* Adding Python 3.10 and 3.11 to package and actions

Add env system for uv installation

* Moved out coveralls testing to its own action

* Updated publishing adding python versions 3.10 and 3.11

* Fix pytest action

* Updated readme

* Fixed errors

Using plural for properties under Outputs

* Fix ruff

.github/workflows/actions.yml

@@ -1,4 +1,4 @@
-name: install-and-test
+name: Installing and Testing
 on: [push]
 
 # https://docs.github.com/en/actions/using-jobs/assigning-permissions-to-jobs
@@ -9,55 +9,57 @@ permissions:
   checks: write
   pull-requests: write
 
+env:
+  UV_SYSTEM_PYTHON: true
+
 jobs:
   install-and-test:
     runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python_version: ["3.9", "3.10", "3.11"]
     steps:
     - uses: actions/checkout@v4
-    - name: Set up Python 3.9
+    - name: Set up Python ${{matrix.python_version}}
       uses: actions/setup-python@v5
       with:
-        python-version: 3.9
+        python-version: ${{matrix.python_version}}
+    - name: Install uv
+      run: |
+        curl -LsSf https://astral.sh/uv/install.sh | sh
     - name: Install dependencies
       run: |
         pip install --upgrade pip
-        pip install uv
-        uv pip install -e '.[dev]' --index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple --system
-        uv pip install coveralls --system
+        uv pip install -e '.[dev]'
     - name: mypy
       run: |
         python -m mypy --ignore-missing-imports --follow-imports=silent --no-strict-optional src/nomad_simulations/schema_packages tests
-    - name: Build coverage file
+    - name: Test with pytest
       run: |
-        pytest --junitxml=pytest.xml --cov-report=term-missing:skip-covered --cov=src tests | tee pytest-coverage.txt
-    - name: Pytest coverage comment
-      uses: MishaKav/pytest-coverage-comment@main
-      with:
-        pytest-coverage-path: pytest-coverage.txt
-        junitxml-path: pytest.xml
-    - name: Submit to coveralls
-      continue-on-error: true
-      env:
-        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      run: |
-        coveralls --service=github
+        python -m pytest -sv tests
   build-and-install:
     runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python_version: ["3.9", "3.10", "3.11"]
     steps:
     - uses: actions/checkout@v4
-    - name: Set up Python 3.9
+    - name: Set up Python ${{matrix.python_version}}
       uses: actions/setup-python@v5
       with:
-        python-version: 3.9
+        python-version: ${{matrix.python_version}}
+    - name: Install uv
+      run: |
+        curl -LsSf https://astral.sh/uv/install.sh | sh
     - name: Build the package
       run: |
-        pip install uv
-        uv pip install --upgrade pip --system
-        uv pip install build --system
+        uv pip install build
         python -m build --sdist
     - name: Install the package
       run: |
-        uv pip install dist/*.tar.gz --index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple --system
+        uv pip install dist/*.tar.gz
   ruff-linting:
       runs-on: ubuntu-latest
       steps:

.github/workflows/coveralls.yml

@@ -0,0 +1,44 @@
+name: Testing with coveralls Report
+on: [push]
+
+# https://docs.github.com/en/actions/using-jobs/assigning-permissions-to-jobs
+# `contents` is for permission to the contents of the repository.
+# `pull-requests` is for permission to pull request
+permissions:
+  contents: write
+  checks: write
+  pull-requests: write
+
+env:
+  UV_SYSTEM_PYTHON: true
+
+jobs:
+  coveralls-test:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.11
+      uses: actions/setup-python@v5
+      with:
+        python-version: 3.11
+    - name: Install uv
+      run: |
+        curl -LsSf https://astral.sh/uv/install.sh | sh
+    - name: Install dependencies
+      run: |
+        uv pip install -e '.[dev]'
+        uv pip install coveralls
+    - name: Build coverage file
+      run: |
+        pytest --junitxml=pytest.xml --cov-report=term-missing:skip-covered --cov=src tests | tee pytest-coverage.txt
+    - name: Pytest coverage comment
+      uses: MishaKav/pytest-coverage-comment@main
+      with:
+        pytest-coverage-path: pytest-coverage.txt
+        junitxml-path: pytest.xml
+    - name: Submit to coveralls
+      continue-on-error: true
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      run: |
+        coveralls --service=github

.github/workflows/publish.yml

@@ -15,27 +15,31 @@ on:
 permissions:
   contents: read
 
+env:
+  UV_SYSTEM_PYTHON: true
+
 jobs:
   deploy:
-
     runs-on: ubuntu-latest
-
+    strategy:
+      fail-fast: false
+      matrix:
+        python_version: ["3.9", "3.10", "3.11"]
     steps:
-    - uses: actions/checkout@v3
-
-    - name: Set up Python 3.9
-      uses: actions/setup-python@v3
+    - uses: actions/checkout@v4
+    - name: Set up Python ${{matrix.python_version}}
+      uses: actions/setup-python@v5
       with:
-        python-version: '3.9'
-
+        python-version: ${{matrix.python_version}}
+    - name: Install uv
+      run: |
+        curl -LsSf https://astral.sh/uv/install.sh | sh
     - name: Install dependencies
       run: |
         pip install --upgrade pip
-        pip install build
-
+        uv pip install build
     - name: Build package
       run: python -m build
-
     - name: Publish package to PyPI
       uses: pypa/gh-action-pypi-publish@release/v1
       with:

README.md

@@ -20,11 +20,11 @@ pip install nomad-simulations --index-url https://gitlab.mpcdf.mpg.de/api/v4/pro
 
 ## Development
 
-If you want to develop locally this package, clone the project and in the workspace folder, create a virtual environment (note this project uses Python 3.9):
+If you want to develop locally this package, clone the project and in the workspace folder, create a virtual environment (you can use Python 3.9, 3.10, or 3.11):
 ```sh
 git clone https://github.com/nomad-coe/nomad-simulations.git
 cd nomad-simulations
-python3.9 -m venv .pyenv
+python3.11 -m venv .pyenv
 . .pyenv/bin/activate
 ```
 

pyproject.toml

@@ -8,6 +8,8 @@ classifiers = [
     "Operating System :: OS Independent",
     "Programming Language :: Python",
     "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
     "License :: OSI Approved :: Apache Software License",
 ]
 name = "nomad-simulations"
@@ -46,6 +48,9 @@ dev = [
     "structlog",
 ]
 
+[tool.uv]
+index-url = "https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple"
+
 [tool.ruff]
 # Exclude a variety of commonly ignored directories.
 exclude = [

src/nomad_simulations/schema_packages/outputs.py

@@ -118,15 +118,15 @@ class Outputs(ArchiveSection):
 
     xas_spectra = SubSection(sub_section=XASSpectrum.m_def, repeats=True)
 
-    total_energy = SubSection(sub_section=TotalEnergy.m_def, repeats=True)
+    total_energies = SubSection(sub_section=TotalEnergy.m_def, repeats=True)
 
-    kinetic_energy = SubSection(sub_section=KineticEnergy.m_def, repeats=True)
+    kinetic_energies = SubSection(sub_section=KineticEnergy.m_def, repeats=True)
 
-    potential_energy = SubSection(sub_section=PotentialEnergy.m_def, repeats=True)
+    potential_energies = SubSection(sub_section=PotentialEnergy.m_def, repeats=True)
 
-    total_force = SubSection(sub_section=TotalForce.m_def, repeats=True)
+    total_forces = SubSection(sub_section=TotalForce.m_def, repeats=True)
 
-    temperature = SubSection(sub_section=Temperature.m_def, repeats=True)
+    temperatures = SubSection(sub_section=Temperature.m_def, repeats=True)
 
     # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
     # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #

src/nomad_simulations/schema_packages/properties/energies.py

@@ -127,6 +127,12 @@ class KineticEnergy(BaseEnergy):
     Physical property section describing the kinetic energy of a (sub)system.
     """
 
+    def __init__(
+        self, m_def: 'Section' = None, m_context: 'Context' = None, **kwargs
+    ) -> None:
+        super().__init__(m_def, m_context, **kwargs)
+        self.name = self.m_def.name
+
     def normalize(self, archive: 'EntryArchive', logger: 'BoundLogger') -> None:
         super().normalize(archive, logger)
 
@@ -136,5 +142,11 @@ class PotentialEnergy(BaseEnergy):
     Physical property section describing the potential energy of a (sub)system.
     """
 
+    def __init__(
+        self, m_def: 'Section' = None, m_context: 'Context' = None, **kwargs
+    ) -> None:
+        super().__init__(m_def, m_context, **kwargs)
+        self.name = self.m_def.name
+
     def normalize(self, archive: 'EntryArchive', logger: 'BoundLogger') -> None:
         super().normalize(archive, logger)

src/nomad_simulations/schema_packages/utils/utils.py

@@ -111,8 +111,9 @@ def multiplicity(self):
 
     @property
     def degeneracy(self):
-        return factorial(self.multiplicity) / (
-            factorial(self.multiplicity - self.occupation) * factorial(self.occupation)
+        return factorial(int(self.multiplicity)) / (
+            factorial(int(self.multiplicity - self.occupation))
+            * factorial(self.occupation)
         )
 
 

tests/conftest.py

@@ -23,6 +23,7 @@
 import pytest
 from nomad.datamodel import EntryArchive
 from nomad.units import ureg
+
 from nomad_simulations.schema_packages.atoms_state import AtomsState, OrbitalsState
 from nomad_simulations.schema_packages.general import Simulation
 from nomad_simulations.schema_packages.model_method import ModelMethod

tests/test_atoms_state.py

@@ -22,6 +22,7 @@
 import pytest
 from nomad.datamodel import EntryArchive
 from nomad.units import ureg
+
 from nomad_simulations.schema_packages.atoms_state import (
     AtomsState,
     CoreHole,

tests/test_band_gap.py

@@ -22,6 +22,7 @@
 import pytest
 from nomad.datamodel import EntryArchive
 from nomad.units import ureg
+
 from nomad_simulations.schema_packages.properties import ElectronicBandGap
 from nomad_simulations.schema_packages.variables import Temperature
 
@@ -78,9 +79,6 @@ def test_validate_values(self, value: Union[list[float], float], result: float):
             (None, None, None),
             (None, 'direct', 'direct'),
             (None, 'indirect', 'indirect'),
-            ([], None, None),
-            ([], 'direct', 'direct'),
-            ([], 'indirect', 'indirect'),
             ([[0, 0, 0]], None, None),
             ([[0, 0, 0]], 'direct', None),
             ([[0, 0, 0]], 'indirect', None),

tests/test_band_structure.py

@@ -21,6 +21,7 @@
 import numpy as np
 import pytest
 from nomad.datamodel import EntryArchive
+
 from nomad_simulations.schema_packages.properties import ElectronicEigenvalues
 
 from . import logger
@@ -91,12 +92,6 @@ def test_default_quantities(self, n_bands: Optional[int], rank: Optional[list]):
                 False,
                 (None, None),
             ),
-            (
-                [],
-                [[3, -2], [3, 1], [4, -2], [5, -1], [4, 0], [2, 0], [2, 1], [4, -3]],
-                False,
-                (None, None),
-            ),
             (
                 [[2, 2], [0, 0]],
                 [[3, -2], [3, 1], [4, -2], [5, -1], [4, 0], [2, 0], [2, 1], [4, -3]],
@@ -188,13 +183,6 @@ def test_order_eigenvalues(
                 None,
                 (None, None),
             ),
-            (
-                [],
-                [[3, -2], [3, 1], [4, -2], [5, -1], [4, 0], [2, 0], [2, 1], [4, -3]],
-                None,
-                None,
-                (None, None),
-            ),
             (
                 [[2, 2], [0, 0]],
                 [[3, -2], [3, 1], [4, -2], [5, -1], [4, 0], [2, 0], [2, 1], [4, -3]],
@@ -217,13 +205,6 @@ def test_order_eigenvalues(
                 2.0,
                 (1.0, 2.0),
             ),
-            (
-                [],
-                [[3, -2], [3, 1], [4, -2], [5, -1], [4, 0], [2, 0], [2, 1], [4, -3]],
-                1.0,
-                2.0,
-                (1.0, 2.0),
-            ),
             (
                 [[2, 2], [0, 0]],
                 [[3, -2], [3, 1], [4, -2], [5, -1], [4, 0], [2, 0], [2, 1], [4, -3]],
@@ -290,13 +271,6 @@ def test_homo_lumo_eigenvalues(
                 None,
                 None,
             ),
-            (
-                [],
-                [[3, -2], [3, 1], [4, -2], [5, -1], [4, 0], [2, 0], [2, 1], [4, -3]],
-                None,
-                None,
-                None,
-            ),
             (
                 [[2, 2], [0, 0]],
                 [[3, -2], [3, 1], [4, -2], [5, -1], [4, 0], [2, 0], [2, 1], [4, -3]],
@@ -319,13 +293,6 @@ def test_homo_lumo_eigenvalues(
                 2.0,
                 1.0,
             ),
-            (
-                [],
-                [[3, -2], [3, 1], [4, -2], [5, -1], [4, 0], [2, 0], [2, 1], [4, -3]],
-                1.0,
-                2.0,
-                1.0,
-            ),
             (
                 [[2, 2], [0, 0]],
                 [[3, -2], [3, 1], [4, -2], [5, -1], [4, 0], [2, 0], [2, 1], [4, -3]],