Merge main

.ci_support/environment-docs.yml

@@ -1,19 +1,20 @@
 channels:
 - conda-forge
 dependencies:
-  - nbsphinx
-  - sphinx
-  - myst-parser
-  - numpy
-  - ase =3.22.1
-  - coverage
-  - numpy =1.26.3
-  - scipy =1.11.4
-  - spglib =2.2.0
-  - phonopy =2.21.0
-  - structuretoolkit =0.0.17
-  - seekpath =2.1.0
-  - lammps =2023.08.02
-  - pandas =2.1.4
-  - pylammpsmpi =0.2.11
-  - jinja2 =3.1.2
+- nbsphinx
+- sphinx
+- sphinx_rtd_theme
+- myst-parser
+- numpy
+- ase =3.22.1
+- coverage
+- numpy =1.26.3
+- scipy =1.13.0
+- spglib =2.2.0
+- phonopy =2.22.1
+- structuretoolkit =0.0.22
+- seekpath =2.1.0
+- lammps =2023.11.21
+- pandas =2.2.2
+- pylammpsmpi =0.2.15
+- jinja2 =3.1.3

.ci_support/environment-gpaw.yml

@@ -1,4 +1,4 @@
 channels:
 - conda-forge
 dependencies:
-- gpaw =23.9.1
+- gpaw =24.1.0

.ci_support/environment-lammps.yml

@@ -1,9 +1,9 @@
 channels:
 - conda-forge
 dependencies:
-- lammps =2023.08.02
-- pandas =2.1.4
-- pylammpsmpi =0.2.11
-- jinja2 =3.1.2
+- lammps =2024.02.07
+- pandas =2.2.2
+- pylammpsmpi =0.2.15
+- jinja2 =3.1.3
 - iprpy-data =2023.07.25
 - dynaphopy =1.17.15

.ci_support/environment-mace.yml

@@ -0,0 +1,4 @@
+channels:
+- conda-forge
+dependencies:
+- pymace =0.3.4

.ci_support/environment-matgl.yml

@@ -1,4 +1,4 @@
 channels:
 - conda-forge
 dependencies:
-- matgl =0.9.1
+- matgl =0.9.2

.ci_support/environment-notebooks.yml

@@ -3,10 +3,10 @@ channels:
 dependencies:
 - jupyter
 - papermill
-- gpaw =23.9.1
-- lammps =2023.08.02
-- pandas =2.1.4
-- pylammpsmpi =0.2.11
-- jinja2 =3.1.2
+- gpaw =24.1.0
+- lammps =2023.11.21
+- pandas =2.2.2
+- pylammpsmpi =0.2.15
+- jinja2 =3.1.3
 - iprpy-data =2023.07.25
 - dynaphopy =1.17.15

.ci_support/environment.yml

@@ -3,9 +3,9 @@ channels:
 dependencies:
 - ase =3.22.1
 - coverage
-- numpy =1.26.3
-- scipy =1.11.4
-- spglib =2.2.0
-- phonopy =2.21.0
-- structuretoolkit =0.0.17
+- numpy =1.26.4
+- scipy =1.13.0
+- spglib =2.4.0
+- phonopy =2.22.1
+- structuretoolkit =0.0.22
 - seekpath =2.1.0

.github/dependabot.yml

@@ -3,6 +3,5 @@ updates:
 - package-ecosystem: pip
   directory: "/"
   schedule:
-    interval: weekly
-    day: monday
-  open-pull-requests-limit: 10
+    interval: "daily"
+  open-pull-requests-limit: 10

.github/workflows/dependabot.yml

@@ -20,6 +20,7 @@ jobs:
           package=$(echo "${{ github.event.pull_request.title }}" | awk '{print $2}')
           from=$(echo "${{ github.event.pull_request.title }}" | awk '{print $4}')
           to=$(echo "${{ github.event.pull_request.title }}" | awk '{print $6}')
+          sed -i "/${package}/s/${from}/${to}/g" binder/environment.yml
           sed -i "/${package}/s/${from}/${to}/g" .ci_support/environment.yml
           sed -i "/${package}/s/${from}/${to}/g" .ci_support/environment-lammps.yml
           sed -i "/${package}/s/${from}/${to}/g" .ci_support/environment-gpaw.yml

.github/workflows/unittests.yml

@@ -63,8 +63,7 @@ jobs:
       run: |
         pip install versioneer[toml]==0.29
         pip install . --no-deps --no-build-isolation
-        coverage run --omit atomistics/_version.py -m unittest discover tests
-        coverage combine
+        coverage run --omit="atomistics/_version.py,tests/*" -m unittest discover tests
     - name: Coveralls
       if: matrix.label == 'linux-64-py-3-11'
       uses: coverallsapp/github-action@v2

.github/workflows/unittests_mace.yml

@@ -0,0 +1,36 @@
+name: MACE Unittest Linux 3.11
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - name: Merge Notebook environment
+      run: |
+        cp .ci_support/environment.yml environment.yml
+        tail --lines=+4 .ci_support/environment-mace.yml >> environment.yml
+    - name: Setup Mambaforge
+      uses: conda-incubator/setup-miniconda@v2
+      with:
+        python-version: '3.11'
+        miniforge-variant: Mambaforge
+        channels: conda-forge
+        channel-priority: strict
+        activate-environment: my-env
+        environment-file: environment.yml
+        use-mamba: true
+    - name: Test
+      shell: bash -l {0}
+      timeout-minutes: 60
+      run: |
+        pip install versioneer[toml]==0.29
+        pip install . --no-deps --no-build-isolation
+        python -m unittest tests/test_evcurve_ase_mace.py
+        python -m unittest tests/test_phonons_ase_mace.py
+        python -m unittest tests/test_quasiharmonic_ase_mace.py
+        python -m unittest tests/test_ase_md_mace.py

README.md

@@ -179,8 +179,8 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
   * [Harmonic Approximation](https://atomistics.readthedocs.io/en/latest/workflows.html#harmonic-approximation)
   * [Structure Optimization](https://atomistics.readthedocs.io/en/latest/workflows.html#structure-optimization)
 * [Materials Properties](https://atomistics.readthedocs.io/en/latest/materialproperties.html)
-  * [Elastic Properties](https://atomistics.readthedocs.io/en/docs/materialproperties.html#elastic-properties)
-  * [Thermal Expansion](https://atomistics.readthedocs.io/en/docs/materialproperties.html#thermal-expansion)
-  * [Helmholtz Free Energy](https://atomistics.readthedocs.io/en/docs/materialproperties.html#helmholtz-free-energy)
-  * [Phase Diagram](https://atomistics.readthedocs.io/en/docs/materialproperties.html#phase-diagram)
+  * [Elastic Properties](https://atomistics.readthedocs.io/en/latest/materialproperties.html#elastic-properties)
+  * [Thermal Expansion](https://atomistics.readthedocs.io/en/latest/materialproperties.html#thermal-expansion)
+  * [Helmholtz Free Energy](https://atomistics.readthedocs.io/en/latest/materialproperties.html#helmholtz-free-energy)
+  * [Phase Diagram](https://atomistics.readthedocs.io/en/latest/materialproperties.html#phase-diagram)
 * [Module Index](https://atomistics.readthedocs.io/en/latest/py-modindex.html)