Merge remote-tracking branch 'upstream/main'

Merging latest changes in upstream.

Author: soge8904

.github/workflows/docs.yml

@@ -39,7 +39,7 @@ jobs:
         run: sphinx-build docs docs_build
 
       - name: Upload build artifact
-        uses: actions/upload-pages-artifact@v2
+        uses: actions/upload-pages-artifact@v3
         with:
           path: ./docs_build
 
@@ -52,4 +52,4 @@ jobs:
     steps:
       - name: Deploy to GitHub Pages
         id: deployment
-        uses: actions/deploy-pages@v2
+        uses: actions/deploy-pages@v4

.github/workflows/testing.yml

@@ -89,6 +89,7 @@ jobs:
           micromamba activate a2
           pytest --splits 3 --group ${{ matrix.split }} --durations-path tests/.pytest-split-durations --splitting-algorithm least_duration --ignore=tests/ase --cov=atomate2 --cov-report=xml
 
+
       - uses: codecov/codecov-action@v1
         if: matrix.python-version == '3.10' && github.repository == 'materialsproject/atomate2'
         with:
@@ -150,7 +151,7 @@ jobs:
       - name: Test Notebooks
         run: |
           micromamba activate a2
-          pytest --nbmake ./tutorials --ignore=./tutorials/openmm_tutorial.ipynb
+          pytest --nbmake ./tutorials --ignore=./tutorials/openmm_tutorial.ipynb --ignore=./tutorials/force_fields
 
       - name: Test ASE
         env:
@@ -165,6 +166,81 @@ jobs:
           token: ${{ secrets.CODECOV_TOKEN }}
           file: ./coverage.xml
 
+  test-force-field-notebook:
+    # prevent this action from running on forks
+    if: github.repository == 'materialsproject/atomate2'
+
+    services:
+      local_mongodb:
+        image: mongo:4.0
+        ports:
+          - 27017:27017
+
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0} # enables conda/mamba env activation by reading bash profile
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11", "3.12"]
+
+    steps:
+      - name: Check out repo
+        uses: actions/checkout@v4
+
+      - name: Set up micromamba
+        uses: mamba-org/setup-micromamba@main
+
+      - name: Create mamba environment
+        run: |
+          micromamba create -n a2 python=${{ matrix.python-version }} --yes
+
+      - name: Install uv
+        run: micromamba run -n a2 pip install uv
+
+      - name: Install conda dependencies
+        run: |
+          micromamba install -n a2 -c conda-forge enumlib packmol bader openbabel openff-toolkit==0.16.2 openff-interchange==0.3.22 --yes
+
+      - name: Install dependencies
+        run: |
+          micromamba activate a2
+          python -m pip install --upgrade pip
+          mkdir -p ~/.abinit/pseudos
+          cp -r tests/test_data/abinit/pseudos/ONCVPSP-PBE-SR-PDv0.4 ~/.abinit/pseudos
+          uv pip install .[strict,strict-forcefields,tests,abinit]
+          uv pip install torch-runstats
+          uv pip install --no-deps nequip==0.5.6
+
+      - name: Install pymatgen from master if triggered by pymatgen repo dispatch
+        if: github.event_name == 'repository_dispatch' && github.event.action == 'pymatgen-ci-trigger'
+        run: |
+          micromamba activate a2
+          uv pip install --upgrade 'git+https://github.com/materialsproject/pymatgen@${{ github.event.client_payload.pymatgen_ref }}'
+
+      - name: Forcefield tutorial
+        env:
+          MP_API_KEY: ${{ secrets.MP_API_KEY }}
+
+        # regenerate durations file with `pytest --store-durations --durations-path tests/.pytest-split-durations`
+        # Note the use of `--splitting-algorithm least_duration`.
+        # This helps prevent a test split having no tests to run, and then the GH action failing, see:
+        # https://github.com/jerry-git/pytest-split/issues/95
+        # However this `splitting-algorithm` means that tests cannot depend sensitively on the order they're executed in.
+        run: |
+          micromamba activate a2
+          pytest --nbmake ./tutorials/force_fields
+
+
+      - uses: codecov/codecov-action@v1
+        if: matrix.python-version == '3.10' && github.repository == 'materialsproject/atomate2'
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          name: coverage
+          file: ./coverage.xml
+
+
+
   docs:
     runs-on: ubuntu-latest
 
@@ -186,7 +262,7 @@ jobs:
         run: sphinx-build docs docs_build
 
   automerge:
-    needs: [lint, test-non-ase, test-notebooks-and-ase, docs]
+    needs: [lint, test-non-ase, test-notebooks-and-ase, test-force-field-notebook, docs]
     runs-on: ubuntu-latest
 
     permissions:

.pre-commit-config.yaml

@@ -3,7 +3,7 @@ default_language_version:
 exclude: ^(.github/|tests/test_data/abinit/)
 repos:
 - repo: https://github.com/charliermarsh/ruff-pre-commit
-  rev: v0.8.0
+  rev: v0.9.3
   hooks:
   - id: ruff
     args: [--fix]
@@ -30,15 +30,15 @@ repos:
   - id: rst-directive-colons
   - id: rst-inline-touching-normal
 - repo: https://github.com/pre-commit/mirrors-mypy
-  rev: v1.13.0
+  rev: v1.14.1
   hooks:
   - id: mypy
     files: ^src/
     additional_dependencies:
     - tokenize-rt==4.1.0
     - types-paramiko
 - repo: https://github.com/codespell-project/codespell
-  rev: v2.3.0
+  rev: v2.4.0
   hooks:
   - id: codespell
     stages: [pre-commit, commit-msg]

CHANGELOG.md

@@ -1,5 +1,34 @@
 # Change log
 
+## v0.0.19
+
+### Bug Fixes 🐛
+* CP2K fixes by @janosh in https://github.com/materialsproject/atomate2/pull/1056
+* bug fix for linear strain passing in qha by @JaGeo in https://github.com/materialsproject/atomate2/pull/1061
+* Fix `generate_phonon_displacements`  magmom removal side effect by @janosh in https://github.com/materialsproject/atomate2/pull/1064
+* Fixed Failing Abinit tests bis by @VicTrqt in https://github.com/materialsproject/atomate2/pull/1108
+### Enhancements 🛠
+* Add trajectory reporter to openmm workflow by @orionarcher in https://github.com/materialsproject/atomate2/pull/1053
+* `PhononMaker` add options to `calculate_pdos` and save force constants to file by @chouyoudou in https://github.com/materialsproject/atomate2/pull/1008
+* Allow `MatPesStaticFlowMaker(static2=None)` by @janosh in https://github.com/materialsproject/atomate2/pull/997
+### Documentation 📖
+* Minor docs cleanup by @esoteric-ephemera in https://github.com/materialsproject/atomate2/pull/1047
+* add openmm description to docs by @JaGeo in https://github.com/materialsproject/atomate2/pull/1069
+* Docs update, forcefield elastic convenience maker, forcefield enum hydration by @esoteric-ephemera in https://github.com/materialsproject/atomate2/pull/1072
+* Added the ChemRxiv citation by @hrushikesh-s in https://github.com/materialsproject/atomate2/pull/1107
+* Fix docs by @janosh in https://github.com/materialsproject/atomate2/pull/1109
+### House-Keeping 🧹
+* Fix minor phonon code formatting issues + typos by @janosh in https://github.com/materialsproject/atomate2/pull/1070
+* Fix bump phonopy by @naik-aakash in https://github.com/materialsproject/atomate2/pull/1006
+* update calorine version by @naik-aakash in https://github.com/materialsproject/atomate2/pull/1083
+* Deprecated `Structure.ntypesp` in pymatgen by @jmmshn in https://github.com/materialsproject/atomate2/pull/1105
+
+### New Contributors
+* @chouyoudou made their first contribution in https://github.com/materialsproject/atomate2/pull/1008
+* @VicTrqt made their first contribution in https://github.com/materialsproject/atomate2/pull/1108
+
+**Full Changelog**: https://github.com/materialsproject/atomate2/compare/v0.0.18...v0.0.19
+
 ## v0.0.18
 
 ### New Features 🎉

README.md

@@ -96,6 +96,7 @@ started:
 
 - [Introduction to running workflows][running-workflows]
 - [Using atomate2 with FireWorks][atomate2_fireworks]
+- [Overview of key concepts][key-concepts]
 - [List of VASP workflows][vasp_workflows]
 
 ## Need help?
@@ -124,18 +125,16 @@ A full list of contributors can be found [here][contributors].
 
 ## Citing atomate2
 
-A journal submission for `atomate2` is planned. In the meantime, please use [`citation.cff`](citation.cff) and the [Zenodo record](https://zenodo.org/badge/latestdoi/306414371) to cite `atomate2`.
+A journal submission of `atomate2` is undergoing peer review. In the meantime, please cite the [ChemRxiv preprint](https://chemrxiv.org/engage/chemrxiv/article-details/678e76a16dde43c9085c75e9):
 
 ```bib
-@software{ganose_atomate2_2024,
-  author = {Ganose, Alex and Riebesell, Janosh and George, J. and Shen, Jimmy and S. Rosen, Andrew and Ashok Naik, Aakash and nwinner and Wen, Mingjian and rdguha1995 and Kuner, Matthew and Petretto, Guido and Zhu, Zhuoying and Horton, Matthew and Sahasrabuddhe, Hrushikesh and Kaplan, Aaron and Schmidt, Jonathan and Ertural, Christina and Kingsbury, Ryan and McDermott, Matt and Goodall, Rhys and Bonkowski, Alexander and Purcell, Thomas and Zügner, Daniel and Qi, Ji},
-  doi = {10.5281/zenodo.10677081},
-  license = {cc-by-4.0},
-  month = jan,
-  title = {atomate2},
-  url = {https://github.com/materialsproject/atomate2},
-  version = {0.0.13},
-  year = {2024}
+@article{ganose2025_atomate2,
+    title        = {Atomate2: Modular Workflows for Materials Science},
+    author       = {Ganose, Alex M. and Sahasrabuddhe, Hrushikesh and Asta, Mark and Beck, Kevin and Biswas, Tathagata and Bonkowski, Alexander and Bustamante, Joana and Chen, Xin and Chiang, Yuan and Chrzan, Daryl and Clary, Jacob and Cohen, Orion and Ertural, Christina and Gallant, Max and George, Janine and Gerits, Sophie and Goodall, Rhys and Guha, Rishabh and Hautier, Geoffroy and Horton, Matthew and Kaplan, Aaron and Kingsbury, Ryan and Kuner, Matthew and Li, Bryant and Linn, Xavier and McDermott, Matthew and Mohanakrishnan, Rohith Srinivaas and Naik, Aakash and Neaton, Jeffrey and Persson, Kristin and Petretto, Guido and Purcell, Thomas and Ricci, Francesco and Rich, Benjamin and Riebesell, Janosh and Rignanese, Gian-Marco and Rosen, Andrew and Scheffler, Matthias and Schmidt, Jonathan and Shen, Jimmy-Xuan and Sobolev, Andrei and Sundararaman, Ravishankar and Tezak, Cooper and Trinquet, Victor and Varley, Joel and Vigil-Fowler, Derek and Wang, Duo and Waroquiers, David and Wen, Mingjian and Yang, Han and Zheng, Hui and Zheng, Jiongzhi and Zhu, Zhuoying and Jain, Anubhav},
+    year         = 2025,
+    journal      = {ChemRxiv},
+    url          = {https://chemrxiv.org/engage/chemrxiv/article-details/678e76a16dde43c9085c75e9},
+    urldate      = {2025-01-22},
 }
 ```
 
@@ -153,6 +152,7 @@ A journal submission for `atomate2` is planned. In the meantime, please use [`ci
 [contributors]: https://materialsproject.github.io/atomate2/about/contributors.html
 [license]: https://raw.githubusercontent.com/materialsproject/atomate2/main/LICENSE
 [running-workflows]: https://materialsproject.github.io/atomate2/user/running-workflows.html
+[key-concepts]: https://materialsproject.github.io/atomate2/user/key_concepts_overview.html#key-concepts-in-atomate2-job-flow-makers-inputset-taskdocument-and-builder
 [atomate2_fireworks]: https://materialsproject.github.io/atomate2/user/fireworks.html
 [vasp_workflows]: https://materialsproject.github.io/atomate2/user/codes/vasp.html
 [RelaxBandStructure]: https://materialsproject.github.io/atomate2/user/codes/vasp.html#relax-and-band-structure