resolve merge conflicts + rename schemas to avoid breaking changes

Author: esoteric-ephemera

.github/workflows/deploy.yml

@@ -21,7 +21,7 @@ jobs:
 
       - uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.11"
           cache: pip
           cache-dependency-path: pyproject.toml
 
@@ -51,7 +51,7 @@ jobs:
 
       - uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.11"
 
       - name: Build
         run: |

.github/workflows/docs.yml

@@ -26,7 +26,7 @@ jobs:
 
       - uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.11"
           cache: pip
           cache-dependency-path: pyproject.toml
 

.github/workflows/testing.yml

@@ -17,7 +17,7 @@ jobs:
 
       - uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.11"
           cache: pip
           cache-dependency-path: pyproject.toml
 
@@ -39,7 +39,7 @@ jobs:
         shell: bash -l {0} # enables conda/mamba env activation by reading bash profile
     strategy:
       matrix:
-        python-version: ["3.10", "3.11", "3.12"]
+        python-version: ["3.11", "3.12"]
         split: [1, 2, 3]
 
     steps:
@@ -48,10 +48,11 @@ jobs:
 
       - name: Set up micromamba
         uses: mamba-org/setup-micromamba@main
-
-      - name: Create mamba environment
-        run: |
-          micromamba create -n a2 python=${{ matrix.python-version }} --yes
+        with:
+          environment-name: a2
+          cache-environment: false
+          create-args: >-
+            python=${{ matrix.python-version }}
 
       - name: Install uv
         run: micromamba run -n a2 pip install uv
@@ -66,8 +67,8 @@ jobs:
           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 .[strict,strict-forcefields,tests,abinit,approxneb,aims]
+          uv pip install torch-runstats torch_dftd
           uv pip install --no-deps nequip==0.5.6
 
       - name: Install pymatgen from master if triggered by pymatgen repo dispatch
@@ -87,11 +88,11 @@ jobs:
         # However this `splitting-algorithm` means that tests cannot depend sensitively on the order they're executed in.
         run: |
           micromamba activate a2
-          pytest --splits 3 --group ${{ matrix.split }} --durations-path tests/.pytest-split-durations --splitting-algorithm least_duration --ignore=tests/ase --ignore=tests/openff_md --ignore=tests/openmm_md --cov=atomate2 --cov-report=xml
+          pytest -n auto --splits 3 --group ${{ matrix.split }} --durations-path tests/.pytest-split-durations --splitting-algorithm least_duration --ignore=tests/ase --ignore=tests/openff_md --ignore=tests/openmm_md --cov=atomate2 --cov-report=xml
 
 
       - uses: codecov/codecov-action@v1
-        if: matrix.python-version == '3.10' && github.repository == 'materialsproject/atomate2'
+        if: matrix.python-version == '3.11' && github.repository == 'materialsproject/atomate2'
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           name: coverage${{ matrix.split }}
@@ -113,18 +114,19 @@ jobs:
         shell: bash -l {0} # enables conda/mamba env activation by reading bash profile
     strategy:
       matrix:
-        python-version: ["3.10","3.11","3.12"]
+        python-version: ["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=${{ matrix.python-version }} --yes
+        with:
+          environment-name: a2
+          cache-environment: false
+          create-args: >-
+            python=${{ matrix.python-version }}
 
       - name: Install uv
         run: micromamba run -n a2 pip install uv
@@ -151,12 +153,12 @@ jobs:
 
         run: |
           micromamba activate a2
-          pytest tests/{openff_md,openmm_md}
+          pytest -n auto tests/{openff_md,openmm_md}
 
   test-notebooks-and-ase:
     # prevent this action from running on forks
     if: github.repository == 'materialsproject/atomate2'
-    
+
     # It seems like anything torch-dependent and tblite can't be installed in the same environment
     # without the tblite tests failing in CI, see, e.g.:
     # https://github.com/tblite/tblite/issues/116
@@ -174,18 +176,19 @@ jobs:
         shell: bash -l {0} # enables conda/mamba env activation by reading bash profile
     strategy:
       matrix:
-        python-version: ["3.10", "3.11", "3.12"]
+        python-version: ["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=${{ matrix.python-version }} --yes
+        with:
+          environment-name: a2
+          cache-environment: false
+          create-args: >-
+            python=${{ matrix.python-version }}
 
       - name: Install uv
         run: micromamba run -n a2 pip install uv
@@ -198,7 +201,7 @@ jobs:
         run: |
           micromamba activate a2
           python -m pip install --upgrade pip
-          uv pip install .[strict,tests]
+          uv pip install .[strict,tests,aims]
           uv pip install tblite>=0.4.0
 
       - name: Install pymatgen from master if triggered by pymatgen repo dispatch
@@ -210,17 +213,17 @@ jobs:
           MP_API_KEY: ${{ secrets.MP_API_KEY }}
         run: |
           micromamba activate a2
-          pytest --nbmake ./tutorials --ignore=./tutorials/openmm_tutorial.ipynb --ignore=./tutorials/force_fields
+          pytest -n auto --nbmake ./tutorials --ignore=./tutorials/openmm_tutorial.ipynb --ignore=./tutorials/force_fields
 
       - name: Test ASE
         env:
           MP_API_KEY: ${{ secrets.MP_API_KEY }}
         run: |
           micromamba activate a2
-          pytest --splits 1 --group 1 --cov=atomate2 --cov-report=xml tests/ase
+          pytest -n auto --splits 1 --group 1 --cov=atomate2 --cov-report=xml tests/ase
 
       - uses: codecov/codecov-action@v1
-        if: matrix.python-version == '3.10' && github.repository == 'materialsproject/atomate2'
+        if: matrix.python-version == '3.11' && github.repository == 'materialsproject/atomate2'
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           file: ./coverage.xml
@@ -241,18 +244,19 @@ jobs:
         shell: bash -l {0} # enables conda/mamba env activation by reading bash profile
     strategy:
       matrix:
-        python-version: ["3.10", "3.11", "3.12"]
+        python-version: ["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=${{ matrix.python-version }} --yes
+        with:
+          environment-name: a2
+          cache-environment: false
+          create-args: >-
+            python=${{ matrix.python-version }}
 
       - name: Install uv
         run: micromamba run -n a2 pip install uv
@@ -267,7 +271,7 @@ jobs:
           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 .[strict,strict-forcefields,tests,abinit,aims]
           uv pip install torch-runstats
           uv pip install --no-deps nequip==0.5.6
 
@@ -288,11 +292,11 @@ jobs:
         # 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
+          pytest -n auto --nbmake ./tutorials/force_fields
 
 
       - uses: codecov/codecov-action@v1
-        if: matrix.python-version == '3.10' && github.repository == 'materialsproject/atomate2'
+        if: matrix.python-version == '3.11' && github.repository == 'materialsproject/atomate2'
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           name: coverage
@@ -308,7 +312,7 @@ jobs:
 
       - uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.11"
           cache: pip
           cache-dependency-path: pyproject.toml
 
@@ -321,7 +325,7 @@ jobs:
         run: sphinx-build docs docs_build
 
   automerge:
-    needs: [lint, test-non-ase, test-notebooks-and-ase, test-force-field-notebook, docs]
+    needs: [docs, lint, test-force-field-notebook, test-non-ase, test-notebooks-and-ase, test-openff]
     runs-on: ubuntu-latest
 
     permissions:

.github/workflows/update-precommit.yml

@@ -15,7 +15,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.11"
 
       - name: Install pre-commit
         run: pip install pre-commit

.gitignore

@@ -8,6 +8,9 @@ docs_build/*
 docs/tutorials/*
 docs/tutorials/*/*
 
+# tutorial output files
+tutorials/*.json.gz
+
 # C extensions
 *.so
 
@@ -75,3 +78,6 @@ docs/reference/atomate2.*
 
 .ipynb_checkpoints
 .aider*
+
+# deepmd-kit files
+**/*.pb

.pre-commit-config.yaml

@@ -3,22 +3,24 @@ default_language_version:
 exclude: ^(.github/|tests/test_data/abinit/)
 repos:
 - repo: https://github.com/charliermarsh/ruff-pre-commit
-  rev: v0.9.3
+  rev: v0.14.2
   hooks:
   - id: ruff
     args: [--fix]
     exclude: tutorials/grueneisen_workflow.ipynb
   - id: ruff-format
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v5.0.0
+  rev: v6.0.0
   hooks:
   - id: check-yaml
-  - id: fix-encoding-pragma
-    args: [--remove]
   - id: end-of-file-fixer
   - id: trailing-whitespace
+- repo: https://github.com/asottile/pyupgrade
+  rev: v3.21.0
+  hooks:
+    - id: pyupgrade
 - repo: https://github.com/asottile/blacken-docs
-  rev: 1.19.1
+  rev: 1.20.0
   hooks:
   - id: blacken-docs
     additional_dependencies: [black]
@@ -31,15 +33,15 @@ repos:
   - id: rst-directive-colons
   - id: rst-inline-touching-normal
 - repo: https://github.com/pre-commit/mirrors-mypy
-  rev: v1.14.1
+  rev: v1.18.2
   hooks:
   - id: mypy
     files: ^src/
     additional_dependencies:
     - tokenize-rt==4.1.0
     - types-paramiko
 - repo: https://github.com/codespell-project/codespell
-  rev: v2.4.0
+  rev: v2.4.1
   hooks:
   - id: codespell
     stages: [pre-commit, commit-msg]

CODE_OF_CONDUCT.md

@@ -35,12 +35,18 @@ This Code of Conduct applies both within project spaces and in public spaces
 when an individual is representing the project or its community.
 
 Instances of abusive, harassing, or otherwise unacceptable behavior may be
-reported by contacting a project maintainer at [INSERT EMAIL ADDRESS]. All
-complaints will be reviewed and investigated and will result in a response that
-is deemed necessary and appropriate to the circumstances. Maintainers are
-obligated to maintain confidentiality with regard to the reporter of an
-incident.
-
+reported by contacting a project maintainer at [email protected]. All
+complaints will be reviewed and investigated by a Materials Project staff member
+and will result in a response that
+is deemed necessary and appropriate to the circumstances.
+
+Project maintainers and Materials Project staff members are obligated to
+maintain confidentiality with regard to the reporter of an incident to the extent
+possible by law and institutional policy. Community members should be aware that
+Materials Project staff members are subject to Lawrence Berkeley National Laboratory's
+[harassment and discrimination policies](https://diversity.lbl.gov/harassment-discrimination-policies/),
+which require that reports of sexual violence or harassment (as defined in the policy)
+be reported to the institution.
 
 This Code of Conduct is adapted from the [Contributor Covenant][homepage],
 version 1.3.0, available at https://www.contributor-covenant.org/version/1/3/0/code-of-conduct.html

README.md

@@ -134,16 +134,17 @@ A full list of contributors can be found [here][contributors].
 
 ## Citing 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):
+If you use atomate2, please cite the [following article](https://doi.org/10.1039/D5DD00019J):
 
 ```bib
 @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},
+	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 C. and Clary, Jacob and Cohen, Orion A. and Ertural, Christina and Gallant, Max C. and George, Janine and Gerits, Sophie and Goodall, Rhys E. A. and Guha, Rishabh D. and Hautier, Geoffroy and Horton, Matthew and Inizan, T. J. and Kaplan, Aaron D. and Kingsbury, Ryan S. and Kuner, Matthew C. and Li, Bryant and Linn, Xavier and McDermott, Matthew J. and Mohanakrishnan, Rohith Srinivaas and Naik, Aakash A. and Neaton, Jeffrey B. and Parmar, Shehan M. and Persson, Kristin A. and Petretto, Guido and Purcell, Thomas A. R. and Ricci, Francesco and Rich, Benjamin and Riebesell, Janosh and Rignanese, Gian-Marco and Rosen, Andrew S. 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 B. 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 = {Digital Discovery},
+	doi = {10.1039/D5DD00019J},
+	url = {https://doi.org/10.1039/D5DD00019J},
+	urldate = {2025-07-01},
 }
 ```