Merge branch 'remote-main' into atomate2_jz_pheasy_anharmonic

.github/workflows/deploy.yml

@@ -28,8 +28,6 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          # ase needed to get FrechetCellFilter used by ML force fields
-          pip install git+https://gitlab.com/ase/ase
           pip install .[strict,docs]
 
       - name: Build

.github/workflows/docs.yml

@@ -33,8 +33,6 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          # ase needed to get FrechetCellFilter used by ML force fields
-          pip install git+https://gitlab.com/ase/ase
           pip install .[strict,docs]
 
       - name: Build

.github/workflows/testing.yml

@@ -23,7 +23,10 @@ jobs:
 
       - uses: pre-commit/[email protected]
 
-  test:
+  test-non-ase:
+    # prevent this action from running on forks
+    if: github.repository == 'materialsproject/atomate2'
+
     services:
       local_mongodb:
         image: mongo:4.0
@@ -37,6 +40,7 @@ jobs:
     strategy:
       matrix:
         python-version: ["3.10", "3.11", "3.12"]
+        split: [1, 2, 3]
 
     steps:
       - name: Check out repo
@@ -72,20 +76,30 @@ jobs:
           micromamba activate a2
           uv pip install --upgrade 'git+https://github.com/materialsproject/pymatgen@${{ github.event.client_payload.pymatgen_ref }}'
 
-      - name: Test
+      - name: Test split ${{ matrix.split }}
         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 --ignore=tests/ase --cov=atomate2 --cov-report=xml
+          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:
           token: ${{ secrets.CODECOV_TOKEN }}
+          name: coverage${{ matrix.split }}
           file: ./coverage.xml
 
   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
@@ -143,7 +157,7 @@ jobs:
           MP_API_KEY: ${{ secrets.MP_API_KEY }}
         run: |
           micromamba activate a2
-          pytest --cov=atomate2 --cov-report=xml tests/ase
+          pytest --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'
@@ -172,7 +186,7 @@ jobs:
         run: sphinx-build docs docs_build
 
   automerge:
-    needs: [lint, test, docs]
+    needs: [lint, test-non-ase, test-notebooks-and-ase, docs]
     runs-on: ubuntu-latest
 
     permissions:

.gitignore

@@ -72,3 +72,4 @@ docs/reference/atomate2.*
 *.doctrees*
 
 .ipynb_checkpoints
+.aider*

.pre-commit-config.yaml

@@ -3,21 +3,21 @@ default_language_version:
 exclude: ^(.github/|tests/test_data/abinit/)
 repos:
 - repo: https://github.com/charliermarsh/ruff-pre-commit
-  rev: v0.6.7
+  rev: v0.7.3
   hooks:
   - id: ruff
     args: [--fix]
   - id: ruff-format
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.6.0
+  rev: v5.0.0
   hooks:
   - id: check-yaml
   - id: fix-encoding-pragma
     args: [--remove]
   - id: end-of-file-fixer
   - id: trailing-whitespace
 - repo: https://github.com/asottile/blacken-docs
-  rev: 1.18.0
+  rev: 1.19.1
   hooks:
   - id: blacken-docs
     additional_dependencies: [black]
@@ -30,7 +30,7 @@ repos:
   - id: rst-directive-colons
   - id: rst-inline-touching-normal
 - repo: https://github.com/pre-commit/mirrors-mypy
-  rev: v1.11.2
+  rev: v1.13.0
   hooks:
   - id: mypy
     files: ^src/
@@ -41,11 +41,11 @@ repos:
   rev: v2.3.0
   hooks:
   - id: codespell
-    stages: [commit, commit-msg]
+    stages: [pre-commit, commit-msg]
     args: [--ignore-words-list, 'titel,statics,ba,nd,te,atomate']
     types_or: [python, rst, markdown]
 - repo: https://github.com/kynan/nbstripout
-  rev: 0.7.1
+  rev: 0.8.0
   hooks:
     - id: nbstripout
       args:

CHANGELOG.md

@@ -1,5 +1,49 @@
 # Change log
 
+## v0.0.18
+
+### New Features 🎉
+* Aims magnetic ordering by @tpurcell90 in https://github.com/materialsproject/atomate2/pull/922
+* Ferroelectric Workflow 2 by @fraricci in https://github.com/materialsproject/atomate2/pull/1012
+* Feat: GW workflow with VASP by @yanghan234 in https://github.com/materialsproject/atomate2/pull/808
+
+### Enhancements 🛠
+* Allow energy minimization maker to report energies by @orionarcher in https://github.com/materialsproject/atomate2/pull/1004
+* Implementation to adjust get_supercell_size to also generate orthorhombic supercells by @QuantumChemist in https://github.com/materialsproject/atomate2/pull/923
+* MPMorph Flows by @BryantLi-BLI in https://github.com/materialsproject/atomate2/pull/938
+
+### House-Keeping 🧹
+* Fix `ruff` PLC0206 by @janosh in https://github.com/materialsproject/atomate2/pull/1009
+* Update MACE to 0.3.6 by @orionarcher in https://github.com/materialsproject/atomate2/pull/1032
+* Allow custom mace model by specifying "model" in calculator kwargs" by @orionarcher in https://github.com/materialsproject/atomate2/pull/1017
+* feat: add dedicated fireworks optional dependency (Fix #1033). by @hongyi-zhao in https://github.com/materialsproject/atomate2/pull/1035
+* Make testing utils importable by @jmmshn in https://github.com/materialsproject/atomate2/pull/1037
+
+### New Contributors
+* @fraricci made their first contribution in https://github.com/materialsproject/atomate2/pull/1012
+* @hongyi-zhao made their first contribution in https://github.com/materialsproject/atomate2/pull/1035
+* @BryantLi-BLI made their first contribution in https://github.com/materialsproject/atomate2/pull/938
+* @yanghan234 made their first contribution in https://github.com/materialsproject/atomate2/pull/808
+
+**Full Changelog**: https://github.com/materialsproject/atomate2/compare/v0.0.17...v0.0.18
+
+## v0.0.17
+
+### Bug Fixes 🐛
+
+* Fix `prev_dir` behavior in input set generator of `MPGGAStaticMaker` by @Andrew-S-Rosen in https://github.com/materialsproject/atomate2/pull/996
+
+### Documentation 📖
+
+* Bump min supported Python to 3.10 by @janosh in https://github.com/materialsproject/atomate2/pull/992
+
+### House-Keeping 🧹
+
+* Excise openff dependency from OpenMM testing by @orionarcher in https://github.com/materialsproject/atomate2/pull/993
+* Use `pytest-split` to parallelize across 3 runners and speedup CI by @esoteric-ephemera in https://github.com/materialsproject/atomate2/pull/985
+
+**Full Changelog**: https://github.com/materialsproject/atomate2/compare/v0.0.16...v0.0.17
+
 ## v0.0.16
 
 This release brings lots of new workflows and support for all ASE calculators.

docs/user/codes/openmm.md

@@ -6,24 +6,17 @@
 >>> conda activate atomate2
 
 # installing atomate2
->>> pip install git+https://github.com/orionarcher/atomate2
-
-# installing classical_md dependencies
->>> conda install -c conda-forge --file .github/classical_md_requirements.txt
+>>> pip install "atomate2[openmm]"
 ```
 
 Alternatively, if you anticipate regularly updating
-atomate2 from source (which at this point, you should),
-you can clone the repository and install from source.
+atomate2 from source, you can clone the repository and install from source.
 
 ``` bash
 # installing atomate2
->>> git clone https://github.com/orionarcher/atomate2
+>>> git clone https://github.com/materialsproject/atomate2
 >>> cd atomate2
->>> git branch openff
->>> git checkout openff
->>> git pull origin openff
->>> pip install -e .
+>>> pip install -e '.[openmm]'
 ```
 
 To test the openmm installation, you can run the following command. If
@@ -458,6 +451,7 @@ run_locally(flows[rank], ensure_success=True)
 For now, you'll need to make sure you have a particular emmet branch installed.
 Later the builders will be integrated into `main`.
 
+<!-- TODO get emmet@md_builders merged -->
 ```bash
 pip install git+https://github.com/orionarcher/emmet@md_builders
 ```

docs/user/codes/vasp-workflows.csv

@@ -1,22 +1,22 @@
 Name,Type,Maker
-`Static`_,job,:obj:`.StaticMaker`
-`Relax`_,job,:obj:`.RelaxMaker`
-`Tight Relax`_,job,:obj:`.TightRelaxMaker`
-`Dielectric`_,job,:obj:`.DielectricMaker`
-`Transmuter`_,job,:obj:`.TransmuterMaker`
-`HSE06 Static`_,job,:obj:`.HSEStaticMaker`
-`HSE06 Relax`_,job,:obj:`.HSERelaxMaker`
-`HSE06 Tight Relax`_,job,:obj:`.HSETightRelaxMaker`
-`Double Relax`_,flow,:obj:`.DoubleRelaxMaker`
-`Band Structure`_,flow,:obj:`.BandStructureMaker`
-`Uniform Band Structure`_,flow,:obj:`.UniformBandStructureMaker`
-`Line-Mode Band Structure`_,flow,:obj:`.LineModeBandStructureMaker`
-`HSE06 Band Structure`_,flow,:obj:`.HSEBandStructureMaker`
-`HSE06 Uniform Band Structure`_,flow,:obj:`.HSEUniformBandStructureMaker`
-`HSE06 Line-Mode Band Structure`_,flow,:obj:`.HSELineModeBandStructureMaker`
-`Relax and Band Structure`_,flow,:obj:`.RelaxBandStructureMaker`
-`Elastic Constant`_,flow,:obj:`.ElasticMaker`
-`Optics`_,flow,:obj:`.OpticsMaker`
-`HSE06 Optics`_,flow,:obj:`.HSEOpticsMaker`
-`Phonons`_,flow,:obj:`.PhononMaker`
-`Lobster`_,flow,:obj:`.VaspLobsterMaker`
+`Static`_,job,:obj:`~atomate2.vasp.jobs.core.StaticMaker`
+`Relax`_,job,:obj:`~atomate2.vasp.jobs.core.RelaxMaker`
+`Tight Relax`_,job,:obj:`~atomate2.vasp.jobs.core.TightRelaxMaker`
+`Dielectric`_,job,:obj:`~atomate2.vasp.jobs.core.DielectricMaker`
+`Transmuter`_,job,:obj:`~atomate2.vasp.jobs.core.TransmuterMaker`
+`HSE06 Static`_,job,:obj:`~atomate2.vasp.jobs.core.HSEStaticMaker`
+`HSE06 Relax`_,job,:obj:`~atomate2.vasp.jobs.core.HSERelaxMaker`
+`HSE06 Tight Relax`_,job,:obj:`~atomate2.vasp.jobs.core.HSETightRelaxMaker`
+`Double Relax`_,flow,:obj:`~atomate2.vasp.flows.core.DoubleRelaxMaker`
+`Band Structure`_,flow,:obj:`~atomate2.vasp.flows.core.BandStructureMaker`
+`Uniform Band Structure`_,flow,:obj:`~atomate2.vasp.flows.core.UniformBandStructureMaker`
+`Line-Mode Band Structure`_,flow,:obj:`~atomate2.vasp.flows.core.LineModeBandStructureMaker`
+`HSE06 Band Structure`_,flow,:obj:`~atomate2.vasp.flows.core.HSEBandStructureMaker`
+`HSE06 Uniform Band Structure`_,flow,:obj:`~atomate2.vasp.flows.core.HSEUniformBandStructureMaker`
+`HSE06 Line-Mode Band Structure`_,flow,:obj:`~atomate2.vasp.flows.core.HSELineModeBandStructureMaker`
+`Relax and Band Structure`_,flow,:obj:`~atomate2.vasp.flows.core.RelaxBandStructureMaker`
+`Elastic Constant`_,flow,:obj:`~atomate2.vasp.flows.elastic.ElasticMaker`
+`Optics`_,flow,:obj:`~atomate2.vasp.flows.core.OpticsMaker`
+`HSE06 Optics`_,flow,:obj:`~atomate2.vasp.flows.core.HSEOpticsMaker`
+`Phonons`_,flow,:obj:`~atomate2.vasp.flows.phonons.PhononMaker`
+`Lobster`_,flow,:obj:`~atomate2.vasp.flows.lobster.VaspLobsterMaker`

docs/user/codes/vasp.md

@@ -324,7 +324,7 @@ run_locally(lobster, create_folders=True, store=SETTINGS.JOB_STORE)
 ```
 
 It is, however,  computationally very beneficial to define two different types of job scripts for the VASP and Lobster runs, as VASP and Lobster runs are parallelized differently (MPI vs. OpenMP).
-[FireWorks](https://github.com/materialsproject/fireworks) allows to run the VASP and Lobster jobs with different job scripts. Please check out the [jobflow documentation on FireWorks](https://materialsproject.github.io/jobflow/tutorials/8-fireworks.html#setting-the-manager-configs) for more information.
+[FireWorks](https://github.com/materialsproject/fireworks) allows one to run the VASP and Lobster jobs with different job scripts. Please check out the [jobflow documentation on FireWorks](https://materialsproject.github.io/jobflow/tutorials/8-fireworks.html#setting-the-manager-configs) for more information.
 
 Specifically, you might want to change the `_fworker` for the LOBSTER runs and define a separate `lobster` worker within FireWorks:
 
@@ -468,7 +468,8 @@ Finally, sometimes you have a workflow containing many VASP jobs. In this case i
 tedious to update the input sets for each job individually. Atomate2 provides helper
 functions called "powerups" that can apply settings updates to all VASP jobs in a flow.
 These powerups also contain filters for the name of the job and the maker used to
-generate them.
+generate them. These functions will apply updates *only* to VASP jobs, including those
+created dynamically - all other jobs in a flow will not be modified.
 
 ```py
 from atomate2.vasp.powerups import update_user_incar_settings