Merge branch 'main' of github.com:materialsproject/atomate2

pull turnk main

Author: VicTrqt

.github/PULL_REQUEST_TEMPLATE.md

@@ -27,10 +27,9 @@ Before a pull request can be merged, the following items must be checked:
 
 * [ ] Code is in the [standard Python style](https://www.python.org/dev/peps/pep-0008/).
   The easiest way to handle this is to run the following in the **correct sequence** on
-  your local machine. Start with running [black](https://black.readthedocs.io/en/stable/index.html) on your new code. This will
-  automatically reformat your code to PEP8 conventions and removes most issues. Then run
-  [ruff](https://ruff.rs).
-* [ ] Docstrings have been added in the [Numpy docstring format](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_numpy.html).
+  your local machine. Start with running [`ruff`](https://docs.astral.sh/ruff) and `ruff format` on your new code. This will
+  automatically reformat your code to PEP8 conventions and fix many linting issues.
+* [ ] Doc strings have been added in the [Numpy docstring format](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_numpy.html).
   Run [ruff](https://beta.ruff.rs/docs/rules/#pydocstyle-d) on your code.
 * [ ] Type annotations are **highly** encouraged. Run [mypy](http://mypy-lang.org) to
   type check your code.

.github/workflows/deploy.yml

@@ -6,30 +6,30 @@ on:
     types: [completed]
 
 jobs:
-
   deploy-docs:
-
     # only run if commit is a push to master and the testing finished
     if: ${{ github.repository_owner == 'materialsproject' && github.event.workflow_run.conclusion == 'success' && github.event.workflow_run.event == 'push' && startsWith(github.event.workflow_run.head_branch, 'v0.') }}
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           ref: ${{ github.event.workflow_run.head_branch }}
 
       - name: Install pandoc
         run: sudo apt-get install pandoc
 
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
-          python-version: '3.10'
+          python-version: "3.10"
           cache: pip
           cache-dependency-path: pyproject.toml
 
       - 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
@@ -42,19 +42,18 @@ jobs:
           publish_dir: ./docs_build/
 
   deploy-pypi:
-
     # only run if commit is a push to master, the testing finished, and tagged as version
     if: github.repository_owner == 'materialsproject' && github.event.workflow_run.conclusion == 'success' && github.event.workflow_run.event == 'push' && startsWith(github.event.workflow_run.head_branch, 'v0.')
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           ref: ${{ github.event.workflow_run.head_branch }}
 
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
-          python-version: '3.10'
+          python-version: "3.10"
 
       - name: Build
         run: |
@@ -68,19 +67,18 @@ jobs:
           password: ${{ secrets.PYPI_PASSWORD }}
 
   deploy-github:
-
     runs-on: ubuntu-latest
     needs:
       - deploy-pypi
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           ref: ${{ github.event.workflow_run.head_branch }}
 
       - name: Write release info
         run: |
-          awk 'BEGIN {p = 0} {a = 0 }; /^v\d*.\d*.\d*./ { p += 1; a = 1}; p + a == 1 { print } ' CHANGELOG.md | sed -e '1,1d' | sed  -e '/./,$!d' -e :a -e '/^\n*$/{$d;N;ba' -e '}' > release_info.txt
+          awk 'BEGIN {p = 0} {a = 0 }; /^\#\#\ v\d*.\d*.\d*./ { p += 1; a = 1}; p + a == 1 { print } ' CHANGELOG.md | sed -e '1,1d' | sed  -e '/./,$!d' -e :a -e '/^\n*$/{$d;N;ba' -e '}' > release_info.txt
           echo "" >> release_info.txt
           awk '/CONTRIBUTOR SECTION/{f=1; c=0} f' CHANGELOG.md >> release_info.txt
 

.github/workflows/docs.yml

@@ -17,14 +17,14 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           ref: ${{ github.event.workflow_run.head_branch }}
 
       - name: Install pandoc
         run: sudo apt-get install pandoc
 
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: "3.10"
           cache: pip
@@ -33,6 +33,8 @@ 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

@@ -3,19 +3,19 @@ name: testing
 on:
   push:
     branches: [main]
-    tags: ['v*']
+    tags: ["v*"]
   pull_request:
-    branches: [main]
+  workflow_dispatch:
 
 jobs:
   lint:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
-          python-version: "3.8"
+          python-version: "3.9"
           cache: pip
           cache-dependency-path: pyproject.toml
 
@@ -31,21 +31,33 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.9", "3.10", "3.11"]
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-          cache: pip
-          cache-dependency-path: pyproject.toml
+
 
       - name: Install dependencies
+        # ERROR: Cannot install atomate2 and atomate2[strict,tests]==0.0.1 because these package versions have conflicting dependencies.
+        # The conflict is caused by:
+        #   atomate2[strict,tests] 0.0.1 depends on pymatgen>=2023.10.4
+        #   atomate2[strict,tests] 0.0.1 depends on pymatgen==2023.10.4; extra == "strict"
+        # ERROR: ResolutionImpossible: for help visit https://pip.pypa.io/en/latest/topics/dependency-resolution/#dealing-with-dependency-conflicts
+        #   chgnet 0.2.1 depends on pymatgen>=2023.5.31
+        #   emmet-core 0.70.0 depends on pymatgen>=2023.10.11
         run: |
           python -m pip install --upgrade pip
-            pip install .[strict,tests]
+          mkdir -p ~/.abinit/pseudos
+          cp -r tests/test_data/abinit/pseudos/ONCVPSP-PBE-SR-PDv0.4 ~/.abinit/pseudos
+          # ase needed to get FrechetCellFilter used by ML force fields
+          pip install git+https://gitlab.com/ase/ase
+          pip install .[strict,tests,abinit]
+          pip install torch-runstats
+          pip install --no-deps nequip
 
       - name: Test
         env:
@@ -62,9 +74,9 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: "3.10"
           cache: pip
@@ -73,6 +85,8 @@ 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/update-precommit.yml

@@ -2,20 +2,20 @@ name: pre-commit-auto-update
 
 on:
   schedule:
-    - cron: '0 0 1,14,28 * *'
+    - cron: "0 0 1,14,28 * *"
   workflow_dispatch:
 
 jobs:
   auto-update:
     runs-on: ubuntu-latest
-    
+
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.8
+          python-version: 3.9
 
       - name: Install pre-commit
         run: pip install pre-commit

.pre-commit-config.yaml

@@ -1,43 +1,27 @@
 default_language_version:
   python: python3
-exclude: '^.github/'
+exclude: ^(.github/|tests/test_data/abinit/)
 repos:
 - repo: https://github.com/charliermarsh/ruff-pre-commit
-  rev: v0.0.287
+  rev: v0.3.5
   hooks:
   - id: ruff
     args: [--fix]
+  - id: ruff-format
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.4.0
+  rev: v4.5.0
   hooks:
   - id: check-yaml
   - id: fix-encoding-pragma
     args: [--remove]
   - id: end-of-file-fixer
   - id: trailing-whitespace
-- repo: https://github.com/psf/black
-  rev: 23.7.0
-  hooks:
-  - id: black
 - repo: https://github.com/asottile/blacken-docs
   rev: 1.16.0
   hooks:
   - id: blacken-docs
     additional_dependencies: [black]
     exclude: README.md
-- repo: https://github.com/pycqa/flake8
-  rev: 6.1.0
-  hooks:
-  - id: flake8
-    entry: pflake8
-    files: ^src/
-    additional_dependencies:
-    - pyproject-flake8==6.0.0a1
-    - flake8-bugbear==22.12.6
-    - flake8-typing-imports==1.14.0
-    - flake8-docstrings==1.6.0
-    - flake8-rst-docstrings==0.3.0
-    - flake8-rst==0.8.0
 - repo: https://github.com/pre-commit/pygrep-hooks
   rev: v1.10.0
   hooks:
@@ -46,18 +30,17 @@ repos:
   - id: rst-directive-colons
   - id: rst-inline-touching-normal
 - repo: https://github.com/pre-commit/mirrors-mypy
-  rev: v1.5.1
+  rev: v1.9.0
   hooks:
   - id: mypy
     files: ^src/
     additional_dependencies:
     - tokenize-rt==4.1.0
-    - types-pkg_resources==0.1.2
     - types-paramiko
 - repo: https://github.com/codespell-project/codespell
-  rev: v2.2.5
+  rev: v2.2.6
   hooks:
   - id: codespell
     stages: [commit, commit-msg]
-    args: [--ignore-words-list, 'titel,statics,ba,nd,te']
+    args: [--ignore-words-list, 'titel,statics,ba,nd,te,atomate']
     types_or: [python, rst, markdown]

ADMIN.md

@@ -2,6 +2,7 @@
 
 Version releases on Pypi and GitHub are handled automatically through GitHub
 actions. The steps to push a new release are:
+
 1. Update `CHANGELOG.md` with a new version and release notes.
 2. Create a tagged Git commit with the above changes: `git tag v0.0.1`
 3. Push the commit and tags to GitHub using: `git push origin --tags`