Merge remote-tracking branch 'upstream/main' into hiphive

hrushikesh-s · Mar 1, 2024 · 30940f5 · 30940f5
2 parents 2a4c89c + 58703ef
commit 30940f5
Show file tree

Hide file tree

Showing 903 changed files with 19,420 additions and 2,716 deletions.
diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.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.

diff --git a/.github/workflows/deploy.yml b/.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
 

diff --git a/.github/workflows/docs.yml b/.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

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
@@ -11,9 +11,9 @@ 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: "3.9"
           cache: pip
@@ -34,9 +34,9 @@ jobs:
         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
@@ -52,6 +52,8 @@ jobs:
         #   emmet-core 0.70.0 depends on pymatgen>=2023.10.11
         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,tests]
 
       - name: Test
@@ -69,9 +71,9 @@ 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
@@ -80,6 +82,8 @@ 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

diff --git a/.github/workflows/update-precommit.yml b/.github/workflows/update-precommit.yml
@@ -2,18 +2,18 @@ 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: 3.9
 

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -2,10 +2,11 @@ default_language_version:
   python: python3
 repos:
 - repo: https://github.com/charliermarsh/ruff-pre-commit
-  rev: v0.1.1
+  rev: v0.2.2
   hooks:
   - id: ruff
     args: [--fix]
+  - id: ruff-format
 - repo: https://github.com/pre-commit/pre-commit-hooks
   rev: v4.5.0
   hooks:
@@ -14,29 +15,12 @@ repos:
     args: [--remove]
   - id: end-of-file-fixer
   - id: trailing-whitespace
-- repo: https://github.com/psf/black
-  rev: 23.10.0
-  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:
@@ -45,13 +29,12 @@ repos:
   - id: rst-directive-colons
   - id: rst-inline-touching-normal
 - repo: https://github.com/pre-commit/mirrors-mypy
-  rev: v1.6.1
+  rev: v1.8.0
   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: v2.2.6