Merge pull request #109 from materialsproject/patch_trans

# Linting change, New minor functions

Author: jmmshn

.github/dependabot.yml

@@ -0,0 +1,13 @@
+version: 2
+updates:
+- package-ecosystem: pip
+  directory: "/"
+  schedule:
+    interval: weekly
+  open-pull-requests-limit: 2
+  allow:
+  - dependency-type: direct
+  - dependency-type: indirect
+  ignore:
+    - dependency-name: mistune
+    - dependency-name: numpy

.github/workflows/testing.yml

@@ -2,46 +2,22 @@ on:
   push:
     branches:
       - main
-
     tags:
       - 'v*'
-
   pull_request:
     branches:
       - main
-
-
 jobs:
-
-  paper:
-    runs-on: ubuntu-latest
-    name: Paper Draft
-    steps:
-      - name: Checkout
-        uses: actions/checkout@v2
-      - name: Build draft PDF
-        uses: openjournals/openjournals-draft-action@master
-        with:
-          journal: joss
-          # This should be the path to the paper within your repo.
-          paper-path: paper/paper.md
-      - name: Upload
-        uses: actions/upload-artifact@v1
-        with:
-          name: paper
-          # This is the output path where Pandoc will write the compiled
-          # PDF. Note, this should be the same directory as the input
-          # paper.md
-          path: paper/paper.pdf
   lint:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v2
-
-      - uses: actions/setup-python@v2
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
         with:
-          python-version: 3.8
+          python-version: "3.10"
+          cache: pip
+          cache-dependency-path: pyproject.toml
 
       - name: Install dependencies
         run: |
@@ -58,7 +34,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ 3.8, 3.9 ]
+        python-version: [ "3.9", "3.10", "3.11" ]
 
     steps:
     - uses: actions/[email protected]
@@ -101,10 +77,11 @@ jobs:
 
       - uses: actions/setup-python@v3
         with:
-          python-version: 3.9
+          python-version: 3.11
 
       - name: Install dependencies
         run: |
+          python -m pip install --upgrade pip
           pip install -e .[strict]
           pip install -e .[docs]
       - name: Build

.pre-commit-config.yaml

@@ -1,63 +1,36 @@
 default_language_version:
   python: python3
-exclude: '^src/atomate2/vasp/schemas/calc_types/'
 repos:
-- repo: https://github.com/charliermarsh/ruff-pre-commit
-  rev: v0.0.250
-  hooks:
-  - id: ruff
-    args: [--fix]
-- repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.4.0
-  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: 22.12.0
-  hooks:
-  - id: black
-- repo: https://github.com/asottile/blacken-docs
-  rev: v1.12.1
-  hooks:
-  - id: blacken-docs
-    additional_dependencies: [black]
-    exclude: README.md
-- repo: https://github.com/pycqa/flake8
-  rev: 6.0.0
-  hooks:
-  - id: flake8
-    entry: pflake8
-    files: ^src/
-    additional_dependencies:
-    - pyproject-flake8==6.0.0
-    - 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:
-  - id: python-use-type-annotations
-  - id: rst-backticks
-  - id: rst-directive-colons
-  - id: rst-inline-touching-normal
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  # Ruff version.
+  rev: v0.1.8
+  hooks:
+    # Run the linter.
+    - id: ruff
+      args: [ --fix ]
+    # Run the formatter.
+    - id: ruff-format
 - repo: https://github.com/pre-commit/mirrors-mypy
-  rev: v0.991
+  rev: v1.5.1
   hooks:
   - id: mypy
     files: ^src/
+    args:
+    - --namespace-packages
+    - --explicit-package-bases
     additional_dependencies:
     - tokenize-rt==4.1.0
     - types-pkg_resources==0.1.2
-    - types-paramiko
 - repo: https://github.com/codespell-project/codespell
-  rev: v2.2.2
+  rev: v2.2.6
   hooks:
   - id: codespell
-    stages: [commit, commit-msg]
-    args: [--ignore-words-list, 'titel,statics,ba,nd,te']
-    types_or: [python, rst, markdown]
+    name: codespell
+    description: Checks for common misspellings in text files.
+    entry: codespell
+    language: python
+    types: [text]
+    args: [
+      --ignore-words-list, 'titel,statics,ba,nd,te,mater,commun,vise,dscribe',
+      --skip, "*.ipynb,./tests,*paper*",
+    ]