Merge branch 'master' into dependabot/pip/pytest-cov-4.1.0

.github/workflows/linting.yml

@@ -8,7 +8,7 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: [3.8]
+        python-version: [3.9]
 
     steps:
     - uses: actions/checkout@v2
@@ -22,21 +22,19 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install -r requirements-ci.txt --quiet
-    - name: mypy
-      run: |
-        mypy maml
-    - name: pydocstyle
-      run: |
-        pydocstyle --count maml
-    - name: pylint
+
+    - name: ruff
       run: |
-        pylint maml
+        ruff --version
+        ruff . --ignore D
+
     - name: black
       run: |
         black --version
         black --check --diff --color maml
-    - name: flake8
+
+    - name: mypy
       run: |
-        flake8 --count --show-source --statistics maml
-        # exit-zero treats all errors as warnings.
-        flake8 --count --exit-zero --max-complexity=20 --statistics maml
+        mypy --version
+        rm -rf .mypy_cache
+        mypy maml

.github/workflows/testing.yml

@@ -1,39 +1,41 @@
 name: Testing
 
-on: [push, pull_request]
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+  release:
+    types: [published]
+  workflow_dispatch:
+    inputs:
+      task:
+        type: choice
+        options: [tests, release]
+        default: tests
+        description: Only run tests or release a new version to PyPI after tests pass.
 
 jobs:
-  build:
+  test:
 
     strategy:
       max-parallel: 20
       matrix:
-        os: [ubuntu-latest, macos-latest]
-        python-version: [3.8, 3.9]
+        os: [ubuntu-latest]
+        python-version: ["3.9", "3.10"]
 
     runs-on: ${{ matrix.os }}
+    env:
+      PMG_MAPI_KEY: ${{ secrets.PMG_MAPI_KEY }}
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
-    - name: Cache pip
-      if: matrix.os == 'ubuntu-latest'
-      uses: actions/cache@v2
-      with:
-        path: ~/.cache/pip
-        key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }}
-        restore-keys: |
-          ${{ runner.os }}-pip-
-    - uses: actions/cache@v2
-      if: startsWith(runner.os, 'macOS')
-      with:
-        path: ~/Library/Caches/pip
-        key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }}
-        restore-keys: |
-          ${{ runner.os }}-pip-
+        cache: pip
+        cache-dependency-path: '**/requirements.txt'
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
@@ -43,11 +45,35 @@ jobs:
         pip install -r requirements-optional.txt
         pip install -e .
     - name: pytest
-      env:
-        PMG_MAPI_KEY: ${{ secrets.PMG_MAPI_KEY }}
       run: |
-        pytest maml --cov=maml
-    - name: Coveralls Python
-      continue-on-error: true
+        pytest tests --cov=maml
+    - name: Upload coverage reports to Codecov
       if: matrix.os == 'ubuntu-latest'
-      uses: AndreMiras/coveralls-python-action@v20201129
+      uses: codecov/codecov-action@v3
+      env:
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+
+  release:
+    if: github.event.name == 'release'
+    needs: test
+    runs-on: ubuntu-latest
+    permissions:
+      # For pypi trusted publishing
+      id-token: write
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        name: Install Python
+        with:
+          python-version: "3.10"
+      - run: |
+          python -m pip install build
+          pip install -e .
+          pip wheel -w dist .
+      - name: Build sdist
+        run: python -m build --sdist
+      - name: Publish to PyPi
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          skip-existing: true
+          verbose: true

.gitignore

@@ -8,7 +8,9 @@
 *.pyd
 dist
 _build
+_site
 build
+Gemfile.lock
 .project
 .pydevproject
 .settings

.pre-commit-config.yaml

@@ -1,43 +1,47 @@
-exclude: ^(docs)
+exclude: ^(docs|.*test_files|cmd_line|tasks.py)
 
 ci:
   autoupdate_schedule: monthly
+  skip: [mypy]
+  autofix_commit_msg: pre-commit auto-fixes
+  autoupdate_commit_msg: pre-commit autoupdate
 
 repos:
-  - repo: https://github.com/PyCQA/autoflake
-    rev: v2.1.1
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.3.5
     hooks:
-      - id: autoflake
-
-  - repo: https://github.com/asottile/pyupgrade
-    rev: v3.3.2
-    hooks:
-      - id: pyupgrade
-        args: [--py38-plus]
+      - id: ruff
+        args: [--fix]
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.5.0
     hooks:
       - id: check-yaml
+        exclude: pymatgen/analysis/vesta_cutoffs.yaml
       - id: end-of-file-fixer
       - id: trailing-whitespace
 
-  - repo: https://github.com/PyCQA/isort
-    rev: 5.12.0
-    hooks:
-      - id: isort
-
   - repo: https://github.com/psf/black
-    rev: 23.3.0
+    rev: 24.3.0
     hooks:
       - id: black
 
-  - repo: https://github.com/PyCQA/flake8
-    rev: 6.0.0
-    hooks:
-      - id: flake8
-
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.2.0
+    rev: v1.9.0
     hooks:
       - id: mypy
+
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.2.6
+    hooks:
+      - id: codespell
+        stages: [commit, commit-msg]
+        exclude_types: [html]
+        additional_dependencies: [tomli] # needed to read pyproject.toml below py3.11
+
+  - repo: https://github.com/MarcoGorelli/cython-lint
+    rev: v0.16.0
+    hooks:
+      - id: cython-lint
+        args: [--no-pycodestyle]
+      - id: double-quote-cython-strings

CHANGES.rst → CHANGES.md

@@ -1,53 +1,46 @@
-Change log
-==========
+# Change log
 
-v2022.9.20
-----------
+## v2023.9.9
+* Added DIRECT sampling approach in `maml.sampling`.
+
+## v2022.9.20
 * Bug fix for BOWSR failing because of indexing in some instances.
 
-v2021.1.28
-----------
+## v2021.1.28
 * Fix SNAP stress components
 * Fix unexpected test outcome in BOWSR and symbolic regression
 
-v2021.12.13
------------
+## v2021.12.13
+
 * Update dependencies
 * Fix bugs
 
-v2021.10.13
------------
+## v2021.10.13
 * add bowsr
 
-v2021.3.2
----------
+## v2021.3.2
 * Set up namespace package architecture for maml.apps. The RFXAS package is now available as a separate package
   `maml-apps.rfxas`. Usage remains similar.
 
-v2021.2.27
-----------
+## v2021.2.27
 * maml is now compatible with both mlip-2 and mlip-dev
 
-v0.0.4
-------
+## v0.0.4
 * bug fix
 * compatibility with new n2p2 and mlip software
 * upgrade rfxas
 
-v0.0.3
-------
+## v0.0.3
 * bug fix
 * add atomsets models
 
-v0.0.2
-------
+## v0.0.2
 * major refactor
 * move mlearn potential energy surfaces to apps
 * fix potential problem of rotated structure in lammps
 * add rfxas app
 * add initial symbolic regression app
 * add megnet-based describers
 
-v0.0.1
-------
+## v0.0.1
 * initial release

CITATION.cff

@@ -0,0 +1,19 @@
+cff-version: 1.2.0
+message: |
+  If you use maml in your research, please consider citing the following.
+authors:
+- family-names: Chen
+  given-names: Chi
+- family-names: Zuo
+  given-names: Yunxing
+- family-names: Ye
+  given-names: Weike
+- family-names: Ji
+  given-names: Qi
+- family-names: Ong
+  given-names: Shyue Ping
+  orcid: https://orcid.org/0000-0001-5726-2587
+title: 'Materials Machine Learning (maml)'
+version: 2022.9.20 # replace with whatever version you use
+date-released: 2022-09-20
+url: https://github.com/materialsvirtuallab/maml