Merge branch 'develop' of https://github.com/SMTG-UCL/ShakeNBreak int…

…o develop

.github/dependabot.yml

@@ -0,0 +1,14 @@
+version: 2
+updates:
+- package-ecosystem: pip
+  directory: "/"
+  schedule:
+    interval: daily
+  groups:
+    python-packages:
+      patterns:
+        - "*"
+  open-pull-requests-limit: 2
+  allow:
+    - dependency-type: direct
+    - dependency-type: indirect

.github/workflows/lint.yml

@@ -31,12 +31,7 @@ jobs:
         run: |
           python -m pip install --upgrade pip
           pip install setuptools setuptools_scm wheel
-          pip install numpy
-          pip install pydocstyle
-          pip install black
-          pip install flake8
-          pip install isort
-          pip install -e .
+          pip install pydocstyle black flake8 isort
           pip install -e .[tests]
 
       - name: sort imports
@@ -51,8 +46,8 @@ jobs:
       - name: black
         run:  |
           black --version
-          black  --line-length 88 --color shakenbreak
-          black  --line-length 88 --check --diff --color shakenbreak
+          black --color shakenbreak
+          black --check --diff --color shakenbreak
 
       - name: flake8
         run:  |

.github/workflows/pip_install_test.yml

@@ -6,16 +6,19 @@ on:
     branches: [main]
     types:
       - completed  # only test when new release has been deployed to PyPI
+  workflow_dispatch:
 
 jobs:
   build-linux:
     runs-on: ubuntu-latest
-    if: ${{ github.event.workflow_run.conclusion == 'success' }}
+    if: ${{ github.event_name == 'workflow_dispatch' || (github.event_name == 'workflow_run' && github.event.workflow_run.conclusion == 'success') }}
+    # only run when tests have passed (or manually triggered)
+
     strategy:
       max-parallel: 5
 
       matrix:
-        python-version: ['3.8', '3.9', '3.10']
+        python-version: ['3.8', '3.9', '3.10', '3.11']
 
     name: Python ${{ matrix.python-version }} pip install
 
@@ -30,17 +33,23 @@ jobs:
         run: |
           sleep 10m  # wait 10 minutes for PyPI to update with the new release
           python -m pip install --upgrade pip
-          pip install shakenbreak  # install only from PyPI
-          pip install shakenbreak[tests]
+          pip install shakenbreak[tests]  # install only from PyPI
 
       - name: Test
         run:  |
-          for test in tests/test_*py
-            do if [[ "$test" != *"test_local"* ]]
-              then pytest $test
-            fi
-          done  # Ignore local tests file, which tests INCAR and POTCAR file writing but not possible on GitHub Actions
-          pytest --mpl tests/test_shakenbreak.py  # test output plots
-          pytest --mpl tests/test_plotting.py  # test output plots
-          # pytest --mpl-generate-path=tests/remote_baseline tests/test_plotting.py  # generate output plots
-          # pytest --mpl-generate-path=tests/remote_baseline tests/test_shakenbreak.py  # generate output plots
+          pytest --mpl -vv tests  # test everything
+          
+      - name: Generate GH Actions test plots
+        if: always()  # always generate the plots, even if the tests fail
+        run:  |
+          # Generate the test plots in case there were any failures:
+          pytest --mpl-generate-path=tests/remote_baseline tests/test_plotting.py
+          pytest --mpl-generate-path=tests/remote_baseline tests/test_shakenbreak.py
+
+      # Upload test plots
+      - name: Archive test plots
+        if: always()  # always upload the plots, even if the tests fail
+        uses: actions/upload-artifact@v3
+        with:
+          name: output-plots
+          path: tests/remote_baseline

.github/workflows/release.yml

@@ -1,15 +1,19 @@
 name: Release and publish
 
 on:
-  push:
-    branches:
-      - main
-    tags:
-      - 'v*' # Push events to matching v*, i.e. v1.0, v20.15.10
+  workflow_run:
+    workflows: [ "Tests" ]
+    branches: [ main ]
+    types:
+      - completed  # only release when tests have passed
+
+  workflow_dispatch:
 
 jobs:
   release:
     runs-on: ubuntu-latest
+    if: ${{ github.event_name == 'workflow_dispatch' || (github.event_name == 'workflow_run' && github.event.workflow_run.conclusion == 'success') }}
+    # only run when tests have passed (or manually triggered)
 
     steps:
       - uses: actions/checkout@v1
@@ -22,46 +26,31 @@ jobs:
         run: |
           python -m pip install --upgrade pip
           pip install setuptools setuptools_scm wheel
-          pip install numpy
-          pip install -e .
           pip install -e .[tests]
 
-      - name: Test
-        run:  |
-          for test in tests/test_*py
-            do if [[ "$test" != *"test_local"* ]]
-              then pytest $test
-            fi
-          done  # Ignore local tests file, which tests INCAR and POTCAR file writing but not possible on GitHub Actions
-          pytest --mpl tests/test_shakenbreak.py  # test output plots
-          pytest --mpl tests/test_plotting.py  # test output plots
-
       - name: Build packages
         run: |
           python setup.py sdist bdist_wheel
 
-      - name: Generate release tag
-        uses: amitsingh-007/[email protected]
-        with:
-          github_token: ${{ secrets.GITHUB_TOKEN }}
-
       - name: Publish
         uses: pypa/gh-action-pypi-publish@master
         with:
           user: __token__
           password: ${{ secrets.TWINE_PASSWORD }}
 
-      - name: Write release info
+      - name: Generate release info
         run: |
           awk 'BEGIN {p = 0} {a = 0 }; /^v\d*.\d*.\d*./ { p += 1; a = 1}; p + a == 1 { print } ' CHANGELOG.rst | sed -e '1,1d' | sed  -e '/./,$!d' -e :a -e '/^\n*$/{$d;N;ba' -e '}' > release_info.txt
+          echo "version=$(grep version setup.py | awk -F\" '{print $2}')" >> $GITHUB_ENV
+
       - name: Release
         uses: actions/create-release@v1
         id: create_release
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         with:
-          tag_name: ${{ env.release_tag }}
-          release_name: ${{ env.release_tag }}
+          tag_name: v${{ env.version }}
+          release_name: ${{ env.version }}
           body_path: release_info.txt
           draft: false
           prerelease: false

.github/workflows/test.yml

@@ -0,0 +1,65 @@
+name: Tests
+
+on:
+  pull_request:
+    branches:
+       - main
+       - develop
+  push:
+    branches:
+      - main
+      - develop
+  workflow_dispatch:
+
+jobs:
+  build-linux:
+    runs-on: ubuntu-latest
+    strategy:
+      max-parallel: 5
+
+      matrix:
+        python-version: ['3.8', '3.9', '3.10', '3.11']
+
+    name: Python ${{ matrix.python-version }} Test Pop
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e .[tests]
+
+      - name: Check package versions
+        run: |
+          pip show -V pymatgen-analysis-defects
+          pip show -V pymatgen
+          pip show -V pytest
+
+      - name: Test
+        run:  |
+          pytest --mpl -vv tests  # test everything
+          
+      - name: Generate GH Actions test plots
+        if: always()  # always generate the plots, even if the tests fail
+        run:  |
+          # Generate the test plots in case there were any failures:
+          pytest --mpl-generate-path=tests/remote_baseline tests/test_plotting.py
+          pytest --mpl-generate-path=tests/remote_baseline tests/test_shakenbreak.py
+
+      # Upload test plots
+      - name: Archive test plots
+        if: always()  # always upload the plots, even if the tests fail
+        uses: actions/upload-artifact@v3
+        with:
+          name: output-plots
+          path: tests/remote_baseline
+
+      # - name: Download a single artifact
+      #   uses: actions/download-artifact@v3
+      #   with:
+      #     name: output-plots

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 # See https://pre-commit.com for more information
 # See https://pre-commit.com/hooks.html for more hooks
-exclude: ^(docs|tests|SnB_input_files|.github|shakenbreak/bash_scripts|CITATION*|MANIFEST*)
+exclude: ^(docs|tests|SnB_input_files|.github|shakenbreak/scripts|CITATION*|MANIFEST*)
 repos:
 
 
@@ -19,7 +19,7 @@ repos:
 
 # Sort/format imports
   - repo: https://github.com/PyCQA/isort
-    rev: 5.10.1
+    rev: 5.12.0
     hooks:
       - id: isort
         args: [--profile, black]
@@ -36,7 +36,7 @@ repos:
     rev: 22.6.0
     hooks:
       - id: black
-        args: [--line-length, "88", --color]
+        args: [--color]
 
 # Check code formatting
   - repo: https://github.com/PyCQA/flake8

.readthedocs.yaml

@@ -17,4 +17,4 @@ sphinx:
 # Explicitly set the version of Python and its requirements
 python:
   install:
-    - requirements: docs/requirements.txt
+    - requirements: docs/docs_requirements.txt