Merge branch 'main' of https://github.com/GrainLearning/grainLearning

Author: chyalexcheng

.github/workflows/Linter.yml

@@ -5,6 +5,7 @@ name: Python linter
 on:
   pull_request:
     branches: [ "main"]
+  workflow_dispatch:
 
 jobs:
   lint:
@@ -14,10 +15,10 @@ jobs:
       fail-fast: false
     steps:
       - uses: actions/checkout@v3
-      - name: Set up Python 3.9
+      - name: Set up Python 3.12
         uses: actions/setup-python@v3
         with:
-          python-version: 3.9
+          python-version: 3.12
       - uses: actions/cache@v3
         with:
           path: ${{ env.pythonLocation }}

.github/workflows/release.yml

@@ -5,21 +5,22 @@ on:
   release:
     types:
       - published
-      
+
 jobs:
   build:
+    runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
-      - name: Set up Python 3.10
-        uses: actions/setup-python@v3
+      - name: Set up Python 3.12
+        uses: actions/setup-python@v4
         with:
-          python-version: 3.10
-          
+          python-version: 3.12
+
       - uses: actions/cache@v3
         with:
           path: ${{ env.pythonLocation }}
           key: ${{ env.pythonLocation }}-${{ hashFiles('pyproject.toml') }}
-      
+
       - name: Install dependencies
         run: |
           python -m pip install poetry
@@ -30,7 +31,7 @@ jobs:
       - uses: actions/upload-artifact@v3
         with:
           path: dist/*
-      
+
   upload_test_pypi:
     needs: [build]
     runs-on: ubuntu-latest
@@ -59,22 +60,22 @@ jobs:
         with:
           user: __token__
           password: ${{ secrets.PYPI_TOKEN }}
-          
+
   publish-zenodo:
         runs-on: ubuntu-latest
         steps:
           - name: Checkout the contents of your repository
-            uses: actions/checkout@v2
+            uses: actions/checkout@v4
           - name: Create a draft snapshot of the repository contents as a new
-                  version in collection 7123966 on Zenodo using metadata
+                  version in concept 7123966 on Zenodo using metadata
                   from repository file .zenodo.json
             env:
               GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
               ZENODO_ACCESS_TOKEN: ${{ secrets.ZENODO_TOKEN }}
-            uses: zenodraft/action@0.10.0
+            uses: zenodraft/action@0.13.3
             with:
               compression: zip
-              collection: 7123966
+              concept: 7123966
               metadata: .zenodo.json
               publish: false
               upsert-doi: true

.github/workflows/sonarcloud.yml

@@ -18,10 +18,10 @@ jobs:
       - uses: actions/checkout@v3
         with:
           fetch-depth: 0  # Shallow clones should be disabled for a better relevancy of analysis
-      - name: Set up Python 3.9
+      - name: Set up Python 3.12
         uses: actions/setup-python@v3
         with:
-          python-version: 3.9
+          python-version: 3.12
       - uses: actions/cache@v3
         with:
           path: ${{ env.pythonLocation }}
@@ -30,7 +30,7 @@ jobs:
         run: |
           python -m pip install poetry
           poetry lock --no-update
-          poetry install -E dev -E rnn
+          poetry install --all-extras
       - name: Check style against standards using prospector
         run: poetry run prospector --zero-exit --output-format grouped --output-format pylint:pylint-report.txt
       - name: Run unit tests with coverage

.readthedocs.yaml

@@ -8,10 +8,8 @@ build:
     post_create_environment:
       # install poetry https://docs.readthedocs.io/en/stable/build-customization.html#id11
       - pip install poetry
-      # Tell poetry to not use a virtual environment 
-      # (We are in a virtual environement anyway)
-      - poetry config virtualenvs.create false
     post_install:
-      # commented out because poetry in readthedocs environement was not able to find right packages otherwise
-      # - poetry lock --no-update
-      - poetry install -E docs -E rnn
+      # Install dependencies with 'docs' dependency group
+      # VIRTUAL_ENV needs to be set manually for now.
+      # See https://github.com/readthedocs/readthedocs.org/pull/11152/
+      - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH poetry install -E docs -E rnn

CITATION.cff

@@ -39,7 +39,7 @@ authors:
     email: klaus.thoeni@newcastle.edu.au
 identifiers:
   - type: doi
-    value: 10.5281/zenodo.7123966
+    value: 10.5281/zenodo.7123965
 repository-code: 'https://github.com/GrainLearning/grainLearning/'
 url: 'https://grainlearning.readthedocs.io/'
 abstract: >-