python 3.10 collections test suite update

.github/actions/build_distribution/action.yml

@@ -0,0 +1,48 @@
+name: "build_distribution"
+
+description: "Build and export the distribution"
+
+runs:
+  using: composite
+  steps:
+    - name: Set up Git repository
+      uses: actions/checkout@v2
+
+    - name: Collect any new commits
+      shell: bash
+      run: |
+        git pull  # get any pushes made since the trigger began; without this job-to-job connections may fail
+
+    - name: Set up Node.js 14
+      uses: actions/setup-node@v2
+      with:
+        node-version: '14'
+
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.9
+
+    - name: Install dependencies
+      shell: bash
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r scripts/requirements.txt
+
+    - name: Build distribution
+      shell: bash
+      run: python3 scripts/build_distribution.py
+
+    - name: Commit changes, ready to push
+      shell: bash
+      run: |
+        git config --local user.email "[email protected]"
+        git config --local user.name "GitHub Action"
+        git add *.nt *.md *.fasta *.gb
+        git diff-index --quiet HEAD . || git commit -m "Build distribution"
+
+    - name: Push changes
+      uses: ad-m/github-push-action@master
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        branch: ${{ github.ref }}

.github/actions/build_packages/action.yml

@@ -0,0 +1,55 @@
+name: "build_packages"
+
+description: "Build and validate final packages"
+runs:
+  using: composite
+  steps:
+    - name: Set up Git repository
+      uses: actions/checkout@v2
+
+    - name: Collect any new commits
+      shell: bash
+      run: |
+        git pull  # get any pushes made since the trigger began; without this job-to-job connections may fail
+
+    - name: Set up Node.js 14
+      uses: actions/setup-node@v2
+      with:
+        node-version: '14'
+
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.9
+
+    - name: Install dependencies
+      shell: bash
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r scripts/requirements.txt
+
+    - name: Collate packages
+      shell: bash
+      run: python3 scripts/collate_packages.py
+
+    - name: Create vector build plans
+      shell: bash
+      run: python3 scripts/expand_combinations.py
+
+    - name: Generate markdown from packages
+      shell: bash
+      run: python3 scripts/generate_markdown.py
+
+    - name: Commit changes, ready to push
+      shell: bash
+      run: |
+        git config --local user.email "[email protected]"
+        git config --local user.name "GitHub Action"
+        git add */views/*.nt */README.md
+        git diff-index --quiet HEAD . || git commit -m "Collate and summarize packages"
+
+    - name: Push changes
+      uses: ad-m/github-push-action@master
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        branch: ${{ github.ref }}

.github/actions/directories_and_excel/action.yml

@@ -0,0 +1,49 @@
+
+name: "directories_and_excel"
+
+description: "Updates data files and commits"
+
+runs:
+  using: composite
+  steps:
+    - name: Collect any new commits
+      shell: bash
+      run: |
+        git pull  # get any pushes made since the trigger began; without this job-to-job connections may fail
+
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.9
+
+    - name: Install dependencies
+      shell: bash
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r scripts/requirements.txt
+
+    - name: Regularize directories
+      shell: bash
+      run: python3 scripts/regularize_directories.py
+
+    - name: Update CSVs
+      shell: bash
+      run: python3 scripts/export_csvs.py
+
+    - name: Update SBOL
+      shell: bash
+      run: python3 scripts/export_sbol.py
+
+    - name: Commit changes, ready to push
+      shell: bash
+      run: |
+        git config --local user.email "[email protected]"
+        git config --local user.name "GitHub Action"
+        git add */views
+        git diff-index --quiet HEAD . || git commit -m "Automatically update exports"
+
+    - name: Push changes
+      uses: ad-m/github-push-action@master
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        branch: ${{ github.ref }}

.github/actions/make-sbol/action.yml

@@ -0,0 +1,33 @@
+# An action to convert excel to sbol file 
+name: "make_sbol"
+
+description:  "Installs the required dependencies, python3.9 and sbol-utilities,
+              that are needed to convert the package xlsx file to a SBOL 
+              compatible reference"
+
+runs: 
+  using: "composite"
+  steps:
+      # Check out and install the latest sbol-utilities package
+      - name: "Check out experimental package code for SBOL utilities"
+        uses: "actions/checkout@v3"
+        with:
+          repository: "SynBioDex/sbol-utilities"
+          ref: "sep054"
+          path: "sbol-utilities"
+
+      # Set python3.9 up for latest compatability
+      - name: "Set up Python"
+        uses: "actions/setup-python@v4"
+        with:
+          python-version: 3.9
+
+      # Install SBOL utlities to use excel-to-sbol
+      - name: "Install SBOL utilities"  
+        shell: "bash"
+        run: "pip install -e sbol-utilities"
+
+      # Run excel-to-sbol, if pass exports correctly
+      - name: "Test if we can export correctly"
+        shell: "bash"
+        run: "excel-to-sbol -c ./.github/workflows/sheet_config.json Vectors.xlsx"

.github/actions/retrieve_parts/action.yml

@@ -0,0 +1,52 @@
+name: "retrieve_parts"
+
+description: "Imports parts and devices and converts any legacy parts to SBOL3"
+
+runs:
+  using: composite
+  steps:
+    - name: Set up Git repository
+      uses: actions/checkout@v2
+
+    - name: Collect any new commits
+      shell: bash
+      run: |
+        git pull  # get any pushes made since the trigger began; without this job-to-job connections may fail
+
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.9
+
+    - name: Set up Node.js 14
+      uses: actions/setup-node@v2
+      with:
+        node-version: '14'
+
+    - name: Install dependencies
+      shell: bash
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r scripts/requirements.txt
+
+    - name: Import parts and devices
+      shell: bash
+      run: python3 scripts/import_parts.py
+
+    - name: Convert SBOL2 imports to SBOL3
+      shell: bash
+      run: python3 scripts/convert_sbol_2to3.py
+
+    - name: Commit changes, ready to push
+      shell: bash
+      run: |
+        git config --local user.email "[email protected]"
+        git config --local user.name "GitHub Action"
+        git add */*.gb */*.fasta */*.nt
+        git diff-index --quiet HEAD . || git commit -m "Automatically import referenced parts"
+
+    - name: Push changes
+      uses: ad-m/github-push-action@master
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        branch: ${{ github.ref }}

.github/workflows/build_packages.yml

@@ -0,0 +1,37 @@
+name: Build packages
+
+on: [push]
+
+jobs:
+  directories_and_excel:
+    name: Check package structure and export from Excel files
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out this repository for building
+        uses: actions/checkout@v3
+      - name: directories_and_excel
+        uses: ./.github/actions/directories_and_excel
+
+  retrieve_parts:
+    name: Retrieve missing parts
+    needs: directories_and_excel
+    runs-on: ubuntu-latest
+    steps:
+      - name: retrieve_parts
+        uses: ./.github/actions/retrieve_parts
+
+  build_packages:
+    name: Build and validate final packages
+    needs: retrieve_parts
+    runs-on: ubuntu-latest
+    steps:
+      - name: build_packages
+        uses: ./.github/actions/build_packages
+
+  build_distribution:
+    name: Build and export distribution
+    needs: build_packages
+    runs-on: ubuntu-latest
+    steps:
+      - name: build_distriubtion
+        uses: ./.github/actions/build_distriubtion

.github/workflows/python_linter.yaml

@@ -11,9 +11,9 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out source repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
       - name: Set up Python 3.9
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: 3.9
       - name: Install dependencies
@@ -37,9 +37,9 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out source repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
       - name: Set up Python 3.9
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: 3.9
       - name: flake8 lint