Init first unittest for add_workflows_from_workflowhub

.github/workflows/lint.yaml

@@ -1,8 +1,16 @@
-name: Lint
-on: [push, pull_request]
+name: Code best practice and unittesting
+
+on:
+  pull_request:
+    branches:
+      - main
+    paths:
+      - 'bin/**'  # This will trigger the workflow only if files in the 'bin' folder are modified.
+
 concurrency:
   group: lint-${{ github.ref }}
   cancel-in-progress: true
+
 jobs:
   lint:
     runs-on: ubuntu-latest
@@ -15,3 +23,20 @@ jobs:
       run: python -m pip install 'tox>=1.8.0'
     - name: Lint
       run: tox -e lint
+
+  unittest:
+    runs-on: ubuntu-20.04
+    strategy:
+      matrix:
+        python-version: ['3.11']
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install requirements
+        run: python -m pip install -r requirements.txt
+      - name: Run unittests
+        run: |
+          PYTHONPATH=bin python -m unittest discover -s bin/tests

.github/workflows/run_tests.yaml

@@ -1,9 +1,47 @@
 name: Run tests
-on: [push, pull_request]
+
+# This GitHub Actions workflow is designed to automate testing for the project.
+# It triggers under two conditions:
+# 1. Pull requests targeting the main branch, ensuring that internal changes
+#    are validated before merging.
+# 2. Pushes to the dev branch, allowing for continuous integration
+#    as changes are made directly to the development branch.
+#
+# The workflow consists of three main jobs:
+# - **test-tools**: Runs tests for tools extracted from the repository.
+# - **test-tutorials**: Runs tests for community tutorials.
+# - **test-workflows**: Runs tests for workflow scripts.
+#
+# Each job includes the following steps:
+# - Checkout the repository code.
+# - Set up the Python environment using the specified version.
+# - Install required dependencies.
+# - Execute scripts for extraction and filtering of tools, tutorials, or workflows.
+#
+# This ensures that the code remains reliable and functional as new changes are introduced.
+
+on:
+  pull_request:
+    branches:
+      - main  # Trigger on pull requests targeting the main branch
+  push:
+    branches:
+      - dev  # Trigger on pushes to the dev branch
 
 jobs:
   test-tools:
     runs-on: ubuntu-20.04
+    # This job runs tests for tools.
+    # It checks for internal pull requests targeting the main branch,
+    # as well as pushes to the dev branch.
+    # The workflow performs the following steps:
+    # 1. Checkout the repository code.
+    # 2. Set up Python environment using the specified version.
+    # 3. Install required Python packages.
+    # 4. Extract tools using a provided script.
+    # 5. Filter community tools using a provided script.
+    # 6. Format tools into an interactive table and generate a word cloud.
+    if: github.event.pull_request.head.repo.full_name == github.repository || github.ref == 'refs/heads/dev'
     strategy:
       matrix:
         python-version: ['3.11']
@@ -14,7 +52,7 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-      - name: Install requirement
+      - name: Install requirements
         run: python -m pip install -r requirements.txt
       - name: Tool extraction
         run: | 
@@ -26,9 +64,20 @@ jobs:
           bash sources/bin/get_community_tools.sh test
       - name: Create interactive table and wordcloud
         run: | 
-          bash sources/bin/format_tools.sh
+          bash sources/bin/format_tools.sh test
+
   test-tutorials:
     runs-on: ubuntu-20.04
+    # This job runs tests for tutorials.
+    # Similar to the tools job, it checks for internal pull requests
+    # to the main branch and pushes to the dev branch.
+    # The workflow performs the following steps:
+    # 1. Checkout the repository code.
+    # 2. Set up Python environment using the specified version.
+    # 3. Install required Python packages.
+    # 4. Extract tutorials using a provided script.
+    # 5. Filter community tutorials using a provided script.
+    if: github.event.pull_request.head.repo.full_name == github.repository || github.ref == 'refs/heads/dev'
     strategy:
       matrix:
         python-version: ['3.11']
@@ -38,7 +87,7 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-      - name: Install requirement
+      - name: Install requirements
         run: python -m pip install -r requirements.txt
       - name: Tutorial extraction
         run: | 
@@ -48,8 +97,13 @@ jobs:
       - name: Tutorial filtering
         run: | 
           bash sources/bin/get_community_tutorials.sh test
+
   test-workflows:
     runs-on: ubuntu-20.04
+    # This job runs tests for workflows.
+    # It performs the same checks as the other jobs, ensuring
+    # quality for workflow scripts.
+    if: github.event.pull_request.head.repo.full_name == github.repository || github.ref == 'refs/heads/dev'
     strategy:
       matrix:
         python-version: ['3.11']
@@ -59,7 +113,7 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-      - name: Install requirement
+      - name: Install requirements
         run: python -m pip install -r requirements.txt
       - name: Workflow extraction
         run: | 

README.md

@@ -3,7 +3,43 @@ Galaxy Codex
 
 Galaxy Communities Dock aka Galaxy Codex is a catalog of Galaxy resources (tools, training, workflows) that can be filtered for any community.
 
-This repository stores the sources to build this catalog. The catalog is automatically updated every week.
-
+This repository stores the sources to build this catalog and its content. The catalog is automatically updated every week.
 
 Any Galaxy community can be added to this project and benefit from the dedicated resources, including interactive tables that can be embedded into subdomains and website via an iframe. **Learn [how to add your community](https://training.galaxyproject.org/training-material//topics/dev/tutorials/community-tool-table/tutorial.html) in the dedicated GTN tutorial**. 
+
+# Catalog content
+
+## Tool table
+
+Column | Description
+--- | ---
+Suite ID | ID of Galaxy suite
+Tool IDs | List of Galaxy tool IDs
+Description | Description of the suite
+Homepage | Homepage for tool
+Suite version | Version of the Galaxy suite
+Suite Conda package | Conda package used as requirement for the suite 
+Latest suite conda package version | Latest Conda package version on anaconda
+Suite version status | Update status derived by comparing the suite version to the latest conda package version
+ToolShed categories | 
+EDAM operations | EDAM operations extracted using bio.tools
+EDAM reduced operations | EDAM operations where only the most specific terms are kept, i.e. all terms that are superclasses of other terms are removed
+EDAM topics | EDAM topics extracted using bio.tools
+EDAM reduced topics | EDAM topics where only the most specific terms are kept, i.e. all terms that are superclasses of other terms are removed
+Suite owner | Owner of the Galaxy suite
+Suite source | Path to the Galaxy suite
+bio.tools ID | ID of the bio.tools entry corresponding to the tool
+bio.tools name | Name of the bio.tools entry corresponding to the tool
+bio.tools description | Description in bio.tools entry corresponding to the tool
+bii ID | ID of BII entry corresponding to the tool
+Number of tools available on ...  | Number of tools available on given Galaxy server
+Suite users (last 5 years) on ...  | Number of users of the suite in the last 5 years on given Galaxy server
+Suite users on ...  | Number of users of the suite on given Galaxy server
+Suite runs (last 5 years) on ...  |  Number of runs of the suite tools in the last 5 years on given Galaxy server
+Suite runs on ...  | Number of runs of the suite tools on given Galaxy server
+Suite users (last 5 years) on main servers  |  Number of users of the suite in the last 5 years on all UseGalaxy servers
+Suite users on main servers  | Number of users of the suite on all UseGalaxy servers
+Suite runs (last 5 years) on main servers  | Number of runs of the suite tools in the last 5 years on all UseGalaxy servers
+Suite runs on main servers  | Number of runs of the suite tools on all UseGalaxy servers
+Deprecated | Deprecation status after review by a domain expert
+To keep | Status to add to a community after review by a domain expert