Merge branch 'galaxyproject:main' into elixir-toolkit-theme

.github/workflows/lint_and_unittest.yaml

@@ -0,0 +1,42 @@
+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
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
+      with:
+          python-version: '3.11'
+    - name: Install tox
+      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

README.md

@@ -1,13 +1,28 @@
 Galaxy Codex
 ============
 
-Galaxy Communities Dock aka Galaxy Codex is a catalog of Galaxy resources (tools, training, workflows) that can be filtered for any community.
+Galaxy Communities Dock (Galaxy CoDex) is a catalog of resources for Galaxy communities.
 
-This repository stores the sources to build this catalog and its content. The catalog is automatically updated every week.
+Currently, we have two main resources:
 
-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**. 
+1. **Galaxy Community Catalog**: from tools, training & workflows
+2. **Galaxy Labs**: (led by Galaxy Australia!) main and tool panel content for communities to spin up subdomain pages
 
-# Catalog content
+This repository stores the sources to build all of this content. The catalog is automatically updated every week.
+
+# Join the CoDex
+Any Galaxy Community can be added to this project and benefit from the dedicated resources.
+**Learn [how to add your community](https://training.galaxyproject.org/training-material/topics/community/faqs/codex.html)** in the dedicated GTN tutorial.
+
+# Galaxy Community Catalog
+To generate interactive tables that can be embedded into Galaxy Labs (subdomains) and websites via an iframe. 
+**Learn [how to generate the Galaxy Community Catalog](https://training.galaxyproject.org/training-material//topics/dev/tutorials/community-tool-table/tutorial.html)** in the dedicated GTN tutorial. 
+
+# Galaxy Lab
+To generate GalaxyLab content, you can follow our documentation (to be added!).
+To spin up a GalaxyLab on your server, you can follow our documentation (to be added!).
+
+# Galaxy Community Catalog content
 
 ## Tool table
 
@@ -42,4 +57,8 @@ Suite users on main servers  | Number of users of the suite on all UseGalaxy ser
 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
+To keep | Status to add to a community after review by a domain expert
+
+# Vocabulary
+**Galaxy Lab**: Formerly known as Subdomains, Galaxy Australia built a new method for generating the main and tool panels for a Galaxy subdomain, known as a Galaxy Lab.
+**Galaxy Community**: Galaxy Community of Practice. You can see a full list of Special Interest Groups in the [SIG Directory](https://galaxyproject.org/community/sig).

communities/spoc/lab/templates/conclusion.html

@@ -17,9 +17,7 @@ <h4 class="mb-3">Single Cell and Spatial Omics community support</h4>
   <h4 class="mb-3">News and Events</h4>
 
   <div class="row justify-content-center">
-    <div class="col">
-      <iframe width="400px" height="600px" src="https://training.galaxyproject.org/training-material/feeds/single-cell-month.w.html"></iframe>
-    </div>
+      <iframe width="100%" height="600px" src="https://training.galaxyproject.org/training-material/feeds/single-cell-month.w.html"></iframe>
   </div>
 </section>
 

sources/README.md

@@ -216,6 +216,13 @@ When the tests succeed a maintainer will merge the dev branch into main. Feel fr
 
 The reason we are not running the tests directly on the pull request branch is, that this does not allow to access the GitHub secrets, that are required to run the tests.
 
+# Run the unit tests locally
+
+```
+cd codex/sources
+PYTHONPATH=bin python -m unittest discover -s bin/tests
+```
+
 ### Tools
 
 To make a test run of the tool to check its functionalities follow [Usage](#Usage) to set-up the environnement and the API key, then run

sources/bin/extract_all_tutorials.sh

@@ -5,7 +5,7 @@ then
         python sources/bin/extract_gtn_tutorials.py \
                 extract \
                 --all "communities/all/resources/test_tutorials.json" \
-                --tools "communities/all/resources/tools.json" \
+                --tools "communities/all/resources/test_tools.json" \
                 --api $PLAUSIBLE_API_KEY \
                 --test
 else

sources/bin/extract_all_workflows.sh

@@ -4,7 +4,7 @@ if [ ! -z $1 ]
 then
         python sources/bin/extract_galaxy_workflows.py extract \
                 --all communities/all/resources/test_workflows.json \
-                --tools communities/all/resources/tools.json \
+                --tools communities/all/resources/test_tools.json \
                 --test
 else
         python sources/bin/extract_galaxy_workflows.py extract \

sources/bin/shared.py

@@ -83,11 +83,11 @@ def read_suite_per_tool_id(tool_fp: str) -> Dict:
     tool_suites = load_json(tool_fp)
     tools = {}
     for suite in tool_suites:
-        for tool in suite["Galaxy tool ids"]:
+        for tool in suite["Suite ID"]:
             tools[tool] = {
-                "Galaxy wrapper id": suite["Galaxy wrapper id"],
-                "Galaxy wrapper owner": suite["Galaxy wrapper id"],
-                "EDAM operation": suite["EDAM operation"],
+                "Suite ID": suite["Suite ID"],
+                "Suite owner": suite["Suite owner"],
+                "EDAM operations": suite["EDAM operations"],
             }
     return tools
 
@@ -154,7 +154,7 @@ def get_edam_operation_from_tools(selected_tools: list, all_tools: dict) -> List
     edam_operation = set()
     for t in selected_tools:
         if t in all_tools:
-            edam_operation.update(set(all_tools[t]["EDAM operation"]))
+            edam_operation.update(set(all_tools[t]["EDAM operations"]))
         else:
             print(f"{t} not found in all tools")
     return list(edam_operation)