update rptools + rp2paths versions

.github/CONTRIBUTING.md

@@ -0,0 +1,51 @@
+# Contributing
+
+Contributions are welcome, and they are greatly appreciated! Every little bit helps, and credit will always be given.
+
+## Ways you can help
+
+### Report Bugs
+
+Report bugs at <https://github.com/brsynth/synbiocad-galaxy-wrappers/issues>.
+
+If you are reporting a bug, please include:
+
+- Your operating system name and version, versions of synbiocad-galaxy-wrappers and the wrapper associated.
+- Any details about your local setup that might be helpful in troubleshooting.
+- Detailed steps to reproduce the bug.
+
+### Fix Bugs
+
+Look through the GitHub issues for bugs. Anything tagged with `bug` is open to whoever wants to implement it.
+
+### Implement Features
+
+Look through the GitHub issues for features. Anything tagged with `enhancement` is open to whoever wants to implement it.
+
+### Write Documentation
+
+Same as Implement Features
+
+### Submit Feedback
+
+The best way to send feedback is to file an issue at <https://github.com/brsynth/synbiocad-galaxy-wrappers/issues>.
+
+If you are proposing a feature:
+
+- Explain in detail how it would work.
+- Keep the scope as narrow as possible, to make it easier to implement.
+- This will hopefully become a community-driven project and contributions are welcome :)
+
+## Pull Request Guidelines
+
+Open a Pull Request will trigger a bunch of tests checking:
+
+1. the `.shed.yml` file
+2. the wrapper with `planemo`
+
+Add a reviewer: `@guillaume-gricourt` or `@breakthewall` or `@tduigou`
+When the Pull Request will be closed, the wrapper will be updated in the following repository:
+1. testtoolshed
+2. toolshed
+
+This policy was modified from [planemo project](https://github.com/galaxyproject/planemo/blob/master/CONTRIBUTING.rst)

.github/workflows/lint.yml

@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: 'Checkout'
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
       - name: Lint Code Base

.github/workflows/pr.yml

@@ -20,11 +20,11 @@ jobs:
       nb: ${{ steps.set-matrix.outputs.nb }}
     steps:
       - name: 'Checkout'
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: 'Select modified files'
         id: files
         #uses: Ana06/[email protected]
-        uses: tj-actions/changed-files@v35
+        uses: tj-actions/changed-files@v39
         with:
           files: tools/**
           separator: ","
@@ -46,11 +46,11 @@ jobs:
       matrix: ${{ steps.set-matrix.outputs.matrix }}
     steps:
       - name: 'Checkout'
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: 'List repos'
         id: set-matrix
         run: |
-          matrix=$(jq -R -s -c '[split("\n")[] | select(.|length>0)]' .github/workflows/test_skip.txt)
+          matrix=$(jq -R -s -c '[split("\n")[] | select(.|length>0)]' .github/workflows/test_tools_skip.txt)
           echo "Number of repos: ${matrix}"
           echo "matrix=$matrix" >> "${GITHUB_OUTPUT}"
 
@@ -64,7 +64,7 @@ jobs:
         repo: ${{ fromJson(needs.list.outputs.matrix) }}
     steps:
       - name: 'Checkout'
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: "Setup python"
         uses: actions/setup-python@v4
         with:
@@ -85,7 +85,7 @@ jobs:
           ./scripts/shed_lint.py -i "tools/${{ matrix.repo }}"
       - name: 'Test tool'
         if: ${{ ! contains(fromJson(needs.skip.outputs.matrix), matrix.repo) }}
-        timeout-minutes: 60
+        timeout-minutes: 120
         continue-on-error: true
         run: |
           planemo test \
@@ -95,16 +95,18 @@ jobs:
             --galaxy_source https://github.com/galaxyproject/galaxy \
             --galaxy_branch release_22.05 \
             --galaxy_python_version 3.7 \
-            "tools/${{ matrix.repo }}" || { touch tool_test_output.html tool_test_output.json; }
+            "tools/${{ matrix.repo }}"
       - name: 'Prepare artefact'
         run: |
+          touch tool_test_output.html tool_test_output.json
           zip -9 ${{ matrix.repo }}.zip tool_test_output.html tool_test_output.json
       - name: 'Upload Artifact Version'
         uses: actions/upload-artifact@v3
         with:
           name: ${{ matrix.repo }}-artifact
           path: ${{ matrix.repo }}.zip
       - name: 'Aggregate results'
+        if: ${{ ! contains(fromJson(needs.skip.outputs.matrix), matrix.repo) }}
         run: |
           ./scripts/aggregate_test.py -i .
 
@@ -119,7 +121,7 @@ jobs:
         repo: ${{ fromJson(needs.list.outputs.matrix) }}
     steps:
       - name: 'Checkout'
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: "Setup python"
         uses: actions/setup-python@v4
         with:
@@ -136,3 +138,5 @@ jobs:
       - name: 'Main ToolShed'
         run: |
           planemo shed_update --force_repository_creation --shed_target toolshed --shed_key "${{ secrets.TOOLSHED }}" "tools/${{ matrix.repo }}" || planemo shed_update --force_repository_creation --shed_target toolshed --shed_key "${{ secrets.TOOLSHED }}" "tools/${{ matrix.repo }}"
+      - name: 'Create release'
+        uses: ./.github/workflows/release.yml

.github/workflows/prworkflows.yml

@@ -0,0 +1,120 @@
+name: PullRequestWorkflow
+
+on:
+  pull_request:
+    types:
+      - edited
+      - opened
+      - reopened
+      - synchronize
+  pull_request_target:
+    types:
+      - closed
+
+jobs:
+
+  list:
+    runs-on: ubuntu-latest
+    outputs:
+      matrix: ${{ steps.set-matrix.outputs.matrix }}
+      nb: ${{ steps.set-matrix.outputs.nb }}
+    steps:
+      - name: 'Checkout'
+        uses: actions/checkout@v4
+      - name: 'Select modified files'
+        id: files
+        #uses: Ana06/[email protected]
+        uses: tj-actions/changed-files@v39
+        with:
+          files: workflows/**
+          separator: ","
+      - name: 'List repos'
+        id: set-matrix
+        run: |
+          echo "list file modified"
+          echo ${{ steps.files.outputs.all_changed_and_modified_files }}
+          matrix=$(echo ${{ steps.files.outputs.all_changed_and_modified_files }} | jq -R -s -c 'split(",") | map(select(contains("workflows"))) | map(split("/")[1]) | sort | unique')
+          echo "list of repo: ${matrix}"
+          echo "matrix=$matrix" >> "${GITHUB_OUTPUT}"
+          nb=$(echo ${matrix} | jq -s -c '.[] | length')
+          echo "Number of repos: ${nb}"
+          echo "nb=$nb" >> "${GITHUB_OUTPUT}"
+
+  skip:
+    runs-on: ubuntu-latest
+    outputs:
+      matrix: ${{ steps.set-matrix.outputs.matrix }}
+    steps:
+      - name: 'Checkout'
+        uses: actions/checkout@v4
+      - name: 'List repos'
+        id: set-matrix
+        run: |
+          matrix=$(jq -R -s -c '[split("\n")[] | select(.|length>0)]' .github/workflows/test_workflows_skip.txt)
+          echo "Number of repos: ${matrix}"
+          echo "matrix=$matrix" >> "${GITHUB_OUTPUT}"
+
+  test:
+    needs: [list, skip]
+    if: ${{ github.event.pull_request.merged == false && needs.list.outputs.nb > 0 }}
+    runs-on: ubuntu-latest
+    strategy:
+      max-parallel: 1
+      matrix:
+        repo: ${{ fromJson(needs.list.outputs.matrix) }}
+    steps:
+      - name: 'Checkout'
+        uses: actions/checkout@v4
+      - name: "Setup python"
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+          cache: 'pip' # caching pip dependencies
+          cache-dependency-path: |
+            env/requirements.txt
+      - name: 'Install packages'
+        run: |
+          pip install -r env/requirements.txt
+      - name: 'Worfklow Lint'
+        run: |
+          planemo workflow_lint \
+            --fail_level error \
+            "workflows/${{ matrix.repo }}"
+      - name: 'Test tool'
+        if: ${{ ! contains(fromJson(needs.skip.outputs.matrix), matrix.repo) }}
+        timeout-minutes: 60
+        run: |
+          planemo test \
+            --engine external_galaxy \
+            --galaxy_url https://galaxy-synbiocad.org \
+            --galaxy_user_key "${{ secrets.GG_SYNBIOCAD_TOKEN }}" \
+            "workflows/${{ matrix.repo }}/${{ matrix.repo }}.ga"
+
+  shed:
+    needs: list
+    if: ${{ github.event.pull_request.merged == true && needs.list.outputs.nb > 0 }}
+    runs-on: ubuntu-latest
+    continue-on-error: true
+    strategy:
+      max-parallel: 1
+      matrix:
+        repo: ${{ fromJson(needs.list.outputs.matrix) }}
+    steps:
+      - name: 'Checkout'
+        uses: actions/checkout@v4
+      - name: "Setup python"
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+          cache: 'pip' # caching pip dependencies
+          cache-dependency-path: |
+            env/requirements.txt
+      - name: 'Install packages'
+        run: |
+          pip install -r env/requirements.txt
+      - name: 'Deploy'
+        run: |
+          ./scripts/upload_workflow.py \
+            --workflow "workflows/${{ matrix.repo }}/${{ matrix.repo }}.ga" \
+            --galaxy_url https://galaxy-synbiocad.org \
+            --galaxy_user_key "${{ secrets.GG_SYNBIOCAD_TOKEN }}"