Merge pull request #25 from bernt-matthias/topic/galaxy-slots

support setting GALAXY_SLOTS

.github/workflows/tools.yaml

@@ -145,8 +145,8 @@ jobs:
         if ! grep -q "tool1.xml" <<<$(echo "${{ steps.discover.outputs.tool-list }}"); then echo "tool1.xml must be in the repo list"; exit 1; fi
         if ! grep -q "tool2.xml" <<<$(echo "${{ steps.discover.outputs.tool-list }}"); then echo "tool2.xml must be in the repo list"; exit 1; fi
     # chunk-count will only consider tools/workflows depending on the workflow input to the action
-    - name: Check that the number of chunks is two, i.e. the number of tools
-      run: if [ "${{ steps.discover.outputs.chunk-count }}" != "2" ]; then exit 1; fi
+    - name: Check that the number of chunks is three, i.e. the number of tools
+      run: if [ "${{ steps.discover.outputs.chunk-count }}" != "3" ]; then exit 1; fi
 
   lint:
     name: Test linting of tools
@@ -217,6 +217,9 @@ jobs:
       with:
         path: ~/.cache/pip
         key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup-ci-tools.outputs.galaxy-head-sha }}
+    - name: Get number of CPU cores
+      uses: SimenB/github-actions-cpu-cores@v1
+      id: cpu-cores
     - name: Planemo test tools
       uses: ./
       id: test-tools
@@ -228,6 +231,7 @@ jobs:
         chunk: ${{ matrix.chunk }}
         chunk-count: ${{ needs.setup-ci-tools.outputs.chunk-count }}
         additional-planemo-options: --simultaneous_uploads --check_uploads_ok
+        galaxy-slots: ${{ steps.cpu-cores.outputs.count }}
     - uses: actions/upload-artifact@v2
       with:
         name: 'Tool test output ${{ matrix.chunk }}'
@@ -264,7 +268,7 @@ jobs:
         mode: combine
         html-report: true
     - name: Check statistics
-      run: if ! grep -q "2\s\+success" <<<$(echo ${{ steps.combine.outputs.statistics }}); then echo "wrong statistics"; exit 1; fi
+      run: if ! grep -q "3\s\+success" <<<$(echo ${{ steps.combine.outputs.statistics }}); then echo "wrong statistics"; exit 1; fi
     - uses: actions/upload-artifact@v2
       with:
         name: 'All tool test results'

README.md

@@ -27,7 +27,7 @@ The version of planemo can be controlled with the input `planemo-version` (defau
 Assumptions
 -----------
 
-The action currently only works on workflows using an Ubuntu image.
+The action currently only works on github actions workflows using an Ubuntu image.
 
 Assumptions on the repository
 -----------------------------
@@ -112,6 +112,7 @@ Optional inputs:
 - `galaxy-source`
 - `python-version`
 - `additional-planemo-options`: additional options passed to `planemo test`, see for instance [here](https://github.com/galaxyproject/planemo-ci-action/blob/657582777416fc51b6171961d90dced7dacbeea2/.github/workflows/tools.yaml#L229)
+- `galaxy-slots`: number of slots (threads) to use in Galaxy jobs (sets the `GALAXY_SLOTS` environment variable)
 
 Output:
 

action.yml

@@ -65,6 +65,9 @@ inputs:
   additional-planemo-options:
     description: 'Additional options passed to planemo in lint/test mode'
     default: ''
+  galaxy-slots:
+    description: 'Number of cores to be used for Galaxy jobs in planemo test'
+    default: '1'
   # inputs that are needed for testing this action
   # not supposed to be used
   github-event-name-override:
@@ -132,6 +135,7 @@ runs:
         GITHUB_EVENT_NAME_OVERRIDE: ${{ inputs.github-event-name-override }}
         GITHUB_REF_OVERRIDE: ${{ inputs.github-ref-override }}
         ADDITIONAL_PLANEMO_OPTIONS: ${{ inputs.additional-planemo-options }}
+        GALAXY_SLOTS: ${{ inputs.galaxy-slots }}
 
     # see https://trstringer.com/github-actions-multiline-strings/
     - run: |

test/tools/galaxy_slots/.shed.yml

@@ -0,0 +1,4 @@
+categories: [Sequence Analysis]
+description: test setting GALAXY_SLOTS
+name: galaxy_slots
+owner: adent

test/tools/galaxy_slots/galaxy_slots.xml

@@ -0,0 +1,34 @@
+<tool id="galaxy_slots" name="galaxy_slots" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT">
+    <macros>
+        <token name="@TOOL_VERSION@">0.1.0</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>
+    <command detect_errors="exit_code"><![CDATA[
+        echo "GALAXY_SLOTS \${GALAXY_SLOTS:-1}" > '$out'
+    ]]></command>
+    <inputs/>
+    <outputs>
+        <data name="out" format="txt"/>
+    </outputs>
+    <tests>
+        <test>
+            <output name="out">
+                <assert_contents>
+                    <has_line line="GALAXY_SLOTS 1" negate="true"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+**Input**
+
+
+**Output**
+
+
+    ]]></help>
+    <citations>
+        <citation type="doi">blah</citation>
+    </citations>
+</tool>