9595 matrix :
9696 python-version : [3.7]
9797 steps :
98- # checkout the repository to master
98+ # checkout the repository
9999 # and use it as the current working directory
100100 - uses : actions/checkout@v2
101101 with :
@@ -115,7 +115,7 @@ jobs:
115115 with :
116116 path : ~/.cache/pip
117117 key : pip_cache_python_${{ matrix.python-version }}_${{ env.GALAXY_HEAD_SHA }}
118- - name : Setup planemo
118+ - name : Install Planemo
119119 run : pip install planemo
120120 - name : Planemo lint
121121 run : |
@@ -126,7 +126,7 @@ jobs:
126126
127127 # flake8 of python scripts in the changed repositories
128128 flake8 :
129- name : Lint python scripts
129+ name : Lint Python scripts
130130 needs : setup
131131 runs-on : ubuntu-latest
132132 strategy :
@@ -154,12 +154,12 @@ jobs:
154154 with :
155155 path : ~/.cache/pip
156156 key : pip_cache_python_${{ matrix.python-version }}_${{ env.GALAXY_HEAD_SHA }}
157- - name : Setup flake8
157+ - name : Install flake8
158158 run : pip install flake8
159159 - name : Flake8
160160 run : |
161161 if [ -s ../workflow_artifacts/changed_repositories.list ]; then
162- flake8 $(cat ../workflow_artifacts/changed_repositories.list)
162+ flake8 $(cat ../workflow_artifacts/changed_repositories.list)
163163 fi
164164
165165 # planemo test the changed repositories, each chunk creates an artifact
@@ -184,7 +184,7 @@ jobs:
184184 ports :
185185 - 5432:5432
186186 steps :
187- # checkout the repository to master
187+ # checkout the repository
188188 # and use it as the current working directory
189189 - uses : actions/checkout@v2
190190 with :
@@ -300,9 +300,9 @@ jobs:
300300 with :
301301 path : ~/.cache/pip
302302 key : pip_cache_python_${{ matrix.python-version }}_${{ env.GALAXY_HEAD_SHA }}
303- - name : Setup planemo
303+ - name : Install Planemo
304304 run : pip install planemo
305- - name : Setup jq
305+ - name : Install jq
306306 run : sudo apt-get install jq
307307 - name : Combine outputs
308308 run : find . -name tool_test_output.json -exec sh -c 'planemo merge_test_reports "$@" tool_test_output.json' sh {} +
@@ -320,15 +320,14 @@ jobs:
320320 run : |
321321 stat=$(jq '.["tests"][]["data"]["status"]' upload/tool_test_output.json | grep -v "success" || true)
322322 if [[ "$(echo -n $stat | wc -l)" -gt "0" ]]; then
323- echo "unsuccessful tests found $(sort <<<$stat | uniq -c)"
323+ echo "Unsuccessful tests found $(sort <<<$stat | uniq -c)"
324324 exit 1
325325 fi
326326
327327 # deploy the tools to the toolsheds (first TTS for testing)
328328 deploy :
329329 name : Deploy
330330 needs : combine_outputs
331- # This job runs on Linux
332331 strategy :
333332 matrix :
334333 python-version : [3.7]
@@ -353,21 +352,19 @@ jobs:
353352 with :
354353 path : ~/.cache/pip
355354 key : pip_cache_python_${{ matrix.python-version }}_${{ env.GALAXY_HEAD_SHA }}
356- - name : Setup planemo
355+ - name : Install Planemo
357356 run : pip install planemo
358- # TODO remove --owner
359357 - name : Deploy on testtoolshed
360358 env :
361359 SHED_KEY : ${{ secrets.tts_api_key }}
362360 run : |
363- while read -r DIR;
364- do
365- planemo shed_update --shed_target testtoolshed --shed_key "${{ env.SHED_KEY }}" --force_repository_creation "$DIR" --owner matthias || exit 1;
361+ while read -r DIR; do
362+ planemo shed_update --shed_target testtoolshed --shed_key "${{ env.SHED_KEY }}" --force_repository_creation "$DIR" || exit 1;
366363 done < ../workflow_artifacts/changed_repositories.list
367364 - name : Deploy on toolshed
368365 env :
369366 SHED_KEY : ${{ secrets.ts_api_key }}
370367 run : |
371- while read -r DIR;
372- do planemo shed_update --shed_target toolshed --shed_key "${{ env.SHED_KEY }}" --force_repository_creation "$DIR" || exit 1;
368+ while read -r DIR; do
369+ planemo shed_update --shed_target toolshed --shed_key "${{ env.SHED_KEY }}" --force_repository_creation "$DIR" || exit 1;
373370 done < ../workflow_artifacts/changed_repositories.list
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