Merge pull request #74 from kipoi/haimasree-patch-1

Workflow improvement
kipoi · Jan 3, 2022 · 061f5e9 · 061f5e9
2 parents 1cfdc09 + 10e3613
commit 061f5e9
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diff --git a/.github/workflows/release-workflow.yml b/.github/workflows/release-workflow.yml
@@ -1,25 +1,20 @@
 name: Build, test and push images on demand
-
-# Controls when the action will run. 
-on: 
+on:
   workflow_dispatch:
-
-# A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:
   buildtestandpush:
     # The type of runner that the job will run on
     strategy:
       fail-fast: true
       matrix:
         image: ["sharedpy3keras1.2", "mpra-dragonn", "extended_coda", "mmsplice",
-        "mmsplice-mtsplice", "deepmel", "framepool", "kipoisplice", "deeptarget",
-        "attentivechrome", "bpnet-oskn", "seqvec", "deepflybrain", "aparent-site_probabilities", 
-        "aparent-veff"]
+          "mmsplice-mtsplice", "deepmel", "framepool", "kipoisplice", "deeptarget",
+          "attentivechrome", "bpnet-oskn", "seqvec", "deepflybrain", "aparent-site_probabilities",
+          "aparent-veff"]
     runs-on: ubuntu-latest
     env:
       SINGULARITY_PULL_FOLDER: "/home/runner/singularity/"
       ZENODO_ACCESS_TOKEN: ${{ secrets.ZENODOACCESSTOKEN }}
-    # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
     - uses: actions/checkout@v2
     - name: Set up Python 3.9
@@ -58,7 +53,6 @@ jobs:
       if: ${{ success() }}
       run: |
         update_all_singularity kipoi/kipoi-docker:${{ matrix.image }} 
-
   buildandtestsharedpy3keras2:
     # The type of runner that the job will run on
     strategy:
@@ -67,7 +61,6 @@ jobs:
         modelgroup: ["Basenji,Basset,HAL,DeepSEA,Optimus_5Prime,labranchor,CleTimer,SiSp,FactorNet,MaxEntScan,pwm_HOCOMOCO",
           "DeepBind", "lsgkm-SVM", "rbp_eclip", "Xpresso"]
     runs-on: ubuntu-latest
-    # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
     - uses: actions/checkout@v2
     - name: Set up Python 3.9
@@ -79,8 +72,6 @@ jobs:
         docker build -f dockerfiles/Dockerfile.kipoi-base-env -t kipoi/kipoi-docker:kipoi-base-env . 
         docker build -f dockerfiles/Dockerfile.sharedpy3keras2 -t kipoi/kipoi-docker:sharedpy3keras2 . 
         pytest -s test-containers/test_containers_from_command_line.py --image=kipoi/kipoi-docker:sharedpy3keras2 --modelgroup=${{ matrix.modelgroup }}
-
-
   buildandpushkipoibaseenvandsharedpy3keras2:
     needs: [buildandtestsharedpy3keras2, buildtestandpush]
     runs-on: ubuntu-latest
@@ -123,6 +114,6 @@ jobs:
     - name: Update the singularity version of ${{ matrix.image }}
       shell: bash -l {0}
       if: ${{ success() }}
-      run: |
+      run: |-
         update_all_singularity kipoi/kipoi-docker:kipoi-base-env
-        update_all_singularity kipoi/kipoi-docker:sharedpy3keras2
+        update_all_singularity kipoi/kipoi-docker:sharedpy3keras2
diff --git a/.github/workflows/sync-with-model-repo.yml b/.github/workflows/sync-with-model-repo.yml
@@ -47,3 +47,5 @@ jobs:
         python kipoi_containers/updateoradd.py
     - name: Create Pull Request
       uses: peter-evans/create-pull-request@v3
+      with:
+            token: ${{ secrets.GITHUBPAT }}
diff --git a/.github/workflows/test-images.yml b/.github/workflows/test-images.yml
@@ -1,5 +1,4 @@
 name: CI
-
 on:
   push:
     branches: ['**']
@@ -30,7 +29,6 @@ jobs:
         flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-
   test:
     strategy:
       fail-fast: false
@@ -52,7 +50,7 @@ jobs:
       uses: actions/setup-python@v2
       with:
         python-version: 3.9
-    - name: Install 
+    - name: Install
       uses: conda-incubator/setup-miniconda@v2
       with:
         activate-environment: py39
@@ -71,7 +69,6 @@ jobs:
       run: |
         pytest -s test-containers/test_models_from_command_line.py --model=${{ matrix.model }}
         docker system prune -a -f
-
   testdockerandsingularity:
 
     runs-on: ubuntu-latest
@@ -94,4 +91,4 @@ jobs:
         pip install coveralls
         docker pull kipoi/kipoi-docker:mmsplice
         coverage run -m pytest -s test-docker/test_docker_handler.py test-singularity test-containers/test_update_all_singularity_images.py
-        coveralls --service=github
+        coveralls --service=github