switch default docker image for version_capture to GAR-hosted image (#…

…198)

* version_capture task changes: exposed docker image as an optional input; set default to GAR-hosted docker image. Original image is ubuntu:jammy-20230816 downloaded from dockerhub. tested fine with miniwdl

* added pytest --git-aware option to suppress the constant warning

* remove --git-aware; seems that it accidentally removes test data required by CI workflows

* update CI for task_versioning.wdl in theiaprok checks

* attempting micromamba install of pytest environment instead of miniconda

* change micromamba env name to "pytest-env" instead of "base"

* attempting to use envrionment.yml for micromamba install instead of manually specifying deps

* typo in path to environment.yml

* what is taking up all this disk space???

* more attempts to free up disk space

* removed du command

* another attempt to free up diskspace

.github/workflows/pytest-workflows.yml

@@ -59,22 +59,41 @@ jobs:
           repository: bactopia/bactopia-tests
           path: bactopia-tests
 
-      # Setup Miniconda3
-      - name: Setup miniconda
-        uses: conda-incubator/setup-miniconda@v2
+      # # Setup Miniconda3
+      # - name: Setup miniconda
+      #   uses: conda-incubator/setup-miniconda@v2
+      #   with:
+      #     activate-environment: actions
+      #     auto-activate-base: false
+
+      # attempting micromamba install instead of miniconda3 in order to save on disk space
+      - uses: mamba-org/setup-micromamba@v1
         with:
-          activate-environment: actions
-          auto-activate-base: false
+          environment-file: tests/config/environment.yml
+
+      # # Depends and env info (mostly for debug)
+      # # rm -rf commands as recommended here: https://github.com/actions/runner-images/issues/2840#issuecomment-1284059930
+      # - name: Install Dependencies and create storage space
+      #   run: |
+      #     conda install -y -c conda-forge -c bioconda cromwell miniwdl=1.5.2 'python>=3.7' pytest pytest-workflow 'importlib-metadata<=4.13.0'
+      #     conda clean -a -y
+      #     uname -a && env
+      #     sudo rm -rf /usr/share/dotnet
+      #     sudo rm -rf "$AGENT_TOOLSDIRECTORY"
 
-      # Depends and env info (mostly for debug)
+      # env info (mostly for debug)
       # rm -rf commands as recommended here: https://github.com/actions/runner-images/issues/2840#issuecomment-1284059930
-      - name: Install Dependencies and create storage space
+      - name: Env info and create storage space
         run: |
-          conda install -y -c conda-forge -c bioconda cromwell miniwdl=1.5.2 'python>=3.7' pytest pytest-workflow 'importlib-metadata<=4.13.0'
-          conda clean -a -y
+          micromamba list
+          micromamba clean -a -y
           uname -a && env
           sudo rm -rf /usr/share/dotnet
+          sudo rm -rf /opt/ghc
+          sudo rm -rf "/usr/local/share/boost"
           sudo rm -rf "$AGENT_TOOLSDIRECTORY"
+          sudo rm -rf /usr/local/lib/android
+          df -h
 
       - name: Test ${{ matrix.tag }}
         run: TMPDIR=~ pytest --tag ${{ matrix.tag }}_${{ matrix.engine }} --symlink --kwdof --color=yes

tasks/task_versioning.wdl

@@ -3,6 +3,7 @@ version 1.0
 task version_capture {
   input {
     String? timezone
+    String docker = "us-docker.pkg.dev/general-theiagen/ubuntu/ubuntu:jammy-20230816"
   }
   meta {
     volatile: true
@@ -20,7 +21,7 @@ task version_capture {
   runtime {
     memory: "1 GB"
     cpu: 1
-    docker: "ubuntu:jammy"
+    docker: docker
     disks: "local-disk 10 HDD"
     dx_instance_type: "mem1_ssd1_v2_x2" 
   }

tests/config/environment.yml

@@ -0,0 +1,12 @@
+name: pytest-env-CI
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - python >=3.7
+  - cromwell
+  - miniwdl=1.5.2
+  - pytest
+  - pytest-workflow
+  - importlib-metadata <=4.13.0

tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml

@@ -624,7 +624,7 @@
     - path: miniwdl_run/wdl/tasks/species_typing/task_ts_mlst.wdl
       md5sum: d49ae0b02e798af0636eb2721bb434b4
     - path: miniwdl_run/wdl/tasks/task_versioning.wdl
-      md5sum: c178145bad99e3858a1327b3774177f3
+      md5sum: 2ed48e1b2d6e69fac4b2888f18b3c0c8
     - path: miniwdl_run/wdl/tasks/taxon_id/task_gambit.wdl
       md5sum: 08987d952c67c6ff6debf6898af15f9a
     - path: miniwdl_run/wdl/tasks/taxon_id/task_kraken2.wdl

tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml

@@ -592,7 +592,7 @@
     - path: miniwdl_run/wdl/tasks/species_typing/task_ts_mlst.wdl
       md5sum: d49ae0b02e798af0636eb2721bb434b4
     - path: miniwdl_run/wdl/tasks/task_versioning.wdl
-      md5sum: c178145bad99e3858a1327b3774177f3
+      md5sum: 2ed48e1b2d6e69fac4b2888f18b3c0c8
     - path: miniwdl_run/wdl/tasks/taxon_id/task_gambit.wdl
       md5sum: 08987d952c67c6ff6debf6898af15f9a
     - path: miniwdl_run/wdl/tasks/taxon_id/task_kraken2.wdl