diff --git a/.github/workflows/kb_sdk_test.yaml b/.github/workflows/kb_sdk_test.yaml index 1e6e994..1c67b63 100644 --- a/.github/workflows/kb_sdk_test.yaml +++ b/.github/workflows/kb_sdk_test.yaml @@ -1,63 +1,33 @@ -name: KBase SDK Tests +name: Run KBase SDK Tests on: push: - branches: - - master - - main pull_request: - branches: - - master - - main - - develop - workflow_dispatch: jobs: - - sdk_tests: + test: runs-on: ubuntu-latest - steps: - - - name: Check out GitHub repo - if: "!contains(github.event.head_commit.message, 'skip ci')" - uses: actions/checkout@v2 - - - name: Check out Actions CI files - if: "!contains(github.event.head_commit.message, 'skip ci')" - uses: actions/checkout@v2 - with: - repository: 'kbaseapps/kb_sdk_actions' - path: 'kb_sdk_actions' - - - name: Set up test environment - if: "!contains(github.event.head_commit.message, 'skip ci')" - shell: bash - env: - KBASE_TEST_TOKEN: ${{ secrets.KBASE_TEST_TOKEN }} - run: | - # Verify kb_sdk_actions clone worked - test -f "$HOME/kb_sdk_actions/bin/kb-sdk" && echo "CI files cloned" - # Pull kb-sdk & create startup script - docker pull kbase/kb-sdk - - sh $GITHUB_WORKSPACE/kb_sdk_actions/bin/make_testdir && echo "Created test_local" - test -f "test_local/test.cfg" && echo "Confirmed config exists" - - - name: Configure authentication - if: "!contains(github.event.head_commit.message, 'skip ci')" - shell: bash - env: - KBASE_TEST_TOKEN: ${{ secrets.KBASE_TEST_TOKEN }} - run: | - # Add token to config - sed -ie "s/^test_token=.*$/&$KBASE_TEST_TOKEN/g" ./test_local/test.cfg - - - name: Run tests - if: "!contains(github.event.head_commit.message, 'skip ci')" - shell: bash - env: - CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} - run: | - sh $GITHUB_WORKSPACE/kb_sdk_actions/bin/kb-sdk test - bash <(curl -s https://codecov.io/bash) + steps: + - uses: actions/checkout@v4 + + - name: Download kb-sdk, set up path, and modify kb-sdk helper script + run: | + mkdir -p $(pwd)/bin + docker run ghcr.io/kbase/kb_sdk_patch-develop:br-0.0.4 genscript > $(pwd)/bin/kb-sdk + docker tag ghcr.io/kbase/kb_sdk_patch-develop:br-0.0.4 kbase/kb-sdk:latest + chmod 755 $(pwd)/bin/kb-sdk + echo "$(pwd)/bin" >> $GITHUB_PATH + sed -i 's/docker run -it/docker run /g' $(pwd)/bin/kb-sdk + + - name: Setup KBase SDK Tests and inject kbase token + env: + KBASE_TEST_TOKEN: ${{ secrets.KBASE_TEST_TOKEN }} + run: | + kb-sdk test || true + mkdir -p ./test_local + sed -i "s/^test_token=.*$/test_token=$KBASE_TEST_TOKEN/g" ./test_local/test.cfg + continue-on-error: true + + - name: Run KBase SDK Tests + run: kb-sdk test diff --git a/RELEASE_NOTES.md b/RELEASE_NOTES.md index c776a08..5b5c2eb 100644 --- a/RELEASE_NOTES.md +++ b/RELEASE_NOTES.md @@ -1,3 +1,6 @@ +### Version 1.9.1 +* Updated version to sync with [DomainAnnotation](https://github.com/kbaseapps/DomainAnnotation/blob/093b943ead242d24227978d1df0b713d067beb89/ui/narrative/methods/annotate_domains_in_a_genome/spec.json#L30-L65) to fix `Server error: /data/db/Cog.aux (Read-only file system)` + ### Version 1.9.0 __Changes__ - added Score_Orthologs_Evolutionary_Rates() App diff --git a/kbase.yml b/kbase.yml index 701db69..0aa4df0 100644 --- a/kbase.yml +++ b/kbase.yml @@ -8,7 +8,7 @@ service-language: python module-version: - 1.9.0 + 1.9.1 owners: [dylan,jmc] diff --git a/lib/kb_phylogenomics/kb_phylogenomicsImpl.py b/lib/kb_phylogenomics/kb_phylogenomicsImpl.py index 0b3b13a..e3198e2 100644 --- a/lib/kb_phylogenomics/kb_phylogenomicsImpl.py +++ b/lib/kb_phylogenomics/kb_phylogenomicsImpl.py @@ -3461,7 +3461,7 @@ def run_DomainAnnotation_Sets(self, ctx, params): domains_obj_name += '.DomainAnnotation' domains_obj_name = 'domains_' + domains_obj_name # DEBUG DomainAnnotation_Params = {'genome_ref': genome_ref, - 'dms_ref': 'KBasePublicGeneDomains/All-1.0.8', # for Pfam 32 + 'dms_ref': 'KBasePublicGeneDomains/All-1.0.10', # for Pfam 32 'ws': params['workspace_name'], #'ws': ws_name_by_genome_ref[genome_ref], 'output_result_id': domains_obj_name