test errors due to directory changes

KoslickiLab · Nov 17, 2023 · 23d5a0f · 23d5a0f
1 parent 8b8ba0e
commit 23d5a0f
Showing 1 changed file with 7 additions and 7 deletions.
diff --git a/.github/workflows/runTest.yml b/.github/workflows/runTest.yml
@@ -7,15 +7,15 @@ jobs:
       run:
         shell: bash -el {0}
     steps:
-#    - uses: actions/checkout@v4
-#    - uses: conda-incubator/setup-miniconda@v2
-#      with:
-#        activate-environment: yacht_env
-#        environment-file: env/yacht_env.yml
+    - uses: actions/checkout@v4
+    - uses: conda-incubator/setup-miniconda@v2
+      with:
+        activate-environment: yacht_env
+        environment-file: env/yacht_env.yml
     - name: make training data
-      run: python -m srcs.make_training_data_from_sketches --ref_file '../tests/testdata/20_genomes_sketches.zip' --ksize 31 --prefix 'gtdb_ani_thresh_0.95' --ani_thresh 0.95 --outdir ../ --force
+      run: python -m srcs.make_training_data_from_sketches --ref_file './tests/testdata/20_genomes_sketches.zip' --ksize 31 --prefix 'gtdb_ani_thresh_0.95' --ani_thresh 0.95 --outdir ./ --force
     - name: run YACHT
-      run: python srcs.run_YACHT.py --json ../gtdb_ani_thresh_0.95_config.json --sample_file '../tests/testdata/sample.sig.zip' --significance 0.99 --min_coverage_list 1 0.6 0.2 0.1
+      run: python srcs.run_YACHT.py --json ./gtdb_ani_thresh_0.95_config.json --sample_file './tests/testdata/sample.sig.zip' --significance 0.99 --min_coverage_list 1 0.6 0.2 0.1
     - name: test-unit
       run: pytest tests/test_unit.py --cov=./  --cov-report xml:covunit.xml
     - name: test-utils