Merge pull request #1302: Remove Snakemake tests (and dependency)

nextstrain · Sep 20, 2023 · b4ca57f · b4ca57f
2 parents 82ed696 + 4f0c374
commit b4ca57f
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Showing 98 changed files with 14 additions and 182,434 deletions.
diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
@@ -66,7 +66,6 @@ jobs:
     - run: cram tests/
       env:
         AUGUR: coverage run -a ${{ github.workspace }}/bin/augur
-    - run: bash tests/builds/runner.sh
     - uses: actions/upload-artifact@v3
       with:
         name: coverage
@@ -97,6 +96,7 @@ jobs:
               pathogen: seasonal-flu,
               build-args: --configfile profiles/ci/builds.yaml -p,
             }
+          - { pathogen: tb }
           - { pathogen: zika }
     name: pathogen-repo-ci (${{ matrix.pathogen }})
     defaults:

diff --git a/.gitignore b/.gitignore
@@ -12,7 +12,6 @@ scratch/
 s3/
 build/
 dist/
-.snakemake
 *stderr
 /docs/_build/
 

diff --git a/devel/test b/devel/test
@@ -28,7 +28,6 @@ python3 -m pip install .[dev]
 # Run unit and functional tests.
 echo Running tests
 ./run_tests.sh || true
-bash tests/builds/runner.sh || true
 
 # Clean up the temporary environment.
 echo Cleaning up

diff --git a/setup.py b/setup.py
@@ -79,7 +79,6 @@
             "pytest-cov >=2.8.1",
             "pytest-mock >= 2.0.0",
             "recommonmark >=0.5.0",
-            "snakemake >=5.4.0",
             "Sphinx >=2.0.1",
             "sphinx-autobuild >=2021.3.14",
             "sphinx-argparse >=0.2.5",

diff --git a/tests/builds/add_to_alignment/Snakefile b/tests/builds/add_to_alignment/Snakefile
diff --git a/tests/builds/add_to_alignment/data/aligned.fasta b/tests/builds/add_to_alignment/data/aligned.fasta
diff --git a/tests/builds/add_to_alignment/data/metadata.tsv b/tests/builds/add_to_alignment/data/metadata.tsv
-Original file line number
+Diff line change
@@ Expand Up / @@ -12,7 +12,6 @@ scratch/ @@
     s3/
     build/
     dist/
-    .snakemake
     *stderr
     /docs/_build/
@@ Expand Down @@