update: workflow

bigbio · Nov 24, 2024 · 19a05c6 · 19a05c6
1 parent 25ae806
commit 19a05c6
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Showing 2 changed files with 5 additions and 7 deletions.
diff --git a/.github/workflows/python-app.yml b/.github/workflows/python-app.yml
@@ -28,7 +28,6 @@ jobs:
         python -m pip install --upgrade pip
         pip install flake8 pytest
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-        python setup.py install
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names
@@ -37,6 +36,6 @@ jobs:
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: Test with unittest
       run: |
-        cd tests/
+        python setup.py install
         python -m unittest
 
diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
@@ -29,7 +29,6 @@ jobs:
         python -m pip install --upgrade pip
         python -m pip install flake8 pytest
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-        python setup.py install
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names
@@ -38,13 +37,13 @@ jobs:
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: Test with unittest
       run: |
-        cd tests/
+        python setup.py install
         python -m unittest
     - name: Test commandline tool help
       run: |
         ibaqpy --help
     - name: Test commandline normalization features
       run: |
-        rm -rfv tests/PXD003947/PXD003947-peptides-norm.csv
-        rm -rfv tests/PXD003947/PXD003947-peptides-norm.parquet
-        ibaqpy features2peptides --parquet tests/PXD003947/PXD003947-feature.parquet --sdrf tests/PXD003947/PXD003947.sdrf.tsv --min_aa 7 --min_unique 2 --remove_ids data/contaminants_ids.tsv --remove_decoy_contaminants --remove_low_frequency_peptides --output tests/PXD003947/PXD003947-peptides-norm.csv --skip_normalization --nmethod median --pnmethod max_min --log2 --save_parquet
+        rm -rfv tests/example/PXD017834-ibaq-norm.csv
+        rm -rfv tests/example/PXD017834-peptides-norm.csv
+        ibaqpy features2peptides --parquet tests/example/feature.parquet --sdrf tests/example/PXD017834-TMT.sdrf.tsv --min_aa 7 --min_unique 2 --remove_ids data/contaminants_ids.tsv --remove_decoy_contaminants --remove_low_frequency_peptides --output tests/example/PXD017834-peptides-norm.csv --skip_normalization --nmethod median --pnmethod max_min --log2 --save_parquet