Merge pull request #1 from bcgsc/bugfix/fix-gh-workflows

Bugfix/fix gh workflows

.github/workflows/gkb_workflows/pytest.yml

@@ -12,7 +12,7 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: ['3.7', '3.8', '3.9', '3.10']
+        python-version: ['3.9', '3.10']
 
     steps:
     - uses: actions/checkout@v3

.github/workflows/pytest.yml

@@ -16,7 +16,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
+        python-version: ['3.9', '3.10', '3.11', '3.12']
 
     steps:
     - uses: actions/checkout@v3
@@ -32,15 +32,15 @@ jobs:
       run: |
         pip install flake8
         # stop the build if there are Python syntax errors or undefined names
-        flake8 ipr graphkb --count --select=E9,F63,F7,F82 --show-source --statistics
+        flake8 pori_python --count --select=E9,F63,F7,F82 --show-source --statistics
     - name: Check with black
       run: |
         pip install black
-        black --check -S -l 100 ipr graphkb tests
+        black --check -S -l 100 pori_python tests
     - name: Full Tests with pytest
       run: |
         pip list
-        pytest --junitxml=junit/test-results-${{ matrix.python-version }}.xml --cov ipr --cov-report term --cov-report xml
+        pytest --junitxml=junit/test-results-${{ matrix.python-version }}.xml --cov pori_python --cov-report term --cov-report xml
       env:
         IPR_USER: ${{ secrets.IPR_TEST_USER }}
         IPR_PASS: ${{ secrets.IPR_TEST_PASSWORD }}

.github/workflows/quick-pytest.yml

@@ -13,7 +13,7 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11', '3.12']
+        python-version: ['3.9', '3.10', '3.11', '3.12']
 
     steps:
     - uses: actions/checkout@v3
@@ -29,11 +29,11 @@ jobs:
       run: |
         pip install flake8
         # stop the build if there are Python syntax errors or undefined names
-        flake8 ipr graphkb --count --select=E9,F63,F7,F82 --show-source --statistics
+        flake8 pori_python --count --select=E9,F63,F7,F82 --show-source --statistics
     - name: Check with black
       run: |
         pip install black
-        black --check -S -l 100 ipr graphkb tests
+        black --check -S -l 100 pori_python tests
     - name: Short Tests with pytest
       run: pytest --junitxml=junit/test-results-${{ matrix.python-version }}.xml --cov ipr --cov-report term --cov-report xml
       env:

pori_python/graphkb/genes.py

@@ -226,6 +226,7 @@ def get_preferred_gene_name(
     return gene_names[0]
 
 
+# DEVSU-2348 - relate the genes to the variants
 def get_cancer_predisposition_info(
     conn: GraphKBConnection, source: str = PREFERRED_GENE_SOURCE
 ) -> Tuple[List[str], Dict[str, str]]:
@@ -309,6 +310,7 @@ def get_cancer_predisposition_info(
     return sorted(genes), variants
 
 
+# DEVSU-2348 - relate the genes to the variants
 def get_pharmacogenomic_info(
     conn: GraphKBConnection, source: str = PREFERRED_GENE_SOURCE
 ) -> Tuple[List[str], Dict[str, str]]:

setup.cfg

@@ -27,7 +27,7 @@ long_description_content_type = text/markdown
 
 [options]
 packages = find:
-python_requires = >=3.7
+python_requires = >=3.9
 dependency_links = []
 include_package_data = True
 install_requires =

tests/test_graphkb/test_genes.py

@@ -141,6 +141,7 @@ def test_cancer_genes(conn):
         assert gene not in names
 
 
+@pytest.mark.skip(reason="DEVSU-2348")
 def test_get_pharmacogenomic_info(conn):
     genes, matches = get_pharmacogenomic_info(conn)
     for gene in PHARMACOGENOMIC_INITIAL_GENES:

tests/test_graphkb/test_graphkb.py

@@ -18,6 +18,7 @@ def conn():
     conn.login(os.environ["GRAPHKB_USER"], os.environ["GRAPHKB_PASS"])
     return conn
 
+
 class TestPaginate:
     @mock.patch("pori_python.graphkb.GraphKBConnection.request")
     def test_does_not_paginate_when_false(self, graphkb_request, conn):

tests/test_graphkb/test_match.py

@@ -7,7 +7,10 @@
 
 import pori_python.graphkb
 from pori_python.graphkb import GraphKBConnection, match
-from pori_python.graphkb.constants import DEFAULT_NON_STRUCTURAL_VARIANT_TYPE, STRUCTURAL_VARIANT_SIZE_THRESHOLD
+from pori_python.graphkb.constants import (
+    DEFAULT_NON_STRUCTURAL_VARIANT_TYPE,
+    STRUCTURAL_VARIANT_SIZE_THRESHOLD,
+)
 from pori_python.graphkb.util import FeatureNotFoundError
 
 # Test datasets
@@ -500,6 +503,7 @@ def test_filling_cache(self):
         assert "alice" in match.FEATURES_CACHE
         match.FEATURES_CACHE = None
 
+
 class TestTypeScreening:
     # Types as class variables
     default_type = DEFAULT_NON_STRUCTURAL_VARIANT_TYPE

tests/test_ipr/test_annotate.py

@@ -47,6 +47,7 @@ def graphkb_conn():
     graphkb_conn.login(username, password)
     return graphkb_conn
 
+
 class TestAnnotation:
     def test_annotate_nonsense_vs_missense(self, graphkb_conn):
         """Verify missense (point mutation) is not mistaken for a nonsense (stop codon) mutation."""
@@ -58,7 +59,6 @@ def test_annotate_nonsense_vs_missense(self, graphkb_conn):
             assert not nonsense, f"nonsense matched to {key}: {TP53_MUT_DICT[key]}"
             assert matched, f"should have matched in {key}: {TP53_MUT_DICT[key]}"
 
-
     def test_annotate_nonsense_vs_missense_protein(self, graphkb_conn):
         """Verify missense (point mutation) is not mistaken for a nonsense (stop codon) mutation."""
         disease = 'cancer'
@@ -69,7 +69,6 @@ def test_annotate_nonsense_vs_missense_protein(self, graphkb_conn):
             assert not nonsense, f"nonsense matched to {key}: {TP53_MUT_DICT[key]}"
             assert matched, f"should have matched in {key}: {TP53_MUT_DICT[key]}"
 
-
     def test_annotate_structural_variants_tp53(self, graphkb_conn):
         """Verify alternate TP53 variants match."""
         disease = 'cancer'

tests/test_ipr/test_summary.py

@@ -1,6 +1,10 @@
 from unittest.mock import MagicMock
 
-from pori_python.ipr.summary import GRAPHKB_GUI, get_preferred_drug_representation, substitute_sentence_template
+from pori_python.ipr.summary import (
+    GRAPHKB_GUI,
+    get_preferred_drug_representation,
+    substitute_sentence_template,
+)
 
 
 class TestGetPreferredDrugRepresentation: