Create python-package.yml

.github/workflows/python-package.yml

@@ -0,0 +1,27 @@
+name: Build and test Python package
+on:
+  push:
+  pull_request:
+    branches: [ "master" ]
+jobs:
+  build:
+
+    runs-on: ubuntu-20.04
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.6", "3.7", "3.8", "3.9", "3.10", "3.11", "3.12"]
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install package
+      run: |
+        python -m pip install --upgrade pip
+        pip install pytest
+        pip install .
+    - name: Test with pytest
+      run: |
+        pytest

tests/test_all.py

@@ -1,46 +1,42 @@
 
 import sys
 import gemmapy
+import pytest
 
 api = gemmapy.GemmaPy()
 
-out = False
-if len(sys.argv)>1 and sys.argv[1].startswith("out"): out = True
-
 # test 8x getDataset... functions
-for f in [s for s in dir(api) if s.startswith('get_dataset')]:
-    print('testing %s...' % f, end='')
+@pytest.mark.parametrize('f', [s for s in dir(api) if s.startswith('get_dataset')])
+def test_get_dataset_functions(f):
     func = getattr(api,f)
-    if not f.endswith('_by_ids'):
-        res = func('GSE46416')
+    if f == 'get_datasets':
+        args = tuple()
+    elif f.endswith('_for_genes'):
+        args = ['GSE46416'], ['BRCA1']
+    elif f.endswith('_by_ids'):
+        args = ['GSE46416'],
     else:
-        res = func(['GSE46416'])
-    print('ok')
-    if out: print(str(res)[:2000])
-
+        args = 'GSE46416',
+    res = func(*args)
+
 # test 2x former getDataset... functions
-for f in ['get_dataset_differential_expression_analyses','get_differential_expression_values']:
-#    if f.endswith('_values'): continue
-    print('testing %s...' % f, end='')
+def test_get_differential_expression_values():
+    f = 'get_differential_expression_values'
     func = getattr(api,f)
     res = func('GSE46416')
-    print('ok')
-    if out: print(str(res)[:2000])
 
 # test 4x getGene... functions
-for f in [s for s in dir(api) if s.startswith('get_gene')]:
-    print('testing %s...' % f, end='')
+@pytest.mark.parametrize('f', [s for s in dir(api) if s.startswith('get_gene')])
+def test_get_gene_functions(f):
     func = getattr(api,f)
     if not f.endswith('_genes'):
         res = func('DYRK1A')
     else:
         res = func(['DYRK1A'])
-    print('ok')
-    if out: print(str(res)[:2000])
 
 # test 5x getPlatform... functions
-for f in [s for s in dir(api) if s.startswith('get_platform')]:
-    print('testing %s...' % f, end='')
+@pytest.mark.parametrize('f', [s for s in dir(api) if s.startswith('get_platform')])
+def test_get_platform_functions(f):
     func = getattr(api,f)
     if f == 'get_platform_element':
         res = func("GPL1355", ["AFFX_Rat_beta-actin_M_at"])
@@ -50,30 +46,21 @@
         res = func(["GPL1355"])
     else:
         res = func("GPL1355")
-    print('ok')
-    if out: print(str(res)[:2000])
-
 
 # test 2x search... functions
-for f in [s for s in dir(api) if s.startswith('search')]:
-    print('testing %s...' % f, end='')
+@pytest.mark.parametrize('f', [s for s in dir(api) if s.startswith('search')])
+def test_search_functions(f):
     func = getattr(api,f)
     if f == 'search_annotations':
         res = func(['traumatic'])
     elif f == 'search_datasets':
         res = func(['bipolar'],'human')
-    else:
-        continue
-    print('ok')
-    if out: print(str(res)[:2000])
 
 # test 2x get_tax... functions
-for f in ['get_taxa','get_taxon_datasets']:
-    print('testing %s...' % f, end='')
+@pytest.mark.parametrize('f', ['get_taxa','get_taxon_datasets'])
+def test_get_taxa_functions(f):
     func = getattr(api,f)
     if f.endswith('_datasets'):
-        res = func('worm')
+        res = func('human')
     else:
         res = func()
-    print('ok')
-    if out: print(str(res)[:2000])

tests/test_one.py

@@ -1,5 +1,6 @@
 import gemmapy
 
-api = gemmapy.GemmaPy()
-res = api.get_platforms_by_ids(['GPL96'])
-print(res)
+def test_one():
+    api = gemmapy.GemmaPy()
+    res = api.get_platforms_by_ids(['GPL96'])
+    print(res)

tests/test_tut.py

@@ -1,4 +1,7 @@
 import gemmapy
+import pandas
+import numpy as np
+
 api_instance = gemmapy.GemmaPy()
 
 print("Downloading expression data\nEx1")
@@ -29,8 +32,6 @@
 
 # -----
 print("\nDifferential expression analyses\nEx1")
-import pandas
-import numpy as np
 de = api_instance.get_differential_expression_values('GSE46416', readableContrasts=True)
 de = de[0]
 # Classify probes for plotting
@@ -58,7 +59,6 @@
 
 # -----
 print("\nPlatform Annotations\nEx1")
-import pandas
 api_response = api_instance.get_platform_annotations('GPL96')
 with pandas.option_context('display.max_rows', None, 'display.max_columns', None): print(api_response[:6])