tests(retropath2): support windows

.github/workflows/test.yml

@@ -19,7 +19,7 @@ jobs:
     runs-on: ${{ matrix.os }}-latest
     strategy:
       matrix:
-        os: ["macos-latest", "ubuntu-latest", "windows-latest"]
+        os: ["macos", "ubuntu", "windows"]
     defaults:
       run:
         shell: bash -l {0}
@@ -37,9 +37,3 @@ jobs:
         run: |
           conda install -y python pytest pytest-mock
           python -m pytest
-      - name: "Archive production artifacts"
-        uses: actions/upload-artifact@v3
-        with:
-          name: test_windows
-          path: |
-            tests/data/results_windows.csv

retropath2_wrapper/Args.py

@@ -132,7 +132,7 @@ def _add_arguments(parser):
         '--timeout',
         type=int,
         default=DEFAULT_TIMEOUT,
-        help=f'Defines the time after which the program will stop and return calculated results (default: {DEFAULT_TIMEOUT})'
+        help=f'Defines the time after which the program (RDKit MCS Aggregation) will stop and return calculated results (default: {DEFAULT_TIMEOUT}).'
     )
     # parser.add_argument('--forward'      , action='store_true')
 

tests/functional/test_retropath2.py

@@ -36,25 +36,25 @@ def test_lycopene(self):
         r_code, result = retropath2(
             sink_file=self.lycopene_sink_csv,
             source_file=self.lycopene_source_csv,
-            rules_file=self.rulesd12_csv,
+            rules_file=self.rulesd12_7325_csv,
             outdir=tmpdir,
             timeout=10,
             logger=self.logger,
         )
+        # Specific test for windows due to Github Runner memory consumption.
+        # Only check first lines.
         if sys.platform == 'win32':
             with open(result['outdir'] + "/" + result['results']) as fid:
                 result_lines = fid.read().splitlines()
-            with open(self.lycopene_r20220104_results_csv) as fid:
+            with open(self.lycopene_r20220104_results_7325_csv) as fid:
                 theorical_lines = fid.read().splitlines()
+            nb_lines = len(result_lines)
 
-            identical_line = 0
-            for i, the in enumerate(theorical_lines):
-                if the != result_lines[i]:
-                    identical_line = i
-                    break
-            self.assertTrue(identical_line > 5)
+            self.assertTrue(nb_lines > 5)
+            self.assertTrue(result_lines, theorical_lines[:nb_lines])
         else:
             filecmp.cmp(result['outdir'] + "/" + result['results'], self.lycopene_r20220104_results_csv)
+            shutil.copyfile(result['outdir'] + "/" + result['results'], "mac.result.csv")
         shutil.rmtree(tmpdir, ignore_errors=True)
 
     """

tests/main_test.py

@@ -11,6 +11,7 @@ class Main_test(unittest.TestCase):
     # rules
     rules_csv = os.path.join(dataset_path, "rules.csv.gz")
     rulesd12_csv = os.path.join(dataset_path, "rules_d12.csv.gz")
+    rulesd12_7325_csv = os.path.join(dataset_path, "rules_d12_7325.csv.gz")
 
     # empty
     empty_csv = os.path.join(dataset_path, "empty_file.csv")
@@ -45,5 +46,6 @@ class Main_test(unittest.TestCase):
     lycopene_r20210127_source_csv = os.path.join(dataset_path, "lycopene", "out", "r20210127", "source-in-sink.csv")
     lycopene_r20210127_target_csv = os.path.join(dataset_path, "lycopene", "out", "r20210127", "target_scope.csv")
     lycopene_r20220104_results_csv = os.path.join(dataset_path, "lycopene", "out", "r20220104", "results.csv")
+    lycopene_r20220104_results_7325_csv = os.path.join(dataset_path, "lycopene", "out", "r20220104", "results.7325.csv")
     lycopene_r20220104_source_csv = os.path.join(dataset_path, "lycopene", "out", "r20220104", "source-in-sink.csv")
     lycopene_r20220104_target_csv = os.path.join(dataset_path, "lycopene", "out", "r20220104", "target_scope.csv")