refactor(tests): locate test files into a root file

tests/functional/test_retropath2.py

@@ -0,0 +1,97 @@
+"""
+Created on Jul 15 2020
+
+@author: Joan Hérisson
+"""
+import filecmp
+import os
+import tempfile
+
+from retropath2_wrapper.__main__ import create_logger
+from retropath2_wrapper.Args import RETCODES
+from retropath2_wrapper.RetroPath2 import retropath2
+from tests.main_test import Main_test
+
+
+class TestRetropath2(Main_test):
+    def setUp(self):
+        self.logger = create_logger(__name__, 'DEBUG')
+
+    def test_src_in_sink(self):
+         with tempfile.TemporaryDirectory() as tmpdir:
+             r_code, result = retropath2(
+                 sink_file=self.lycopene_sink_csv,
+                 source_file=self.source_mnxm790_csv,
+                 rules_file=self.rules_csv,
+                 outdir=tmpdir,
+                 logger=self.logger,
+             )
+             self.assertEqual(r_code, RETCODES['SrcInSink'])
+
+    def test_lycopene(self):
+        with tempfile.TemporaryDirectory() as tempd:
+            r_code, result = retropath2(
+                sink_file=self.lycopene_sink_csv,
+                source_file=self.lycopene_source_csv,
+                rules_file=self.rulesd12_csv,
+                outdir=tempd,
+            )
+            self.assertTrue(
+                filecmp.cmp(os.path.join(result['outdir'], result['results']), self.lycopene_r20220104_results_csv)
+            )
+
+    """
+    # Set attributes
+    maxDiff = None
+    csv        = '.csv'
+    gz         = '.gz'
+    data_path  = os_path.join(here, 'data')
+    iml1515_sinkfile   = os_path.join(data_path, 'lycopene', 'in', 'sink') + csv
+    lycopene_sourcefile = os_path.join(data_path, 'lycopene', 'in', 'source') + csv
+    alanine_sourcefile = os_path.join(data_path, 'alanine', 'in', 'source') + csv
+    rulesfile  = os_path.join(data_path, 'rules') + csv + gz
+    rulesfile_d12 = os_path.join(data_path, 'rules_d12') + csv + gz
+    ref_file   = os_path.join(data_path, 'lycopene', 'out', 'r20220104', 'results') + csv
+
+    # def test_light(self):
+    #     r_code, result = retropath2(
+    #         self.sinkfile+self.csv,
+    #         self.sourcefile+self.csv,
+    #         extract_gz(
+    #             self.rulesfile,
+    #             gettempdir()),
+    #         self.outdir,
+    #         dmin=16
+    #         )
+    #     self.assertTrue(cmp(result, self.ref_file+self.csv))
+
+
+    # def test_GZ(self):
+    #     r_code, result = retropath2(
+    #         self.sinkfile+self.csv,
+    #         self.sourcefile+self.csv,
+    #         self.rulesfile,
+    #         self.outdir,
+    #         dmin=16,
+    #         logger=self.logger
+    #         )
+    #     self.assertTrue(cmp(result, self.ref_file+self.csv))
+
+
+    # def test_woCSV(self):
+    #     if not os_path.exists(self.outdir):
+    #         os_mkdir(self.outdir)
+    #     rulesfile = gunzip_to_csv(
+    #         self.rulesfile_d12,
+    #         self.outdir
+    #         )
+    #     ext = '.dat'
+    #     r_code, result = retropath2(
+    #         self.sinkfile + ext,
+    #         self.sourcefile + ext,
+    #         rulesfile,
+    #         self.outdir,
+    #         dmin=12
+    #         )
+    #     self.assertTrue(cmp(result, self.ref_file+'_d12'+self.csv))
+    """

tests/main_test.py

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+import os
+import unittest
+
+
+class Main_test(unittest.TestCase):
+    dataset_path = os.path.join(os.path.dirname(__file__), "data")
+
+    # rules
+    rules_csv = os.path.join(dataset_path, "rules.csv.gz")
+    rulesd12_csv = os.path.join(dataset_path, "rules_d12.csv.gz")
+
+    # empty
+    empty_csv = os.path.join(dataset_path, "empty_file.csv")
+    empty_sink_csv = os.path.join(dataset_path, "empty_sink.csv")
+    source_weird_csv = os.path.join(dataset_path, "source.weird.csv")
+    johndoe = os.path.join(dataset_path, "johndoe")
+
+    # source
+    source_csv = os.path.join(dataset_path, "source.csv")
+    source_dat = os.path.join(dataset_path, "source.dat")
+    source_mnxm790_csv = os.path.join(dataset_path, "source.mnxm790.csv")
+
+    # sink
+    sink_csv = os.path.join(dataset_path, "sink.csv")
+    sink_dat = os.path.join(dataset_path, "sink.dat")
+
+    # scope
+    scope_csv = os.path.join(dataset_path, "scope.csv")
+    scoped12_csv = os.path.join(dataset_path, "scope_d12.csv")
+
+    # inchi
+    inchi_csv = os.path.join(dataset_path, "inchi_test_cases.csv")
+
+    # alanine
+    alanine_sink_csv = os.path.join(dataset_path, "alanine", "in", "sink.csv")
+    alanine_source_csv = os.path.join(dataset_path, "alanine", "in", "source.csv")
+
+    # lycopene
+    lycopene_sink_csv = os.path.join(dataset_path, "lycopene", "in", "sink.csv")
+    lycopene_source_csv = os.path.join(dataset_path, "lycopene", "in", "source.csv")
+    lycopene_r20210127_results_csv = os.path.join(dataset_path, "lycopene", "out", "r20210127", "results.csv")
+    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_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")
+