Merge pull request #18 from jcorreia11/fix_release

Fix release

setup.cfg

@@ -1,14 +1,14 @@
 [metadata]
 name = biocatalyzer
-version = 0.0.2-beta
+version = 0.0.4-beta
 description = BioCatalyzer: a rule-based tool to predict compound metabolism
 long_description = file: README.md
 long_description_content_type = text/markdown
 keywords = reaction-rules, metabolism, enzymatic-reactions, chemoinformatics, cheminformatics
 author = João Correia
 author_email = [email protected]
 url = https://github.com/jcorreia11/BioCatalyzer
-download_url = https://github.com/jcorreia11/BioCatalyzer/archive/refs/tags/v0.0.2-beta.tar.gz
+download_url = https://github.com/jcorreia11/BioCatalyzer/archive/refs/tags/v0.0.4-beta.tar.gz
 license = MIT
 license_file = LICENSE
 platforms = unix, linux, osx, cygwin, win32
@@ -49,6 +49,12 @@ testing =
 
 [options.package_data]
 biocatalyzer = py.typed
+biocatalyzer.data.byproducts_to_remove=
+    *.tsv
+biocatalyzer.data.patterns_to_remove=
+    *.tsv
+biocatalyzer.data.reactionrules=
+    all_reaction_rules_forward_no_smarts_duplicates_sample.tsv
 
 [flake8]
 max-line-length = 160

src/biocatalyzer/io_utils/loaders.py

@@ -106,7 +106,7 @@ def load_organisms(path):
         pd.DataFrame:
             pandas dataframe with the organisms to use.
         """
-        if not path:
+        if path is None or path == 'None':
             return 'ALL'
         if Loaders._verify_file(path):
             orgs = pd.read_csv(path, header=0, sep='\t')
@@ -135,7 +135,7 @@ def load_byproducts_to_remove(path):
         pd.DataFrame:
             pandas dataframe with the byproducts to remove.
         """
-        if not path:
+        if path is None or path == 'None':
             return []
         byproducts = pd.read_csv(path, header=0, sep='\t')
         if 'smiles' not in byproducts.columns:
@@ -157,7 +157,7 @@ def load_patterns_to_remove(path):
         pd.DataFrame:
             pandas dataframe with the patterns to remove.
         """
-        if not path:
+        if path is None or path == 'None':
             return []
         patterns = pd.read_csv(path, header=0, sep='\t')
         if 'smarts' not in patterns.columns:

tests/unit_tests/clis/test_cli.py

@@ -58,3 +58,13 @@ def test_biocatalyzer_full(self):
                                 f"--ms_data_path={self.ms_data_path} --mode={self.mode} --tolerance={self.tolerance} "
                                 f"--n_jobs={self.n_jobs}")
         self.assertEqual(exit_status, 0)
+
+    def test_biocatalyzer_full2(self):
+        exit_status = os.system(f"biocatalyzer_cli {self.compounds_path} {self.output_folder} "
+                                f"--neutralize={self.neutralize} --reaction_rules={self.reaction_rules_path} "
+                                f"--patterns_to_remove={None} "
+                                f"--molecules_to_remove={None} "
+                                f"--min_atom_count={self.min_atom_count} --match_ms_data={self.match_ms_data} "
+                                f"--ms_data_path={self.ms_data_path} --mode={self.mode} --tolerance={self.tolerance} "
+                                f"--n_jobs={self.n_jobs}")
+        self.assertEqual(exit_status, 0)