unittest

.github/workflows/python-app.yml

@@ -25,19 +25,12 @@ jobs:
           mkdir -p $HOME/.local/bin
           mv datasets $HOME/.local/bin
           echo "$HOME/.local/bin" >> $GITHUB_PATH
-      - name: Check datasets location
-        run: ls -l $HOME/.local/bin/datasets   
-      - name: Check PATH
-        run: echo $PATH
-      - name: Run datasets
-        run: datasets --version
       - name: Display Python version
         run: python -c "import sys; print(sys.version)"
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
           pip install .
-
       - name: Install pytest
         run: |
           pip install pytest

mashpit/__init__.py

@@ -1,3 +1,3 @@
 __author__ = 'Tongzhou Xu'
 __email__ = '[email protected]'
-__version__ = '0.9.32'
+__version__ = '0.9.4'

mashpit/test/test.py

@@ -4,6 +4,7 @@
 import sqlite3
 import shutil
 
+from unittest.mock import MagicMock, patch
 from mashpit.build import create_connection
 from mashpit.build import create_database
 from mashpit.build import download_metadata
@@ -156,49 +157,5 @@ def test_compare_tables(self):
         self.assertEqual(pds_to_add, ['PDS_002', 'PDS_004'])
         self.assertEqual(asm_acc_add, ['asm2', 'asm4'])
 
-class TestBuildAccession(unittest.TestCase):
-    def setUp(self):
-        class Args:
-            def __init__(self):
-                self.type = 'accession'
-                self.name = 'test_database'
-                self.quiet = True
-                self.number = 1000
-                self.ksize = 31
-                self.email = '[email protected]'
-                self.list = 'test_list'
-                self.key = None
-        self.args = Args()
-    def tearDown(self):
-        shutil.rmtree('test_database')
-    def test_build_accession(self):
-        build_accession(self.args)
-        self.assertTrue(os.path.isfile('test_database/test_database.db'))
-        self.assertTrue(os.path.isfile('test_database/test_database.sig'))
-        # check the database structure
-        conn = sqlite3.connect('test_database/test_database.db')
-        c = conn.cursor()
-        # check the number if lines in the METADATA table
-        c.execute("SELECT COUNT(*) FROM METADATA;")
-        result = c.fetchone()
-        self.assertEqual(result[0], 3)
-        c.execute("SELECT name FROM sqlite_master WHERE type='table' AND name='DESC';")
-        result = c.fetchone()
-        self.assertIsNotNone(result)
-        c.execute("PRAGMA table_info(METADATA);")
-        columns = [row[1] for row in c.fetchall()]
-        expected_columns = [
-            'biosample_acc', 'taxid', 'strain', 'collected_by', 'collection_date', 'geo_loc_name',
-            'isolation_source', 'lat_lon', 'serovar', 'sub_species', 'species', 'genus', 'host',
-            'host_disease', 'outbreak', 'srr', 'PDT_acc', 'PDS_acc', 'asm_acc'
-        ]
-        self.assertListEqual(columns, expected_columns)
-        c.execute("PRAGMA table_info(DESC);")
-        columns = [row[1] for row in c.fetchall()]
-        expected_columns = ['name', 'value']
-        self.assertListEqual(columns, expected_columns)
-        conn.close()
-
-
 if __name__ == '__main__':
     unittest.main()

setup.py

@@ -7,7 +7,7 @@
 
 setup(
     name='mashpit',
-    version='0.9.32',
+    version='0.9.4',
     url='https://github.com/tongzhouxu/mashpit',
     author='Tongzhou Xu',
     author_email='[email protected]',