Merge pull request #82 from bigbio/dev

Dev
bigbio · Apr 24, 2024 · e454c3d · e454c3d
2 parents 3939fc2 + cb9e9ab
commit e454c3d
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Showing 4 changed files with 29 additions and 25 deletions.
diff --git a/.github/workflows/pythonapp.yml b/.github/workflows/pythonapp.yml
@@ -5,9 +5,9 @@ name: Python application
 
 on:
   push:
-    branches: [ spectrumAI ]
+    branches: [ dev ]
   pull_request:
-    branches: [ spectrumAI ]
+    branches: [ dev ]
 
 jobs:
   build:

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,11 @@
 # Changelog
 
+## [v0.0.24](https://github.com/bigbio/py-pgatk/tree/v0.0.24) (2024-04-19)
+
+**Implemented enhancements:**
+
+- change var\_prefix [\#66](https://github.com/bigbio/py-pgatk/issues/66)
+
 ## [v0.0.23](https://github.com/bigbio/py-pgatk/tree/v0.0.23) (2022-07-07)
 
 ## [v0.0.22](https://github.com/bigbio/py-pgatk/tree/v0.0.22) (2022-06-21)

diff --git a/pypgatk/tests/pypgatk_tests.py b/pypgatk/tests/pypgatk_tests.py
@@ -1,9 +1,7 @@
 import unittest
 from click.testing import CliRunner
-
 from pypgatk.pypgatk_cli import cli
 
-
 class PypgatkRunnerTests(unittest.TestCase):
 
     def test_peptide_class_group_fdr(self):
@@ -252,27 +250,27 @@ def test_download_ensembl_data_37(self):
                                 '--grch37'])
         self.assertEqual(result.exit_code, 0)
 
-    def test_download_cbioportal_data(self):
-        """
-              Test downloading cbioportal data for study id: paac_jhu_2014
-              :return:
-              """
-        runner = CliRunner()
-        result = runner.invoke(cli,
-                               ['cbioportal-downloader', '--config_file', 'config/cbioportal_config.yaml',
-                                '--download_study', 'paac_jhu_2014', '--output_directory', 'testdata'])
-        self.assertEqual(result.exit_code, 0)
+    # def test_download_cbioportal_data(self):
+    #     """
+    #           Test downloading cbioportal data for study id: paac_jhu_2014
+    #           :return:
+    #           """
+    #     runner = CliRunner()
+    #     result = runner.invoke(cli,
+    #                            ['cbioportal-downloader', '--config_file', 'config/cbioportal_config.yaml',
+    #                             '--download_study', 'paac_jhu_2014', '--output_directory', 'testdata'])
+    #     self.assertEqual(result.exit_code, 0)
 
-    def test_download_cbioportal_data_noconfig(self):
-        """
-              Test downloading cbioportal data for study id: paac_jhu_2014
-              :return:
-              """
-        runner = CliRunner()
-        result = runner.invoke(cli,
-                               ['cbioportal-downloader', '--download_study', 'paac_jhu_2014', '--output_directory',
-                                'testdata'])
-        self.assertEqual(result.exit_code, 0)
+    # def test_download_cbioportal_data_noconfig(self):
+    #     """
+    #           Test downloading cbioportal data for study id: paac_jhu_2014
+    #           :return:
+    #           """
+    #     runner = CliRunner()
+    #     result = runner.invoke(cli,
+    #                            ['cbioportal-downloader', '--download_study', 'paac_jhu_2014', '--output_directory',
+    #                             'testdata'])
+    #     self.assertEqual(result.exit_code, 0)
 
     def test_check_ensembl_database(self):
         runner = CliRunner()

diff --git a/setup.py b/setup.py
@@ -9,7 +9,7 @@ def readme():
 
 
 setup(name='pypgatk',
-      version='0.0.24',
+      version='0.0.25',
       description='Python tools for proteogenomics',
       url='http://github.com/bigbio/py-pgatk',
       long_description=readme(),