have get_repo() accept files, including those that don't exist

KarrLab · Jun 15, 2019 · 1825929 · 1825929
1 parent 3bbc7d3
commit 1825929
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Showing 2 changed files with 21 additions and 14 deletions.
diff --git a/tests/util/test_git.py b/tests/util/test_git.py
@@ -17,7 +17,7 @@
 from pathlib import Path
 
 # todo: next: get push working on CircleCI
-RUNNING_ON_CIRCLE = True
+RUNNING_ON_CIRCLE = False
 
 
 # todo: next: rename wc_utils.util.git: update wc_utils, obj_model, wc_kb, wc_sim, & wc_lang
@@ -43,16 +43,20 @@ def tearDown(self):
         self.test_git_repos.delete_test_repo()
 
     def test_get_repo(self):
-        repo = get_repo(dirname='.')
+        repo = get_repo(path='.')
         self.assertTrue(isinstance(repo, git.Repo))
-        repo = get_repo(dirname=os.path.dirname(__file__), search_parent_directories=False)
+        repo = get_repo(path=os.path.dirname(__file__))
         self.assertTrue(isinstance(repo, git.Repo))
-        repo = get_repo(dirname=os.path.dirname(__file__), search_parent_directories=True)
+        repo = get_repo(path=os.path.dirname(__file__), search_parent_directories=False)
+        self.assertTrue(isinstance(repo, git.Repo))
+        repo = get_repo(__file__)
+        self.assertTrue(isinstance(repo, git.Repo))
+        repo = get_repo(path=os.path.join(os.path.dirname(__file__), 'no such file'))
         self.assertTrue(isinstance(repo, git.Repo))
 
         tempdir = tempfile.mkdtemp()
         with self.assertRaisesRegex(ValueError, 'is not in a Git repository'):
-            get_repo(dirname=tempdir)
+            get_repo(path=tempdir)
         shutil.rmtree(tempdir)
 
     def test_repo_status(self):
@@ -111,7 +115,7 @@ def test_repo_status(self):
         with self.assertRaisesRegex(ValueError, r"data_file '.+' must be in the repo that's in '.+'"):
             repo_status(self.repo, RepoMetadataCollectionType.DATA_REPO, data_file='/tmp/test.xlsx')
 
-        repo = get_repo(dirname='.')
+        repo = get_repo(path='.')
         with self.assertRaisesRegex(ValueError, "data_file must be provided if repo_type is "
                 "RepoMetadataCollectionType.DATA_REPO"):
             repo_status(repo, RepoMetadataCollectionType.DATA_REPO)

diff --git a/wc_utils/util/git.py b/wc_utils/util/git.py
@@ -17,34 +17,37 @@
 from .config import core
 
 
-def get_repo(dirname='.', search_parent_directories=True):
+def get_repo(path='.', search_parent_directories=True):
     """ Get a Git repository
 
     Args:
-        dirname (:obj:`str`): path to Git repository
+        path (:obj:`str`): path to file or directory in a Git repository; if `path` doesn't exist
+            or is a file then its directory is used
         search_parent_directories (:obj:`bool`, optional): if :obj:`True`, search for the root 
-            of the repository among the parent directories of :obj:`dirname`; default=:obj:`True`
+            of the repository among the parent directories of :obj:`path`; default=:obj:`True`
 
     Returns:
         :obj:`git.Repo`: a `GitPython` repository
 
     Raises:
-        :obj:`ValueError`: if obj:`dirname` is not a path to a Git repository
+        :obj:`ValueError`: if obj:`path` is not a path to a Git repository
     """
     repo = None
-    resolved_path = Path(dirname).expanduser().resolve()
+    resolved_path = Path(path).expanduser().resolve()
+    if not resolved_path.exists() or resolved_path.is_file():
+        resolved_path = resolved_path.parent
     dirnames = itertools.chain([str(resolved_path)], resolved_path.parents)
     if search_parent_directories:
         dirnames = [str(resolved_path)]
     for parent_dirname in dirnames:
         try:
             repo = git.Repo(str(parent_dirname), search_parent_directories=search_parent_directories)
             break
-        except (git.exc.InvalidGitRepositoryError, git.exc.NoSuchPathError):
+        except (git.exc.InvalidGitRepositoryError, git.exc.NoSuchPathError) as e:
             pass
 
     if not repo:
-        raise ValueError('"{}" is not in a Git repository'.format(dirname))
+        raise ValueError('"{}" is not in a Git repository'.format(path))
     return repo
 
 
@@ -144,7 +147,7 @@ def get_repo_metadata(dirname='.', search_parent_directories=True, repo_type=Non
         :obj:`ValueError`: if obj:`dirname` is not a path to a Git repository,
             or if the repo is not suitable for gathering metadata
     """
-    repo = get_repo(dirname=dirname, search_parent_directories=search_parent_directories)
+    repo = get_repo(path=dirname, search_parent_directories=search_parent_directories)
     if repo_type:
         unsuitable_changes = repo_status(repo, repo_type, data_file=data_file)
         if unsuitable_changes: