Merge pull request #562 from JrGoodle/misc-fixes

Misc fixes

codecov.yml

@@ -1,10 +1,21 @@
-codecov:
-  require_ci_to_pass: no
-
 coverage:
   precision: 2
   round: down
   range: "70...100"
+  status:
+    project:
+      default: off
+      clowder:
+        paths:
+          - 'src/'
+          - '!src/clowder/util/clowder.schema.json'
+          - '!src/clowder/util/clowder.config.schema.json'
+        target: 70
+        threshold: 20
+    patch:
+       default: off
+        #  enabled: no
+        #  target: '50'
 
 parsers:
   gcov:
@@ -14,6 +25,7 @@ parsers:
       method: no
       macro: no
 
+comment: off
 # comment:
 #   # layout: "reach,diff,flags,tree"
 #   # layout: "files"
@@ -29,6 +41,3 @@ ignore:
   - "docs/**/*"
   - "script/**/*"
   - "test/**/*"
-
-# fixes:
-#    - "/home/circleci/::"

docs/clowder.cli.rst

@@ -36,6 +36,14 @@ clowder\.cli\.clean\_controller module
     :undoc-members:
     :show-inheritance:
 
+clowder\.cli\.config\_controller module
+--------------------------------------
+
+.. automodule:: clowder.cli.config_controller
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 clowder\.cli\.diff\_controller module
 -------------------------------------
 
@@ -132,6 +140,14 @@ clowder\.cli\.status\_controller module
     :undoc-members:
     :show-inheritance:
 
+clowder\.cli\.util module
+--------------------------------------
+
+.. automodule:: clowder.cli.util
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 clowder\.cli\.yaml\_controller module
 -------------------------------------
 

docs/clowder.config.rst

@@ -0,0 +1,30 @@
+clowder\.config package
+====================
+
+Submodules
+----------
+
+clowder\.config\.clowder\_config module
+-------------------------------------
+
+.. automodule:: clowder.config.clowder_config
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+clowder\.config\.config module
+---------------------------------------
+
+.. automodule:: clowder.config.config
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: clowder.config
+    :members:
+    :undoc-members:
+    :show-inheritance:

docs/clowder.git.rst

@@ -4,6 +4,14 @@ clowder\.git package
 Submodules
 ----------
 
+clowder\.git\.git\_repo module
+-------------------------
+
+.. automodule:: clowder.git.git_repo
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 clowder\.git\.project\_repo module
 ----------------------------------
 
@@ -28,14 +36,6 @@ clowder\.git\.project\_repo\_recursive module
     :undoc-members:
     :show-inheritance:
 
-clowder\.git\.repo module
--------------------------
-
-.. automodule:: clowder.git.repo
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
 clowder\.git\.util module
 -------------------------
 

docs/clowder.model.rst

@@ -20,6 +20,14 @@ clowder\.model\.fork module
     :undoc-members:
     :show-inheritance:
 
+clowder\.model\.git\_settings module
+-----------------------------
+
+.. automodule:: clowder.model.git_settings
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 clowder\.model\.project module
 ------------------------------
 
@@ -36,6 +44,14 @@ clowder\.model\.source module
     :undoc-members:
     :show-inheritance:
 
+clowder\.model\.util module
+-----------------------------
+
+.. automodule:: clowder.model.util
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 
 Module contents
 ---------------

docs/clowder.rst

@@ -39,6 +39,30 @@ clowder\.clowder\_repo module
     :undoc-members:
     :show-inheritance:
 
+clowder\.environment module
+-----------------------------
+
+.. automodule:: clowder.environment
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+clowder\.error module
+-----------------------------
+
+.. automodule:: clowder.error
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+clowder\.logging module
+-----------------------------
+
+.. automodule:: clowder.logging
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 
 Module contents
 ---------------

docs/clowder.util.rst

@@ -4,14 +4,6 @@ clowder\.util package
 Submodules
 ----------
 
-clowder\.util\.clowder\_utils module
-------------------------------------
-
-.. automodule:: clowder.util.clowder_utils
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
 clowder\.util\.connectivity module
 ----------------------------------
 
@@ -52,10 +44,10 @@ clowder\.util\.formatting module
     :undoc-members:
     :show-inheritance:
 
-clowder\.util\.parallel\_commands module
+clowder\.util\.parallel module
 ----------------------------------------
 
-.. automodule:: clowder.util.parallel_commands
+.. automodule:: clowder.util.parallel
     :members:
     :undoc-members:
     :show-inheritance:

src/clowder/cli/status.py

@@ -56,7 +56,7 @@ def status(args) -> None:
     else:
         clowder_repo.print_status()
 
-    padding = len(max(CLOWDER_CONTROLLER.get_project_paths(projects), key=len))
+    padding = len(max(CLOWDER_CONTROLLER.get_projects_output(projects), key=len))
 
     for project in projects:
         print(project.status(padding=padding))

src/clowder/clowder_controller.py

@@ -11,6 +11,7 @@
 import clowder.util.formatting as fmt
 from clowder.environment import ENVIRONMENT
 from clowder.error import ClowderError, ClowderErrorType
+from clowder.logging import LOG_DEBUG
 from clowder.model import Defaults, Project, Source
 from clowder.model.util import (
     print_parallel_projects_output,
@@ -55,6 +56,7 @@ def __init__(self):
             validate_yaml_file(yaml, ENVIRONMENT.clowder_yaml)
             self._load_clowder_yaml(yaml)
         except ClowderError as err:
+            LOG_DEBUG('Failed to init clowder controller', err)
             self.error = err
         except (KeyboardInterrupt, SystemExit):
             raise ClowderError(ClowderErrorType.USER_INTERRUPT, fmt.error_user_interrupt())
@@ -68,21 +70,23 @@ def get_all_fork_project_names(self) -> Tuple[str, ...]:
 
         try:
             return tuple(sorted([p.name for p in self.projects if p.fork is not None]))
-        except TypeError:
+        except TypeError as err:
+            LOG_DEBUG('Failed to get fork project names', err)
             return ()
 
     @staticmethod
-    def get_project_paths(projects: Tuple[Project, ...]) -> Tuple[str, ...]:
-        """Returns all project paths for specified projects
+    def get_projects_output(projects: Tuple[Project, ...]) -> Tuple[str, ...]:
+        """Returns all project paths/names output for specified projects
 
-        :param Tuple[Project, ...] projects: Projects to get paths of
+        :param Tuple[Project, ...] projects: Projects to get paths/names output of
         :return: All project paths
         :rtype: Tuple[str, ...]
         """
 
         try:
-            return tuple(sorted([p.formatted_project_path() for p in projects]))
-        except TypeError:
+            return tuple(sorted([p.formatted_project_output() for p in projects]))
+        except TypeError as err:
+            LOG_DEBUG('Failed to get projects output', err)
             return ()
 
     def get_timestamp(self, timestamp_project: str) -> str:
@@ -157,7 +161,8 @@ def _get_all_project_names(self) -> Tuple[str, ...]:
         try:
             names = [g for p in self.projects for g in p.groups]
             return tuple(sorted(set(names)))
-        except TypeError:
+        except TypeError as err:
+            LOG_DEBUG('Failed to get project names', err)
             return ()
 
     def _load_clowder_yaml(self, yaml: dict) -> None:
@@ -190,6 +195,7 @@ def _load_clowder_yaml(self, yaml: dict) -> None:
             names.append('default')
             self.project_choices_with_default = tuple(sorted(set(names)))
         except (AttributeError, KeyError, TypeError) as err:
+            LOG_DEBUG('Failed to load clowder yaml', err)
             self.name = None
             self.defaults = None
             self.sources = ()

src/clowder/git/git_repo.py

@@ -609,7 +609,7 @@ def _format_error_message(self, message: str) -> str:
         """
 
         if self.parallel:
-            fmt.error_parallel_exception(self.repo_path, message)
+            fmt.error_parallel_exception(str(self.repo_path), message)
         else:
             return message
 
@@ -645,7 +645,7 @@ def _repo(self) -> Repo:
             repo = Repo(self.repo_path)
         except GitError as err:
             LOG_DEBUG('Git error', err)
-            repo_path_output = fmt.path_string(self.repo_path)
+            repo_path_output = fmt.path_string(str(self.repo_path))
             message = f"{fmt.ERROR} Failed to create Repo instance for {repo_path_output}"
             message = self._format_error_message(message)
             raise ClowderError(ClowderErrorType.GIT_ERROR, message, error=err)

src/clowder/git/project_repo.py

@@ -64,7 +64,7 @@ def create_clowder_repo(self, url: str, branch: str, depth: int = 0) -> None:
             except OSError as err:
                 LOG_DEBUG('Failed to remove existing .clowder directory', err)
                 raise ClowderError(ClowderErrorType.DIRECTORY_EXISTS,
-                                   fmt.error_directory_exists(self.repo_path),
+                                   fmt.error_directory_exists(str(self.repo_path)),
                                    error=err)
 
         if self.repo_path.is_symlink():

src/clowder/git/project_repo_impl.py

@@ -439,7 +439,7 @@ def _init_repo(self) -> None:
             return
 
         try:
-            self._print(f' - Initialize repo at {fmt.path_string(self.repo_path)}')
+            self._print(f' - Initialize repo at {fmt.path_string(str(self.repo_path))}')
             if not self.repo_path.is_dir():
                 try:
                     os.makedirs(str(self.repo_path))