Merge pull request #493 from JrGoodle/subdirectories

Allow clowder to be called from subdirectories

clowder_test/clowder_test/cli/cats_controller.py

@@ -205,6 +205,15 @@ def status(self) -> None:
 
         self._execute_command('./status.sh', self.path)
 
+    @expose(
+        help='Run cats subdirectory tests'
+    )
+    @create_cats_cache
+    def subdirectory(self) -> None:
+        """clowder cats subdirectory tests"""
+
+        self._execute_command('./subdirectory.sh', self.path)
+
     @expose(
         help='Run cats yaml tests'
     )

clowder_test/clowder_test/execute.py

@@ -56,7 +56,7 @@ def wrapper(*args, **kwargs):
 
 
 def execute_test_command(command: str, path: str, parallel: bool = False, write: bool = False,
-                         coverage: bool = False, test_env: Optional[dict] = None, debug: bool = False,
+                         coverage: bool = False, test_env: Optional[dict] = None, debug: bool = True,
                          quiet: bool = False) -> None:
     """Execute test command
 

src/clowder/__init__.py

@@ -7,8 +7,39 @@
 
 import os
 import pkg_resources
+from typing import Optional
 
 
-ROOT_DIR = os.getcwd()
-
 CLOWDER_SCHEMA = pkg_resources.resource_string(__name__, "clowder.schema.json")
+
+
+CURRENT_DIR: str = os.getcwd()
+CLOWDER_DIR: Optional[str] = None
+CLOWDER_REPO_DIR: Optional[str] = None
+CLOWDER_REPO_VERSIONS_DIR: Optional[str] = None
+CLOWDER_YAML: Optional[str] = None
+
+
+temp_dir = CURRENT_DIR
+old_dir = None
+# Walk up directory tree to find possible clowder repo (.clowder directory) and set global variable
+while old_dir != temp_dir:
+    old_dir = temp_dir
+    clowder_repo_dir = os.path.join(temp_dir, '.clowder')
+    if os.path.exists(clowder_repo_dir) and os.path.isdir(clowder_repo_dir):
+        CLOWDER_DIR = temp_dir
+        CLOWDER_REPO_DIR = clowder_repo_dir
+        break
+    else:
+        temp_dir = os.path.dirname(temp_dir)
+
+# If clowder repo exists, try to set other global path variables
+if CLOWDER_REPO_DIR is not None:
+    clowder_yaml = os.path.join(CLOWDER_DIR, 'clowder.yaml')
+    if os.path.islink(clowder_yaml):
+        CLOWDER_YAML = clowder_yaml
+
+    clowder_versions = os.path.join(CLOWDER_REPO_DIR, 'versions')
+    if os.path.isdir(clowder_versions):
+        CLOWDER_REPO_VERSIONS_DIR = clowder_versions
+

src/clowder/cli/branch_controller.py

@@ -8,8 +8,10 @@
 from cement.ext.ext_argparse import ArgparseController, expose
 
 from clowder.clowder_controller import CLOWDER_CONTROLLER
-from clowder.clowder_repo import print_clowder_repo_status
-from clowder.util.decorators import valid_clowder_yaml_required
+from clowder.util.decorators import (
+    print_clowder_repo_status,
+    valid_clowder_yaml_required
+)
 from clowder.util.clowder_utils import (
     filter_projects,
     options_help_message

src/clowder/cli/checkout_controller.py

@@ -8,8 +8,10 @@
 from cement.ext.ext_argparse import ArgparseController, expose
 
 from clowder.clowder_controller import CLOWDER_CONTROLLER
-from clowder.clowder_repo import print_clowder_repo_status
-from clowder.util.decorators import valid_clowder_yaml_required
+from clowder.util.decorators import (
+    print_clowder_repo_status,
+    valid_clowder_yaml_required
+)
 from clowder.util.clowder_utils import (
     filter_projects,
     options_help_message

src/clowder/cli/clean_controller.py

@@ -10,8 +10,10 @@
 from cement.ext.ext_argparse import ArgparseController, expose
 
 from clowder.clowder_controller import CLOWDER_CONTROLLER, ClowderController
-from clowder.clowder_repo import print_clowder_repo_status
-from clowder.util.decorators import valid_clowder_yaml_required
+from clowder.util.decorators import (
+    print_clowder_repo_status,
+    valid_clowder_yaml_required
+)
 from clowder.util.clowder_utils import (
     filter_projects,
     options_help_message

src/clowder/cli/diff_controller.py

@@ -8,8 +8,10 @@
 from cement.ext.ext_argparse import ArgparseController, expose
 
 from clowder.clowder_controller import CLOWDER_CONTROLLER
-from clowder.clowder_repo import print_clowder_repo_status
-from clowder.util.decorators import valid_clowder_yaml_required
+from clowder.util.decorators import (
+    print_clowder_repo_status,
+    valid_clowder_yaml_required
+)
 from clowder.util.clowder_utils import (
     filter_projects,
     options_help_message

src/clowder/cli/forall_controller.py

@@ -11,12 +11,14 @@
 from cement.ext.ext_argparse import ArgparseController, expose
 
 from clowder.clowder_controller import CLOWDER_CONTROLLER, ClowderController
-from clowder.clowder_repo import print_clowder_repo_status
 from clowder.util.clowder_utils import (
     filter_projects,
     options_help_message
 )
-from clowder.util.decorators import valid_clowder_yaml_required
+from clowder.util.decorators import (
+    print_clowder_repo_status,
+    valid_clowder_yaml_required
+)
 from clowder.util.parallel_commands import forall_parallel
 
 

src/clowder/cli/herd_controller.py

@@ -11,14 +11,16 @@
 from cement.ext.ext_argparse import ArgparseController, expose
 
 from clowder.clowder_controller import CLOWDER_CONTROLLER, ClowderController
-from clowder.clowder_repo import print_clowder_repo_status_fetch
 from clowder.util.clowder_utils import (
     filter_projects,
     options_help_message,
     validate_projects
 )
 from clowder.util.connectivity import network_connection_required
-from clowder.util.decorators import valid_clowder_yaml_required
+from clowder.util.decorators import (
+    print_clowder_repo_status_fetch,
+    valid_clowder_yaml_required
+)
 from clowder.util.parallel_commands import herd_parallel
 
 

src/clowder/cli/init_controller.py

@@ -10,8 +10,10 @@
 from cement.ext.ext_argparse import ArgparseController, expose
 from termcolor import colored, cprint
 
-from clowder.clowder_repo import CLOWDER_REPO
+import clowder.clowder_repo as clowder_repo
+from clowder import CURRENT_DIR
 from clowder.error.clowder_exit import ClowderExit
+from clowder.git.util import existing_git_repository
 from clowder.util.connectivity import network_connection_required
 
 
@@ -45,14 +47,15 @@ def _init(self) -> None:
         :raise ClowderExit:
         """
 
-        if os.path.isdir(CLOWDER_REPO.clowder_path):
+        clowder_repo_dir = os.path.join(CURRENT_DIR, '.clowder')
+        if existing_git_repository(clowder_repo_dir):
             cprint('Clowder already initialized in this directory\n', 'red')
             raise ClowderExit(1)
 
         url_output = colored(self.app.pargs.url, 'green')
-        print('Create clowder repo from ' + url_output + '\n')
+        print(f"Create clowder repo from {url_output}\n")
         if self.app.pargs.branch is None:
             branch = 'master'
         else:
             branch = str(self.app.pargs.branch[0])
-        CLOWDER_REPO.init(self.app.pargs.url, branch)
+        clowder_repo.init(self.app.pargs.url, branch)

src/clowder/cli/link_controller.py

@@ -7,8 +7,11 @@
 
 from cement.ext.ext_argparse import ArgparseController, expose
 
-from clowder.clowder_repo import print_clowder_repo_status
-from clowder.util.decorators import clowder_required
+from clowder import CLOWDER_DIR
+from clowder.util.decorators import (
+    clowder_required,
+    print_clowder_repo_status
+)
 from clowder.util.clowder_utils import (
     get_saved_version_names,
     link_clowder_yaml,
@@ -49,4 +52,4 @@ def _link(self) -> None:
             version = None
         else:
             version = self.app.pargs.version[0]
-        link_clowder_yaml(version)
+        link_clowder_yaml(CLOWDER_DIR, version)

src/clowder/cli/prune_controller.py

@@ -11,11 +11,13 @@
 from termcolor import cprint
 
 from clowder.clowder_controller import CLOWDER_CONTROLLER, ClowderController
-from clowder.clowder_repo import print_clowder_repo_status
 from clowder.error.clowder_error import ClowderError
 from clowder.model.project import Project
 from clowder.util.connectivity import network_connection_required
-from clowder.util.decorators import valid_clowder_yaml_required
+from clowder.util.decorators import (
+    print_clowder_repo_status,
+    valid_clowder_yaml_required
+)
 from clowder.util.clowder_utils import (
     existing_branch_projects,
     filter_projects,

src/clowder/cli/repo_controller.py

@@ -7,12 +7,12 @@
 
 from cement.ext.ext_argparse import ArgparseController, expose
 
-from clowder.clowder_repo import (
-    CLOWDER_REPO,
+import clowder.clowder_repo as clowder_repo
+from clowder.util.decorators import (
+    clowder_required,
     print_clowder_repo_status,
     print_clowder_repo_status_fetch
 )
-from clowder.util.decorators import clowder_required
 from clowder.util.connectivity import network_connection_required
 
 
@@ -54,7 +54,7 @@ def add(self) -> None:
     def _add(self) -> None:
         """Clowder repo add command private implementation"""
 
-        CLOWDER_REPO.add(self.app.pargs.files)
+        clowder_repo.add(self.app.pargs.files)
 
 
 class RepoCommitController(ArgparseController):
@@ -82,7 +82,7 @@ def commit(self) -> None:
     def _commit(self) -> None:
         """Clowder repo commit command private implementation"""
 
-        CLOWDER_REPO.commit(self.app.pargs.message[0])
+        clowder_repo.commit(self.app.pargs.message[0])
 
 
 class RepoPullController(ArgparseController):
@@ -110,7 +110,7 @@ def pull(self) -> None:
     def _pull(self) -> None:
         """Clowder repo pull command private implementation"""
 
-        CLOWDER_REPO.pull()
+        clowder_repo.pull()
 
 
 class RepoPushController(ArgparseController):
@@ -138,7 +138,7 @@ def push(self) -> None:
     def _push(self) -> None:
         """Clowder repo push command private implementation"""
 
-        CLOWDER_REPO.push()
+        clowder_repo.push()
 
 
 class RepoRunController(ArgparseController):
@@ -168,7 +168,7 @@ def run(self) -> None:
     def _run(self) -> None:
         """Clowder repo run command private implementation"""
 
-        CLOWDER_REPO.run_command(self.app.pargs.command[0])
+        clowder_repo.run_command(self.app.pargs.command[0])
 
 
 class RepoCheckoutController(ArgparseController):
@@ -199,7 +199,7 @@ def repo_checkout(self) -> None:
     def _checkout(self) -> None:
         """Clowder repo checkout command private implementation"""
 
-        CLOWDER_REPO.checkout(self.app.pargs.ref[0])
+        clowder_repo.checkout(self.app.pargs.ref[0])
 
 
 class RepoCleanController(ArgparseController):
@@ -229,7 +229,7 @@ def repo_clean(self) -> None:
     def _clean(self) -> None:
         """Clowder repo clean command private implementation"""
 
-        CLOWDER_REPO.clean()
+        clowder_repo.clean()
 
 
 class RepoStatusController(ArgparseController):
@@ -259,4 +259,4 @@ def repo_status(self) -> None:
     def _status(self) -> None:
         """Clowder repo status command private implementation"""
 
-        CLOWDER_REPO.git_status()
+        clowder_repo.git_status()

src/clowder/cli/reset_controller.py

@@ -11,14 +11,16 @@
 from cement.ext.ext_argparse import ArgparseController, expose
 
 from clowder.clowder_controller import CLOWDER_CONTROLLER, ClowderController
-from clowder.clowder_repo import print_clowder_repo_status_fetch
 from clowder.util.clowder_utils import (
     filter_projects,
     options_help_message,
     validate_projects
 )
 from clowder.util.connectivity import network_connection_required
-from clowder.util.decorators import valid_clowder_yaml_required
+from clowder.util.decorators import (
+    print_clowder_repo_status_fetch,
+    valid_clowder_yaml_required
+)
 from clowder.util.parallel_commands import reset_parallel
 
 

src/clowder/cli/save_controller.py

@@ -10,10 +10,10 @@
 
 from cement.ext.ext_argparse import ArgparseController, expose
 
+import clowder.clowder_repo as clowder_repo
 import clowder.util.formatting as fmt
-from clowder import ROOT_DIR
+from clowder import CLOWDER_REPO_DIR
 from clowder.clowder_controller import CLOWDER_CONTROLLER
-from clowder.clowder_repo import CLOWDER_REPO
 from clowder.error.clowder_exit import ClowderExit
 from clowder.util.decorators import valid_clowder_yaml_required
 from clowder.util.clowder_utils import validate_projects
@@ -53,15 +53,15 @@ def _save(self) -> None:
             print(fmt.error_save_default(self.app.pargs.version))
             raise ClowderExit(1)
 
-        CLOWDER_REPO.print_status()
+        clowder_repo.print_status()
         CLOWDER_CONTROLLER.validate_projects_exist()
         # TODO: Get all projects
         validate_projects(CLOWDER_CONTROLLER.projects)
 
         # Replace path separators with dashes to avoid creating directories
         version_name = self.app.pargs.version.replace('/', '-')
 
-        versions_dir = os.path.join(ROOT_DIR, '.clowder', 'versions')
+        versions_dir = os.path.join(CLOWDER_REPO_DIR, 'versions')
         _make_dir(versions_dir)
 
         yaml_file = os.path.join(versions_dir, f"{version_name}.clowder.yaml")

src/clowder/cli/start_controller.py

@@ -8,9 +8,11 @@
 from cement.ext.ext_argparse import ArgparseController, expose
 
 from clowder.clowder_controller import CLOWDER_CONTROLLER
-from clowder.clowder_repo import print_clowder_repo_status
 from clowder.util.connectivity import network_connection_required
-from clowder.util.decorators import valid_clowder_yaml_required
+from clowder.util.decorators import (
+    print_clowder_repo_status,
+    valid_clowder_yaml_required
+)
 from clowder.util.clowder_utils import (
     filter_projects,
     options_help_message,

src/clowder/cli/stash_controller.py

@@ -8,8 +8,10 @@
 from cement.ext.ext_argparse import ArgparseController, expose
 
 from clowder.clowder_controller import CLOWDER_CONTROLLER
-from clowder.clowder_repo import print_clowder_repo_status
-from clowder.util.decorators import valid_clowder_yaml_required
+from clowder.util.decorators import (
+    print_clowder_repo_status,
+    valid_clowder_yaml_required
+)
 from clowder.util.clowder_utils import (
     filter_projects,
     options_help_message