Remove the submodules

.github/workflows/basic_testing.yaml

@@ -68,6 +68,8 @@ jobs:
       - name: Install the code
         run: |
           cd $GITHUB_WORKSPACE
+          pip install pyyaml
+          ./jcb_client_init.py
           pip install .[testing]
 
       - name: Run unit tests

.gitignore

@@ -1,3 +1,7 @@
+# JCB clients
+src/jcb/configuration/algorithms/
+src/jcb/configuration/apps/gdas/
+
 # Mac files
 .DS_Store
 

README.md

@@ -26,8 +26,12 @@
 ### Installation
 
 ``` shell
-git clone --recurse-submodules https://github.com/noaa-emc/jcb
+git clone https://github.com/noaa-emc/jcb
 cd jcb
+
+# Optional step if you want to run the client integration tests
+./jcb_client_init.py  # May first require `pip install pyyaml` if it is not available
+
 pip install --prefix=/path/to/where/you/want/installed .
 ```
 

jcb_client_init.py

@@ -0,0 +1,252 @@
+#!/usr/bin/env python
+
+
+# --------------------------------------------------------------------------------------------------
+
+
+import os
+import subprocess
+import typing
+
+import yaml
+
+
+# --------------------------------------------------------------------------------------------------
+
+
+bold = '\033[1m'
+red = '\033[91m'
+green = '\033[92m'
+end = '\033[0m'
+
+
+# --------------------------------------------------------------------------------------------------
+
+
+def write_message(message: str, center: bool = False) -> None:
+
+    """Write a message, optionally centered, and print it line by line.
+
+    Args:
+        message (str): The message to be written and printed.
+        center (bool): If True, center each line of the message. Defaults to False.
+    """
+
+    # Max line length
+    max_line_length = 100
+
+    # Break the message into a list of lines max 100 characters but do not cut a word in half
+    lines = []
+    while len(message) > max_line_length:
+        last_space = message[:max_line_length].rfind(' ')
+        lines.append(message[:last_space])
+        message = message[last_space+1:]
+    lines.append(message)
+
+    # If center is true center the lines
+    if center:
+        lines = [line.center(max_line_length) for line in lines]
+
+    # Remove any lines that are empty
+    lines = [line for line in lines if line != '']
+
+    # Print the lines
+    for line in lines:
+        print(line)
+
+
+# --------------------------------------------------------------------------------------------------
+
+
+def get_jcb_branch() -> typing.Optional[str]:
+
+    """Get the current Git branch name.
+
+    Executes a Git command to retrieve the current branch name.
+    Returns the branch name unless it is 'HEAD' or 'develop',
+    in which case it returns None.
+
+    Returns:
+        Optional[str]: The current Git branch name, or None if the branch
+        is 'HEAD', 'develop', or if an error occurs.
+    """
+
+    # Command to get git branch
+    git_branch_command = ['git', 'rev-parse', '--abbrev-ref', 'HEAD']
+
+    # Return current branch
+    try:
+        branch = subprocess.check_output(git_branch_command).strip().decode('utf-8')
+        return branch if branch != 'HEAD' and branch != 'develop' else None
+    except subprocess.CalledProcessError:
+        return None
+
+
+# --------------------------------------------------------------------------------------------------
+
+
+def branch_exists_on_remote(git_ls_remote_command: typing.List[str]) -> bool:
+
+    """Check if a branch exists on the remote repository.
+
+    Executes a Git command to check for the existence of a branch
+    on the remote repository.
+
+    Args:
+        git_ls_remote_command (List[str]): The Git command to list remote branches.
+
+    Returns:
+        bool: True if the branch exists on the remote repository, False otherwise.
+    """
+
+    # Return status of branch existence
+    try:
+        output = subprocess.check_output(git_ls_remote_command)
+        return bool(output)
+    except subprocess.CalledProcessError:
+        return False
+
+
+# --------------------------------------------------------------------------------------------------
+
+
+def update_default_refs(jcb_apps: typing.Dict[str, typing.Dict[str, typing.Any]]) -> None:
+
+    """Update the default Git references for jcb apps based on the current branch.
+
+    Gets the current branch of the jcb repo and updates the default branch
+    for each app in jcb_apps if the branch exists on the remote.
+
+    Args:
+        jcb_apps (Dict[str, Dict[str, Any]]): A dictionary containing app configurations,
+        where the key is the app name and the value is a dictionary with configuration details.
+
+    Returns:
+        None
+    """
+
+    # Get the current branch of the jcb repo
+    jcb_branch = get_jcb_branch()
+
+    # Nothing to do unless there is a branch  called something other than develop
+    if jcb_branch is None:
+        return
+
+    # Write message
+    write_message(f'The branch for jcb is {red + jcb_branch + end}. Looking for this branch '
+                  'for the clients.')
+
+    # Loop over jcb_apps and update default branch
+    for app, app_conf in jcb_apps.items():
+
+        # Check if the default branch exists
+        full_url = f'https://github.com/{app_conf["git_url"]}.git'
+        git_ls_remote_command = ['git', 'ls-remote', '--heads', full_url, jcb_branch]
+
+        # If the branch exists, update the default branch
+        found = red + 'not found' + end
+        if branch_exists_on_remote(git_ls_remote_command):
+            found = green + 'found' + end
+            app_conf['git_ref'] = jcb_branch
+        write_message(f'  Branch {jcb_branch} {found} for {app}')
+    write_message(' ')
+
+
+# --------------------------------------------------------------------------------------------------
+
+
+def clone_or_update_repos(jcb_apps: typing.Dict[str, typing.Dict[str, typing.Any]]) -> None:
+
+    """Clone or update repositories based on the provided configuration.
+
+    Loops over jcb_apps and clones the repositories if the target path does not exist.
+    If the repository already exists at the target path, it prints a warning message.
+
+    Args:
+        jcb_apps (Dict[str, Dict[str, Any]]): A dictionary containing app configurations,
+        where the key is the app name and the value is a dictionary with configuration details.
+
+    Returns:
+        None
+    """
+
+    # Loop over jcb_apps and clone or update the repositories
+    for app, app_conf in jcb_apps.items():
+
+        target_path = app_conf['target_path']
+
+        # Check if the target path exists
+        if not os.path.exists(target_path):
+
+            # Clone command
+            full_url = f'https://github.com/{app_conf["git_url"]}.git'
+            git_clone = ['git', 'clone', full_url, '-b', app_conf['git_ref'],
+                         target_path]
+
+            # Clone the repository
+            command_string = ' '.join(git_clone)
+            write_message(f'Cloning {app} with command: {command_string}')
+            subprocess.run(git_clone, stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL)
+
+        else:
+
+            # Print warning that repo is already cloned
+            write_message(f'Repository {app} already cloned at {target_path}. Update '
+                          'manually or remove to clone again using this script.')
+
+        write_message(' ')
+
+
+# --------------------------------------------------------------------------------------------------
+
+
+if __name__ == "__main__":
+
+    # Write initial message
+    write_message(' ')
+    write_message('-'*100)
+    write_message(' ')
+    write_message(bold + 'Running jcb client initialization script' + end, True)
+    write_message(' ')
+    write_message('This script will clone any of the jcb clients that are registered in '
+                  'jcb_apps.yaml.\n')
+
+    # Get the path of this file
+    file_path = os.path.dirname(os.path.realpath(__file__))
+
+    # Open the jcb_apps.yaml file
+    with open(os.path.join(file_path, 'jcb_clients.yaml')) as file:
+        jcb_apps = yaml.load(file, Loader=yaml.FullLoader)
+
+    # Required keys
+    required_keys = ['git_url', 'git_ref']
+
+    # Set the path to where the applications will be cloned
+    jcb_config_path = os.path.join(file_path, 'src', 'jcb', 'configuration')
+
+    # Loop over jcb_apps and make sure required keys are present and add target_path
+    for app, app_conf in jcb_apps.items():
+        for key in required_keys:
+            if key not in app_conf:
+                raise Exception(f'Key \'{key}\' not found in jcb_apps.yaml')
+        app_conf['target_path'] = os.path.join(jcb_config_path, 'apps', app)
+
+    # Add jcb-algorithms to the dictionary
+    jcb_apps['algorithms'] = {
+        'git_url': 'noaa-emc/jcb-algorithms',
+        'git_ref': 'develop',
+        'target_path': os.path.join(jcb_config_path, 'algorithms')
+    }
+
+    # Update the default refs for the clients
+    update_default_refs(jcb_apps)
+
+    # Clone or update the repositories
+    clone_or_update_repos(jcb_apps)
+
+    write_message('Initialization of jcb clients is complete')
+    write_message(' ')
+    write_message('-'*100)
+
+
+# --------------------------------------------------------------------------------------------------

jcb_client_path.py

@@ -0,0 +1,37 @@
+#!/usr/bin/env python
+
+
+# --------------------------------------------------------------------------------------------------
+
+
+import os
+import sys
+
+import yaml
+
+
+# --------------------------------------------------------------------------------------------------
+
+
+if __name__ == "__main__":
+
+    # Get the repo path from the argument
+    git_url_in = sys.argv[1]
+
+    # Get the path of this file
+    file_path = os.path.dirname(os.path.realpath(__file__))
+
+    # Open the jcb_apps.yaml file
+    with open(os.path.join(file_path, 'jcb_clients.yaml')) as file:
+        jcb_apps = yaml.load(file, Loader=yaml.FullLoader)
+
+    # Loop over jcb_apps and make sure required keys are present and add target_path
+    for app, app_conf in jcb_apps.items():
+        if git_url_in.lower() == app_conf['git_url'].lower():
+            print(os.path.join(file_path, 'src', 'jcb', 'configuration', 'apps', app))
+
+    # Fail if we got to here
+    exit(1)
+
+
+# --------------------------------------------------------------------------------------------------

jcb_clients.yaml

@@ -0,0 +1,3 @@
+gdas:
+  git_url: noaa-emc/jcb-gdas
+  git_ref: develop