dayhoff-tools 1.13.13__py3-none-any.whl → 1.13.14__py3-none-any.whl

dayhoff_tools/cli/github_commands.py

@@ -0,0 +1,286 @@
+"""CLI commands for GitHub authentication.
+
+This module provides commands for authenticating with GitHub from within
+development containers using the GitHub CLI (gh).
+
+The implementation:
+1. Wraps `gh auth login` with sensible defaults for devcontainer environments
+2. Automatically configures git to use GitHub CLI for credential management
+3. Uses HTTPS protocol and device flow authentication (works in headless envs)
+"""
+
+import shutil
+import subprocess
+import sys
+from typing import List, Tuple
+
+import typer
+
+# --- Configuration ---
+# OAuth scopes to request during login:
+# - repo: Full access to private/public repositories
+# - read:org: Read-only access to organization membership
+# - workflow: Ability to update GitHub Actions workflow files
+GITHUB_SCOPES = "repo,read:org,workflow"
+GITHUB_PROTOCOL = "https"
+
+# --- Color constants for formatted output ---
+RED = "\033[0;31m"
+GREEN = "\033[0;32m"
+YELLOW = "\033[0;33m"
+BLUE = "\033[0;36m"
+NC = "\033[0m"  # No Color
+
+
+# --- Helper Functions ---
+def _find_executable(name: str) -> str:
+    """Find the full path to an executable in PATH."""
+    path = shutil.which(name)
+    if not path:
+        raise FileNotFoundError(
+            f"{name} command not found. Please ensure it's installed."
+        )
+    return path
+
+
+def _run_command(
+    cmd_list: List[str],
+    capture: bool = False,
+    check: bool = True,
+    suppress_output: bool = False,
+) -> Tuple[int, str, str]:
+    """Run a command and return its result.
+
+    Args:
+        cmd_list: List of command arguments
+        capture: Whether to capture output
+        check: Whether to raise on non-zero exit code
+        suppress_output: Whether to hide output even if not captured
+
+    Returns:
+        Tuple of (return_code, stdout_str, stderr_str)
+    """
+    stdout_opt = (
+        subprocess.PIPE if capture else subprocess.DEVNULL if suppress_output else None
+    )
+    stderr_opt = (
+        subprocess.PIPE if capture else subprocess.DEVNULL if suppress_output else None
+    )
+
+    try:
+        result = subprocess.run(
+            cmd_list, stdout=stdout_opt, stderr=stderr_opt, check=check, text=True
+        )
+        return (
+            result.returncode,
+            result.stdout if capture else "",
+            result.stderr if capture else "",
+        )
+    except subprocess.CalledProcessError as e:
+        if capture:
+            return (e.returncode, e.stdout or "", e.stderr or "")
+        return (e.returncode, "", "")
+
+
+def _is_gh_authenticated() -> bool:
+    """Check if GitHub CLI is authenticated.
+
+    Returns:
+        True if `gh auth status` succeeds, False otherwise.
+    """
+    try:
+        gh_path = _find_executable("gh")
+        returncode, _, _ = _run_command(
+            [gh_path, "auth", "status"],
+            capture=True,
+            check=False,
+            suppress_output=True,
+        )
+        return returncode == 0
+    except FileNotFoundError:
+        return False
+
+
+def _get_gh_user() -> str:
+    """Get the currently authenticated GitHub username.
+
+    Returns:
+        The username or 'Not authenticated' if not logged in.
+    """
+    try:
+        gh_path = _find_executable("gh")
+        returncode, stdout, _ = _run_command(
+            [gh_path, "auth", "status", "--show-token"],
+            capture=True,
+            check=False,
+            suppress_output=True,
+        )
+        if returncode != 0:
+            return "Not authenticated"
+
+        # Parse the output to find the logged in account
+        # Format: "Logged in to github.com account username (keyring)"
+        for line in stdout.split("\n"):
+            if "Logged in to" in line and "account" in line:
+                parts = line.split("account")
+                if len(parts) > 1:
+                    # Extract username from "account username (keyring)" or similar
+                    user_part = parts[1].strip().split()[0]
+                    return user_part
+        return "Unknown"
+    except FileNotFoundError:
+        return "gh CLI not found"
+
+
+def _get_gh_scopes() -> str:
+    """Get the OAuth scopes for the current GitHub authentication.
+
+    Returns:
+        Comma-separated list of scopes or 'Unknown' if not available.
+    """
+    try:
+        gh_path = _find_executable("gh")
+        returncode, stdout, _ = _run_command(
+            [gh_path, "auth", "status"],
+            capture=True,
+            check=False,
+            suppress_output=True,
+        )
+        if returncode != 0:
+            return "N/A"
+
+        # Parse output for scopes - format varies by gh version
+        # Look for lines containing "Token scopes:" or similar
+        for line in stdout.split("\n"):
+            if "scopes" in line.lower():
+                # Extract everything after the colon
+                if ":" in line:
+                    scopes = line.split(":", 1)[1].strip()
+                    return scopes if scopes else "none"
+        return "Unknown"
+    except FileNotFoundError:
+        return "N/A"
+
+
+# --- Typer Application ---
+gh_app = typer.Typer(help="Manage GitHub authentication using the gh CLI.")
+
+
+@gh_app.command("status")
+def gh_status():
+    """Show current GitHub authentication status."""
+    print(f"{BLUE}--- GitHub Authentication Status ---{NC}")
+
+    try:
+        gh_path = _find_executable("gh")
+    except FileNotFoundError:
+        print(f"{RED}Error: GitHub CLI (gh) is not installed.{NC}")
+        print(
+            f"Install it with: {YELLOW}brew install gh{NC} (Mac) or see https://cli.github.com"
+        )
+        sys.exit(1)
+
+    if _is_gh_authenticated():
+        user = _get_gh_user()
+        print(f"  Status: {GREEN}Authenticated{NC}")
+        print(f"  User: {GREEN}{user}{NC}")
+
+        # Show detailed status
+        print(f"\n{BLUE}Detailed status:{NC}")
+        _run_command([gh_path, "auth", "status"], check=False)
+    else:
+        print(f"  Status: {RED}Not authenticated{NC}")
+        print(f"\nTo authenticate, run:")
+        print(f"  {YELLOW}dh gh login{NC}")
+
+
+@gh_app.command("login")
+def gh_login():
+    """Authenticate with GitHub and configure git credential helper.
+
+    This command:
+    1. Authenticates with GitHub using device flow (works in headless environments)
+    2. Requests scopes: repo, read:org, workflow
+    3. Configures git to use the GitHub CLI for credential management
+    """
+    try:
+        gh_path = _find_executable("gh")
+    except FileNotFoundError:
+        print(f"{RED}Error: GitHub CLI (gh) is not installed.{NC}")
+        print(
+            f"Install it with: {YELLOW}brew install gh{NC} (Mac) or see https://cli.github.com"
+        )
+        sys.exit(1)
+
+    # Step 1: Authenticate with GitHub
+    print(f"{BLUE}Authenticating with GitHub...{NC}")
+    print(f"{YELLOW}Requesting scopes: {GITHUB_SCOPES}{NC}")
+    print(f"{YELLOW}Using protocol: {GITHUB_PROTOCOL}{NC}")
+    print()
+
+    login_cmd = [
+        gh_path,
+        "auth",
+        "login",
+        "--web",  # Use device flow (works in devcontainers)
+        "--git-protocol",
+        GITHUB_PROTOCOL,
+        "--scopes",
+        GITHUB_SCOPES,
+    ]
+
+    returncode, _, _ = _run_command(login_cmd, capture=False, check=False)
+
+    if returncode != 0:
+        print(f"\n{RED}Authentication failed. Please check the output above.{NC}")
+        sys.exit(1)
+
+    # Step 2: Configure git credential helper
+    print(f"\n{BLUE}Configuring git to use GitHub CLI for credentials...{NC}")
+    setup_cmd = [gh_path, "auth", "setup-git"]
+    setup_rc, _, setup_err = _run_command(setup_cmd, capture=True, check=False)
+
+    if setup_rc != 0:
+        print(
+            f"{YELLOW}Warning: Failed to configure git credential helper: {setup_err}{NC}"
+        )
+        print(f"You may need to run manually: {YELLOW}gh auth setup-git{NC}")
+    else:
+        print(f"{GREEN}Git credential helper configured.{NC}")
+
+    # Step 3: Show final status
+    print(f"\n{GREEN}GitHub authentication complete!{NC}")
+    print(f"\n{BLUE}--- Current Status ---{NC}")
+    gh_status()
+
+
+@gh_app.command("logout")
+def gh_logout():
+    """Log out from GitHub and clear credentials.
+
+    This removes the GitHub authentication token and unconfigures
+    the git credential helper.
+    """
+    try:
+        gh_path = _find_executable("gh")
+    except FileNotFoundError:
+        print(f"{RED}Error: GitHub CLI (gh) is not installed.{NC}")
+        sys.exit(1)
+
+    if not _is_gh_authenticated():
+        print(f"{YELLOW}Not currently authenticated with GitHub.{NC}")
+        return
+
+    print(f"{BLUE}Logging out from GitHub...{NC}")
+
+    # Log out from github.com
+    logout_cmd = [gh_path, "auth", "logout", "--hostname", "github.com"]
+    returncode, _, _ = _run_command(logout_cmd, capture=False, check=False)
+
+    if returncode != 0:
+        print(f"{RED}Logout may have failed. Check the output above.{NC}")
+        sys.exit(1)
+
+    print(f"\n{GREEN}Successfully logged out from GitHub.{NC}")
+    print(f"\n{BLUE}To log back in:{NC}")
+    print(f"  {YELLOW}dh gh login{NC}")

dayhoff_tools/cli/main.py

@@ -5,6 +5,7 @@ from importlib.metadata import PackageNotFoundError, version
 
 import typer
 from dayhoff_tools.cli.cloud_commands import aws_app, gcp_app
+from dayhoff_tools.cli.github_commands import gh_app
 from dayhoff_tools.cli.engine1 import engine_app, studio_app
 from dayhoff_tools.cli.utility_commands import (
     add_dependency,
@@ -67,6 +68,7 @@ app.command("wimport")(import_from_warehouse_typer)
 # Cloud commands
 app.add_typer(gcp_app, name="gcp", help="Manage GCP authentication and impersonation.")
 app.add_typer(aws_app, name="aws", help="Manage AWS SSO authentication.")
+app.add_typer(gh_app, name="gh", help="Manage GitHub authentication.")
 
 # Engine and Studio commands (original implementation)
 app.add_typer(engine_app, name="engine", help="Manage compute engines for development.")

{dayhoff_tools-1.13.13.dist-info → dayhoff_tools-1.13.14.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dayhoff-tools
-Version: 1.13.13
+Version: 1.13.14
 Summary: Common tools for all the repos at Dayhoff Labs
 Author: Daniel Martin-Alarcon
 Author-email: dma@dayhofflabs.com

{dayhoff_tools-1.13.13.dist-info → dayhoff_tools-1.13.14.dist-info}/RECORD

@@ -25,7 +25,8 @@ dayhoff_tools/cli/engines_studios/simulators/simulator_utils.py,sha256=HA08pIMJW
 dayhoff_tools/cli/engines_studios/simulators/studio_list_simulator.py,sha256=ntizeR0BJLdJOwCRBKPajc2xT-BL7SNnONxfgxXDgr8,11609
 dayhoff_tools/cli/engines_studios/simulators/studio_status_simulator.py,sha256=6WvpnRawJVaQf_H81zuR1_66igRRVxPxjAt8e69xjp4,5394
 dayhoff_tools/cli/engines_studios/studio_commands.py,sha256=4ul6i8HDHZTffavu1y_j4kwvsDNvjMvYMWbZGXN8nKY,25597
-dayhoff_tools/cli/main.py,sha256=0WfxPvlHNGkDxqkJJ0qbHNsoF5DXVznNCSQbv8L2-zk,7140
+dayhoff_tools/cli/github_commands.py,sha256=pfrxI68LObGm_gtPlQN-gHPahHV4l9k9T4GqO99NNL0,8948
+dayhoff_tools/cli/main.py,sha256=6DLwNscPJccv3-07vnOnwxz3Vgbl7lRazFenZ66mYls,7264
 dayhoff_tools/cli/swarm_commands.py,sha256=5EyKj8yietvT5lfoz8Zx0iQvVaNgc3SJX1z2zQR6o6M,5614
 dayhoff_tools/cli/utility_commands.py,sha256=e2P4dCCtoqMUGNyb0lFBZ6GZpl5Zslm1qqE5qIvsy38,50765
 dayhoff_tools/deployment/base.py,sha256=uZnFvnPQx6pH_HmJbdThweAs3BrxMaDohpE3iX_-yk4,18377
@@ -48,7 +49,7 @@ dayhoff_tools/intake/uniprot.py,sha256=BZYJQF63OtPcBBnQ7_P9gulxzJtqyorgyuDiPeOJq
 dayhoff_tools/logs.py,sha256=DKdeP0k0kliRcilwvX0mUB2eipO5BdWUeHwh-VnsICs,838
 dayhoff_tools/sqlite.py,sha256=jV55ikF8VpTfeQqqlHSbY8OgfyfHj8zgHNpZjBLos_E,18672
 dayhoff_tools/warehouse.py,sha256=UETBtZD3r7WgvURqfGbyHlT7cxoiVq8isjzMuerKw8I,24475
-dayhoff_tools-1.13.13.dist-info/METADATA,sha256=8KS0hvygpcFiLh-3K4VTQNvqORSmhPgCLeQyvcXWB5k,2981
-dayhoff_tools-1.13.13.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
-dayhoff_tools-1.13.13.dist-info/entry_points.txt,sha256=iAf4jteNqW3cJm6CO6czLxjW3vxYKsyGLZ8WGmxamSc,49
-dayhoff_tools-1.13.13.dist-info/RECORD,,
+dayhoff_tools-1.13.14.dist-info/METADATA,sha256=pIzquyAaZbv2V8ZCtD0j3B7EZgb9f_YwZDzIIbCr6pI,2981
+dayhoff_tools-1.13.14.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
+dayhoff_tools-1.13.14.dist-info/entry_points.txt,sha256=iAf4jteNqW3cJm6CO6czLxjW3vxYKsyGLZ8WGmxamSc,49
+dayhoff_tools-1.13.14.dist-info/RECORD,,