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fix: virtual subdirectory deps marked as orphaned, skipping instruction processing #100

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Merged
danielmeppiel merged 4 commits into from
Feb 24, 2026
Merged

fix: virtual subdirectory deps marked as orphaned, skipping instruction processing #100

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5108201
fix: virtual subdirectory deps marked as orphaned, skipping instructi…
sergio-sisternes-epam Feb 24, 2026
ab5c66d
fix: address PR #100 review comments
sergio-sisternes-epam Feb 24, 2026
a700499
fix: prune and deps list handle virtual subdirectory packages
sergio-sisternes-epam Feb 24, 2026
bede7f9
fix: preserve ADO source label in rglob-based deps scanner
sergio-sisternes-epam Feb 24, 2026
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66 changes: 30 additions & 36 deletions src/apm_cli/cli.py
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Original file line number Diff line number Diff line change
Expand Up @@ -762,57 +762,51 @@ def prune(ctx, dry_run):
for dep in declared_deps:
repo_parts = dep.repo_url.split("/")
if dep.is_virtual:
# Virtual package: include full path based on platform
package_name = dep.get_virtual_package_name()
if dep.is_azure_devops() and len(repo_parts) >= 3:
# ADO structure: org/project/virtual-pkg-name
expected_installed.add(
f"{repo_parts[0]}/{repo_parts[1]}/{package_name}"
)
elif len(repo_parts) >= 2:
# GitHub structure: owner/virtual-pkg-name
expected_installed.add(f"{repo_parts[0]}/{package_name}")
if dep.is_virtual_subdirectory() and dep.virtual_path:
# Virtual subdirectory packages keep natural path structure.
if dep.is_azure_devops() and len(repo_parts) >= 3:
expected_installed.add(
f"{repo_parts[0]}/{repo_parts[1]}/{repo_parts[2]}/{dep.virtual_path}"
)
elif len(repo_parts) >= 2:
expected_installed.add(
f"{repo_parts[0]}/{repo_parts[1]}/{dep.virtual_path}"
)
else:
# Virtual file/collection packages are flattened.
package_name = dep.get_virtual_package_name()
if dep.is_azure_devops() and len(repo_parts) >= 3:
expected_installed.add(
f"{repo_parts[0]}/{repo_parts[1]}/{package_name}"
)
elif len(repo_parts) >= 2:
expected_installed.add(f"{repo_parts[0]}/{package_name}")
else:
# Regular package: use full repo_url path
if dep.is_azure_devops() and len(repo_parts) >= 3:
# ADO structure: org/project/repo
expected_installed.add(
f"{repo_parts[0]}/{repo_parts[1]}/{repo_parts[2]}"
)
elif len(repo_parts) >= 2:
# GitHub structure: owner/repo
expected_installed.add(f"{repo_parts[0]}/{repo_parts[1]}")
except Exception as e:
_rich_error(f"Failed to parse apm.yml: {e}")
sys.exit(1)

# Find installed packages in apm_modules/ (now org-namespaced)
# GitHub: apm_modules/owner/repo (2 levels)
# Azure DevOps: apm_modules/org/project/repo (3 levels)
# Walks the tree to find directories containing apm.yml or .apm,
# handling GitHub (2-level), ADO (3-level), and subdirectory (4+ level) packages.
installed_packages = {} # {"path": "display_name"}
if apm_modules_dir.exists():
for level1_dir in apm_modules_dir.iterdir():
if level1_dir.is_dir() and not level1_dir.name.startswith("."):
for level2_dir in level1_dir.iterdir():
if level2_dir.is_dir() and not level2_dir.name.startswith("."):
# Check if level2 has apm.yml (GitHub 2-level structure)
if (level2_dir / "apm.yml").exists() or (
level2_dir / ".apm"
).exists():
path_key = f"{level1_dir.name}/{level2_dir.name}"
installed_packages[path_key] = path_key
else:
# Check for ADO 3-level structure
for level3_dir in level2_dir.iterdir():
if (
level3_dir.is_dir()
and not level3_dir.name.startswith(".")
):
if (level3_dir / "apm.yml").exists() or (
level3_dir / ".apm"
).exists():
path_key = f"{level1_dir.name}/{level2_dir.name}/{level3_dir.name}"
installed_packages[path_key] = path_key
for candidate in apm_modules_dir.rglob("*"):
if not candidate.is_dir() or candidate.name.startswith("."):
continue
if not ((candidate / "apm.yml").exists() or (candidate / ".apm").exists()):
continue
rel_parts = candidate.relative_to(apm_modules_dir).parts
if len(rel_parts) >= 2:
path_key = "/".join(rel_parts)
installed_packages[path_key] = path_key

# Find orphaned packages (installed but not declared)
orphaned_packages = {}
Expand Down
124 changes: 56 additions & 68 deletions src/apm_cli/commands/deps.py
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Original file line number Diff line number Diff line change
Expand Up @@ -52,94 +52,82 @@ def list_packages():
# Load project dependencies to check for orphaned packages
# GitHub: owner/repo or owner/virtual-pkg-name (2 levels)
# Azure DevOps: org/project/repo or org/project/virtual-pkg-name (3 levels)
declared_deps = set()
declared_sources = {} # dep_path → 'github' | 'azure-devops'
try:
apm_yml_path = project_root / "apm.yml"
if apm_yml_path.exists():
project_package = APMPackage.from_apm_yml(apm_yml_path)
for dep in project_package.get_apm_dependencies():
# Build the expected installed package name
repo_parts = dep.repo_url.split('/')
source = 'azure-devops' if dep.is_azure_devops() else 'github'
if dep.is_virtual:
# Virtual package: include full path based on platform
package_name = dep.get_virtual_package_name()
if dep.is_azure_devops() and len(repo_parts) >= 3:
# ADO structure: org/project/virtual-pkg-name
declared_deps.add(f"{repo_parts[0]}/{repo_parts[1]}/{package_name}")
elif len(repo_parts) >= 2:
# GitHub structure: owner/virtual-pkg-name
declared_deps.add(f"{repo_parts[0]}/{package_name}")
if dep.is_virtual_subdirectory() and dep.virtual_path:
# Virtual subdirectory packages keep natural path structure.
# GitHub: owner/repo/subdir
# ADO: org/project/repo/subdir
if dep.is_azure_devops() and len(repo_parts) >= 3:
declared_sources[
f"{repo_parts[0]}/{repo_parts[1]}/{repo_parts[2]}/{dep.virtual_path}"
] = source
elif len(repo_parts) >= 2:
declared_sources[
f"{repo_parts[0]}/{repo_parts[1]}/{dep.virtual_path}"
] = source
else:
# Virtual file/collection packages are flattened.
package_name = dep.get_virtual_package_name()
if dep.is_azure_devops() and len(repo_parts) >= 3:
# ADO structure: org/project/virtual-pkg-name
declared_sources[f"{repo_parts[0]}/{repo_parts[1]}/{package_name}"] = source
elif len(repo_parts) >= 2:
# GitHub structure: owner/virtual-pkg-name
declared_sources[f"{repo_parts[0]}/{package_name}"] = source
else:
# Regular package: use full repo_url path
if dep.is_azure_devops() and len(repo_parts) >= 3:
# ADO structure: org/project/repo
declared_deps.add(f"{repo_parts[0]}/{repo_parts[1]}/{repo_parts[2]}")
declared_sources[f"{repo_parts[0]}/{repo_parts[1]}/{repo_parts[2]}"] = source
elif len(repo_parts) >= 2:
# GitHub structure: owner/repo
declared_deps.add(f"{repo_parts[0]}/{repo_parts[1]}")
declared_sources[f"{repo_parts[0]}/{repo_parts[1]}"] = source
except Exception:
pass # Continue without orphan detection if apm.yml parsing fails

# Scan for installed packages in org-namespaced structure
# GitHub: apm_modules/owner/repo (2 levels)
# Azure DevOps: apm_modules/org/project/repo (3 levels)
# Walks the tree to find directories containing apm.yml,
# handling GitHub (2-level), ADO (3-level), and subdirectory (4+ level) packages.
installed_packages = []
orphaned_packages = []
for level1_dir in apm_modules_path.iterdir():
if level1_dir.is_dir() and not level1_dir.name.startswith('.'):
for level2_dir in level1_dir.iterdir():
if level2_dir.is_dir() and not level2_dir.name.startswith('.'):
# Check if level2 has apm.yml (GitHub 2-level structure)
apm_yml_path = level2_dir / "apm.yml"
if apm_yml_path.exists():
try:
# GitHub 2-level: org/repo format
org_repo_name = f"{level1_dir.name}/{level2_dir.name}"
package = APMPackage.from_apm_yml(apm_yml_path)
context_count, workflow_count = _count_package_files(level2_dir)

is_orphaned = org_repo_name not in declared_deps
if is_orphaned:
orphaned_packages.append(org_repo_name)

installed_packages.append({
'name': org_repo_name,
'version': package.version or 'unknown',
'source': 'orphaned' if is_orphaned else 'github',
'context': context_count,
'workflows': workflow_count,
'path': str(level2_dir),
'is_orphaned': is_orphaned
})
except Exception as e:
click.echo(f"⚠️ Warning: Failed to read package {level1_dir.name}/{level2_dir.name}: {e}")
else:
# Check for ADO 3-level structure: org/project/repo
for level3_dir in level2_dir.iterdir():
if level3_dir.is_dir() and not level3_dir.name.startswith('.'):
apm_yml_path = level3_dir / "apm.yml"
if apm_yml_path.exists():
try:
# ADO 3-level: org/project/repo format
org_repo_name = f"{level1_dir.name}/{level2_dir.name}/{level3_dir.name}"
package = APMPackage.from_apm_yml(apm_yml_path)
context_count, workflow_count = _count_package_files(level3_dir)

is_orphaned = org_repo_name not in declared_deps
if is_orphaned:
orphaned_packages.append(org_repo_name)

installed_packages.append({
'name': org_repo_name,
'version': package.version or 'unknown',
'source': 'orphaned' if is_orphaned else 'azure-devops',
'context': context_count,
'workflows': workflow_count,
'path': str(level3_dir),
'is_orphaned': is_orphaned
})
except Exception as e:
click.echo(f"⚠️ Warning: Failed to read package {level1_dir.name}/{level2_dir.name}/{level3_dir.name}: {e}")
for candidate in apm_modules_path.rglob("*"):
if not candidate.is_dir() or candidate.name.startswith('.'):
continue
apm_yml_path = candidate / "apm.yml"
if not apm_yml_path.exists():
continue
rel_parts = candidate.relative_to(apm_modules_path).parts
if len(rel_parts) < 2:
continue
org_repo_name = "/".join(rel_parts)
try:
package = APMPackage.from_apm_yml(apm_yml_path)
context_count, workflow_count = _count_package_files(candidate)

is_orphaned = org_repo_name not in declared_sources
if is_orphaned:
orphaned_packages.append(org_repo_name)

installed_packages.append({
'name': org_repo_name,
'version': package.version or 'unknown',
'source': 'orphaned' if is_orphaned else declared_sources.get(org_repo_name, 'github'),
'context': context_count,
'workflows': workflow_count,
'path': str(candidate),
'is_orphaned': is_orphaned
})
except Exception as e:
click.echo(f"⚠️ Warning: Failed to read package {org_repo_name}: {e}")

if not installed_packages:
if has_rich:
Expand Down
53 changes: 30 additions & 23 deletions src/apm_cli/primitives/discovery.py
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Original file line number Diff line number Diff line change
Expand Up @@ -171,19 +171,12 @@ def scan_dependency_primitives(base_dir: str, collection: PrimitiveCollection) -

# Process dependencies in declaration order
for dep_name in dependency_order:
# Handle org-namespaced structure
# Join all path parts to handle variable-length paths:
# GitHub: "owner/repo" (2 parts)
# Azure DevOps: "org/project/repo" (3 parts)
# Virtual subdirectory: "owner/repo/subdir" or deeper (3+ parts)
parts = dep_name.split("/")
if len(parts) >= 3:
# ADO structure: apm_modules/org/project/repo
dep_path = apm_modules_path / parts[0] / parts[1] / parts[2]
elif len(parts) == 2:
# GitHub structure: apm_modules/owner/repo
dep_path = apm_modules_path / parts[0] / parts[1]
else:
# Fallback for non-namespaced dependencies
dep_path = apm_modules_path / dep_name
dep_path = apm_modules_path.joinpath(*parts)

if dep_path.exists() and dep_path.is_dir():
scan_directory_with_source(dep_path, collection, source=f"dependency:{dep_name}")
Expand Down Expand Up @@ -211,26 +204,40 @@ def get_dependency_declaration_order(base_dir: str) -> List[str]:
apm_dependencies = package.get_apm_dependencies()

# Extract installed paths from dependency references
# Virtual packages use get_virtual_package_name() for the final directory component
# Virtual file/collection packages use get_virtual_package_name() (flattened),
# while virtual subdirectory packages use natural repo/subdir paths.
dependency_names = []
for dep in apm_dependencies:
if dep.alias:
dependency_names.append(dep.alias)
elif dep.is_virtual:
# Virtual packages: construct path with virtual package name
# GitHub: owner/virtual-pkg-name
# ADO: org/project/virtual-pkg-name
repo_parts = dep.repo_url.split("/")
virtual_name = dep.get_virtual_package_name()
if dep.is_azure_devops() and len(repo_parts) >= 3:
# ADO structure: org/project/virtual-pkg-name
dependency_names.append(f"{repo_parts[0]}/{repo_parts[1]}/{virtual_name}")
elif len(repo_parts) >= 2:
# GitHub structure: owner/virtual-pkg-name
dependency_names.append(f"{repo_parts[0]}/{virtual_name}")

if dep.is_virtual_subdirectory() and dep.virtual_path:
# Virtual subdirectory packages keep natural path structure.
# GitHub: owner/repo/subdir
# ADO: org/project/repo/subdir
if dep.is_azure_devops() and len(repo_parts) >= 3:
dependency_names.append(
f"{repo_parts[0]}/{repo_parts[1]}/{repo_parts[2]}/{dep.virtual_path}"
)
elif len(repo_parts) >= 2:
dependency_names.append(
f"{repo_parts[0]}/{repo_parts[1]}/{dep.virtual_path}"
)
else:
dependency_names.append(dep.virtual_path)
else:
# Fallback
dependency_names.append(virtual_name)
# Virtual file/collection packages are flattened by package name.
# GitHub: owner/virtual-pkg-name
# ADO: org/project/virtual-pkg-name
virtual_name = dep.get_virtual_package_name()
if dep.is_azure_devops() and len(repo_parts) >= 3:
dependency_names.append(f"{repo_parts[0]}/{repo_parts[1]}/{virtual_name}")
elif len(repo_parts) >= 2:
dependency_names.append(f"{repo_parts[0]}/{virtual_name}")
else:
dependency_names.append(virtual_name)
else:
# Regular packages: use full org/repo path
# This matches our org-namespaced directory structure
Expand Down
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