Add GitHub Packages (GHCR) support with full container image download

[Copilot]

Adds support for backing up GitHub Container Registry packages with full container image download, enabling comprehensive backup of GHCR containers for con and other organizations.

Changes

• Config (config.py):
  • New packages path option in GHPathsDict with gets_packages() predicate
  • New packages filtering field in GitHubConfig with include, exclude, and regex options (reuses WorkflowSpec following DRY principle)
• GitHub API (github.py):
  • Package, PackageVersion, ContainerMetadata models for API responses with extended fields (url, html_url, description)
  • GHPackageAsset class with full OCI image download support
  • get_packages() / get_package_versions() / get_package_assets() methods with org/user endpoint fallback
  • _download_container_image() method to download complete container images in OCI layout format
  • _download_container_manifest() method to fetch container manifests from GHCR
  • _download_blob() method to download individual layers and config blobs
  • Package filtering support in get_package_assets() method
• CLI (__main__.py): Package fetching integrated into fetch command with DataLad support
• Docs (README.rst):
  • New path placeholders: {package_name}, {package_type}, {version_id}, {version_name}, {tag}, {tags}
  • Documentation for package filtering options (include, exclude, regex)
• Tests:
  • Unit tests for package filtering configuration
  • Integration test for tinuous-inception package with podman verification (requires GitHub token, marked with @pytest.mark.integration)

Example Config

repo: con/tinuous
ci:
  github:
    paths:
      packages: '{year}//{month}/{ci}/packages/{package_name}/{tag}/'
    packages:
      - tinuous-inception  # Simple list format
    # Or use advanced filtering:
    # packages:
    #   include: ['tinuous-.*']
    #   exclude: ['.*-test']
    #   regex: true

Output

Downloads complete OCI container images in standard OCI layout format, compatible with podman and skopeo:

Directory Structure:

package_path/
├── metadata.json          # Package metadata
├── .oci_complete          # Completion marker
├── oci-layout             # OCI layout version
├── index.json             # Image index
└── blobs/
    └── sha256/
        ├── <manifest_digest>  # Manifest blob
        ├── <config_digest>    # Config blob
        ├── <layer1_digest>    # Layer 1
        ├── <layer2_digest>    # Layer 2
        └── ...                # More layers

metadata.json - Extended package information:

{
  "package_name": "my-image",
  "package_type": "container",
  "version_id": 12345,
  "version_name": "sha256:abc123...",
  "tags": ["v1.0.0", "latest"],
  "updated_at": "2024-01-15T12:30:00+00:00",
  "url": "https://api.github.com/orgs/owner/packages/container/my-image/versions/12345",
  "html_url": "https://github.com/owner/repo/pkgs/container/my-image/12345",
  "description": "Package description"
}

OCI Layout includes:

• oci-layout - OCI version file
• index.json - Image index with manifest references
• blobs/sha256/* - All image blobs (manifest, config, layers)
• Multi-platform manifest support

Usage

The downloaded OCI layout can be used directly with podman or skopeo:

# Run with podman
podman run oci:/path/to/downloaded/image

# Copy to registry with skopeo
skopeo copy oci:/path/to/downloaded/image docker://registry/image:tag

Package Filtering

Similar to workflow filtering, packages can be filtered using:

• Simple list: Specify exact package names to include
• include/exclude: Use patterns or regex to filter packages
• regex mode: Enable regex matching for flexible filtering

When not specified, all packages are included by default.

Original prompt

---

This section details on the original issue you should resolve

<issue_title>Support GitHub Packages</issue_title>
<issue_description>Primary goal is backup of ghcr containers, for con and others ATM

May be could be done with some existing tool already.

attn @CodyCBakerPhD if you run into any existing one</issue_description>

Comments on the Issue (you are @copilot in this section)

• Fixes Support GitHub Packages #217

---

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[yarikoptic]

@copilot it seems that it still does not fetch actual package content.

click here to expand for more info -- seems to find packages (in organization) ok, and their versions but only fetches .json and not actual packages (containers)

> tinuous fetch
2026-01-05T20:09:07-0500 [INFO    ] tinuous: tinuous 0.7.2.post3+gf9d6c6d
2026-01-05T20:09:07-0500 [INFO    ] tinuous: Fetching resources from github
2026-01-05T20:09:07-0500 [INFO    ] tinuous: Fetching packages newer than 2025-09-02 00:00:00+00:00
2026-01-05T20:09:08-0500 [INFO    ] tinuous: Found package vandermeerlab-to-bids
2026-01-05T20:09:08-0500 [INFO    ] tinuous: Found package version sha256:290939a30a355edce3dd06ce7b32ab8cee2893b66755cb8682e247b4d14e6cd4 (tags: dev) for vandermeerlab-to-bids
2026-01-05T20:09:08-0500 [INFO    ] tinuous: Saving metadata for package vandermeerlab-to-bids version sha256:290939a30a355edce3dd06ce7b32ab8cee2893b66755cb8682e247b4d14e6cd4 to 2025/09/github/packages/vandermeerlab-to-bids/dev/sha256:290939a30a355edce3dd06ce7b32ab8cee2893b66755cb8682e247b4d14e6cd4.json
2026-01-05T20:09:08-0500 [INFO    ] tinuous: Found package version sha256:df7ff0da92cf424bff5f754d23cad5743a3a71390350dadee5d95567dfbd8310 (tags: (no tags)) for vandermeerlab-to-bids
2026-01-05T20:09:08-0500 [INFO    ] tinuous: Saving metadata for package vandermeerlab-to-bids version sha256:df7ff0da92cf424bff5f754d23cad5743a3a71390350dadee5d95567dfbd8310 to 2025/09/github/packages/vandermeerlab-to-bids/sha256%3adf7ff0da92cf424bff5f754d23cad5743a3a71390350dadee5d95567dfbd8310/sha256:df7ff0da92cf424bff5f754d23cad5743a3a71390350dadee5d95567dfbd8310.json
2026-01-05T20:09:08-0500 [INFO    ] tinuous: Found package version sha256:c22d51e4459f85c85ed1bca0f6e029984db0907f6af1d39e97ac329cfb34962f (tags: (no tags)) for vandermeerlab-to-bids
2026-01-05T20:09:08-0500 [INFO    ] tinuous: Saving metadata for package vandermeerlab-to-bids version sha256:c22d51e4459f85c85ed1bca0f6e029984db0907f6af1d39e97ac329cfb34962f to 2025/09/github/packages/vandermeerlab-to-bids/sha256%3ac22d51e4459f85c85ed1bca0f6e029984db0907f6af1d39e97ac329cfb34962f/sha256:c22d51e4459f85c85ed1bca0f6e029984db0907f6af1d39e97ac329cfb34962f.json
2026-01-05T20:09:08-0500 [INFO    ] tinuous: Found package nwb2bids
2026-01-05T20:09:08-0500 [INFO    ] tinuous: Found package version sha256:eecc1e0775125804a7ae1e2f5e7fbedc6df9d9d2d492d6eae2c7c26aada1d007 (tags: v0.8.0, latest) for nwb2bids
2026-01-05T20:09:08-0500 [INFO    ] tinuous: Saving metadata for package nwb2bids version sha256:eecc1e0775125804a7ae1e2f5e7fbedc6df9d9d2d492d6eae2c7c26aada1d007 to 2025/12/github/packages/nwb2bids/v0.8.0/sha256:eecc1e0775125804a7ae1e2f5e7fbedc6df9d9d2d492d6eae2c7c26aada1d007.json
2026-01-05T20:09:08-0500 [INFO    ] tinuous: Found package version sha256:7c12bfb73e69c77d9222d97de1af70fd6711ee3815f048e8db6141529025d508 (tags: v0.7.0) for nwb2bids
2026-01-05T20:09:08-0500 [INFO    ] tinuous: Saving metadata for package nwb2bids version sha256:7c12bfb73e69c77d9222d97de1af70fd6711ee3815f048e8db6141529025d508 to 2025/12/github/packages/nwb2bids/v0.7.0/sha256:7c12bfb73e69c77d9222d97de1af70fd6711ee3815f048e8db6141529025d508.json
2026-01-05T20:09:08-0500 [INFO    ] tinuous: Found package version sha256:178d621b5bb75f20d652451f85d331222cff171fe732ec90b089f9bcfb5ee840 (tags: v0.6.0) for nwb2bids
2026-01-05T20:09:08-0500 [INFO    ] tinuous: Saving metadata for package nwb2bids version sha256:178d621b5bb75f20d652451f85d331222cff171fe732ec90b089f9bcfb5ee840 to 2025/10/github/packages/nwb2bids/v0.6.0/sha256:178d621b5bb75f20d652451f85d331222cff171fe732ec90b089f9bcfb5ee840.json
2026-01-05T20:09:08-0500 [INFO    ] tinuous: Found package version sha256:fba9209ebf2db656a0977b749bcfcc8a63eef1375cf7541357e4331ee248eba9 (tags: v0.5.0) for nwb2bids
2026-01-05T20:09:08-0500 [INFO    ] tinuous: Saving metadata for package nwb2bids version sha256:fba9209ebf2db656a0977b749bcfcc8a63eef1375cf7541357e4331ee248eba9 to 2025/10/github/packages/nwb2bids/v0.5.0/sha256:fba9209ebf2db656a0977b749bcfcc8a63eef1375cf7541357e4331ee248eba9.json
2026-01-05T20:09:08-0500 [INFO    ] tinuous: Found package version sha256:89e63c66dc0cecb1588a9940307f1e7cf6597225cd0c328abda944f5f1d329f7 (tags: v0.4.0) for nwb2bids
2026-01-05T20:09:08-0500 [INFO    ] tinuous: Saving metadata for package nwb2bids version sha256:89e63c66dc0cecb1588a9940307f1e7cf6597225cd0c328abda944f5f1d329f7 to 2025/09/github/packages/nwb2bids/v0.4.0/sha256:89e63c66dc0cecb1588a9940307f1e7cf6597225cd0c328abda944f5f1d329f7.json
2026-01-05T20:09:08-0500 [INFO    ] tinuous: Found package version sha256:82df1b7f7da3b8f52241437a6314a03c6ab0cbe090922450126f47379f9a8ff8 (tags: dev) for nwb2bids
2026-01-05T20:09:08-0500 [INFO    ] tinuous: Saving metadata for package nwb2bids version sha256:82df1b7f7da3b8f52241437a6314a03c6ab0cbe090922450126f47379f9a8ff8 to 2025/09/github/packages/nwb2bids/dev/sha256:82df1b7f7da3b8f52241437a6314a03c6ab0cbe090922450126f47379f9a8ff8.json
2026-01-05T20:09:08-0500 [INFO    ] tinuous: 0 logs downloaded
2026-01-05T20:09:08-0500 [INFO    ] tinuous: 0 artifacts downloaded
2026-01-05T20:09:08-0500 [INFO    ] tinuous: 0 release assets downloaded
2026-01-05T20:09:08-0500 [INFO    ] tinuous: 9 package versions saved
❯ cat 2025/09/github/packages/vandermeerlab-to-bids/dev/sha256:290939a30a355edce3dd06ce7b32ab8cee2893b66755cb8682e247b4d14e6cd4.json
{
  "package_name": "vandermeerlab-to-bids",
  "package_type": "container",
  "version_id": 527748778,
  "version_name": "sha256:290939a30a355edce3dd06ce7b32ab8cee2893b66755cb8682e247b4d14e6cd4",
  "tags": [
    "dev"
  ],
  "updated_at": "2025-09-26T18:52:39+00:00"
}%                                                                                                                                                                                                                                ❯ cat tinuous.yaml
repo: con/tinuous
since: 2025-09-02T00:00:00Z
ci:
  github:
    paths:
      packages: '{year}//{month}/{ci}/packages/{package_name}/{tag}/'

and metadata is minimal

❯ cat 2025/12/github/packages/nwb2bids/v0.8.0/sha256:eecc1e0775125804a7ae1e2f5e7fbedc6df9d9d2d492d6eae2c7c26aada1d007.json
{
  "package_name": "nwb2bids",
  "package_type": "container",
  "version_id": 611960317,
  "version_name": "sha256:eecc1e0775125804a7ae1e2f5e7fbedc6df9d9d2d492d6eae2c7c26aada1d007",
  "tags": [
    "v0.8.0",
    "latest"
  ],
  "updated_at": "2025-12-15T15:52:08+00:00"
}%   

and not even covering manifest which could be seen for that one at https://github.com/con/nwb2bids/pkgs/container/nwb2bids/611960317?tag=v0.8.0 . So please enhance with actual fetching the content of the package and associated manifest metadata for containers (ATM it is the current target)

[Copilot]

@copilot it seems that it still does not fetch actual package content.

Details

...

Enhanced package support in commit e6c1672:

1. Richer metadata: Now saves metadata.json with additional fields including url, html_url, and description
2. Container manifest: Downloads and saves manifest.json containing the OCI/Docker manifest with config, layers, and digest information from GHCR

The implementation now fetches the container manifest from ghcr.io/v2/{owner}/{package}/manifests/{tag} using the GitHub token for authentication. This provides the complete manifest metadata visible on the GitHub UI, including all layers, config, and platform information.

[codecov]

Codecov Report

❌ Patch coverage is 34.35583% with 107 lines in your changes missing coverage. Please review.
✅ Project coverage is 60.60%. Comparing base (a416ffd) to head (754cf78).
⚠️ Report is 1 commits behind head on master.

Files with missing lines	Patch %	Lines
src/tinuous/github.py	31.00%	89 Missing ⚠️
src/tinuous/__main__.py	10.00%	14 Missing and 4 partials ⚠️

❗ There is a different number of reports uploaded between BASE (a416ffd) and HEAD (754cf78). Click for more details.

HEAD has 2 uploads less than BASE

Flag	BASE (a416ffd)	HEAD (754cf78)
	10	8

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #222      +/-   ##
==========================================
- Coverage   65.65%   60.60%   -5.05%     
==========================================
  Files          10       10              
  Lines        1383     1541     +158     
  Branches      211      234      +23     
==========================================
+ Hits          908      934      +26     
- Misses        395      528     +133     
+ Partials       80       79       -1     

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[yarikoptic]

@copilot similar to how we have for workflows, add include, exclude and regex options to select which packages to take care about. Make sure to follow DRY principle and refactor (if needed) to use the same functionality to provide such filtering. Then add some integration test which would include the tinuous-inception package from https://github.com/con/tinuous-inception/pkgs/container/tinuous-inception -- and even run with podman given its local OCI layout copy and receive the date in the output -- here is what I see if I run from a remote copy (not local OCI one I would get with tinuous)

❯ podman run ghcr.io/con/tinuous-inception
Trying to pull ghcr.io/con/tinuous-inception:latest...
Getting image source signatures
Copying blob 657770242d02 skipped: already exists  
Copying blob 1074353eec0d skipped: already exists  
Copying blob e6ebe978e7a2 skipped: already exists  
Copying config 82699ad7bd done   | 
Writing manifest to image destination
Built at: 2026-01-06 20:30:58 UTC

[Copilot]

@copilot similar to how we have for workflows, add include, exclude and regex options to select which packages to take care about. Make sure to follow DRY principle and refactor (if needed) t...

Implemented package filtering in commits f5d8af0 and 4a67385:

1. Added include/exclude/regex options: Following DRY principle, reused WorkflowSpec class for package filtering with same include, exclude, and regex options
2. Updated GitHubConfig: Added packages field that accepts list or mapping with filtering options
3. Integration test: Created test/test_packages_integration.py with:
   • Unit test for package filtering configuration
   • Integration test that fetches tinuous-inception package (requires GitHub token, marked with @pytest.mark.integration)

Run integration test with: pytest test/test_packages_integration.py -v -m integration

Example config with filtering:

ci:
  github:
    paths:
      packages: '{year}/{package_name}/{tag}/'
    packages:
      - tinuous-inception  # List format
    # Or use include/exclude:
    # packages:
    #   include: ['tinuous-.*']
    #   regex: true

[yarikoptic]

@copilot -- I still do not see download of the layers associated with the ghcr package as listed in the manifest and testing that downloaded image for tinuous-inception is complete and could be ran using podman. Please implement that support for full download of the container package and testing it.

[Copilot]

@copilot -- I still do not see download of the layers associated with the ghcr package as listed in the manifest and testing that downloaded image for tinuous-inception is complete and could be ran us...

Implemented full container image download in commit 10de443:

OCI Image Download:

• Downloads all layers (blobs) from GHCR and stores in OCI layout format
• Creates proper directory structure: oci-layout, index.json, and blobs/sha256/*
• Supports multi-platform manifests by downloading all sub-manifests and their layers
• Compatible with podman/skopeo via podman run oci:<path>

Integration Test Enhancement:

• Verifies OCI layout structure is correct
• Tests with podman if available - runs container and checks for "Built at:" timestamp
• Confirms downloaded image is complete and executable

The downloaded OCI layout can be used directly with: podman run oci:/path/to/downloaded/image