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Upload to Zenodo

Overview

Use upload_zenodo to publish CartLoader outputs — including PMTiles, decoded spatial factors, and the catalog — to a Zenodo deposition, either an existing one or a newly created draft. In catalog mode, files are pulled from catalog.yaml and grouped into cartload basics, cartload optional files (e.g., UMAP, alias), and additional basemaps (non-SGE PMTiles).

Requirements

  • A completed run of run_cartload2, which produces:
    • Rasterized SGE tiles
    • (Optional) Decoded spatial factor maps
    • (Optional) Joined molecule-factor outputs
    • (Optional) Cell assets
    • (Optional) Background assets, such as histology
    • A catalog file (catalog.yaml) summarizing the output structure and metadata
  • A Zenodo access token saved in a file (for API authentication).
  • (Optional) A Zenodo deposition ID to upload to an existing deposition.

Question

Actions

  • Upload files to a Zenodo deposition.
  • (Optional) Create a new deposition if no --zenodo-deposition-id is provided or --zenodo-deposition-id points to a published record.
  • (Optional) Fullfill or update metadata.

Example Usage

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cartloader upload_zenodo \
  --upload-method catalog \
  --in-dir /path/to/run_cartload2/output/directory \
  --zenodo-token /path/to/zenodo_token.txt \
  --title  "Title Info" \
  --creators "Creator Name" \
  --description "Description Info"
  • --upload-method catalog: Upload files defined in the catalog.
  • (Recommended) Provide metadata via --title, --creators, and --description.

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zenodo_deposition_id=DEPOSITION_ID                # replace with your deposition ID (published IDs get a new draft automatically)

cartloader upload_zenodo \
  --upload-method catalog \
  --in-dir /path/to/run_cartload2/output/directory \
  --zenodo-token /path/to/zenodo_token.txt \
  --zenodo-deposition-id ${zenodo_deposition_id}
- --upload-method catalog: Upload files defined in the catalog.

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cartloader upload_zenodo \
  --upload-method files \
  --in-dir /path/to/run_cartload2/output/directory \
  --files catalog.yaml genes_all.pmtiles some_factor.pmtiles \
  --zenodo-token /path/to/zenodo_token.txt \
  --zenodo-deposition-id ${zenodo_deposition_id}
- --upload-method files: Upload files defined in --files.

Parameters

Input Selection

  • --in-dir (str): Path to the directory containing run_cartload2 outputs.

  • --upload-method (str, default: all): Which files to upload.

    --upload-method Options

    • all: Upload every file in --in-dir,
    • catalog: Upload files listed in a catalog.yaml,
    • files: Upload only the filenames provided via --files.

  • --files FILE [FILE ...]: Filenames to upload (relative to --in-dir or absolute). Use with --upload-method files.

  • --catalog-yaml (str): Path to a catalog.yaml. Required if --upload-method catalog. If omitted, uses <in-dir>/catalog.yaml.

Zenodo Configuration

  • --zenodo-token (str): Path to your Zenodo access token file.
  • --zenodo-deposition-id (str): Zenodo deposition ID to upload files to. If the ID is for a published deposition, a new draft version is created automatically. If omitted, a new draft deposition is created.
  • --publish (flag): Publish the deposition automatically after upload. Recommended to publish manually after reviewing via the Zenodo web interface.

Zenodo Metadata

  • --title (str): Title for Zenodo deposition. Required only when creating a new deposition (i.e., if --zenodo-deposition-id is not provided or the existing deposition lacks these fields).
  • --upload-type (str, default: dataset): One of: dataset, software, publication, poster, presentation, image, video, lesson, other.
  • --creators (list of str): Creators in "Lastname, Firstname" format.

Behavior Flags

  • --dry-run (flag): Simulate and print operations; do not execute uploads.
  • --restart (flag): Re-upload overlapping files instead of skipping existing ones.

Output

  • Files uploaded to the Zenodo deposition (existing or newly created draft).
  • A cartload.zenodo.done marker file when --upload-method catalog completes the basics stage.