pluot-reference-materials

The (git-ignored) references directory (at the root of the repo) is intended as a space to temporarily place read-only copies of code or documentation files/folders. These copies allow us to reference the logic or specifications of dependencies, related tools, or data formats by reading local files within the references directory.

Pulling in a new reference

If the user asks you to pull in a new reference material/document, they will specify a URL to a file or github repository. If the user specifies a github repository, use degit to pull in a lightweight copy of the repo or a user-specified subset of it (this avoids pulling in the full repo commit history). Store the files/folders in a new subdirectory of references.

Examples

• The AnnData on-disk format: https://github.com/scverse/anndata/blob/main/docs/fileformat-prose.md
• The SpatialData design document: https://github.com/scverse/spatialdata/blob/main/docs/design_doc.md
• The OME-NGFF specification and RFCs: https://github.com/ome/ngff
• OME-Zarr RFC-5 transformations: https://github.com/clbarnes/ome_zarr_transformations_conformance
• Vitessce Bitmask Layer files:
  • https://github.com/vitessce/vitessce/blob/main/packages/gl/src/BitmaskLayerBeta.js
  • https://github.com/vitessce/vitessce/blob/main/packages/gl/src/bitmask-layer-beta-shaders.js
  • https://github.com/vitessce/vitessce/blob/main/packages/gl/src/bitmask-utils.js
  • https://github.com/vitessce/vitessce/blob/main/packages/gl/src/bitmask-utils.test.js
• AnnData.js handling of sparse arrays: https://github.com/ilan-gold/anndata.js/blob/main/src/sparse_array.ts
• Vitessce handling of sparse arrays: https://github.com/vitessce/vitessce/blob/main/packages/file-types/zarr/src/anndata-loaders/ObsFeatureMatrixAnndataLoader.js
• D3 scales: https://github.com/d3/d3-scale
• D3 axes: https://github.com/d3/d3-axis