Make some Experiment/Query classes abstract #244
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{experiment,query}.py classes abstract79cb3c2 to
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I pushed one more commit, explicitly tagging @jp-dark had suggested using |
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@ryan-williams I think the suggestion has merit but I'd prefer to take it as follow-on work and not let it block this current PR. |
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ryan-williams
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Jan 27, 2025
`EagerIterator` was moved from `somacore` to `tiledbsoma` in single-cell-data/SOMA#244 / single-cell-data/TileDB-SOMA#3307 (released 1.0.24 / 1.15.0). THis `import` shim helps us support versions before and since those.
ryan-williams
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Feb 11, 2025
…www` builds (#26) * Rename `{EAQ,Batch}Iterable` * Add `EagerIterator` shim `EagerIterator` was moved from `somacore` to `tiledbsoma` in single-cell-data/SOMA#244 / single-cell-data/TileDB-SOMA#3307 (released 1.0.24 / 1.15.0). THis `import` shim helps us support versions before and since those. * More descriptive test var names * rm `IterDataPipe` * Rename: `Experiment{AxisQueryIterable,}Dataset` * Move batch-"squeeze" logic down to `BatchIterable` This makes `ExperimentDataset` a pure pass-through wrapper around `BatchIterable`, in preparation for folding the latter intothe former. * Fold `BatchIterable` into `ExperimentDataset` * Rename kwarg: `{X,layer}_name` * Require `io_batch_size % shuffle_chunk_size == 0` * More consistent kwarg ordering * `parametrize("use_eager_fetch")` * `tests._utils.parametrize` * Add space to `# type: ignore`s * Add `docs/`: Sphinx/RTD build * Add `www/`: shuffling simulation - Vite app, builds under `www/dist/shuffle/` - `make dist` (under `docs/`) builds Sphix/RTD site (`make html`), copies it to `www/dist/`, and builds Vite app - `ghp.yml` GHA uploads combined build to GHP * Update README, CHANGELOG * cr: notebook copy tweak https://github.com/single-cell-data/TileDB-SOMA-ML/pull/26/files#r1936198406 * cr: add private note to `_csr` docstr https://github.com/single-cell-data/TileDB-SOMA-ML/pull/26/files#r1934615892 * cr: rm `CSR_IO_Buffer` ivar decls https://github.com/single-cell-data/TileDB-SOMA-ML/pull/26/files#r1934599631 * cr: docstr nit https://github.com/single-cell-data/TileDB-SOMA-ML/pull/26/files#r1934663531 * cr: rename "GPU batches" to "mini batches" https://github.com/single-cell-data/TileDB-SOMA-ML/pull/26/files#r1934665025 * cr: mention `layer_name` kwarg rename in CHANGELOG https://github.com/single-cell-data/TileDB-SOMA-ML/pull/26/files#r1934668910 * cr: docstr nit https://github.com/single-cell-data/TileDB-SOMA-ML/pull/26/files#r1934686963 * cr: update CHANGELOG https://github.com/single-cell-data/TileDB-SOMA-ML/pull/26/files#r1943429030 * cr: export `.common` types in `tiledbsoma_ml/__init__.py` https://github.com/single-cell-data/TileDB-SOMA-ML/pull/26/files#r1943430810 * cr: vendor `tiledbsoma._eager_iter` https://github.com/single-cell-data/TileDB-SOMA-ML/pull/26/files#r1943421917
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Move several classes/files to TileDB-SOMA (single-cell-data/TileDB-SOMA#3307), leave abstract interfaces here.