(chore): generate 1.10.5 release notes #3416
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Co-authored-by: Isaac Virshup <[email protected]>
As noted by @ilan-gold, just setting `blank_issues = true` makes a little link visible:
Co-authored-by: Philipp A <[email protected]>
* makes count nonzeros dense * added test * added releasenote
Co-authored-by: Philipp A <[email protected]>
Co-authored-by: Philipp A <[email protected]>
Co-authored-by: Philipp A <[email protected]>
Co-authored-by: Philipp A <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Philipp A <[email protected]>
* try out uv * syntax * env * better * Fix resolution * wtf * Fix order * compile
…ters to user specified key (scverse#2889) Co-authored-by: Ilan Gold <[email protected]> Co-authored-by: Phil Schaf <[email protected]>
updates: - [github.com/astral-sh/ruff-pre-commit: v0.3.2 → v0.3.3](astral-sh/ruff-pre-commit@v0.3.2...v0.3.3) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Stop reporting durations * Fix compatibility with scipy 1.13 * release note
…se#2856) * (chore): add dask sparse chunks creation * (feat): add dask summation * (refactor): `materialize_as_ndarray` needs to operate on indidiual dask arrays * (feat): `filter_genes` and `filter_cells` * (feat): normalization * (fix) `lop1p` tests working * (refactor): clean up writing test * (refactor): us `da.chunk.sum` * (fix): remove `Client` * (refactor): remove unnecessary `count_nonzero` * (fix): change expected fail on sparse normalization * (fix): update comment * (feat): `_get_mean_var` dask * (feat): clean up tests for what should/should not work * (refactor): `_compat.sum` to `_utils.elem_sum` * (chore): add `elem_sum` test * (refactor): `elem_sum` -> `axis_sum` * (feat): add `scale` support * (fix): maintain dtype * (chore): add back condition * (fix): use `sum` when needed * (chore): release notes * (fx): don't use `mean_func` name twice * (chore): revert sparse-chunks-in-dask * (chore): type hint * (chore): check `test_compare_to_upstream` * (chore): remove comment * (chore): allow passing `dtype` arg in `axis_sum` * (fix): revert fixture changes * (refactor): cleaner with `array_type` conversion before if-then * (chore): clarify hvg support * (chore): handle array types better * (chore): clean up `materialize_as_ndarray` * (chore): fix typing/dispatch problem in 3.9 * (chore): `list` type -> `Callable` * (feat): `row_divide` for better division handling * (fix): use `tuple` for `ARRAY_TYPEXXXX` * (refactor): `mean_func` -> `axis_mean` + types * (chore): remove unnecessary aggregation * (fix): raise `ValueError` for summing over more than one axis * (fix): grammar * (fix): better type hints * (revert): use old `test_normalize_total` siince we have `csr` * (revert): extraneous diff * (fix): try `Union` * (chore): add column division ability * (chore): add scale test * (fix): duplicate in release note * (refactor): guard clause + comments * (chore): add `out` check for `dask` * (chore): add `divisor` type hints * (fix): remove some erroneous diffs * (chore): `axis_{sum,mean}` type hint fixes * (refactor): generalize to scaling * (chore): remove erroneous comment * (chore): remove non-public API * (fix): import from `sc._utils` * (fix): `inidices` -> `indices` * (fix): remove erroneous `axis_sum` calls * (fix): return statements for `axis_scale` * (refactor): return out of `axis_sum` if `X._meta` is `np.ndarray` * (core): comment fix * (fix): use `normalize_total` in HVG test for true reproducibility * (refactor): separate out `out` test for dask * (fix): correct chunking/rechunking behavior * (chore): add guard clause for `sparse` `out != X != None` in scaling * (fix): guard clause condition * (fix): try finishing `|` typing for 3.9 * (fix): call `register` to allow unions? * (fix): clarify warning * (feat): test for `max_value`/`zero_center` combos * (fix): allow settings of `X` in `scale_array` * (chore): add tests for `normalize` correctness * (fix): refactor for pure dask in `median` * (refactor): add clarifying condition * (chore): skip warning computations + tests * (fix): actually skip computation in `normalize_total` condition * (fix): actually skip in `filter_genes` + tests * (fix): use all-in-one median implemetation * (refactor): remove erreous dask warnings * (chore): add note about `exclude_highly_expressed` * (feat): `axis_scale` -> `axis_mul_or_truediv` * (feat): `allow_divide_by_zero` * (chore): add notes + type hints * Have hvg compute earlier and only once * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * (refactor): make codecov better by removing dead code/refactoring * (fix): `np.clip` in dask does not take min/max as `kwargs` * Update docs/release-notes/1.11.0.md Co-authored-by: Isaac Virshup <[email protected]> * (chore): move release note * (chore): remove erroneous comment --------- Co-authored-by: ilan-gold <[email protected]> Co-authored-by: Isaac Virshup <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Fix aggregating obsm/ varm * Remove print * Add test for labeled case
* Update leiden future warning * Better warning * Update scanpy/_utils/__init__.py --------- Co-authored-by: Ilan Gold <[email protected]>
Co-authored-by: Philipp A <[email protected]>
updates: - [github.com/astral-sh/ruff-pre-commit: v0.3.3 → v0.3.4](astral-sh/ruff-pre-commit@v0.3.3...v0.3.4) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Start going to tutorial submodule * bump submodule * Got plotting tutorial layout to a decent point * clear out git submodule * Using stubs to reference notebooks * Use symlinks instead * Add knn-transformers * Remove docutils.conf as it's no longer needed * Update basic tutorial * Update reference to ecosystem * Add bib * Start a how-to section * Update old tutorial link * experimental tutorial module * update spatial tutorials links * Update basic tutorials layout * Add trajectories * Fix some links * fix some more links * unfuck cite directive * update submodule * Fix sphinx handling of ftp link * Add submodule to readthedocs * add rapids-singlecell to news * Update advanced plotting tutorial * apply pre-commit fixes on notebooks * Fix link * Cut down on tutorials * Release notes (+ a release note fix) * Fix rapids-singlecell link * Updae tutorials page * add setuptools dep for doc builds * Use intersphinx for a link * update notebooks * add back blank line * update submodule * Add dask notebook * Update notebook submodule * Update notebook submodule * update submodule * Prep release notes * update submodule * add release note for doc style overhaul * bump date
* Fix aggregate for more than two groups * release note
* Add marsilea notebook * bump notebooks * release note * update submodule * update submodule * update submodule
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Philipp A. <[email protected]>
…quare method. (scverse#3284) Co-authored-by: Intron7 <[email protected]> Co-authored-by: Philipp A. <[email protected]> Co-authored-by: Severin Dicks <[email protected]>
updates: - [github.com/astral-sh/ruff-pre-commit: v0.7.2 → v0.7.3](astral-sh/ruff-pre-commit@v0.7.2...v0.7.3) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
…ease notes) (scverse#3359) Co-authored-by: Philipp A <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
… package (scverse#3362) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Phil Schaf <[email protected]>
…erse#3393) * (fix): bound sklearn because of dask-ml on the release candidate * (chore): release note * (fix): `mod` in note * (fix): release notes number
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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@meeseeksdev backport to main