(chore): add rust-cache to CI and use the standard uv action #32
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
LDeakin
commented
Nov 8, 2024
ilan-gold
reviewed
Nov 8, 2024
|
The old |
|
I might just leave it then, unless the next version of astral's has caching |
|
@ilan-gold with rust-cache: CI from 8m -> 1m30s |
LDeakin
changed the title
ilan-gold
approved these changes
Nov 14, 2024
LDeakin
added a commit
that referenced
this pull request
Nov 15, 2024
* (fix): use the standard uv GH action * cache with pyproject.toml * ci: remove install rust * (chore): add rust-cache to CI * (fix): add note in CI about rust-toolchain action
ilan-gold
added a commit
that referenced
this pull request
Nov 16, 2024
* Add a `CodecPipeline` stub * Pass chunk spec * (fix): return bytes as numpy array (#18) * (fix): return bytes as numpy array * (fix): reshape after making view * (fix): remove unused code * (fix): error handling in `get_store_and_path` * (fix): change `example/simple.py` to a 2D array * (fix): pass value to `store_chunk_subset` * (fix): clippy warnings * (fix): handle missing chunks in `retrieve_chunk_subset` and cleanup * (fix): panics to errors in `get_store_and_path` * (fix): add partial reads/writes to `simply.py` * (fix): minimum working codec pipeline - Add internal `get_chunk_representation`, `retrieve_chunk_bytes`, and `store_chunk_bytes` - Separate `retrieve_chunk` and `retrieve_chunk_subset` - Separate `store_chunk` and `store_chunk_subset` - Add assertions to simple.py * (fix): handle relative filesystem paths * (fix): minimal error handling and fix clippy warnings * (fix): handle relative filesystem paths take 2 * (fix): constant handling * (fix): add `retrieve_chunks` for parallel read - Add config options - CodecPipelineImpl interior mutability * (fix): add `store_chunks` for parallel write * (fix) convert write value to contiguous array if needed * (fix): bump zarrs to 21e86cb9 * CI for codec pipeline (#20) * (fix): ci for running tests * (fix): no need to extract tests * (Fix): remove duplicate name * (fix): use a submodule... * (chore): remove memory store + port zarr codec tests * (chore): remove `dlpark` * (fix): getattr for itemsize * (chore): remove runtime F ordering * (chore): skip vlen * (feat): parse int --------- Co-authored-by: Lachlan Deakin <ljdgit@gmail.com> * (fix): support writing arrays with non-native endianness * (fix): disable bad/unsupported invalid metadata tests * (fix): do not store empty chunks * (fix) remove dead code in codec pipeline * (fix): move some selection logic from Rust to Python * (feat): `chunks_desc` handling + concurrency via `zarr.config` (#21) * (fix): minimum working codec pipeline - Add internal `get_chunk_representation`, `retrieve_chunk_bytes`, and `store_chunk_bytes` - Separate `retrieve_chunk` and `retrieve_chunk_subset` - Separate `store_chunk` and `store_chunk_subset` - Add assertions to simple.py * (fix): handle relative filesystem paths * (fix): minimal error handling and fix clippy warnings * (fix): handle relative filesystem paths take 2 * (fix): constant handling * (fix): add `retrieve_chunks` for parallel read - Add config options - CodecPipelineImpl interior mutability * (fix): add `store_chunks` for parallel write * (fix) convert write value to contiguous array if needed * (fix): bump zarrs to 21e86cb9 * CI for codec pipeline (#20) * (fix): ci for running tests * (fix): no need to extract tests * (Fix): remove duplicate name * (fix): use a submodule... * (chore): remove memory store + port zarr codec tests * (chore): remove `dlpark` * (fix): getattr for itemsize * (chore): remove runtime F ordering * (chore): skip vlen * (feat): parse int --------- Co-authored-by: Lachlan Deakin <ljdgit@gmail.com> * (fix): support writing arrays with non-native endianness * (fix): disable bad/unsupported invalid metadata tests * (fix): do not store empty chunks * (fix) remove dead code in codec pipeline * (fix): move some selection logic from Rust to Python * (chore): `chunks_desc` cleanup * (feat): adding concurrency via zarr config * (chore): remove extra comment * (fix): refactor chunk info creation + threads->threading + ruff * (fix): use `or` for `threading.max_workers` getting --------- Co-authored-by: Lachlan Deakin <ljdgit@gmail.com> * (chore): pipeline-specific tests (#23) * (chore): add pipeline-specific tests * (chore): add more tests, including weird zarr one * (fix): arr shape used in test * (chore): change names * (chore): remove unnecessary fill_value checking * (chore): make roundtrip_full_array shorter * (fix): handle singleton axis indexing Fixes `test_roundtrip_singleton_axis` test * (fix): deprecated numpy array to scalar in `make_slice_selection` Fixes the `test_roundtrip_partial` test --------- Co-authored-by: Lachlan Deakin <ljdgit@gmail.com> * (chore): add orthogonal indexing tests (#24) * (chore): add orthogonal indexing tests * (fix): oindex roundtrip * (fix): dont skip test because it works actually * (fix): clean up returning * Delete tests/__init__.py * (chore): add ellipsis indexing tests (#25) * Format (#26) * Pyo3-0.22 (#29) * Refactor and deduplicate ChunksItem (#31) * Improve error mapping code (#28) Co-authored-by: ilan-gold <ilanbassgold@gmail.com> * (chore): add `pyarray_itemsize()` * (chore): add safety comments to `ndarray_to_*` methods Also add `py_untyped_array_to_array_object` * (chore): label fields in `ChunksItemRaw` * (fix): fix store/retrieve with scalars + refactor - Fixed fill value bytes being larger than needed when storing - Handle reduced dimensionality inputs/outputs - Uses LDeakin/zarrs@8c1391f - This inconsistency was picked up by `zarrs` in debug build * (fix): address several unwraps * (chore): cleanup `slice_to_range` * (chore): change `retrieve_chunk_bytes` to return `ArrayBytes` * (chore): add SAFETY docs and `store_chunk_subset_bytes` input validation * (chore): file structure (#27) Co-authored-by: Lachlan Deakin <ljdgit@gmail.com> * (feat): refactor `CodecPipelineStore` to a trait - Move filesystem store implementation to a submodule * (fix): bring back filesystem relative path support Broken with 4c1ce39 * (fix): bump `requires-python` to 3.11 This is the minimum set by `zarr` 3.0.0b1 * Rust tests (#33) * Simplify shape calculation * (chore): add rust-cache to CI and use the standard uv action (#32) * (fix): use the standard uv GH action * cache with pyproject.toml * ci: remove install rust * (chore): add rust-cache to CI * (fix): add note in CI about rust-toolchain action * (feat): fall back to pure python indexing in case of unhandled rust indexing for read (#30) * (chore): file structure * (chore): parametrize tests to get full scope of possibilities * (chore): xfail tests that fail on zarr-python default pipeline * (fix) singular * (fix): check for contiguous index arrays * (fix): contiguous numpy arrays converted to slices * (feat): add reading for non-contiguous buffers * (chore): remove unused imports * (fix): cleanup unwraps in `retrieve_chunks` * Refactor full indexing (#34) * (chore): `make_chunk_info_for_rust` cleanup * (fix): all tests working except "tests/test_pipeline.py::test_roundtrip[vindex-contiguous_in_chunk_array-contiguous_in_chunk_array]" * (fix): skip read in `store_chunk_subset_bytes` for full chunks * (fix): improve dropped index detection + disallow integer write case * (chore): message more specific * (fix): use `Exception` * (chore): erroneous comment * (chore): `drop_axes` default * (chore): `drop_axes` param * (chore): apply review * (chore): `else` branch * (chore): add basic nd tests (#35) * (chore): add basic 3d tests * (refactor): use `pytest_generate_tests` * (fix): clarify collapsed dimension behavior * (chore): clean ups --------- Co-authored-by: Lachlan Deakin <ljdgit@gmail.com> Co-authored-by: Philipp A. <flying-sheep@web.de> * (fix): support zarr 3.0.0b2 + bump zarrs to 0.18.0-beta.0 (#36) * (fix): support zarr 3.0.0b2 * (fix): open store read_only in test_roundtrip_read_only_zarrs * (fix): pin zarrs revision I think an old version is cached? * (chore): add Cargo.toml to uv dependency glob * (fix): unquote uv dependency glob * (chore): bump `zarrs` to 0.18.0-beta.0 * (fix): remove unused rust features and `paste` * (chore): first pass at docs * (chore): add `yml` * (chore): small cleanup in `README.md` * (chore): add some little examples + integer indexing note * (chore): more examples * (chore): link * Update hatch.toml Co-authored-by: Philipp A. <flying-sheep@web.de> * (chore): update package name * merge * (fix): add zarrs import to example * (fix): fix typo in docs * (fix): remove python/zarrs_python directory * (fix): clarify what is not supported * (chore): futher clarify --------- Co-authored-by: Lachlan Deakin <ljdgit@gmail.com> Co-authored-by: Philipp A. <flying-sheep@web.de>
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
The current CI spontaneously broke, probably related to the uv 0.5.0 release