gador/nixpkgs
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

python312Packages.zarr: 2.18.7 -> 3.1.0 (#373248)

Browse Source
This commit is contained in:
Doron Behar
2025-08-14 11:17:11 +03:00
committed by GitHub
parent 5c09e7c195 002a7b2aa2
commit 7ef1b4163a
10 changed files with 175 additions and 26 deletions
Download Patch File Download Diff File Expand all files Collapse all files
pkgs/development/python-modules/anndata/default.nix
+10 -2
View File
@@ -12,6 +12,7 @@
hatchling,
joblib,
lib,
legacy-api-wrap,
natsort,
numba,
numpy,
@@ -32,14 +33,14 @@
buildPythonPackage rec {
pname = "anndata";
version = "0.11.4";
version = "0.12.2";
pyproject = true;
src = fetchFromGitHub {
owner = "scverse";
repo = "anndata";
tag = version;
hash = "sha256-9RDR0veZ8n2sq0kUbAkS2nP57u47cQxmubzuWWYBKBY=";
hash = "sha256-uGkeSlYcphRnIFfe9UcLvnupKeMzAIm5wT8fp3gmPKw=";
};
build-system = [
@@ -50,6 +51,7 @@ buildPythonPackage rec {
dependencies = [
array-api-compat
h5py
legacy-api-wrap
natsort
numpy
pandas
@@ -92,18 +94,24 @@ buildPythonPackage rec {
];
disabledTests = [
# requires data from a previous test execution:
"test_no_diff"
# doctests that require scanpy, creating a circular dependency chain. These
# do not work in disabledTestPaths for some reason.
"anndata._core.anndata.AnnData.concatenate"
"anndata._core.anndata.AnnData.obs_names_make_unique"
"anndata._core.anndata.AnnData.var_names_make_unique"
"anndata._core.extensions.register_anndata_namespac"
"anndata._core.merge.concat"
"anndata._core.merge.gen_reindexer"
"anndata._core.sparse_dataset.sparse_dataset"
"anndata._io.specs.registry.read_elem_as_dask"
"anndata._io.specs.registry.read_elem_lazy"
"anndata._io.utils.report_read_key_on_error"
"anndata._io.utils.report_write_key_on_error"
"anndata._warnings.ImplicitModificationWarning"
"anndata.experimental.backed._io.read_lazy"
"anndata.experimental.merge.concat_on_disk"
"anndata.experimental.multi_files._anncollection.AnnCollection"
"anndata.utils.make_index_unique"
pkgs/development/python-modules/legacy-api-wrap/default.nix
+42
View File
@@ -0,0 +1,42 @@
{
lib,
buildPythonPackage,
fetchFromGitHub,
hatch-docstring-description,
hatch-vcs,
hatchling,
pytestCheckHook,
}:
buildPythonPackage rec {
pname = "legacy-api-wrap";
version = "1.4.1";
pyproject = true;
src = fetchFromGitHub {
owner = "flying-sheep";
repo = "legacy-api-wrap";
tag = "v${version}";
hash = "sha256-ySkhfUyRBd4QS3f46KlaA5NrHxHr+dlkgmD4fGk2KsA=";
};
build-system = [
hatch-docstring-description
hatch-vcs
hatchling
];
pythonImportsCheck = [
"legacy_api_wrap"
];
nativeCheckInputs = [ pytestCheckHook ];
meta = {
description = "Wrap legacy APIs in python projects";
homepage = "https://github.com/flying-sheep/legacy-api-wrap";
changelog = "https://github.com/flying-sheep/legacy-api-wrap/releases/tag/${src.tag}";
license = lib.licenses.mpl20;
maintainers = with lib.maintainers; [ bcdarwin ];
};
}
pkgs/development/python-modules/multiscale-spatial-image/default.nix
+4 -2
View File
@@ -9,6 +9,7 @@
python-dateutil,
spatial-image,
xarray,
xarray-dataclass,
zarr,
dask-image,
fsspec,
@@ -22,7 +23,7 @@
buildPythonPackage rec {
pname = "multiscale-spatial-image";
version = "2.0.2";
version = "2.0.3";
pyproject = true;
disabled = pythonOlder "3.8";
@@ -31,7 +32,7 @@ buildPythonPackage rec {
owner = "spatial-image";
repo = "multiscale-spatial-image";
tag = "v${version}";
hash = "sha256-aJp9RrCy88XFpM5GU7jADHQZFNZgXvlqSsCbmay3gww=";
hash = "sha256-wKSzhlNXIXOFEK8+xfKF6zTFr0+mdFhhvjWiHAKphk0=";
};
build-system = [ hatchling ];
@@ -42,6 +43,7 @@ buildPythonPackage rec {
python-dateutil
spatial-image
xarray
xarray-dataclass
zarr
];
pkgs/development/python-modules/numcodecs/default.nix
+2 -2
View File
@@ -26,14 +26,14 @@
buildPythonPackage rec {
pname = "numcodecs";
version = "0.15.1";
version = "0.16.1";
pyproject = true;
disabled = pythonOlder "3.8";
src = fetchPypi {
inherit pname version;
hash = "sha256-7u135NZjZkGizGBfvGB4x6jyzEDz36Kz9h5S5gkbBP8=";
hash = "sha256-xH8g1lZFRWjGtGl84CCB5ru1EvGYc4xqVvr+gCnJf7E=";
};
build-system = [
pkgs/development/python-modules/ome-zarr/default.nix
+5 -2
View File
@@ -23,14 +23,14 @@
buildPythonPackage rec {
pname = "ome-zarr";
version = "0.11.1";
version = "0.12rc1";
pyproject = true;
src = fetchFromGitHub {
owner = "ome";
repo = "ome-zarr-py";
tag = "v${version}";
hash = "sha256-3RXkz+UQvLixfYYhm5y/5vu9r0ga6s3xKx1azbmKFgg=";
hash = "sha256-uwAcICrFHZYYULfacWII5C3Y+Rs2Bf8ZLQEijfkldn8=";
};
build-system = [
@@ -78,6 +78,9 @@ buildPythonPackage rec {
"tests/test_starting_points.py::TestStartingPoints::test_label"
"tests/test_starting_points.py::TestStartingPoints::test_labels"
"tests/test_starting_points.py::TestStartingPoints::test_top_level"
# tries to access network:
"ome_zarr/io.py"
];
pythonImportsCheck = [
pkgs/development/python-modules/spatial-image/default.nix
+4 -4
View File
@@ -7,12 +7,12 @@
pytestCheckHook,
numpy,
xarray,
xarray-dataclasses,
xarray-dataclass,
}:
buildPythonPackage rec {
pname = "spatial-image";
version = "1.2.1";
version = "1.2.3";
pyproject = true;
disabled = pythonOlder "3.10";
@@ -21,7 +21,7 @@ buildPythonPackage rec {
owner = "spatial-image";
repo = "spatial-image";
tag = "v${version}";
hash = "sha256-PGc2uey2xcfE0PcYDaCp7U0lgeGL1I6MMP3vbTN+Alk=";
hash = "sha256-mhT86v4/5s4dFw9sDYm5Ba7sM0ME9ifN9KEzhxVigOc=";
};
build-system = [ hatchling ];
@@ -29,7 +29,7 @@ buildPythonPackage rec {
dependencies = [
numpy
xarray
xarray-dataclasses
xarray-dataclass
];
nativeCheckInputs = [ pytestCheckHook ];
pkgs/development/python-modules/tifffile/default.nix
+5 -5
View File
@@ -14,14 +14,14 @@
buildPythonPackage rec {
pname = "tifffile";
version = "2025.5.10";
version = "2025.6.11";
pyproject = true;
disabled = pythonOlder "3.9";
src = fetchPypi {
inherit pname version;
hash = "sha256-AYM100KDqj/YwmO65cPCtmHrxFVI/eMVBAFvyue/EQM=";
hash = "sha256-Ds5MLnoQZWlX1Wigk7B1E8ByjTDBvYzBJyWQH//bcUM=";
};
build-system = [ setuptools ];
@@ -58,11 +58,11 @@ buildPythonPackage rec {
# flaky, often killed due to OOM or timeout
env.SKIP_LARGE = "1";
meta = with lib; {
meta = {
description = "Read and write image data from and to TIFF files";
homepage = "https://github.com/cgohlke/tifffile/";
changelog = "https://github.com/cgohlke/tifffile/blob/v${version}/CHANGES.rst";
license = licenses.bsd3;
maintainers = with maintainers; [ lebastr ];
license = lib.licenses.bsd3;
maintainers = with lib.maintainers; [ lebastr ];
};
}
pkgs/development/python-modules/xarray-dataclass/default.nix
+48
View File
@@ -0,0 +1,48 @@
{
lib,
buildPythonPackage,
fetchFromGitHub,
pythonOlder,
hatchling,
pytestCheckHook,
numpy,
typing-extensions,
xarray,
}:
buildPythonPackage rec {
pname = "xarray-dataclass";
version = "3.0.0";
pyproject = true;
src = fetchFromGitHub {
owner = "xarray-contrib";
repo = "xarray-dataclass";
tag = "v${version}";
hash = "sha256-NHJvrkoRhq5cPSBBMWzrWVn+3sPvveMRgTXc/NdLfuA=";
};
build-system = [
hatchling
];
pythonRelaxDeps = [ "xarray" ];
dependencies = [
numpy
typing-extensions
xarray
];
nativeCheckInputs = [ pytestCheckHook ];
pythonImportsCheck = [ "xarray_dataclass" ];
meta = with lib; {
description = "Xarray data creation made easy by dataclass";
homepage = "https://xarray-contrib.github.io/xarray-dataclass";
changelog = "https://github.com/xarray-contrib/xarray-dataclass/releases/tag/v${version}";
license = licenses.mit;
maintainers = with maintainers; [ bcdarwin ];
};
}
pkgs/development/python-modules/zarr/default.nix
+51 -9
View File
@@ -5,51 +5,93 @@
pythonOlder,
# build-system
setuptools-scm,
hatchling,
hatch-vcs,
# dependencies
asciitree,
donfig,
numpy,
fasteners,
numcodecs,
typing-extensions,
# tests
pytestCheckHook,
pytest-asyncio,
pytest-cov-stub,
hypothesis,
aiohttp,
fsspec,
moto,
requests,
tomlkit,
uv,
writableTmpDirAsHomeHook,
}:
buildPythonPackage rec {
pname = "zarr";
version = "2.18.7";
version = "3.1.0";
pyproject = true;
disabled = pythonOlder "3.8";
disabled = pythonOlder "3.11";
src = fetchPypi {
inherit pname version;
hash = "sha256-srj2bxTaxK9msYDSM4gZmBuYH3Dhlsmmbmv6qeWVcvU=";
hash = "sha256-rOWxEdxp1TFcsWVd/Q+BbFrPl5jSrZL0O2CKUsjIrCs=";
};
build-system = [
setuptools-scm
hatchling
hatch-vcs
];
dependencies = [
asciitree
donfig
numpy
fasteners
numcodecs
typing-extensions
]
++ numcodecs.optional-dependencies.msgpack;
++ numcodecs.optional-dependencies.crc32c;
optional-dependencies = {
remote = [ fsspec ];
};
nativeCheckInputs = [
pytestCheckHook
pytest-asyncio
pytest-cov-stub
hypothesis
aiohttp
moto
requests
tomlkit
uv
writableTmpDirAsHomeHook
]
++ moto.optional-dependencies.s3
++ moto.optional-dependencies.server
++ optional-dependencies.remote;
pytestFlagsArray = [
# Don't measure the time it takes for hypothesis related tests to succeed.
# See https://github.com/astropy/astropy/issues/17649 for a similar
# discussion, and see:
# https://github.com/zarr-developers/zarr-python/blob/v3.0.4/tests/conftest.py#L182C1-L187C2
"--hypothesis-profile=ci"
];
disabledTests = [
# 3 tests that require multiple Python versions to co-exist
"test_scripts_can_run"
"test_roundtrip_v2"
"test_roundtrip_v3"
];
pythonImportsCheck = [ "zarr" ];
# FIXME remove once zarr's reverse dependencies support v3
passthru.skipBulkUpdate = true;
meta = {
description = "Implementation of chunked, compressed, N-dimensional arrays for Python";
homepage = "https://github.com/zarr-developers/zarr";
pkgs/top-level/python-packages.nix
+4
View File
@@ -8029,6 +8029,8 @@ self: super: with self; {
ledgerwallet = callPackage ../development/python-modules/ledgerwallet { };
legacy-api-wrap = callPackage ../development/python-modules/legacy-api-wrap { };
legacy-cgi = callPackage ../development/python-modules/legacy-cgi { };
leidenalg = callPackage ../development/python-modules/leidenalg { igraph-c = pkgs.igraph; };
@@ -19903,6 +19905,8 @@ self: super: with self; {
xarray = callPackage ../development/python-modules/xarray { };
xarray-dataclass = callPackage ../development/python-modules/xarray-dataclass { };
xarray-dataclasses = callPackage ../development/python-modules/xarray-dataclasses { };
xarray-einstats = callPackage ../development/python-modules/xarray-einstats { };