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python312Packages.s3fs: 2024.12.0 -> 2025.2.0 #382057

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Merged
NickCao merged 3 commits into from
Feb 15, 2025
Merged

python312Packages.s3fs: 2024.12.0 -> 2025.2.0 #382057

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815a35a
python312Packages.s3fs: 2024.12.0 -> 2025.2.0
GaetanLepage Feb 14, 2025
3b988f7
python312Packages.ome-zarr: fix
GaetanLepage Feb 14, 2025
232ef93
python312Packages.pyiceberg: fix on darwin
GaetanLepage Feb 14, 2025
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27 changes: 17 additions & 10 deletions pkgs/development/python-modules/ome-zarr/default.nix
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Original file line number Diff line number Diff line change
@@ -1,28 +1,32 @@
{
lib,
buildPythonPackage,
pythonOlder,
fetchFromGitHub,
pytestCheckHook,

# build-system
setuptools,
setuptools-scm,

# dependencies
aiohttp,
dask,
distributed,
fsspec,
numpy,
requests,
scikit-image,
setuptools,
toolz,
zarr,

# tests
pytestCheckHook,
}:

buildPythonPackage rec {
pname = "ome-zarr";
version = "0.10.3";
pyproject = true;

disabled = pythonOlder "3.9";

src = fetchFromGitHub {
owner = "ome";
repo = "ome-zarr-py";
Expand All @@ -32,21 +36,24 @@ buildPythonPackage rec {

build-system = [
setuptools
setuptools-scm
];

dependencies = [
numpy
aiohttp
dask
distributed
zarr
fsspec
aiohttp
numpy
requests
scikit-image
toolz
zarr
] ++ fsspec.optional-dependencies.s3;

nativeCheckInputs = [ pytestCheckHook ];
nativeCheckInputs = [
pytestCheckHook
];

disabledTests = [
# attempts to access network
Expand Down Expand Up @@ -90,7 +97,7 @@ buildPythonPackage rec {
meta = {
description = "Implementation of next-generation file format (NGFF) specifications for storing bioimaging data in the cloud";
homepage = "https://pypi.org/project/ome-zarr";
changelog = "https://github.com/ome/ome-zarr-py/blob/${src.tag}/CHANGELOG.md";
changelog = "https://github.com/ome/ome-zarr-py/blob/v${version}/CHANGELOG.md";
license = lib.licenses.bsd2;
maintainers = [ lib.maintainers.bcdarwin ];
mainProgram = "ome_zarr";
Expand Down
121 changes: 65 additions & 56 deletions pkgs/development/python-modules/pyiceberg/default.nix
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
{
lib,
stdenv,
buildPythonPackage,
fetchFromGitHub,

Expand Down Expand Up @@ -49,7 +50,6 @@
pytest-mock,
pytest-timeout,
requests-mock,
pythonOlder,
}:

buildPythonPackage rec {
Expand Down Expand Up @@ -185,61 +185,70 @@ buildPythonPackage rec {
"tests/integration"
];

disabledTests = [
# botocore.exceptions.EndpointConnectionError: Could not connect to the endpoint URL
"test_checking_if_a_file_exists"
"test_closing_a_file"
"test_fsspec_file_tell"
"test_fsspec_getting_length_of_file"
"test_fsspec_pickle_round_trip_s3"
"test_fsspec_raise_on_opening_file_not_found"
"test_fsspec_read_specified_bytes_for_file"
"test_fsspec_write_and_read_file"
"test_writing_avro_file"

# Require unpackaged gcsfs
"test_fsspec_converting_an_outputfile_to_an_inputfile_gcs"
"test_fsspec_new_input_file_gcs"
"test_fsspec_new_output_file_gcs"
"test_fsspec_pickle_roundtrip_gcs"

# Timeout (network access)
"test_fsspec_converting_an_outputfile_to_an_inputfile_adls"
"test_fsspec_new_abfss_output_file_adls"
"test_fsspec_new_input_file_adls"
"test_fsspec_pickle_round_trip_aldfs"

# TypeError: pyarrow.lib.large_list() takes no keyword argument
# From tests/io/test_pyarrow_stats.py:
"test_bounds"
"test_column_metrics_mode"
"test_column_sizes"
"test_metrics_mode_counts"
"test_metrics_mode_full"
"test_metrics_mode_non_default_trunc"
"test_metrics_mode_none"
"test_null_and_nan_counts"
"test_offsets"
"test_read_missing_statistics"
"test_record_count"
"test_value_counts"
"test_write_and_read_stats_schema"
# From tests/io/test_pyarrow.py:
"test_list_type_to_pyarrow"
"test_projection_add_column"
"test_projection_list_of_structs"
"test_read_list"
"test_schema_compatible_missing_nullable_field_nested"
"test_schema_compatible_nested"
"test_schema_mismatch_missing_required_field_nested"
"test_schema_to_pyarrow_schema_exclude_field_ids"
"test_schema_to_pyarrow_schema_include_field_ids"
# From tests/io/test_pyarrow_visitor.py
"test_round_schema_conversion_nested"

# Hangs forever (from tests/io/test_pyarrow.py)
"test_getting_length_of_file_gcs"
];
disabledTests =
[
# botocore.exceptions.EndpointConnectionError: Could not connect to the endpoint URL
"test_checking_if_a_file_exists"
"test_closing_a_file"
"test_fsspec_file_tell"
"test_fsspec_getting_length_of_file"
"test_fsspec_pickle_round_trip_s3"
"test_fsspec_raise_on_opening_file_not_found"
"test_fsspec_read_specified_bytes_for_file"
"test_fsspec_write_and_read_file"
"test_writing_avro_file"

# Require unpackaged gcsfs
"test_fsspec_converting_an_outputfile_to_an_inputfile_gcs"
"test_fsspec_new_input_file_gcs"
"test_fsspec_new_output_file_gcs"
"test_fsspec_pickle_roundtrip_gcs"

# Timeout (network access)
"test_fsspec_converting_an_outputfile_to_an_inputfile_adls"
"test_fsspec_new_abfss_output_file_adls"
"test_fsspec_new_input_file_adls"
"test_fsspec_pickle_round_trip_aldfs"

# TypeError: pyarrow.lib.large_list() takes no keyword argument
# From tests/io/test_pyarrow_stats.py:
"test_bounds"
"test_column_metrics_mode"
"test_column_sizes"
"test_metrics_mode_counts"
"test_metrics_mode_full"
"test_metrics_mode_non_default_trunc"
"test_metrics_mode_none"
"test_null_and_nan_counts"
"test_offsets"
"test_read_missing_statistics"
"test_record_count"
"test_value_counts"
"test_write_and_read_stats_schema"
# From tests/io/test_pyarrow.py:
"test_list_type_to_pyarrow"
"test_projection_add_column"
"test_projection_list_of_structs"
"test_read_list"
"test_schema_compatible_missing_nullable_field_nested"
"test_schema_compatible_nested"
"test_schema_mismatch_missing_required_field_nested"
"test_schema_to_pyarrow_schema_exclude_field_ids"
"test_schema_to_pyarrow_schema_include_field_ids"
# From tests/io/test_pyarrow_visitor.py
"test_round_schema_conversion_nested"

# Hangs forever (from tests/io/test_pyarrow.py)
"test_getting_length_of_file_gcs"
]
++ lib.optionals stdenv.hostPlatform.isDarwin [
# ImportError: The pyarrow installation is not built with support for 'GcsFileSystem'
"test_converting_an_outputfile_to_an_inputfile_gcs"
"test_new_input_file_gcs"
"test_new_output_file_gc"
];

__darwinAllowLocalNetworking = true;

meta = {
description = "Python library for programmatic access to Apache Iceberg";
Expand Down
113 changes: 100 additions & 13 deletions pkgs/development/python-modules/s3fs/default.nix
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Original file line number Diff line number Diff line change
@@ -1,35 +1,46 @@
{
lib,
aiobotocore,
aiohttp,
buildPythonPackage,
fetchFromGitHub,

# buildInputs
docutils,
fetchPypi,

# build-system
setuptools,

# dependencies
aiobotocore,
aiohttp,
fsspec,

# tests
flask,
flask-cors,
fsspec,
moto,
pytestCheckHook,
pythonOlder,
setuptools,
}:

buildPythonPackage rec {
pname = "s3fs";
version = "2024.12.0";
version = "2025.2.0";
pyproject = true;

disabled = pythonOlder "3.9";

src = fetchPypi {
inherit pname version;
hash = "sha256-Gw86j1lGzKW6KYcdZ5KrHkUo7XYjJ9iu+vyBtzuZ/VY=";
src = fetchFromGitHub {
owner = "fsspec";
repo = "s3fs";
tag = version;
hash = "sha256-nnfvccORDspj54sRxL3d0hn4MpzKYGKE2Kl0v/wLaNw=";
};

buildInputs = [ docutils ];

build-system = [ setuptools ];

pythonRelaxDeps = [
"fsspec"
];

dependencies = [
aiobotocore
aiohttp
Expand All @@ -48,12 +59,88 @@ buildPythonPackage rec {
disabledTests = [
# require network access
"test_async_close"

# AssertionError: assert ['x', 'y'] == []
"test_with_data"

# AssertionError: assert ['1', 'x', 'y'] == []
"test_clear_empty"
"test_no_dircache"

# KeyError: 'ChecksumAlgorithm'
"test_info"

# KeyError:
# del d[1]
"test_complex_keys"

# TypeError: string indices must be integers, not 'str'
"test_bucket_versioning"
"test_bulk_delete"
"test_copy_with_source_and_destination_as_list"
"test_cp_directory_recursive"
"test_dynamic_add_rm"
"test_get_directory_to_existing_directory"
"test_get_directory_to_new_directory"
"test_get_directory_without_files_with_same_name_prefix"
"test_get_file_info_with_selector"
"test_get_file_to_existing_directory"
"test_get_file_to_file_in_existing_directory"
"test_get_file_to_file_in_new_directory"
"test_get_file_to_new_directory"
"test_get_glob_edge_cases"
"test_get_glob_to_existing_directory"
"test_get_glob_to_new_directory"
"test_get_list_of_files_to_existing_directory"
"test_get_list_of_files_to_new_directory"
"test_get_with_source_and_destination_as_list"
"test_move[False]"
"test_move[True]"
"test_new_bucket"
"test_new_bucket_auto"
"test_pipe_exclusive"
"test_put_directory_recursive"
"test_put_directory_to_existing_directory"
"test_put_directory_to_new_directory"
"test_put_directory_without_files_with_same_name_prefix"
"test_put_file_to_existing_directory"
"test_put_file_to_file_in_existing_directory"
"test_put_file_to_file_in_new_directory"
"test_put_file_to_new_directory"
"test_put_glob_edge_cases"
"test_put_glob_to_existing_directory"
"test_put_glob_to_new_directory"
"test_put_list_of_files_to_existing_directory"
"test_put_list_of_files_to_new_directory"
"test_rm"
"test_rm_invalidates_cache"
"test_rm_recursive_folder"
"test_s3_big_ls"
"test_s3fs_etag_preserving_multipart_copy"
"test_tags"

# ExceptionGroup: errors while tearing down <Function test_copy_two_files_new_directory> (2 sub-exceptions)
"test_copy_directory_to_existing_directory"
"test_copy_directory_to_new_directory"
"test_copy_directory_without_files_with_same_name_prefix"
"test_copy_file_to_existing_directory"
"test_copy_file_to_file_in_existing_directory"
"test_copy_file_to_file_in_new_directory"
"test_copy_file_to_new_directory"
"test_copy_glob_edge_cases"
"test_copy_glob_to_existing_directory"
"test_copy_glob_to_new_directory"
"test_copy_list_of_files_to_existing_directory"
"test_copy_list_of_files_to_new_directory"
"test_copy_two_files_new_directory"
];

__darwinAllowLocalNetworking = true;

meta = {
description = "Pythonic file interface for S3";
homepage = "https://github.com/fsspec/s3fs";
changelog = "https://github.com/fsspec/s3fs/raw/${version}/docs/source/changelog.rst";
changelog = "https://github.com/fsspec/s3fs/blob/${version}/docs/source/changelog.rst";
license = lib.licenses.bsd3;
maintainers = with lib.maintainers; [ teh ];
};
Expand Down