python3Packages.pyogrio: 0.12.1 -> 0.13.0 (#539704)

pkgs/development/python-modules/azure-kusto-data/default.nix

@@ -1,36 +1,49 @@
 {
   lib,
-  aiohttp,
-  aioresponses,
-  asgiref,
-  azure-core,
-  azure-identity,
   buildPythonPackage,
   fetchFromGitHub,
+
+  # build-system
+  uv-build,
+
+  # dependencies
+  azure-core,
+  azure-identity,
   ijson,
   msal,
+  python-dateutil,
+  requests,
+
+  # optional-dependencies
+
+  # tests
+  # aio:
+  aiohttp,
+  asgiref,
+  # pandas:
   pandas,
+
+  # tests
+  aioresponses,
   pytest-asyncio,
   pytest-xdist,
   pytestCheckHook,
-  python-dateutil,
-  requests,
-  uv-build,
 }:
 
-buildPythonPackage rec {
+buildPythonPackage (finalAttrs: {
   pname = "azure-kusto-data";
-  version = "6.0.3";
+  version = "6.0.4";
   pyproject = true;
+  __structuredAttrs = true;
 
   src = fetchFromGitHub {
     owner = "Azure";
     repo = "azure-kusto-python";
-    tag = "v${version}";
-    hash = "sha256-n69KpWZpAVMjr7d1QRQ/J/SgeTLkadJUhCgD62F6O7w=";
+    tag = "v${finalAttrs.version}";
+    hash = "sha256-iggsVxLmDbP6+oSPaIiujPLsZAWwm5VLZSl+HYm0DIQ=";
   };
 
-  sourceRoot = "${src.name}/${pname}";
+  sourceRoot = "${finalAttrs.src.name}/azure-kusto-data";
 
   postPatch = ''
     substituteInPlace pyproject.toml \
@@ -42,7 +55,6 @@ buildPythonPackage rec {
   pythonRelaxDeps = [
     "ijson"
   ];
-
   dependencies = [
     azure-core
     azure-identity
@@ -66,22 +78,30 @@ buildPythonPackage rec {
     pytest-xdist
     pytestCheckHook
   ]
-  ++ lib.concatAttrValues optional-dependencies;
+  ++ lib.concatAttrValues finalAttrs.passthru.optional-dependencies;
 
   pythonImportsCheck = [ "azure.kusto.data" ];
 
+  disabledTests = [
+    # AssertionError: Attributes of DataFrame.iloc[:, 1] (column name="rowguid") are different
+    "test_sanity_data_frame"
+  ];
+
   disabledTestPaths = [
     # Tests require network access
     "tests/aio/test_async_token_providers.py"
     "tests/test_token_providers.py"
     "tests/test_e2e_data.py"
+
+    # AssertionError: assert <class 'pandas.Timestamp'> is <class 'pandas.api.typing.NaTType'>
+    "tests/test_helpers.py"
   ];
 
   meta = {
     description = "Kusto Data Client";
     homepage = "https://github.com/Azure/azure-kusto-python/tree/master/azure-kusto-data";
-    changelog = "https://github.com/Azure/azure-kusto-python/releases/tag/${src.tag}";
+    changelog = "https://github.com/Azure/azure-kusto-python/releases/tag/${finalAttrs.src.tag}";
     license = lib.licenses.mit;
     maintainers = [ ];
   };
-}
+})

pkgs/development/python-modules/fiona/default.nix

@@ -25,9 +25,10 @@
   pytestCheckHook,
   pytz,
   snuggs,
+  versionCheckHook,
 }:
 
-buildPythonPackage rec {
+buildPythonPackage (finalAttrs: {
   pname = "fiona";
   version = "1.10.1";
   pyproject = true;
@@ -35,18 +36,20 @@ buildPythonPackage rec {
   src = fetchFromGitHub {
     owner = "Toblerity";
     repo = "Fiona";
-    tag = version;
+    tag = finalAttrs.version;
     hash = "sha256-5NN6PBh+6HS9OCc9eC2TcBvkcwtI4DV8qXnz4tlaMXc=";
   };
 
   postPatch = ''
     substituteInPlace pyproject.toml \
       --replace-fail "cython~=3.0.2" cython
-
+  ''
+  +
     # pyparsing deprecated parseString in favor of parse_string
-    substituteInPlace fiona/fio/features.py fiona/_vendor/snuggs.py \
-      --replace-fail parseString parse_string
-  '';
+    ''
+      substituteInPlace fiona/fio/features.py fiona/_vendor/snuggs.py \
+        --replace-fail parseString parse_string
+    '';
 
   build-system = [
     cython
@@ -72,17 +75,21 @@ buildPythonPackage rec {
     s3 = [ boto3 ];
   };
 
+  pythonImportsCheck = [ "fiona" ];
+
   nativeCheckInputs = [
     fsspec
     pytestCheckHook
     pytz
     shapely
     snuggs
+    versionCheckHook
   ]
-  ++ optional-dependencies.s3;
+  ++ finalAttrs.passthru.optional-dependencies.s3;
 
+  # prevent importing local fiona
   preCheck = ''
-    rm -r fiona # prevent importing local fiona
+    rm -r fiona
   '';
 
   disabledTestMarks = [
@@ -91,84 +98,36 @@ buildPythonPackage rec {
     "gdal"
   ];
 
+  pytestFlags = [
+    # UserWarning: The parameter --where is used more than once. Remove its duplicate as parameters should be unique.
+    "-Wignore::UserWarning"
+  ];
+
   disabledTests = [
     # Some tests access network, others test packaging
     "http"
     "https"
     "wheel"
 
+    # AssertionError: assert """"bool": true""" in data
+    "test_write_bool_subtype"
+
+    # AssertionError: assert '"coordinates": [ [ [ -111.74, 42.0 ], [ -111.66, 42.0 ]' in f.read(2000)
+    "test_open_kwargs"
+
+    # fiona.errors.DatasetDeleteError: Driver does not support dataset removal operation
+    "test_remove"
+
     # see: https://github.com/Toblerity/Fiona/issues/1273
     "test_append_memoryfile_drivers"
-
-    # AssertionError CLI exists with non-zero error code
-    # This is a regression introduced by https://github.com/NixOS/nixpkgs/pull/448189
-    "test_bbox_json_yes"
-    "test_bbox_no"
-    "test_bbox_where"
-    "test_bbox_yes"
-    "test_bbox_yes_two_files"
-    "test_bool_seq"
-    "test_bounds_explode_with_obj"
-    "test_calc_seq"
-    "test_collect_ld"
-    "test_collect_no_rs"
-    "test_collect_noparse"
-    "test_collect_noparse_records"
-    "test_collect_noparse_rs"
-    "test_collect_rec_buffered"
-    "test_collect_rs"
-    "test_creation_options"
-    "test_different_crs"
-    "test_distrib"
-    "test_distrib_no_rs"
-    "test_dst_crs_default_to_src_crs"
-    "test_dst_crs_epsg3857"
-    "test_dst_crs_no_src"
-    "test_existing_property"
-    "test_explode"
-    "test_explode_output_rs"
-    "test_explode_pp"
-    "test_explode_with_id"
-    "test_filter"
-    "test_fio_load_layer"
-    "test_fio_load_layer_append"
-    "test_load__auto_detect_format"
-    "test_load__auto_detect_format"
-    "test_load__auto_detect_format"
-    "test_load__auto_detect_format"
-    "test_load__auto_detect_format"
-    "test_map_count"
-    "test_multi_layer"
-    "test_one"
-    "test_precision"
-    "test_reduce_area"
-    "test_reduce_area"
-    "test_reduce_union"
-    "test_reduce_union_zip_properties"
-    "test_seq"
-    "test_seq"
-    "test_seq_no_rs"
-    "test_seq_rs"
-    "test_seq_rs"
-    "test_two"
-    "test_vfs"
-    "test_where_no"
-    "test_where_yes"
-    "test_where_yes_two_files"
-    "test_with_id"
-    "test_with_obj"
   ];
 
-  pythonImportsCheck = [ "fiona" ];
-
-  doInstallCheck = true;
-
   meta = {
-    changelog = "https://github.com/Toblerity/Fiona/blob/${src.rev}/CHANGES.txt";
     description = "OGR's neat, nimble, no-nonsense API for Python";
+    changelog = "https://github.com/Toblerity/Fiona/blob/${finalAttrs.src.tag}/CHANGES.txt";
     mainProgram = "fio";
     homepage = "https://fiona.readthedocs.io/";
     license = lib.licenses.bsd3;
     teams = [ lib.teams.geospatial ];
   };
-}
+})

pkgs/development/python-modules/geopandas/default.nix

@@ -2,16 +2,15 @@
   lib,
   buildPythonPackage,
   fetchFromGitHub,
-  fetchpatch,
-  pytestCheckHook,
-  setuptools,
-  writableTmpDirAsHomeHook,
 
+  # build-system
+  setuptools,
+
+  # dependencies
   packaging,
   pandas,
   pyogrio,
   pyproj,
-  rtree,
   shapely,
 
   # optional-dependencies
@@ -24,18 +23,24 @@
   pyarrow,
   sqlalchemy,
   xyzservices,
+
+  # tests
+  pytestCheckHook,
+  rtree,
+  writableTmpDirAsHomeHook,
 }:
 
 buildPythonPackage (finalAttrs: {
   pname = "geopandas";
-  version = "1.1.3";
+  version = "1.1.4";
   pyproject = true;
+  __structuredAttrs = true;
 
   src = fetchFromGitHub {
     owner = "geopandas";
     repo = "geopandas";
     tag = "v${finalAttrs.version}";
-    hash = "sha256-66FbHNewpSEVZ9RwngK7E4bcELa9Z2OQ9xVP9+fgeHQ=";
+    hash = "sha256-7XWPPLuJjc6x+Vb16z0bEjYe1lX710vz5Rwjg/WFHH0=";
   };
 
   build-system = [ setuptools ];

pkgs/development/python-modules/msticpy/default.nix

@@ -1,5 +1,12 @@
 {
   lib,
+  buildPythonPackage,
+  fetchFromGitHub,
+
+  # build-system
+  setuptools,
+
+  # dependencies
   attrs,
   azure-common,
   azure-core,
@@ -11,12 +18,9 @@
   azure-monitor-query,
   beautifulsoup4,
   bokeh,
-  buildPythonPackage,
-  cache,
   cryptography,
   deprecated,
   dnspython,
-  fetchFromGitHub,
   folium,
   geoip2,
   html5lib,
@@ -26,9 +30,8 @@
   ipywidgets,
   keyring,
   lxml,
-  markdown,
-  msal-extensions,
   msal,
+  msal-extensions,
   msrest,
   msrestazure,
   nest-asyncio,
@@ -40,7 +43,6 @@
   pygments,
   pyjwt,
   pyyaml,
-  setuptools,
   tldextract,
   tqdm,
   typing-extensions,
@@ -49,23 +51,25 @@
 
 buildPythonPackage (finalAttrs: {
   pname = "msticpy";
-  version = "3.0.0";
+  version = "3.0.1";
   pyproject = true;
+  __structuredAttrs = true;
 
   src = fetchFromGitHub {
     owner = "microsoft";
     repo = "msticpy";
     tag = "v${finalAttrs.version}";
-    hash = "sha256-aX5Nd0tNuweBp2SqGwe4/Z4LcdJaX3p5LLNQAOdGVGo=";
+    hash = "sha256-utE77oSCAAYKmsyf8ZPep7spUSIoJXBU6NzeLpDIvUs=";
   };
 
+  build-system = [ setuptools ];
+
   pythonRelaxDeps = [
     "azure-kusto-data"
     "bokeh"
+    "nest_asyncio"
+    "pandas"
   ];
-
-  build-system = [ setuptools ];
-
   dependencies = [
     attrs
     azure-common

pkgs/development/python-modules/pyogrio/default.nix

@@ -2,55 +2,74 @@
   lib,
   buildPythonPackage,
   fetchFromGitHub,
-  pytestCheckHook,
-
-  certifi,
-  cython,
   gdal,
-  numpy,
-  packaging,
+
+  # build-system
+  cython,
   setuptools,
   versioneer,
-  wheel,
+
+  # dependencies
+  certifi,
+  numpy,
+  packaging,
+
+  # tests
+  fiona,
+  pandas,
+  pytest-benchmark,
+  pytestCheckHook,
 }:
 
-buildPythonPackage rec {
+buildPythonPackage (finalAttrs: {
   pname = "pyogrio";
-  version = "0.12.1";
+  version = "0.13.0";
   pyproject = true;
+  __structuredAttrs = true;
 
   src = fetchFromGitHub {
     owner = "geopandas";
     repo = "pyogrio";
-    tag = "v${version}";
-    hash = "sha256-c3bd8gxsHCzLKmy8baiIUbTXzZWms/NlDg7Az6TWrfM=";
+    tag = "v${finalAttrs.version}";
+    hash = "sha256-9WaJMrh3FN4hWpdGNq2TynoLqT91tLQ7iTTl/NWYQTI=";
   };
 
   postPatch = ''
     substituteInPlace pyproject.toml \
-      --replace-fail "versioneer[toml]==0.28" "versioneer[toml]"
+      --replace-fail \
+        "versioneer[toml]==0.28" \
+        "versioneer[toml]"
   '';
 
-  nativeBuildInputs = [
+  build-system = [
     cython
-    gdal # for gdal-config
     setuptools
     versioneer
-    wheel
+  ];
+
+  nativeBuildInputs = [
+    gdal # for gdal-config
   ];
 
   buildInputs = [ gdal ];
 
-  propagatedBuildInputs = [
+  dependencies = [
     certifi
     numpy
     packaging
   ];
 
-  nativeCheckInputs = [ pytestCheckHook ];
+  pythonImportsCheck = [ "pyogrio" ];
+
+  nativeCheckInputs = [
+    fiona
+    pandas
+    pytestCheckHook
+    pytest-benchmark
+  ];
 
   preCheck = ''
-    python setup.py build_ext --inplace
+    rm pyogrio/__init__.py
   '';
 
   disabledTestMarks = [
@@ -58,13 +77,26 @@ buildPythonPackage rec {
     "network"
   ];
 
-  pythonImportsCheck = [ "pyogrio" ];
+  disabledTests = [
+    # Circular dependencies with geopandas
+    "test_detect_zip_path"
+    "test_path_absolute"
+    "test_path_relative_dataframe"
+    "test_uri_local_file_dataframe"
+    "test_vsi_handling_read_dataframe"
+    "test_zip_path_dataframe"
+  ];
+
+  disabledTestPaths = [
+    # NameError: name 'shapely' is not defined
+    "pyogrio/tests/test_geopandas_io.py"
+  ];
 
   meta = {
     description = "Vectorized spatial vector file format I/O using GDAL/OGR";
     homepage = "https://pyogrio.readthedocs.io/";
-    changelog = "https://github.com/geopandas/pyogrio/blob/${src.tag}/CHANGES.md";
+    changelog = "https://github.com/geopandas/pyogrio/blob/${finalAttrs.src.tag}/CHANGES.md";
     license = lib.licenses.mit;
     teams = [ lib.teams.geospatial ];
   };
-}
+})