naturalis / sdmdl

Species Distribution Modelling using Deep Learning
MIT License
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Update fiona to 1.9.5 #422

Closed pyup-bot closed 8 months ago

pyup-bot commented 1 year ago

This PR updates fiona from 1.8.6 to 1.9.5.

Changelog ### 1.9.4.post1 ``` ------------------------ Extraneous files were unintentionally packaged in the 1.9.4 wheels. This post1 release excludes them so that wheel contents are as in version 1.9.3. ``` ### 1.9.4 ``` ------------------ - The performance of Feature.from_dict() has been improved (1267). - Several sources of meaningless log messages from fiona._geometry about NULL geometries are avoided (1264). - The Parquet driver has been added to the list of supported drivers and will be available if your system's GDAL library links libarrow. Note that fiona wheels on PyPI do not include libarrow as it is rather large. - Ensure that fiona._vendor modules are found and included. - Bytes type feature properties are now hex encoded when serializing to GeoJSON (1263). - Docstrings for listdir and listlayers have been clarified and harmonized. - Nose style test cases have been converted to unittest.TestCase (1256). - The munch package used by fio-filter and fio-calc is now vendored and patched to remove usage of the deprecated pkg_resources module (1255). ``` ### 1.9.3 ``` ------------------ - Rasterio CRS objects are compatible with the Collection constructor and are now accepted (1248). - Enable append mode for fio-load (1237). - Reading a GeoJSON with an empty array property can result in a segmentation fault since version 1.9.0. This has been fixed (1228). ``` ### 1.9.2 ``` ------------------ - Get command entry points using importlib.metadata (1220). - Instead of warning, transform_geom() raises an exception when some points can't be reprojected unless the caller opts in to partial reprojection. This restores the behavior of version 1.8.22. - Add support for open options to all CLI commands that call fiona.open (1215). - Fix a memory leak that can occur when iterating over a dataset using strides (1205). - ZipMemoryFile now supports zipped GDB data (1203). ``` ### 1.9.1 ``` ------------------ - Log a warning message when identically named fields are encountered (1201). - Avoid dependence on listdir order in tests (1193). - Prevent empty geometries arrays from appearing in __geo_interface__ (1197). - setuptools added to pyproject.toml. Its pkg_resources module is used by the CLI (1191). ``` ### 1.9.0 ``` ------------------ - CITATION.txt has been replaced by a new CITATION.cff file and the credits have been updated. - In setup.py the distutils (deprecated) logger is no longer used. ``` ### 1.9b2 ``` ------------------ - Add Feature.__geo_interface__ property (1181). - Invalid creation options are filtered and ignored (1180). - The readme doc has been shortened and freshened up, with a modern example for version 1.9.0 (1174). - The Geometry class now provides and looks for __geo_interface__ (1174). - The top level fiona module now exports Feature, Geometry, and Properties (1174). - Functions that take Feature or Geometry objects will continue to take dicts or objects that provide __geo_interface__ (1177). This reverses the deprecation introduced in 1.9a2. - Python ignores SIGPIPE by default. By never catching BrokenPipeError via `except Exception` when, for example, piping the output of rio-shapes to the Unix head program, we avoid getting an unhandled BrokenPipeError message when the interpreter shuts down (2689). ``` ### 1.9b1 ``` ------------------ New features: * Add listdir and listlayers method to io.MemoryFile (resolving 754). * Add support for TIN and triangle geometries (1163). * Add an allow_unsupported_drivers option to fiona.open() (1126). * Added support for the OGR StringList field type (1141). Changes and bug fixes: * Missing and unused imports have been added or removed. * Make sure that errors aren't lost when a collection can't be saved properly (1169). * Ensure that ZipMemoryFile have the proper GDAL name after creation so that we can use listdir() (1092). * The fiona._loading module, which supports DLL loading on Windows, has been moved into __init__.py and is no longer used anywhere else (1168). * Move project metadata to pyproject.toml (1165). * Update drvsupport.py to reflect new format capabilities in GDAL 3.6.0 (1122). * Remove debug logging from env and _env modules. ``` ### 1.9a3 ``` ------------------ Packaging: * Builds now require Cython >= 0.29.29 because of * https://github.com/cython/cython/issues/4609 (see #1143). * PyPI wheels now include GDAL 3.5.2, PROJ 9.0.1, and GEOS 3.11.0. * PyPI wheels are now available for Python 3.11. ``` ### 1.9a2 ``` ------------------ Deprecations: - Fiona's API methods will accept feature and geometry dicts in 1.9.0, but this usage is deprecated. Instances of Feature and Geometry will be required in 2.0. - The precision keyword argument of fiona.transform.transform_geom is deprecated and will be removed in version 2.0. - Deprecated usage has been eliminated in the project. Fiona's tests pass when run with a -Werror::DeprecationWarning filter. Changes: - Fiona's FionaDeprecationWarning now sub-classes DeprecationWarning. - Some test modules have beeen re-formatted using black. New features: - Fiona Collections now carry a context exit stack into which we can push fiona Envs and MemoryFiles (1059). - Fiona has a new CRS class, like rasterio's, which is compatible with the CRS dicts of previous versions (714). ``` ### 1.9a1 ``` ------------------ Deprecations: - The fiona.drivers() function has been deprecated and will be removed in version 2.0. It should be replaced by fiona.Env(). - The new fiona.meta module will be renamed to fiona.drivers in version 2.0. Packaging: - Source distributions contain no C source files and require Cython to create them from .pyx files (1096). Changes: - Shims for various versions of GDAL have been removed and are replaced by Cython compilation conditions (1093). - Use of CURL_CA_BUNDLE environment variable is replaced by a more specific GDAL/PROJ_CURL_CA_BUNDLE (1095). - Fiona's feature accessors now return instances of fiona.model.Feature instead of Python dicts (787). The Feature class is compatible with code that expects GeoJSON-like dicts but also provides id, geometry, and properties attributes. The last two of these are instances of fiona.model.Geometry and fiona.model.Properties. - GDAL 3.1.0 is the minimum GDAL version. - Drop Python 2, and establish Python 3.7 as the minimum version (1079). - Remove six and reduce footprint of fiona.compat (985). New features: - The appropriate format driver can be detected from filename in write mode (948). - Driver metadata including dataset open and dataset and layer creations options are now exposed through methods of the fiona.meta module (950). - CRS WKT format support (979). - Add 'where' SQL clause to set attribute filter (961, 1097). Bug fixes: - Env and Session classes have been updated for parity with rasterio and to resolve a credential refresh bug (1055). ``` ### 1.8.22 ``` ------------------- Builds now require Cython >= 0.29.29 because of https://github.com/cython/cython/issues/4609 (#1143). ``` ### 1.8.21 ``` ------------------- Changes: - Driver mode support tests have been made more general and less susceptible to driver quirks involving feature fields and coordinate values (1060). - OSError is raised on attempts to open a dataset in a Python file object in "a" mode (see 1027). - Upgrade attrs, cython, etc to open up Python 3.10 support (1049). Bug fixes: - Allow FieldSkipLogFilter to handle exception messages as well as strings (reported in 1035). - Clean up VSI files left by MemoryFileBase, resolving 1041. - Hard-coded "utf-8" collection encoding added in 423 has been removed (1057). ``` ### 1.8.20 ``` ------------------- Packaging: - Wheels include GDAL 3.3.0 and GEOS 3.9.1. Bug fixes: - Allow use with click 8 and higher (1015). ``` ### 1.8.19 ``` ------------------- Packaging: - Wheels include GDAL 3.2.1 and PROJ 7.2.1. Bug fixes: - In fiona/env.py the GDAL data path is now configured using set_gdal_config instead by setting the GDAL_DATA environment variable (1007). - Spurious iterator reset warnings have been eliminatged (987). ``` ### 1.8.18 ``` ------------------- - The precision option of transform has been fixed for the case of GeometryCollections (971, 972). - Added missing --co (creation) option to fio-load (390). - If the certifi package can be imported, its certificate store location will be passed to GDAL during import of fiona._env unless CURL_CA_BUNDLE is already set. - Warn when feature fields named "" are found (955). ``` ### 1.8.17 ``` ------------------- - To fix issue 952 the fio-cat command no longer cuts feature geometries at the anti-meridian by default. A --cut-at-antimeridian option has been added to allow cutting of geometries in a geographic destination coordinate reference system. ``` ### 1.8.16 ``` ------------------- - More OGR errors and warnings arising in calls to GDAL C API functions are surfaced (946). - A circular import introduced in some cases in 1.8.15 has been fixed (945). ``` ### 1.8.15 ``` ------------------- - Change shim functions to not return tuples (942) as a solution for the packaging problem reported in 941. - Raise a Python exception when VSIFOpenL fails (937). ``` ### 1.8.14 ``` ------------------- - When creating a new Collection in a MemoryFile with a default (random) name Fiona will attempt to use a format driver-supported file extension (934). When initializing a MemoryFile with bytes of data formatted for a vector driver that requires a certain file name or extension, the user should continue to pass an appropriate filename and/or extension. - Read support for FlatGeobuf has been enabled in the drvsupport module. - The MemoryFile implementation has been improved so that it can support multi-part S3 downloads (906). This is largely a port of code from rasterio. - Axis ordering for results of fiona.transform was wrong when CRS were passed in the "EPSG:dddd" form (919). This has been fixed by (926). - Allow implicit access to the only dataset in a ZipMemoryFile. The path argument of ZipMemoryFile.open() is now optional (928). - Improve support for datetime types: support milliseconds (744), timezones (914) and improve warnings if type is not supported by driver (572). - Fix "Failed to commit transaction" TransactionError for FileGDB driver. - Load GDAL DLL dependencies on Python 3.8+ / Windows with add_dll_directory() (851). - Do not require optional properties (848). - Ensure that slice does not overflow available data (884). - Resolve issue when "ERROR 4: Unable to open EPSG support file gcs.csv." is raised on importing fiona (897). - Resolve issue resulting in possible mixed up fields names (affecting only DXF, GPX, GPSTrackMacker and DGN driver) (916). - Ensure crs_wkt is passed when writing to MemoryFile (907). ``` ### 1.8.13.post1 ``` ------------------------- - This release is being made to improve binary wheel compatibility with shapely 1.7.0. There have been no changes to the fiona package code since 1.8.13. ``` ### 1.8.13 ``` ------------------- - The Python version specs for argparse and ordereddict in 1.8.12 were wrong and have been corrected (843). ``` ### 1.8.12 ``` ------------------- - Specify Python versions for argparse, enum34, and ordereddict requirements (842). ``` ### 1.8.11 ``` ------------------- - Fix an access violation on Windows (826). ``` ### 1.8.10 ``` ------------------- Deprecations: - Use of vfs keyword argument with open or listlayers has been previously noted as deprecated, but now triggers a deprecation warning. Bug fixes: - fiona.open() can now create new datasets using CRS URNs (823). - listlayers() now accepts file and Path objects, like open() (825). - Use new set_proj_search_path() function to set the PROJ data search path. For GDAL versions before 3.0 this sets the PROJ_LIB environment variable. For GDAL version 3.0 this calls OSRSetPROJSearchPaths(), which overrides PROJ_LIB. - Remove old and unused _drivers extension module. - Check for header.dxf file instead of pcs.csv when looking for installed GDAL data. The latter is gone with GDAL 3.0 but the former remains (818). ``` ### 1.8.9.post2 ``` ------------------------ - The 1.8.9.post1 release introduced a bug affecting builds of the package from a source distribution using GDAL 2.x. This bug has been fixed in commit 960568d. ``` ### 1.8.9.post1 ``` ------------------------ - A change has been made to the package setup script so that the shim module for GDAL 3 is used when building the package from a source distribution. There are no other changes to the package. ``` ### 1.8.9 ``` ------------------ - A shim module and support for GDAL 3.0 has been added. The package can now be built and used with GDAL 3.0 and PROJ 6.1 or 6.2. Note that the 1.8.9 wheels we will upload to PyPI will contain GDAL 2.4.2 and PROJ 4.9.3 as in the 1.8.8 wheels. ``` ### 1.8.8 ``` ------------------ - The schema of geopackage files with a geometry type code of 3000 could not be reported using Fiona 1.8.7. This bug is fixed. ``` ### 1.8.7 ``` ------------------ Bug fixes: - Regression in handling of polygons with M values noted under version 1.8.5 below was in fact not fixed then (see new report 789), but is fixed in version 1.8.7. - Windows filenames containing "!" are now parsed correctly, fixing issue 742. Upcoming changes: - In version 1.9.0, the objects yielded when a Collection is iterated will be mutable mappings but will no longer be instances of Python's dict. Version 1.9 is intended to be backwards compatible with 1.8 except where user code tests `isinstance(feature, dict)`. In version 2.0 the new Feature, Geometry, and Properties classes will become immutable mappings. See https://github.com/Toblerity/fiona-rfc/blob/master/rfc/0001-fiona-2-0-changes.md for more discussion of the upcoming changes for version 2.0. ```
Links - PyPI: https://pypi.org/project/fiona - Changelog: https://data.safetycli.com/changelogs/fiona/
pyup-bot commented 8 months ago

Closing this in favor of #459