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Hello community,
here is the log from the commit of package python-tifffile for openSUSE:Factory
checked in at 2023-01-23 18:31:45
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Comparing /work/SRC/openSUSE:Factory/python-tifffile (Old)
and /work/SRC/openSUSE:Factory/.python-tifffile.new.32243 (New)
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Package is "python-tifffile"
Mon Jan 23 18:31:45 2023 rev:8 rq:1060309 version:2022.10.10
Changes:
--------
--- /work/SRC/openSUSE:Factory/python-tifffile/python-tifffile.changes
2021-02-10 21:30:34.638300972 +0100
+++
/work/SRC/openSUSE:Factory/.python-tifffile.new.32243/python-tifffile.changes
2023-01-23 18:32:04.412105840 +0100
@@ -1,0 +2,267 @@
+Sat Jan 21 13:23:43 UTC 2023 - Ben Greiner <[email protected]>
+
+- Update to 2022.10.10.
+ * Pass 4925 tests.
+ * Fix RecursionError in peek_iterator.
+ * Fix reading NDTiffv3 summary settings.
+ * Fix svs_description_metadata parsing (#149).
+ * Fix ImportError if Python was built without zlib or lzma.
+ * Fix bool of COMPRESSION and PREDICTOR instances.
+ * Deprecate non-sequence extrasamples arguments.
+ * Parse SCIFIO metadata as ImageJ.
+- Release 2022.8.12
+ * Fix writing ImageJ format with hyperstack argument.
+ * Fix writing description with metadata disabled.
+ * Add option to disable writing shaped metadata in TiffWriter.
+- Release 2022.8.8
+ * Fix regression using imread out argument (#147).
+ * Fix imshow show argument.
+ * Support fsspec OpenFile.
+- Release 2022.8.3
+ * Fix regression writing default resolutionunit (#145).
+ * Add strptime function parsing common datetime formats.
+- Release 2022.7.31
+ * Fix reading corrupted WebP compressed segments missing alpha
+ channel (#122).
+ * Fix regression reading compressed ImageJ files.
+- Release 2022.7.28
+ * Rename FileSequence.labels attribute to dims (breaking).
+ * Rename tifffile_geodb module to geodb (breaking).
+ * Rename TiffFile._astuple method to astuple (breaking).
+ * Rename noplots command line argument to maxplots (breaking).
+ * Fix reading ImageJ hyperstacks with non-TZC order.
+ * Fix colorspace of JPEG segments encoded by Bio-Formats.
+ * Fix fei_metadata for HELIOS FIB-SEM (#141, needs test).
+ * Add xarray style properties to TiffPage (WIP).
+ * Add option to specify OME-XML for TiffFile.
+ * Add option to control multiscales in ZarrTiffStore.
+ * Support writing to uncompressed ZarrTiffStore.
+ * Support writing empty images with tiling.
+ * Support overwriting some tag values in NDPI (#137).
+ * Support Jetraw compression (experimental).
+ * Standardize resolution parameter and property.
+ * Deprecate third resolution argument on write (use
+ resolutionunit).
+ * Deprecate tuple type compression argument on write (use
+ compressionargs).
+ * Deprecate enums in TIFF namespace (use enums from module).
+ * Improve default number of threads to write compressed segments
+ (#139).
+ * Parse metaseries time values as datetime objects (#143).
+ * Increase internal read and write buffers to 256 MB.
+ * Convert some warnings to debug messages.
+ * Declare all classes final.
+ * Add script to generate documentation via Sphinx.
+ * Convert docstrings to Google style with Sphinx directives.
+- Release 2022.5.4
+ * Allow to write NewSubfileType=0 (#132).
+ * Support writing iterators of strip or tile bytes.
+ * Convert iterables (not iterators) to NumPy arrays when writing.
+ * Explicitly specify optional keyword parameters for imread and
+ imwrite.
+ * Return number of written bytes from FileHandle write functions.
+- Release 2022.4.28
+ * Add option to specify fsspec version 1 URL template name
+ (#131).
+ * Ignore invalid dates in UIC tags (#129).
+ * Fix zlib_encode and lzma_encode to work with non-contiguous
+ arrays (#128).
+ * Fix delta_encode to preserve byteorder of ndarrays.
+ * Move Imagecodecs fallback functions to private module and add
+ tests.
+- Release 2022.4.26
+ * Fix AttributeError in TiffFile.shaped_metadata (#127).
+ * Fix TiffTag.overwrite with pre-packed binary value.
+ * Write sparse TIFF if tile iterator contains None.
+ * Raise ValueError when writing photometric mode with too few
+ samples.
+ * Improve test coverage.
+- Release 2022.4.22
+ * Add type hints for Python 3.10 (WIP).
+ * Fix Mypy errors (breaking).
+ * Mark many parameters positional-only or keyword-only
+ (breaking).
+ * Remove deprecated pages parameter from imread (breaking).
+ * Remove deprecated compress and ijmetadata write parameters
+ (breaking).
+ * Remove deprecated fastij and movie parameters from TiffFile
+ (breaking).
+ * Remove deprecated multifile parameters from TiffFile
+ (breaking).
+ * Remove deprecated tif parameter from TiffTag.overwrite
+ (breaking).
+ * Remove deprecated file parameter from FileSequence.asarray
+ (breaking).
+ * Remove option to pass imread class to FileSequence (breaking).
+ * Remove optional parameters from __str__ functions (breaking).
+ * Rename TiffPageSeries.offset to dataoffset (breaking)
+ * Change TiffPage.pages to None if no SubIFDs are present
+ (breaking).
+ * Change TiffPage.index to int (breaking).
+ * Change TiffPage.is_contiguous, is_imagej, and is_shaped to bool
+ (breaking).
+ * Add TiffPage imagej_description and shaped_description
+ properties.
+ * Add TiffFormat abstract base class.
+ * Deprecate lazyattr and use functools.cached_property instead
+ (breaking).
+ * Julian_datetime raises ValueError for dates before year 1
+ (breaking).
+ * Regressed import time due to typing.
+- Release 2022.4.8
+ * Add _ARRAY_DIMENSIONS attributes to ZarrTiffStore.
+ * Allow C instead of S axis when writing OME-TIFF.
+ * Fix writing OME-TIFF with separate samples.
+ * Fix reading unsqueezed pyramidal OME-TIFF series.
+- Release 2022.3.25
+ * Fix another ValueError using ZarrStore with zarr >= 2.11.0
+ (tiffslide #25).
+ * Add parser for Hamamatsu streak metadata.
+ * Improve hexdump.
+- Release 2022.3.16
+ * Use multi-threading to compress strips and tiles.
+ * Raise TiffFileError when reading corrupted strips and tiles
+ (#122).
+ * Fix ScanImage single channel count (#121).
+ * Add parser for AstroTIFF FITS metadata.
+- Release 2022.2.9
+ * Fix ValueError using multiscale ZarrStore with zarr >= 2.11.0.
+ * Raise KeyError if ZarrStore does not contain key.
+ * Limit number of warnings for missing files in multifile series.
+ * Allow to save colormap to 32-bit ImageJ files (#115).
+- Release 2022.2.2
+ * Fix TypeError when second ImageDescription tag contains
+ non-ASCII (#112).
+ * Fix parsing IJMetadata with many IJMetadataByteCounts (#111).
+ * Detect MicroManager NDTiffv2 header (not tested).
+ * Remove cache from ZarrFileSequenceStore (use
+ zarr.LRUStoreCache).
+ * Raise limit on maximum number of pages.
+ * Use J2K format when encoding JPEG2000 segments.
+ * Formally deprecate imsave and TiffWriter.save.
+ * Drop support for Python 3.7 and NumPy < 1.19 (NEP29).
+- Release 2021.11.2
+ * Lazy-load non-essential tag values (breaking).
+ * Warn when reading from closed file.
+ * Support ImageJ prop metadata type (#103).
+ * Support writing indexed ImageJ format.
+ * Fix multi-threaded access of multi-page Zarr stores with
+ chunkmode 2.
+ * Raise error if truncate is used with compression, packints, or
+ tile.
+ * Read STK metadata without UIC2tag.
+ * Improve log and warning messages (WIP).
+ * Improve string representation of large tag values.
+- Release 2021.10.12
+ * Revert renaming of file parameter in FileSequence.asarray
+ (breaking).
+ * Deprecate file parameter in FileSequence.asarray.
+- Release 2021.10.10
+ * Disallow letters as indices in FileSequence; use categories
+ (breaking).
+ * Do not warn of missing files in FileSequence; use files_missing
+ property.
+ * Support predictors in ZarrTiffStore.write_fsspec.
+ * Add option to specify Zarr group name in write_fsspec.
+ * Add option to specify categories for FileSequence patterns
+ (#76).
+ * Add option to specify chunk shape and dtype for
+ ZarrFileSequenceStore.
+ * Add option to tile ZarrFileSequenceStore and
+ FileSequence.asarray.
+ * Add option to pass additional zattrs to Zarr stores.
+ * Detect Roche BIF files.
+- Release 2021.8.30
+ * Fix horizontal differencing with non-native byte order.
+ * Fix multi-threaded access of memory-mappable, multi-page Zarr
+ stores (#67).
+- Release 2021.8.8
+ * Fix tag offset and valueoffset for NDPI > 4 GB (#96).
+- Release 2021.7.30
+ * Deprecate first parameter to TiffTag.overwrite (no longer
+ required).
+ * TiffTag init API change (breaking).
+ * Detect Ventana BIF series and warn that tiles are not stitched.
+ * Enable reading PreviewImage from RAW formats (#93, #94).
+ * Work around numpy.ndarray.tofile is very slow for
+ non-contiguous arrays.
+ * Fix issues with PackBits compression (requires imagecodecs
+ 2021.7.30).
+- Release 2021.7.2
+ * Decode complex integer images found in SAR GeoTIFF.
+ * Support reading NDPI with JPEG-XR compression.
+ * Deprecate TiffWriter RGB auto-detection, except for RGB24/48
+ and RGBA32/64.
+- Release 2021.6.14
+ * Set stacklevel for deprecation warnings (#89).
+ * Fix svs_description_metadata for SVS with double header (#88,
++++ 70 more lines (skipped)
++++ between /work/SRC/openSUSE:Factory/python-tifffile/python-tifffile.changes
++++ and
/work/SRC/openSUSE:Factory/.python-tifffile.new.32243/python-tifffile.changes
Old:
----
tifffile-2021.1.14.tar.gz
New:
----
tifffile-2022.10.10.tar.gz
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Other differences:
------------------
++++++ python-tifffile.spec ++++++
--- /var/tmp/diff_new_pack.axrIzn/_old 2023-01-23 18:32:05.952116497 +0100
+++ /var/tmp/diff_new_pack.axrIzn/_new 2023-01-23 18:32:05.980116691 +0100
@@ -1,7 +1,7 @@
#
# spec file for package python-tifffile
#
-# Copyright (c) 2021 SUSE LLC
+# Copyright (c) 2023 SUSE LLC
#
# All modifications and additions to the file contributed by third parties
# remain the property of their copyright owners, unless otherwise agreed
@@ -16,33 +16,44 @@
#
-%define packagename tifffile
-%define skip_python2 1
-%define skip_python36 1
-%{?!python_module:%define python_module() python-%{**} python3-%{**}}
Name: python-tifffile
-Version: 2021.1.14
+Version: 2022.10.10
Release: 0
Summary: Read and write TIFF(r) files
License: BSD-2-Clause
-URL: https://www.lfd.uci.edu/~gohlke/
-Source:
https://github.com/cgohlke/tifffile/archive/v%{version}.tar.gz#/%{packagename}-%{version}.tar.gz
-BuildRequires: %{python_module imagecodecs >= 2020.5.30}
-BuildRequires: %{python_module lxml}
-BuildRequires: %{python_module matplotlib >= 3.2}
-BuildRequires: %{python_module numpy >= 1.15.1}
-BuildRequires: %{python_module pytest}
+URL: https://github.com/cgohlke/tifffile/
+Source:
https://github.com/cgohlke/tifffile/archive/v%{version}.tar.gz#/tifffile-%{version}.tar.gz
+BuildRequires: %{python_module base >= 3.8}
+BuildRequires: %{python_module numpy >= 1.19.2}
+BuildRequires: %{python_module pip}
BuildRequires: %{python_module setuptools}
-BuildRequires: %{python_module zarr >= 2.5.0}
+BuildRequires: %{python_module wheel}
BuildRequires: fdupes
BuildRequires: python-rpm-macros
-Requires: python-imagecodecs >= 2020.5.30
-Requires: python-lxml
-Requires: python-matplotlib >= 3.2
-Requires: python-numpy >= 1.15.1
-Requires: python-zarr >= 2.5.0
+Requires: python-numpy
Requires(post): update-alternatives
-Requires(postun): update-alternatives
+Requires(postun):update-alternatives
+Recommends: python-fsspec
+Recommends: python-imagecodecs >= 2022.2.22
+Recommends: python-lxml
+Recommends: python-matplotlib >= 3.3
+Recommends: python-zarr
+# SECTION test
+BuildRequires: %{python_module imagecodecs >= 2022.2.22}
+BuildRequires: %{python_module cmapfile}
+BuildRequires: %{python_module czifile}
+BuildRequires: %{python_module dask}
+BuildRequires: %{python_module fsspec}
+BuildRequires: %{python_module lfdfiles}
+BuildRequires: %{python_module lxml}
+BuildRequires: %{python_module matplotlib >= 3.3}
+BuildRequires: %{python_module oiffile}
+BuildRequires: %{python_module pytest-xdist}
+BuildRequires: %{python_module pytest}
+BuildRequires: %{python_module roifile}
+BuildRequires: %{python_module xarray}
+BuildRequires: %{python_module zarr}
+# /SECTION
BuildArch: noarch
%python_subpackages
@@ -53,37 +64,50 @@
arrays to TIFF, BigTIFF, and ImageJ hyperstack compatible files.
%prep
-%setup -q -n %{packagename}-%{version}
+%setup -q -n tifffile-%{version}
# Fix warning wrong-file-end-of-line-encoding
sed -i 's/\r//' README.rst
+sed -i '1{/env python/d}' tifffile/{lsm2bin,tiff2fsspec,tiffcomment}.py
%build
-%python_build
+%pyproject_wheel
%install
-%python_install
-%python_clone -a %{buildroot}%{_bindir}/%{packagename}
+%pyproject_install
+%python_clone -a %{buildroot}%{_bindir}/tifffile
%python_clone -a %{buildroot}%{_bindir}/lsm2bin
%python_clone -a %{buildroot}%{_bindir}/tiffcomment
+%python_clone -a %{buildroot}%{_bindir}/tiff2fsspec
%python_expand %fdupes %{buildroot}%{$python_sitelib}
-%prepare_alternative %{packagename}
+%prepare_alternative tifffile
%prepare_alternative lsm2bin
%prepare_alternative tiffcomment
%post
-%python_install_alternative %{packagename}
+%python_install_alternative tifffile
%python_install_alternative lsm2bin
%python_install_alternative tiffcomment
+%python_install_alternative tiff2fsspec
%postun
-%python_uninstall_alternative %{packagename}
+%python_uninstall_alternative tifffile
%python_uninstall_alternative lsm2bin
%python_uninstall_alternative tiffcomment
+%python_uninstall_alternative tiff2fsspec
%check
-# skip online tests and tests that OOM
-%pytest -k 'not (test_issue_infinite_loop or test_func_pformat_xml or
test_filehandle_seekable or test_write_compress_lerc or test_write_imagej_raw
or test_write_bigtiff or test_write_ome or test_class_omexml_attributes or
test_class_omexml_multiimage or test_class_omexml or
test_write_compression_lerc)'
+# Crashes Out-Of-Memory
+donttest="test_write_ome"
+donttest="$donttest or test_write_imagej_raw"
+donttest="$donttest or test_write_bigtiff"
+# can't connect to localhost
+donttest="$donttest or test_write_fsspec"
+# no lerc support in imagecodecs
+donttest="$donttest or test_write_compression_lerc"
+# can't connect to external server
+donttest="$donttest or test_class_omexml"
+%pytest -n auto -k "not ($donttest)"
%files %{python_files}
%doc README.rst
@@ -91,7 +115,8 @@
%python_alternative %{_bindir}/tifffile
%python_alternative %{_bindir}/lsm2bin
%python_alternative %{_bindir}/tiffcomment
-%{python_sitelib}/*egg-info/
-%{python_sitelib}/%{packagename}/
+%python_alternative %{_bindir}/tiff2fsspec
+%{python_sitelib}/tifffile-%{version}.dist-info/
+%{python_sitelib}/tifffile
%changelog
++++++ tifffile-2021.1.14.tar.gz -> tifffile-2022.10.10.tar.gz ++++++
++++ 45220 lines of diff (skipped)
