py-tifffile: updated to 2023.4.12 2023.4.12 - Pass 4988 tests. - Do not write duplicate ImageDescription tags from extratags (breaking). - Support multifocal SVS files - Log warning when filtering out extratags. - Fix writing OME-TIFF with image description in extratags. - Ignore invalid predictor tag value if prediction is not used. - Raise KeyError if ZarrStore is missing requested chunk. 2023.3.21 - Fix reading MMstack with missing data 2023.3.15 - Fix corruption using tile generators with prediction/compression - Add parser for Micro-Manager MMStack series (breaking). - Return micromanager_metadata IndexMap as numpy array (breaking). - Revert optimizations for Micro-Manager OME series. - Do not use numcodecs zstd in write_fsspec (kerchunk issue 317). - More type annotations. 2023.2.28 - Fix reading some Micro-Manager metadata from corrupted files. - Speed up reading Micro-Manager indexmap for creation of OME series. 2023.2.27 - Use Micro-Manager indexmap offsets to create virtual TiffFrames. - Fixes for future imagecodecs. 2023.2.3 - Fix overflow in calculation of databytecounts for large NDPI files. 2023.2.2 - Fix regression reading layered NDPI files. - Add option to specify offset in FileHandle.read_array. 2023.1.23 - Support reading NDTiffStorage. - Support reading PIXTIFF compression. - Support LERC with Zstd or Deflate compression. - Do not write duplicate and select extratags. - Allow to write uncompressed image data beyond 4 GB in classic TIFF. - Add option to specify chunkshape and dtype in FileSequence.asarray. - Add option for imread to write to output in FileSequence.asarray - Add function to read GDAL structural metadata. - Add function to read NDTiff.index files. - Fix IndexError accessing TiffFile.mdgel_metadata in non-MDGEL files. - Fix unclosed file ResourceWarning in TiffWriter. - Fix non-bool predictor arguments - Relax detection of OME-XML - Rename some TiffFrame parameters (breaking). - Deprecate squeeze_axes (will change signature). - Use defusexml in xml2dict. 2022.10.10 - Fix RecursionError in peek_iterator. - Fix reading NDTiffv3 summary settings. - Fix svs_description_metadata parsing - 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. 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. 2022.8.8 - Fix regression using imread out argument - Fix imshow show argument. - Support fsspec OpenFile. 2022.8.3 - Fix regression writing default resolutionunit - Add strptime function parsing common datetime formats. 2022.7.31 - Fix reading corrupted WebP compressed segments missing alpha channel - Fix regression reading compressed ImageJ files. 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 - 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 - 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 - Parse metaseries time values as datetime objects - 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. 2022.5.4 - Allow to write NewSubfileType=0 - 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. 2022.4.28 - Add option to specify fsspec version 1 URL template name - Ignore invalid dates in UIC tags - Fix zlib_encode and lzma_encode to work with non-contiguous arrays - Fix delta_encode to preserve byteorder of ndarrays. - Move Imagecodecs fallback functions to private module and add tests. 2022.4.26 - Fix AttributeError in TiffFile.shaped_metadata - 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. 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. 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. 2022.3.25 - Fix another ValueError using ZarrStore with zarr >= 2.11.0 - Add parser for Hamamatsu streak metadata. - Improve hexdump. 2022.3.16 - Use multi-threading to compress strips and tiles. - Raise TiffFileError when reading corrupted strips and tiles - Fix ScanImage single channel count - Add parser for AstroTIFF FITS metadata. 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 2022.2.2 - Fix TypeError when second ImageDescription tag contains non-ASCII - Fix parsing IJMetadata with many IJMetadataByteCounts - 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).diff -r1.12 -r1.13 pkgsrc/graphics/py-tifffile/Makefile
(adam)
@@ -1,28 +1,33 @@ | @@ -1,28 +1,33 @@ | |||
1 | # $NetBSD: Makefile,v 1.12 2022/01/05 15:41:12 wiz Exp $ | 1 | # $NetBSD: Makefile,v 1.13 2023/04/24 07:03:08 adam Exp $ | |
2 | 2 | |||
3 | DISTNAME= tifffile-2021.11.2 | 3 | DISTNAME= tifffile-2023.4.12 | |
4 | PKGNAME= ${PYPKGPREFIX}-${DISTNAME} | 4 | PKGNAME= ${PYPKGPREFIX}-${DISTNAME} | |
5 | PKGREVISION= 2 | |||
6 | CATEGORIES= graphics python | 5 | CATEGORIES= graphics python | |
7 | MASTER_SITES= ${MASTER_SITE_PYPI:=t/tifffile/} | 6 | MASTER_SITES= ${MASTER_SITE_PYPI:=t/tifffile/} | |
8 | 7 | |||
9 | MAINTAINER= pkgsrc-users@NetBSD.org | 8 | MAINTAINER= pkgsrc-users@NetBSD.org | |
10 | HOMEPAGE= https://www.lfd.uci.edu/~gohlke/ | 9 | HOMEPAGE= https://www.lfd.uci.edu/~gohlke/ | |
11 | COMMENT= Read and write TIFF(r) files | 10 | COMMENT= Read and write TIFF(r) files | |
12 | LICENSE= modified-bsd | 11 | LICENSE= modified-bsd | |
13 | 12 | |||
14 | USE_LANGUAGES= # none | 13 | DEPENDS+= ${PYPKGPREFIX}-numpy-[0-9]*:../../math/py-numpy | |
14 | TEST_DEPENDS+= ${PYPKGPREFIX}-fsspec-[0-9]*:../../sysutils/py-fsspec | |||
15 | TEST_DEPENDS+= ${PYPKGPREFIX}-test-[0-9]*:../../devel/py-test | |||
15 | 16 | |||
16 | PYTHON_VERSIONS_INCOMPATIBLE= 27 | 17 | USE_LANGUAGES= # none | |
17 | 18 | |||
18 | USE_PKG_RESOURCES= yes | 19 | USE_PKG_RESOURCES= yes | |
19 | 20 | |||
21 | PYTHON_VERSIONS_INCOMPATIBLE= 27 | |||
22 | ||||
20 | post-install: | 23 | post-install: | |
21 | .for bin in lsm2bin tiff2fsspec tiffcomment tifffile | 24 | .for bin in lsm2bin tiff2fsspec tiffcomment tifffile | |
22 | cd ${DESTDIR}${PREFIX}/bin && \ | 25 | cd ${DESTDIR}${PREFIX}/bin && \ | |
23 | ${MV} ${bin} ${bin}-${PYVERSSUFFIX} || ${TRUE} | 26 | ${MV} ${bin} ${bin}-${PYVERSSUFFIX} || ${TRUE} | |
24 | .endfor | 27 | .endfor | |
25 | 28 | |||
29 | do-test: | |||
30 | cd ${WRKSRC} && ${SETENV} ${TEST_ENV} pytest-${PYVERSSUFFIX} tests | |||
31 | ||||
26 | .include "../../lang/python/egg.mk" | 32 | .include "../../lang/python/egg.mk" | |
27 | .include "../../math/py-numpy/buildlink3.mk" | |||
28 | .include "../../mk/bsd.pkg.mk" | 33 | .include "../../mk/bsd.pkg.mk" |
@@ -1,35 +1,38 @@ | @@ -1,35 +1,38 @@ | |||
1 | @comment $NetBSD: PLIST,v 1.3 2021/06/13 18:43:24 adam Exp $ | 1 | @comment $NetBSD: PLIST,v 1.4 2023/04/24 07:03:08 adam Exp $ | |
2 | bin/lsm2bin-${PYVERSSUFFIX} | 2 | bin/lsm2bin-${PYVERSSUFFIX} | |
3 | bin/tiff2fsspec-${PYVERSSUFFIX} | 3 | bin/tiff2fsspec-${PYVERSSUFFIX} | |
4 | bin/tiffcomment-${PYVERSSUFFIX} | 4 | bin/tiffcomment-${PYVERSSUFFIX} | |
5 | bin/tifffile-${PYVERSSUFFIX} | 5 | bin/tifffile-${PYVERSSUFFIX} | |
6 | ${PYSITELIB}/${EGG_INFODIR}/PKG-INFO | 6 | ${PYSITELIB}/${EGG_INFODIR}/PKG-INFO | |
7 | ${PYSITELIB}/${EGG_INFODIR}/SOURCES.txt | 7 | ${PYSITELIB}/${EGG_INFODIR}/SOURCES.txt | |
8 | ${PYSITELIB}/${EGG_INFODIR}/dependency_links.txt | 8 | ${PYSITELIB}/${EGG_INFODIR}/dependency_links.txt | |
9 | ${PYSITELIB}/${EGG_INFODIR}/entry_points.txt | 9 | ${PYSITELIB}/${EGG_INFODIR}/entry_points.txt | |
10 | ${PYSITELIB}/${EGG_INFODIR}/requires.txt | 10 | ${PYSITELIB}/${EGG_INFODIR}/requires.txt | |
11 | ${PYSITELIB}/${EGG_INFODIR}/top_level.txt | 11 | ${PYSITELIB}/${EGG_INFODIR}/top_level.txt | |
12 | ${PYSITELIB}/tifffile/__init__.py | 12 | ${PYSITELIB}/tifffile/__init__.py | |
13 | ${PYSITELIB}/tifffile/__init__.pyc | 13 | ${PYSITELIB}/tifffile/__init__.pyc | |
14 | ${PYSITELIB}/tifffile/__init__.pyo | 14 | ${PYSITELIB}/tifffile/__init__.pyo | |
15 | ${PYSITELIB}/tifffile/__main__.py | 15 | ${PYSITELIB}/tifffile/__main__.py | |
16 | ${PYSITELIB}/tifffile/__main__.pyc | 16 | ${PYSITELIB}/tifffile/__main__.pyc | |
17 | ${PYSITELIB}/tifffile/__main__.pyo | 17 | ${PYSITELIB}/tifffile/__main__.pyo | |
18 | ${PYSITELIB}/tifffile/_imagecodecs.py | |||
19 | ${PYSITELIB}/tifffile/_imagecodecs.pyc | |||
20 | ${PYSITELIB}/tifffile/_imagecodecs.pyo | |||
21 | ${PYSITELIB}/tifffile/geodb.py | |||
22 | ${PYSITELIB}/tifffile/geodb.pyc | |||
23 | ${PYSITELIB}/tifffile/geodb.pyo | |||
18 | ${PYSITELIB}/tifffile/lsm2bin.py | 24 | ${PYSITELIB}/tifffile/lsm2bin.py | |
19 | ${PYSITELIB}/tifffile/lsm2bin.pyc | 25 | ${PYSITELIB}/tifffile/lsm2bin.pyc | |
20 | ${PYSITELIB}/tifffile/lsm2bin.pyo | 26 | ${PYSITELIB}/tifffile/lsm2bin.pyo | |
21 | ${PYSITELIB}/tifffile/numcodecs.py | 27 | ${PYSITELIB}/tifffile/numcodecs.py | |
22 | ${PYSITELIB}/tifffile/numcodecs.pyc | 28 | ${PYSITELIB}/tifffile/numcodecs.pyc | |
23 | ${PYSITELIB}/tifffile/numcodecs.pyo | 29 | ${PYSITELIB}/tifffile/numcodecs.pyo | |
24 | ${PYSITELIB}/tifffile/tiff2fsspec.py | 30 | ${PYSITELIB}/tifffile/tiff2fsspec.py | |
25 | ${PYSITELIB}/tifffile/tiff2fsspec.pyc | 31 | ${PYSITELIB}/tifffile/tiff2fsspec.pyc | |
26 | ${PYSITELIB}/tifffile/tiff2fsspec.pyo | 32 | ${PYSITELIB}/tifffile/tiff2fsspec.pyo | |
27 | ${PYSITELIB}/tifffile/tiffcomment.py | 33 | ${PYSITELIB}/tifffile/tiffcomment.py | |
28 | ${PYSITELIB}/tifffile/tiffcomment.pyc | 34 | ${PYSITELIB}/tifffile/tiffcomment.pyc | |
29 | ${PYSITELIB}/tifffile/tiffcomment.pyo | 35 | ${PYSITELIB}/tifffile/tiffcomment.pyo | |
30 | ${PYSITELIB}/tifffile/tifffile.py | 36 | ${PYSITELIB}/tifffile/tifffile.py | |
31 | ${PYSITELIB}/tifffile/tifffile.pyc | 37 | ${PYSITELIB}/tifffile/tifffile.pyc | |
32 | ${PYSITELIB}/tifffile/tifffile.pyo | 38 | ${PYSITELIB}/tifffile/tifffile.pyo | |
33 | ${PYSITELIB}/tifffile/tifffile_geodb.py | |||
34 | ${PYSITELIB}/tifffile/tifffile_geodb.pyc | |||
35 | ${PYSITELIB}/tifffile/tifffile_geodb.pyo |
@@ -1,5 +1,5 @@ | @@ -1,5 +1,5 @@ | |||
1 | $NetBSD: distinfo,v 1.10 2021/11/17 17:25:03 adam Exp $ | 1 | $NetBSD: distinfo,v 1.11 2023/04/24 07:03:08 adam Exp $ | |
2 | 2 | |||
3 | BLAKE2s (tifffile-2021.11.2.tar.gz) = 94eda32fafead53cfbd45ec836340eda55f4403c448236f0f2520396ea7fed09 | 3 | BLAKE2s (tifffile-2023.4.12.tar.gz) = 3498559d8b58143a8707394bf38f9b59917c3e1d3a07a88a425bb910e7910385 | |
4 | SHA512 (tifffile-2021.11.2.tar.gz) = f9c69306096535c6d2f11cc52d8f9c6cbb04b2b767d09acb0a27b1a7be7152b0dd324ec2faf1ca96998f86f028bd4b31f79895731cc5c7c026717812fb1949cb | 4 | SHA512 (tifffile-2023.4.12.tar.gz) = 71c2c24552b44592288887b83e1f67ecf9acfe9a47da5ced49da18cd603f911f5fa0803e5eb4984af3a00a35abe21091b91be90abed345b6c7196dbac40f47ba | |
5 | Size (tifffile-2021.11.2.tar.gz) = 271504 bytes | 5 | Size (tifffile-2023.4.12.tar.gz) = 342873 bytes |