CVS commit: pkgsrc/graphics/py-tifffile

["Adam Ciarcinski" <adam%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   adam
Date:           Mon Apr 24 07:03:08 UTC 2023

Modified Files:
        pkgsrc/graphics/py-tifffile: Makefile PLIST distinfo

Log Message:
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).


To generate a diff of this commit:
cvs rdiff -u -r1.12 -r1.13 pkgsrc/graphics/py-tifffile/Makefile
cvs rdiff -u -r1.3 -r1.4 pkgsrc/graphics/py-tifffile/PLIST
cvs rdiff -u -r1.10 -r1.11 pkgsrc/graphics/py-tifffile/distinfo

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

Modified files:

Index: pkgsrc/graphics/py-tifffile/Makefile
diff -u pkgsrc/graphics/py-tifffile/Makefile:1.12 pkgsrc/graphics/py-tifffile/Makefile:1.13
--- pkgsrc/graphics/py-tifffile/Makefile:1.12   Wed Jan  5 15:41:12 2022
+++ pkgsrc/graphics/py-tifffile/Makefile        Mon Apr 24 07:03:08 2023
@@ -1,8 +1,7 @@
-# $NetBSD: Makefile,v 1.12 2022/01/05 15:41:12 wiz Exp $
+# $NetBSD: Makefile,v 1.13 2023/04/24 07:03:08 adam Exp $
 
-DISTNAME=      tifffile-2021.11.2
+DISTNAME=      tifffile-2023.4.12
 PKGNAME=       ${PYPKGPREFIX}-${DISTNAME}
-PKGREVISION=   2
 CATEGORIES=    graphics python
 MASTER_SITES=  ${MASTER_SITE_PYPI:=t/tifffile/}
 
@@ -11,18 +10,24 @@ HOMEPAGE=   https://www.lfd.uci.edu/~gohlk
 COMMENT=       Read and write TIFF(r) files
 LICENSE=       modified-bsd
 
-USE_LANGUAGES= # none
+DEPENDS+=      ${PYPKGPREFIX}-numpy-[0-9]*:../../math/py-numpy
+TEST_DEPENDS+= ${PYPKGPREFIX}-fsspec-[0-9]*:../../sysutils/py-fsspec
+TEST_DEPENDS+= ${PYPKGPREFIX}-test-[0-9]*:../../devel/py-test
 
-PYTHON_VERSIONS_INCOMPATIBLE=  27
+USE_LANGUAGES= # none
 
 USE_PKG_RESOURCES=     yes
 
+PYTHON_VERSIONS_INCOMPATIBLE=  27
+
 post-install:
 .for bin in lsm2bin tiff2fsspec tiffcomment tifffile
        cd ${DESTDIR}${PREFIX}/bin && \
        ${MV} ${bin} ${bin}-${PYVERSSUFFIX} || ${TRUE}
 .endfor
 
+do-test:
+       cd ${WRKSRC} && ${SETENV} ${TEST_ENV} pytest-${PYVERSSUFFIX} tests
+
 .include "../../lang/python/egg.mk"
-.include "../../math/py-numpy/buildlink3.mk"
 .include "../../mk/bsd.pkg.mk"

Index: pkgsrc/graphics/py-tifffile/PLIST
diff -u pkgsrc/graphics/py-tifffile/PLIST:1.3 pkgsrc/graphics/py-tifffile/PLIST:1.4
--- pkgsrc/graphics/py-tifffile/PLIST:1.3       Sun Jun 13 18:43:24 2021
+++ pkgsrc/graphics/py-tifffile/PLIST   Mon Apr 24 07:03:08 2023
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.3 2021/06/13 18:43:24 adam Exp $
+@comment $NetBSD: PLIST,v 1.4 2023/04/24 07:03:08 adam Exp $
 bin/lsm2bin-${PYVERSSUFFIX}
 bin/tiff2fsspec-${PYVERSSUFFIX}
 bin/tiffcomment-${PYVERSSUFFIX}
@@ -15,6 +15,12 @@ ${PYSITELIB}/tifffile/__init__.pyo
 ${PYSITELIB}/tifffile/__main__.py
 ${PYSITELIB}/tifffile/__main__.pyc
 ${PYSITELIB}/tifffile/__main__.pyo
+${PYSITELIB}/tifffile/_imagecodecs.py
+${PYSITELIB}/tifffile/_imagecodecs.pyc
+${PYSITELIB}/tifffile/_imagecodecs.pyo
+${PYSITELIB}/tifffile/geodb.py
+${PYSITELIB}/tifffile/geodb.pyc
+${PYSITELIB}/tifffile/geodb.pyo
 ${PYSITELIB}/tifffile/lsm2bin.py
 ${PYSITELIB}/tifffile/lsm2bin.pyc
 ${PYSITELIB}/tifffile/lsm2bin.pyo
@@ -30,6 +36,3 @@ ${PYSITELIB}/tifffile/tiffcomment.pyo
 ${PYSITELIB}/tifffile/tifffile.py
 ${PYSITELIB}/tifffile/tifffile.pyc
 ${PYSITELIB}/tifffile/tifffile.pyo
-${PYSITELIB}/tifffile/tifffile_geodb.py
-${PYSITELIB}/tifffile/tifffile_geodb.pyc
-${PYSITELIB}/tifffile/tifffile_geodb.pyo

Index: pkgsrc/graphics/py-tifffile/distinfo
diff -u pkgsrc/graphics/py-tifffile/distinfo:1.10 pkgsrc/graphics/py-tifffile/distinfo:1.11
--- pkgsrc/graphics/py-tifffile/distinfo:1.10   Wed Nov 17 17:25:03 2021
+++ pkgsrc/graphics/py-tifffile/distinfo        Mon Apr 24 07:03:08 2023
@@ -1,5 +1,5 @@
-$NetBSD: distinfo,v 1.10 2021/11/17 17:25:03 adam Exp $
+$NetBSD: distinfo,v 1.11 2023/04/24 07:03:08 adam Exp $
 
-BLAKE2s (tifffile-2021.11.2.tar.gz) = 94eda32fafead53cfbd45ec836340eda55f4403c448236f0f2520396ea7fed09
-SHA512 (tifffile-2021.11.2.tar.gz) = f9c69306096535c6d2f11cc52d8f9c6cbb04b2b767d09acb0a27b1a7be7152b0dd324ec2faf1ca96998f86f028bd4b31f79895731cc5c7c026717812fb1949cb
-Size (tifffile-2021.11.2.tar.gz) = 271504 bytes
+BLAKE2s (tifffile-2023.4.12.tar.gz) = 3498559d8b58143a8707394bf38f9b59917c3e1d3a07a88a425bb910e7910385
+SHA512 (tifffile-2023.4.12.tar.gz) = 71c2c24552b44592288887b83e1f67ecf9acfe9a47da5ced49da18cd603f911f5fa0803e5eb4984af3a00a35abe21091b91be90abed345b6c7196dbac40f47ba
+Size (tifffile-2023.4.12.tar.gz) = 342873 bytes