3.5.6

What's Changed

• version boost, and include GRCm39 in ESS docs by @WardDeb in #1297
• ensure -a/-b are positive by @WardDeb in #1301
• drop bws from plotFingerPrint doc by @WardDeb in #1302
• Np2 by @WardDeb in #1325
• Version print multibigwigsummary / plotcoverage by @zimoun in #1304
• ARM osx installation instructions by @WardDeb in #1328

New Contributors

• @zimoun made their first contribution in #1304

Full Changelog: 3.5.5...3.5.6

3.5.5

What's Changed

• drop support for python 3.7
• doc fixes (argparse properly displayed, minor changes in installation instructions)
• deepblue support stops
• initiate deprecation of tight_layout in plotheatmap, in favor of constrained_layout. Minor changes in paddings, etc can occur (but for the better).
• documentation changes to improve ESS tab, table constraints have been lifted & sphinx_rtd_theme to v2.0.0
• upload artifact in gh test runner pinned to 3
• Try to get the number of processors from sched_getaffinity, to avoid using to many in job submissions for example. #1199
• Fix typo in estimateScaleFactor that fixes broken argparsing. #1286

Full Changelog: 3.5.4...3.5.5

3.5.4

• error handling + cases for bwAverage with > 2 samples (@lldelisle )
• Tick.label deprecated for matplotlib 3.8 (@lldelisle )
• matplotlib minimal version is now 3.5
• cicd update for pypi push

3.5.3

• matplotlib version pin has been removed, some colormap changes in cm.py for newer version. Some plotting differences might occur
• dependencies and metadata are defined in the toml file (setup.py & requirements deprecated)
• scripts / entrypoints are defined here as well (bin folder deprecated)
• wheels are built with setuptools / toml file now (python >= 3.7)
• deeptools' version is defined in the toml file as well (no more _version.py, keep importlib as a requirement until we drop python 3.7 support). --version flags have been changed to use importlib in all executables.
• usage standardized per executable
• nosetests are deprecated and ported to pytests
• pytests now run on proposed wheel with version 3.7 - 3.11
• dependency on the custom typescript action (https://github.com/deeptools/github-actions) has been deprecated in favor of micromamba/python/miniconda-setup actions
• planemo tests and pytests use conda environment(.github/test_and_build.yml), historical 'foo' name is dropped.
• planemo tests expected pngs are slightly changed (due to mpl updates) expected qual metrics in plotfingerprint changed, not 100% where exactly the rounding difference comes from
• planemo tests run on galaxy 23.1
• stricter label checks and validator in galaxy wrapper
• deprecation of np types for builtin types

3.5.2

What's Changed

• new subcommand: Bigwig average #1169
• dendogram of plotCorrelation now matches each cell correctly
• Fix label options
• add pool
• several other bugs fixed: #1159, #1185, #1172, #1181, #1183
• Fix galaxy tests
• upload artifact
• allow 1 or 2 lines diff for bowtie2 program
• change github action to get artifacts
• fix plotPCA
• try to fix old samtools installed
• add forgotten channels
• CI test planemo in a separate test
• CI test pypi push only on release tag
• alignmentSieve: increase default chunklength in alignmentSieve (#1180 )
• alignmentSieve: output compressed bamfile (#1147 )
• suppress lack of index warnings from pysam
• fixedStep in bedGraph output to avoid merging bins with equal values.

Full Changelog: 3.5.1...3.5.2

3.5.1

• cmp usage is updated to fit the recent mpl updates.
• The requirements.txt is updated.
• "NA" occurences in plotFingerprint.py have been replaced by numpy.NAN (PR #1002)
• computeMatrixOperations.xml is fixed (brought up in #1003)
• plotly error is fixed. (issue #1013)
• relase version is updated in planemo.sh
• fixed galaxy tests
• A bug is taken care of in computeMatrixOperations.py / dataRange
• in plotProfile.py legen location is changed from auto to best (issue #1042)

3.5.0

• Fixed a small issue in computeGCBias (issue #969)
• Added dataRange to computeMatricOperation to return min,max,median and 10th and 90th percentile.
• Fixed a small typo in bamCompare. (issue #966)
• Save the output matrix of the plotheatmap in a format to be compatible with running plotheatmap on it again.(issue #953)
• Different colors can now be set by user for plotProfile --plotType heatmap (issue #956)
• Added the auto option to the zMin and zMax of plotHeatmap. (issue #908)
• Added --sortUsingSamples and --clusterUsingSamples to the plotHeatmap galaxy wrapper. (issue #976)

3.4.3

• Changed iteritems() in estimateEscaleFactor to its python3 compatible items().
• Added the missing argument (--clusterUsingSamples) to plotProfile.

3.4.1

• Prevented temporary bedGraph files from being written to (possibly small) shared-memory drives even when TMPDIR is set to somewhere else. Now shared memory is only used if requested by setting TMPDIR (or other appropriate environment variables) to /dev/shm.
• Fixed a bug in bamPEFragmentSize that caused incompatibility with newer matplotlib releases. (issue #928)

3.4.0

• Fixed a bug in one of the Galaxy wrappers.
• Added the --lineAtTickMarks option to plotHeatmap so that there are dashed vertical lines for each tick mark in the plot. (issue #924)