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)

3.3.2

• Fixed --yAxisLabel in plotProfile (issue #889)
• Fixed a small X-axis tick offset issue. This caused the location of tick marks in profile plots to be shifted to the left by 0.5 to 1 bin. This was generally not notable, only really appearing when very few bins (e.g., 4) were used. The issue was mostly that the end tick would appear after the end of the plot, since its coordinate was the end of the bin. (issue #888)
• multiBamSummary and multiBigwigSummary no longer exclude small bins at the end of genomic chunks. multiBamSummary now has a --genomicChunkSize option in case users need to control the size of the genome used for multiprocessing for consistency. (issue #887)
• Added 4 new colormaps, which were copied from the seaborn project (issue #879). These are: rocket, mako, vlag, and icefire.
• Fixed an issue in the Galaxy wrapper of plotCorrelation where the X and Y.
• Fixed an issue with the --Offset option, where a single negative value wouldn't include only a single position, but rather that base through the end of the read. (stems from issue #902)
• Clustered output from plotHeatmap and plotProfile now allow computing the silhouette score of each row. This is printed in the returned BED file as the last column.