Deeptools

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

* Programmed around a bug in matplotlib that prevented the plotCorrelation scatter plot from working. See https://bioinformatics.stackexchange.com/questions/12830/plot-correlation-between-several-bam-files/12831

* 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)

* 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)

* 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.

* Fixed `--plotNumbers` not working in `plotCorrelation`. This was issue 838.
* Fixed compatibility with matplotlib 3 and restrict to at least that version.
* The Y-axis labels should once again appear in both plotHeatmap and plotProfile (issue 844). This was related to the previous point.
* Testing is no longer performed with python 2.7, which will reach end of life in a couple months.
* Various documentation updates (issues 868, 867 and 851).
* Increased support for BED files with track header lines (issue 866).