Tobias

- Fixed bug when reading motifs in "long" format. An error is now written if the pfm/jaspar motif does not follow 4-row format.
- Added transfac as possible input through biopython parser.
- Fixed bug caused by updated parameter name bug stemming from the adjustText library
- Fixed bug caused by an updated parameter name stemming from pandas
- added new tool "SubMerge" for subsetting and merging results of BINDetect analysis

- Fixed error with 'matplotlib.cbook.mplDeprecation', which is found at 'matplotlib.MatplotlibDeprecationWarning' in matplotlib>=3.8. TOBIAS now checks for the matplotlib version when filtering warnings.
- Improved error messages when reading corrupt bigwig file in BINDetect

- Pinned adjustText<0.8 due to Attribute error (116 and 182)
- Solved std::bad_alloc error in BINDetect due to 0-counts in motifs (192)
- Solved deprecation error for pypdf2: PdfFileMerger -> PdfMerger and set lower limit for pypdf version
- Fixed BINDetect error causing "Falling back to 'constant' normalization" arising from "ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 1 dimensions." due to upgrade of numpy.

- Fixed deprecation errors for writer.save() and DataFrameGroupBy.mean
- Improved error when .bed.gz is input to regions.from_bed (180)
- Fix error in plotting BINDetect volcano for many motifs (181)

- Fixed True/False highlighted column from 0.14.0 to include bindetect excel output as well.
- Added '--bias-pkl' option to ATACorrect (174)

- Added '--cmap' option in PlotHeatmap (130)
- Added 'drop-chrom' in ATACorrect to gain more control over which chromosomes should be excluded (142)
- Added a True/False "<cond1>_<cond2>_highlighted" column in bindetect_results.txt/.xlsx files. These columns mark the highlighted TFs for each volcano plot.
- Added check for empty '--TFBS' files in CreateNetwork