Testing now pytest and bug fixes for scripts

Major changes for the testing from nose to pytest

What's Changed

• Added --extend-by function by @Acribbs in #131
• Ac tables2table by @Acribbs in #130
• bump version by @Acribbs in #133

Full Changelog: v0.7.2...v0.7.4

bug fixes for setup.py

In order to get conda to build need to revert changes to setup.py

Last change before script gff2psl and APG module deprecation

• Warning of deprecation for gff2psl and Blat module
• Warning of deprecation for AGP module
• Removed IGV and CBiotools modules
• Cleaned up repo with redundant files

python3.10 fixes and script removal

• removed redundant scripts and removed some code to make it easier to maitain
• changed tostring to tobytes for python3 compatibility
• Various numpy.int to .int64 and .float to .float64 changes

Updated to work with pysam>=0.17

#110 updated pysam imports to reflect the updated pysam code

v0.6.4

Reverted back to old setup.py

v0.6.3

The following have been updated for this release:

• Updated to work with latest pysam
• Updated to work with latest biopython
• Added version strings to scripts that are missing them
• Readthedocs now build the documentation

increased version tag

Failed to increase version tag in repo in last release

tests now implemented in GitHub actions

This release adds the following:

• Pinned biopython to 1.78
• bug fixes to fasta2bed for ungapped function
• tests are now implemented on GitHub actions

Compatibility with pandas 1.0

The v0.6.0 release makes cgat-apps compatible with pandas-1.0.0.

It also:

• adds bcl2fastq, a wrapper that outputs fastq files from bcl files (#59)
• pins pysam to version 0.5.12 (#56)

and other minor bugfixes (e.g. #57)