Hicstuff

- Fix file extension in hicstuff rebin.
- Fix incompatibility between lines and trim in hicstuff view.
- More flexible binning suffix support.
- Update commands.py and fix pandas >= 1.5, accordingly.

- Correct build to make it work.
- Correct hicstuff rebin fragments size issue.

- Check third parties at the beginning of pipeline.
- Change output file names of hicstuff cutsite.
- Reverse reads if necessary in the hicstuff cutsite.
- Improve figures plot.

- Add support for compressed genome
- Repare camembert plot
- Fix deprecation error form matplotlib 3.5.0
- correctly report when matrix rows do not match header in hics_flexible_loader
- Pin matplotlib version and docutils

* Improve dockerfile base layer to address compatibility bug with libcrypto.
* Standardize the format of default values in CLI help messages.
* Fix bug in distancelaw causing integer conversion of custom log bases

* The docker image is now based on the miniconda3 layer, which greatly reduces build times.
* P(s) normalization factor is only computed based on P(s) values within xlim. Before that, all values above the lower bound were used. Because longer distances have much lower interaction values, this makes a small difference in practice.