Protgraph

Changes and Improvements can be seen on PR 44

Finally, after 3 months of work and pizza, a new release: ProtGraph 0.2.1

This version does not have any breaking changes to the previous one and mostly adds new functionalities.

**Improvements/Changes**:
- The summarizing (merging) of single amino acids in nodes into one Node is significantly faster (Factor ~20x). E.G.: Executing ProtGraph on Titin will now only need roughly ~2 minutes (instead of ~30 minutes)!
- Psycopg2 has been replaced by Psycopg3, therefore an overall performance increase using Postgres should be seen. We also set up connections to use the binary protocol for better efficiency!
- New stopping criterion for started processes in ProtGraph. We noticed, that some processes do not get destroyed after they finished. This is most probably due to some multiprocessing shenanigans in Python itself. We changed the implementation slightly in hope that zombie processes occur less often!

**New Features**:
- New CLI Option, Add no description to the statistics output csv. This reduces the statistics file size considerably (for complete UP, a reduction of ~20 GB could be noticed)
- ProtGraph now collapses parallel edges into one edge, containing information of all parallel edges. This may only happen for some proteins, however, ProtGraph now has an "edge case" for that.
- A new exporter has been added: Cassandra (Cluster)
- We now are able to calculate the number of possible peptides by variants/mutagen and conflicts, giving more insights of the large search space!

The new release of ProtGraph should shortly be availble in PIP (PyPI) and probably tomorrow on BioConda due to new dependencies!

Changes and Improvements can be seen on PR 40

Here a short summary:
* The CLI has been reworked (BREAKING CHANGES) and is now easier to add/remove applied features/digestions from the SP-EMBL-Format
* New parsable Feature: MUTAGEN
* New parsable Feature: CONFLICT
* New "Aminoacid Replacment" via ProtGraph
* ProtGraph is now able to substitute a aminoacid with multiple aminoacids. E.G.: J -> I, L and more. These rules can be defined by the user.

The new release of ProtGraph should shortly be availble in PIP and BioConda!

Due to human error, Release 0.1.1 has been re-bumped to 0.1.2.

This re-bump allows us to publish the package automagically to PyPI and Conda.

This release fixes some minor issues. More details can be found in PR 31

First release of ProtGraph 0.1.0.

We now have a working version of ProtGraph with many export functionalities.

ProtGraph from now on can export peptides to: Postgres (and Citus!), MySql and Fasta. Furthermore, graphs can be directly exported into GML, GraphML, Dot, Pickle, Postgres, MySQL and even as two large CSVs or single CSVs for each protein.

The Fasta Header for ProtGraph has been reworked. We now have more precise information in those headers, which should be easy to understand.

The CLI has also been reworked. Instead of returning all possible flags and options at once, ProtGraph now returns only a minimal set of Flags and Options. There is of course a flag to display all flags and options available for ProtGraph.

With this release onward, we will also make sure to publich our latest Version into PyPI as well as in BioConda!

Nothing new, only added the Pipfile to the package for preperation to add it into conda.