Mpwt

Modify:

- replace GPL license by LGPL license.

**Warning**:
In this version, some option names have been changed:
- "--dat" ("dat_creation" in python code) has been replaced by "--flat" ("flat_creation" in python code) to better reflect the attribute-values flat files created by this option.

Add:

- new options to extract other files to the ouput folder (issue 63):
- "--mx" ("xml_creation") to extract XML files created by MetaFlux.
- "--mo" ("owl_extraction") to extract owl files.
- "--mc" ("col_extraction") to extract tabulated files (".col" extension).

Fix:

- issue with "-r" (size_reduction) option: all files were extracted instead of only requested output files.

Modify:

- replace "--dat" ("dat_creation") by "--flat" ("flat_creation") to better reflect data created by this command.
- use PGDB ID as output name when using mpwt without input_folder (like "mpwt -o output_folder").
- update readme.

Add:

- \_\_version\_\_ in mpwt init file to handle version (issue 59).

Fix:

- error when creating dat files without input folder (issue 61).

Modify:

- refactor how paths are handled (issue 60). This is a first step to the compatibility of mpwt on Windows. But this will need more tests and modification.

mpwt has now a new dependency with **chardet** (linked to issue 56).

Fix:

- issue with encoding when writing the terminal logs (issue 56).
- issue with Pathway Tools pop-up showing after attribute-value flat files creation (issue 57).

Add:

- an option (--tp/patho_transporter_inference) to use Transporter Inference Parser with PathoLogic (issue 53).
- a badge showing last Pathway Tools release compatible with mpwt.
- a picture trying to show how mpwt works.
- clean option when using topf.
- GitHub Actions to release mpwt on PyPI with GitHub Release.

Fix:

- no join and close of Pool map if an error occurred (issue 52).
- issue when error can occur after PGDB creation but not take into account (issue 54).

Modify:

- replace Pool map by starmap (issue 51).

Add:

- a check for unfinished builds. If during a previous run a build failed, mpwt will delete it and relaunch it (issue 49).
- a badge with a link to the preprint.

Fix:

- numerous issues in topf (issue 30).
- numerous issues with taxon_id file when using circular, codon_table or element_type.
- numerous issues with raise error messages not showing.
- typos.