Draft: remove all content for review (DO NOT MERGE!)

This branch and merge request is for reviewing your code and code structure. It is only for the purpose of reviewing and should never be merged! Note that any changes made to the repo by you after creation of this merge request are not considered for this review. Please also note that we will not review code style here (we will use automatic tools for that in a future session), but rather we will keep feedback high level at this point. Please address any issues raised (if you haven't already addressed them on your own in the meantime).

Next to the in-line and general code comments we will give during the review sessions (done by me and Mihaela), we keep track of the status of the more formal requirements (i.e., not the actual code) with respect to repository setup, packaging and documentation in the following checklist. Please complete any pieces that remain after the "List checked by reviewers" was set to "Yes" by us (indicating that we are done checking your repo against the checklist). To address these, please check the relevant notebooks and homeworks for more info.

List checked by reviewers

• Yes
• No

Version control

• Repo configured correctly: repo public; default branch protected against pushes; fast-forward merges; encourage squash commits; delete source branch by default
• License available in file LICENSE without any file extension
• .gitignore available and includes common Python artifacts; no such artifacts (e.g., from building/packaging) are under version control
• Files organized as expected, with at least one and not more than three directories, all in lower case; one directory containing all the tool/app code and named after the app (required), one directory tests containing all test-related content (required if tests or test files are available), and one directory named img or images, containing the screenshots from exercise 1 (fine if omitted or deleted at this point); all other files (LICENSE, README.md, .gitignore, setup.py, etc.) in repository root directory

Packaging

• setup.py available (used pyproject.toml as alternative)
• CLI executable available
• CLI arguments available
• Tool can be successfully installed with pip install .
• CLI executable can be successfully executed with -h option

Documentation

• README.md has at least a synopsis, usage and installation instructions and contact information (can use zavolab-biozentrum@unibas.ch if you don't want to put your own); other sections, as outlined in the course materials, welcome
• Google-style docstrings available for all modules, classes, functions, methods
• Type hints provided at least for all functions & methods

tests/resources/Annotation1.gtf

-1	havana	gene	1	100	.	+	.	gene_id "GENE1";
-1	havana	transcript	1	100	.	+	.	gene_id "GENE1"; transcript_id "TRANSCRIPT1"; transcript_support_level "1";
-1	havana	exon	1	20	.	+	.	gene_id "GENE1"; transcript_id "TRANSCRIPT1"; exon_number "1"; exon_id "ENSE00002234944"; transcript_support_level "1";
-1	havana	exon	50	70	.	+	.	gene_id "GENE1"; transcript_id "TRANSCRIPT1"; exon_number "2"; exon_id "ENSE00003582793"; transcript_support_level "1";
-1	havana	exon	80	100	.	+	.	gene_id "GENE1"; transcript_id "TRANSCRIPT1"; exon_number "3"; exon_id "ENSE00002312635"; transcript_support_level "1";