Pytximport

API
- Allows the source column and the target column from the GTF to be explicitly set when creating a transcript-to-gene or transcript-name-to-transcript-mapping
- Removes unused `sparse` and `sparse_threshold` arguments

Other changes
- Adds regular cron job CI testing to detect changed dependencies

API
- Added support for RSEM gene-level quantification files. Previously, it was already possible to read RSEM transcript level data from a .tsv file. Now, not only can RMEM transcript data be read in by setting `data_type` to `rsem`, but if `gene_level` is set to True, existing gene-level data can be read in and aggregated by `pytximport`.
- Added support for gzipped files when reading in tabular data with `data_type` set `tsv`.

Other changes
- `pytximport` is now available through Bioconda and an install badge has been added to the README and the documentation.
- Added unit tests to check RSEM gene-level quantification for correctness.

API
- Added utility functions to create transcript-to-gene maps from Biomart or .gtf files.
- Added a flag to allow overwriting existing files.

Other changes
- Added unit tests for file saving via programatic (non-CLI) usage.

API
- Added support for inferential replicates via the `inferential_replicates`, `inferential_replicate_variance` and `inferential_replicate_transformer` arguments with support for salmon and kallisto.
- Fixed a bug where custom column names were not applied.
- Fixed a bug when saving .csv files from AnnData objects.

Other changes
- Added unit tests for file saving via programatic (non-CLI) usage.

API
- Added a new count transformation for differential transcript usage analysis: `dtu_scaled_tpm` (`dtuScaledTPM` in R-version of `tximport`)
- Added a utility function for renaming transcript-level exports with the transcript name: `utils.replace_transcript_ids_with_names`.
- When using biotype filtering, the TPM values will now be rescaled to match the sum of the TPM values before filtering.
- Apply biotype filtering, ignore transcript version and ignore after bar for transcript-level exports as well.
- Bug fix: Saving to files when exporting transcript-level counts works now.

Other changes
- Moved transcript version removal into the utility function `remove_transcript_version` and biotype filtering into the utility function `filter_by_biotype`.
- Always run unittests locally for each commit with pre-commit.

API
- Change the default `output_type` to "anndata".
- When a biotype filter is used, the abundance of the remaining transcripts after filtering will now be rescaled to match the total abundance pre-filtering for each sample.
- Bug fix: Now returns AnnData objects when returning transcript-level data if `output_type` is "anndata".

Other changes
- Run CI on `dev` branch.