Kb-python

`count`
* Hotfix for 10x Feature Barcode map when `-x 10x:FB` (146)

`ref`
* Fixed an issue with a dangling keyword argument when concatenating files (132).

`count`
* Fixed an issue where using `-x smartseq` would check for the `--nucleus` flag, which was deprecated in the previous version (133).

General
- Deprecated `--lamanno` and `--nucleus` flags. Use `--workflow` instead.
- Updated `setup.py` so that tests don't get installed.
- Fixed an issue where `requirements.txt` would not be included in the Pypi upload.

*This version has been yanked due to an issue with installation. Do not try to install this version!*

General
- Added a check for whether the temporary directory exists. If it does, now prints out an error and exits. (119)
- Logging is now handled by a specialized logger implemented in the `ngs-tools` library, which provides logger namespacing.
- Updated supported technologies text and syntax for `kb --list` so that they are more compact. Added link to the kallisto manual for custom technology definitions.
- Updated citation in `info`.

`ref`
- Fixed `--tmp` option to set the temporary directory properly (122)
- Major refactor of FASTA and GTF parsing. All relevant functions were replaced with appropriate ones from the `ngs-tools` library. The ones provided in this library are far more robust in dealing with GTF entries (especially missing attributes). FASTA and GTF files no longer have to be sorted nor decompressed. These all result in an approximately order-of-magnitude speedup in splitting the genomic FASTA. Additionally, more helpful error messages are printed, which should help user debuggability.
- Fixed an issue where no logging messages were displayed when downloading a reference with `-d`.

`count`
- Whitelists are now provided by the `ngs-tools` library.

General
* Added the optional arguments `--kallisto` and `--bustools`, which may be used to override the packaged kallisto and bustools binaries. The argument may be a command in the user's PATH, which will be expanded to the full absolute path, or an absolute/relative path to the binary (109, thanks apeltzer, dpryan79, Maarten-vd-Sande).
`ref`
* Any spaces in GTF groups are now removed. For instance, if a transcript has ID `TRANSCRIPT ID` then the resulting transcript sequence will be named `TRANSCRIPTID`. (97, thanks axelalmet)
`count`
* Fixed an issue where converting the count matrix using `--loom` and `--workflow lamanno` would cause an error (91)
* Fixed an issue with parsing FASTQ paths when using `-x smartseq`, where the second read file would be erroneously used as the first (114, thanks jma1991)
* Added entries to indicate the current working directory when the `kb` command was called, along with the `kallisto` and `bustools` binary paths and versions in `kb_info.json`.

`count`
- Fixed `loompy does not accept empty matrices as data` error when providing `--loom` with `--workflow lamanno` (91)
- When using `--h5ad` or `--loom` with `-x smartseq`, the output matrix has genes as columns, instead of transcripts. For genes that have multiple transcripts, the counts are added. (93)
- For `-x smartseq`, it is now possible to provide a batch TSV instead of FASTQs directly. The batch TSV must contain exactly three columns: cell ID, FASTQ 1 (read 1), FASTQ 2 (read 2).
- Added an error when an uneven number of FASTQs are provided for `-x smartseq` (only paired-end reads are currently supported)
- Turned off all logging and warning messages from `h5py` and `anndata`.