RLS Version 2.0.0

Effectively a minor release, turning the _SemiBin2 beta_ into a full
SemiBin2 release.

Full ChangeLog:

- `SemiBin`: Better error checking throughout
- `SemiBin`: Write a log file
- `concatenate_fasta`: support compression
- `concatenate_fasta`: slightly better error message when contig ID already contains separator
- `SemiBin`: add `bin_short` as alias for `bin`

ChangeLog

@@ -1,4 +1,5 @@
-Unreleased
+Version 2.0.0
+	* SemiBin: Better error checking throughout
 	* SemiBin: Write a log file
 	* concatenate_fasta: support compression
 	* concatenate_fasta: slightly better error message when contig ID already

README.md

@@ -57,7 +57,7 @@ Please find more options and details below and [read the docs](https://semibin.r
 
 ## Advanced Installation
 
-SemiBin runs on Python 3.7-3.11.
+SemiBin runs on Python 3.7-3.11. Python 3.12 should work as well, but not well tested yet.
 
 ### Bioconda
 

SemiBin/semibin_version.py

@@ -1 +1 @@
-__version__ = '1.5.1'
+__version__ = '2.0.0'

docs/subcommands.md

@@ -222,7 +222,7 @@ These have the same meaning as for `single_easy_bin`
 
 ### bin_short
 
-The `bin_short` subcommand (`bin` is an accepted alias, for backwards compatibility) requires the contig file and output (files `data.csv`, `model.h5`) from the `generate_sequence_features_single`, `generate_sequence_features_multi` and `train` subcommand as inputs and output the final bins in the `output_recluster_bins` directory.
+The `bin_short` subcommand (for backwards compatibility reasons, `bin` is accepted as an alias) requires the contig file and output (files `data.csv`, `model.h5`) from the `generate_sequence_features_single`, `generate_sequence_features_multi` and `train` subcommand as inputs and output the final bins in the `output_recluster_bins` directory.
 
 #### Required arguments
 

docs/usage.md

@@ -257,7 +257,7 @@ Having access to a GPU can speed up this mode.
 (4) Bin
 
 ```bash
-SemiBin2 bin \
+SemiBin bin_short \
     -i contig.fa \
     --model contig_output/model.h5 \
     --data contig_output/data.csv \

docs/whatsnew.md

@@ -1,11 +1,13 @@
 # What's New
 
-## Unreleased version
+## Version 2.0.0
 
 ### User-visible changes
 
 - Running SemiBin now writes a log file in the output directory
 - The `concatenate_fasta` subcommand now supports compression
+- Adds `bin_short` subcommand as alias for `bin` (by analogy with `bin_long`)
+
 
 ## Version 1.5.1 (SemiBin2 beta)