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VERSION
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VERSION
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1.2.2
- support gzipped protein files as input (thanks to alienzj for the PR)
1.2.1
- renamed private classes (thanks to misialq for the PR)
1.2.0
- modified how bin IDs are identified to improve output tables
1.1.11
- fixed error with inverse_transformed being deprecated in newer versions of Matplotlib
1.1.10
- fixed bug with missing bCalledGenes flag that was impacting a number of commands
1.1.9
- fixed support for gzip input FASTA files
1.1.8
- updated setup.py to include long description and fixed PyPi URL
1.1.7
- added Jie Zhu's (alienzj) PR to allow input files to be specified via a file
- added Jeremy Jacobson's (jjacobson95) PR to fix prettytable import issue
- added fix by Jie Li (jili6t) regarding more stringent matching of bin extensions
1.1.6
- allow CheckM data path to be set through a CHECKM_DATA_PATH environmental variable
1.1.5
- fixed small bug with maxibor's PR
1.1.4
- added Maxime Borry's (maxibor) PR to allow path to DATA_CONFIG file to be set
1.1.3
- fixed error resulting from incorrect GFF files produced by Prodigal on FASTA files with Windows style line endings
- replaced usage of normed keyword with density as required for Matplotlib >= 3.2.0
1.1.2
- removed erroneous error message when setting root to CheckM reference data
- fixed infinit loop issue when trying to install CheckM reference data to directory without write permission
1.1.1
- fixes legacy Python 2 syntax issues (thanks to Sebastian Jaenicke!)
1.1.0
- code base ported to Python 3
- massive thanks to baudrly, vinisalazar, and asafpr for initial Python 2 to 3 porting
- bug in ssu_finder fixed that on rare occasions caused a SSU sequence to be reported more than once
- now using i-Evalue to break ties in the rare cases when hits to a target sequence have the exact same full E-value; this makes the code more deterministic
- improvements to information reported in marker_plot
- fixed CLI issue with outliers method
1.0.18
- fix to CLI of bin_qa_plot (thanks to Finesim97 for PR)
1.0.17
- fixed bug with CLI of plotting methods introduced in 1.0.16
1.0.16
- made ~/.checkm the default directory for CheckM reference data
- "checkm data setRoot <directory>" is no longer interactive and the directory must be given on the command line
1.0.15
- fixed CheckM data setRoot command to work from command line (thanks to cbt for PR)
- added logging to files
- improved reporting of CheckM results to include timestamp
- removed "--force-overwrite" option and now allow output directories to already exist
1.0.14
- fixed bug with test command missing "--force-overwrite" option
1.0.13
- failed commands now exit with error code 1
- added "--force-overwrite" option
1.0.12
- removed bVerbose option for all commands
1.0.11
- fix to lineage_wf CLI regarding missing coverage_file argument
1.0.10
- updated version number for pypi
1.0.9
- removed ScreamingBackpack as a dependency and modified CheckM to never removes user files
- added "life" as an acceptable rank for the taxonomy_wf so the universal Prokaryotic marker set can be used
- fixed bug with processing empty gene files
- fixed bug with processing identical user genomes which cause pplacer to create polytomies