Ecosyste.ms: Issues

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GitHub / JLSteenwyk/ClipKIT issues and pull requests

#59 - [YYYY-MM-DD]: [BUG TITLE] cannot read phylip or maf files

Issue - State: closed - Opened by aebaci about 1 month ago - 2 comments
Labels: bug

#58 - Bump setuptools from 69.5.1 to 70.0.0

Pull Request - State: open - Opened by dependabot[bot] 4 months ago
Labels: dependencies

#57 - Bump zipp from 3.1.0 to 3.19.1

Pull Request - State: open - Opened by dependabot[bot] 5 months ago
Labels: dependencies

#56 - Bump certifi from 2023.7.22 to 2024.7.4

Pull Request - State: open - Opened by dependabot[bot] 5 months ago
Labels: dependencies

#55 - Bump urllib3 from 1.26.4 to 1.26.19 in /docs

Pull Request - State: open - Opened by dependabot[bot] 5 months ago
Labels: dependencies

#54 - Bump tornado from 6.1 to 6.4.1 in /docs

Pull Request - State: open - Opened by dependabot[bot] 6 months ago
Labels: dependencies

#53 - Bump requests from 2.23.0 to 2.32.0

Pull Request - State: open - Opened by dependabot[bot] 6 months ago
Labels: dependencies

#52 - Bump jinja2 from 2.11.3 to 3.1.4 in /docs

Pull Request - State: open - Opened by dependabot[bot] 7 months ago
Labels: dependencies

#51 - Bump tqdm from 4.66.2 to 4.66.3

Pull Request - State: open - Opened by dependabot[bot] 7 months ago
Labels: dependencies

#50 - Bump idna from 2.10 to 3.7 in /docs

Pull Request - State: closed - Opened by dependabot[bot] 7 months ago - 1 comment
Labels: dependencies

#49 - Bump certifi from 2020.4.5.1 to 2023.7.22

Pull Request - State: closed - Opened by dependabot[bot] 7 months ago
Labels: dependencies

#48 - fixed errors that were throwing errors for docs

Pull Request - State: closed - Opened by JLSteenwyk 7 months ago

#47 - Added support for Python 3.11

Pull Request - State: closed - Opened by JLSteenwyk 7 months ago

#46 - Cannot Install the clipkit

Issue - State: closed - Opened by zhangwenda0518 7 months ago - 1 comment
Labels: bug

#45 - remove gaps and codon[YYYY-MM-DD]: [BUG TITLE]

Issue - State: closed - Opened by nbat64 8 months ago - 9 comments
Labels: bug

#43 - Question about clarifying defaults for --gap_characters

Issue - State: closed - Opened by smorzechowski 9 months ago - 2 comments
Labels: bug

#42 - Enable codon option in programmatic interface

Pull Request - State: closed - Opened by TJBIII 10 months ago

#41 - Code used to benchmark

Issue - State: closed - Opened by sen-pai 11 months ago - 1 comment
Labels: question

#40 - 2023-12-05: Difference between parameters `smart-gap`, `gappy` and `kpic-gappy`

Issue - State: closed - Opened by sanyalab 12 months ago - 3 comments
Labels: question

#39 - [2023-12-05]: Cannot Install latest version of clipkit

Issue - State: closed - Opened by sanyalab 12 months ago - 2 comments
Labels: bug

#38 - Change to trimming behavior with gappyness threshold?

Issue - State: closed - Opened by chtsai0105 about 1 year ago - 2 comments
Labels: bug

#37 - Numpy performance improvements

Pull Request - State: closed - Opened by TJBIII about 1 year ago

#36 - 2023-08-24: Use numpy to accelerate the trimming process

Issue - State: closed - Opened by chtsai0105 about 1 year ago - 2 comments
Labels: enhancement

#35 - Bump certifi from 2020.12.5 to 2023.7.22 in /docs

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#34 - Add tests for api module

Pull Request - State: closed - Opened by TJBIII over 1 year ago

#33 - Bump pygments from 2.7.4 to 2.15.0

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#32 - Bump requests from 2.23.0 to 2.31.0

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#31 - Dev ClipKIT 2.0

Pull Request - State: closed - Opened by JLSteenwyk over 1 year ago

#30 - Bump requests from 2.25.1 to 2.31.0 in /docs

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#29 - Should I make consensus sequence before using Clipkit or after ClipKit

Issue - State: closed - Opened by Rohit-Satyam over 1 year ago - 3 comments

#28 - Bump certifi from 2020.4.5.1 to 2022.12.7

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#27 - added to change log for 1.4.0 in docs

Pull Request - State: closed - Opened by JLSteenwyk over 1 year ago

#26 - Seq type handling

Pull Request - State: closed - Opened by JLSteenwyk over 1 year ago

#25 - extract parsimony sites

Issue - State: closed - Opened by atongsa almost 2 years ago - 1 comment

#24 - Refactor stats calculation and return stats from execute

Pull Request - State: closed - Opened by TJBIII almost 2 years ago

#23 - Bump certifi from 2020.12.5 to 2022.12.7 in /docs

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies

#22 - Bump numpy from 1.18.2 to 1.21.0

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago
Labels: dependencies

#21 - Bump numpy from 1.18.2 to 1.21.0 in /docs

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago
Labels: dependencies

#20 - Preserve sequence description for FASTA

Issue - State: closed - Opened by edgardomortiz almost 3 years ago - 2 comments

#19 - Trim CDS sequence

Issue - State: closed - Opened by jsharbrough about 3 years ago - 4 comments

#18 - Bump babel from 2.9.0 to 2.9.1 in /docs

Pull Request - State: closed - Opened by dependabot[bot] about 3 years ago - 1 comment
Labels: dependencies

#17 - Bump py from 1.8.1 to 1.10.0 in /docs

Pull Request - State: closed - Opened by dependabot[bot] about 3 years ago
Labels: dependencies

#16 - on pinning dependency versions

Issue - State: closed - Opened by ialbert about 3 years ago - 2 comments

#14 - Output sequence as digits

Issue - State: closed - Opened by andersgs over 3 years ago - 6 comments

#13 - Bump urllib3 from 1.26.4 to 1.26.5 in /docs

Pull Request - State: closed - Opened by dependabot[bot] over 3 years ago - 1 comment
Labels: dependencies

#12 - Bump pygments from 2.6.1 to 2.7.4

Pull Request - State: closed - Opened by dependabot[bot] over 3 years ago
Labels: dependencies

#11 - Bump py from 1.8.1 to 1.10.0

Pull Request - State: closed - Opened by dependabot[bot] over 3 years ago
Labels: dependencies

#10 - help message

Issue - State: closed - Opened by haruosuz over 3 years ago - 1 comment

#9 - Bump pygments from 2.6.1 to 2.7.4 in /docs

Pull Request - State: closed - Opened by dependabot[bot] over 3 years ago - 2 comments
Labels: dependencies

#8 - Bump pyyaml from 5.3.1 to 5.4 in /docs

Pull Request - State: closed - Opened by dependabot[bot] over 3 years ago
Labels: dependencies

#7 - Bump jinja2 from 2.11.2 to 2.11.3 in /docs

Pull Request - State: closed - Opened by dependabot[bot] over 3 years ago - 1 comment
Labels: dependencies

#6 - Bump bleach from 3.1.4 to 3.3.0

Pull Request - State: closed - Opened by dependabot[bot] almost 4 years ago
Labels: dependencies

#5 - Cannot read in fasta files

Issue - State: closed - Opened by LifeMine-swyka about 4 years ago - 2 comments

#4 - fixed united testing to work with np arrays

Pull Request - State: closed - Opened by JLSteenwyk over 4 years ago

#3 - Add file handler for logging and remove logArr. Clean up arg parsing

Pull Request - State: closed - Opened by JLSteenwyk over 4 years ago

#2 - Re org

Pull Request - State: closed - Opened by JLSteenwyk over 4 years ago

#1 - Dev

Pull Request - State: closed - Opened by JLSteenwyk over 4 years ago