https://github.com/jlsteenwyk/clipkit

a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference
https://github.com/jlsteenwyk/clipkit

Keywords

bioinformatics evolution evolutionary-biology genomics phylogenetics phylogenomics python systematics

Keywords from Contributors

multiple-sequence-alignments transforms measur archiving compose animals optimize generic conversion observation

Last synced: 11 months ago
JSON representation

Acceptance Criteria

Revelant topics? true
External users? true
Open source license? true
Active? true
Fork? false

Repository metadata

a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference

Host: GitHub
URL: https://github.com/jlsteenwyk/clipkit
Owner: JLSteenwyk
License: mit
Created: 2020-04-11T14:41:10.000Z (about 5 years ago)
Default Branch: master
Last Pushed: 2024-05-20T23:00:23.000Z (12 months ago)
Last Synced: 2024-06-02T15:01:16.234Z (11 months ago)
Topics: bioinformatics, evolution, evolutionary-biology, genomics, phylogenetics, phylogenomics, python, systematics
Language: Python
Homepage: https://jlsteenwyk.com/ClipKIT/
Size: 25.7 MB
Stars: 54
Watchers: 7
Forks: 4
Open Issues: 3
Releases: 0
Metadata Files:
- Readme: README.md
- Changelog: change_log.txt
- License: LICENSE.md

Owner metadata

Name: Jacob L. Steenwyk
Login: JLSteenwyk
Email:
Kind: user
Description: Berkeley Science Fellow and Postdoctoral Scholar. Evolutionary genomics and software development.
Website: https://jlsteenwyk.com
Location: Berkeley, CA
Twitter: JLSteenwyk
Company: University of California, Berkeley
Icon url: https://avatars.githubusercontent.com/u/17225603?u=370657f310a69a5facb58b2d8e3a0ef1e7fdd1ac&v=4
Repositories: 10
Last ynced at: 2023-03-06T17:39:56.653Z
Profile URL: https://github.com/JLSteenwyk

GitHub Events

Total

Create event: 44
Release event: 10
Issues event: 30
Watch event: 54
Delete event: 21
Issue comment event: 53
Push event: 252
Pull request event: 58
Fork event: 3

Last Year

Create event: 21
Delete event: 7
Fork event: 2
Issue comment event: 24
Issues event: 15
Pull request event: 28
Push event: 84
Release event: 6
Watch event: 16

Committers metadata

Last synced: 11 months ago

Total Commits: 266
Total Committers: 8
Avg Commits per committer: 33.25
Development Distribution Score (DDS): 0.459

Commits in past year: 63
Committers in past year: 4
Avg Commits per committer in past year: 15.75
Development Distribution Score (DDS) in past year: 0.286

Name	Email	Commits
JLSteenwyk	j**k@g**m	144
Thomas Buida	t**a@g**m	45
Jacob Steenwyk	j**k@J**y	37
Jacob Steenwyk	j**k@J**t	21
Jacob Steenwyk	j**k@J**l	8
dependabot[bot]	4****]	8
Jacob L Steenwyk	j**k@J**l	2
Thomas Buida	T****I	1

Committer domains:

Issue and Pull Request metadata

Last synced: 11 months ago

Total issues: 17
Total pull requests: 35
Average time to close issues: 2 days
Average time to close pull requests: 26 days
Total issue authors: 15
Total pull request authors: 3
Average comments per issue: 2.88
Average comments per pull request: 0.34
Merged pull request: 21
Bot issues: 0
Bot pull requests: 22

Past year issues: 8
Past year pull requests: 14
Past year average time to close issues: 4 days
Past year average time to close pull requests: 18 days
Past year issue authors: 6
Past year pull request authors: 3
Past year average comments per issue: 2.75
Past year average comments per pull request: 0.29
Past year merged pull request: 7
Past year bot issues: 0
Past year bot pull requests: 8

More stats: https://issues.ecosyste.ms/repositories/lookup?url=https://github.com/jlsteenwyk/clipkit

Top Issue Authors

chtsai0105 (2)
sanyalab (2)
andersgs (1)
atongsa (1)
edgardomortiz (1)
haruosuz (1)
ialbert (1)
jolienvanhooff (1)
jsharbrough (1)
LifeMine-swyka (1)
nbat64 (1)
Rohit-Satyam (1)
sen-pai (1)
smorzechowski (1)
zhangwenda0518 (1)

Top Pull Request Authors

dependabot[bot] (22)
JLSteenwyk (9)
TJBIII (4)

Top Issue Labels

bug (5)
question (2)
enhancement (1)

Top Pull Request Labels

dependencies (22)

Package metadata

Total packages: 1
Total downloads:
- pypi: 480 last-month
Total dependent packages: 0
Total dependent repositories: 1
Total versions: 44
Total maintainers: 1

pypi.org: clipkit

Alignment trimming software for phylogenetics.

Homepage: https://github.com/jlsteenwyk/clipkit
Documentation: https://clipkit.readthedocs.io/
Licenses: mit
Latest release: 2.3.0 (published about 1 year ago)
Last Synced: 2024-06-02T15:07:34.549Z (11 months ago)
Versions: 44
Dependent Packages: 0
Dependent Repositories: 1
Downloads: 480 Last month
Docker Downloads: 0
Rankings:
- Docker downloads count: 2.276%
- Stargazers count: 9.91%
- Dependent packages count: 10.118%
- Average: 12.922%
- Downloads: 16.8%
- Forks count: 16.875%
- Dependent repos count: 21.552%
Maintainers (1)
- JLSteenwyk

Dependencies

Pipfile pypi

Cython ==0.29.16
Pygments ==2.7.4
appdirs ==1.4.3
astroid ==2.3.3
attrs ==19.3.0
biopython ==1.76
black ==19.10b0
bleach ==3.3.0
certifi ==2020.4.5.1
chardet ==3.0.4
click ==7.1.1
clipkit ==0.0.1
docutils ==0.16
idna ==2.9
isort ==4.3.21
keyring ==21.2.0
lazy-object-proxy ==1.4.3
mccabe ==0.6.1
more-itertools ==8.2.0
numpy ==1.21.0
pathspec ==0.8.0
pkginfo ==1.5.0.1
pluggy ==0.13.1
py ==1.10.0
pylint ==2.4.4
pyparsing ==2.4.7
pytest ==5.4.1
pytest-mock ==3.0.0
readme-renderer ==26.0
regex ==2020.4.4
requests ==2.23.0
requests-toolbelt ==0.9.1
six ==1.14.0
toml ==0.10.0
tqdm ==4.45.0
twine ==3.1.1
typed-ast ==1.4.1
urllib3 ==1.25.9
wcwidth ==0.1.9
webencodings ==0.5.1
wrapt ==1.11.2

docs/Pipfile pypi

sphinx-autobuild * develop
Pygments *
Sphinx *
sphinx_rtd_theme *

docs/Pipfile.lock pypi

argh ==0.26.2 develop
livereload ==2.6.3 develop
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pyyaml ==5.4 develop
six ==1.15.0 develop
sphinx-autobuild ==0.7.1 develop
tornado ==6.1 develop
watchdog ==2.0.2 develop
alabaster ==0.7.12
babel ==2.9.0
certifi ==2020.12.5
chardet ==4.0.0
docutils ==0.16
idna ==2.10
imagesize ==1.2.0
jinja2 ==2.11.3
markupsafe ==1.1.1
packaging ==20.9
pygments ==2.6.1
pyparsing ==2.4.7
pytz ==2021.1
requests ==2.25.1
snowballstemmer ==2.1.0
sphinx ==3.0.2
sphinx-rtd-theme ==0.4.3
sphinxcontrib-applehelp ==1.0.2
sphinxcontrib-devhelp ==1.0.2
sphinxcontrib-htmlhelp ==1.0.3
sphinxcontrib-jsmath ==1.0.1
sphinxcontrib-qthelp ==1.0.3
sphinxcontrib-serializinghtml ==1.1.4
urllib3 ==1.26.4

docs/requirements.txt pypi

appdirs ==1.4.3
attrs ==19.3.0
biopython ==1.76
click ==7.1.2
importlib-metadata ==1.6.0
more-itertools ==8.2.0
numpy ==1.21.0
packaging ==20.3
pathspec ==0.8.0
pluggy ==0.13.1
py ==1.10.0
pyparsing ==2.4.7
pytest ==5.4.1
pytest-mock ==3.0.0
regex ==2020.5.7
six ==1.14.0
toml ==0.10.0
tqdm ==4.45.0
typed-ast ==1.4.1
wcwidth ==0.1.9
zipp ==3.1.0

docs/requirements_manual.txt pypi

appdirs ==1.4.3
attrs ==19.3.0
biopython ==1.76
black ==19.10b0
click ==7.1.2
importlib-metadata ==1.6.0
more-itertools ==8.2.0
numpy ==1.21.0
packaging ==20.3
pathspec ==0.8.0
pluggy ==0.13.1
py ==1.10.0
pyparsing ==2.4.7
pytest ==5.4.1
pytest-mock ==3.0.0
regex ==2020.5.7
six ==1.14.0
toml ==0.10.0
tqdm ==4.45.0
typed-ast ==1.4.1
wcwidth ==0.1.9
zipp ==3.1.0

requirements.txt pypi

appdirs ==1.4.3
attrs ==19.3.0
biopython ==1.79
click ==7.1.2
importlib-metadata ==1.6.0
more-itertools ==8.2.0
numpy ==1.18.2
packaging ==20.3
pathspec ==0.8.0
pluggy ==0.13.1
py ==1.8.1
pyparsing ==2.4.7
pytest ==5.4.1
pytest-mock ==3.0.0
regex ==2020.5.7
six ==1.14.0
toml ==0.10.0
tqdm ==4.45.0
typed-ast ==1.4.1
wcwidth ==0.1.9
zipp ==3.1.0

.github/workflows/ci.yml actions

JamesIves/github-pages-deploy-action releases/v3 composite
actions/checkout master composite
actions/setup-python master composite
codecov/codecov-action v1.0.7 composite
dschep/install-pipenv-action v1 composite

docs/setup.py pypi

setup.py pypi

Pipfile.lock pypi

appdirs ==1.4.3
astroid ==2.3.3
attrs ==19.3.0
biopython ==1.76
black ==19.10b0
bleach ==3.3.0
certifi ==2023.7.22
chardet ==3.0.4
click ==7.1.1
clipkit ==0.0.1
cython ==0.29.16
docutils ==0.16
idna ==2.9
isort ==4.3.21
keyring ==21.2.0
lazy-object-proxy ==1.4.3
mccabe ==0.6.1
more-itertools ==8.2.0
numpy ==1.21.0
packaging ==24.0
pathspec ==0.8.0
pkginfo ==1.5.0.1
pluggy ==0.13.1
py ==1.10.0
pygments ==2.7.4
pylint ==2.4.4
pyparsing ==2.4.7
pytest ==5.4.1
pytest-mock ==3.0.0
readme-renderer ==26.0
regex ==2020.4.4
requests ==2.23.0
requests-toolbelt ==0.9.1
setuptools ==69.5.1
six ==1.14.0
toml ==0.10.0
tqdm ==4.66.2
twine ==3.1.1
typed-ast ==1.4.1
urllib3 ==1.25.9
wcwidth ==0.1.9
webencodings ==0.5.1
wrapt ==1.11.2

Score: 12.300436923564986

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