JOSS: https://github.com/glasgowcompbio/vimms/

dda fragmentation metabolomics python simulation

Score: 5.5012582105447265

Last synced: 28 minutes ago
JSON representation

Repository metadata:

A programmable and modular LC/MS simulator in Python

Host: GitHub
URL: https://github.com/glasgowcompbio/vimms/
Owner: glasgowcompbio
License: mit
Created: 2020-07-03T19:25:39.000Z (almost 6 years ago)
Default Branch: main
Last Pushed: 2026-06-13T19:24:43.000Z (9 days ago)
Last Synced: 2026-06-13T20:08:25.224Z (9 days ago)
Topics: dda, fragmentation, metabolomics, python, simulation
Language: Python
Homepage: https://glasgowcompbio.github.io/vimms/
Size: 291 MB
Stars: 24
Watchers: 4
Forks: 7
Open Issues: 11
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
- Zenodo: .zenodo.json

Owner metadata:

Name: glasgowcompbio
Login: glasgowcompbio
Email:
Kind: organization
Description:
Website:
Location:
Twitter:
Company:
Icon url: https://avatars.githubusercontent.com/u/47832966?v=4
Repositories: 11
Last Synced at: 2023-03-04T12:09:27.112Z
Profile URL: https://github.com/glasgowcompbio

GitHub Events

Total

Create event: 29
Delete event: 21
Fork event: 1
Issue comment event: 2
Issues event: 1
Pull request event: 54
Push event: 51
Release event: 3
Watch event: 3
Total: 165

Last Year

Create event: 27
Delete event: 21
Issue comment event: 1
Pull request event: 54
Push event: 49
Total: 152

Committers metadata

Last synced: 21 days ago

Total Commits: 1,070
Total Committers: 7
Avg Commits per committer: 152.857
Development Distribution Score (DDS): 0.56

Commits in past year: 9
Committers in past year: 2
Avg Commits per committer in past year: 4.5
Development Distribution Score (DDS) in past year: 0.111

Name	Email	Commits
Joe Wandy	j**y@g**m	471
VinnyDavies	v**s@g**k	210
Simon Rogers	s**s@g**m	190
unknown	m**2@g**m	173
Rónán Daly	r**y@g**k	14
Kei kuan To	2**t@s**k	9
dependabot[bot]	4****]	3

Issue and Pull Request metadata

Last synced: 4 months ago

Total issues: 71
Total pull requests: 98
Average time to close issues: 7 months
Average time to close pull requests: 21 days
Total issue authors: 11
Total pull request authors: 4
Average comments per issue: 1.97
Average comments per pull request: 0.36
Merged pull request: 50
Bot issues: 0
Bot pull requests: 37

Past year issues: 2
Past year pull requests: 53
Past year average time to close issues: 1 minute
Past year average time to close pull requests: about 3 hours
Past year issue authors: 1
Past year pull request authors: 2
Past year average comments per issue: 0.0
Past year average comments per pull request: 0.04
Past year merged pull request: 33
Past year bot issues: 0
Past year bot pull requests: 7

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

Top Issue Authors

joewandy (40)
sdrogers (9)
vinnydavies (8)
mcbrider5002 (6)
RonanDaly (2)
pisistrato (1)
oolonek (1)
samsonjm (1)
NitTza (1)
MKoesters (1)
jspaezp (1)

Top Pull Request Authors

joewandy (52)
dependabot[bot] (37)
sdrogers (7)
vinnydavies (2)

Top Issue Labels

enhancement (22)
bug (22)
refactoring (8)
question (6)
discussion (3)
priority (2)
codex (2)
documentation (1)
good first issue (1)
invalid (1)

Top Pull Request Labels

codex (43)
dependencies (37)
python (7)
enhancement (1)

Dependencies

Pipfile pypi

build * develop
mkdocs * develop
mkdocstrings * develop
twine * develop
autopep8 *
events *
flake8 *
gpy *
intervaltree *
ipyparallel *
ipywidgets *
joblib *
jsonpickle *
jupyterlab *
loguru *
mass-spec-utils *
matplotlib *
networkx *
numpy *
pandas *
pipenv-setup *
psims *
pymzml ==2.4.7
pysmiles *
pytest *
pytest-cov *
requests *
scikit-learn *
scipy *
seaborn *
statsmodels *
tabulate *
tqdm *

requirements.txt pypi

Babel ==2.9.1
Cerberus ==1.3.4
Cython ==0.29.24
Events ==0.4
GPy ==1.10.0
Jinja2 ==3.0.1
Markdown ==3.3.4
MarkupSafe ==2.0.1
Pillow ==8.3.2
PyYAML ==5.4.1
Pygments ==2.10.0
QtPy ==1.9.0
SQLAlchemy ==1.4.23
SecretStorage ==3.3.1
Send2Trash ==1.8.0
anyio ==3.3.1
appdirs ==1.4.4
argon2-cffi ==21.1.0
astunparse ==1.6.3
async-generator ==1.10
attrs ==21.2.0
backcall ==0.2.0
black ==19.10b0
bleach ==4.1.0
build ==0.7.0
cached-property ==1.5.2
certifi ==2021.5.30
cffi ==1.14.6
chardet ==3.0.4
charset-normalizer ==2.0.6
click ==8.0.1
colorama ==0.4.4
cryptography ==3.4.8
cycler ==0.10.0
debugpy ==1.4.3
decorator ==5.1.0
defusedxml ==0.7.1
distlib ==0.3.2
docutils ==0.17.1
entrypoints ==0.3
flake8 ==3.9.2
ghp-import ==2.0.1
greenlet ==1.1.1
idna ==3.2
importlib-metadata ==4.8.1
iniconfig ==1.1.1
intervaltree ==3.1.0
ipykernel ==6.4.1
ipyparallel ==7.0.1
ipython ==7.27.0
ipython-genutils ==0.2.0
ipywidgets ==7.5.1
jedi ==0.18.0
jeepney ==0.7.1
joblib ==1.0.1
json5 ==0.9.6
jsonpickle ==2.0.0
jsonschema ==3.2.0
jupyter ==1.0.0
jupyter-client ==7.0.3
jupyter-console ==6.1.0
jupyter-core ==4.8.1
jupyter-server ==1.11.0
jupyterlab ==3.1.12
jupyterlab-pygments ==0.1.2
jupyterlab-server ==2.8.1
keyring ==23.2.1
kiwisolver ==1.3.2
loguru ==0.5.3
lxml ==4.6.3
mass-spec-utils ==0.0.12
matplotlib ==3.4.3
matplotlib-inline ==0.1.3
mccabe ==0.6.1
mergedeep ==1.3.4
mistune ==0.8.4
mkdocs ==1.2.2
mkdocs-autorefs ==0.2.1
mkdocstrings ==0.15.2
molmass ==2021.6.18
more-itertools ==8.4.0
nbclassic ==0.3.2
nbclient ==0.5.4
nbconvert ==6.1.0
nbformat ==5.1.3
nest-asyncio ==1.5.1
networkx ==2.6.3
notebook ==6.4.4
numpy ==1.21.2
orderedmultidict ==1.0.1
outcome ==1.0.1
packaging ==20.9
pandas ==1.3.3
pandocfilters ==1.5.0
paramz ==0.9.5
parso ==0.8.2
pathspec ==0.9.0
patsy ==0.5.1
pbr ==5.6.0
pep517 ==0.11.0
pexpect ==4.8.0
pickleshare ==0.7.5
pip-shims ==0.5.3
pipenv-setup ==3.1.1
pipfile ==0.0.2
pkginfo ==1.7.1
plette ==0.2.3
pluggy ==1.0.0
prometheus-client ==0.11.0
prompt-toolkit ==3.0.20
psims ==0.1.43
psutil ==5.8.0
ptyprocess ==0.7.0
py ==1.10.0
pyDOE ==0.3.8
pycodestyle ==2.7.0
pycparser ==2.20
pyflakes ==2.3.1
pymdown-extensions ==8.2
pymzml ==2.4.7
pyparsing ==2.4.7
pyrsistent ==0.18.0
pysmiles ==1.0.1
pytest ==6.2.5
pytest-cov ==2.12.1
python-dateutil ==2.8.2
pytkdocs ==0.11.1
pytz ==2021.1
pyyaml-env-tag ==0.1
pyzmq ==22.3.0
qtconsole ==4.7.5
readme-renderer ==29.0
regex ==2021.8.28
requests ==2.26.0
requests-toolbelt ==0.9.1
requests-unixsocket ==0.2.0
requirementslib ==1.5.16
rfc3986 ==1.5.0
scikit-learn ==0.24.2
scipy ==1.4.1
seaborn ==0.11.2
six ==1.16.0
sniffio ==1.2.0
sortedcontainers ==2.4.0
statsmodels ==0.12.2
tabulate ==0.8.9
terminado ==0.12.1
testpath ==0.5.0
threadpoolctl ==2.2.0
toml ==0.10.2
tomli ==1.2.1
tomlkit ==0.7.2
tornado ==6.1
tqdm ==4.62.2
traitlets ==5.1.0
trio ==0.16.0
twine ==3.4.2
typed-ast ==1.4.3
urllib3 ==1.26.6
vistir ==0.5.2
watchdog ==2.1.5
wcwidth ==0.2.5
webencodings ==0.5.1
websocket-client ==1.2.1
widgetsnbextension ==3.5.1
xlrd ==1.2.0
zipp ==3.5.0

setup.py pypi

events *
gpy *
intervaltree *
ipyparallel *
joblib *
jsonpickle *
loguru *
mass-spec-utils *
matplotlib *
networkx *
numpy *
pandas *
psims *
pymzml ==2.4.7
pysmiles *
requests *
scikit-learn *
scipy *
seaborn *
statsmodels *
tabulate *
tqdm *

.github/workflows/python-package.yml actions

actions/checkout v2 composite
actions/setup-python v2 composite

environment.yml conda

autopep8
flake8
intervaltree
ipyparallel
ipywidgets
joblib
jsonpickle
jupyterlab
loguru
matplotlib
networkx
numba
numpy
pandas
pip
plotly
pytest
pytest-cov
requests
scikit-learn
scipy
seaborn
statsmodels
tabulate
tqdm

ecosyste.ms

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Experiments

Summary