BA_PY: Optimize Your Workflow with Python!

mbapy is a Python package that includes a collection of useful Python scripts as sub-modules, and it's goal is Basic for All in Python.
mbapy primarily focus on data works, including data-retrieval, data-management, data-visualization, data-analysis and data-computation. It is built for both python-users and command-line-users.

Get start

install

Now, mbapy only support pypi install:

pip install mbapy

mbapy is a multi-funtional package, and it does not require every third-party packages to make every sub-module work. However, it provides some requriements option to install more specified requirements to make some sub-modules work:

1. bio: some packages for biology(sci).
   install as pip install mbapy[bio]
2. game: some packages for game(pygame).
   install as pip install mbapy[game]
3. full: full requirements to make almost every sub-module in mbapy work(except dl_torch).
   install as pip install mbapy[full]

If you find the latest release version has some problems, you can try install the up-to-date version on github or gitee:

pip install git+https://github.com/BHM-Bob/BA_PY.git

pip install git+https://gitee.com/BHM-Bob/BA_PY.git

docs

The documentation for mbapy can be found on read the docs or just in the docs folder.

web sites

• open source at:
  1. github： https://github.com/BHM-Bob/BA_PY
  2. gitee： https://gitee.com/BHM-Bob/BA_PY
  3. SourceForge： https://sourceforge.net/projects/ba-py/
• docs at: read the docs: https://ba-py.rtfd.io
• PyPI: https://pypi.org/project/mbapy/

Contents

mbapy python package

__version__

some version info

base

some utils for easier coding

file

image

imgae utils, including reading, saving and process a image into a feature tensor via pytorch.

video

video utils, including extract frames or unique frames from a video.

plot

pandas.dataFrame utils for plot and some simple plot based on plt

web

utils for web-crawler

request

get a web hyml page or a selenium browser warpper for easier usage.

parse

utils for parsing html

task

small task manager

spider

a light-weight web spider architecture

stats

cluster

BAKmeans, KOptim, KBayesian from KMeans, and a func for many cluster

df

pandas.dataFrame utils for stats

reg

regression

test

some test func(using scipy and mostly give a support for mbapy-style data input)

dl-torch

pytorch utils for deeplearning

bb

basic blocks : tiny network structures

data

utils for dataset loading

loss

some loss function

m

model : deeplearning model constructed with basic blocks

utils

deeplearning training utils

optim

learning rate scheduler

paper

sci-paper utils, contains paper searching, downloading and parsing

paper_search

search papers via pubmed, baidu xueshu, wos

paper_download

download papers via scihub

paper_parse

parse paper from a pdf file into a dict of each sections

bio

peptide

class and funcs to calcu peptide MW, mutations

high_level

some high-level utils for bio

sci_instrument

hplc

HPLC instrument data processing and visualization

mass

mass spectrometry instrument data processing and visualization

scripts

some useful scripts for command user
launch by python -m mbapy.scripts.XXX or mbapy-cli XXX.

examples

web/crawler

1. chaoxin ppt multi threads downloader (jpg->pdf)
2. wujin search http://www.basechem.org
3. chemSub search http://chemsub.online.fr
4. cnipa https://pss-system.cponline.cnipa.gov.cn/seniorSearch

Additional Info

Requirements

1. mbapy requires python 3.8~3.11 because of the use of type hint and require matplotlib>=3.7.5, and the developer do not test it on other python version.
2. mbapy only requires a part of third-party packages in a specific version. This is because the developer do not want to make a big change during the installation. Bellow are the specific requirements:

• matplotlib>=3.7.5: HPLC and Mass data visualization need set legend draggable, this is only supported in 3.7+
• seaborn>=0.13.0: plot_utils.bar_utils.plot_bar need set seaborn stripplot native_scale, this is only supported in 0.13+
• nicegui[highcharts]: scripts/hplc: explore-hplc need a highcharts as interactive plot for manual peaking.
• torch any: though dl_torch is important for mbapy, but the developer kowns torch is a big package, and do not has a specific function requirement.