Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

support python3 and bugs fix #1

Open
wants to merge 48 commits into
base: master
Choose a base branch
from
Open
Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
48 commits
Select commit Hold shift + click to select a range
b7b77fd
support python3 and bugs fix
KimBioInfoStudio Jan 4, 2018
91d87ad
Update README.md
KimBioInfoStudio Jan 8, 2018
e9f291d
build wheel and upload to pypi
KimBioInfoStudio Jun 13, 2019
bb39968
upate readme
KimBioInfoStudio Jun 13, 2019
087f476
Update README.md
KimBioInfoStudio Jun 13, 2019
1c9cacd
test ci
KimBioInfoStudio Jun 20, 2019
9b23a71
Merge branch 'develop' of https://github.com/KimBioInfoStudio/PyCirco…
KimBioInfoStudio Jun 20, 2019
f0f8f37
test codecov
KimBioInfoStudio Jun 20, 2019
07a9671
add .travis.yml
KimBioInfoStudio Jun 20, 2019
2ce8a25
rename run_circos as test
KimBioInfoStudio Jun 20, 2019
e649ba3
codecov
KimBioInfoStudio Jun 20, 2019
75a85f9
install requ in ci
KimBioInfoStudio Jun 20, 2019
f545acd
add install circos
KimBioInfoStudio Jun 20, 2019
8c13833
add cd to demo
KimBioInfoStudio Jun 20, 2019
359101e
add some badage
KimBioInfoStudio Jun 21, 2019
61650a2
Update README.md
KimBioInfoStudio Aug 21, 2019
03a6aff
Update main.yml
KimBioInfoStudio Aug 21, 2019
e952a70
Update main.yml
KimBioInfoStudio Aug 21, 2019
8f6b931
Update main.yml
KimBioInfoStudio Aug 21, 2019
4c6f47d
update readme
KimBioInfoStudio Sep 17, 2019
5c799c8
Update README.md
KimBioInfoStudio Sep 17, 2019
e0620a3
update matplotlib for each version of python
KimBioInfoStudio Sep 17, 2019
b00fd5e
add more version of python
KimBioInfoStudio Sep 17, 2019
f5e9a92
remove python2.6 python3.4
KimBioInfoStudio Sep 17, 2019
05f0c4d
remove python2.6
KimBioInfoStudio Sep 17, 2019
9db1699
remove python2.6 python3.4
KimBioInfoStudio Sep 17, 2019
c52d9a1
Update setup.py
KimBioInfoStudio Sep 17, 2019
e10c0e7
Update setup.py
KimBioInfoStudio Sep 17, 2019
a5d2e37
Update setup.py
KimBioInfoStudio Sep 17, 2019
ae91922
remove python2 all
Sep 17, 2019
030abaf
add makefile
Sep 18, 2019
9663fa6
Update README.md
KimBioInfoStudio Sep 18, 2019
0910004
Update .travis.yml
KimBioInfoStudio Sep 18, 2019
204436f
Update .travis.yml
KimBioInfoStudio Sep 18, 2019
df3cb6a
add demo.png
Oct 8, 2019
0eccbf1
Update main.yml
KimBioInfoStudio Oct 23, 2019
b14a3d1
Update main.yml
KimBioInfoStudio Oct 23, 2019
95d06dc
Delete .travis.yml
KimBioInfoStudio Oct 23, 2019
a769f45
Update main.yml
KimBioInfoStudio Oct 23, 2019
0258257
Update main.yml
KimBioInfoStudio Oct 25, 2019
01177ab
update setup
Dec 12, 2019
c207559
make pylint happy
Dec 12, 2019
4cde0d9
Update main.yml
KimBioInfoStudio Dec 12, 2019
bae4be2
make lint happy
Sep 19, 2022
548ad28
make lint happy
Sep 19, 2022
ab19e55
make lint happy
Sep 19, 2022
31d6435
fix an error with latest matplotlib
Sep 19, 2022
bd92270
update pyton version
Sep 19, 2022
File filter

Filter by extension

Filter by extension


Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
56 changes: 56 additions & 0 deletions .github/workflows/main.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,56 @@
name: Auto CI Test On Github Actions

on: [push]

jobs:
build:
runs-on: ubuntu-latest
strategy:
max-parallel: 1
matrix:
python-version: [3.6, 3.7, 3.8, 3.9, 3.10]

steps:
- uses: actions/checkout@v1
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v1
with:
python-version: ${{ matrix.python-version }}

- name: Install dependencies
run: |
python -m pip install --upgrade pip
python -m pip install codecov pylint autopep8
python -m pip install -r requirements.txt

- name: Pre Format Code Style With Autopep8
run: |
python -m autopep8 -v -i -r ./

- name: Check Code Style With Pylint
run: |
#python -m pylint -v ./*.py
#python -m pylint -v ./src/*.py
#python -m pylint -v ./test/*.py

- name: Test With Demo Files
run: |
python setup.py install
cd test
python ./test.py

- name: Test Code Covrage
run: |
export CODECOV_TOKEN="e00c5f99-4f96-4cae-9bbc-d77668302050"
cd test
coverage run ./test.py
codecov

- name: Auto Deploy .whl File to PyPi
run: |
echo -e "[ INFO ] This Funcation Under Developing will coming soon"

- name: Auto Freeze a Github Release
run: |
echo -e "[ INFO ] This Funcation Under Developing will coming soon"

2 changes: 0 additions & 2 deletions MANIFEST.in

This file was deleted.

33 changes: 33 additions & 0 deletions Makefile
Original file line number Diff line number Diff line change
@@ -0,0 +1,33 @@
.PHONY: hlep pre lint install test clean
.DEFAULT: help
help:
@echo "----------------------------------------"
@echo "PyCircos"
@echo "Design For NGS Circos Plot Within Python"
@echo "----------------------------------------"
@echo "make help"
@echo "\tprint this help info to screen"
@echo "make pre"
@echo "\tinstall needed env, use only once"
@echo "make lint"
@echo "\trun pylint to format all file"
@echo "make install"
@echo "\tinstall pycircos"
@echo "make test"
@echo "\trun a test demo"
@echo "make clean"
@echo "\tclean temp cache and unusing file"
pre:
python3 -m pip install -r ./requirements.txt
lint:
python3 -m pip install pylint
python3 -m pylint
install:pre
python3 ./setup.py install
test:
python3 ./test/test.py
clean:
@rm -rf ./build ./dist ./pycircos.egg-info



58 changes: 58 additions & 0 deletions README.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,58 @@
# Python Modules for Circos Plot

[![Build Status](https://travis-ci.com/KimBioInfoStudio/PyCircos.svg?branch=develop)](https://travis-ci.com/KimBioInfoStudio/PyCircos)
![codecov](https://codecov.io/gh/KimBioInfoStudio/PyCircos/branch/develop/graph/badge.svg)



## 1. Pre Installation

> As official, Pyhton2 will end life form 2020-1-1, So we develop a new version support Python3.5+, We deeply recommand all users using the python version 3.5+, Thx!

### Python 3.5+ packages(automatically installed)

1. numpy
2. pandas
3. matplotlib


## 2. Installation
### intall dev branch

1. install from source code

```
git clone https://github.com/KimBioInfoStudio/PyCircos.git
cd PyCircos
pip install -r requirements.txt
python3 setup.py install [--user]
```

2. or install form source code with using 'make'

```
git clone https://github.com/KimBioInfoStudio/PyCircos.git
cd PyCircos
make install
```

3. install release branch

```
pip install pycircos
```

## 3. Examples
### command

```
cd ./test/
python3 test.py
open ./demo.png
```
### results

![](./test/demo.png)



29 changes: 0 additions & 29 deletions README.rst

This file was deleted.

3 changes: 0 additions & 3 deletions RELEASE

This file was deleted.

78 changes: 0 additions & 78 deletions demo/run_circos.py

This file was deleted.

57 changes: 0 additions & 57 deletions install.sh

This file was deleted.

3 changes: 3 additions & 0 deletions requirements.txt
Original file line number Diff line number Diff line change
@@ -0,0 +1,3 @@
numpy
pandas
matplotlib
Loading