Commit eb5ebd14 authored by Martino Bertoni's avatar Martino Bertoni 🌋

cleaned package root

parent 40fc39a4
Pipeline #2015 passed with stages
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.project
.pydevproject
*.pyc
.settings
# Byte-compiled / optimized / DLL files
__pycache__/
*.py[cod]
*$py.class
# C extensions
*.so
# Distribution / packaging
.Python
build/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
lib/
lib64/
parts/
sdist/
var/
wheels/
*.egg-info/
.installed.cfg
*.egg
MANIFEST
# PyInstaller
# Usually these files are written by a python script from a template
# before PyInstaller builds the exe, so as to inject date/other infos into it.
*.manifest
*.spec
# Installer logs
pip-log.txt
pip-delete-this-directory.txt
# Unit test / coverage reports
htmlcov/
.tox/
.coverage
.coverage.*
.cache
nosetests.xml
coverage.xml
*.cover
.hypothesis/
.pytest_cache/
# Translations
*.mo
*.pot
# Django stuff:
*.log
local_settings.py
db.sqlite3
# Flask stuff:
instance/
.webassets-cache
# Scrapy stuff:
.scrapy
# Sphinx documentation
docs/_build/
# PyBuilder
target/
# Jupyter Notebook
.ipynb_checkpoints
# pyenv
.python-version
# celery beat schedule file
celerybeat-schedule
# SageMath parsed files
*.sage.py
# Environments
.env
.venv
env/
venv/
ENV/
env.bak/
venv.bak/
# Spyder project settings
.spyderproject
.spyproject
# Rope project settings
.ropeproject
# mkdocs documentation
/site
# mypy
.mypy_cache/
......@@ -2,15 +2,25 @@
Credits
=======
Development Lead
Development TEAM
----------------
* Miquel Duran Frigola <miquel.duran@irbbarcelona.org>
* Oriol Guitart <oriol.guitart@irbbarcelona.org>
* Martino Bertoni <martino.bertoni@irbbarcelona.org>
* Adria Fernandez <adria.fernandez@irbbarcelona.org>
* Pau Badia <pau.badia@irbbarcelona.org>
* Nicolas Soler <nicolas.soler@irbbarcelona.org>
Contributors
------------
None yet. Why not be the first?
* Adria Fernandez <adria.fernandez@irbbarcelona.org>
* Lidia Mateo <lidia.mateo@irbbarcelona.org>
* David Amat <david.amat@irbbarcelona.org>
* Alejandro Castrelo <alejandro.castrelo@irbbarcelona.org>
* Modesto Orozco <modesto.orozco.ruiz@irbbarcelona.org>
* Aleix Gimeno <aleix.gimeno@irbbarcelona.org>
* Paula Torren <paula.torren@irbbarcelona.org>
* Elena Pareja <elena.pareja@irbbarcelona.org>
* Roger Compte <roger.compte@irbbarcelona.org>
......@@ -15,7 +15,8 @@ Types of Contributions
Report Bugs
~~~~~~~~~~~
Report bugs at http://gitlab.sbnb.org/packages/chemical_checker/issues.
Report bugs in
`Gitlab <http://gitlabsbnb.irbbarcelona.org/packages/chemical_checker/issues>`_
If you are reporting a bug, please include:
......@@ -38,14 +39,15 @@ and "help wanted" is open to whoever wants to implement it.
Write Documentation
~~~~~~~~~~~~~~~~~~~
chemicalchecker could always use more documentation, whether as part of the
official chemicalchecker docs, in docstrings, or even on the web in blog posts,
The Chemical Checker could always use more documentation, whether as part of the
official docs, in docstrings, or even on the gitlab repository, in notebooks,
articles, and such.
Submit Feedback
~~~~~~~~~~~~~~~
The best way to send feedback is to file an issue at http://gitlab.sbnb.org/packages/chemical_checker/issues.
The best way to send feedback is to file an issue in
`Gitlab <http://gitlabsbnb.irbbarcelona.org/packages/chemical_checker/issues>`_
If you are proposing a feature:
......@@ -54,23 +56,3 @@ If you are proposing a feature:
* Remember that this is a volunteer-driven project, and that contributions
are welcome :)
Tips
----
To run a subset of tests::
$ py.test tests.test_chemicalchecker
Deploying
---------
A reminder for the maintainers on how to deploy.
Make sure all your changes are committed (including an entry in HISTORY.rst).
Then run::
$ bumpversion patch # possible: major / minor / patch
$ git push
$ git push --tags
=======
History
=======
0.1.0 (2018-11-21)
------------------
* First release.
GNU GENERAL PUBLIC LICENSE
Version 3, 29 June 2007
Python Package with everything needed to create and query the Chemical Checker.
Copyright (C) 2018 Martino Bertoni
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
Also add information on how to contact you by electronic and paper mail.
You should also get your employer (if you work as a programmer) or school,
if any, to sign a "copyright disclaimer" for the program, if necessary.
For more information on this, and how to apply and follow the GNU GPL, see
<http://www.gnu.org/licenses/>.
The GNU General Public License does not permit incorporating your program
into proprietary programs. If your program is a subroutine library, you
may consider it more useful to permit linking proprietary applications with
the library. If this is what you want to do, use the GNU Lesser General
Public License instead of this License. But first, please read
<http://www.gnu.org/philosophy/why-not-lgpl.html>.
include AUTHORS.rst
include CONTRIBUTING.rst
include HISTORY.rst
include LICENSE
include README.rst
include ../LICENSE
include chemicalchecker/util/config/cc_config.json
include chemicalchecker/util/logging/logging_conf.ini
......
===============
Chemical Checker
===============
Python Package with everything needed to create and query the Chemical Checker.
* Free software: GNU General Public License v3
* Documentation: http://gitlab.sbnb.org/packages/chemical_checker/wikis/home
Features
--------
* Unified logging, profiling, and config
* HPC and DB agnostic
Unit-testing
------------
Got to your chemicalchecker package directory
To run all tests::
$ pytest
To run a subset of tests::
$ pytest tests.test_chemicalchecker
Deploying
---------
A reminder for the maintainers on how to deploy.
Make sure all your changes are committed (including an entry in HISTORY.rst).
Then run::
$ bumpversion patch # possible: major / minor / patch
TODO EXPAND... get version and tag accordingly::
$ git pull --rebase
$ git push
$ git push --tags
Upload it in DevPI::
$ devpi login USER --password='PASSWORD'
$ devpi use USER/dev
$ devpi upload
$ devpi push chemicalchecker==0.1.0 root/dev
$ devpi test chemicalchecker==0.1.0 root/dev
Install it
----------
with the following::
$ sudo pip install --trusted-host devpi.sbnb.org --index http://devpi.sbnb.org:3141/root/dev/ chemicalchecker
#!/bin/bash
PACKAGE_NAME=$1
FULL_VERSION=$2
MINOR_VERSION=${FULL_VERSION%.*}
MAJOR_VERSION=${FULL_VERSION%.*.*}
cd docs
make html
cd ..
#init_devpi.sh
devpi upload --with-docs
devpi test ${PACKAGE_NAME}==$FULL_VERSION
devpi push ${PACKAGE_NAME}==$FULL_VERSION root/dev
pip==18.1
bumpversion==0.5.3
wheel==0.32.1
flake8==3.5.0
tox==3.5.2
coverage==4.5.1
Sphinx==1.8.1
twine==1.12.1
pytest==3.8.2
pytest-runner==4.2
sqlalchemy
paramiko
psycopg2-binary
autologging==1.1.0
patool
pandas
wget
standardiser
h5py
numpy==1.16.0
scipy
scikit-learn
seaborn
matplotlib==2.0.0
gensim
timeout_decorator
mock
tensorflow
adanet
csvsort
e3fp
cython
MulticoreTSNE
fancyimpute
networkx
\ No newline at end of file
[bumpversion]
current_version = 0.1.0
commit = True
tag = True
[bumpversion:file:setup.py]
search = version='{current_version}'
replace = version='{new_version}'
[bumpversion:file:chemicalchecker/__init__.py]
search = __version__ = '{current_version}'
replace = __version__ = '{new_version}'
[bdist_wheel]
universal = 1
[flake8]
exclude = docs
[aliases]
# Define setup.py command aliases here
test = pytest
[tool:pytest]
collect_ignore = ['setup.py']
......@@ -5,12 +5,6 @@
from setuptools import setup, find_packages
with open('README.rst') as readme_file:
readme = readme_file.read()
with open('HISTORY.rst') as history_file:
history = history_file.read()
requirements = [
'numpy',
'h5py',
......@@ -24,7 +18,9 @@ requirements = [
'sklearn',
'csvsort',
'matplotlib<3.0',
'seaborn'
'seaborn',
'tqdm',
'apache-airflow'
]
setup_requirements = ['pytest-runner']
......@@ -41,7 +37,7 @@ setup(
classifiers=[
'Development Status :: 2 - Pre-Alpha',
'Intended Audience :: Developers',
'License :: OSI Approved :: GNU General Public License v3 (GPLv3)',
'License :: MIT License',
'Natural Language :: English',
"Programming Language :: Python :: 2",
'Programming Language :: Python :: 2.7',
......@@ -51,14 +47,26 @@ setup(
'Programming Language :: Python :: 3.6',
'Programming Language :: Python :: 3.7',
],
description="Python Package with everything needed to create and query the Chemical Checker.",
description="Chemical Checker Package.",
install_requires=requirements,
license="GNU General Public License v3",
long_description=readme + '\n\n' + history,
long_description='''The Chemical Checker (CC) is a data-driven resource of small molecule
bioactivity data. The main goal of the CC is to express data in a format
that can be used off-the-shelf in daily computational drug discovery
tasks. The resource is organized in **5 levels** of increasing
complexity, ranging from the chemical properties of the compounds to
their clinical outcomes. In between, we consider targets, off-targets,
perturbed biological networks and several cell-based assays, including
gene expression, growth inhibition, and morphological profiles. The CC
is different to other integrative compounds database in almost every
aspect. The classical, relational representation of the data is
surpassed here by a less explicit, more machine-learning-friendly
abstraction of the data''',
include_package_data=True,
keywords='chemicalchecker',
name='chemicalchecker',
packages=find_packages(exclude=['chemicalchecker.tool.hotnet*', 'chemicalchecker.tool.targetmate*']),
packages=find_packages(
exclude=['chemicalchecker.tool.hotnet*', 'chemicalchecker.tool.targetmate*']),
setup_requires=setup_requirements,
test_suite='tests',
tests_require=test_requirements,
......
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