cleaned package root

.gitignore

-.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/

package/AUTHORS.rst

@@ -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>

package/CONTRIBUTING.rst

@@ -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
-

package/HISTORY.rst

-=======
-History
-=======
-
-0.1.0 (2018-11-21)
-------------------
-
-* First release.

package/LICENSE

-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>.
-

package/MANIFEST.in

 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
 

package/README.rst

-===============
-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

package/release_library.sh

-#!/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

package/requirements_dev.txt

-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

package/setup.cfg

-[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']
-

package/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,