Merge Michel lab/Cresset changes into LOMAP

.gitattributes

@@ -0,0 +1,2 @@
+Lomap/_version.py export-subst
+lomap/_version.py export-subst

.gitignore

@@ -0,0 +1,111 @@
+# 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/
+.nox/
+.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
+
+# IPython
+profile_default/
+ipython_config.py
+
+# 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/
+.dmypy.json
+dmypy.json

.travis.yml

@@ -1,42 +1,45 @@
 language: python
-
-sudo: false
+matrix:
+  include:
+    - os: linux
+      python: 3.6
+      env:
+        - PYTHON_VER=3.6
+    - os: linux
+      python: 3.5
+      env:
+        - PYTHON_VER=3.5
 
 branches:
   only:
+    - devel
     - master
-
-
-before_install:
-  - source devtools/travis-ci/install.sh 
-  - export PYTHONUNBUFFERED=true
-
-
-install: true
-
-
-script: 
-  - conda config --add channels ${ORGNAME}
-  - conda build devtools/conda-recipe 
-  - conda create -n _test --yes
-  - source activate _test
-  - conda install --use-local lomap --yes
-  - conda install --yes pip nose
-  - pip install nose-timer
-  - nosetests -v
-
-env:
-  matrix:
-    - CONDA_PY=27
-    - CONDA_PY=34
-
-  global:
-    - ORGNAME="nividic"
-    - PACKAGENAME="lomap"
-
+    - feat_pytest 
+
+before_install: 
+  - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
+  - bash miniconda.sh -b -p $HOME/miniconda
+  - export PATH="$HOME/miniconda/bin:$PATH"
+  - hash -r
+  - conda config --set always_yes yes --set changeps1 no
+  - conda update -q conda
+  - conda info -a
+  - conda create -q -n test-env python=$TRAVIS_PYTHON_VERSION
+  - source activate test-env
+  - conda install networkx
+  - conda install numpy
+  - conda install matplotlib
+  - conda install -c rdkit rdkit=2018.03.4
+  - conda install pip pytest
+  - pip install codecov
+install: yes
+
+script:
+  - python setup.py install
+  - pytest -v test/test_lomap.py 
 
 after_success:
   - echo "...DONE..."
-
+  - codecov
 notifications:
-  email: false
+  email: false

CHANGELOG

@@ -0,0 +1,19 @@
+*********
+CHANGELOG
+*********
+
+0.0.x
+=====
+
+Internal Alpha version
+----------------------
+- Basic functionality of preparing a Perturbation map for alchemical free energy calculations
+
+1.0.0
+=====
+
+- added versioning
+- support for python 3.5 and networkx2
+- improved visualisation of output networks
+- better enforcement of PEP8 style python
+- no longer support for python 2.7

MANIFEST.in

@@ -3,4 +3,6 @@ recursive-include test  *
 include MANIFEST.in
 include README.md
 include LICENCE.txt
-include example.py
+include examples/example.py
+include versioneer.py
+include lomap/_version.py

README.md

@@ -1,59 +1,58 @@
 [![Anaconda Badge](https://anaconda.org/nividic/lomap/badges/version.svg)](https://anaconda.org/nividic/lomap)
-
 [![Build Status](https://travis-ci.org/MobleyLab/Lomap.svg?branch=master)](https://travis-ci.org/MobleyLab/Lomap)
+[![codecov](https://codecov.io/gh/MobleyLab/Lomap/branch/devel/graph/badge.svg)](https://codecov.io/gh/MobleyLab/Lomap)
 
 
 # Lomap
 Alchemical free energy calculations hold increasing promise 
 as an aid to drug discovery efforts. However, applications of 
 these techniques in discovery projects have been relatively 
-few, partly because of the difficulty of planning and setting up 
+rare, partly because of the difficulty of planning and setting up 
 calculations. The lead optimization mapper (LOMAP) was 
 introduced as an automated algorithm to plan efficient relative 
 free energy calculations between potential ligands within 
 a substantial of compounds. The original LOMAP code was mainly
 based on commercial APIs such as OpenEye and Schrodinger. The aim 
-of this project is to deveop a new version of LOMAP based on free
+of this project is to develop a new version of LOMAP based on free
 avalaible APIs such as RDKit offering the scientific community a 
-free tool to plan in advance binding free energy calculations
+free tool to plan in advance binding free energy calculations.
 
 
 ## Prerequisites
-* RDKit Release >2015.09.2
-* Graphviz 2.38
-* pygraphviz
-* NetworkX 
-* Matplotlib > 2.0
-* PyQt 4.11
+* RDKit Release
+* NetworkX
+* Matplotlib 
+* python > 3.5 
 
 Authors
 -------
 * Gaetano Calabro' <gcalabro@uci.edu>
 * David Mobley <dmobley@uci.edu>
 
-## Installation
-
-Add to the conda channels:
-
-conda config --add channels nividic
+* Mark Mackey
+* Lester Hedges
+* Antonia S J S Mey
+* Jenke Scheen
 
-and then:
-
-conda install lomap
-
-or
+## Installation
 
-Add to the conda channels:
+`python setup.py install`
 
-conda config --add channels mobleylab
+Usage
+-----
+As a commandline tool LOMAP can be simply used as:
+`
+lomap test/basic/
+`
 
-and then:
+For a basic example run:
+`python examples/example.py`
 
-conda install lomap
+For generating radial graphs with a hub, run:
+`python examples/example_radial.py`
 
+If you would rather use the API directly, try:
 
-Usage
------
 ```python
 import lomap
 
@@ -101,10 +100,3 @@ nx_graph = db_mol.build_graph()
 ```
 
 
-
-## Issues
-* Lomap is in debugging stage and it has been tested on Ubuntu 14.04 and OSX Yosemite
-* Lomap has been developed in python 2.7 and 3.4
-
-## Disclaimers
-* This code is currently in alpha release status. Use at your own risk. We will almost certainly be making changes to the API in the near future.

devtools/conda-recipe/meta.yaml

@@ -19,7 +19,7 @@ requirements:
     - rdkit
     - matplotlib
     - pyqt ==4.11.4
-    - networkx ==1.11
+    - networkx >=2.0
     - graphviz
     - pygraphviz
     - pillow
@@ -28,10 +28,10 @@ requirements:
   run:
     - python
     - boost
-    - rdkit 
+    - rdkit
     - matplotlib
-    - pyqt
-    - networkx ==1.11
+    - pyqt ==4.11.4
+    - networkx >=2.0
     - graphviz
     - pygraphviz
     - pillow

devtools/travis-ci/install.sh

@@ -1,4 +1,4 @@
-MINICONDA=Miniconda2-latest-Linux-x86_64.sh
+MINICONDA=Miniconda3-latest-Linux-x86_64.sh
 MINICONDA_MD5=$(curl -s https://repo.continuum.io/miniconda/ | grep -A3 $MINICONDA | sed -n '4p' | sed -n 's/ *<td>\(.*\)<\/td> */\1/p')
 wget http://repo.continuum.io/miniconda/$MINICONDA
 if [[ $MINICONDA_MD5 != $(md5sum $MINICONDA | cut -d ' ' -f 1) ]]; then
@@ -10,5 +10,5 @@ PIP_ARGS="-U"
 
 export PATH=$HOME/miniconda/bin:$PATH
 
-conda install --yes conda-build jinja2 anaconda-client pip 
+conda install --yes pip 
 

example.py → examples/example.py

@@ -8,7 +8,7 @@
 # The DBMolecule class must be created with a valid
 # directory name
 
-db_mol = lomap.DBMolecules('test/basic/', output=True)
+db_mol = lomap.DBMolecules('../test/basic/', output=True)
 
 # db_mol = lomap.DBMolecules('test/basic/', output=True, display=True)
 

example_radial_graph.py → examples/example_radial_graph.py

@@ -7,7 +7,7 @@
 # The DBMolecule class must be created with a valid
 # directory name
 
-db_mol = lomap.DBMolecules('test/radial/', output=True, radial=True )
+db_mol = lomap.DBMolecules('../test/radial/', output=True, radial=True )
 #use the radial option with hub ligand set as 
 #db_mol = lomap.DBMolecules('test/radial/', output=True, radial=True, hub="ejm_46.mol2")
 

lomap/__init__.py

@@ -59,11 +59,14 @@
       nx_graph = db_mol.build_graph() 
 """
 
-from lomap.dbmol import DBMolecules
-from lomap.dbmol import SMatrix
-from lomap.dbmol import Molecule
-from lomap.mcs import MCS
+from .dbmol import DBMolecules
+from .dbmol import SMatrix
+from .dbmol import Molecule
+from .mcs import MCS
 
 del dbmol
-del graphgen
 del mcs
+
+from ._version import get_versions
+__version__ = get_versions()['version']
+del get_versions