diff --git a/.travis.yml b/.travis.yml index 2e7270a..0554252 100644 --- a/.travis.yml +++ b/.travis.yml @@ -7,7 +7,7 @@ addons: apt: sources: - ubuntu-toolchain-r-test - + before_install: - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install md5sha1sum; fi @@ -27,10 +27,17 @@ script: - conda config --add channels ${ORGNAME} # Create a test environment - conda create --quiet --yes -n test python=$python + # Activate root environment + #- source activate root # Activate the test environment - source activate test + # Get conda info + - conda info + # Get environment info + - conda list --explicit # Build recipie - conda build devtools/conda-recipe + #- conda-build devtools/conda-recipe -c conda-forge/label/gcc7 # Install locally-built package - conda install --yes --quiet --use-local ${PACKAGENAME} #- conda install --yes --quiet pip nose nose-timer @@ -41,17 +48,16 @@ os: - osx - linux - env: matrix: - python=2.7 CONDA_PY=27 # - python=3.4 CONDA_PY=34 - python=3.5 CONDA_PY=35 - python=3.6 CONDA_PY=36 + global: - - PACKAGENAME="sstmap" - ORGNAME="solvationtools" after_success: - - source devtools/travis-ci/deploy_anaconda.sh \ No newline at end of file + - source devtools/travis-ci/deploy_anaconda.sh diff --git a/Makefile b/Makefile index d4ec700..b498d76 100644 --- a/Makefile +++ b/Makefile @@ -1,4 +1,3 @@ -CC = g++ SOURCEDIR = ./sstmap INSTALLDIR = ~/anaconda2/bin bruteclust: $(SOURCEDIR)/make_clust_brute.cpp @@ -18,4 +17,4 @@ clean: rm -f kdhsa102 rm -f 6dimprobable -test: pytest -m tests \ No newline at end of file +test: pytest -m tests diff --git a/README.md b/README.md index b8ce8b6..dcf3c05 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,4 @@ -[![Build Status](https://travis-ci.org/kamran-haider/SSTMap.svg?branch=v1.1_dev)](https://travis-ci.org/kamran-haider/SSTMap) +[![Build Status](https://travis-ci.org/kamran-haider/SSTMap.svg?branch=master)](https://travis-ci.org/kamran-haider/SSTMap) [![Anaconda-Server Badge](https://anaconda.org/solvationtools/sstmap/badges/installer/conda.svg)](https://conda.anaconda.org/solvationtools) [![Anaconda-Server Badge](https://anaconda.org/solvationtools/sstmap/badges/downloads.svg)](https://anaconda.org/solvationtools/sstmap) [![DOI for Citing SSTMap](https://img.shields.io/badge/DOI-10.1021%2Fj.jctc.2017.11.021-blue.svg)](http://doi.org/10.1021/acs.jctc.7b00592) @@ -38,8 +38,8 @@ You can also download the release package manually from GitHub, unzip it, naviga ```bash https://github.com/KurtzmanLab/SSTMap/archive/1.1.4.tar.gz or https://github.com/KurtzmanLab/SSTMap/archive/1.1.4.zip -tar -xvf 1.1.4.tar.gz or unzip 1.0.0.zip -cd SSTMap-1.0 +tar -xvf 1.1.4.tar.gz or unzip 1.1.4.zip +cd SSTMap-1.1.4 python setup.py install ``` Or you can clone the GitHub repository, navigate into the directory, and execute the command: @@ -54,6 +54,7 @@ git checkout tags/1.1.4 python setup.py install ``` **For the developmental version:** + ``` python setup.py install ``` @@ -109,7 +110,7 @@ Principal Developer(s) Co-Developers ------------- * Steven Ramsey -* Anthony Cruz Balberdi +* Anthony Cruz Balberdy * Tobias Wulsdorf Principal Investigators diff --git a/devtools/conda-recipe/meta.yaml b/devtools/conda-recipe/meta.yaml index 451654f..325f751 100644 --- a/devtools/conda-recipe/meta.yaml +++ b/devtools/conda-recipe/meta.yaml @@ -1,6 +1,6 @@ package: name: sstmap - version: 1.1.3 + version: 1.1.4 source: path: ../../ @@ -8,19 +8,23 @@ source: requirements: build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + host: - python - - numpy 1.14.0 - - setuptools - - gcc - - toolchain - - libgcc + - numpy + - setuptools + - conda-build + - toolchain3 + - libgcc - gsl 2.2.1 - - libopenblas - + - libopenblas + - libgcc-ng + - libstdcxx-ng run: - python - libgcc - - numpy + - numpy - scipy - mdtraj - parmed diff --git a/setup.py b/setup.py index f2b52d3..343b08c 100644 --- a/setup.py +++ b/setup.py @@ -9,6 +9,7 @@ sources=['sstmap/_sstmap_ext.c'], include_dirs=[numpy.get_include()], extra_link_args=['-lgsl','-lgslcblas'])) + extensions.append(Extension('_sstmap_entropy', sources=['sstmap/_sstmap_entropy.cpp', 'sstmap/kdhsa102.cpp'], language="c++")) diff --git a/sstmap/__init__.py b/sstmap/__init__.py index a17afa4..ccac5db 100644 --- a/sstmap/__init__.py +++ b/sstmap/__init__.py @@ -45,7 +45,7 @@ __license__ = "MIT" __maintainer__ = "Kamran Haider" __email__ = "kamranhaider.mb@gmail.com" -__version__ = "1.1.3" +__version__ = "1.1.4" from sstmap import site_water_analysis, grid_water_analysis, utils diff --git a/sstmap/grid_water_analysis.py b/sstmap/grid_water_analysis.py index 5d0fce0..be7ffcd 100644 --- a/sstmap/grid_water_analysis.py +++ b/sstmap/grid_water_analysis.py @@ -221,7 +221,7 @@ def calculate_euler_angles(self, water, coords): H_temp = np.zeros(3) H_temp[0] = ((w2*w2+x2*x2)-(y2*y2+z2*z2))*h1wat[0] - H_temp[0] = (2*(x2*y2 - w2*z2)*h1wat[1]) + H_temp[0] + H_temp[0] = (2*(x2*y2 + w2*z2)*h1wat[1]) + H_temp[0] H_temp[0] = (2*(x2*z2-w2*y2)*h1wat[2]) + H_temp[0] H_temp[1] = 2*(x2*y2 - w2*z2)* h1wat[0] @@ -235,7 +235,7 @@ def calculate_euler_angles(self, water, coords): H_temp2 = np.zeros(3,) H_temp2[0] = ((w2*w2+x2*x2)-(y2*y2+z2*z2))*h2wat[0] H_temp2[0] = (2*(x2*y2 + w2*z2)*h2wat[1]) + H_temp2[0] - H_temp2[0] = (2*(x2*z2-w2*y2)+h2wat[2]) +H_temp2[0] + H_temp2[0] = (2*(x2*z2-w2*y2)*h2wat[2]) +H_temp2[0] H_temp2[1] = 2*(x2*y2 - w2*z2) *h2wat[0] H_temp2[1] = ((w2*w2-x2*x2+y2*y2-z2*z2)*h2wat[1]) +H_temp2[1]