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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,3 +1,14 @@ | ||
| env: | ||
| global: | ||
| - secure: "HIj3p+p2PV8DBVg/KGUx6n83KwB0ASE5FwOn0SMB9zxnzAqe8sapwdBQdMdq0sXB7xT1spJqRxuxOMVEVn35BNLu7bxMLfa4287C8YXcomnvmv9xruxAsjsIewnNQ80vtPVbQddBPxa4jKbqgPby5QhhAP8KANAqYe44pIV70fY=" | ||
| - GH_DOC_BRANCH: develop | ||
| - GH_REPOSITORY: github.com/MDAnalysis/mdanalysis.git | ||
| - GIT_CI_USER: TravisCI | ||
| - GIT_CI_EMAIL: [email protected] | ||
| - MDA_DOCDIR: package/doc/html | ||
| matrix: | ||
| - SETUP=full CYTHONIZE=true | ||
| - SETUP=minimal CYTHONIZE=false | ||
| language: python | ||
| python: | ||
| - "2.7" | ||
|
|
@@ -6,27 +17,31 @@ addons: | |
| apt: | ||
| packages: | ||
| - gfortran | ||
| - libgfortran3 | ||
| - libhdf5-serial-dev | ||
| - libnetcdf-dev | ||
| - liblapack-dev | ||
| - libatlas-dev | ||
| before_install: | ||
| - wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh | ||
| - chmod +x miniconda.sh | ||
| - ./miniconda.sh -b | ||
| - ./miniconda.sh -b -p /home/travis/miniconda | ||
| - export PATH=/home/travis/miniconda/bin:$PATH | ||
| - conda update --yes conda | ||
| install: | ||
| - conda create --yes -q -n pyenv mkl python=2.7 numpy=1.9.1 scipy=0.14.0 nose=1.3.7 sphinx=1.3 | ||
| - if [[ $SETUP == 'full' ]]; then conda create --yes -q -n pyenv python=2.7 numpy=1.9.2 scipy=0.16.0 nose=1.3.7 sphinx=1.3; fi | ||
| - if [[ $SETUP == 'minimal' ]]; then conda create --yes -q -n pyenv python=2.7 numpy=1.9.2 nose=1.3.7 sphinx=1.3; fi | ||
| - source activate pyenv | ||
| - conda install --yes python=$TRAVIS_PYTHON_VERSION cython biopython matplotlib networkx netcdf4 | ||
| - pip install package/ | ||
| - if [[ $SETUP == 'full' ]]; then conda install --yes python=$TRAVIS_PYTHON_VERSION cython biopython matplotlib networkx netcdf4; fi | ||
| - if [[ $SETUP == 'minimal' ]]; then conda install --yes python=$TRAVIS_PYTHON_VERSION biopython networkx; fi | ||
| - if [[ $CYTHONIZE == 'true' ]]; then find . -name '*.pyx' -exec touch '{}' \; ;fi | ||
| - pip install -v package/ | ||
| - pip install testsuite/ | ||
| - pip install coveralls tempdir | ||
| - chmod +x testsuite/MDAnalysisTests/mda_nosetests | ||
| # command to run tests | ||
| script: | ||
| - ./testsuite/MDAnalysisTests/mda_nosetests -v --with-coverage --cover-package MDAnalysis --processes=2 --process-timeout=120 --with-memleak | ||
| - ./testsuite/MDAnalysisTests/mda_nosetests --with-coverage --cover-package MDAnalysis --processes=2 --process-timeout=300 --with-memleak | ||
| - | | ||
| test ${TRAVIS_PULL_REQUEST} == "false" && \ | ||
| test ${TRAVIS_BRANCH} == ${GH_DOC_BRANCH} && \ | ||
|
|
@@ -41,12 +56,3 @@ after_success: | |
| test ${TRAVIS_BRANCH} == ${GH_DOC_BRANCH} && \ | ||
| test "${TRAVIS_BUILD_NUMBER}.1" == "${TRAVIS_JOB_NUMBER}" && \ | ||
| bash ./maintainer/deploy_docs.sh | ||
| env: | ||
| global: | ||
| - secure: "HIj3p+p2PV8DBVg/KGUx6n83KwB0ASE5FwOn0SMB9zxnzAqe8sapwdBQdMdq0sXB7xT1spJqRxuxOMVEVn35BNLu7bxMLfa4287C8YXcomnvmv9xruxAsjsIewnNQ80vtPVbQddBPxa4jKbqgPby5QhhAP8KANAqYe44pIV70fY=" | ||
| - GH_DOC_BRANCH: develop | ||
| - GH_REPOSITORY: github.com/MDAnalysis/mdanalysis.git | ||
| - GIT_CI_USER: TravisCI | ||
| - GIT_CI_EMAIL: [email protected] | ||
| - MDA_DOCDIR: package/doc/html | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,105 @@ | ||
| # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- | ||
| # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 | ||
| # | ||
| # MDAnalysis --- http://www.MDAnalysis.org | ||
| # Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein | ||
| # and contributors (see AUTHORS for the full list) | ||
| # | ||
| # Released under the GNU Public Licence, v2 or any higher version | ||
| # | ||
| # Please cite your use of MDAnalysis in published work: | ||
| # | ||
| # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. | ||
| # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. | ||
| # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 | ||
| # | ||
|
|
||
| """ | ||
| Analysis building blocks --- :mod:`MDAnalysis.analysis.base` | ||
| ============================================================ | ||
| A collection of useful building blocks for creating Analysis | ||
| classes. | ||
| """ | ||
| import numpy as np | ||
| import logging | ||
|
|
||
|
|
||
| logger = logging.getLogger(__name__) | ||
|
|
||
|
|
||
| class AnalysisBase(object): | ||
| """Base class for defining multi frame analysis | ||
| The analysis base class is designed as a template for creating | ||
| multiframe analysis. | ||
| The class implements the following methods: | ||
| _setup_frames(trajectory, start=None, stop=None, step=None) | ||
| Pass a Reader object and define the desired iteration pattern | ||
| through the trajectory | ||
| run | ||
| The user facing run method. Calls the analysis methods | ||
| defined below | ||
| Your analysis can implement the following methods, which are | ||
| called from run: | ||
| _prepare | ||
| Called before iteration on the trajectory has begun. | ||
| Data structures can be set up at this time, however most | ||
| error checking should be done in the __init__ | ||
| _single_frame | ||
| Called after the trajectory is moved onto each new frame. | ||
| _conclude | ||
| Called once iteration on the trajectory is finished. | ||
| Apply normalisation and averaging to results here. | ||
| """ | ||
| def _setup_frames(self, trajectory, start=None, | ||
| stop=None, step=None): | ||
| self._trajectory = trajectory | ||
| start, stop, step = trajectory.check_slice_indices( | ||
| start, stop, step) | ||
| self.start = start | ||
| self.stop = stop | ||
| self.step = step | ||
| self.nframes = len(xrange(start, stop, step)) | ||
|
|
||
| def _single_frame(self): | ||
| """Calculate data from a single frame of trajectory | ||
| Don't worry about normalising, just deal with a single frame. | ||
| """ | ||
| pass | ||
|
|
||
| def _prepare(self): | ||
| """Set things up before the analysis loop begins""" | ||
| pass | ||
|
|
||
| def _conclude(self): | ||
| """Finalise the results you've gathered. | ||
| Called at the end of the run() method to finish everything up. | ||
| """ | ||
| pass | ||
|
|
||
| def run(self): | ||
| """Perform the calculation""" | ||
| logger.info("Starting preparation") | ||
| self._prepare() | ||
| for i, ts in enumerate( | ||
| self._trajectory[self.start:self.stop:self.step]): | ||
| self._ts = ts | ||
| #logger.info("--> Doing frame {} of {}".format(i+1, self.nframes)) | ||
| self._single_frame() | ||
| logger.info("Finishing up") | ||
| self._conclude() | ||
|
|
||
|
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