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Merge pull request #751 from kain88-de/conda
conda build scripts (fixes #608)
2 parents e39ace4 + abf7aa7 commit e3a345d

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‎README.rst‎

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|build| |cov| [*]_
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|docs| |devdocs| |usergroup| |developergroup|
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|docs| |devdocs| |usergroup| |developergroup| |anaconda|
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MDAnalysis_ is a Python toolkit to analyze molecular dynamics
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trajectories generated by a wide range of popular simulation packages
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.. code:: python
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import MDAnalysis as mda
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# Load simulation results with a single line
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u = mda.Universe('topol.tpr','traj.trr')
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# Select atoms
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ag = u.select_atoms('name OH')
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# Atom data made available as Numpy arrays
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ag.positions
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ag.velocities
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ag.forces
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# Iterate through trajectories
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for ts in u.trajectory:
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print(ag.center_of_mass())
@@ -61,7 +61,7 @@ MDAnalysis issue tracker.)
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.. Footnotes
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.. [*] **build**: Unit testing is for the whole package; **coverage** is shown for the core library
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.. [*] **build**: Unit testing is for the whole package; **coverage** is shown for the core library
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modules (which excludes `MDAnalysis.analysis`_ and `MDAnalysis.visualization`_ at
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the moment). For more details and discussion see issue `#286`_.
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@@ -77,11 +77,11 @@ MDAnalysis issue tracker.)
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.. |usergroup| image:: https://img.shields.io/badge/Google%20Group-Users-lightgrey.svg
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:alt: User Google Group
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:target: http://users.mdanalysis.org
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.. |developergroup| image:: https://img.shields.io/badge/Google%20Group-Developers-lightgrey.svg
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:alt: Developer Google Group
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:target: http://developers.mdanalysis.org
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.. |docs| image:: https://img.shields.io/badge/docs-latest-brightgreen.svg
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:alt: Documentation (latest release)
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:target: http://docs.mdanalysis.org
@@ -93,7 +93,11 @@ MDAnalysis issue tracker.)
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.. |build| image:: https://travis-ci.org/MDAnalysis/mdanalysis.svg?branch=develop
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:alt: Build Status
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:target: https://travis-ci.org/MDAnalysis/mdanalysis
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.. |cov| image:: https://coveralls.io/repos/MDAnalysis/mdanalysis/badge.svg?branch=develop
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:alt: Coverage Status
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:target: https://coveralls.io/r/MDAnalysis/mdanalysis?branch=develop
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.. |anaconda| image:: https://anaconda.org/mdanalysis/mdanalysis/badges/version.svg
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:alt: Anaconda
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:target: https://anaconda.org/MDAnalysis/mdanalysis

‎maintainer/change_release.sh‎

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@@ -10,7 +10,7 @@ like '0.7.6' or 0.7.6-dev'.
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Run from the top directory of the git checkout.
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"
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FILES="package/setup.py package/MDAnalysis/version.py testsuite/setup.py testsuite/MDAnalysisTests/__init__.py"
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FILES="package/setup.py package/MDAnalysis/version.py testsuite/setup.py testsuite/MDAnalysisTests/__init__.py maintainer/conda/MDAnalysis/meta.yaml"
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die () {
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echo "ERROR: $1"
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findcommand() {
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for name in $*; do
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path=$(which $name)
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if [ -n "$path" ]; then
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echo $path
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return 0
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fi
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path=$(which $name)
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if [ -n "$path" ]; then
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echo $path
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return 0
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fi
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done
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die "None of the commands $* found." 2
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}
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sed_eregex () {
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# does this sed understand extended regular expressions?
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# - FreeBSD (Mac OS X) sed -E
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# - GNU sed --regexp-extended (undocumented: also -E ...)
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local SED=$1
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if [ "good" = "$(echo 'bad' | $SED -E 's/(abc)?bad|foo/good/')" ]; then
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echo "$SED -E"
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return 0
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elif [ "good" = "$(echo 'bad' | $SED --regexp-extended 's/(abc)?bad|foo/good/')" ]; then
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echo "$SED --regexp-extended"
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return 0
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elif [ "good" = "$(echo 'bad' | $SED 's/(abc)?bad|foo/good/')" ]; then
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echo "$SED"
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return 0
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fi
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echo "false"
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return 1
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# does this sed understand extended regular expressions?
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# - FreeBSD (Mac OS X) sed -E
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# - GNU sed --regexp-extended (undocumented: also -E ...)
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local SED=$1
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if [ "good" = "$(echo 'bad' | $SED -E 's/(abc)?bad|foo/good/')" ]; then
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echo "$SED -E"
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return 0
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elif [ "good" = "$(echo 'bad' | $SED --regexp-extended 's/(abc)?bad|foo/good/')" ]; then
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echo "$SED --regexp-extended"
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return 0
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elif [ "good" = "$(echo 'bad' | $SED 's/(abc)?bad|foo/good/')" ]; then
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echo "$SED"
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return 0
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fi
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echo "false"
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return 1
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}
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while getopts h OPT; do
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case $OPT in
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h) echo "$usage";
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exit 0
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;;
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\?) exit 2;;
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h) echo "$usage";
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exit 0
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;;
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\?) exit 2;;
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esac
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done
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test -n "$RELEASE" || die "Required argument missing. See -h for help." 2
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# find a sed with -i and -E
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for cmd in gsed sed; do
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for cmd in gsed sed; do
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SED=$(sed_eregex $(findcommand $cmd))
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[ "$SED" != "false" ] && break
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done
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[ "$SED" = "false" ] && { echo "ERROR: cannot find suitable sed."; exit 1; }
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[ "$SED" = "false" ] && { echo "ERROR: cannot find suitable sed."; exit 1; }
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# should check for -i but we just hope for the best ...
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# modern(ish) seds have -i
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echo "Using sed = $SED"
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git grep -E -l 'RELEASE.*[0-9]+\.[0-9]+\.[0-9]+(\.[0-9]+)?(dev|rc*[0-9])?' $FILES \
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| xargs -I FILE $SED '/RELEASE/s/[0-9]+\.[0-9]+\.[0-9]+(\.[0-9]+)?(dev|rc*[0-9])?/'${RELEASE}'/' -i.bak FILE
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git grep -E -l '__version__ =.*[0-9]+\.[0-9]+\.[0-9]+(\.[0-9]+)?(dev|rc*[0-9])?' $FILES \
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| xargs -I FILE $SED '/__version__/s/[0-9]+\.[0-9]+\.[0-9]+(\.[0-9]+)?(dev|rc*[0-9])?/'${RELEASE}'/' -i.bak FILE
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git status
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git grep -E -l 'version:.*[0-9]+\.[0-9]+\.[0-9]+(\.[0-9]+)?(dev|rc*[0-9])?' $FILES \
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| xargs -I FILE $SED '/version:/s/[0-9]+\.[0-9]+\.[0-9]+(\.[0-9]+)?(dev|rc*[0-9])?/'${RELEASE}'/' -i.bak FILE
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git status

‎maintainer/conda/MDAnalysis/build.sh‎

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#!/bin/bash
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MDA_USE_OPENMP=FALSE pip install package/
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pip install testsuite/

‎maintainer/conda/MDAnalysis/meta.yaml‎

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package:
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name: mdanalysis
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# This has to be changed after a release
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version: "0.14.0"
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source:
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# to build from source you can speficy the path to the code directly.
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# path: ../../../
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# This ensures that you will build from a clean checkout
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git_url: https://github.com/MDAnalysis/mdanalysis
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git_branch: master
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# git_tag: release-0.14.0
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requirements:
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build:
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- python
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- setuptools
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- pip
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- numpy
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- cython
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- biopython
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- networkx
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- griddataformats
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- nose
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- tempdir
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run:
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- python
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- numpy
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- scipy
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- griddataformats
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- networkx
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- biopython
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- matplotlib
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- seaborn
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- six
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- netcdf4
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- nose
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- tempdir
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test:
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imports:
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- MDAnalysis
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- MDAnalysis.analysis
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# check that distance cython modules have been build
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- MDAnalysis.lib.c_distances_openmp
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- MDAnalysis.lib.c_distances
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requires:
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# this is the same list as the run requirements
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- python
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- numpy
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- scipy
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- griddataformats
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- networkx
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- biopython
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- matplotlib
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- seaborn
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- six
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- netcdf4
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- nose
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- tempdir
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commands:
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# run the testsuite with 2 processes
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- python -c 'import MDAnalysisTests; MDAnalysisTests.run(label="full", extra_argv=["-v", "--processes=2", "--process-timeout=120"])'
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about:
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home: http://www.mdanalysis.org
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license: GPLv2
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license_file: package/LICENSE
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summary: 'MDAnalysis is a Python library to analyze molecular dynamics trajectories.'
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# See
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# http://docs.continuum.io/conda/build.html for
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# more information about meta.yaml

‎maintainer/conda/tempdir/bld.bat‎

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"%PYTHON%" setup.py install
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if errorlevel 1 exit 1
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:: Add more build steps here, if they are necessary.
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:: See
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:: http://docs.continuum.io/conda/build.html
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:: for a list of environment variables that are set during the build process.

‎maintainer/conda/tempdir/build.sh‎

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#!/bin/bash
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$PYTHON setup.py install
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# Add more build steps here, if they are necessary.
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# See
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# http://docs.continuum.io/conda/build.html
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# for a list of environment variables that are set during the build process.

‎maintainer/conda/tempdir/meta.yaml‎

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package:
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name: tempdir
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version: "0.7.1"
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source:
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fn: tempdir-0.7.1.tar.gz
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url: https://pypi.python.org/packages/source/t/tempdir/tempdir-0.7.1.tar.gz
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md5: 4076f2d7fa9306c77f7b16a5f2e4c154
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build:
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noarch_python: True
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requirements:
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build:
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- python
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- setuptools
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run:
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- python
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test:
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# Python imports
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imports:
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- tempdir
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about:
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home: https://bitbucket.org/another_thomas/tempdir
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license: MIT License
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summary: 'Tempdirs are temporary directories, based on tempfile.mkdtemp'
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# See
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# http://docs.continuum.io/conda/build.html for
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# more information about meta.yaml

‎package/CHANGELOG‎

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* release numbers follow "Semantic Versioning" http://semver.org
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------------------------------------------------------------------------------
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??/??/16 jandom, abhinavgupta94, orbeckst
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??/??/16 jandom, abhinavgupta94, orbeckst, kain88-de, hainm
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* 0.15.0
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@@ -27,6 +27,10 @@ API Changes
2727
* rmsd doesn't superimpose by default anymore. The superposition
2828
is controlled by the 'superposition' keyword now. (see issue #562)
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Enhancements
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* Add conda build scripts (Issue #608)
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Fixes
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* test_shear_from_matrix doesn't fail for MKL builds anymore (Issue #757)

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