Thanks. I got a recipe working, and have submitted it to conda/conda-recipes here https://github.com/conda/conda-recipes/pull/310 <https://github.com/conda/conda-recipes/pull/310>
Until it becomes more “official” (eg maintained by openbabel or conda), I pushed my binaries to binstar so Anaconda users on a Mac should be able to get up and running in just a few seconds with `conda install -c rmg openbabel`. Working linux builds coming soon, I hope. (And then Windows.) > On May 26, 2015, at 4:24 PM, Patrick Fuller <patrickful...@gmail.com> wrote: > > Hi Richard, > > I played around with this a while ago, and I managed to get it to work > without handling environment variables. My build.sh had a not-very-elegant > install_name_tool workaround. > > cmake .. -DPYTHON_BINDINGS=ON -DRUN_SWIG=ON > -DCMAKE_INSTALL_PREFIX=~/miniconda3 > -DPYTHON_INCLUDE_DIR=~/miniconda3/include/python3.4m > -DCMAKE_LIBRARY_PATH=~/miniconda/lib > make && make install > install_name_tool -change libpython3.4m.dylib > ~/miniconda3/lib/libpython3.4m.dylib > ~/miniconda3/lib/python3.4/site-packages/_openbabel.so > for l in xmlformat pubchem cmlreactformat cmlformat cdxmlformat; do > install_name_tool -change libxml2.2.dylib ~/miniconda3/lib/libxml2.dylib > ~/miniconda3/lib/openbabel/2.3.90/$l.so; done > I have a version of this on their binstar site, but I don’t know if it works. > I generalized the commands with conda's environment variables, but dropped > the whole effort at some point. > > Hope this helps, > Pat > > > On Tue, May 26, 2015 at 1:40 PM, Richard West <r.h.w...@gmail.com > <mailto:r.h.w...@gmail.com>> wrote: > In the thread below (was "Re: [OpenBabel-Devel] Google Summer of Code”) > there was some discussion of making conda binaries, for the anaconda > distribution. > > Pat wrote: >> Conda. The best user experience (if the binaries work), cross-OS, >> language-agnostic, and a great virtual environment. I don’t think there’s >> enough support to direct all users to conda, but it would be worth >> supporting conda binaries, mentioning it in the getting started, and hoping >> adoption grows. > > > For much the same reasons as his first sentence, we're trying to package > another tool (Reaction Mechanism Generator) for Conda. We’re almost there, > but one of the last dependencies is OpenBabel, so we're now making an > OpenBabel build recipe. I wrote the first Mac homebrew recipe for OpenBabel > many years ago, but haven’t really touched it since then, and am far from > comfortable with the build process. > > My current impasse is the need to set $BABEL_LIBDIR and $BABEL_DATADIR > https://github.com/conda/conda-recipes/issues/309 > <https://github.com/conda/conda-recipes/issues/309> > > I expect when we get around to Windows build, we’ll need a lot more help. > > Is this mailing list a good place to seek help? Or github? Or elsewhere? > Don’t want to spam the wrong people! > > Is anyone already doing this? > > Thanks, > Richard > > -- > Richard H. West, Ph.D. r.w...@neu.edu <mailto:r.w...@neu.edu> > Assistant Professor, Department of Chemical Engineering, > Northeastern University, 360 Huntington Ave, Boston, MA 02115 > http://neu.edu/comocheng <http://neu.edu/comocheng> Phone: 617-373-5163 > <tel:617-373-5163> > > >> On Feb 3, 2015, at 10:14 AM, Patrick Fuller <patrickful...@gmail.com >> <mailto:patrickful...@gmail.com>> wrote: >> >> Noel's python content is great, and I think a redesign would push >> information like that to the forefront. >> >> I'm willing to migrate the website, which I can play with on a personal >> github.io <http://github.io/> fork. I think you had some experience with >> avogadro and pandoc - how did that turn out? >> >> Pat >> >> On Sun, Feb 1, 2015 at 11:43 AM, Geoffrey Hutchison >> <geoff.hutchi...@gmail.com <mailto:geoff.hutchi...@gmail.com>> wrote: >> I certainly agree with a need for a better website. Noel's user >> documentation (https://open-babel.readthedocs.org/en/latest/ >> <https://open-babel.readthedocs.org/en/latest/>) gives a lot about getting >> started and using Python. If you have suggestions, it's welcome. At the >> moment, I don't have the time to do a website redesign. >> >> As far as packaging, it's not really our job to intercede with OS-specific >> packages. Debian, Ubuntu, etc. have managers and a set policy about updates >> and what to install with the main package (i.e., not scripting bindings - >> that's a separate package). >> >> Now, you mention having a more frequent release schedule. That'd be great, >> but I'd really need people to step up to help as release managers. Given 2-3 >> people willing to help, we can certainly get a more concrete schedule - >> which I think would also help with your frustration at older binary >> packaging. >> >> So if people can provide a little help: >> - Website, possibly migrating to GitHub pages / Jekyll (i.e., re-using the >> Sphinx documentation) >> - Volunteering to serve as release managers >> >> -Geoff >> >> >>> From: Patrick Fuller <patrickful...@gmail.com >>> <mailto:patrickful...@gmail.com>> >> ... >>> In more detail: >>> I think that the complicated install / getting started process is >>> dissuading new users. This project would focus on the new user experience, >>> particularly the first 30 minutes after someone decides to try open babel. >>> The goal should be to get novice programmers properly set up and writing an >>> interesting script (an a-ha moment) in this time.This would lead to a >>> couple of sub-projects: >>> >>> Information organization. There is a ton of information in the open babel >>> website, but the home page is daunting for new users. As a good example to >>> follow, I’d point to django’s website <https://www.djangoproject.com/> - >>> there’s a big “Get Started” button right when the page loads. This is an >>> intentional choice, and described by the django founder in this talk >>> <http://pyvideo.org/video/403/pycon-2011--writing-great-documentation>. >>> Scripting as a first-class citizen. I think a tutorial should cover basic >>> tasks through the command line, C++, and python. The information is already >>> on the website, but it just needs to be presented to new users quicker. >>> Installation. A large portion of scientific coders aren’t particularly good >>> at software (see software carpentry <http://software-carpentry.org/>), and >>> don’t have the ability / desire to debug things like cmake output. There >>> are packages out there, but they’re tied to an old version of open babel >>> and don’t install everything. Hard drive space is cheap- open babel should >>> install everything through every installation method with build options to >>> disable. Approaches: >>> OS-specific package managers, e.g. brew, apt-get, yum. Maintaining all of >>> these separately is a hassle, but I’ve been told good things about effing >>> package management <https://github.com/jordansissel/fpm> as a translator. >>> Other challenges include: can’t use most recent commit (I think homebrew is >>> an exception), and doesn’t play well with virtual environments out of the >>> box. >>> Language-specific package managers, e.g. pip. It’s a hassle to compile >>> through these package managers, but they play well with language-specific >>> virtual environments and git (e.g. pip install >>> git+https://github.com/openbabel/openbabel >>> <https://github.com/openbabel/openbabel>). >>> Conda. The best user experience (if the binaries work), cross-OS, >>> language-agnostic, and a great virtual environment. I don’t think there’s >>> enough support to direct all users to conda, but it would be worth >>> supporting conda binaries, mentioning it in the getting started, and hoping >>> adoption grows. >>> Versioning. New releases every x months, and ideally a simple workflow to >>> propagate a new version to all supported package managers. >>> If I can help further, let me know. >>> >>> Pat >>> >> >> ------------------------------------------------------------------------------ >> Dive into the World of Parallel Programming. The Go Parallel Website, >> sponsored by Intel and developed in partnership with Slashdot Media, is your >> hub for all things parallel software development, from weekly thought >> leadership blogs to news, videos, case studies, tutorials and more. Take a >> look and join the conversation now. http://goparallel.sourceforge.net/ >> <http://goparallel.sourceforge.net/> >> _______________________________________________ >> OpenBabel-Devel mailing list >> OpenBabel-Devel@lists.sourceforge.net >> <mailto:OpenBabel-Devel@lists.sourceforge.net> >> https://lists.sourceforge.net/lists/listinfo/openbabel-devel >> <https://lists.sourceforge.net/lists/listinfo/openbabel-devel> >> >> >> ------------------------------------------------------------------------------ >> Dive into the World of Parallel Programming. The Go Parallel Website, >> sponsored by Intel and developed in partnership with Slashdot Media, is your >> hub for all things parallel software development, from weekly thought >> leadership blogs to news, videos, case studies, tutorials and more. Take a >> look and join the conversation now. >> http://goparallel.sourceforge.net/_______________________________________________ >> >> <http://goparallel.sourceforge.net/_______________________________________________> >> OpenBabel-Devel mailing list >> OpenBabel-Devel@lists.sourceforge.net >> <mailto:OpenBabel-Devel@lists.sourceforge.net> >> https://lists.sourceforge.net/lists/listinfo/openbabel-devel >> <https://lists.sourceforge.net/lists/listinfo/openbabel-devel> > >
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