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openworm / owmeta

Unified, simple data access python library for data & facts about C. elegans anatomy
MIT License
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Simplify installation for alpha0.5 #35

Closed slarson closed 10 years ago

slarson commented 10 years ago

As reported on the openworm-discuss list folks are running into roadblocks installing this library due to a dependency on the BerkeleyDB being installed on their system and version mismatches. This is too high a bar for most users to have to worry about; they won't use this and they'll go elsewhere. We need to simplify the installation procedures so that pip install is really all that is needed.

One approach may be to look at adding a new RDFLib backend that is pure python. Some options include:

slarson commented 10 years ago

Looks like ZODB may be an out of the box easy-to-install solution as it already has an RDFLib backend. Then again it seems to have some incompatibilities that may be problematic.

mwatts15 commented 10 years ago

We don't need to worry about the binary dependencies if we rely on a simple RDF serialization. Loading in the database once on install isn't problematic.

On Wed, Aug 13, 2014 at 6:22 PM, Stephen Larson notifications@github.com wrote:

Looks like ZODB http://www.zodb.org/en/latest/documentation/guide/prog-zodb.html#installing-zodb may be an out of the box easy-to-install solution as it already has an RDFLib backend https://github.com/RDFLib/rdflib-zodb. Then again it seems to have some incompatibilities that may be problematic.

— Reply to this email directly or view it on GitHub https://github.com/openworm/PyOpenWorm/issues/35#issuecomment-52125301.

Cheers, Mark Watts Department of Computer Science University of Texas at Austin

slarson commented 10 years ago

@mwatts15 any update on this one?

mwatts15 commented 10 years ago

Unit tests pass with rdflib-zodb. It seems to need additional configuration to store the DB in a file.

slarson commented 10 years ago

is that checked in somewhere now? not seeing any references to zodb in the last two commits from you.

On Fri, Aug 15, 2014 at 8:09 AM, mwatts15 notifications@github.com wrote:

Unit tests pass with rdflib-zodb. It seems to need additional configuration to store the DB in a file.

— Reply to this email directly or view it on GitHub https://github.com/openworm/PyOpenWorm/issues/35#issuecomment-52316471.

mwatts15 commented 10 years ago

No, I tested it locally.

slarson commented 10 years ago

ok-- since we're operating on limited time, if you want to commit to your personal repo fork and have me review just let me know.

On Fri, Aug 15, 2014 at 8:14 AM, mwatts15 notifications@github.com wrote:

No, I tested it locally.

— Reply to this email directly or view it on GitHub https://github.com/openworm/PyOpenWorm/issues/35#issuecomment-52317080.

mwatts15 commented 10 years ago

If you want to have a look, I pushed a branch zodb.