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The Integrative Modeling Platform

Home Page: https://integrativemodeling.org

License: GNU General Public License v3.0

Python 42.08% C++ 50.62% C 1.38% CMake 0.96% Shell 1.01% HTML 0.01% LLVM 0.05% Gnuplot 0.01% Cuda 0.04% Yacc 0.03% MAXScript 1.94% Jupyter Notebook 0.16% Makefile 0.05% Batchfile 0.02% Roff 0.16% CSS 0.03% Perl 0.01% NSIS 0.03% SWIG 0.99% Rich Text Format 0.42%
protein-structure python c-plus-plus structural-biology integrative-modeling

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imp's Issues

feature/pointer_docs

This branch has changes to make it clearer what the various smart pointers do. It is ready to commit to svn.

RMFs can be very large

Look into data set compression, setting chunk size intelligently, make sure there is no wasted space.

circularity in test dependencies

There is an inherent circularity in the dependency computations with tests in that the dependencies for a test depend on modules that haven't been parsed yet. This is probably responsible for much of the flakiness we see. Possibilities include

  • do things in two passes, first stuff that can only look backwards and then tests and running examples that can look at the whole project
  • munge more

It is not clear how to do the first, we can add a pass argument in the environment...

Add support for locking rmf files

The model is for having separate read and write processes. Would have a lock attribute and a version counter. Need tool to break lock. Make checking lock exposed to the user rather than low level.

external builds are flakey

Since the required modules are sorted arbitrarily which doesn't really work as they need to be in the right order. Need to track dependencies with external builds too.

rmf_all_frames

  • Fix RMF.h to include new files.
  • add enum to specify STATIC
  • make decorator check cover all frames if necessary
  • add test for get all values in decorators

feature/rmf_fill_bug

This feature contains test code that shows a bug in hdf5 with filling. Ready to commit to svn.

Speed up scons

Make install just take what is there. Use os.glob instead of scons glob.

remove parsing of python examples

We don't use any of the results any more. We can skip building lots of tables in data and remove the whole function lookup table.

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