- Sep 24, 2019
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E Madison Bray authored
existing generate_loaders() function. This is a little out of sync still with the wip_hyperopt branch, and I have yet to resolve the differences between the two, but this helps me to understand the current functionality and where improvements and abstractions can be made.
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E Madison Bray authored
fixes to the README.
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E Madison Bray authored
builds of pytorch and friends. Fix DOS line endings on existing environment/requirements files.
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E Madison Bray authored
Add a brief docstring in simul_data.py that the code there is just for testing / demonstration purposes and pointed out by Jean; we might remove it later (though I believe it might be useful for tutorial purposes and, with some refactoring, for generating a dataset template).
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- Sep 18, 2019
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E Madison Bray authored
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E Madison Bray authored
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E Madison Bray authored
The conda environment file is specifically for a CPU-only setup; need to add a separate one for GPU once I get on a machine that actually has a CUDA-capable GPU.
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- Sep 17, 2019
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E Madison Bray authored
simul_data.py script. This will likely be rewritten in the future, but having this test makes for a nice demonstration, and a nice check against future changes (it provides something of a partial certificate of the current functionality of the code).
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E Madison Bray authored
module-level global variable. This will likely be refactored even further to make it easier to override specific parameters in different contexts. But this still makes it easier to override all defaults, esp. for testing.
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E Madison Bray authored
be what was intended, but never completed. In particular the intent seemed to be that the scenario_idx column in generated scenario params be a simple integer, rather than a name like "scenario_0000".
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E Madison Bray authored
of the "seed" parameter from the simulation params.
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E Madison Bray authored
for it to take a value. Use action='store_true' instead.
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E Madison Bray authored
argv, rather than defaulting to argv. Also return an exit code instead of calling ``sys.exit()`` directly. This makes testing for these functions easier. This is just a preliminary move intended to test setting up a test framework.
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E Madison Bray authored
Enough to be able to `pip install -e .` for more effective development.
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E Madison Bray authored
package called dnadna. As many of the modules are also scripts, their `if __name__ == '__main__'` blocks are converted to `main()` functions, which are called from executable scripts now living in the `scripts/` directory. This `scripts/` directory will mostly go away in the next stage, however, as we add a `setup.cfg` and implement `console_scripts` entrypoints, and possibly sub-commands. Not all of these scripts are currently actually working with each other; most are in some state of disrepair to be cleaned up later, but with the exception of cleaning up some imports they are otherwise left unmodified by this commit. Also adds the beginnings of a .gitignore file.
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- Sep 16, 2019
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E Madison Bray authored
Although these may be worth keeping in a repository, I don't believe the belong in the main sources for a distributable package based on this work. Instead they should go in a personal repository which uses this one as a dependency, or in a specialized branch, etc.
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- Aug 05, 2019
- Aug 01, 2019
- Jul 31, 2019
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Jean Cury authored
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- Jul 25, 2019
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Jean Cury authored
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- Jul 20, 2019
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jeanrjc authored
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- Jul 18, 2019
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jeanrjc authored
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- May 23, 2019
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jeanrjc authored
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- May 22, 2019
- May 21, 2019
- May 17, 2019