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cucapra / pollen

generating hardware accelerators for pangenomic graph queries
MIT License
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Monorepo #83

Closed anshumanmohan closed 1 year ago

anshumanmohan commented 1 year ago

This PR carves mygfa, slow-odgi, and data-gen into three sibling directories:

pollen
|
+-- mygfa/
|   |
|   +-- mygfa/
|   +-- pyproject.toml
|
+-- slow_odgi/
|   |
|   +-- slow_odgi/
|   +-- pyproject.toml
|
+-- data_gen/
|   |
|   +-- data_gen/
|   +-- pyproject.toml
|
+-- test/
|
+-- all/
+-- of/
+-- susans/
+-- stuff/
|
+-- .gitignore
+-- Makefile
+-- LICENSE
+-- README

data_gen is now its own little command, and can be installed with flit install --user --symlink while in path/to/pollen/data_gen/ . data_gen also has a new parser, with depth and simple as the only subcommands.

Testing is still via turnt, nothing controversial there, but simple is not tested because there is no oracle or basis to test again. I just sorta made it up.

Test with:

  1. make test-slow-odgi
  2. make test-data-gen
  3. data_gen simple test/k.gfa
anshumanmohan commented 1 year ago

Thanks Adrian! I've incorporated your suggestions, though now I notice that the top-level README is a little stale. A curious person may go beyond slow-odgi and try to run the node-depth accelerator, but be disappointed. I'll check to see if we can patch that up right quick.

sampsyo commented 1 year ago

Nice!! All looks good from here.