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durrantlab / wisp

WISP is a trajectory analysis tool that calculates and visualizes allosteric pathways.
https://durrantlab.github.io/wisp/
Academic Free License v3.0
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Conda+poetry setup and performance #2

Closed aalexmmaldonado closed 6 months ago

aalexmmaldonado commented 11 months ago

These tests work on my local computer. Something is going on with the workflow.

conda run -p /home/alex/repos/wisp/.venv pytest -c pyproject.toml --cov=wisp --cov-report=xml tests/
============================= test session starts ==============================
platform linux -- Python 3.11.6, pytest-7.4.2, pluggy-1.3.0
rootdir: /home/alex/repos/wisp
configfile: pyproject.toml
plugins: cov-4.1.0
collected 1 item

tests/test_wisp.py .                                                     [100%]

---------- coverage: platform linux, python 3.11.6-final-0 -----------
Coverage XML written to file coverage.xml

============================== 1 passed in 3.39s ===============================

/home/alex/repos/wisp/.venv/lib/python3.11/site-packages/coverage/control.py:883: CoverageWarning: No data was collected. (no-data-collected)
  self._warn("No data was collected.", slug="no-data-collected")
aalexmmaldonado commented 11 months ago

So, there are indeed negative weights when we have (i, i) edges. They are essentially zero, but due to NumPy floats, they are on the order of $-1 \times 10^{-16}$. We will set all diagonals of correlation_matrix to 0.0 in run_wisp().

aalexmmaldonado commented 11 months ago

All bugs for serial processing have been fixed at this point. I left the new test running for 30 minutes, and it would not finish. We must debug and profile the code to see the most significant contributions.

aalexmmaldonado commented 6 months ago

We need to merge so we can debug effectively. Will make another PR. #1 is still not fixed.