paulsengroup / modle Goto Github PK

High-performance stochastic modeling of DNA loop extrusion interactions

License: Other

CMake 4.69% Dockerfile 0.90% Python 2.15% Shell 2.42% C++ 89.33% Jupyter Notebook 0.51%

bioinformatics biology cpp cpp17 dna high-performance loop-extrusion stochastic-model tad topologically-associated-domains

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modle's Issues

Add missing SPDX headers before release

Refactor CI

The following jobs can probably be rewritten as reusable workflows:

run-unit-tests
run-modle-integration-test
run-modle-tools-integration-test

The same is may be true for steps like:

Generate cache keys

Update modle_integration_test.sh to use cmp instead of shasum

Store digest of input file(s) in cooler metadata attribute

The troubleshooting information for the Incorrect or incomplete Conan profile is buried in a hidden paragraph in a different subsection from that where the error occurs. I discovered the troubleshooting information by Googling the error message... which brought me back to the page I started from.

It would make sense to either

Instruct the user to update the Conan profile on fresh install, or
Put the troubleshooting information front and center next to the command that can fail, or
Make a visible note next to the command to check the troubleshooting section.

Investigate performance regression when serializing sparse matrices on MacOS

Before bumping deps with #62, unit tests covering the serialization of sparse contact matrices took less than 200s, now they take in the order of 600s

See e.g. running times for these two CI runs:

Before PR: https://github.com/paulsengroup/modle/actions/runs/3741978784
After PR: https://github.com/paulsengroup/modle/actions/runs/3772356164

Update generated-by attribute in cooler file

This attribute should contain the version of MoDLE used to generate the cooler, not coolerpp's ver

Pin recipe revisions in conanfile.py

Update scripts to build Dockerfile

Add modle_tools subcommand to generate config.toml given a cooler produced by modle

modle_tools eval: remove CLI short option for --reference-matrix

Port bugfix for modle_tools eval to main

Port bugfix from ed185da.

Embed metadata when generating .cool files using modle_tools

Add CLI option to specify assembly attribute in output cooler

Unable to find h5diff in your PATH

Hi,

When running the command for the integration test ../test/scripts/modle_integration_test_simple.sh src/modle/modle I get the error

Unable to find h5diff in your PATH
/home/gfilion/miniconda3/envs/tmp/bin/xz

There does not seem to be a reference to h5diff in the installation notes.
Running apt install hdf5-tools on Ubuntu works.

$ h5diff --version
h5diff: Version 1.10.4

Running command again fails with error

h5diff: unknown option "exclude-attribute"