Parse input files for DT when not in traj

[ljwoods2]

Fixes #70

Changes made in this Pull Request:

• Parse MDP file from GMX using regex to get DT
• Parse input file from LAMMPS using regex to get its DT
• Remove some unused code (now that we always test for time, step, dt)

The GROMACS simulation engine test_compare_imd_to_true_traj is going to fail until we merge this with #53, which adds MinimalReader and allows keeping the IMD stream's DT value (instead of replacing it with time between transmitted frames as a result of the TRR reader)

Same goes for LAMMPS

(sorry for the black diff, apparently when I wrote everything previously I had configured a nonstandard, short max line length in my vscode)

PR Checklist

• Tests?
• Docs?
• CHANGELOG updated?
• Issue raised/referenced?

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 61.46%. Comparing base (56430e9) to head (73556cc).

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[Copilot]

Pull Request Overview

This PR adds functionality to parse the DT value from input files for GROMACS and LAMMPS using regular expressions, and removes obsolete code related to testing for time, step, and dt.

• Updated test files for NAMD, LAMMPS, and GROMACS to use regex extraction for dt.
• Removed unused fixtures and refactored test_compare_imd_to_true_traj to simplify dt handling.

Reviewed Changes

Copilot reviewed 4 out of 4 changed files in this pull request and generated 1 comment.

File	Description
imdclient/tests/test_namd.py	Reformatted logger formatter and test function definition style
imdclient/tests/test_lammps.py	Added regex-based dt extraction and reformatted formatter setup
imdclient/tests/test_gromacs.py	Added dt fixture using regex for mdp file and reformatted logger
imdclient/tests/base.py	Refactored dt handling in tests by replacing old fixtures

[Copilot]

The call to assert_allclose includes three array arguments; the extra argument (imd_u.trajectory[i - first_frame].dt) should be removed so that the function compares only true_u.trajectory[i].dt and dt.

[amruthesht]

@ljwoods2, two things -

1. Maybe we can use the imdreader-split branch to introduce these changes?
2. I think it would be a better idea to parse the *.log output file to get this information rather than the input file. Since that would confirm the actual value being used rather than the one that was set by the user.

[ljwoods2]

@amruthesht is there ever a case where dt would change from what the user set it to? Unless there's a clear case that we'd encounter I don't see value in rewriting it, if we ever want to drastically modify these tests in the future to include such a case we can do it then.

I'd be happy to swap this PR to make it into your imdreader-split branch, will do that late tonight.

[amruthesht]

@ljwoods2 - I can't think think of a specific case that is common so I think it should be fine for now to stick with parsing the input file.
The suggested change should be convenient though since the parsed .mdp file is just pasted out in the eventual *.log output for GROMACS

However, right now the gmx tests seem to be failing and still using the MDA "transmission dt" for some reason. I can take a stab at it if you want.

[ljwoods2]

@amruthesht that's expected, read the issue description. This doesn't use your minimalreader, so IMD universe is created by dumping stream into a TRR file and then rereading (which loses DT information)

[amruthesht]

@amruthesht that's expected, read the issue description. This doesn't use your minimalreader, so IMD universe is created by dumping stream into a TRR file and then rereading (which loses DT information)

My bad - I thought you were doing comparisons without dumping it as a TRR.
This makes sense then to include in the imdreader-split branch