IMDv2 generic support implmentation with tests

[amruthesht]

This PR provides generic IMDv2 support for handling various v2 streaming scenarios in imdclient

Fixes #140 , #143

Changes made in this Pull Request:

• IMDv2 schema as described in IMDv2 support and tests for receiving positions #140
• intergation tests for IMDv2 simulationengine implementationss
• unit test for IMDClientv2
• box wrapping for TRR and IMD based checking when using v2 or IMD-unwrap=True in session info
• v2 trate sending via IMDClient object
• Added v2 tests addressing Add tests for IMDv2 streams #82

Note: IMDv2 in GROMACS seems to expects transmission rate from the user via the client, as discussed in #143
It ignores IMD-nst in the *.mdp file. Thus the IMDClient object was modified to send IMD_TRATE right after IMD_GO as set in the object initiation when using v2.

PR Checklist

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

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 86.58%. Comparing base (9fd3c34) to head (c79f62f).

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

[Copilot]

Pull request overview

This PR extends imdclient to handle more IMDv2 streaming patterns (notably variable energy-packet ordering) and adds/updates integration tests and simulation inputs to validate IMDv2 behavior across supported engines.

Changes:

• Update IMDv2 frame parsing to tolerate multiple leading energy packets before coordinates and to reuse cached energies when energies are omitted.
• Add IMDv2 integration test coverage alongside existing IMDv3 tests for NAMD, GROMACS, and LAMMPS.
• Add new IMDv2 engine input/config files and rename/refactor test datafile constants to separate v2/v3 variants.

Reviewed changes

Copilot reviewed 15 out of 15 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
imdclient/IMDClient.py	Adjust IMDv2 producer parsing to handle multiple/optional energy packets before coordinates.
imdclient/tests/base.py	Refactor integration test base class and add an IMDv2-specific integration test class.
imdclient/tests/test_namd.py	Split shared NAMD fixtures and add IMDv2 + IMDv3 integration test classes with version-specific inputs.
imdclient/tests/test_lammps.py	Split shared LAMMPS fixtures and add IMDv2 + IMDv3 integration test classes with version-specific inputs.
imdclient/tests/test_gromacs.py	Split shared GROMACS fixtures and add IMDv2 + IMDv3 integration test classes with version-specific inputs.
imdclient/tests/minimalreader.py	Handle missing box data when converting to MDAnalysis dimensions during stream processing.
imdclient/tests/datafiles.py	Rename/split datafile constants to explicitly distinguish v2 vs v3 simulation inputs.
imdclient/data/namd/md/namd_v2_nst_1.namd	Add NAMD IMDv2 test configuration (NST=1).
imdclient/data/namd/md/namd_v2_nst_8.namd	Add NAMD IMDv2 test configuration (NST=8).
imdclient/data/lammps/md/lammps_v2_nst_1.in	Add LAMMPS IMDv2 test input (NST=1).
imdclient/data/lammps/md/lammps_v2_nst_8.in	Add LAMMPS IMDv2 test input (NST=8).
imdclient/data/lammps/md/lammps_v3_nst_1.in	Expand LAMMPS IMDv3 fix options to explicitly enable time/box/coords/vel/forces.
imdclient/data/lammps/md/lammps_v3_nst_8.in	Expand LAMMPS IMDv3 fix options to explicitly enable time/box/coords/vel/forces.
imdclient/data/gromacs/md/gromacs_v2_nst1.mdp	Add GROMACS IMDv2 test MDP (NST=1).
imdclient/data/gromacs/md/gromacs_v2_nst8.mdp	Add GROMACS IMDv2 test MDP (NST=8).

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

[orbeckst]

As discussed in meeting, wrap the GROMACS streamed coordinates into the unit cell by

1. extracting the ts.dimensions from the saved trajectory
2. create two on-the-fly transformations
   • set_box_dimensions
   • wrap
3. use the transformations with the in-memory universe that you build with the numpy array of the IMD data

This should generate an in-memory trajectory of wrapped coordinates.

[amruthesht]

@orbeckst - This PR is finally done after a bit of back and forth trying to figure out issues with using v2 in GROMACS.
Please let me know if you still see any outstanding issues.

Thank you to you and @HeydenLabASU for the discussion and suggestions on solving this issue.