Fix: No search for MLatom in the virtual environment

[cplett]

• fix: Without an MLatom executable in the $PATH, the respective oet_mlatom script didn't work, even though MLatom was available in the installed virtual environment. With this fix, the MLatom executable is now searched also for in the respective virtual environment.
• fix: Installing the dev features during the setup of the virtual environment is now done in editable mode similar to the standard installation.
• build: bump MLatom dependency from 2.0.3 to 3.12.0.

[stgeo]

Thanks for the fix! The changes look OK to me (see one comment below).

I tried a fresh install with

./install.py --venv-dir venv-mlatom --extra mlatom -d

and got a couple of issues when running the tests:

1. With the venv activated python test_mlatom.py throws (in addition to the same warnings as below

FileNotFoundError: [Errno 2] No such file or directory: PosixPath('/redacted/orca-external-tools/venv-mlatom/lib/python3.12/site-packages/oet/../../bin/oet_mlatom')

Looks like ROOT_DIR is not what we expect.
2. Replacing ROOT_DIR with Path(__file__).resolve().parent I get

/redacted/orca-external-tools/venv-mlatom/lib/python3.12/site-packages/torchani/aev.py:16: UserWarning: cuaev not installed
  warnings.warn("cuaev not installed")
/redacted/orca-external-tools/venv-mlatom/lib/python3.12/site-packages/torchani/__init__.py:39: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import get_distribution, DistributionNotFound
/redacted/orca-external-tools/venv-mlatom/lib/python3.12/site-packages/torchani/__init__.py:55: UserWarning: Dependency not satisfied, torchani.ase will not be available
  warnings.warn("Dependency not satisfied, torchani.ase will not be available")
Checking the model files and downloading them if necessary.
/redacted/orca-external-tools/venv-mlatom/lib/python3.12/site-packages/torchani/resources/
F..
======================================================================
FAIL: test_H2O_engrad (__main__.MLatomTests.test_H2O_engrad)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/redacted/orca-external-tools/tests/mlatom/test_mlatom.py", line 104, in test_H2O_engrad
    self.assertAlmostEqual(energy, expected_energy, places=9)
AssertionError: -76.38342071073 != -76.38342071002 within 9 places (7.099885124262073e-10 difference)

----------------------------------------------------------------------
Ran 3 tests in 14.001s

FAILED (failures=1)

The deviation might be due to the mlatom update (BTW please mention the version bump in the commit message and/or PR description).

We really should integrate the tests into the CI...

I guess the torchANI/CUAEV installation is more complicated - we may want to check if we can automatically get a system-specific setup or at least expose the configuration options to the user at install time. Nothing to do now though.

[cplett]

@stgeo Thanks for the review.

Regarding 1: The problem with ROOT_DIR did only occur when installing the dev features during the setup of the virtual environment. This wasn't done as an editable install so the ROOT_DIR changed to the installation in site-packages. This was fixed now.

Regarding 2: I lowered the precision for the checks to 10^-7 as 10^-9 seemed to be a little bit to strict.

[stgeo]

LGTM, thanks for looking into the issues!

[stgeo]

It's not ideal if the tests only work for an editable install. We probably need a different strategy to find the binaries than using ROOT_DIR. Please open an issue or add it to the requirements for the restructuring of the test suite.

[cplett]

Agreed. Added the point to #41.