The environment yml file misses mdtraj package

[iGulitch]

Built a Singularity container with the latest versions of mbuild, foyer, and gmso. Used the environment combined of all the environment.yml files of all the three apps. Ran mbuild.load and got the following message :

###########################################################

The code at conversion.py:454 requires the "mdtraj" package
mdtraj can be installed using:
# conda install -c conda-forge mdtraj
or
# pip install mdtraj

###########################################################
Traceback (most recent call last):
  File "/opt/conda/envs/mosdef/lib/python3.13/site-packages/mbuild/utils/io.py", line 209, in import_
    return importlib.import_module(module)
           ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^
  File "/opt/conda/envs/mosdef/lib/python3.13/importlib/__init__.py", line 88, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
           ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<frozen importlib._bootstrap>", line 1387, in _gcd_import
  File "<frozen importlib._bootstrap>", line 1360, in _find_and_load
  File "<frozen importlib._bootstrap>", line 1324, in _find_and_load_unlocked
ModuleNotFoundError: No module named 'mdtraj'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/<path to run script>/<run script>", line 242, in <module>
    main()
    ~~~~^^
  File "/<path to run script>/<run script>", line 239, in main
    <function>(<argument>)
    ~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^
  File "/<path to run script>/<run script>", line 148, in <function>
    ...
  File "/<path to run script>/<run script>", line 172, in <function>
    mol = mbuild.load(<input>)
  File "/opt/conda/envs/mosdef/lib/python3.13/site-packages/mbuild/conversion.py", line 126, in load
    return load_file(
        filename=filename_or_object,
    ...<5 lines>...
        **kwargs,
    )
  File "/opt/conda/envs/mosdef/lib/python3.13/site-packages/mbuild/conversion.py", line 454, in load_file
    md = import_("mdtraj")
  File "/opt/conda/envs/mosdef/lib/python3.13/site-packages/mbuild/utils/io.py", line 242, in import_
    raise DelayImportError(m)
mbuild.utils.io.DelayImportError: 
The code at conversion.py:454 requires the "mdtraj" package
mdtraj can be installed using:
# conda install -c conda-forge mdtraj
or
# pip install mdtraj

Inclusion of mdtraj in the environment file solves the issue. Perhaps, you may want to include mdtraj in the standard environment file of mbuild?

[chrisjonesBSU]

There are several packages in the -dev.yml file that don't show up in the regular one. I can't remember the reasoning behind which are excluded and which aren't, but I think the idea is to have one be a smaller option for basic mbuild functionality while the other includes more packages for complete functionality support and testing. You could use the -dev file in your docker file, or install mdtraj manually in a separate command in the docker file.

Also, just an FYI, I made a MosDeF containers repo that I've been meaning to finalize and transfer ownership over to MoSDeF-hub. Maybe these might be what you need? If they seem helpful, but are missing something, feel free to open an issue.

[chrisjonesBSU]

Looking around, it looks like mdtraj is the backend to load .pdb files. It is included in the dependencies for the mBuild conda-forge package. @CalCraven, maybe at least the environment.yml should mirror what is listed in the recipe

[iGulitch]

Hi, @chrisjonesBSU , and thanks for your reply!

You could use the -dev file in your docker file, or install mdtraj manually in a separate command in the docker file.

I used to exploit environment-dev.yml file before foyer 1.0.1 was released. My latest experience was that the dependencies were never resolved neither with conda, nor with mamba. I moved to a lighter file environment.yml now, and the container is created nice and smoothly within just minutes. mdtraj is not necessary for a container to be built successfully, but like I wrote above, it's missed upon the call mbuild.load. Therefore, I included mdtraj into my own environmental file.

Also, just an FYI, I made a MosDeF containers repo that I've been meaning to finalize and transfer ownership over to MoSDeF-hub.

Thank you, but I'm using Singularity to build containers as a technical requirement at work :)

[CalCraven]

Yeah, essentially what @iGulitch has run into is the reason to have a lighter version of what's a requirement for mBuild. It makes it faster and cleaner to install, especially if you're building an environment with many other dependencies. However, I do agree that everything that's in the recipe probably should be in environment.yml, so we might want to take care of that.

The more hard dependencies we have though, the more likely something is going to make a new release that causes maintenance. Just the one fact of life we have to deal with.

I used to exploit environment-dev.yml file before foyer 1.0.1 was released. My latest experience was that the dependencies were never resolved neither with conda, nor with mamba.

I'll see if I can replicate that, because the environment-dev.yml would be the ideal place to put all of the necessary depencies. Do you happen to have the commands to build the environment that was hanging?

[iGulitch]

Hi, @CalCraven , long time no talk! :)

The command to set up the environment was obviously smth like mamba env create -f /tmp/@USER/environment_mosdef.yml, where environment_mosdef.yml contained the dependencies list manually combined of all the dependencies lists environment-dev.yml of mbuild, foyer, and gmso. Besides, I was installing foyer manually in my Singularity definition file via git clone command, not via pip as you do this now :

name: <name>
channels:
  - <channels>
dependencies:
  - <dependencies>
  - pip:
      - <github repositories>

Unfortunately, I didn't save that list of dependencies, but it was for mbuild 1.1.0, foyer 0.12.1, and gmso 0.12.0.

RN, my list of dependencies is as follows [ there might be some excessive things, I admit ] :

name: <name>
channels:
  - conda-forge
  - openbabel
  - rdkit
dependencies:
  - boltons
  - ele
#  - forcefield-utilities >= 0.4.0
#  - foyer >= 0.11.3
  - garnett
#  - gmso >= 0.12.0
  - lark
  - lxml
  - mdtraj
  - numpy >= 2.0, < 2.3
  - networkx >= 2.5
  - packmol >= 20.15
  - openmm
  - parmed >= 3.4.3
  - pycifrw
  - pydantic >= 2
  - python >= 3.10, <= 3.13
  - python-symengine
  - rdkit >= 2021
  - requests
  - scipy
  - symengine
  - sympy
  - treelib
  - unyt >= 2.9.5
  - pip:
      - git+https://github.com/mosdef-hub/gmso.git@main
      - git+https://github.com/mosdef-hub/mbuild.git@main
      - git+https://github.com/mosdef-hub/foyer.git@main
      - git+https://github.com/mosdef-hub/forcefield-utilities.git@main

and the container creation works smoothly, the dependencies are resolved quickly. Basically, the list is manually combined of all the dependencies lists environment.yml of the newest versions of mbuild, foyer, and gmso, and I added installation via pip section in yml file rather than using git clone separately.

[CalCraven]

Thanks @iGulitch that should be plenty to work off of! Creating environments is always a hassle, so good to double check there isn't any single package holding things up.