Tutorial04 optimize.in file not found

[shastry2358]

Hello all! I'm a newcomer to the OpenFF initiative and was referred here by a colleague to attempt to parametrize a drug molecule i am currently working with. I am going through the tutorial for optimizing forcefields (https://docs.openforcefield.org/projects/evaluator/en/v0.1.1/tutorials/tutorial04.html#Setting-up-the-ForceBalance-Inputs) and have run into a somewhat silly error. When i try to locate the optimize.in file that supposedly ships with the openff framework, I run into a ton of errors. Below I am showing all openff packages installed in the environment and all imports before the line of code that is throwing errors.

> micromamba list

  openff-amber-ff-ports             0.0.4           pyhca7485f_0              conda-forge
  openff-evaluator                  0.3.11          pyhd8ed1ab_0              conda-forge
  openff-evaluator-base             0.3.11          pyhd8ed1ab_0              conda-forge
  openff-forcefields                2024.09.0       pyhff2d567_0              conda-forge
  openff-interchange                0.4.2           pyhd8ed1ab_3              conda-forge
  openff-interchange-base           0.4.2           pyhd8ed1ab_3              conda-forge
  openff-toolkit                    0.16.9          pyhd8ed1ab_1              conda-forge
  openff-toolkit-base               0.16.9          pyhd8ed1ab_1              conda-forge
  openff-units                      0.3.1           pyhd8ed1ab_1              conda-forge
  openff-utilities                  0.1.15          pyhd8ed1ab_0              conda-forge

Attempting to run the "input_file_path ... " line below throws the below errors, any help is appreciated!

>>> from openff.evaluator.utils import get_data_filename
>>> from openff.evaluator.datasets import PhysicalPropertyDataSet
>>> from openff.evaluator.attributes import UNDEFINED
>>> from openff.toolkit.typing.engines.smirnoff import ForceField
>>> input_file_path = get_data_filename("tutorials/tutorial04/optimize.in")
Traceback (most recent call last):
  File "~/micromamba/envs/fftk/lib/python3.10/site-packages/pkg_resources/__init__.py", line 419, in get_provider
    module = sys.modules[moduleOrReq]
KeyError: 'openff.evaluator'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "~/micromamba/envs/fftk/lib/python3.10/site-packages/openff/evaluator/utils/utils.py", line 29, in get_data_filename
    fn = resource_filename("openff.evaluator", os.path.join("data", relative_path))
  File "~/micromamba/envs/fftk/lib/python3.10/site-packages/pkg_resources/__init__.py", line 1379, in resource_filename
    return get_provider(package_or_requirement).get_resource_filename(
  File "~/micromamba/envs/fftk/lib/python3.10/site-packages/pkg_resources/__init__.py", line 421, in get_provider
    __import__(moduleOrReq)
  File "~/micromamba/envs/fftk/lib/python3.10/site-packages/openff/evaluator/__init__.py", line 12, in <module>
    register_default_plugins()
  File "~/micromamba/envs/fftk/lib/python3.10/site-packages/openff/evaluator/plugins.py", line 21, in register_default_plugins
    importlib.import_module("openff.evaluator.properties")
  File "~/micromamba/envs/fftk/lib/python3.10/importlib/__init__.py", line 126, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "~/micromamba/envs/fftk/lib/python3.10/site-packages/openff/evaluator/properties/__init__.py", line 1, in <module>
    from .binding import HostGuestBindingAffinity
  File "~/micromamba/envs/fftk/lib/python3.10/site-packages/openff/evaluator/properties/binding.py", line 10, in <module>
    from openff.evaluator.layers import register_calculation_schema
  File "~/micromamba/envs/fftk/lib/python3.10/site-packages/openff/evaluator/layers/__init__.py", line 1, in <module>
    from .layers import CalculationLayer, CalculationLayerResult, CalculationLayerSchema
  File "~/micromamba/envs/fftk/lib/python3.10/site-packages/openff/evaluator/layers/layers.py", line 18, in <module>
    from openff.evaluator.storage.data import BaseStoredData, StoredSimulationData
  File "~/micromamba/envs/fftk/lib/python3.10/site-packages/openff/evaluator/storage/__init__.py", line 1, in <module>
    from .storage import StorageBackend  # isort:skip
  File "~/micromamba/envs/fftk/lib/python3.10/site-packages/openff/evaluator/storage/storage.py", line 11, in <module>
    from openff.evaluator.storage.data import (
  File "~/micromamba/envs/fftk/lib/python3.10/site-packages/openff/evaluator/storage/data.py", line 9, in <module>
    from openff.evaluator.forcefield import ForceFieldSource
  File "~/micromamba/envs/fftk/lib/python3.10/site-packages/openff/evaluator/forcefield/__init__.py", line 7, in <module>
    from .gradients import ParameterGradient, ParameterGradientKey
  File "~/micromamba/envs/fftk/lib/python3.10/site-packages/openff/evaluator/forcefield/gradients.py", line 173, in <module>
    pint.compat.upcast_types.append(ParameterGradient)
AttributeError: module 'pint.compat' has no attribute 'upcast_types'. Did you mean: 'is_upcast_type'?

[mattwthompson]

That's a very old version of Evaluator; the docs link you have uses 0.1.1 and your environment uses 0.3.1. The most recent release is 0.5.1, could you upgrade to that version?

[mattwthompson]

Great to hear! Re-creating environments is fine (some people even think it's preferred). Those versions look good, mostly pretty recent.

If possible, you may benefit from upgrading to Python 3.11 or 3.12, we don't make new packages for 3.10 any more.

[shastry2358]

is it not possible to use openff-evaluator=0.5.1 and openff-toolkit=0.16.1? When attempting to install those versions of the package together, I get the following error:

> mamba create -n openff -c conda-forge openff-toolkit=0.16.9 openff-evaluator=0.5.1 python

conda-forge/linux-64                                        Using cache
conda-forge/noarch                                          Using cache
error    libmamba Could not solve for environment specs
    The following packages are incompatible
    ├─ openff-evaluator 0.5.1**  is installable and it requires
    │  └─ openff-evaluator-base 0.5.1 pyhd8ed1ab_0, which requires
    │     └─ openff-interchange-base ~=0.3.18  with the potential options
    │        ├─ openff-interchange-base [0.3.18|0.3.19|...|0.3.29], which can be installed;
    │        └─ openff-interchange-base 0.3.25 would require
    │           └─ openff-toolkit-base ~=0.15.2 , which can be installed;
    └─ openff-toolkit 0.16.9**  is not installable because there are no viable options
       ├─ openff-toolkit 0.16.9 would require
       │  ├─ openff-interchange ~=0.4.0  but there are no viable options
       │  │  ├─ openff-interchange 0.4.0 would require
       │  │  │  └─ openff-interchange-base 0.4.0 pyhd8ed1ab_0, which conflicts with any installable versions previously reported;
       │  │  ├─ openff-interchange 0.4.0 would require
       │  │  │  └─ openff-interchange-base 0.4.0 pyhd8ed1ab_1, which conflicts with any installable versions previously reported;
       │  │  ├─ openff-interchange 0.4.1 would require
       │  │  │  └─ openff-interchange-base 0.4.1 pyhd8ed1ab_0, which conflicts with any installable versions previously reported;
       │  │  ├─ openff-interchange 0.4.2 would require
       │  │  │  └─ openff-interchange-base 0.4.2 pyhd8ed1ab_0, which conflicts with any installable versions previously reported;
       │  │  ├─ openff-interchange 0.4.2 would require
       │  │  │  └─ openff-interchange-base 0.4.2 pyhd8ed1ab_1, which conflicts with any installable versions previously reported;
       │  │  ├─ openff-interchange 0.4.2 would require
       │  │  │  └─ openff-interchange-base 0.4.2 pyhd8ed1ab_2, which conflicts with any installable versions previously reported;
       │  │  ├─ openff-interchange 0.4.2 would require
       │  │  │  └─ openff-interchange-base 0.4.2 pyhd8ed1ab_3, which conflicts with any installable versions previously reported;
       │  │  ├─ openff-interchange 0.4.3 would require
       │  │  │  └─ openff-interchange-base 0.4.3 pyhd8ed1ab_0, which conflicts with any installable versions previously reported;
       │  │  └─ openff-interchange 0.4.3 would require
       │  │     └─ openff-interchange-base 0.4.3 pyhd8ed1ab_1, which conflicts with any installable versions previously reported;
       │  └─ openff-toolkit-base 0.16.9 pyhd8ed1ab_0, which conflicts with any installable versions previously reported;
       └─ openff-toolkit 0.16.9 would require
          ├─ openff-interchange ~=0.4.0 , which cannot be installed (as previously explained);
          └─ openff-toolkit-base 0.16.9 pyhd8ed1ab_1, which conflicts with any installable versions previously reported.
critical libmamba Could not solve for environment specs

[shastry2358]

It appears openff-toolkit=0.16.5 and openff-evaluator=0.5.1 are installable together.

[mattwthompson]

They totally should work, but we have a bot fail in our packaging ecosystem. Thanks for finding, hope to have that fixed shortly: conda-forge/openff-evaluator-feedstock#62

There are certainly some other combinations of versions that should work; most anything that the solver finds should work and be okay for learning more about the framework. Some slightly older versions (Python 3.10, Evaluator 0.4.x, Interchange 0.3.18+, Toolkit 0.16.x) should be fine as they're each within the past year or two of releases

[mattwthompson]

Above packaging issues is addressed, within the hour you should be able to pull down 0.5.1 alongside the most recent version of every OpenFF package it depends on. You should see the string pyhd8ed1ab somewhere in the full name of the conda package (the most recent file listed here: pyhd8ed1ab_2.conda)