Multiple environment conflicts in speed_ppi.yml

[mglgc]

First of all, thank you very much for making your program freely available to the scientific community. Unfortunately, there is no way for a successuful installation due to the presence of multiple conflicts during the env creation, as some others report some time before (isues #25 and #26).

[patrickbryant1]

Hi,

There are constant updates to these packages which creates conflicts. At the time of the last update - there were no conflicts. Can you please specify what packages are causing the issues and I will try to create a new env?

Best,

Patrick

[mglgc]

Hi Patrick
Thank you for your reply. At the current time, the issue is as follow:

LibMambaUnsatisfiableError: Encountered problems while solving:

• package openmmforcefields-0.11.2-pyhd8ed1ab_1 requires ambertools >=20.0,<23, but none of the providers can be installed

Could not solve for environment specs
The following packages are incompatible
├─ ambertools ==23.3 py312h1577c9a_6 is requested and can be installed;
└─ openmmforcefields ==0.11.2 pyhd8ed1ab_1 is not installable because it requires
└─ ambertools >=20.0,<23 , which conflicts with any installable versions previously reported.

[patrickbryant1]

Hi,

I see you are using mamba, but this is a conda env. Have you tried with conda?

You can skip these dependencies otherwise - they are only for relaxing the structures.

[mglgc]

Hi Patrick,
Using a conda install instead a big list of dependencies errors is got (file attached);

conda_onflicts.txt

On the other hand, following with mamba and skipping the amber instalations, errors are finally coming from pip for one version package:

Pip subprocess error:
ERROR: Could not find a version that satisfies the requirement tf-nightly==2.16.0.dev20231211 (from versions: 2.20.0.dev20250327, 2.20.0.dev20250328, 2.20.0.dev20250329, 2.20.0.dev20250330, 2.20.0.dev20250331, 2.20.0.dev20250401, 2.20.0.dev20250402, 2.20.0.dev20250403, 2.20.0.dev20250404, 2.20.0.dev20250405, 2.20.0.dev20250406, 2.20.0.dev20250407, 2.20.0.dev20250408, 2.20.0.dev20250409, 2.20.0.dev20250410, 2.20.0.dev20250412, 2.20.0.dev20250413, 2.20.0.dev20250418, 2.20.0.dev20250423, 2.20.0.dev20250425, 2.20.0.dev20250508, 2.20.0.dev20250511, 2.20.0.dev20250514, 2.20.0.dev20250515, 2.20.0.dev20250516, 2.20.0.dev20250526, 2.20.0.dev20250530, 2.20.0.dev20250602, 2.20.0.dev20250619)
ERROR: No matching distribution found for tf-nightly==2.16.0.dev20231211

failed

CondaEnvException: Pip failed.

Hi,

I see you are using mamba, but this is a conda env. Have you tried with conda?

You can skip these dependencies otherwise - they are only for relaxing the structures.

[patrickbryant1]

Hi,

We will try to add a new env next week. In the meantime either remove the link to tf-nightly (regular tf is fine) or use this env which should also work: https://github.com/patrickbryant1/EvoBind/blob/master/environment.yml

Best,

Patrick

[patrickbryant1]

Hi,

Can you try to install these into a conda env:

dm-haiku==0.0.11
ml-collections
biopython==1.81
chex==0.1.5
dm-tree==0.1.8
immutabledict==2.0.0
scipy
tensorflow
numpy==1.26.4
jaxlib==0.4.35
pandas

and then:
pip install --upgrade "jax[cuda12_pip]" -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html

[mglgc]

Hi Patrick,
Thank you for your reply.
Unfortunately, some issues are following trying to install jaxlib==0.4.35

conda install jaxlib==0.4.35
Collecting package metadata (current_repodata.json): - WARNING conda.models.version:get_matcher(537): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.7.1., but conda is ignoring the . and treating it as 1.7.1
done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): | WARNING conda.models.version:get_matcher(537): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.8.0., but conda is ignoring the . and treating it as 1.8.0
WARNING conda.models.version:get_matcher(537): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.6.0., but conda is ignoring the . and treating it as 1.6.0
WARNING conda.models.version:get_matcher(537): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.9.0., but conda is ignoring the . and treating it as 1.9.0
done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed

ResolvePackageNotFound:

• python=3.1

Hi,

Can you try to install these into a conda env:

dm-haiku==0.0.11 ml-collections biopython==1.81 chex==0.1.5 dm-tree==0.1.8 immutabledict==2.0.0 scipy tensorflow numpy==1.26.4 jaxlib==0.4.35 pandas

and then: pip install --upgrade "jax[cuda12_pip]" -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html