🐛 Bug: Ersilia Test on PY3.12

[GemmaTuron]

Describe the bug.

I am trying to use the test command at Ersilia. I have tried to install it with
pip install -e .[test]
In an environment that has Python 3.12, as in principle Py3.12 is supported by Ersilia. I have run into the following errors:

1. The rdkit-pypi I think is downgraded, I get the following error that disappears if I change lines 63 and 73 of the pyproject.toml file:

INFO: pip is looking at multiple versions of ersilia to determine which version is compatible with other requirements. This could take a while.
ERROR: Could not find a version that satisfies the requirement rdkit-pypi (from ersilia) (from versions: none)
ERROR: No matching distribution found for rdkit-pypi

2. Once this is bypassed I get stuck at this issue (attached .txt).
   ersiliatest_py312.txt

I believe this is due to Python 3.12 because in an environment with 3.11 it works. Also, The Ersilia install without [test] seems to work in Py3.12. Tagging both @Abellegese as the developer of the testing and @DhanshreeA

Describe the steps to reproduce the behavior

No response

Operating environment

Ubuntu 24.04 LTS

[DhanshreeA]

Wait, this is clearly an error. rdkit is never supposed to be explicitly installed in ersilia, and therefore, not to be explicitly specified in the pyproject.toml at all. I see this was added as an optional test extra within ersilia, ie not to be installed with the standard ersilia installation. But in either case, the test should not require it either since ersilia takes care of installing rdkit whenever it is doing anything with compound inputs. In fact, even within that part of the code, we switched to using the more updated versions of rdkit.

[DhanshreeA]

I think first step is to make sure that the test extra should not need rdkit, ie the test should go through the flow of installing rdkit the way ersilia normally does when dealing with compound inputs.
Secondly, if for whatever reason, rdkit is explicitly required, then we need to use rdkit>=2023 onward and definitely not rdkit-pypi.

[GemmaTuron]

so the rdkit-pypi was added in this commit which was authored by you @DhanshreeA and @Abellegese if I am not wrong: 4f7edf4#diff-50c86b7ed8ac2cf95bd48334961bf0530cdc77b5a56f852c5c61b89d735fd711

[Abellegese]

Yes @GemmaTuron I did that because of the new pytest functionality. We have partial mocking on the test_run.py, meaning the run is taking place without serving (we test CLI components, and few functional level testing of run command). Apparently rdkit was installed during serving:

def setup(self):
    RdkitRequirement()
    ChemblWebResourceClientRequirement()

So the test was failing and I put that as extra in the .toml file. Maybe as @DhanshreeA suggested we might need to invoke this from the above code, as a pytest fixture.

[Abellegese]

Will take care of this.

[GemmaTuron]

This should be tied to refactoring the test command to ensure it works in all Python env -- see #1484
@Abellegese can you tackle it in addition to the refactorings specified?

[Abellegese]

Yes I pushed the changes a couple hours ago, will create a PR.

[Abellegese]

Hi @GemmaTuron but the log also shows that you had trouble installing scipt, I guess due to gfortran. To resolve this, you need to install a Fortran compiler. You can do this by installing the gfortran package, which is part of the GNU Compiler Collection. On Ubuntu or similar Linux distributions, you can install it using the following command:

sudo apt-get install gfortran

Updated: Also needed to remove the scipy version from the pyproject.toml, since the version specified in there is not supported by py3.12. So its also fixed to be *.