Installation instructions are incomplete

[w8jcik]

There are following instructions in the readme file:

Installation with conda
The easiest way to install auto_martini is with conda:
conda env create -f environment.yaml

Unfortunatelly the file called environment.yaml was deleted from the repository.

Was the file deleted because it was invalid or because of an oversight?

Without this file it is not clear how to install auto_martini with Conda.

[tbereau]

Good point. What about with pip?

https://github.com/tbereau/auto_martini#installation-with-pip

[w8jcik]

Pip instructions ask to call:

python setup.py install

There is no setup.py file either.

Also I am pretty sure Pip won't install binary packages that are needed.

[tbereau]

Ok, I realize now that the code's been updated to poetry. Then it's easy, you clone, you run

poetry shell
poetry add rdkit
poetry install

(I needed to add rdkit on my end, maybe you don't). Afterwards you should be good to go. For every new terminal you open, you need to run poetry shell to load the virtual environment.

[w8jcik]

Thank you for quick help and updating the README.md :)

Just few more comments on the topic:

• https://github.com/tbereau/auto_martini#example has wrong module name.
  It should be auto_martini instead of auto-martini.
• Section about tests is outdated, I think it should be something like poetry run pytest now.
• Tests are failing when run, is it expected?

======================================================= short test summary info ========================================================
FAILED auto_martini/tests/test_basic.py::test_auto_martini_run_sdf[sdf_file0-3] - SystemExit: 1
FAILED auto_martini/tests/test_basic.py::test_auto_martini_run_sdf[sdf_file1-5] - SystemExit: 1
FAILED auto_martini/tests/test_basic.py::test_auto_martini_run_smiles[N1=C(N)NNC1N-valid_GUA.top-GUA-2] - SystemExit: 1
FAILED auto_martini/tests/test_basic.py::test_auto_martini_run_smiles[CCC-valid_PRO.top-PRO-1] - SystemExit: 1

[tbereau]

Thanks for pointing these out!

Indeed, the tests fail because the alogps webserver has been down for a while, and the tests use it. I haven't found a good alternative yet.