The Compositional Perturbation Autoencoder (CPA) is a deep generative framework to learn effects of perturbations at the single-cell level. CPA performs OOD predictions of unseen combinations of drugs, learns interpretable embeddings, estimates dose-response curves, and provides uncertainty estimates.
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Invalid dashes in "–extra-index-url" Installation instructions #41
An observer familiar with command line arguments will notice that it is unusual to have a long-form command line option with only a single dash ('-'). A keen observer will notice that the character on the installation page is, in fact, not an "en dash" ('-') but an "em dash" ('–'). I suspect that the author of the documentation intended for "--" to be entered, but that readthedocs interpreted this as an "em dash".
Suggested fix:
Please alter all instances of the "em dash" ('–') with two "en dashes" ('--') on the lines concerning the installation of pytorch. Replacing the offending character as described above resolved the issue for me:
What I did:
I attempted to install cpa-tools proceeding according to the instructions on the Installation page.
System: Linux (Debian ) pytorch variant: cpu
I was able to successfully create a virtual environment by running:
conda create -n cpa python=3.9And I invoked this newly created environment using:
conda activate cpaMy issue started when trying to install torch:
pip install torch==1.13.1+cpu –extra-index-url https://download.pytorch.org/whl/cpuExpected behavior:
When copying the installation instructions for the CPU only version of pytorch, I expected to get:
Observed behavior: When copying this statement to the command line,
pip install torch==1.13.1+cpu –extra-index-url https://download.pytorch.org/whl/cpuI obtained the error:
ERROR: Invalid requirement: '–extra-index-url'An observer familiar with command line arguments will notice that it is unusual to have a long-form command line option with only a single dash ('-'). A keen observer will notice that the character on the installation page is, in fact, not an "en dash" ('-') but an "em dash" ('–'). I suspect that the author of the documentation intended for "--" to be entered, but that readthedocs interpreted this as an "em dash".
Suggested fix:
Please alter all instances of the "em dash" ('–') with two "en dashes" ('--') on the lines concerning the installation of pytorch. Replacing the offending character as described above resolved the issue for me:
pip install torch==1.13.1+cpu --extra-index-url https://download.pytorch.org/whl/cpu