updating readme and minor cleanups

choderalab / pinot

Probabilistic Inference for NOvel Therapeutics

MIT License

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updating readme and minor cleanups #92

Closed karalets closed 4 years ago

karalets commented 4 years ago

Editing the readme slightly to make the instructions actually installable on a fresh environment.

More issues I saw here that require an update:

In the readme the command

conda install rdkit does currently not work, fails with

PackagesNotFoundError: The following packages are not available from current channels:
  - rdkit

Another issue I am mindful of: int he requirements.txt we are not specifying versions of dependencies, which is not a good idea in general.

I'd like us to transition to specific versions and to maintain a version of pinot as well. Can we add those changes in this PR and discuss them before I merge this?

Thanks guys.

miretchin commented 4 years ago

re: installing rdkit, we have to specify a channel, can't just do conda install rdkit. conda install -c conda-forge rdkit or conda install -c rdkit rdkit

works instead

karalets commented 4 years ago

re: installing rdkit, we have to specify a channel, can't just do conda install rdkit. conda install -c conda-forge rdkit or conda install -c rdkit rdkit

works instead

adding that as a change to the PR! thanks

miretchin commented 4 years ago

Another thing I noticed:

you can't do pip install -r requirements

pip expects an actual file:

pip install -r requirements.txt

lgtm-com[bot] commented 4 years ago

This pull request fixes 1 alert when merging 1e649c914cf72cbd7a1a967679b84ce63a639ff1 into 1b8bba8b1aedf070adb0b4b2ef58437f8297ea16 - view on LGTM.com

fixed alerts:

1 for Unused import

karalets commented 4 years ago

Another thing I noticed:

you can't do pip install -r requirements

pip expects an actual file:

pip install -r requirements.txt

that was already in this pr