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rdkit / homebrew-rdkit

Homebrew formula for rdkit
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Invalid option --with-python3 #115

Closed jbibbe4 closed 2 years ago

jbibbe4 commented 2 years ago

I have been following the instruction in the README in order to install RDKit on MacOS Catalina (10.15.7) with Homebrew 3.1.8. I have Python 3.9.4. brew tap rdkit/rdkit worked normally, but brew install rdkit --with-python3 resulted in the following error: Error: invalid option: --with-python3.

When I type brew info rdkit, this is the output:

rdkit: stable 2021.03.5 (bottled), HEAD
Open-source chemoinformatics library
https://rdkit.org/
Not installed
From: https://github.com/Homebrew/homebrew-core/blob/HEAD/Formula/rdkit.rb
License: BSD-3-Clause
==> Dependencies
Build: cmake ✘, swig ✘
Required: boost ✘, boost-python3 ✘, eigen ✘, freetype ✘, numpy ✘, postgresql ✘, py3cairo ✘, python@3.9 ✘
==> Options
--HEAD
    Install HEAD version
==> Caveats
You may need to add RDBASE to your environment variables.
For Bash, put something like this in your $HOME/.bashrc:
  export RDBASE=/usr/local/share/RDKit
==> Analytics
install: 172 (30 days), 476 (90 days), 1,264 (365 days)
install-on-request: 172 (30 days), 475 (90 days), 1,259 (365 days)
build-error: 0 (30 days)

So the only option that they give is --HEAD, not --with-python3. Does this have to do with Homebrew removing options? How can I install rdkit with the Python 3 wrapper?

jbibbe4 commented 2 years ago

I don't understand this at all, but when I do 

brew install rdkit/rdkit/rdkit --with-python3

it works. Maybe I should have typed brew tap rdkit/rdkit/rdkit instead of only twice rdkit.

My clue for this was that when I typed brew options --all, I got:

rdkit/rdkit/rdkit
--with-avalon
    Build with Avalon support
--with-inchi
    Build with InChI support
--with-java
    Build Java wrapper
--with-postgresql
    Build with PostgreSQL database cartridge
--with-pycairo
    Build with py2cairo/py3cairo support
--with-python3
    Build with python3 support
--without-eigen
    Build without eigen support
--without-numpy
    Use your own numpy instead of Homebrew's numpy
--HEAD
    Install HEAD version
UnixJunkie commented 2 years ago

There is an official brew formula that doesn't require 'brew tap rdkit/rdkit'. It supports python by default, you should give it a try.

jbibbe4 commented 2 years ago

There is an official brew formula that doesn't require 'brew tap rdkit/rdkit'. It supports python by default, you should give it a try.

Why isn't that in the README?

I'm sorry, I'm quite new to Homebrew and its terminology.

UnixJunkie commented 2 years ago

Just updated the README; that will save me some user support indeed. :)