Comments (14)
I just uploaded the recent RDKit version to https://pypi.org/project/rdkit/. You should now be able to install RDKit using
pip install rdkit
I am planning to keep the repos rdkit-pypi
and rdkit
at PyPi in sync for some time but retire rdkit-pypi
in the future.
from rdkit-pypi.
awesome. Thanks @kuelumbus
from rdkit-pypi.
That said, it would still be nice to be able to pip install rdkit
so I think asking @greglandrum about that is a good idea.
from rdkit-pypi.
Ha! I see you have already done so. :-)
from rdkit-pypi.
This is a good point. I believe the best solution is to get access to rdkit
on PyPi. I believe the maintainer is Greg (from the RDKit core team). I will contact him.
I am not sure though if this will solve the issue. I do not have much experience with Conda. Can you please try to install a python package (numpy
or so that has the same name) with conda and pip (i.e., the pip in the conda environment). Do they coexist? If so this would not help. I assume Conda always picks the conda-forge
version over the PyPi version.
from rdkit-pypi.
I see similar behavior with numpy, so maybe the best solution is just to avoid using both conda and pip :)
pip list:
numpy 1.22.4
conda list:
numpy 1.22.4 pypi_0 pypi
numpy-base 1.22.3 py39h3b1a694_0
and:
>>> np.__version__
'1.22.3'
from rdkit-pypi.
@kuelumbus actually I think numpy
is a special case due to its complexity. For a simpler package like seaborn
there does not appear to be any conflict (although conda shows the wrong version) as there is only a single package name.
from rdkit-pypi.
@kuelumbus actually I think
numpy
is a special case due to its complexity. For a simpler package likeseaborn
there does not appear to be any conflict (although conda shows the wrong version) as there is only a single package name.
Does this mean that even if RDKit would have the same name, it is possible to have a conda
and pip
version installed in one conda environment? (I assume conda installs packages to a different directory than pip
.)
Also, why do you have two rdkit versions installed in one conda environment (or how did this happen)? Is this a standard case conda users end up with?
from rdkit-pypi.
Does this mean that even if RDKit would have the same name, it is possible to have a conda and pip version installed in one conda environment? (I assume conda installs packages to a different directory than pip.)
No, you'll just have one install. Conda and pip both install packages in .../site-packages/
, but they store their metadata separately so the version shown by conda|pip list
could be different even though they are pointing to the same source files.
Also, why do you have two rdkit versions installed in one conda environment (or how did this happen)? Is this a standard case conda users end up with?
That's a contrived case for illustration, but it could happen if users install packages that depend on rdkit from both sources.
from rdkit-pypi.
Thanks for clarifying. I believe the only thing that I can do is to rename the package on PyPi to rdkit
. But it seems to me the best solution is to use either conda or pip and don't mix them.
from rdkit-pypi.
That said, it would still be nice to be able to
pip install rdkit
so I think asking @greglandrum about that is a good idea.
@kuelumbus I am happy to do this; send me email and we can figure out how to do the transfer
from rdkit-pypi.
Came here to suggest using rdkit
as distribution name for the wheel releases. I'm super happy to see it happening :)
Developers being able to do packaging depending simply on rdkit
right away set's them up for a future where the conda and pip installs are properly aware of each other:
As @skearnes was saying with conda and pip install to the same location in site-packages. This seems weird but if you consider the second install as an update it makes sense. The problem is that the tools might not be properly aware of the existing version.
From conda side there is a configuration that will fix this with the new distribution name: https://docs.conda.io/projects/conda/en/latest/user-guide/configuration/pip-interoperability.html
However most of the time the pip installs come after the conda, and here the problem is coming from rdkit not installing the package properly. It's missing distribution info. Long story short the problem is that after the conda install alone, pip list
doesn't show it.
I came across the issue with conda+pip before and commented on the situation in the conversation on an older PR that was about packaging: rdkit/rdkit#2690 (comment)
TL;DR
Sorry for the long message and back seat commenting. I just hope to make all aware that moving the pypi name is really great but only half the fix. Until the rdkit source install (conda) is not fixed, pip will continue to always overwrite.
from rdkit-pypi.
Thanks @kuelumbus and @greglandrum! I'll send a PR soon to update the RDKit installation docs.
from rdkit-pypi.
Ah I see @kuelumbus already submitted a PR (rdkit/rdkit#5373); thanks!
from rdkit-pypi.
Related Issues (20)
- Incompatible with NumPy 2
- Patch versions of `2024.03` are missing at PyPI HOT 3
- `Contrib` folder missing HOT 5
- Python 3.11 wheels
- Turn on RDK_BUILD_XYZ2MOL_SUPPORT HOT 4
- PyPI Release for 3.11 support HOT 2
- SystemError: initialization of rdchem raised unreported exception HOT 5
- Python 3.11 support on PyPI comes with RDKit release 2022.9.2 HOT 3
- Set upper bound for numpy version HOT 2
- libXrender.so.1 not available HOT 1
- Musl linux wheels are missing HOT 4
- Version mismatch due to setuptools cutting trailing zeros? HOT 2
- Missing/invalid X11 libraries dependencies for libcairo on GNU/Linux HOT 4
- Installation on raspberry pi bullseye failed HOT 12
- Wheels for pyodide/pyscript HOT 9
- `rdkit.rdBase.boostVersion` is empty string in latest release installed from PyPI using pip HOT 2
- Latest version not on pypi HOT 5
- no YAeHMOP support on Mac ARM for rdkit 2023.05 HOT 3
- Python stubs are missing for Windows wheels HOT 1
- Missing wheels on PyPI due to size limit for RDKit versions larger than 2023.9.6 HOT 2
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from rdkit-pypi.