You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
The Bioconda version of Latch is out of sync with PyPI. The Bioconda version is 2.19.11 from 1 year and 5 months ago, while the PyPI version is 2.53.12, released 12 days ago. I use conda to manage all my environments, and don't trust pip to deal with my conda-based dependencies, as I've had too many problems mixing pip and conda.
Describe the solution you'd like
I would love it if you would update the bioconda latch package to the latest version as on PyPI, and keep them in sync, to reduce installation friction. I use conda/bioconda manage my environments and packages, and I think having the latest package on bioconda will help a lot of people.
Describe alternatives you've considered
My workaround is creating a latch-only environment, but then I have to see that my Python needs to be <3.12, and conda defaults to 3.13 now, but even that didn't work :(
Additional context
First I did:
pip install latch
But then I saw it installed HUGE amount of dependencies, including a warning that there are probably conflicts with my environment:
ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
spyder 4.2.5 requires pyqt5<5.13, which is not installed.
spyder 4.2.5 requires pyqtwebengine<5.13, which is not installed.
conda-repo-cli 1.0.5 requires pathlib, which is not installed.
anaconda-project 0.9.1 requires ruamel-yaml, which is not installed.
Then I uninstalled latch:
(base)
Wed 13 Nov - 11:39 ~
pip uninstall latch
Found existing installation: latch 2.53.12
Uninstalling latch-2.53.12:
Would remove:
/Users/olga/opt/anaconda3/bin/latch
/Users/olga/opt/anaconda3/lib/python3.8/site-packages/latch-2.53.12.dist-info/*
/Users/olga/opt/anaconda3/lib/python3.8/site-packages/latch/*
/Users/olga/opt/anaconda3/lib/python3.8/site-packages/latch_cli/*
/Users/olga/opt/anaconda3/lib/python3.8/site-packages/tests/*
Proceed (y/n)? y
Successfully uninstalled latch-2.53.12
Created a new environment, conda create -n latch python pip, only to look at the PyPI version spec and realize that I need Python<3.13 installed, and conda defaulted to 3.13.
Then I removed the environment: conda env remove -n latch and created a new one with the specified Python version: conda create -n latch 'python<3.13' pip.
`conda create -n latch 'python<3.13' pip` output
(base)
Wed 13 Nov - 11:46 ~
conda create -n latch 'python<3.13' pip
Collecting package metadata (current_repodata.json): done
Solving environment: done
==> WARNING: A newer version of conda exists. <==
current version: 22.9.0
latest version: 24.9.2
Please update conda by running
$ conda update -n base -c defaults conda
## Package Plan ##
environment location: /Users/olga/opt/anaconda3/envs/latch
added / updated specs:
- pip
- python[version='<3.13']
The following packages will be downloaded:
package | build
---------------------------|-----------------
pip-24.2 | py312hecd8cb5_0 2.8 MB
python-3.12.7 | hcd54a6c_0 14.0 MB
setuptools-75.1.0 | py312hecd8cb5_0 2.2 MB
wheel-0.44.0 | py312hecd8cb5_0 146 KB
------------------------------------------------------------
Total: 19.1 MB
The following NEW packages will be INSTALLED:
bzip2 pkgs/main/osx-64::bzip2-1.0.8-h6c40b1e_6 None
ca-certificates pkgs/main/osx-64::ca-certificates-2024.9.24-hecd8cb5_0 None
expat pkgs/main/osx-64::expat-2.6.3-h6d0c2b6_0 None
libcxx pkgs/main/osx-64::libcxx-14.0.6-h9765a3e_0 None
libffi pkgs/main/osx-64::libffi-3.4.4-hecd8cb5_1 None
ncurses pkgs/main/osx-64::ncurses-6.4-hcec6c5f_0 None
openssl pkgs/main/osx-64::openssl-3.0.15-h46256e1_0 None
pip pkgs/main/osx-64::pip-24.2-py312hecd8cb5_0 None
python pkgs/main/osx-64::python-3.12.7-hcd54a6c_0 None
readline pkgs/main/osx-64::readline-8.2-hca72f7f_0 None
setuptools pkgs/main/osx-64::setuptools-75.1.0-py312hecd8cb5_0 None
sqlite pkgs/main/osx-64::sqlite-3.45.3-h6c40b1e_0 None
tk pkgs/main/osx-64::tk-8.6.14-h4d00af3_0 None
tzdata pkgs/main/noarch::tzdata-2024b-h04d1e81_0 None
wheel pkgs/main/osx-64::wheel-0.44.0-py312hecd8cb5_0 None
xz pkgs/main/osx-64::xz-5.4.6-h6c40b1e_1 None
zlib pkgs/main/osx-64::zlib-1.2.13-h4b97444_1 None
Proceed ([y]/n)? y
Downloading and Extracting Packages
setuptools-75.1.0 | 2.2 MB | ############################################################################################################### | 100%
pip-24.2 | 2.8 MB | ############################################################################################################### | 100%
wheel-0.44.0 | 146 KB | ############################################################################################################### | 100%
python-3.12.7 | 14.0 MB | ############################################################################################################### | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
# $ conda activate latch
#
# To deactivate an active environment, use
#
# $ conda deactivate
Retrieving notices: ...working... done
The Bioconda version of Latch is out of sync with PyPI. The Bioconda version is 2.19.11 from 1 year and 5 months ago, while the PyPI version is 2.53.12, released 12 days ago. I use
conda
to manage all my environments, and don't trust pip to deal with my conda-based dependencies, as I've had too many problems mixingpip
andconda
.Describe the solution you'd like
I would love it if you would update the bioconda latch package to the latest version as on PyPI, and keep them in sync, to reduce installation friction. I use conda/bioconda manage my environments and packages, and I think having the latest package on bioconda will help a lot of people.
Describe alternatives you've considered
My workaround is creating a latch-only environment, but then I have to see that my Python needs to be <3.12, and conda defaults to 3.13 now, but even that didn't work :(
Additional context
First I did:
But then I saw it installed HUGE amount of dependencies, including a warning that there are probably conflicts with my environment:
Full `pip install latch` output
Then I uninstalled
latch
:Created a new environment,
conda create -n latch python pip
, only to look at the PyPI version spec and realize that I need Python<3.13 installed, andconda
defaulted to 3.13.`conda create -n latch python pip` output
Then I removed the environment:
conda env remove -n latch
and created a new one with the specified Python version:conda create -n latch 'python<3.13' pip
.`conda create -n latch 'python<3.13' pip` output
`conda activate latch && pip install latch` output
The text was updated successfully, but these errors were encountered: