Installation of Stereopy >=1.6.0 using Conda

[ViHammer]

The installation of Stereopy >=1.6.0 using conda is broken. Conda (or Mamba) do not find the package.

Following these instructions:
https://anaconda.org/channels/stereopy/packages/stereopy/overview

conda install stereopy::stereopy=1.6.0 --dry-run
Retrieving notices: ...working... done
Channels:
 - conda-forge
 - stereopy
 - bioconda
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: failed

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

  - stereopy::stereopy==1.6.0

Current channels:

  - https://conda.anaconda.org/conda-forge
  - https://conda.anaconda.org/stereopy
  - https://conda.anaconda.org/bioconda/linux-64

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.

Following the guidelines of these guidelines https://stereopy.readthedocs.io/en/latest/content/00_Installation.html, but specifying the Stereopy version also doesnt work:

mamba install stereopy==1.6 -c stereopy -c grst -c numba -c conda-forge -c bioconda -c fastai -c defaults --dry-run

Looking for: ['stereopy==1.6']

conda-forge/linux-64                                        Using cache
conda-forge/noarch                                          Using cache
bioconda/linux-64                                           Using cache
bioconda/noarch                                             Using cache
stereopy/linux-64                                             No change
stereopy/noarch                                               No change
grst/noarch                                                   No change
numba/linux-64                                                No change
pkgs/r/linux-64                                               No change
pkgs/r/noarch                                                 No change
pkgs/main/noarch                                              No change
numba/noarch                                                  No change
fastai/linux-64                                               No change
grst/linux-64                                                 No change
fastai/noarch                                                 No change
pkgs/main/linux-64                                   9.6MB @  11.0MB/s  0.6s

Pinned packages:
  - python 3.8.*


Could not solve for environment specs
The following package could not be installed
└─ stereopy 1.6  does not exist (perhaps a typo or a missing channel).

[wanruiwen-genomics-cn]

Dear @ViHammer,

Thank you for reporting this issue!

Short answer: The Stereopy conda channel on Anaconda.org has not been updated with packages for version 1.6.0 or later. This is a packaging/distribution gap, not a code bug. In the meantime, you can install Stereopy via PyPI (pip install stereopy) or from source.

---

Assessment

• Type: usage/question (packaging/distribution)
• Severity: medium
• Affected module: Conda channel publishing (not a code issue)

What Is Happening

The stereopy conda channel on Anaconda.org does not contain builds for Stereopy >= 1.6.0. When you run conda install stereopy::stereopy=1.6.0 or mamba install stereopy==1.6, the package manager searches the configured channels but cannot find a matching package because it was never uploaded to the conda channel for these versions.

The current release version in the repository is 1.6.2, but conda packages need to be explicitly built and uploaded to the Anaconda channel by the maintainers. The PyPI distribution (pip install stereopy) is up to date.

Is This Expected?

Yes, from the package manager's perspective — it correctly reports the package is unavailable in the configured channels. However, it is not ideal that the conda channel lags behind PyPI releases.

Recommended Workflow

Step 1: Install via pip (recommended workaround)

Create a conda environment with Python 3.8, then use pip:

conda create --name st python=3.8
conda activate st
pip install stereopy

Step 2: Alternatively, install from source for the latest development version

conda create --name st python=3.8
conda activate st
git clone -b dev https://github.com/STOmics/stereopy.git
cd stereopy
pip install -e .

Alternative Approaches

• Option A (pip in conda env): Use pip install stereopy inside your conda environment. This is fully supported and gives you the latest release.
• Option B (from source): Clone the repository and install with pip install -e . for the cutting-edge development version.
• Option C (conda with older version): If you specifically need conda-managed dependencies, conda install stereopy -c stereopy -c conda-forge -c bioconda may still work for versions <= 1.5.x that were published to the channel.

Useful References

Resource	Purpose
Installation Guide	Official installation instructions (pip + conda + dev)
PyPI - Stereopy	Latest pip-installable release
Anaconda - stereopy	Conda channel (may not have latest versions)

Notes

• Stereopy requires Python 3.8 (requires-python = ">=3.8, <3.9"). Make sure your environment uses Python 3.8.x.
• Using pip install inside a conda environment is a common and well-supported pattern for packages where conda builds are not immediately available.
• We will flag this to the maintainers so that the conda channel can be updated with newer builds.

Please let us know if you have further questions!

Best regards,
Stereopy Maintainer