Improve Docker images usability #249
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
When trying to run `sc.pp.highly_variable_genes()` in docs/tutorials/annotation.ipynb the following ImportError is encountered: ImportError: Please install skmisc package via `pip install --user scikit-misc Looking at the pyproject.toml for the `scanpy` project it looks like the `scikit-misc` package can be co-installed by specifying `scanpy[skmisc]` (see: https://github.com/scverse/scanpy/blob/a956fa781a8406fc5030093356c0372456d9184b/pyproject.toml#L142)
User friendliness improvements: - Added short guide on how to make use of Nvidia GPU with Docker image - Updated recommend-interactive image and example command so that downloaded datasets can be shared with local machine (and vice versa) - This commit also bumps the default `SnapATAC2` version that will be built when following the README to v2.6.0.
Codecov ReportAll modified and coverable lines are covered by tests ✅
❗ Your organization needs to install the Codecov GitHub app to enable full functionality. Additional details and impacted files@@ Coverage Diff @@
## main #249 +/- ##
=======================================
Coverage 98.23% 98.23%
=======================================
Files 4 4
Lines 227 227
=======================================
Hits 223 223
Misses 4 4 ☔ View full report in Codecov by Sentry. |
kaizhang
pushed a commit
that referenced
this pull request
Mar 14, 2024
* Address import error encountered in annotation.ipynb When trying to run `sc.pp.highly_variable_genes()` in docs/tutorials/annotation.ipynb the following ImportError is encountered: ImportError: Please install skmisc package via `pip install --user scikit-misc Looking at the pyproject.toml for the `scanpy` project it looks like the `scikit-misc` package can be co-installed by specifying `scanpy[skmisc]` (see: https://github.com/scverse/scanpy/blob/a956fa781a8406fc5030093356c0372456d9184b/pyproject.toml#L142) * Make recommend-interactive docker image even more user friendly User friendliness improvements: - Added short guide on how to make use of Nvidia GPU with Docker image - Updated recommend-interactive image and example command so that downloaded datasets can be shared with local machine (and vice versa) - This commit also bumps the default `SnapATAC2` version that will be built when following the README to v2.6.0. * Add guide sections for running SnapATAC2 Docker image on other platforms * Fix formatting error in Docker README.md
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
This PR was originally intended to address: #238
But it turns out that the issue was with an upstream dependency (
scvi-tools) that has since resolved the problem. So, I spent a bit of time further polishing the Docker images and guide and really making sure that the notebooks (especially the annotations.ipynb) work now.Link to preview updated SnapATAC2 /docker README: https://github.com/njmei/SnapATAC2/tree/address-docker-issues/docker#snapatac2-dockerfiles
Highlights:
annotations.ipynbcan make use of a GPU:Question:
I was looking to see if SnapATAC2 is now publishing Docker images for various new version releases, but I'm not seeing up to date images at: https://hub.docker.com/r/kaizhang/snapatac2. Is there anything I can do to help that process along?