basilisk
basilisk: a Bioconductor package for managing Python environments - Published in JOSS (2022)
Science Score: 95.0%
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✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 1 DOI reference(s) in JOSS metadata -
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4 of 12 committers (33.3%) from academic institutions -
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✓JOSS paper metadata
Published in Journal of Open Source Software
Keywords
Keywords from Contributors
Repository
Clone of the Bioconductor repository for the basilisk package.
Basic Info
- Host: GitHub
- Owner: LTLA
- License: gpl-3.0
- Language: R
- Default Branch: master
- Homepage: https://bioconductor.org/packages/devel/bioc/html/basilisk.html
- Size: 561 KB
Statistics
- Stars: 28
- Watchers: 7
- Forks: 13
- Open Issues: 11
- Releases: 0
Topics
Metadata Files
README.md
Managing Python environments within Bioconductor
|Environment|Status|
|---|---|
|BioC-release|
|
|BioC-devel|
|
basilisk provides a standardized mechanism for handling Python dependencies within Bioconductor packages.
It automatically manages different Python versions and virtual environments for each BioC package,
ensuring that users are not burdened with the responsibility of satisfying any Python-based SystemRequirements.
We integrate with reticulate to allow intuitive calling of Python code within R,
with additional protection to ensure that multiple Python environments can be called within the same R session.
Most "users" of this package are expected to be Bioconductor package developers; end users should not need to interact with the basilisk machinery, all going well. Users can follow the typical installation process for Bioconductor packages:
```r install.packages("BiocManager") # if not already installed BiocManager::install("basilisk")
Bioconductor package developers may prefer to use the devel version:
BiocManager::install("basilisk", version="devel") ```
The vignette provides instructions on how to adapt a client package to use basilisk.
A minimal example is provided in the inst/example directory and contains code like:
```r
Provision an environment.
myenv <- BasiliskEnvironment(envname="myenv_name", pkgname="name.of.package", packages=c("pandas==0.25.1") )
Run reticulate code using that environment.
res <- basiliskRun(env=myenv, fun=function(args) { out <- reticulate::import("pandas") # Do something with pandas return(somer_object) }) ```
Detailed documentation for each function is available through the usual methods, i.e., ?basiliskRun.
See the Bioconductor landing page for more links;
some examples of basilisk client packages include crisprScore and velociraptor.
Bugs can be posted to the Issues of this repository. Pull requests are welcome.
Owner
- Name: Aaron Lun
- Login: LTLA
- Kind: user
- Location: San Francisco
- Company: @Genentech
- Twitter: realAaronLun
- Repositories: 183
- Profile: https://github.com/LTLA
It/Its (ノಠ益ಠ)ノ彡┻━┻
JOSS Publication
basilisk: a Bioconductor package for managing Python environments
Authors
Genentech Inc., South San Francisco, USA
Editor
Nikoleta Glynatsi
Tags
Bioconductor bioinformaticsGitHub Events
Total
- Issues event: 2
- Issue comment event: 2
- Push event: 20
- Create event: 1
Last Year
- Issues event: 2
- Issue comment event: 2
- Push event: 20
- Create event: 1
Committers
Last synced: 7 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| LTLA | i****s@g****m | 462 |
| Nitesh Turaga | n****a@g****m | 10 |
| J Wokaty | j****y@s****u | 10 |
| vjcitn | s****c@c****u | 4 |
| Aaron Lun | a****n@c****k | 4 |
| Hervé Pagès | h****s | 3 |
| Michael Stadler | s****l@g****m | 2 |
| Aaron Lun | l****n@g****m | 2 |
| A Wokaty | a****y@s****u | 2 |
| Martin Grigorov | m****g | 1 |
| Jean-Philippe Fortin | f****6@g****m | 1 |
| Charlotte Soneson | c****n@g****m | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 2
- Total pull requests: 1
- Average time to close issues: about 1 month
- Average time to close pull requests: 15 days
- Total issue authors: 1
- Total pull request authors: 1
- Average comments per issue: 4.5
- Average comments per pull request: 8.0
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 2
- Pull requests: 1
- Average time to close issues: about 1 month
- Average time to close pull requests: 15 days
- Issue authors: 1
- Pull request authors: 1
- Average comments per issue: 4.5
- Average comments per pull request: 8.0
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- csoneson (2)
- vjcitn (1)
Pull Request Authors
- LTLA (1)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- basilisk.utils * imports
- dir.expiry * imports
- methods * imports
- parallel * imports
- reticulate * imports
- utils * imports
- BiocStyle * suggests
- callr * suggests
- knitr * suggests
- rmarkdown * suggests
- testthat * suggests
- basilisk * imports
- reticulate * imports
- testthat * suggests