-
Notifications
You must be signed in to change notification settings - Fork 633
Comparing changes
Open a pull request
base repository: snakemake/snakemake
base: v8.11.0
head repository: snakemake/snakemake
compare: v8.11.1
- 10 commits
- 14 files changed
- 10 contributors
Commits on Apr 26, 2024
-
Configuration menu - View commit details
-
Copy full SHA for 74b99ec - Browse repository at this point
Copy the full SHA 74b99ecView commit details
Commits on Apr 28, 2024
-
fix: check template rendering output for leaked input file paths (#2850)
<!--Add a description of your PR here--> ### QC <!-- Make sure that you can tick the boxes below. --> * [x] The PR contains a test case for the changes or the changes are already covered by an existing test case. * [x] The documentation (`docs/`) is updated to reflect the changes or this is not necessary (e.g. if the change does neither modify the language nor the behavior or functionalities of Snakemake).
Configuration menu - View commit details
-
Copy full SHA for 433302e - Browse repository at this point
Copy the full SHA 433302eView commit details -
fix: small typo in error (#2853)
<!--Add a description of your PR here--> This is just a small typo fix. Working on a fix for snakemake/snakemake-executor-plugin-kubernetes#19 and eventually ended up at the following error when deploying to kubernetes: ``` Error: Error when applying default storage provider gcs to upload workflow sources. {query_validity} ``` Fixing this here so the error is more clear since it looks like kubernetes uses the docker container from main.
Configuration menu - View commit details
-
Copy full SHA for 325a715 - Browse repository at this point
Copy the full SHA 325a715View commit details -
docs: fix typo and link for RO Crate (#2851)
Fixes a typo that breaks the link and link text for RO Crate in the docs. ### QC <!-- Make sure that you can tick the boxes below. --> * [ ] **N/A** The PR contains a test case for the changes or the changes are already covered by an existing test case. * [x] The documentation (`docs/`) is updated to reflect the changes or this is not necessary (e.g. if the change does neither modify the language nor the behavior or functionalities of Snakemake).
Configuration menu - View commit details
-
Copy full SHA for cec0041 - Browse repository at this point
Copy the full SHA cec0041View commit details -
fix: return set instead of list when just --quiet (#2829)
### Description Fixes #2825. `parse_quietness` should return a set since that is what `setup_logger()` expects. ### QC <!-- Make sure that you can tick the boxes below. --> * [x] The PR contains a test case for the changes or the changes are already covered by an existing test case. * [x] The documentation (`docs/`) is updated to reflect the changes or this is not necessary (e.g. if the change does neither modify the language nor the behavior or functionalities of Snakemake).
Configuration menu - View commit details
-
Copy full SHA for eeb57e2 - Browse repository at this point
Copy the full SHA eeb57e2View commit details -
fix: replace pkg_resources for python 3.12 (#2831)
### Description Follow up to #2312, Python 3.12 also [removed](https://docs.python.org/3.12/whatsnew/3.12.html#removed) bundled `setuptools` (aka `pkg_resources`) ### QC <!-- Make sure that you can tick the boxes below. --> - [ ] The PR contains a test case for the changes or the changes are already covered by an existing test case. - [ ] The documentation (`docs/`) is updated to reflect the changes or this is not necessary (e.g. if the change does neither modify the language nor the behavior or functionalities of Snakemake). Co-authored-by: Johannes Köster <[email protected]>
Configuration menu - View commit details
-
Copy full SHA for ac144fc - Browse repository at this point
Copy the full SHA ac144fcView commit details -
fix: Prevent binary log files to crash snakemake execution with `show…
…-failed-logs` (#2827) ### Description As described in #2826 currently the whole snakemake execution crashes if a log file is binary and `show-failed-logs` is used. This fix prevents the crash by capturing the `UnicodeDecodeError` and returning an error message that the log file is not a text instead. ### QC * [x] The PR contains a test case for the changes or the changes are already covered by an existing test case. * [x] The documentation (`docs/`) is updated to reflect the changes or this is not necessary (e.g. if the change does neither modify the language nor the behavior or functionalities of Snakemake). --------- Co-authored-by: Vito Zanotelli <[email protected]>
Configuration menu - View commit details
-
Copy full SHA for 8a80bda - Browse repository at this point
Copy the full SHA 8a80bdaView commit details
Commits on Apr 29, 2024
-
fix: omit norun jobs when determining remote storage input file retri…
…eval (#2854) <!--Add a description of your PR here--> ### QC <!-- Make sure that you can tick the boxes below. --> * [x] The PR contains a test case for the changes or the changes are already covered by an existing test case. * [x] The documentation (`docs/`) is updated to reflect the changes or this is not necessary (e.g. if the change does neither modify the language nor the behavior or functionalities of Snakemake).
Configuration menu - View commit details
-
Copy full SHA for 37a7c7f - Browse repository at this point
Copy the full SHA 37a7c7fView commit details -
fix: use keyword arguments in
_IOFile.open(#2847)fixes #2846 Previously, keword arguments to `.open` were not actually used leading to unexpected (by me) behaviour. I don't think the documentation needs to change to reflect this, because it's what one would expect in the first place. ### QC <!-- Make sure that you can tick the boxes below. --> * [ ] The PR contains a test case for the changes or the changes are already covered by an existing test case. * [x] The documentation (`docs/`) is updated to reflect the changes or this is not necessary (e.g. if the change does neither modify the language nor the behavior or functionalities of Snakemake). --------- Co-authored-by: Johannes Köster <[email protected]>
Configuration menu - View commit details
-
Copy full SHA for 50c84dc - Browse repository at this point
Copy the full SHA 50c84dcView commit details -
chore(main): release 8.11.1 (#2849)
🤖 I have created a release *beep* *boop* --- ## [8.11.1](v8.11.0...v8.11.1) (2024-04-29) ### Bug Fixes * check template rendering output for leaked input file paths ([#2850](#2850)) ([433302e](433302e)) * do not distinguish between local and remote rules in dryrun ([74b99ec](74b99ec)) * omit norun jobs when determining remote storage input file retrieval ([#2854](#2854)) ([37a7c7f](37a7c7f)) * Prevent binary log files to crash snakemake execution with `show-failed-logs` ([#2827](#2827)) ([8a80bda](8a80bda)) * replace pkg_resources for python 3.12 ([#2831](#2831)) ([ac144fc](ac144fc)) * return set instead of list when just --quiet ([#2829](#2829)) ([eeb57e2](eeb57e2)) * small typo in error ([#2853](#2853)) ([325a715](325a715)) * use keyword arguments in `_IOFile.open` ([#2847](#2847)) ([50c84dc](50c84dc)) ### Documentation * fix typo and link for RO Crate ([#2851](#2851)) ([cec0041](cec0041)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please). Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Configuration menu - View commit details
-
Copy full SHA for fc70c90 - Browse repository at this point
Copy the full SHA fc70c90View commit details
This comparison is taking too long to generate.
Unfortunately it looks like we can’t render this comparison for you right now. It might be too big, or there might be something weird with your repository.
You can try running this command locally to see the comparison on your machine:
git diff v8.11.0...v8.11.1