fix: restore accidentally changed behavior of --cores. If not specified, Snakemake now complains again, asking for --cores to be specified (of --jobs in case of remote exec). As before, if a default is desired, it can be easily set via a profile#3531
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johanneskoester merged 2 commits intomainfrom Apr 14, 2025
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…ed, Snakemake now complains again, asking for --cores to be specified (of --jobs in case of remote exec). As before, if a default is desired, it can be easily set via a profile
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📝 Walkthrough## Walkthrough
The change removes a fallback assignment in the command-line interface logic where the number of CPU cores (`args.cores`) would default to the system's available CPU count if not explicitly set. After this modification, if no value is provided for `args.cores` through prior logic, it will remain `None`. Additionally, test code was updated to avoid raising `None` exceptions and to explicitly specify `--cores 1` in certain test Snakemake command invocations. No other logic or function signatures are affected.
## Changes
| File(s) | Change Summary |
|------------------------------|-----------------------------------------------------------------------------------------------|
| src/snakemake/cli.py | Removed fallback code that set `args.cores` to the available CPU count if it was still `None`. |
| tests/common.py | Modified error handling to raise exceptions only if they are not `None` after failed runs. |
| tests/tests.py | Added `--cores 1` option to Snakemake shell commands in two test functions. |
## Sequence Diagram(s)
```mermaid
sequenceDiagram
participant User
participant CLI
User->>CLI: Provide command-line arguments (may omit --cores)
CLI->>CLI: Process arguments
alt --cores provided or set by earlier logic
CLI->>CLI: Use specified value for args.cores
else --cores not set
CLI->>CLI: args.cores remains None (no fallback assignment)
end |
johanneskoester
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🤖 I have created a release *beep* *boop* --- ## [9.2.0](v9.1.11...v9.2.0) (2025-04-14) ### Features * auto detect string resources in resource definitions given by --default-resources and --set-resources in the string yields a syntax error when being interpreted as a python expression; this will obviate the need to quote such expressions in many cases; further, fix interpretation of quoted resources by removing quotes after intepretation ([#3532](#3532)) ([81f09bd](81f09bd)) ### Bug Fixes * restore accidentally changed behavior of --cores. If not specified, Snakemake now complains again, asking for --cores to be specified (of --jobs in case of remote exec). As before, if a default is desired, it can be easily set via a profile ([#3531](#3531)) ([11b2b30](11b2b30)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please).
Contributor
|
Just got caught out by this change with the (new to me) error:
Easy to work arround with an explicit |
7 tasks
kjohnsen
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…ed, Snakemake now complains again, asking for --cores to be specified (of --jobs in case of remote exec). As before, if a default is desired, it can be easily set via a profile (snakemake#3531) ### Description <!--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). <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit - **Refactor** - Updated the logic for assigning CPU cores, removing the automatic fallback to available CPU count when not explicitly set. - **Bug Fixes** - Improved error handling to avoid raising null exceptions after failed executions. - **Tests** - Modified test commands to explicitly specify single-core usage during runs. <!-- end of auto-generated comment: release notes by coderabbit.ai -->
kjohnsen
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Dec 15, 2025
🤖 I have created a release *beep* *boop* --- ## [9.2.0](snakemake/snakemake@v9.1.11...v9.2.0) (2025-04-14) ### Features * auto detect string resources in resource definitions given by --default-resources and --set-resources in the string yields a syntax error when being interpreted as a python expression; this will obviate the need to quote such expressions in many cases; further, fix interpretation of quoted resources by removing quotes after intepretation ([snakemake#3532](snakemake#3532)) ([81f09bd](snakemake@81f09bd)) ### Bug Fixes * restore accidentally changed behavior of --cores. If not specified, Snakemake now complains again, asking for --cores to be specified (of --jobs in case of remote exec). As before, if a default is desired, it can be easily set via a profile ([snakemake#3531](snakemake#3531)) ([11b2b30](snakemake@11b2b30)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please).
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Description
QC
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).Summary by CodeRabbit