Commits on Feb 5, 2026

1. fix: standardize handling of resources (#3421) …

   This centralizes the code for resource handling into the `resource.py`
   file under a new `Resource` class. Notably, `DefaultResources` has been
   removed, its functionality rolled into the new class. The same class is
   now used for handling global resource limits, default resources, and
   rule resource constraints
   
   As a result of this standarization, the following bugs/inconsistencies
   are fixed:
   
   1) humanreadable resources can now be specified in a group job in
   cluster submit without crashing the program (#3367)
   2) `mem`, `mem_mb`, and `mem_mib` can now be used interchangeably across
   `--resources`, `--set-resource-scopes`, `--default-resources`,
   `--set-resources`, and the `resource` keyword within a `Snakefile`, as
   the names are internally standardized.
   4) humanreadable resources can now be used in all resource contexts
   (e.g. `--resources`)
   6) Providing the same effective resource twice (e.g. mem, mem_mb and/or
   mem_mib) in the same rule or in the global resource specification raises
   an error.
   7) **BREAKING** `mem_mb` and `mem_mib` can no longer be provided a
   string or a function that returns a string within a rule.
   8) The `{resources}` object available within a shell command or
   parameter context now has access to all versions of a sized resource,
   e.g. `mem`, `mem_mb`, `mem_mib`. `mem` is now always a string with a
   unit.
   
   
   A few additional changes:
   
   - The old `Resource` class in snakemake/io.py (that subclasses
   `Namedlist` was renamed to `ResourceList` to prevent confusion. This
   class is still used within the `Job` class and is ultimately passed onto
   the executor. This ensures compatibility with the existing plugin
   interface.
   - I added the ability to watch for a specific Exception class within the
   tests to help increase the resolution of some of my "failure" tests.
   This is completely backwards-compatible
   - Additional typing annotations were added throughout the code I
   touched.
   - A small rearrangement in the code within snakemake/workflow.py to
   group the resource-related code together.
   
   ### Outstanding issues (not to be resolved here)
   1. It was, and remains, possible to sneak a string value as a thread
   using `--set-threads` with a python expression
   1. --resources cannot be given an expression, per design. Currently,
   though, nothing stops one from from providing an expression directly via
   the api. This problem preexists this PR.
   3. There is currently no testing of the cli parsing functions. This
   should be written in a new PR.
   4. The check for positive integers is only done for the CLI. Resources
   requested within rules will not be so validated. This is unchanged from
   previous
   
   ### Gotchas
   1. This does represent a breaking change for API use, as the dataclasses
   will not perform any automatic conversion. Specifically,
   ResourceSettings.resources, .overwrite_threads, .overwrite_resources,
   and .default_resources will be broken in dependent apps.
   
   
   
   <!--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
   
   # Release Notes
   
   * **New Features**
   * Support for human-readable resource specifications (e.g., "1 GB", "1
   GiB")
   * New resource units: mem_mib, disk_mib alongside existing mem_mb,
   disk_mb
   
   * **Bug Fixes**
     * Improved resource handling and validation with better error messages
     * Enhanced resource constraint detection and reporting
   
   * **Refactor**
     * Unified resource management system for simplified configuration
     * Streamlined CLI resource parsing and argument handling
   <!-- end of auto-generated comment: release notes by coderabbit.ai -->

   

   pvandyken authored Feb 5, 2026
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2. chore(main): release 9.16.3 (#3966) …

   🤖 I have created a release *beep* *boop*
   ---
   
   
   ##
   [9.16.3](v9.16.2...v9.16.3)
   (2026-02-05)
   
   
   ### Bug Fixes
   
   * standardize handling of resources
   ([#3421](#3421))
   ([4cada18](4cada18))
   
   ---
   This PR was generated with [Release
   Please](https://github.com/googleapis/release-please). See
   [documentation](https://github.com/googleapis/release-please#release-please).

   

   snakemake-bot authored Feb 5, 2026
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