fix: parsing ordinary yaml strings by cmeesters · Pull Request #3506 · snakemake/snakemake

cmeesters · 2025-04-02T07:52:45Z

In a rule's resource section, we are able to define gres="gpu:1". In a config file, however, we need to define gres: "'gpu:1'" or (on the command line) --set-resources <rulename>:"'gpu=2'". This PR is to try, whether a common setting of simple, non-nested strings is even possible.

QC

This PR primarily is intended to check whether it will pass current QC checks.

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).

I did not cross the docs question - will be necessary, when successful.

Summary by CodeRabbit

New Features
- Improved text handling: the app now classifies ordinary/plain strings to avoid unintended evaluation.
Bug Fixes
- Resource evaluation now safely passes through plain strings, reducing spurious errors and mis-evaluation.
Tests
- Added test coverage validating plain-string detection across various inputs to ensure consistent behavior.

coderabbitai · 2025-04-02T07:52:53Z

📝 Walkthrough

Walkthrough

Adds is_ordinary_string(val) to classify plain strings vs. Python expressions and integrates it into resource evaluation: generic_callable and eval_resource_expression now treat ordinary strings as safe passthroughs on NameError/SyntaxError. Adds a unit test covering the new function.

Changes

Cohort / File(s)	Change Summary
Resources module `src/snakemake/resources.py`	Added `is_ordinary_string(val)` (regex-based heuristic). Updated `generic_callable(...)` and `eval_resource_expression` error paths to return ordinary strings instead of attempting evaluation or raising on `NameError`/`SyntaxError`.
Tests `tests/tests.py`	Imported `is_ordinary_string` and added `test_resource_is_ordinary_string()` asserting true for plain strings and false for code-like strings and non-strings.

Sequence Diagram(s)

sequenceDiagram
    autonumber
    participant T as Test / Caller
    participant E as eval_resource_expression
    participant G as generic_callable
    participant R as is_ordinary_string

    T->>E: evaluate resource value (val)
    alt value is callable expression
        E->>G: delegate evaluation
        G->>R: is_ordinary_string(val)?
        alt ordinary string (True)
            R-->>G: True
            G-->>E: return original val (passthrough)
        else not ordinary (False)
            R-->>G: False
            G-->>G: attempt to evaluate expression
            alt evaluation raises NameError/SyntaxError
                G-->>E: return original val (error handled)
            else success
                G-->>E: return evaluated result
            end
        end
    else value not callable
        E-->>T: return value
    end

Estimated code review effort

🎯 3 (Moderate) | ⏱️ ~20 minutes

Possibly related PRs

feat: 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: Similar changes broadening exception handling in resource evaluation and improving detection/quoting of plain resource strings.

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Post copyable unit tests in a comment
Commit unit tests in branch fix/resource_parsing

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coderabbitai

Actionable comments posted: 0

🧹 Nitpick comments (1)

src/snakemake/resources.py (1)
686-688: Consider simplifying the return statement.

The condition can be simplified by directly returning the result of is_ordinary_string().
-    if is_ordinary_string(value):
-        return True
+    return is_ordinary_string(value)
Note: This is a minor style improvement. Since is_ordinary_string() already returns a boolean, there's no need for the explicit if condition.

🧰 Tools

🪛 Ruff (0.8.2)

686-689: Return the condition bool(is_ordinary_string(value)) directly

Replace with return bool(is_ordinary_string(value))

(SIM103)

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`**/*.py`: Do not try to improve formatting. Do not suggest type annotations for functions that are defined inside of functions or methods. Do not suggest type annotation of the `s...

**/*.py: Do not try to improve formatting.
Do not suggest type annotations for functions that are defined inside of functions or methods.
Do not suggest type annotation of the self argument of methods.
Do not suggest type annotation of the cls argument of classmethods.
Do not suggest return type annotation if a function or method does not contain a return statement.

src/snakemake/resources.py

🪛 Ruff (0.8.2)

src/snakemake/resources.py

686-689: Return the condition bool(is_ordinary_string(value)) directly

Replace with return bool(is_ordinary_string(value))

(SIM103)

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🔇 Additional comments (2)

src/snakemake/resources.py (2)

662-668: Good implementation of the new is_ordinary_string helper.

The function is well-defined with a clear docstring that explains its purpose. It correctly identifies strings that should be treated as ordinary YAML strings rather than Python expressions, which addresses the PR objective of fixing parsing for resource strings.

544-545: Appropriate usage of the new helper in generic_callable.

This change correctly prevents ordinary strings from being unnecessarily evaluated as Python expressions, which would lead to errors. Now strings like "gpu:1" can be passed through directly, addressing the issue described in the PR objectives.

… into fix/resource_parsing

coderabbitai

Actionable comments posted: 1

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`**/*.py`: Do not try to improve formatting. Do not suggest type annotations for functions that are defined inside of functions or methods. Do not suggest type annotation of the `s...

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Do not suggest type annotation of the self argument of methods.
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src/snakemake/resources.py

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🔇 Additional comments (1)

src/snakemake/resources.py (1)

660-666: Looks good!

This new function provides a clear way to identify ordinary string values (not function calls) that should be treated as literal strings rather than Python expressions.

src/snakemake/resources.py

Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>

coderabbitai

Actionable comments posted: 0

🧹 Nitpick comments (1)

src/snakemake/resources.py (1)
684-687: Consider the logical implications of the 'or' operator.

Using or in is_ordinary_string(value) or eval(value) means that eval(value) won't be executed if is_ordinary_string(value) returns True. This is good for performance, but if eval(value) evaluates to a falsy value (0, empty string, etc.) and is_ordinary_string(value) is False, the function will return that falsy value instead of True.

Consider explicitly returning True if needed:
-    return is_ordinary_string(value) or eval(value)
+    if is_ordinary_string(value):
+        return True
+    return bool(eval(value))

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`**/*.py`: Do not try to improve formatting. Do not suggest type annotations for functions that are defined inside of functions or methods. Do not suggest type annotation of the `s...

**/*.py: Do not try to improve formatting.
Do not suggest type annotations for functions that are defined inside of functions or methods.
Do not suggest type annotation of the self argument of methods.
Do not suggest type annotation of the cls argument of classmethods.
Do not suggest return type annotation if a function or method does not contain a return statement.

src/snakemake/resources.py

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🔇 Additional comments (2)

src/snakemake/resources.py (2)

660-667: Function logic looks correct for checking ordinary strings.

The new is_ordinary_string function appropriately checks if a string value should be treated literally rather than evaluated as a Python expression. The regex pattern catches the common case of function-like strings.

684-687: Handle potential eval() exceptions.

The modification now attempts to evaluate string values using eval() without proper error handling. This could cause unexpected exceptions if the string is not a valid Python expression, especially since this function is called within an exception handler in eval_resource_expression() (line 542).

Consider adding try/except around the eval call:
-    return is_ordinary_string(value) or eval(value)
+    try:
+        return is_ordinary_string(value) or eval(value)
+    except (NameError, SyntaxError):
+        return False

cmeesters · 2025-04-02T13:21:20Z

@johanneskoester is my attempt futile - or are there any ideas ;-)

coderabbitai

Actionable comments posted: 0

🧹 Nitpick comments (1)

src/snakemake/resources.py (1)
686-691: Simplify the conditional return statement.

The current implementation can be simplified to directly return the boolean result.
-    if is_ordinary_string(value):
-        return True
-    else:
-        return False
+    return is_ordinary_string(value)
🧰 Tools

🪛 Ruff (0.8.2)

688-691: Return the condition bool(is_ordinary_string(value)) directly

Replace with return bool(is_ordinary_string(value))

(SIM103)

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src/snakemake/resources.py (2 hunks)

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`**/*.py`: Do not try to improve formatting. Do not suggest type annotations for functions that are defined inside of functions or methods. Do not suggest type annotation of the `s...

**/*.py: Do not try to improve formatting.
Do not suggest type annotations for functions that are defined inside of functions or methods.
Do not suggest type annotation of the self argument of methods.
Do not suggest type annotation of the cls argument of classmethods.
Do not suggest return type annotation if a function or method does not contain a return statement.

src/snakemake/resources.py

🪛 Ruff (0.8.2)

src/snakemake/resources.py

688-691: Return the condition bool(is_ordinary_string(value)) directly

Replace with return bool(is_ordinary_string(value))

(SIM103)

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🔇 Additional comments (1)

src/snakemake/resources.py (1)

660-668: Implementation looks good, but regex pattern could be more explicit.

The new function is_ordinary_string correctly identifies strings that shouldn't be evaluated as Python expressions. The regex pattern matches function calls, dictionary literals, and lambda expressions to exclude them from being considered "ordinary".

Consider adding a comment explaining the specific patterns being matched in the regex for better maintainability.

cmeesters · 2025-04-02T16:45:21Z

oops! The last attempt passed? Then I am putting this PR to review. @johanneskoester

johanneskoester

I like this. Two things to get this merged.

we need very comprehensive test cases that clearly show that this does not cause regressions and always works as expected.
The regex needs a comment that explains the rationale behind its elements.

… into fix/resource_parsing

coderabbitai

Actionable comments posted: 0

🧹 Nitpick comments (1)

src/snakemake/resources.py (1)
710-715: Simplify the conditional return statement

The conditional return can be simplified for better readability.
-    if is_ordinary_string(value):
-        return True
-    else:
-        return False
+    return is_ordinary_string(value)
🧰 Tools

🪛 Ruff (0.8.2)

712-715: Return the condition bool(is_ordinary_string(value)) directly

Replace with return bool(is_ordinary_string(value))

(SIM103)

📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL
Plan: Pro

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Reviewing files that changed from the base of the PR and between 120b5d6 and 09ab54e.

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src/snakemake/resources.py (2 hunks)

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`**/*.py`: Do not try to improve formatting. Do not suggest type annotations for functions that are defined inside of functions or methods. Do not suggest type annotation of the `s...

**/*.py: Do not try to improve formatting.
Do not suggest type annotations for functions that are defined inside of functions or methods.
Do not suggest type annotation of the self argument of methods.
Do not suggest type annotation of the cls argument of classmethods.
Do not suggest return type annotation if a function or method does not contain a return statement.

src/snakemake/resources.py

🪛 Ruff (0.8.2)

src/snakemake/resources.py

712-715: Return the condition bool(is_ordinary_string(value)) directly

Replace with return bool(is_ordinary_string(value))

(SIM103)

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🔇 Additional comments (2)

src/snakemake/resources.py (2)

660-692: Good addition with clear documentation

The is_ordinary_string function is well-documented and addresses the need to identify strings that should be treated as literal values rather than Python expressions. This helps solve the YAML string parsing issue mentioned in the PR objectives.

542-558: Handle potential eval() exceptions properly

The previous review highlighted a concern about exception handling when evaluating expressions that hasn't been addressed in this PR. Since you're now identifying ordinary strings that shouldn't be evaluated, this is a good opportunity to improve the error handling here.

Consider modifying the exception handling in the eval_resource_expression function:
    try:
        value = eval(
            val,
            args,
        )
    # Triggers for string arguments like n1-standard-4
    except NameError:
        return val
    except Exception as e:
-        if is_humanfriendly_resource(val):
+        try:
+            if is_humanfriendly_resource(val):
+                return val
+        except Exception:
+            pass
        if not is_file_not_found_error(e, kwargs["input"]):
            # Missing input files are handled by the caller
            raise WorkflowError(
Let me check if there are other instances of eval() that might need similar handling:
#!/bin/bash
# Check for other eval() calls in the codebase that might need similar handling
rg "eval\(" src/snakemake/
🧰 Tools

🪛 Ruff (0.8.2)

546-557: Within an except clause, raise exceptions with raise ... from err or raise ... from None to distinguish them from errors in exception handling

(B904)

cmeesters · 2025-04-03T13:59:30Z

@johanneskoester well, ad 2, I added a bit in a docstring, see commit a0587db

However, writing a full test which will guarantee this will have no side effects? I was hoping the existing test-suite, will cover that ;-). Nevertheless, I prepared 90cb705 , which introduces a new test prior to the resources section.

Any ideas for additional tests?

cmeesters · 2025-04-04T09:00:25Z

@johanneskoester updated branch. Any ideas for additional tests?

johanneskoester · 2025-04-04T13:55:06Z

What about additionally catching SyntaxError in line 539 of resources.py?
That would already suffice for gpu:1. But there will be cases where it is not sufficient.

johanneskoester · 2025-04-04T13:55:19Z

THe tests are fine here.

Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>

coderabbitai

Actionable comments posted: 0

🧹 Nitpick comments (1)

src/snakemake/resources.py (1)
710-715: Simplify boolean return statement.

The conditional return can be simplified to improve readability.
-    if is_ordinary_string(value):
-        return True
-    else:
-        return False
+    return is_ordinary_string(value)
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src/snakemake/resources.py

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src/snakemake/resources.py

712-715: Return the condition bool(is_ordinary_string(value)) directly

Replace with return bool(is_ordinary_string(value))

(SIM103)

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🔇 Additional comments (2)

src/snakemake/resources.py (2)

539-539: Proper exception handling syntax implemented.

The code now correctly catches both NameError and SyntaxError exceptions using the proper tuple syntax. This fixes the syntax error from the previous version.

660-692: Well-implemented new function for string validation.

The new is_ordinary_string function is well-documented and provides a clear way to identify "ordinary" strings that shouldn't be evaluated as Python expressions. The regex pattern correctly identifies function calls, dictionary literals, and lambda expressions.

tbooth · 2025-04-08T16:57:37Z

Actionable comments posted: 0

🧹 Nitpick comments (1)

I'm with the AI-powered rabbit on this one! Code of the form:

if func_that_returns_True_or_False():
    return True
else:
    return False

should be simplified.

But mainly I wanted to say I'm glad to see this fix - the current syntax for defining resources is tricky and annoying.

… into fix/resource_parsing

cmeesters · 2025-04-09T10:18:04Z

@tbooth yes, generally I agree. Just thought being more explicit would help readability. Yet, the introduced function is so small, that my latest commit just introduced a thick comment. I hope, this will do.

@johanneskoester any further ideas regarding additional checks? Or are you willing to merge?

johanneskoester · 2025-04-14T20:09:11Z

@cmeesters I have added one more test case. I think we also would have to recognize such expressions as non-strings. To speed things up, I have separated the SyntaxError approach into a separate PR, because that should be always fine: #3532.

cademirch · 2025-04-15T19:02:28Z

@cmeesters I have added one more test case. I think we also would have to recognize such expressions as non-strings. To speed things up, I have separated the SyntaxError approach into a separate PR, because that should be always fine: #3532.

Do we need to check expressions? Any valid expression should eval before getting checked by is_ordinary_string?

In any case, I've added a regex to try and catch expressions.

cmeesters · 2025-04-17T09:11:50Z

@johanneskoester & @cademirch thank you for your input, guys. I'm afraid, I am currently on a retreat and taking a few days off after Easter.

cademirch · 2025-04-23T21:57:56Z

test failure is unrelated to changes here. seems like some sort of ephemeral connection issue in windows runners

coderabbitai

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📚 Learning: 2024-10-06T14:09:54.370Z

Learnt from: johanneskoester
PR: snakemake/snakemake#3117
File: tests/test_wrapper/Snakefile:11-11
Timestamp: 2024-10-06T14:09:54.370Z
Learning: Changes made within test cases, such as in `tests/test_wrapper/Snakefile`, are for testing purposes and do not require updates to the project documentation.

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src/snakemake/resources.py (1)

is_ordinary_string (664-697)

🪛 Ruff (0.12.2)

tests/tests.py

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🔇 Additional comments (1)

tests/tests.py (1)

16-16: LGTM: import of is_ordinary_string

Import is used by the new unit test and aligns with the module where the helper is defined.

coderabbitai · 2025-09-05T06:30:12Z

tests/tests.py

+def test_resource_is_ordinary_string():
+    # Ordinary strings
+    assert is_ordinary_string("hello") is True
+    assert is_ordinary_string("123") is True
+    assert is_ordinary_string("simple_string") is True
+
+    # Strings that are not ordinary
+    assert is_ordinary_string("func_name(arg1, arg2)") is False  # Function call
+    assert is_ordinary_string("{'key': 'value'}") is False  # Dictionary literal
+    assert is_ordinary_string("lambda x: x + 1") is False  # Lambda expression
+    assert is_ordinary_string("2 * input.size") is False  # calculation
+
+    # Non-string inputs
+    assert is_ordinary_string(123) is False  # Integer
+    assert is_ordinary_string(["list", "of", "strings"]) is False  # List
+    assert is_ordinary_string(None) is False  # NoneType
+
+


💡 Verification agent

🧩 Analysis chain

Cover dashed/slashed resource strings; current regex likely misclassifies them

The regex in is_ordinary_string includes operators like '-' and '/', which will erroneously flag common resource values as non-ordinary (e.g., "--nice=150 --gres=gpu:1", "nvidia-tesla-1000", "CUDA/11.8"). That undermines the PR goal. Please expand the test to capture these cases; they should be True. If they fail, we need to relax the operator detection in is_ordinary_string (e.g., drop '-' and '/' from the operator class or constrain matches to arithmetic contexts and strip whitespace).

Apply this minimal test expansion:

def test_resource_is_ordinary_string(): # Ordinary strings assert is_ordinary_string("hello") is True assert is_ordinary_string("123") is True assert is_ordinary_string("simple_string") is True + assert is_ordinary_string("gpu:1") is True + assert is_ordinary_string("--nice=150 --gres=gpu:1") is True + assert is_ordinary_string("nvidia-tesla-1000") is True + assert is_ordinary_string("CUDA/11.8") is True @@ # Strings that are not ordinary assert is_ordinary_string("func_name(arg1, arg2)") is False # Function call assert is_ordinary_string("{'key': 'value'}") is False # Dictionary literal assert is_ordinary_string("lambda x: x + 1") is False # Lambda expression assert is_ordinary_string("2 * input.size") is False # calculation

Follow-up (in src/snakemake/resources.py, not in this file): consider either stripping the value before matching and/or narrowing the arithmetic pattern so that minus and slash inside plain text (paths, flags, model names) do not trigger. I can propose a concrete regex tweak once we agree on desired edge cases.

🏁 Script executed:

#!/bin/bash # Locate the implementation of is_ordinary_string to inspect its regex rg -nP --type=py 'def is_ordinary_string' -C5 src/snakemake/resources.py

Length of output: 464

🏁 Script executed:

#!/bin/bash # Show the implementation of is_ordinary_string for regex inspection sed -n '660,740p' src/snakemake/resources.py

Length of output: 2067

Add tests for dashed/slashed resource strings and relax operator regex

Expand test_resource_is_ordinary_string to assert True for "gpu:1", "--nice=150 --gres=gpu:1", "nvidia-tesla-1000", and "CUDA/11.8".

In is_ordinary_string, remove - and / from the [\+\-\*/\%] class (or narrow it to only match arithmetic with surrounding whitespace) so common resource identifiers aren’t misclassified.

🧰 Tools

🪛 Ruff (0.12.2)

936-936: Use of assert detected

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🤖 Prompt for AI Agents

In tests/tests.py around lines 934-951, expand the test_resource_is_ordinary_string block to include positive assertions for "gpu:1", "--nice=150 --gres=gpu:1", "nvidia-tesla-1000", and "CUDA/11.8" so dashed and slashed resource tokens are considered ordinary; then in the implementation of is_ordinary_string (where the operator regex lives) remove '-' and '/' from the operator character class or replace the simple [\+\-\*/\%] with a more specific pattern that only matches arithmetic operators when surrounded by whitespace (e.g. require \s+before/after) so hyphens and slashes in resource names aren’t treated as operators and those new tests pass.

@cmeesters I have seen this after the merge, but could you review the suggestion for a potential follow-up PR?

Seems like the humans are having a chat. I'll hop back into my burrow for now. If you need me again, just tag @coderabbitai in a new comment, and I'll come hopping out!

🤖 I have created a release *beep* *boop* --- ## [9.11.0](v9.10.1...v9.11.0) (2025-09-05) ### Features * add landing page to the report containing custom metadata defined with a YTE yaml template ([#3452](#3452)) ([c754d80](c754d80)) * Issue a warning when unsupported characters are used in wildcard names ([#1587](#1587)) ([fa57355](fa57355)) ### Bug Fixes * avoid checking output files in immediate-submit mode ([#3569](#3569)) ([58c42cf](58c42cf)) * clarify --keep-going flag help text to distinguish runtime vs DAG construction errors ([#3705](#3705)) ([a3a8ef4](a3a8ef4)) * enable docstring assignment in `use rule ... with:` block ([#3710](#3710)) ([2191962](2191962)) * fix missing attribute error in greedy scheduler settings when using touch, dryrun or immediate submit. ([6471004](6471004)) * only trigger script with CODE label ([#3707](#3707)) ([2d01f8c](2d01f8c)) * parser.py incorrectly parsing multiline f-strings ([#3701](#3701)) ([06ece76](06ece76)) * parsing ordinary yaml strings ([#3506](#3506)) ([ddf334e](ddf334e)) * remove temp files when using checkpoints ([#3716](#3716)) ([5ff3e20](5ff3e20)) * Restore python rules changes triggering reruns. (GH: [#3213](#3213)) ([#3485](#3485)) ([2f663be](2f663be)) * unit testing ([#3680](#3680)) ([06ba7e6](06ba7e6)) * use queue_input_wait_time when updating queue input jobs ([#3712](#3712)) ([a945a19](a945a19)) ### Documentation * output files within output directories is an error ([#2848](#2848)) ([#2913](#2913)) ([37272e5](37272e5)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please).

In a rule's resource section, we are able to define `gres="gpu:1"`. In a config file, however, we need to define `gres: "'gpu:1'"` or (on the command line) `--set-resources <rulename>:"'gpu=2'"`. This PR is to try, whether a common setting of simple, non-nested strings is even possible. ### QC This PR primarily is intended to check whether it will pass current QC checks. * [ ] 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). I did not cross the docs question - will be necessary, when successful.  ## Summary by CodeRabbit * **New Features** * Improved text handling: the app now classifies ordinary/plain strings to avoid unintended evaluation. * **Bug Fixes** * Resource evaluation now safely passes through plain strings, reducing spurious errors and mis-evaluation. * **Tests** * Added test coverage validating plain-string detection across various inputs to ensure consistent behavior.  --------- Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com> Co-authored-by: Johannes Koester <johannes.koester@uni-due.de> Co-authored-by: Cade Mirchandani <cmirchan@ucsc.edu> Co-authored-by: Johannes Köster <johannes.koester@tu-dortmund.de>

🤖 I have created a release *beep* *boop* --- ## [9.11.0](snakemake/snakemake@v9.10.1...v9.11.0) (2025-09-05) ### Features * add landing page to the report containing custom metadata defined with a YTE yaml template ([snakemake#3452](snakemake#3452)) ([c754d80](snakemake@c754d80)) * Issue a warning when unsupported characters are used in wildcard names ([snakemake#1587](snakemake#1587)) ([fa57355](snakemake@fa57355)) ### Bug Fixes * avoid checking output files in immediate-submit mode ([snakemake#3569](snakemake#3569)) ([58c42cf](snakemake@58c42cf)) * clarify --keep-going flag help text to distinguish runtime vs DAG construction errors ([snakemake#3705](snakemake#3705)) ([a3a8ef4](snakemake@a3a8ef4)) * enable docstring assignment in `use rule ... with:` block ([snakemake#3710](snakemake#3710)) ([2191962](snakemake@2191962)) * fix missing attribute error in greedy scheduler settings when using touch, dryrun or immediate submit. ([6471004](snakemake@6471004)) * only trigger script with CODE label ([snakemake#3707](snakemake#3707)) ([2d01f8c](snakemake@2d01f8c)) * parser.py incorrectly parsing multiline f-strings ([snakemake#3701](snakemake#3701)) ([06ece76](snakemake@06ece76)) * parsing ordinary yaml strings ([snakemake#3506](snakemake#3506)) ([ddf334e](snakemake@ddf334e)) * remove temp files when using checkpoints ([snakemake#3716](snakemake#3716)) ([5ff3e20](snakemake@5ff3e20)) * Restore python rules changes triggering reruns. (GH: [snakemake#3213](snakemake#3213)) ([snakemake#3485](snakemake#3485)) ([2f663be](snakemake@2f663be)) * unit testing ([snakemake#3680](snakemake#3680)) ([06ba7e6](snakemake@06ba7e6)) * use queue_input_wait_time when updating queue input jobs ([snakemake#3712](snakemake#3712)) ([a945a19](snakemake@a945a19)) ### Documentation * output files within output directories is an error ([snakemake#2848](snakemake#2848)) ([snakemake#2913](snakemake#2913)) ([37272e5](snakemake@37272e5)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please).

fix: parsing ordingary yaml strings

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fix: another, more restrictive attempt

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fix: trying regex to exclude python expressions

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cmeesters changed the title ~~fix: parsing ordingary yaml strings~~ fix: parsing ordinary yaml strings Apr 2, 2025

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Inconsistent handling of gres in profiles snakemake/snakemake-executor-plugin-slurm#248

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one more test and some refactoring

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add regex for matching expressions

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chore: remove spurious log file

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Possible breaking changes with Snakemake 9 harvardinformatics/snparcher#240

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chore(main): release 9.11.0 #3722

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fix: standardize handling of resources #3421

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