fix: disable execute after print compilation by Hocnonsense · Pull Request #3041 · snakemake/snakemake

Hocnonsense · 2024-08-23T01:59:49Z

with flag print-compilation, it is not intend to execute the code, which can be incomplete, and running it will waste time and print errors to the screen.

Also, I add some asserts to some properties as they are typing as Optional.

QC

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).

Summary by CodeRabbit

New Features
- Introduced a reusable decorator that standardizes resource settings in the Workflow API.
Enhancements
- Improved type annotations for better clarity and type safety across multiple classes.
- Added assertions in critical methods to ensure necessary settings are initialized before use.
Refactor
- Streamlined several function signatures and internal logic for enhanced readability and maintainability.

with flag `print-compilation`, it is not intend to execute the code, which can be incomplete, and running it will waste time and print errors to the screen. Also, I add some asserts to some properties as they are typing as Optional.

coderabbitai · 2024-08-23T02:00:13Z

Walkthrough

The changes involve multiple modifications across several files in the Snakemake codebase. A new decorator function _no_dag is introduced to standardize resource settings in the WorkflowApi class. Type annotations are enhanced in the snakemake/parser.py, snakemake/persistence.py, and snakemake/workflow.py files for improved clarity and type safety. Various assertions are added throughout the Workflow class to check critical settings, increasing the robustness of the code.

Changes

File	Change Summary
`snakemake/api.py`	Introduced `_no_dag` decorator to set `cores` to 1 for specific methods; decorated `lint` method with `_no_dag`.
`snakemake/parser.py`	Updated `lineno` function with type annotation; reformatted `parse` function signature and added type hints; refactored `linemap` updates.
`snakemake/persistence.py`	Changed `path` parameter annotation from `Path = None` to `Path
`snakemake/workflow.py`	Enhanced type annotations for properties and method signatures; added assertions to validate critical settings before access.
`snakemake/common/__init__.py`	Changed `environ` parameter annotation in `set_env` function to use `Dict[str, unicode]`.
`snakemake/io.py`	Updated type annotations from `dict` to `Dict` for various parameters and attributes to improve type clarity.

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coderabbitai

Actionable comments posted: 2

Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

Commits

Files that changed from the base of the PR and between 9a60046 and fad0939.

Files selected for processing (4)

snakemake/api.py (2 hunks)
snakemake/parser.py (2 hunks)
snakemake/persistence.py (1 hunks)
snakemake/workflow.py (33 hunks)

Additional context used

Path-based instructions (4)

snakemake/persistence.py (1)

Pattern **/*.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.

snakemake/api.py (1)

Pattern **/*.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.

snakemake/parser.py (1)

Pattern **/*.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.

snakemake/workflow.py (1)

Pattern **/*.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.

Ruff

snakemake/parser.py

1311-1311: Ambiguous variable name: l

(E741)

snakemake/workflow.py

20-20: typing.Dict imported but unused

Remove unused import: typing.Dict

(F401)

Additional comments not posted (38)

snakemake/persistence.py (1)

44-44: Type annotation update is appropriate.

The change from Path = None to Path | None = None enhances type clarity and aligns with modern Python type hinting practices.

snakemake/api.py (2)

290-295: Introduction of _no_dag decorator is well-structured.

The _no_dag decorator is defined outside of the dag function, enhancing code organization and reusability. It sets cores to 1, aligning with the PR objective.

297-297: Application of _no_dag decorator to lint method is appropriate.

The lint method now inherits the behavior of setting cores to 1, which is consistent with the intended functionality.

snakemake/parser.py (2)

73-74: Type annotation added for lineno function.

The addition of type annotation for the token parameter enhances clarity and type safety.

1299-1305: Type annotations and reformatting added to parse function.

The type annotations for workflow and linemap enhance clarity and type safety. The reformatting improves readability.

snakemake/workflow.py (33)

151-151: LGTM!

The change from Mapping[str, str] to dict[str, str] is appropriate for specifying the type more precisely.

152-152: LGTM!

The change to allow overwrite_workdir to be of type str or Path enhances flexibility in handling file paths.

253-253: LGTM!

The assertion ensures that storage_settings is not None, which helps prevent potential runtime errors.

274-274: LGTM!

The assertion ensures that storage_settings is not None, which helps prevent potential runtime errors.

386-389: LGTM!

The condition ensures that execution_settings is not None before accessing use_threads, which is a good practice.

473-473: LGTM!

The assertion ensures that dag_settings is not None, which helps prevent potential runtime errors.

478-478: LGTM!

The assertion ensures that deployment_settings is not None, which helps prevent potential runtime errors.

666-669: LGTM!

The condition ensures that storage_settings and default_storage_provider are not None before proceeding, which is a good practice.

679-680: LGTM!

The change to allow shadow_prefix to be of type str, Path, or None enhances flexibility.

698-698: LGTM!

The assertion ensures that dag_settings is not None, which helps prevent potential runtime errors.

799-799: LGTM!

The assertion ensures that deployment_settings is not None, which helps prevent potential runtime errors.

818-818: LGTM!

The assertion ensures that dag_settings is not None, which helps prevent potential runtime errors.

837-837: LGTM!

The assertion ensures that dag_settings is not None, which helps prevent potential runtime errors.

857-857: LGTM!

The assertion ensures that dag_settings is not None, which helps prevent potential runtime errors.

912-912: LGTM!

The assertion ensures that dag_settings is not None, which helps prevent potential runtime errors.

928-928: LGTM!

The assertion ensures that dag_settings is not None, which helps prevent potential runtime errors.

938-938: LGTM!

The assertion ensures that dag_settings is not None, which helps prevent potential runtime errors.

948-948: LGTM!

The assertion ensures that dag_settings is not None, which helps prevent potential runtime errors.

958-958: LGTM!

The assertion ensures that dag_settings is not None, which helps prevent potential runtime errors.

971-971: LGTM!

The assertion ensures that dag_settings is not None, which helps prevent potential runtime errors.

987-987: LGTM!

The assertion ensures that dag_settings is not None, which helps prevent potential runtime errors.

1006-1006: LGTM!

The assertion ensures that dag_settings is not None, which helps prevent potential runtime errors.

1017-1017: LGTM!

The assertion ensures that dag_settings is not None, which helps prevent potential runtime errors.

1040-1040: LGTM!

The assertion ensures that dag_settings is not None, which helps prevent potential runtime errors.

1048-1048: LGTM!

The assertion ensures that deployment_settings is not None, which helps prevent potential runtime errors.

1054-1054: LGTM!

The assertion ensures that dag_settings is not None, which helps prevent potential runtime errors.

1064-1064: LGTM!

The assertion ensures that dag_settings is not None, which helps prevent potential runtime errors.

1086-1091: LGTM!

The assertions ensure that critical settings are not None, which helps prevent potential runtime errors.

1360-1361: LGTM!

The assertion ensures that the frame is not None, which helps prevent potential runtime errors.

1388-1389: LGTM!

The assertion ensures that the frame is not None, which helps prevent potential runtime errors.

1435-1435: LGTM!

Adding a type hint for linemap improves code clarity and type safety.

1447-1447: LGTM!

The return statement aligns with the PR objective to disable execution after print compilation.

1969-1969: LGTM!

The assertion ensures that deployment_settings is not None, which helps prevent potential runtime errors.

snakemake/parser.py

snakemake/workflow.py

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

johanneskoester

Thank you so much! I have just a few questions about the changes.

johanneskoester · 2024-08-27T14:08:46Z

snakemake/workflow.py

-            deploy.append("conda")
-        if DeploymentMethod.APPTAINER in self.deployment_settings.deployment_method:
-            deploy.append("singularity")
+        if self.deployment_settings is not None:


why would this be none here?

These following checks of None are added as these params are setted as None when it was created. mypy warned me that. Probably an assert is proper here, or I will ignore these type of warnings? Thanks for your advice!

johanneskoester · 2024-08-27T14:09:20Z

snakemake/workflow.py

+        assert self.dag_settings is not None
        self._prepare_dag(
-            forceall=self.dag_settings.forceall,
+            forceall=self.dag_settings.forceall,  # True?


yes, why not?

Sorry for the trailing comment added here, I've deleted it

johanneskoester · 2024-08-27T14:10:28Z

snakemake/workflow.py

            path = str(path)
-        if self.storage_settings.default_storage_provider is not None:
+        if (
+            self.storage_settings is not None


Why would this be None here?

johanneskoester · 2024-08-27T14:10:46Z

snakemake/workflow.py

        return (
-            self.execution_settings.use_threads
+            (
+                self.execution_settings is not None


Why would this be None here?

snakemake/workflow.py

snakemake/parser.py

coderabbitai

Actionable comments posted: 0

Review details

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Review profile: CHILL

Commits

Files that changed from the base of the PR and between fad0939 and 6069ad6.

Files selected for processing (2)

snakemake/parser.py (2 hunks)
snakemake/workflow.py (33 hunks)

Files skipped from review as they are similar to previous changes (2)

snakemake/parser.py
snakemake/workflow.py

coderabbitai

Actionable comments posted: 0

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Commits

Files that changed from the base of the PR and between 6069ad6 and f894795.

Files selected for processing (1)

snakemake/workflow.py (36 hunks)

Files skipped from review as they are similar to previous changes (1)

snakemake/workflow.py

johanneskoester · 2024-08-28T15:39:01Z

snakemake/parser.py

+def parse(
+    path,
+    workflow: "workflow.Workflow",
+    linemap: dict[int, int],


Suggested change

linemap: dict[int, int],

linemap: Dict[int, int],

I rather used typing.Dict so far for backwards compatibility. Can you change the rest?

Ah wait, I will do that quickly.

Sorry for my miss, and I'm grateful for your help!

sonarqubecloud · 2024-08-28T15:44:37Z

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarCloud

coderabbitai

Actionable comments posted: 0

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Review profile: CHILL

Commits

Files that changed from the base of the PR and between f894795 and 4b4051d.

Files selected for processing (4)

snakemake/common/init.py (1 hunks)
snakemake/io.py (2 hunks)
snakemake/parser.py (2 hunks)
snakemake/workflow.py (36 hunks)

Files skipped from review due to trivial changes (2)

snakemake/common/init.py
snakemake/io.py

Files skipped from review as they are similar to previous changes (2)

snakemake/parser.py
snakemake/workflow.py

🤖 I have created a release *beep* *boop* --- ## [8.19.0](v8.18.2...v8.19.0) (2024-08-29) ### Features * check consistency of output file mtimes (must be newer than input files) ([#3050](#3050)) ([666cf62](666cf62)) * print host name when executing workflow ([#3048](#3048)) ([b0ff787](b0ff787)) ### Bug Fixes * `mem` and `disk` inference fixes ([#3040](#3040)) ([7530794](7530794)) * avoid error accessing superclass in ioutils ([#3056](#3056)) ([a66a5f5](a66a5f5)) * disable execute after print compilation ([#3041](#3041)) ([86ed3cd](86ed3cd)) * download report assets upon package build such that reports become possible offline (cont. of [#2904](#2904)) ([#3026](#3026)) ([e8dad4b](e8dad4b)) ### Documentation * Add 'Editor integrations' section to Installation page ([#3045](#3045)) ([9a4006d](9a4006d)) * Fix typo (seesee to see) ([#3037](#3037)) ([de201fb](de201fb)) * various documentation fixes ([#3052](#3052)) ([b11460c](b11460c)) --- 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>

with flag `print-compilation`, it is not intend to execute the code, which can be incomplete, and running it will waste time and print errors to the screen. Also, I add some asserts to some properties as they are typing as Optional.  ### QC  * [ ] 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).  ## Summary by CodeRabbit - **New Features** - Introduced a reusable decorator that standardizes resource settings in the Workflow API. - **Enhancements** - Improved type annotations for better clarity and type safety across multiple classes. - Added assertions in critical methods to ensure necessary settings are initialized before use. - **Refactor** - Streamlined several function signatures and internal logic for enhanced readability and maintainability.  --------- Co-authored-by: Johannes Köster <johannes.koester@uni-due.de> Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>

🤖 I have created a release *beep* *boop* --- ## [8.19.0](snakemake/snakemake@v8.18.2...v8.19.0) (2024-08-29) ### Features * check consistency of output file mtimes (must be newer than input files) ([snakemake#3050](snakemake#3050)) ([666cf62](snakemake@666cf62)) * print host name when executing workflow ([snakemake#3048](snakemake#3048)) ([b0ff787](snakemake@b0ff787)) ### Bug Fixes * `mem` and `disk` inference fixes ([snakemake#3040](snakemake#3040)) ([7530794](snakemake@7530794)) * avoid error accessing superclass in ioutils ([snakemake#3056](snakemake#3056)) ([a66a5f5](snakemake@a66a5f5)) * disable execute after print compilation ([snakemake#3041](snakemake#3041)) ([86ed3cd](snakemake@86ed3cd)) * download report assets upon package build such that reports become possible offline (cont. of [snakemake#2904](snakemake#2904)) ([snakemake#3026](snakemake#3026)) ([e8dad4b](snakemake@e8dad4b)) ### Documentation * Add 'Editor integrations' section to Installation page ([snakemake#3045](snakemake#3045)) ([9a4006d](snakemake@9a4006d)) * Fix typo (seesee to see) ([snakemake#3037](snakemake#3037)) ([de201fb](snakemake@de201fb)) * various documentation fixes ([snakemake#3052](snakemake#3052)) ([b11460c](snakemake@b11460c)) --- 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>

fix: disable execute after print compilation

fad0939

with flag `print-compilation`, it is not intend to execute the code, which can be incomplete, and running it will waste time and print errors to the screen. Also, I add some asserts to some properties as they are typing as Optional.

Hocnonsense requested a review from johanneskoester as a code owner August 23, 2024 01:59

coderabbitai bot reviewed Aug 23, 2024

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johanneskoester and others added 3 commits August 27, 2024 16:04

Update snakemake/workflow.py

28ae90c

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

style: Avoid ambiguous variable names @coderabbitai

434fc58

Merge branch 'main' into main

6069ad6

johanneskoester reviewed Aug 27, 2024

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Hocnonsense and others added 2 commits August 27, 2024 22:56

refactor: make changes reasonable

3beddaf

Merge branch 'main' into main

f894795

coderabbitai bot reviewed Aug 27, 2024

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johanneskoester requested changes Aug 28, 2024

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use Dict type for consistency

4b4051d

johanneskoester approved these changes Aug 28, 2024

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johanneskoester merged commit 86ed3cd into snakemake:main Aug 29, 2024

github-actions bot mentioned this pull request Aug 29, 2024

chore(main): release 8.19.0 #3051

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feat: Prefer papermill to nbconvert #2857

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feat: seperate namespase of module from influence of use modification #3046

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feat: Initial attempt at adding a --any-of feature #3115

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feat: support for specifying conda envs as directories #3132

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feat!: Logging refactor & add LoggerPluginInterface #3107

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fix: update rust-script usage to recent version (v0.35.0) #3183 #3208

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feat: finalized support for access pattern annotation (sequential, random, multi), allowing storage plugins to decide about the most efficient provisioning approach (e.g. mounting vs. downloading a local copy) #3461

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fix: logging refinements #3571

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fix: reuse async runner to prevent port exhaustion #3911

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Hocnonsense self-assigned this Mar 18, 2026

Hocnonsense mentioned this pull request Mar 22, 2026

fix: Compiled workflow.include should carry print_compilation keyword #2469

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Hocnonsense commented Aug 23, 2024 •

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