feat: Support Hy in script directive by jsquaredosquared · Pull Request #3824 · snakemake/snakemake

jsquaredosquared · 2025-11-03T00:46:10Z

Add support for Hy in the script directive. This will allow the use of a Lisp-like syntax for writing scripts, e.g.:

(require hyrule [-> ->>])

(defn is-odd? [n] (!= (% n 2) 0))

(setv result
      (->> (get snakemake.input 0)
           open
           .readlines
           (map int)
           (filter is-odd?)
           sum))

(print result
       :file
       (-> (get snakemake.output 0)
           (open "w")))

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
- Added runtime support for Hy scripts.
Documentation
- Added Hy and Xonsh language sections with examples and cross-references.
- Fixed Bash example formatting and removed a duplicated Xonsh example.
Tests
- Added end-to-end test exercising Hy script execution with a Snakefile, Hy script, and sample input/output.

coderabbitai · 2025-11-03T00:46:22Z

📝 Walkthrough

Walkthrough

Adds Hy (.hy) script support: new HyScript subclass, language detection and dispatch registration for "hy", documentation updates adding Xonsh and Hy examples, and a test bundle (Snakefile, Hy script, input) exercising a Hy script that sums odd numbers.

Changes

Cohort / File(s)	Summary
Documentation `docs/snakefiles/rules.rst`	Added Xonsh and Hy language sections and examples; adjusted Bash example header formatting; removed duplicate Xonsh block and restored placement for the new blocks.
Core language support `src/snakemake/script/__init__.py`	Added `HyScript` (subclass of `PythonScript`) with `write_script(preamble, fd)` that emits a Hy-specific preamble and `execute_script(fname, edit=False)` that invokes the hy runtime; registered `"hy": HyScript` in the exec-class mapping; updated `get_language(...)` to detect `.hy` files; included `.hy` in the supported-types error message; imported `get_report_id`.
Tests / Examples `tests/test_script_hy/Snakefile`, `tests/test_script_hy/scripts/test.hy`, `tests/test_script_hy/test.in`	New test bundle: `rule test_hy` uses `envs/hy.yaml` and runs `scripts/test.hy`; `test.hy` reads `test.in`, filters odd integers, sums them, and writes `test.out`; `test.in` contains integers 1–20.

Sequence Diagram(s)

sequenceDiagram
  participant SM as Snakemake
  participant HS as HyScript
  participant HY as hy runtime
  participant FS as Filesystem

  rect `#E8F5E9`
    Note over SM,HS: detect `.hy` -> select HyScript
  end

  SM->>HS: script(...): instantiate HyScript
  HS->>HS: write_script(preamble, fd)\n(emit Hy preamble + source)
  HS->>HY: execute_script(fname) (spawn hy runtime)
  HY->>FS: read inputs / write outputs
  HY-->>HS: exit status / stdout
  HS-->>SM: return completion / propagate errors

Estimated code review effort

🎯 3 (Moderate) | ⏱️ ~20 minutes

Review focus:
- Correctness and safety of HyScript.write_script preamble format.
- Subprocess invocation in HyScript.execute_script and error handling/propagation.
- get_language filename detection coverage for .hy.
- Tests: paths and referenced conda env envs/hy.yaml.

Possibly related PRs

feat: xonsh support #3310 — Modifies script dispatch machinery and language registration; strongly related to adding new script-language support.

Pre-merge checks and finishing touches

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 33.33% which is insufficient. The required threshold is 80.00%.	You can run `@coderabbitai generate docstrings` to improve docstring coverage.

✅ Passed checks (2 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title clearly and concisely describes the main change: adding Hy language support to Snakemake's script directive.
Description check	✅ Passed	The PR description includes a clear explanation of the feature, a practical code example, and both QC checklist items are marked as complete with evidence of test and documentation updates.

✨ Finishing touches

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Create PR with unit tests
Post copyable unit tests in a comment

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📒 Files selected for processing (1)

docs/snakefiles/rules.rst (3 hunks)

🧰 Additional context used

🧠 Learnings (4)

📚 Learning: 2024-10-06T14:09:54.370Z

Learnt from: johanneskoester
Repo: snakemake/snakemake PR: 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.

Applied to files:

docs/snakefiles/rules.rst

📚 Learning: 2024-12-14T13:10:48.450Z

Learnt from: johanneskoester
Repo: snakemake/snakemake PR: 2927
File: tests/test_subpath/Snakefile:11-11
Timestamp: 2024-12-14T13:10:48.450Z
Learning: In Snakemake, when a rule defines a single output file (even if the output is specified as a dictionary), `{output}` in the shell command can be used directly to refer to that file.

Applied to files:

docs/snakefiles/rules.rst

📚 Learning: 2024-11-07T00:32:44.137Z

Learnt from: mbhall88
Repo: snakemake/snakemake PR: 3188
File: tests/test_script/scripts/test.sh:4-4
Timestamp: 2024-11-07T00:32:44.137Z
Learning: In test scripts within the Snakemake project, concise code is preferred over verbose error handling when simplicity suffices.

Applied to files:

docs/snakefiles/rules.rst

📚 Learning: 2024-10-29T17:14:13.585Z

Learnt from: zmbc
Repo: snakemake/snakemake PR: 2857
File: snakemake/notebook.py:84-90
Timestamp: 2024-10-29T17:14:13.585Z
Learning: In `snakemake/notebook.py`, when suggesting enhancements to the `execute_script` method in the `JupyterNotebook` class, ensure that changes align with both papermill and nbconvert use cases.

Applied to files:

docs/snakefiles/rules.rst

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🔇 Additional comments (1)

docs/snakefiles/rules.rst (1)

1403-1483: All previous suggestions successfully incorporated. ✓

The Xonsh and Hy sections comprehensively address all prior review feedback:

Hy script example demonstrating both indexed access (snakemake.input[0]) and named access (snakemake.output["results_file"])

Input/output variable naming follows suggested conventions (lines 1415-1417, 1456)

Clear, practical examples showing language-specific syntax for interacting with the snakemake object

Proper RST structure consistent with other language sections in the document

The code examples are accurate and illustrative of real-world usage patterns.

Thanks for using CodeRabbit! It's free for OSS, and your support helps us grow. If you like it, consider giving us a shout-out.

❤️ Share

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coderabbitai

Actionable comments posted: 1

🧹 Nitpick comments (1)

tests/test_script_hy/Snakefile (1)
6-14: Misleading rule name.

The rule is named test_xonsh but it's actually testing Hy script support, not Xonsh. For clarity and maintainability, consider renaming it to test_hy.

Apply this diff:
-rule test_xonsh:
+rule test_hy:
   input:
     "test.in"
   output:
Note: This also aligns better with the directory name test_script_hy and the script being tested.

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📒 Files selected for processing (6)

docs/snakefiles/rules.rst (1 hunks)
src/snakemake/script/__init__.py (3 hunks)
tests/test_script_hy/Snakefile (1 hunks)
tests/test_script_hy/envs/xonsh.yaml (1 hunks)
tests/test_script_hy/scripts/test.hy (1 hunks)
tests/test_script_hy/test.in (1 hunks)

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📓 Path-based instructions (1)

**/*.py

⚙️ CodeRabbit configuration file

**/*.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.

Files:

src/snakemake/script/__init__.py

🧠 Learnings (5)

📚 Learning: 2024-10-06T14:09:54.370Z

Learnt from: johanneskoester
Repo: snakemake/snakemake PR: 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.

Applied to files:

docs/snakefiles/rules.rst
tests/test_script_hy/Snakefile

📚 Learning: 2024-12-14T13:10:48.450Z

Learnt from: johanneskoester
Repo: snakemake/snakemake PR: 2927
File: tests/test_subpath/Snakefile:11-11
Timestamp: 2024-12-14T13:10:48.450Z
Learning: In Snakemake, when a rule defines a single output file (even if the output is specified as a dictionary), `{output}` in the shell command can be used directly to refer to that file.

Applied to files:

docs/snakefiles/rules.rst

📚 Learning: 2024-10-29T17:14:13.585Z

Learnt from: zmbc
Repo: snakemake/snakemake PR: 2857
File: snakemake/notebook.py:84-90
Timestamp: 2024-10-29T17:14:13.585Z
Learning: In `snakemake/notebook.py`, when suggesting enhancements to the `execute_script` method in the `JupyterNotebook` class, ensure that changes align with both papermill and nbconvert use cases.

Applied to files:

docs/snakefiles/rules.rst

📚 Learning: 2024-12-21T15:10:31.992Z

Learnt from: johanneskoester
Repo: snakemake/snakemake PR: 2925
File: tests/test_nonstr_params/Snakefile:14-15
Timestamp: 2024-12-21T15:10:31.992Z
Learning: The file "test.jsonl" in tests/test_nonstr_params is automatically created by Snakemake, rather than manually generated in the Snakefile.

Applied to files:

tests/test_script_hy/Snakefile

📚 Learning: 2025-01-17T12:00:09.368Z

Learnt from: leoschwarz
Repo: snakemake/snakemake PR: 3176
File: tests/test_output_index.py:99-157
Timestamp: 2025-01-17T12:00:09.368Z
Learning: New test dependencies for Snakemake should be introduced in separate PRs rather than being added as part of feature or refactoring PRs.

Applied to files:

tests/test_script_hy/Snakefile

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src/snakemake/script/__init__.py (1)

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src/snakemake/script/__init__.py

1618-1618: Unused method argument: edit

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🔇 Additional comments (8)

docs/snakefiles/rules.rst (2)

1763-1763: LGTM! Documentation simplification.

The change to use "..." as a placeholder for input/output makes the example more concise while maintaining clarity.

1770-1783: LGTM! Well-structured documentation addition.

The Hy language section follows the established documentation pattern and provides clear guidance for users. The description accurately conveys Hy's purpose as a Lisp-like syntax for Python.

src/snakemake/script/__init__.py (4)

1613-1620: Implementation looks correct.

The HyScript class appropriately inherits from PythonScript since Hy is a Lisp dialect that runs on Python. The preamble is wrapped in (pys #[[{preamble}]]) which is Hy's syntax for embedding Python code, allowing the Python-based snakemake object to be accessible in Hy scripts.

Note: The unused edit parameter flagged by static analysis is consistent with other script classes (e.g., XonshScript) and matches the parent class signature.

1686-1687: LGTM! Language detection correctly implemented.

The .hy file extension detection follows the established pattern and is correctly placed in the language detection logic.

1752-1752: LGTM! Script dispatch correctly configured.

The HyScript class is properly registered in the dispatch table, enabling Snakemake to route .hy scripts to the correct executor.

1756-1756: LGTM! Error message updated correctly.

The error message now includes .hy in the list of supported script file types, ensuring users receive accurate guidance.

tests/test_script_hy/test.in (1)

1-20: LGTM! Appropriate test input.

The test input file contains integers 1-20, which provides good coverage for testing the Hy script's functionality (reading input, converting to integers, filtering odd numbers, and computing the sum).

tests/test_script_hy/scripts/test.hy (1)

1-17: LGTM! Well-crafted Hy test script.

The script effectively demonstrates Hy's capabilities:

Uses threading macros from hyrule for clean data pipeline syntax

Correctly accesses Snakemake's input/output via the injected snakemake object

Implements proper file handling with context managers

Shows idiomatic Hy code with functional programming patterns

The logic correctly:

Reads integers from the input file

Filters odd numbers

Computes their sum (which should be 100 for inputs 1-20)

Writes the result to the output file

johanneskoester

Thanks a lot, very nice! One request below.

coderabbitai

Actionable comments posted: 0

🧹 Nitpick comments (1)

src/snakemake/script/__init__.py (1)

1620-1627: LGTM! Clean implementation following established patterns.

The HyScript class correctly:

Inherits from PythonScript to reuse preamble generation

Wraps the Python preamble in Hy's pys macro with bracket string syntax #[[...]] for inline Python embedding

Executes scripts via the hy command, consistent with other script types

The unused edit parameter (flagged by static analysis) is part of the abstract interface and consistent with other script classes.

Note: The bracket string format assumes the preamble doesn't contain ]] which could theoretically break the delimiter. Based on the preamble content this is not a practical concern, but if edge cases arise, consider using a different delimiter or escaping mechanism.

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**/*.py

⚙️ CodeRabbit configuration file

**/*.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.
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Do not suggest return type annotation if a function or method does not contain a return statement.

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src/snakemake/script/__init__.py

1625-1625: Unused method argument: edit

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🔇 Additional comments (3)

src/snakemake/script/__init__.py (3)

1693-1694: LGTM!

The language detection for .hy files follows the same pattern as other supported languages.

1759-1759: LGTM!

Correctly registers HyScript in the dispatch table for Hy language support.

1763-1763: LGTM!

Error message correctly updated to include .hy in the list of supported script file types.

johanneskoester · 2025-11-07T15:50:53Z

Thanks a lot!

🤖 I have created a release *beep* *boop* --- ## [9.14.0](v9.13.7...v9.14.0) (2025-11-27) ### Features * Support Hy in script directive ([#3824](#3824)) ([2329c9e](2329c9e)) ### Bug Fixes * Add support for pathlib in `notebook` field ([#3811](#3811)) ([7b2180a](7b2180a)) * Addressed race condition in workdir_handler.py ([#3844](#3844)) ([8dbfcfb](8dbfcfb)) * cleanup update-marked output files of failed jobs if there was no backup to restore them ([#3843](#3843)) ([41f1ce8](41f1ce8)) * correct Windows callable path handling ([#3832](#3832)) ([5caad70](5caad70)) * expand env vars on resources ([#3823](#3823)) ([fcfa1bc](fcfa1bc)) * fix backup for output marked by `update` ([#3839](#3839)) ([09c64b7](09c64b7)) * Minor fixes/additions to logging module. ([#3802](#3802)) ([3b3986d](3b3986d)) * mount local storage prefix into containers ([#3840](#3840)) ([f1e8b62](f1e8b62)) * properly format input/output files in case of missing rule to produce them ([#3849](#3849)) ([69d5d24](69d5d24)) * Unpack AnnotatedString in _apply_wildcards ([#3798](#3798)) ([7886508](7886508)) ### Performance Improvements * retrieve storage inputs immediately before scheduling jobs instead of before running the entire workflow ([#3850](#3850)) ([4ac6cda](4ac6cda)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please).

Add support for [Hy](https://hylang.org/) in the script directive. This will allow the use of a Lisp-like syntax for writing scripts, e.g.: ```hy (require hyrule [-> ->>]) (defn is-odd? [n] (!= (% n 2) 0)) (setv result (->> (get snakemake.input 0) open .readlines (map int) (filter is-odd?) sum)) (print result :file (-> (get snakemake.output 0) (open "w"))) ``` ### 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).  ## Summary by CodeRabbit * **New Features** * Added runtime support for Hy scripts. * **Documentation** * Added Hy and Xonsh language sections with examples and cross-references. * Fixed Bash example formatting and removed a duplicated Xonsh example. * **Tests** * Added end-to-end test exercising Hy script execution with a Snakefile, Hy script, and sample input/output.  --------- Co-authored-by: Johannes Köster <[email protected]> Co-authored-by: Johannes Köster <[email protected]>

🤖 I have created a release *beep* *boop* --- ## [9.14.0](snakemake/snakemake@v9.13.7...v9.14.0) (2025-11-27) ### Features * Support Hy in script directive ([snakemake#3824](snakemake#3824)) ([2329c9e](snakemake@2329c9e)) ### Bug Fixes * Add support for pathlib in `notebook` field ([snakemake#3811](snakemake#3811)) ([7b2180a](snakemake@7b2180a)) * Addressed race condition in workdir_handler.py ([snakemake#3844](snakemake#3844)) ([8dbfcfb](snakemake@8dbfcfb)) * cleanup update-marked output files of failed jobs if there was no backup to restore them ([snakemake#3843](snakemake#3843)) ([41f1ce8](snakemake@41f1ce8)) * correct Windows callable path handling ([snakemake#3832](snakemake#3832)) ([5caad70](snakemake@5caad70)) * expand env vars on resources ([snakemake#3823](snakemake#3823)) ([fcfa1bc](snakemake@fcfa1bc)) * fix backup for output marked by `update` ([snakemake#3839](snakemake#3839)) ([09c64b7](snakemake@09c64b7)) * Minor fixes/additions to logging module. ([snakemake#3802](snakemake#3802)) ([3b3986d](snakemake@3b3986d)) * mount local storage prefix into containers ([snakemake#3840](snakemake#3840)) ([f1e8b62](snakemake@f1e8b62)) * properly format input/output files in case of missing rule to produce them ([snakemake#3849](snakemake#3849)) ([69d5d24](snakemake@69d5d24)) * Unpack AnnotatedString in _apply_wildcards ([snakemake#3798](snakemake#3798)) ([7886508](snakemake@7886508)) ### Performance Improvements * retrieve storage inputs immediately before scheduling jobs instead of before running the entire workflow ([snakemake#3850](snakemake#3850)) ([4ac6cda](snakemake@4ac6cda)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please).

jsquaredosquared added 6 commits November 3, 2025 07:19

feat: add hy support in script directive

ac37573

docs: update to mention hylang

cf6cac6

test: add tests for hy script

1cf7832

fix: fix hy test snakefile

305f59d

fix: suggest change to error message

ecd313f

fix: remove unnecessary line in test

568c291

jsquaredosquared requested a review from johanneskoester as a code owner November 3, 2025 00:46

jsquaredosquared changed the title ~~Support Hy in script directive~~ feat: Support Hy in script directive Nov 3, 2025

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jsquaredosquared added 3 commits November 3, 2025 08:53

fix: rename hy env file

0a6c3b3

fix: fix rulename

43ef05e

refactor: simplify test script

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johanneskoester requested changes Nov 6, 2025

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Comment thread docs/snakefiles/rules.rst Outdated

Merge branch 'snakemake:main' into support-hy-script

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coderabbitai Bot reviewed Nov 7, 2025

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jsquaredosquared added 4 commits November 7, 2025 12:25

docs: add better hy and xonsh script examples

1ae3131

chore: merge with main

dee238a

fix: remove unrecognized pygment lexer xonsh

ffde4fd

fix: fix error in hy example

351e764

johanneskoester approved these changes Nov 7, 2025

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Comment thread docs/snakefiles/rules.rst Outdated

Comment thread docs/snakefiles/rules.rst Outdated

johanneskoester and others added 3 commits November 7, 2025 16:50

Update docs/snakefiles/rules.rst

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Update docs/snakefiles/rules.rst

034780b

Merge branch 'main' into support-hy-script

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johanneskoester enabled auto-merge (squash) November 7, 2025 15:50

johanneskoester merged commit 2329c9e into snakemake:main Nov 8, 2025
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snakemake-bot mentioned this pull request Nov 8, 2025

chore(main): release 9.14.0 #3835

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feat: Support Hy in script directive#3824

feat: Support Hy in script directive#3824
johanneskoester merged 17 commits intosnakemake:mainfrom
jsquaredosquared:support-hy-script

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