fix: added missing keywords for highlighting

[rroutsong]

A lot of missing keywords for snakemake highlighting. Just added into 0.4.0 token lists.

Addresses some or all of issues #23, #18, #14, #22, #25

Summary by CodeRabbit

• New Features

  • Introduced support for additional rule configuration options, including the new retries parameter.
  • Enhanced keyword recognition by adding pepfile, pepschema, and container to improve rule formatting and syntax highlighting.

• Chores

  • Updated the application version from 0.4.1 to 0.5.0.

[corneliusroemer]

Oh you beat me to it, I opened #31 before seeing this. You're still missing 'retries'

[corneliusroemer]

Easier to review if you just change this one file: https://github.com/snakemake/snakemake-lang-vscode-plugin/pull/24/files

[rroutsong]

No worries, I am sure I missed a few more too I couldn't find a good extensive list of all keywords and their support or deprecation by version.

[corneliusroemer]

Oh damn, I might be wrong, PR #24 doesn't seem to fix syntax highlighting. Have to dig a bit deeper, but thanks for giving this a go. We should figure out how to test it, that'd be useful!

[rroutsong]

OK I am not so familiar with VScode extension development, so I might have borked it up. But I made this into a local vsix and distributed it to my group and it worked for our highlighting purposes.

[mbhall88]

pepfile and pepschema also seem to be missing. Could you also add that to this PR?

[rroutsong]

pepfile and pepschema also seem to be missing. Could you also add that to this PR?

added

[coderabbitai]

📝 Walkthrough

Walkthrough

The pull request updates the package version in the package.json file and modifies several configuration files related to Snakemake rule parameters. Changes include reordering parameters in a JSON file, adding a new parameter ("retries") in a YAML configuration, and updating regular expression patterns in multiple files to recognize new keywords ("pepfile" and "pepschema"). No modifications were made to the declarations of exported or public entities aside from the version update.

Changes

File(s)	Change Summary
package.json	Updated version from "0.4.1" to "0.5.0".
src/js/keywords-regex.json src/keywords.yaml	Reordered rule parameters, added "retries" to the ruleparams section in YAML, and updated the "configs" and "functions" entries in JSON.
src/yaml/snakemake.language.yaml syntaxes/snakemake.tmLanguage.json languages/snakemake.json	Updated regex patterns to recognize the new keywords "pepfile" and "pepschema" without altering existing logic.

---

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[coderabbitai]

Actionable comments posted: 1

🔭 Outside diff range comments (2)

src/keywords.yaml (2)

14-16: 🛠️ Refactor suggestion

Duplicate Entry in Configs

The configs section lists the keyword pepschema twice. Removing the duplicate will help keep the configuration clean and unambiguous.

---

23-70: 🛠️ Refactor suggestion

Duplicate Keywords in Ruleparams

Within the ruleparams section, several keywords appear more than once (for example, container, notebook, default_target, handover, template_engine, and localrule). Duplicates in this list are unnecessary and may cause confusion for maintainers or downstream processing. It is recommended to deduplicate these entries to improve clarity and maintainability.

Suggested diff snippet:

-  - notebook
...
-  - default_target
-  - handover
...
-  - template_engine
...
-  - localrule

(Remove the redundant occurrences.)

🧹 Nitpick comments (4)

languages/snakemake.json (1)

96-102: Enhanced Regex Pattern for OnEnter Rules

The updated beforeText regex now incorporates additional keywords (e.g., container, shellcmd, name, norun, conda_env, container_img, is_containerized, etc.) needed for proper syntax highlighting. While the pattern is comprehensive, consider adding documentation or refactoring it into a more modular form if further keyword additions are anticipated.

src/yaml/snakemake.language.yaml (1)

38-45: Remove Duplicate Indentation Action

In the onEnterRules block, the action object mistakenly includes two indent: indent entries. Removing the redundant entry will simplify the configuration without affecting behavior.

Suggested diff:

-      indent: indent
- 
-      indent: indent
+      indent: indent

🧰 Tools

🪛 YAMLlint (1.35.1)

[error] 42-42: syntax error: could not find expected ':'

(syntax)

syntaxes/snakemake.tmLanguage.json (2)

27-27: Review Keyword Update for Configs Section

The regex pattern now includes the keyword module as intended. Please verify that this addition does not conflict with any existing syntax rules or usage elsewhere in the highlighting definitions.

---

46-46: Duplicate Keywords in Rule Parameters Pattern

The regex pattern for rule parameters contains duplicate keywords (e.g., notebook, template_engine, default_target, and handover appear twice). Removing these duplicates would simplify maintenance and improve readability. Consider revising the pattern as follows:

-  (benchmark|conda|container|shellcmd|name|norun|conda_env|container_img|is_containerized|env_modules|shadow_depth|docstring|notebook|template_engine|cache|path_modifier|handover|default_target|localrule|cwl|group|input|log|message|notebook|output|params|priority|resources|run|script|shadow|shell|singularity|threads|version|wildcard_constraints|wrapper|default_target|template_engine|handover)
+  (benchmark|conda|container|shellcmd|name|norun|conda_env|container_img|is_containerized|env_modules|shadow_depth|docstring|notebook|template_engine|cache|path_modifier|handover|default_target|localrule|cwl|group|input|log|message|output|params|priority|resources|run|script|shadow|shell|singularity|threads|version|wildcard_constraints|wrapper)

This will ensure each keyword appears only once and reduce any potential confusion in the highlighting rules.

📜 Review details

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

📥 Commits

Reviewing files that changed from the base of the PR and between 7ba2658 and 224c802.

📒 Files selected for processing (21)

• package.json (1 hunks)
• src/js/keywords-regex.json (1 hunks)
• src/keywords.yaml (1 hunks)
• src/yaml/snakemake.language.yaml (1 hunks)
• syntaxes/snakemake.tmLanguage.json (2 hunks)
• languages/snakemake.json (1 hunks)
• src/js/keywords-regex.json (1 hunks)
• src/keywords.yaml (2 hunks)
• src/yaml/snakemake.language.yaml (1 hunks)
• syntaxes/snakemake.tmLanguage.json (2 hunks)
• src/js/keywords-regex.json (1 hunks)
• src/keywords.yaml (1 hunks)
• syntaxes/snakemake.tmLanguage.json (1 hunks)
• languages/snakemake.json (1 hunks)
• src/yaml/snakemake.language.yaml (1 hunks)
• syntaxes/snakemake.tmLanguage.json (1 hunks)
• languages/snakemake.json (1 hunks)
• src/js/keywords-regex.json (1 hunks)
• src/keywords.yaml (1 hunks)
• src/yaml/snakemake.language.yaml (1 hunks)
• syntaxes/snakemake.tmLanguage.json (1 hunks)

🧰 Additional context used

🪛 YAMLlint (1.35.1)

src/yaml/snakemake.language.yaml

[error] 42-42: syntax error: could not find expected ':'

(syntax)

🔇 Additional comments (1)

package.json (1)

6-6: Version Bump Update

The version has been updated to "0.4.1", which properly reflects the release that includes the new highlighting keywords.

[dlaehnemann]

LGTM

[coderabbitai]

Actionable comments posted: 0

🔭 Outside diff range comments (2)

src/keywords.yaml (2)

14-16: 🛠️ Refactor suggestion

Remove duplicate keyword "pepschema" in the configs section.

The list under configs contains "pepschema" twice (lines 15 and 16). This duplication might be unintended and could lead to ambiguity in processing or maintenance overhead. Please remove one occurrence.

-  - pepfile
-  - pepschema
-  - pepschema
+  - pepfile
+  - pepschema

---

65-70: 🛠️ Refactor suggestion

Eliminate duplicate entries in the ruleparams section.

The keywords listed after line 64 (including localrule, template_engine, default_target, and another set of localrule and template_engine) appear to be duplicates of entries already present in this section. Duplicate entries can lead to unexpected behavior in highlighting and increase maintenance complexity. It is recommended to remove the repeated keywords.

-  - localrule
-  - template_engine
-  - default_target
-  - localrule
-  - template_engine

🧹 Nitpick comments (1)

src/keywords.yaml (1)

23-49: Review existing duplicates in the ruleparams list.

Beyond the newly added duplicates (lines 65–70), the list already contains potential duplicates such as "container" (at lines 26 and 48) and "handover" (at lines 47 and later repeated at line 63). Although these may predate the current changes, it’s advisable to verify their necessity and remove any unintended repetition.

📜 Review details

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

📥 Commits

Reviewing files that changed from the base of the PR and between 224c802 and 7fe63c2.

⛔ Files ignored due to path filters (2)

• CHANGELOG.md is excluded by !CHANGELOG.md
• package-lock.json is excluded by !**/package-lock.json

📒 Files selected for processing (18)

• package.json (1 hunks)
• src/js/keywords-regex.json (1 hunks)
• src/keywords.yaml (1 hunks)
• syntaxes/snakemake.tmLanguage.json (2 hunks)
• src/js/keywords-regex.json (1 hunks)
• src/keywords.yaml (2 hunks)
• syntaxes/snakemake.tmLanguage.json (2 hunks)
• src/js/keywords-regex.json (1 hunks)
• src/keywords.yaml (1 hunks)
• syntaxes/snakemake.tmLanguage.json (1 hunks)
• syntaxes/snakemake.tmLanguage.json (1 hunks)
• src/js/keywords-regex.json (1 hunks)
• src/keywords.yaml (1 hunks)
• syntaxes/snakemake.tmLanguage.json (1 hunks)
• package.json (1 hunks)
• src/js/keywords-regex.json (1 hunks)
• src/keywords.yaml (1 hunks)
• syntaxes/snakemake.tmLanguage.json (1 hunks)

🚧 Files skipped from review as they are similar to previous changes (17)

• package.json
• src/keywords.yaml
• syntaxes/snakemake.tmLanguage.json
• src/keywords.yaml
• syntaxes/snakemake.tmLanguage.json
• syntaxes/snakemake.tmLanguage.json
• src/keywords.yaml
• src/keywords.yaml
• syntaxes/snakemake.tmLanguage.json
• src/js/keywords-regex.json
• src/js/keywords-regex.json
• package.json
• syntaxes/snakemake.tmLanguage.json
• syntaxes/snakemake.tmLanguage.json
• src/js/keywords-regex.json
• src/js/keywords-regex.json
• src/js/keywords-regex.json

🔇 Additional comments (2)

src/keywords.yaml (2)

12-12: Approve addition of “module” in the configs section.

Adding the module keyword fills one of the missing parameters. This change looks good.

---

50-64: Validate the new ruleparams keywords.

New keywords such as shellcmd, name, norun, conda_env, container_img, is_containerized, env_modules, shadow_depth, docstring, notebook, template_engine, cache, path_modifier, handover, and default_target have been added. Please double-check that these keywords are in the intended order and that none of them conflict with existing definitions.