tree-sitter-nextflow 0.4.1__tar.gz

tree_sitter_nextflow-0.4.1/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2024 Edmund Miller
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

tree_sitter_nextflow-0.4.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: tree-sitter-nextflow
+Version: 0.4.1
+Summary: Nextflow grammar for tree-sitter
+Author-email: Edmund Miller <edmund@nf-co.re>, Ben Sherman <bentshermann@gmail.com>
+License: MIT
+Project-URL: Homepage, https://github.com/nextflow-io/tree-sitter-nextflow
+Keywords: incremental,parsing,tree-sitter,nextflow
+Classifier: Intended Audience :: Developers
+Classifier: Topic :: Software Development :: Compilers
+Classifier: Topic :: Text Processing :: Linguistic
+Classifier: Typing :: Typed
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Provides-Extra: core
+Requires-Dist: tree-sitter~=0.25; extra == "core"
+Dynamic: license-file
+
+# tree-sitter-nextflow
+
+[![Parse rate](https://github.com/nextflow-io/tree-sitter-nextflow/actions/workflows/parse-rate.yml/badge.svg?branch=main)](https://github.com/nextflow-io/tree-sitter-nextflow/actions/workflows/parse-rate.yml)
+
+Nextflow grammar for [tree-sitter](https://github.com/tree-sitter/tree-sitter). Mirrors the official [Nextflow ANTLR grammar](https://github.com/nextflow-io/nextflow/tree/master/modules/nf-lang/src/main/antlr).
+
+## Installation
+
+Install the Python binding and tree-sitter runtime from PyPI after the first release:
+
+```bash
+pip install "tree-sitter-nextflow[core]"
+```
+
+Use the grammar in Python tools:
+
+```python
+from tree_sitter import Language, Parser
+import tree_sitter_nextflow
+
+parser = Parser(Language(tree_sitter_nextflow.language()))
+tree = parser.parse(b'workflow {\n  println "Hello"\n}\n')
+assert not tree.root_node.has_error
+```
+
+The parser produces a syntax tree for your lint rules. It does not run Nextflow's semantic checks.
+Python 3.10 or later is required. Releases provide wheels for Linux and macOS on x86-64 and ARM64,
+plus a source distribution for platforms with a C compiler.
+
+To build the Python, Rust, or C binding from source:
+
+```bash
+git clone https://github.com/nextflow-io/tree-sitter-nextflow.git
+```
+
+- **Python:** `pip install .`
+- **Rust:** add a path or git dependency on this repo in `Cargo.toml`.
+- **C:** `make` builds the shared library.
+
+See [editor and tool integrations](docs/integrations/README.md) for the query files
+and the requirements for Bash highlighting inside process scripts.
+
+## ast-grep
+
+The repo includes an [ast-grep](https://ast-grep.github.io/) setup for searching, linting, and outlining Nextflow code by syntax tree:
+
+```bash
+ast-grep -l nextflow -p 'Channel.from($$$)' .
+```
+
+See [`docs/ast-grep/`](docs/ast-grep/) for setup, the bundled lint rules, and the pattern library.

tree_sitter_nextflow-0.4.1/README.md

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+# tree-sitter-nextflow
+
+[![Parse rate](https://github.com/nextflow-io/tree-sitter-nextflow/actions/workflows/parse-rate.yml/badge.svg?branch=main)](https://github.com/nextflow-io/tree-sitter-nextflow/actions/workflows/parse-rate.yml)
+
+Nextflow grammar for [tree-sitter](https://github.com/tree-sitter/tree-sitter). Mirrors the official [Nextflow ANTLR grammar](https://github.com/nextflow-io/nextflow/tree/master/modules/nf-lang/src/main/antlr).
+
+## Installation
+
+Install the Python binding and tree-sitter runtime from PyPI after the first release:
+
+```bash
+pip install "tree-sitter-nextflow[core]"
+```
+
+Use the grammar in Python tools:
+
+```python
+from tree_sitter import Language, Parser
+import tree_sitter_nextflow
+
+parser = Parser(Language(tree_sitter_nextflow.language()))
+tree = parser.parse(b'workflow {\n  println "Hello"\n}\n')
+assert not tree.root_node.has_error
+```
+
+The parser produces a syntax tree for your lint rules. It does not run Nextflow's semantic checks.
+Python 3.10 or later is required. Releases provide wheels for Linux and macOS on x86-64 and ARM64,
+plus a source distribution for platforms with a C compiler.
+
+To build the Python, Rust, or C binding from source:
+
+```bash
+git clone https://github.com/nextflow-io/tree-sitter-nextflow.git
+```
+
+- **Python:** `pip install .`
+- **Rust:** add a path or git dependency on this repo in `Cargo.toml`.
+- **C:** `make` builds the shared library.
+
+See [editor and tool integrations](docs/integrations/README.md) for the query files
+and the requirements for Bash highlighting inside process scripts.
+
+## ast-grep
+
+The repo includes an [ast-grep](https://ast-grep.github.io/) setup for searching, linting, and outlining Nextflow code by syntax tree:
+
+```bash
+ast-grep -l nextflow -p 'Channel.from($$$)' .
+```
+
+See [`docs/ast-grep/`](docs/ast-grep/) for setup, the bundled lint rules, and the pattern library.

tree_sitter_nextflow-0.4.1/bindings/python/tree_sitter_nextflow/__init__.py

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+"""Nextflow grammar for tree-sitter"""
+
+from importlib.resources import files as _files
+
+from ._binding import language
+
+
+def _get_query(name, file):
+    query = _files(f"{__package__}.queries") / file
+    globals()[name] = query.read_text()
+    return globals()[name]
+
+
+def __getattr__(name):
+    if name == "HIGHLIGHTS_QUERY":
+        return _get_query("HIGHLIGHTS_QUERY", "highlights.scm")
+    if name == "INJECTIONS_QUERY":
+        return _get_query("INJECTIONS_QUERY", "injections.scm")
+    if name == "TAGS_QUERY":
+        return _get_query("TAGS_QUERY", "tags.scm")
+
+    raise AttributeError(f"module {__name__!r} has no attribute {name!r}")
+
+
+__all__ = [
+    "language",
+    "HIGHLIGHTS_QUERY",
+    "INJECTIONS_QUERY",
+    "TAGS_QUERY",
+]
+
+
+def __dir__():
+    return sorted(__all__ + [
+        "__all__", "__builtins__", "__cached__", "__doc__", "__file__",
+        "__loader__", "__name__", "__package__", "__path__", "__spec__",
+    ])

tree_sitter_nextflow-0.4.1/bindings/python/tree_sitter_nextflow/__init__.pyi

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+from typing import Final
+
+HIGHLIGHTS_QUERY: Final[str]
+INJECTIONS_QUERY: Final[str]
+TAGS_QUERY: Final[str]
+
+def language() -> object: ...

tree_sitter_nextflow-0.4.1/bindings/python/tree_sitter_nextflow/binding.c

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+#include <Python.h>
+
+typedef struct TSLanguage TSLanguage;
+
+TSLanguage *tree_sitter_nextflow(void);
+
+static PyObject* _binding_language(PyObject *Py_UNUSED(self), PyObject *Py_UNUSED(args)) {
+    return PyCapsule_New(tree_sitter_nextflow(), "tree_sitter.Language", NULL);
+}
+
+static struct PyModuleDef_Slot slots[] = {
+#ifdef Py_GIL_DISABLED
+    {Py_mod_gil, Py_MOD_GIL_NOT_USED},
+#endif
+    {0, NULL}
+};
+
+static PyMethodDef methods[] = {
+    {"language", _binding_language, METH_NOARGS,
+     "Get the tree-sitter language for this grammar."},
+    {NULL, NULL, 0, NULL}
+};
+
+static struct PyModuleDef module = {
+    .m_base = PyModuleDef_HEAD_INIT,
+    .m_name = "_binding",
+    .m_doc = NULL,
+    .m_size = 0,
+    .m_methods = methods,
+    .m_slots = slots,
+};
+
+PyMODINIT_FUNC PyInit__binding(void) {
+    return PyModuleDef_Init(&module);
+}

tree_sitter_nextflow-0.4.1/bindings/python/tree_sitter_nextflow.egg-info/PKG-INFO

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+Metadata-Version: 2.4
+Name: tree-sitter-nextflow
+Version: 0.4.1
+Summary: Nextflow grammar for tree-sitter
+Author-email: Edmund Miller <edmund@nf-co.re>, Ben Sherman <bentshermann@gmail.com>
+License: MIT
+Project-URL: Homepage, https://github.com/nextflow-io/tree-sitter-nextflow
+Keywords: incremental,parsing,tree-sitter,nextflow
+Classifier: Intended Audience :: Developers
+Classifier: Topic :: Software Development :: Compilers
+Classifier: Topic :: Text Processing :: Linguistic
+Classifier: Typing :: Typed
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Provides-Extra: core
+Requires-Dist: tree-sitter~=0.25; extra == "core"
+Dynamic: license-file
+
+# tree-sitter-nextflow
+
+[![Parse rate](https://github.com/nextflow-io/tree-sitter-nextflow/actions/workflows/parse-rate.yml/badge.svg?branch=main)](https://github.com/nextflow-io/tree-sitter-nextflow/actions/workflows/parse-rate.yml)
+
+Nextflow grammar for [tree-sitter](https://github.com/tree-sitter/tree-sitter). Mirrors the official [Nextflow ANTLR grammar](https://github.com/nextflow-io/nextflow/tree/master/modules/nf-lang/src/main/antlr).
+
+## Installation
+
+Install the Python binding and tree-sitter runtime from PyPI after the first release:
+
+```bash
+pip install "tree-sitter-nextflow[core]"
+```
+
+Use the grammar in Python tools:
+
+```python
+from tree_sitter import Language, Parser
+import tree_sitter_nextflow
+
+parser = Parser(Language(tree_sitter_nextflow.language()))
+tree = parser.parse(b'workflow {\n  println "Hello"\n}\n')
+assert not tree.root_node.has_error
+```
+
+The parser produces a syntax tree for your lint rules. It does not run Nextflow's semantic checks.
+Python 3.10 or later is required. Releases provide wheels for Linux and macOS on x86-64 and ARM64,
+plus a source distribution for platforms with a C compiler.
+
+To build the Python, Rust, or C binding from source:
+
+```bash
+git clone https://github.com/nextflow-io/tree-sitter-nextflow.git
+```
+
+- **Python:** `pip install .`
+- **Rust:** add a path or git dependency on this repo in `Cargo.toml`.
+- **C:** `make` builds the shared library.
+
+See [editor and tool integrations](docs/integrations/README.md) for the query files
+and the requirements for Bash highlighting inside process scripts.
+
+## ast-grep
+
+The repo includes an [ast-grep](https://ast-grep.github.io/) setup for searching, linting, and outlining Nextflow code by syntax tree:
+
+```bash
+ast-grep -l nextflow -p 'Channel.from($$$)' .
+```
+
+See [`docs/ast-grep/`](docs/ast-grep/) for setup, the bundled lint rules, and the pattern library.

tree_sitter_nextflow-0.4.1/bindings/python/tree_sitter_nextflow.egg-info/SOURCES.txt

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+LICENSE
+README.md
+pyproject.toml
+setup.py
+bindings/python/tree_sitter_nextflow/__init__.py
+bindings/python/tree_sitter_nextflow/__init__.pyi
+bindings/python/tree_sitter_nextflow/binding.c
+bindings/python/tree_sitter_nextflow/py.typed
+bindings/python/tree_sitter_nextflow.egg-info/PKG-INFO
+bindings/python/tree_sitter_nextflow.egg-info/SOURCES.txt
+bindings/python/tree_sitter_nextflow.egg-info/dependency_links.txt
+bindings/python/tree_sitter_nextflow.egg-info/not-zip-safe
+bindings/python/tree_sitter_nextflow.egg-info/requires.txt
+bindings/python/tree_sitter_nextflow.egg-info/top_level.txt
+src/parser.c
+src/scanner.c
+test/test_resolve_changelog.py

tree_sitter_nextflow-0.4.1/bindings/python/tree_sitter_nextflow.egg-info/dependency_links.txt

@@ -0,0 +1 @@
+

tree_sitter_nextflow-0.4.1/bindings/python/tree_sitter_nextflow.egg-info/not-zip-safe

@@ -0,0 +1 @@
+

tree_sitter_nextflow-0.4.1/bindings/python/tree_sitter_nextflow.egg-info/requires.txt

@@ -0,0 +1,3 @@
+
+[core]
+tree-sitter~=0.25

tree_sitter_nextflow-0.4.1/bindings/python/tree_sitter_nextflow.egg-info/top_level.txt

@@ -0,0 +1,2 @@
+_binding
+tree_sitter_nextflow

tree_sitter_nextflow-0.4.1/pyproject.toml

@@ -0,0 +1,34 @@
+[build-system]
+requires = ["setuptools>=62.4.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "tree-sitter-nextflow"
+description = "Nextflow grammar for tree-sitter"
+version = "0.4.1"
+keywords = ["incremental", "parsing", "tree-sitter", "nextflow"]
+classifiers = [
+  "Intended Audience :: Developers",
+  "Topic :: Software Development :: Compilers",
+  "Topic :: Text Processing :: Linguistic",
+  "Typing :: Typed",
+]
+authors = [
+  { name = "Edmund Miller", email = "edmund@nf-co.re" },
+  { name = "Ben Sherman", email = "bentshermann@gmail.com" },
+]
+requires-python = ">=3.10"
+license.text = "MIT"
+readme = "README.md"
+
+[project.urls]
+Homepage = "https://github.com/nextflow-io/tree-sitter-nextflow"
+
+[project.optional-dependencies]
+core = ["tree-sitter~=0.25"]
+
+[tool.cibuildwheel]
+build = "cp310-*"
+build-frontend = "build"
+test-requires = ["tree-sitter~=0.25"]
+test-command = "python -m unittest discover -s {project}/bindings/python/tests -v"

tree_sitter_nextflow-0.4.1/queries/highlights.scm

@@ -0,0 +1,252 @@
+;; Syntax highlighting for Nextflow.
+;; The tree-sitter CLI gives later patterns precedence, so general captures
+;; come first and specific ones override them.
+
+(identifier) @variable
+
+((identifier) @variable.builtin
+  (#any-of? @variable.builtin
+    "params" "task" "workflow" "nextflow" "log" "launchDir" "moduleDir"
+    "projectDir" "workDir" "baseDir" "secrets"))
+
+((identifier) @type.builtin
+  (#any-of? @type.builtin "Channel" "channel"))
+
+;; ========================================
+;; KEYWORDS
+;; ========================================
+
+[
+  "process"
+  "workflow"
+  "agent"
+  "include"
+  "from"
+  "import"
+  "nextflow"
+  "params"
+  "record"
+  "enum"
+  "tuple"
+  "def"
+  "as"
+  "new"
+] @keyword
+
+[
+  "if"
+  "else"
+  "for"
+  "try"
+  "catch"
+  "finally"
+  "return"
+  "throw"
+  "assert"
+] @keyword.control
+
+[
+  "in"
+  "!in"
+  "instanceof"
+  "!instanceof"
+] @keyword.operator
+
+;; Section labels
+[
+  "input"
+  "output"
+  "stage"
+  "topic"
+  "when"
+  "script"
+  "shell"
+  "exec"
+  "stub"
+  "prompt"
+  "take"
+  "main"
+  "emit"
+  "publish"
+  "onComplete"
+  "onError"
+] @label
+
+(output_definition "output" @keyword)
+
+(labeled_statement label: (identifier) @label)
+
+;; ========================================
+;; DEFINITIONS
+;; ========================================
+
+(process_definition name: (identifier) @function)
+(workflow_definition name: (identifier) @function)
+(agent_definition name: (identifier) @function)
+(function_definition name: (identifier) @function)
+(include_item name: (identifier) @function)
+(include_item alias: (identifier) @function)
+
+(parameter name: (identifier) @variable.parameter)
+(workflow_take name: (identifier) @variable.parameter)
+(process_input name: (identifier) @variable.parameter)
+
+(param_declaration name: (identifier) @property)
+(param_assignment (identifier) @property)
+(feature_flag (identifier) @property)
+(record_field name: (identifier) @property)
+(workflow_emit name: (identifier) @property)
+(workflow_publish name: (identifier) @property)
+(process_output name: (identifier) @property)
+(output_declaration name: (identifier) @property)
+
+(record_definition name: (identifier) @type)
+(enum_definition name: (identifier) @type)
+(enum_constant) @constant
+(type (identifier) @type)
+
+;; ========================================
+;; CALLS AND PROPERTIES
+;; ========================================
+
+(member_expression property: (identifier) @property)
+(named_argument name: (identifier) @property)
+
+(call_expression function: (identifier) @function.call)
+(call_expression function: (member_expression property: (identifier) @function.method))
+(command_expression function: (identifier) @function.call)
+(command_expression function: (member_expression property: (identifier) @function.method))
+
+;; Process directives: tag "x", cpus 4, memory { 2.GB * task.attempt }
+(process_definition
+  (expression_statement
+    [
+      (command_expression function: (identifier) @keyword.directive)
+      (call_expression function: (identifier) @keyword.directive)
+    ]))
+
+;; Agent directives: model 'openai/gpt-5-mini', tools 'fs:*', tools()
+(agent_definition
+  (expression_statement
+    [
+      (command_expression function: (identifier) @keyword.directive)
+      (call_expression function: (identifier) @keyword.directive)
+    ]))
+
+;; Legacy input/output qualifiers: val x, path "*.bam", tuple val(meta), path(x)
+(input_section
+  (expression_statement
+    (command_expression function: (identifier) @type.builtin)))
+(output_section
+  (expression_statement
+    (command_expression function: (identifier) @type.builtin)))
+(input_section
+  (expression_statement
+    (command_expression
+      arguments: (argument_list (call_expression function: (identifier) @type.builtin)))))
+(output_section
+  (expression_statement
+    (command_expression
+      arguments: (argument_list (call_expression function: (identifier) @type.builtin)))))
+((output_section (process_output name: (identifier) @type.builtin))
+  (#any-of? @type.builtin "stdout" "stdin"))
+
+;; ========================================
+;; OPERATORS AND PUNCTUATION
+;; ========================================
+
+[
+  "="
+  "+="
+  "-="
+  "*="
+  "/="
+  "%="
+  "**="
+  "<<="
+  ">>="
+  ">>>="
+  "&="
+  "|="
+  "^="
+  "?="
+] @operator.assignment
+
+[
+  "=="
+  "!="
+  "<"
+  ">"
+  "<="
+  ">="
+  "&&"
+  "||"
+  "=~"
+  "==~"
+  "<=>"
+  "?:"
+  "?"
+  "!"
+  "+"
+  "-"
+  "*"
+  "/"
+  "%"
+  "**"
+  ".."
+  "..<"
+  "<<"
+  ">>"
+  ">>>"
+  "&"
+  "^"
+  "~"
+  "?."
+  "*."
+] @operator
+
+;; Channel pipes and closure arrows
+[
+  "|"
+  "->"
+] @operator.channel
+
+[
+  "("
+  ")"
+  "["
+  "]"
+  "{"
+  "}"
+] @punctuation.bracket
+
+[
+  ","
+  ":"
+  "."
+] @punctuation.delimiter
+
+;; ========================================
+;; LITERALS
+;; ========================================
+
+(string) @string
+(string_content) @string
+(escape_sequence) @string.escape
+(interpolation) @embedded
+(slashy_string) @string.regex
+
+(integer_literal) @number
+(float_literal) @number.float
+(boolean_literal) @constant.builtin
+(null_literal) @constant.builtin
+
+;; ========================================
+;; COMMENTS
+;; ========================================
+
+(line_comment) @comment
+(block_comment) @comment
+(shebang) @comment
+
+(ERROR) @error

tree_sitter_nextflow-0.4.1/queries/injections.scm

@@ -0,0 +1,26 @@
+;; Bash injection into process script/shell/stub bodies: the string that ends
+;; the section. Only the content chunks are captured, so quote delimiters and
+;; ${...} interpolations stay Nextflow. injection.combined merges the chunks
+;; around interpolations into one bash document.
+;;
+;; exec: bodies are Groovy, so they are left alone.
+
+(script_section
+  ["script" "shell"]
+  (expression_statement
+    (string (string_content) @injection.content)) .
+  (#set! injection.language "bash")
+  (#set! injection.combined))
+
+(stub_section
+  (expression_statement
+    (string (string_content) @injection.content)) .
+  (#set! injection.language "bash")
+  (#set! injection.combined))
+
+;; A process with no section labels: the body is an implicit script.
+(process_definition
+  (expression_statement
+    (string (string_content) @injection.content)) .
+  (#set! injection.language "bash")
+  (#set! injection.combined))

tree_sitter_nextflow-0.4.1/queries/tags.scm

@@ -0,0 +1,42 @@
+;; Code navigation for Nextflow: definitions and references.
+
+;; ========================================
+;; DEFINITIONS
+;; ========================================
+
+(process_definition name: (identifier) @name) @definition.method
+
+(workflow_definition name: (identifier) @name) @definition.function
+
+(agent_definition name: (identifier) @name) @definition.function
+
+(function_definition name: (identifier) @name) @definition.function
+
+(record_definition name: (identifier) @name) @definition.class
+
+(enum_definition name: (identifier) @name) @definition.class
+
+(param_declaration name: (identifier) @name) @definition.variable
+
+(param_assignment . (identifier) @name) @definition.variable
+
+;; ========================================
+;; REFERENCES
+;; ========================================
+
+(call_expression function: (identifier) @name) @reference.call
+
+(call_expression
+  function: (member_expression property: (identifier) @name)) @reference.call
+
+(command_expression function: (identifier) @name) @reference.call
+
+(command_expression
+  function: (member_expression property: (identifier) @name)) @reference.call
+
+;; Process/workflow outputs: FOO.out, FOO.out.bam. Tags queries cannot use
+;; helper captures, so this relies on the upper-case naming convention.
+((member_expression object: (identifier) @name) @reference.call
+  (#match? @name "^[A-Z][A-Z0-9_]*$"))
+
+(include_declaration source: (string) @name) @reference.implementation