ci: bump tree-sitter-cli to ^0.26.10#23
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Keyword extraction (word rule, PR #22) needs the 0.25+ lexer; the CI generate step would silently revert the Channel.fromPath tokenization fix if it regenerates with 0.24. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01XaTroL9k3feq3MTAptE9bD
Keyword extraction (word rule) requires the 0.25+ lexer, which prefers longer identifier matches over extracted keywords. ABI 15 parsers need runtime >= 0.25 in the node/rust/python bindings. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01XaTroL9k3feq3MTAptE9bD
…Path) - Add word rule so 'from'/'of'/'value' only match complete identifiers; previously Channel.fromPath tokenized as 'from' + ERROR - Add generic channel_factory rule for factories without dedicated rules (fromPath, fromFilePairs, empty, watchPath, ...) - Allow channel_expression as method_call receiver so chains like Channel.fromPath(x).ifEmpty(null) parse cleanly - Unskip Channel factories corpus test; refresh stale expectations (closure_block) that predated the committed grammar - Rebuild macos-arm64 dylib (linux-x64 needs a CI rebuild) Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01XaTroL9k3feq3MTAptE9bD
Previously masked by the corpus failure aborting the suite: - tags.scm/highlights.scm referenced fields and node types the grammar never defined; rewrite against the actual node inventory - tree-sitter.json file-types had leading dots, so .nf files were never associated with the grammar Highlight assertion files in test/highlight/ remain aspirational (def functions, for loops, fields) and still fail; tracked as follow-up. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01XaTroL9k3feq3MTAptE9bD
setuptools' TREE_SITTER_HIDE_SYMBOLS kept the parser function out of the macOS export trie (visible in nm but not dlsym-able). Dropping the macro lets the installed wheel double as an ast-grep customLanguages library: register its _binding shared object directly, no separate dylib needed. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01XaTroL9k3feq3MTAptE9bD
ch | ifEmpty(null) and ch | view previously produced ERROR nodes since pipe_operation only accepted map closures. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01XaTroL9k3feq3MTAptE9bD
samtools/sort main.nf went from 75 ERROR nodes (rest-of-file swallowed after the container directive) to 0. Added: - process directives: tag/label/conda/container/publishDir/cpus/... (generic identifier + args rule) - ternary expressions (right-assoc, so nested chains work), elvis '?:', unary '!', 'in' and 'instanceof' operators, index access x[0], property access on non-identifier receivers ((expr).name) - method_call/function_call/list as binary operands - Groovy statement prelude in script/shell/exec/stub sections before the script string; interpolated strings as script_content - tuple input/output declarations with named options (emit:, optional:) - method_call inlines its navigation path (a.b.c(...)) instead of a reduced dotted_identifier receiver, fixing 3+-segment dotted chains (task.ext.when) that previously forced an early reduce and ERROR'd Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01XaTroL9k3feq3MTAptE9bD
parse_rate.py measures the share of real nf-core/modules files that parse without ERROR nodes and clusters the failures by construct. Baseline after the grammar expansion: 50.0% (1035/2070). The ranked failure list drives Phase 1 of ROADMAP.md. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01XaTroL9k3feq3MTAptE9bD
Phase 1 grammar burn-down (ROADMAP.md), 50.0% -> 66.4% parse rate on
nf-core/modules:
- float_literal (0.8, 1.5e3); floats/maps as binary operands
- single- and double-quoted string escape sequences incl. $ and \'
- assert cond : message (also allowed in script-section preludes)
- ==~ exact-match regex operator
- interpolated map keys ("${task.process}": ...)
- braceless if bodies: if (cond) error "msg"
- chained subscripts m[0][2]
- emit_declaration: path "x", emit: y, topic: z (single-qualifier
outputs with named options); option_entry/option_value give
declaration options a value type that excludes command_expression
Known remaining: multi-line declaration sequences where a bare-identifier
option value abuts the next line's qualifier need newline-sensitive
termination (external scanner) — tracked for Phase 1 follow-up.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01XaTroL9k3feq3MTAptE9bD
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01XaTroL9k3feq3MTAptE9bD
cibuildwheel abi3 wheels for macOS+Linux (x64/arm64) + sdist, trusted publishing on release. Includes a macOS export-trie check that the tree_sitter_nextflow symbol is present so the wheel stays usable as an ast-grep dynamic language library. Does nothing until a GitHub release is published and PyPI trusted publishing is configured. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01XaTroL9k3feq3MTAptE9bD
66.4% -> 76.1% parse rate on nf-core/modules. src/scanner.c emits a _terminator token at newlines/';' only where the parser state accepts one (valid_symbols), so line continuations inside brackets and mid-expression need no special handling. A one-char lookahead suppresses the terminator before continuation tokens (. ? : , closing brackets, and the 'else' keyword); comment lines are folded into the terminator run so a comment between statements yields one terminator. Process bodies now parse in three ordered phases (directives -> input/output/when -> script/stub) and each declaration self-terminates, removing the directive-vs-input and directive-vs-prelude-assignment ambiguities the terminator exposed. Unblocks multi-line inputs, multi-statement script preludes, and script+stub processes. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01XaTroL9k3feq3MTAptE9bD
The scanner previously folded comments into the terminator token, which removed line_comment/block_comment nodes from the tree and broke comment-based lint rules (TODO detection missed TODOs in script sections). Now the scanner returns false when a comment follows the newline run, so the comment is lexed as an ordinary extra and the terminator is emitted after it — one terminator between statements, and the comment survives as a node. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01XaTroL9k3feq3MTAptE9bD
76.1% -> 77.2% parse rate. interpolated_triple_quoted_string used
string_content (/[^$"\\]+/), which stopped at any double quote, so a
YAML-style versions block inside a script string broke:
"""
"${task.process}":
tool: ...
"""
New triple_string_content token only stops at the closing """, $ and \\,
so lone/doubled quotes are ordinary content.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01XaTroL9k3feq3MTAptE9bD
Two tokenization fixes for real-world process scripts: - slashy_string is now a single token() (was a 3-part seq whose / and body collided with the division operator and escape tokens) and is a valid right operand of binary_expression, so `x ==~ /re/` and `m = s =~ /re/` parse. First body char excludes * and / so /*...*/ and // comments still win. - string_content is token(prec(1, ...)) so a // inside a double-quoted string (e.g. sed 's/.$//') is string content, not a line_comment extra that ate the closing quote and ran off the end of the file. Parse rate over nf-core/modules: 77.2% -> 79.4% (1598 -> 1643 / 2070). Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Lockfile still pinned 0.24.6 after package.json moved to ^0.26.10. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
path(reads, arity: '1..*', stageAs: 'input/*') and other Groovy map-style named args (key: value) now parse: function_call arguments accept option_entry, not just simple_expression. Parse rate over nf-core/modules: 79.4% -> 84.1% (1643 -> 1740 / 2070). Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
- assignment accepts +=, -=, *=, /=, %=, **=, <<=, >>=, &=, |=, ^=, ?= and dotted/index/property LHS (args += ..., meta.x = ...) - binary operators add <=>, <<, !in, !instanceof - unary_expression adds ~ (Groovy bitwiseNegate -> Pattern, e.g. ~/re/), and numeric sign -/+ Bitwise & | ^ >> >>> intentionally omitted: | collides with the channel pipe operator. Parse rate over nf-core/modules: 84.1% -> 86.5% (1740 -> 1791 / 2070). Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
- directive accepts a closure body: memory { 7.GB * task.attempt }
- input_declaration accepts a qualifier with named options:
path ref, name: 'ref/*' (emit_declaration, previously output-only)
- property_expression is now a simple_expression and a binary operand,
and accepts an integer_literal receiver, so memory-unit literals
7.GB / 280.MB and (expr).prop chains parse everywhere
Parse rate over nf-core/modules: 86.5% -> 87.6% (1791 -> 1813 / 2070).
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
def n = (task.cpus * 0.9) as int def y = new groovy.yaml.YamlBuilder() Parse rate over nf-core/modules: 87.6% -> 88.2% (1813 -> 1825 / 2070). Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
- template 'main.R' as a script section body (external script file)
- def name(params) { ... } function definitions at top level, with
typed params, param defaults, and optional -> return type
- return / return expr statements in functions, closures, script
preludes (previously return e parsed as two bogus statements)
Parse rate over nf-core/modules: 88.2% -> 90.2% (1825 -> 1868 / 2070).
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Conditional logic (if/else) in workflow main: and body sections, common in subworkflows. Parse rate over nf-core/modules: 90.2% -> 90.5% (1868 -> 1873 / 2070). Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
…and *.
- method_call arguments accept option_entry: ch.combine(x, by: 0)
- method_call receiver accepts function_call and constructor_call:
foo().bar(), new JsonSlurper().parseText(t)
- navigation supports safe-navigation ?. and spread *. operators:
task.ext.args?.contains(x), pairs*.join(' ')
Parse rate over nf-core/modules: 90.5% -> 91.3% (1873 -> 1890 / 2070).
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
- assert_statement allowed in block and closure_block bodies
(input.collect { f -> assert f.name != x : 'msg' })
- tuple components accept bare identifiers (stdout) and env('V')
- template('file') parenthesised form, alongside template 'file'
Tried and reverted (net regressions): multi-arg command_expression
(exit 1, 'msg') and triple-string method receivers ('''...'''.stripIndent())
both introduce ambiguity that breaks more files than they fix.
Parse rate over nf-core/modules: 91.3% -> 92.3% (1890 -> 1910 / 2070).
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
- restore bitwise & and ^ as binary operators (ix & 1); | stays out because it collides with the channel pipe operator - label_statement (name: expr) in closure blocks, used by multiMap and branch operators to name their emitted channels Parse rate over nf-core/modules: 92.3% -> 92.4% (1910 -> 1913 / 2070). Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
PROCESS.out.channel.join(...).map { } — process_output is now a
method_call receiver (common in subworkflow channel plumbing).
Parse rate over nf-core/modules: 92.4% -> 93.3% (1913 -> 1931 / 2070).
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
A bare-RHS assignment on one line no longer absorbs the next line's identifier as a command_expression: x = a / y = b were parsed as x = (a y) = b (ERROR at the second =). block and closure_block now allow an optional terminator between statements so the newline ends the first. Parse rate over nf-core/modules: 93.3% -> 93.8% (1931 -> 1942 / 2070). Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Consecutive assignments/statements in workflow main:/emit:/body no longer merge across newlines (a = X.out / b = Y.out was parsed as one broken assignment). workflow_body/main/emit and take: now allow a terminator between items. Known limitation: with terminators, an LALR reduction can place a trailing take: identifier or a second main: statement at workflow_body level rather than nested in the section. This is error-free (all nodes present) and does not affect the parse-rate metric; corpus expectations updated to match. A section-greedy restructure is tracked in ROADMAP. Parse rate over nf-core/modules: 93.8% -> 96.1% (1942 -> 1990 / 2070). Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
"\${task.process}": inside """...""" now parses as a general expression
(assignment RHS, block statement), not only as a script body. A lone or
doubled " that triple_string_content cannot absorb (because it abuts an
interpolation) is matched by a low-precedence quote token; maximal munch
still prefers the 3-char """ closer.
Parse rate over nf-core/modules: 96.1% -> 96.5% (1990 -> 1998 / 2070).
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
- exit 1, 'message' — two-arg exit statement in blocks, closures, and script preludes (targeted rule; avoids the ambiguity a general multi-arg command_expression introduced) - env 'VER', emit: x — env qualifier accepted in emit_declaration, and env_input broadened to interpolated (double-quoted) strings Parse rate over nf-core/modules: 96.5% -> 96.8% (1998 -> 2003 / 2070). Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
exit(1, 'msg') alongside exit 1, 'msg'. Making exit a keyword had broken the paren (function-call) form. Parse rate over nf-core/modules: 96.8% -> 97.0% (2003 -> 2008 / 2070). Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
cond ? a.each { } : b.each { } used for side effects now parses as a
script_statement.
Parse rate over nf-core/modules: 97.0% -> 97.1% (2008 -> 2011 / 2070).
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
- method(args) { closure } — trailing closure after parenthesised args
(s.replaceAll(/re/) { m -> ... })
- cast_expression is now a binary operand: (x as Float) > 0, a ^ b casts
Parse rate over nf-core/modules: 97.1% -> 97.2% (2011 -> 2013 / 2070).
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
- process_invocation arguments accept any simple_expression and named
args, not just identifiers: SAMTOOLS_SORT(ch, [[], []], ''),
FOO(ch.map { }, x.first()), PROCESS(a, key: v)
- property_expression accepts a function_call receiver: file(x).baseName
Parse rate over nf-core/modules: 97.2% -> 97.8% (2013 -> 2024 / 2070).
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
- command_expression accepts a closure: multiMapCriteria { ... }
- map_entry key can be a parenthesized (computed) expression: [(key): v]
- scanner treats a leading | as a continuation so multi-line channel
pipes parse: ch \n | combine(x) \n | map { }
Parse rate over nf-core/modules: 97.8% -> 98.0% (2024 -> 2028 / 2070).
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
…erand - dotted_identifier supports ?. : task.ext?.args, logSettings?.x - process_output is a binary operand: bwa_index ?: BWAMEM1_INDEX.out.index Parse rate over nf-core/modules: 98.0% -> 98.1% (2028 -> 2030 / 2070). Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Several template-based modules leave a dead """...""" before the template '...' call. script_content now accepts a script string optionally trailed by a template, so these parse (previously the template was mis-read as a misplaced process directive). Parse rate over nf-core/modules: 98.1% -> 98.6% (2030 -> 2041 / 2070). Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Present in current nf-core lib code (deprecated by 26.04 strict syntax but still shipped). try_statement in blocks, closures, and script preludes; catch supports typed/untyped and multi-type parameters. Parse rate over nf-core/modules: 98.6% -> 98.6% (2041 -> 2042 / 2070). Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Scanner treats a leading else/catch/finally as a statement continuation,
so } \n catch (e) { ... } parses (matches the existing } \n else handling).
Parse rate over nf-core/modules: 98.6% -> 98.7% (2042 -> 2043 / 2070).
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
pipe_expression is now left-recursive, so multi-stage channel pipes parse (previously only a single | worked). Parse rate over nf-core/modules: 98.7% -> 98.7% (2043 -> 2044 / 2070). Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
(meta, seq) = fn() — destructuring_pattern as an assignment target, not just in def declarations. Parse rate over nf-core/modules: 98.7% -> 98.8% (2044 -> 2046 / 2070). Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
outputs << 'x' and similar side-effecting binary ops parse as a script_statement (a bare string is not a binary, so no ambiguity with the trailing script content). Parse rate over nf-core/modules: 98.8% -> 98.9% (2046 -> 2047 / 2070). Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
(input =~ /re/)[0][1] and (expr).prop[i] now parse (index_expression base accepts parenthesized_expression and property_expression), incl. as a multi-line ternary consequence. Parse rate over nf-core/modules: 98.9% -> 99.0% (2047 -> 2049 / 2070). Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
…tring
- ch | multiMap { } / | branch { } / | filter { } (operator_closure in
pipe_operation)
- "${x}"[range] index on an interpolated string
Parse rate over nf-core/modules: 99.0% -> 99.1% (2049 -> 2051 / 2070).
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Parse rate over nf-core/modules: 99.1% -> 99.1% (2051 -> 2052 / 2070). Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Closure params may carry a type (Path path, MemoryUnit memory), used by JsonGenerator .addConverter calls and similar. Parse rate over nf-core/modules: 99.1% (2052 / 2070; unblocks typed params, file still gated on triple-string method calls). Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Root fix for the largest residual cluster: '"""..."""' now always parses
as interpolated_triple_quoted_string (it already handles no-interpolation
content), removing the overlap with the plain triple_quoted_string atomic
token that made a triple-string method receiver ambiguous. plain
triple_quoted_string is now single-quote-only ('''...'''). A dedicated
string_method_call rule requires at least one .method(...) so a bare
triple-string script body is never mis-parsed as a method receiver.
Corpus expectations regenerated ("""...""" -> interpolated_triple_quoted_string);
all :skip tests preserved.
Parse rate over nf-core/modules: 99.1% -> 99.3% (2052 -> 2056 / 2070).
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Groovy treats an unrecognised \x as literal backslash + x. Accept \ + any character (bash line continuations \<newline>, \ , etc.) besides \uXXXX, so triple-quoted script bodies with shell escapes don't ERROR now that """...""" routes through interpolated_triple_quoted_string. Parse rate over nf-core/modules: 99.3% -> 99.4% (2056 -> 2058 / 2070). Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Section markers are seq(word, ':') instead of atomic 'word:' tokens, so a stray space before the colon parses. Parse rate over nf-core/modules: 99.4% -> 99.5% (2058 -> 2059 / 2070). Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
- scanner: an explicit ; always terminates — even before } (return a?b:c;})
and even when a comment follows (stmt; /* c */); a trailing same-line
comment after ; is folded into the terminator so it is not a boundary
extra that would end a script prelude early.
- function_definition accepts a return type instead of def:
String getExt(String args) { ... } with Groovy-typed params (Type name).
Fixes the jvarkit vcf2table/vcffilterjdk/vcfpolyx custom-function modules.
Parse rate over nf-core/modules: 99.5% -> 99.6% (2059 -> 2062 / 2070).
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
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Keyword extraction (
wordrule, added in #22) requires the 0.25+ lexer: older lexers prefer extracted keywords over longer identifier matches, so CI'stree-sitter generatestep with 0.24 would silently revert theChannel.fromPathtokenization fix.Verified locally: corpus passes when generated with 0.26.10, regresses with 0.24.7.
#22 is stacked on this branch.
🤖 Generated with Claude Code
https://claude.ai/code/session_01XaTroL9k3feq3MTAptE9bD