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Fix LaTeX rendering errors in collection semantics docs

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Fix underscore handling in semantics.py that caused "'_' allowed only
in math mode" errors in rendered HTML. Issues: CollectionDefinition
used bare escaped underscores outside \text{}, expression_to_latex had
double-replacement bugs (unpaired→\text{un\text{paired}}), and
sample_sheet was unhandled.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
This commit is contained in:
John Chilton
2026-03-17 15:15:28 -04:00
co-authored by Claude Opus 4.6
parent fffdb4822d
commit 9d49f7f89b
2 changed files with 445 additions and 261 deletions
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doc/source/dev/collection_semantics.md
+423 -249
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lib/galaxy/model/dataset_collections/types/semantics.py
+22 -12
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@@ -72,8 +72,8 @@ class ToolDefinition(BaseModel):
outputs: dict[str, str] = Field(alias="out")
def as_latex(self) -> str:
inputs = ", ".join([f"{k}: \\text{{ {v} }}" for (k, v) in self.inputs.items()])
outputs = ", ".join([f"{k}: \\text{{ {v} }}" for (k, v) in self.outputs.items()])
inputs = ", ".join([f"{k}: \\text{{ {_escape_underscores(v)} }}" for (k, v) in self.inputs.items()])
outputs = ", ".join([f"{k}: \\text{{ {_escape_underscores(v)} }}" for (k, v) in self.outputs.items()])
return f"tool \\text{{ is }} ({inputs}) \\Rightarrow \\{{ {outputs} \\}}"
@@ -104,10 +104,8 @@ class CollectionDefinition(NamedTuple):
elements: dict[str, Any]
def as_latex(self) -> str:
collection_type = self.collection_type.replace("_", "\\_")
return (
f"\\text{{CollectionInstance<}}{collection_type},{_assumption_elements_to_latex(self.elements)}\\text{{>}}"
)
ct = _latex_collection_type(self.collection_type)
return f"\\text{{CollectionInstance<}}{ct},{_assumption_elements_to_latex(self.elements)}\\text{{>}}"
class CollectionDeclarations(BaseModel):
@@ -120,11 +118,14 @@ Expression = Union[str, DatasetsDeclaration, ToolDeclaration, CollectionDeclarat
# --- Structured Then Expression Models ---
def _escape_underscores(text: str) -> str:
return text.replace("_", "\\_")
def _latex_type_word(word: str) -> str:
if word == "paired_or_unpaired":
return "\\text{paired\\_or\\_unpaired}"
if word == "single_datasets":
return "\\text{single\\_datasets}"
if "_" in word:
escaped = word.replace("_", "\\_")
return "\\text{" + escaped + "}"
return "\\text{" + word + "}"
@@ -313,6 +314,9 @@ YAMLRootModel = RootModel[list[Union[DocEntry, ExampleEntry]]]
WORDS_TO_TEXTIFY = ["list", "forward", "reverse", "mapOver", "collection", "dataset", "inner"]
_POU_PLACEHOLDER = "\x00POU\x00"
_UNPAIRED_PLACEHOLDER = "\x00UNPAIRED\x00"
_SINGLE_DATASETS_PLACEHOLDER = "\x00SINGLEDATASETS\x00"
_SAMPLE_SHEET_PLACEHOLDER = "\x00SAMPLESHEET\x00"
def expression_to_latex(expression: str, wrap: bool = True):
@@ -320,13 +324,19 @@ def expression_to_latex(expression: str, wrap: bool = True):
expression = expression.replace("~>", "\\mapsto")
expression = expression.replace("{", "\\left\\{")
expression = expression.replace("}", "\\right\\}")
expression = expression.replace("single_datasets", "\\text{single\\_datasets}")
# Replace multi-word identifiers with placeholders before WORDS_TO_TEXTIFY
# to prevent double-replacement (e.g. "dataset" inside "single_datasets")
expression = expression.replace("single_datasets", _SINGLE_DATASETS_PLACEHOLDER)
expression = expression.replace("sample_sheet", _SAMPLE_SHEET_PLACEHOLDER)
expression = expression.replace("paired_or_unpaired", _POU_PLACEHOLDER)
expression = expression.replace("unpaired", "\\text{unpaired}")
expression = expression.replace("unpaired", _UNPAIRED_PLACEHOLDER)
expression = expression.replace("paired", "\\text{paired}")
expression = expression.replace(_UNPAIRED_PLACEHOLDER, "\\text{unpaired}")
expression = expression.replace(_POU_PLACEHOLDER, "\\text{paired\\_or\\_unpaired}")
for word in WORDS_TO_TEXTIFY:
expression = expression.replace(word, "\\text{" + word + "}")
expression = expression.replace(_SINGLE_DATASETS_PLACEHOLDER, "\\text{single\\_datasets}")
expression = expression.replace(_SAMPLE_SHEET_PLACEHOLDER, "\\text{sample\\_sheet}")
if wrap:
return f"$ {expression} $"
else: