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ci: add coverage and ruff (#1383)

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* add coverage calculation and push

Signed-off-by: Michele Dolfi <dol@zurich.ibm.com>

* new codecov version and usage of token

Signed-off-by: Michele Dolfi <dol@zurich.ibm.com>

* enable ruff formatter instead of black and isort

Signed-off-by: Michele Dolfi <dol@zurich.ibm.com>

* apply ruff lint fixes

Signed-off-by: Michele Dolfi <dol@zurich.ibm.com>

* apply ruff unsafe fixes

Signed-off-by: Michele Dolfi <dol@zurich.ibm.com>

* add removed imports

Signed-off-by: Michele Dolfi <dol@zurich.ibm.com>

* runs 1 on linter issues

Signed-off-by: Michele Dolfi <dol@zurich.ibm.com>

* finalize linter fixes

Signed-off-by: Michele Dolfi <dol@zurich.ibm.com>

* Update pyproject.toml

Co-authored-by: Cesar Berrospi Ramis <75900930+ceberam@users.noreply.github.com>
Signed-off-by: Michele Dolfi <97102151+dolfim-ibm@users.noreply.github.com>

---------

Signed-off-by: Michele Dolfi <dol@zurich.ibm.com>
Signed-off-by: Michele Dolfi <97102151+dolfim-ibm@users.noreply.github.com>
Co-authored-by: Cesar Berrospi Ramis <75900930+ceberam@users.noreply.github.com>
This commit is contained in:
Michele Dolfi
2025-04-14 18:01:26 +02:00
committed by GitHub
parent 293c28ca7c
commit 5458a88464
104 changed files with 665 additions and 633 deletions
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23
docling/backend/xml/jats_backend.py
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@@ -102,13 +102,13 @@ class JatsDocumentBackend(DeclarativeDocumentBackend):
doc_info: etree.DocInfo = self.tree.docinfo
if doc_info.system_url and any(
[kwd in doc_info.system_url for kwd in JATS_DTD_URL]
kwd in doc_info.system_url for kwd in JATS_DTD_URL
):
self.valid = True
return
for ent in doc_info.internalDTD.iterentities():
if ent.system_url and any(
[kwd in ent.system_url for kwd in JATS_DTD_URL]
kwd in ent.system_url for kwd in JATS_DTD_URL
):
self.valid = True
return
@@ -232,10 +232,9 @@ class JatsDocumentBackend(DeclarativeDocumentBackend):
# TODO: once superscript is supported, add label with formatting
aff = aff.removeprefix(f"{label[0].text}, ")
affiliation_names.append(aff)
affiliation_ids_names = {
id: name
for id, name in zip(meta.xpath(".//aff[@id]/@id"), affiliation_names)
}
affiliation_ids_names = dict(
zip(meta.xpath(".//aff[@id]/@id"), affiliation_names)
)
# Get author names and affiliation names
for author_node in meta.xpath(
@@ -300,7 +299,6 @@ class JatsDocumentBackend(DeclarativeDocumentBackend):
def _add_abstract(
self, doc: DoclingDocument, xml_components: XMLComponents
) -> None:
for abstract in xml_components["abstract"]:
text: str = abstract["content"]
title: str = abstract["label"] or DEFAULT_HEADER_ABSTRACT
@@ -349,7 +347,7 @@ class JatsDocumentBackend(DeclarativeDocumentBackend):
return
def _parse_element_citation(self, node: etree._Element) -> str:
def _parse_element_citation(self, node: etree._Element) -> str: # noqa: C901
citation: Citation = {
"author_names": "",
"title": "",
@@ -440,7 +438,7 @@ class JatsDocumentBackend(DeclarativeDocumentBackend):
citation["page"] = node.xpath("fpage")[0].text.replace("\n", " ").strip()
if len(node.xpath("lpage")) > 0:
citation["page"] += (
"–" + node.xpath("lpage")[0].text.replace("\n", " ").strip()
"–" + node.xpath("lpage")[0].text.replace("\n", " ").strip() # noqa: RUF001
)
# Flatten the citation to string
@@ -595,9 +593,8 @@ class JatsDocumentBackend(DeclarativeDocumentBackend):
try:
self._add_table(doc, parent, table)
except Exception as e:
_log.warning(f"Skipping unsupported table in {str(self.file)}")
pass
except Exception:
_log.warning(f"Skipping unsupported table in {self.file!s}")
return
@@ -609,7 +606,7 @@ class JatsDocumentBackend(DeclarativeDocumentBackend):
)
return
def _walk_linear(
def _walk_linear( # noqa: C901
self, doc: DoclingDocument, parent: NodeItem, node: etree._Element
) -> str:
skip_tags = ["term"]