scitex 2.5.0__py3-none-any.whl → 2.7.0__py3-none-any.whl

scitex/writer/dataclasses/contents/_SupplementaryContents.py

@@ -5,9 +5,8 @@
 # ----------------------------------------
 from __future__ import annotations
 import os
-__FILE__ = (
-    "./src/scitex/writer/dataclasses/_SupplementaryContents.py"
-)
+
+__FILE__ = "./src/scitex/writer/dataclasses/_SupplementaryContents.py"
 __DIR__ = os.path.dirname(__FILE__)
 # ----------------------------------------
 
@@ -51,25 +50,15 @@ class SupplementaryContents:
     def __post_init__(self):
         """Initialize all DocumentSection instances."""
         if self.methods is None:
-            self.methods = DocumentSection(
-                self.root / "methods.tex", self.git_root
-            )
+            self.methods = DocumentSection(self.root / "methods.tex", self.git_root)
         if self.results is None:
-            self.results = DocumentSection(
-                self.root / "results.tex", self.git_root
-            )
+            self.results = DocumentSection(self.root / "results.tex", self.git_root)
         if self.title is None:
-            self.title = DocumentSection(
-                self.root / "title.tex", self.git_root
-            )
+            self.title = DocumentSection(self.root / "title.tex", self.git_root)
         if self.authors is None:
-            self.authors = DocumentSection(
-                self.root / "authors.tex", self.git_root
-            )
+            self.authors = DocumentSection(self.root / "authors.tex", self.git_root)
         if self.keywords is None:
-            self.keywords = DocumentSection(
-                self.root / "keywords.tex", self.git_root
-            )
+            self.keywords = DocumentSection(self.root / "keywords.tex", self.git_root)
         if self.journal_name is None:
             self.journal_name = DocumentSection(
                 self.root / "journal_name.tex", self.git_root
@@ -85,9 +74,7 @@ class SupplementaryContents:
         if self.latex_styles is None:
             self.latex_styles = self.root / "latex_styles"
         if self.wordcount is None:
-            self.wordcount = DocumentSection(
-                self.root / "wordcount.tex", self.git_root
-            )
+            self.wordcount = DocumentSection(self.root / "wordcount.tex", self.git_root)
 
     def verify_structure(self) -> tuple[bool, list[str]]:
         """
@@ -100,13 +87,23 @@ class SupplementaryContents:
 
         # Check required directories
         if not self.figures.exists():
-            expected_path = self.figures.relative_to(self.git_root) if self.git_root else self.figures
+            expected_path = (
+                self.figures.relative_to(self.git_root)
+                if self.git_root
+                else self.figures
+            )
             issues.append(f"Missing figures/ (expected at: {expected_path})")
         if not self.tables.exists():
-            expected_path = self.tables.relative_to(self.git_root) if self.git_root else self.tables
+            expected_path = (
+                self.tables.relative_to(self.git_root) if self.git_root else self.tables
+            )
             issues.append(f"Missing tables/ (expected at: {expected_path})")
         if not self.latex_styles.exists():
-            expected_path = self.latex_styles.relative_to(self.git_root) if self.git_root else self.latex_styles
+            expected_path = (
+                self.latex_styles.relative_to(self.git_root)
+                if self.git_root
+                else self.latex_styles
+            )
             issues.append(f"Missing latex_styles/ (expected at: {expected_path})")
 
         return len(issues) == 0, issues

scitex/writer/dataclasses/core/_Document.py

@@ -5,9 +5,8 @@
 # ----------------------------------------
 from __future__ import annotations
 import os
-__FILE__ = (
-    "./src/scitex/writer/dataclasses/_Document.py"
-)
+
+__FILE__ = "./src/scitex/writer/dataclasses/_Document.py"
 __DIR__ = os.path.dirname(__FILE__)
 # ----------------------------------------
 

scitex/writer/dataclasses/core/_DocumentSection.py

@@ -5,9 +5,8 @@
 # ----------------------------------------
 from __future__ import annotations
 import os
-__FILE__ = (
-    "./src/scitex/writer/dataclasses/_DocumentSection.py"
-)
+
+__FILE__ = "./src/scitex/writer/dataclasses/_DocumentSection.py"
 __DIR__ = os.path.dirname(__FILE__)
 # ----------------------------------------
 
@@ -89,9 +88,7 @@ class DocumentSection:
             )
             return self._read_plain_text()
         except Exception as e:
-            logger.error(
-                f"Unexpected error reading {self.path}: {e}", exc_info=True
-            )
+            logger.error(f"Unexpected error reading {self.path}: {e}", exc_info=True)
             return None
 
     def _read_plain_text(self):
@@ -99,9 +96,7 @@ class DocumentSection:
         try:
             return self.path.read_text(encoding="utf-8")
         except UnicodeDecodeError:
-            logger.warning(
-                f"UTF-8 decode failed for {self.path}, trying latin-1"
-            )
+            logger.warning(f"UTF-8 decode failed for {self.path}, trying latin-1")
             return self.path.read_text(encoding="latin-1")
         except Exception as e:
             logger.error(f"Failed to read {self.path} as text: {e}")
@@ -142,11 +137,7 @@ class DocumentSection:
                 logger.debug(f"Git log failed: {result.stderr}")
                 return []
 
-            return (
-                result.stdout.strip().split("\n")
-                if result.stdout.strip()
-                else []
-            )
+            return result.stdout.strip().split("\n") if result.stdout.strip() else []
         except subprocess.TimeoutExpired:
             logger.warning(f"Git log timed out for {self.path}")
             return []
@@ -265,9 +256,7 @@ class DocumentSection:
         if spec.lower() == "today":
             from datetime import datetime, timedelta
 
-            today = datetime.now().replace(
-                hour=0, minute=0, second=0, microsecond=0
-            )
+            today = datetime.now().replace(hour=0, minute=0, second=0, microsecond=0)
             return self._find_commit_at_timestamp(today)
 
         # Handle relative time like "2 days ago", "1 week ago", "24 hours ago"
@@ -310,9 +299,7 @@ class DocumentSection:
         from datetime import datetime, timedelta
 
         # Pattern: "N <unit> ago"
-        match = re.match(
-            r"(\d+)\s*(day|week|hour|minute)s?\s*ago", spec, re.IGNORECASE
-        )
+        match = re.match(r"(\d+)\s*(day|week|hour|minute)s?\s*ago", spec, re.IGNORECASE)
         if not match:
             return None
 
@@ -392,9 +379,7 @@ class DocumentSection:
                 logger.warning(f"No commit found before {timestamp_str}")
                 return None
         except subprocess.TimeoutExpired:
-            logger.warning(
-                f"Git log timed out looking for commit at {target_datetime}"
-            )
+            logger.warning(f"Git log timed out looking for commit at {target_datetime}")
             return None
         except Exception as e:
             logger.error(f"Error finding commit at timestamp: {e}")

scitex/writer/dataclasses/results/_CompilationResult.py

@@ -5,9 +5,8 @@
 # ----------------------------------------
 from __future__ import annotations
 import os
-__FILE__ = (
-    "./src/scitex/writer/dataclasses/_CompilationResult.py"
-)
+
+__FILE__ = "./src/scitex/writer/dataclasses/_CompilationResult.py"
 __DIR__ = os.path.dirname(__FILE__)
 # ----------------------------------------
 

scitex/writer/dataclasses/results/_LaTeXIssue.py

@@ -5,9 +5,8 @@
 # ----------------------------------------
 from __future__ import annotations
 import os
-__FILE__ = (
-    "./src/scitex/writer/dataclasses/_LaTeXIssue.py"
-)
+
+__FILE__ = "./src/scitex/writer/dataclasses/_LaTeXIssue.py"
 __DIR__ = os.path.dirname(__FILE__)
 # ----------------------------------------
 
@@ -74,9 +73,7 @@ def main(args):
 def parse_args():
     import argparse
 
-    parser = argparse.ArgumentParser(
-        description="Demonstrate LaTeXIssue dataclass"
-    )
+    parser = argparse.ArgumentParser(description="Demonstrate LaTeXIssue dataclass")
     parser.add_argument(
         "--type",
         type=str,

scitex/writer/dataclasses/results/_SaveSectionsResponse.py

@@ -4,9 +4,8 @@
 # ----------------------------------------
 from __future__ import annotations
 import os
-__FILE__ = (
-    "./src/scitex/writer/dataclasses/results/_SaveSectionsResponse.py"
-)
+
+__FILE__ = "./src/scitex/writer/dataclasses/results/_SaveSectionsResponse.py"
 __DIR__ = os.path.dirname(__FILE__)
 # ----------------------------------------
 
@@ -67,7 +66,9 @@ class SaveSectionsResponse:
         return "\n".join(lines)
 
     @classmethod
-    def create_success(cls, sections_saved: int, message: str = "") -> SaveSectionsResponse:
+    def create_success(
+        cls, sections_saved: int, message: str = ""
+    ) -> SaveSectionsResponse:
         """Create a successful response."""
         return cls(
             success=True,
@@ -77,7 +78,9 @@ class SaveSectionsResponse:
         )
 
     @classmethod
-    def create_failure(cls, error_message: str, errors: List[str] = None, sections_saved: int = 0) -> SaveSectionsResponse:
+    def create_failure(
+        cls, error_message: str, errors: List[str] = None, sections_saved: int = 0
+    ) -> SaveSectionsResponse:
         """Create a failed response."""
         return cls(
             success=False,
@@ -90,16 +93,24 @@ class SaveSectionsResponse:
     def validate(self) -> None:
         """Validate response data - raises ValueError if invalid."""
         if self.success and self.sections_saved == 0:
-            raise ValueError("SaveSectionsResponse marked as success but no sections were saved")
+            raise ValueError(
+                "SaveSectionsResponse marked as success but no sections were saved"
+            )
 
         if not self.success and not self.errors:
-            raise ValueError("SaveSectionsResponse marked as failed but no errors provided")
+            raise ValueError(
+                "SaveSectionsResponse marked as failed but no errors provided"
+            )
 
         if self.sections_saved < 0:
-            raise ValueError(f"Invalid sections_saved: {self.sections_saved} (must be >= 0)")
+            raise ValueError(
+                f"Invalid sections_saved: {self.sections_saved} (must be >= 0)"
+            )
 
         if self.sections_skipped < 0:
-            raise ValueError(f"Invalid sections_skipped: {self.sections_skipped} (must be >= 0)")
+            raise ValueError(
+                f"Invalid sections_skipped: {self.sections_skipped} (must be >= 0)"
+            )
 
 
 __all__ = ["SaveSectionsResponse"]

scitex/writer/dataclasses/results/_SectionReadResponse.py

@@ -4,9 +4,8 @@
 # ----------------------------------------
 from __future__ import annotations
 import os
-__FILE__ = (
-    "./src/scitex/writer/dataclasses/results/_SectionReadResponse.py"
-)
+
+__FILE__ = "./src/scitex/writer/dataclasses/results/_SectionReadResponse.py"
 __DIR__ = os.path.dirname(__FILE__)
 # ----------------------------------------
 
@@ -65,7 +64,14 @@ class SectionReadResponse:
             return f"Failed to read {self.section_id}: {self.error}"
 
     @classmethod
-    def create_success(cls, content: str, section_name: str, section_id: str, doc_type: str, file_path: Optional[Path] = None) -> SectionReadResponse:
+    def create_success(
+        cls,
+        content: str,
+        section_name: str,
+        section_id: str,
+        doc_type: str,
+        file_path: Optional[Path] = None,
+    ) -> SectionReadResponse:
         """Create a successful response."""
         return cls(
             success=True,
@@ -80,8 +86,8 @@ class SectionReadResponse:
     @classmethod
     def create_failure(cls, section_id: str, error_message: str) -> SectionReadResponse:
         """Create a failed response."""
-        parts = section_id.split('/')
-        doc_type = parts[0] if len(parts) > 1 else 'manuscript'
+        parts = section_id.split("/")
+        doc_type = parts[0] if len(parts) > 1 else "manuscript"
         section_name = parts[1] if len(parts) > 1 else section_id
 
         return cls(
@@ -96,11 +102,19 @@ class SectionReadResponse:
 
     def validate(self) -> None:
         """Validate response data - raises ValueError if invalid."""
-        if self.success and not self.content and self.section_name not in ['compiled_pdf', 'compiled_tex']:
-            raise ValueError(f"SectionReadResponse marked as success but content is empty for {self.section_id}")
+        if (
+            self.success
+            and not self.content
+            and self.section_name not in ["compiled_pdf", "compiled_tex"]
+        ):
+            raise ValueError(
+                f"SectionReadResponse marked as success but content is empty for {self.section_id}"
+            )
 
         if not self.success and not self.error:
-            raise ValueError(f"SectionReadResponse marked as failed but no error message for {self.section_id}")
+            raise ValueError(
+                f"SectionReadResponse marked as failed but no error message for {self.section_id}"
+            )
 
         if not self.section_name:
             raise ValueError("section_name cannot be empty")
@@ -108,7 +122,7 @@ class SectionReadResponse:
         if not self.section_id:
             raise ValueError("section_id cannot be empty")
 
-        if self.doc_type not in ['manuscript', 'supplementary', 'revision', 'shared']:
+        if self.doc_type not in ["manuscript", "supplementary", "revision", "shared"]:
             raise ValueError(f"Invalid doc_type: {self.doc_type}")
 
 

scitex/writer/dataclasses/tree/_ConfigTree.py

@@ -5,9 +5,8 @@
 # ----------------------------------------
 from __future__ import annotations
 import os
-__FILE__ = (
-    "./src/scitex/writer/dataclasses/tree/_ConfigTree.py"
-)
+
+__FILE__ = "./src/scitex/writer/dataclasses/tree/_ConfigTree.py"
 __DIR__ = os.path.dirname(__FILE__)
 # ----------------------------------------
 
@@ -72,7 +71,11 @@ class ConfigTree:
         missing = []
         for name, section in required:
             if not section.path.exists():
-                expected_path = section.path.relative_to(self.git_root) if self.git_root else section.path
+                expected_path = (
+                    section.path.relative_to(self.git_root)
+                    if self.git_root
+                    else section.path
+                )
                 missing.append(f"{name} (expected at: {expected_path})")
 
         return len(missing) == 0, missing

scitex/writer/dataclasses/tree/_ManuscriptTree.py

@@ -5,9 +5,8 @@
 # ----------------------------------------
 from __future__ import annotations
 import os
-__FILE__ = (
-    "./src/scitex/writer/dataclasses/tree/_ManuscriptTree.py"
-)
+
+__FILE__ = "./src/scitex/writer/dataclasses/tree/_ManuscriptTree.py"
 __DIR__ = os.path.dirname(__FILE__)
 # ----------------------------------------
 
@@ -45,17 +44,11 @@ class ManuscriptTree:
     def __post_init__(self):
         """Initialize all instances."""
         if self.contents is None:
-            self.contents = ManuscriptContents(
-                self.root / "contents", self.git_root
-            )
+            self.contents = ManuscriptContents(self.root / "contents", self.git_root)
         if self.base is None:
-            self.base = DocumentSection(
-                self.root / "base.tex", self.git_root
-            )
+            self.base = DocumentSection(self.root / "base.tex", self.git_root)
         if self.readme is None:
-            self.readme = DocumentSection(
-                self.root / "README.md", self.git_root
-            )
+            self.readme = DocumentSection(self.root / "README.md", self.git_root)
         if self.archive is None:
             self.archive = self.root / "archive"
 
@@ -76,7 +69,11 @@ class ManuscriptTree:
 
         # Check root level files
         if not self.base.path.exists():
-            expected_path = self.base.path.relative_to(self.git_root) if self.git_root else self.base.path
+            expected_path = (
+                self.base.path.relative_to(self.git_root)
+                if self.git_root
+                else self.base.path
+            )
             missing.append(f"base.tex (expected at: {expected_path})")
 
         return len(missing) == 0, missing

scitex/writer/dataclasses/tree/_RevisionTree.py

@@ -5,9 +5,8 @@
 # ----------------------------------------
 from __future__ import annotations
 import os
-__FILE__ = (
-    "./src/scitex/writer/dataclasses/tree/_RevisionTree.py"
-)
+
+__FILE__ = "./src/scitex/writer/dataclasses/tree/_RevisionTree.py"
 __DIR__ = os.path.dirname(__FILE__)
 # ----------------------------------------
 
@@ -47,21 +46,13 @@ class RevisionTree:
     def __post_init__(self):
         """Initialize all instances."""
         if self.contents is None:
-            self.contents = RevisionContents(
-                self.root / "contents", self.git_root
-            )
+            self.contents = RevisionContents(self.root / "contents", self.git_root)
         if self.base is None:
-            self.base = DocumentSection(
-                self.root / "base.tex", self.git_root
-            )
+            self.base = DocumentSection(self.root / "base.tex", self.git_root)
         if self.revision is None:
-            self.revision = DocumentSection(
-                self.root / "revision.tex", self.git_root
-            )
+            self.revision = DocumentSection(self.root / "revision.tex", self.git_root)
         if self.readme is None:
-            self.readme = DocumentSection(
-                self.root / "README.md", self.git_root
-            )
+            self.readme = DocumentSection(self.root / "README.md", self.git_root)
         if self.archive is None:
             self.archive = self.root / "archive"
         if self.docs is None:
@@ -84,10 +75,18 @@ class RevisionTree:
 
         # Check root level files
         if not self.base.path.exists():
-            expected_path = self.base.path.relative_to(self.git_root) if self.git_root else self.base.path
+            expected_path = (
+                self.base.path.relative_to(self.git_root)
+                if self.git_root
+                else self.base.path
+            )
             missing.append(f"base.tex (expected at: {expected_path})")
         if not self.revision.path.exists():
-            expected_path = self.revision.path.relative_to(self.git_root) if self.git_root else self.revision.path
+            expected_path = (
+                self.revision.path.relative_to(self.git_root)
+                if self.git_root
+                else self.revision.path
+            )
             missing.append(f"revision.tex (expected at: {expected_path})")
 
         return len(missing) == 0, missing

scitex/writer/dataclasses/tree/_ScriptsTree.py

@@ -5,9 +5,8 @@
 # ----------------------------------------
 from __future__ import annotations
 import os
-__FILE__ = (
-    "./src/scitex/writer/dataclasses/tree/_ScriptsTree.py"
-)
+
+__FILE__ = "./src/scitex/writer/dataclasses/tree/_ScriptsTree.py"
 __DIR__ = os.path.dirname(__FILE__)
 # ----------------------------------------
 
@@ -91,7 +90,9 @@ class ScriptsTree:
         ]
         for name, path in required_dirs:
             if not path.exists():
-                expected_path = path.relative_to(self.git_root) if self.git_root else path
+                expected_path = (
+                    path.relative_to(self.git_root) if self.git_root else path
+                )
                 missing.append(f"Missing {name}/ (expected at: {expected_path})")
 
         # Check required compilation scripts
@@ -102,7 +103,11 @@ class ScriptsTree:
         ]
         for name, section in required_scripts:
             if not section.path.exists():
-                expected_path = section.path.relative_to(self.git_root) if self.git_root else section.path
+                expected_path = (
+                    section.path.relative_to(self.git_root)
+                    if self.git_root
+                    else section.path
+                )
                 missing.append(f"Missing {name} (expected at: {expected_path})")
 
         return len(missing) == 0, missing

scitex/writer/dataclasses/tree/_SharedTree.py

@@ -5,9 +5,8 @@
 # ----------------------------------------
 from __future__ import annotations
 import os
-__FILE__ = (
-    "./src/scitex/writer/types/tree/_SharedTree.py"
-)
+
+__FILE__ = "./src/scitex/writer/types/tree/_SharedTree.py"
 __DIR__ = os.path.dirname(__FILE__)
 # ----------------------------------------
 
@@ -48,17 +47,11 @@ class SharedTree:
     def __post_init__(self):
         """Initialize all DocumentSection and Path instances."""
         if self.authors is None:
-            self.authors = DocumentSection(
-                self.root / "authors.tex", self.git_root
-            )
+            self.authors = DocumentSection(self.root / "authors.tex", self.git_root)
         if self.title is None:
-            self.title = DocumentSection(
-                self.root / "title.tex", self.git_root
-            )
+            self.title = DocumentSection(self.root / "title.tex", self.git_root)
         if self.keywords is None:
-            self.keywords = DocumentSection(
-                self.root / "keywords.tex", self.git_root
-            )
+            self.keywords = DocumentSection(self.root / "keywords.tex", self.git_root)
         if self.journal_name is None:
             self.journal_name = DocumentSection(
                 self.root / "journal_name.tex", self.git_root
@@ -92,7 +85,11 @@ class SharedTree:
         missing = []
         for name, section in required:
             if not section.path.exists():
-                expected_path = section.path.relative_to(self.git_root) if self.git_root else section.path
+                expected_path = (
+                    section.path.relative_to(self.git_root)
+                    if self.git_root
+                    else section.path
+                )
                 missing.append(f"{name} (expected at: {expected_path})")
 
         return len(missing) == 0, missing

scitex/writer/dataclasses/tree/_SupplementaryTree.py

@@ -5,9 +5,8 @@
 # ----------------------------------------
 from __future__ import annotations
 import os
-__FILE__ = (
-    "./src/scitex/writer/dataclasses/tree/_SupplementaryTree.py"
-)
+
+__FILE__ = "./src/scitex/writer/dataclasses/tree/_SupplementaryTree.py"
 __DIR__ = os.path.dirname(__FILE__)
 # ----------------------------------------
 
@@ -47,13 +46,9 @@ class SupplementaryTree:
     def __post_init__(self):
         """Initialize all instances."""
         if self.contents is None:
-            self.contents = SupplementaryContents(
-                self.root / "contents", self.git_root
-            )
+            self.contents = SupplementaryContents(self.root / "contents", self.git_root)
         if self.base is None:
-            self.base = DocumentSection(
-                self.root / "base.tex", self.git_root
-            )
+            self.base = DocumentSection(self.root / "base.tex", self.git_root)
         if self.supplementary is None:
             self.supplementary = DocumentSection(
                 self.root / "supplementary.tex", self.git_root
@@ -63,9 +58,7 @@ class SupplementaryTree:
                 self.root / "supplementary_diff.tex", self.git_root
             )
         if self.readme is None:
-            self.readme = DocumentSection(
-                self.root / "README.md", self.git_root
-            )
+            self.readme = DocumentSection(self.root / "README.md", self.git_root)
         if self.archive is None:
             self.archive = self.root / "archive"
 
@@ -86,10 +79,18 @@ class SupplementaryTree:
 
         # Check root level files
         if not self.base.path.exists():
-            expected_path = self.base.path.relative_to(self.git_root) if self.git_root else self.base.path
+            expected_path = (
+                self.base.path.relative_to(self.git_root)
+                if self.git_root
+                else self.base.path
+            )
             missing.append(f"base.tex (expected at: {expected_path})")
         if not self.supplementary.path.exists():
-            expected_path = self.supplementary.path.relative_to(self.git_root) if self.git_root else self.supplementary.path
+            expected_path = (
+                self.supplementary.path.relative_to(self.git_root)
+                if self.git_root
+                else self.supplementary.path
+            )
             missing.append(f"supplementary.tex (expected at: {expected_path})")
 
         return len(missing) == 0, missing

scitex/writer/utils/.legacy_git_retry.py

@@ -5,9 +5,8 @@
 # ----------------------------------------
 from __future__ import annotations
 import os
-__FILE__ = (
-    "./src/scitex/writer/git_utils.py"
-)
+
+__FILE__ = "./src/scitex/writer/git_utils.py"
 __DIR__ = os.path.dirname(__FILE__)
 # ----------------------------------------
 
@@ -70,11 +69,7 @@ def git_retry(
             stderr = (
                 e.stderr
                 if isinstance(e.stderr, str)
-                else (
-                    e.stderr.decode("utf-8", errors="ignore")
-                    if e.stderr
-                    else ""
-                )
+                else (e.stderr.decode("utf-8", errors="ignore") if e.stderr else "")
             )
 
             if "index.lock" in stderr and attempt < max_retries - 1:

scitex/writer/utils/_parse_latex_logs.py

@@ -5,9 +5,8 @@
 # ----------------------------------------
 from __future__ import annotations
 import os
-__FILE__ = (
-    "./src/scitex/writer/parse_latex.py"
-)
+
+__FILE__ = "./src/scitex/writer/parse_latex.py"
 __DIR__ = os.path.dirname(__FILE__)
 # ----------------------------------------