rxiv-maker 1.16.7__py3-none-any.whl → 1.16.8__py3-none-any.whl

rxiv_maker/__version__.py

@@ -1,3 +1,3 @@
 """Version information."""
 
-__version__ = "1.16.7"
+__version__ = "1.16.8"

rxiv_maker/cli/commands/docx.py

@@ -1,15 +1,86 @@
 """DOCX export command for rxiv-maker CLI."""
 
+import platform
+import shutil
+import subprocess
+
 import rich_click as click
 from rich.console import Console
 
 from ...core.logging_config import get_logger
+from ...core.managers.dependency_manager import DependencyStatus, get_dependency_manager
 from ...exporters.docx_exporter import DocxExporter
 
 logger = get_logger()
 console = Console()
 
 
+def _check_and_offer_poppler_installation(console: Console, quiet: bool, verbose: bool) -> None:
+    """Check poppler availability and offer automatic installation via brew.
+
+    Args:
+        console: Rich console for output
+        quiet: Whether to suppress output
+        verbose: Whether verbose mode is enabled
+    """
+    # Check if poppler is installed
+    manager = get_dependency_manager()
+    result = manager.check_dependency("pdftoppm")
+
+    if result.status == DependencyStatus.AVAILABLE:
+        if verbose:
+            console.print("[dim]✓ Poppler utilities available[/dim]")
+        return
+
+    # Poppler is missing - offer to install
+    system = platform.system()
+
+    if system == "Darwin" and shutil.which("brew"):
+        # macOS with Homebrew
+        if not quiet:
+            console.print("[yellow]⚠️  Poppler not found[/yellow]")
+            console.print("   Poppler is needed to embed PDF figures in DOCX files.")
+            console.print("   Without it, PDF figures will appear as placeholders.")
+            console.print()
+
+        if click.confirm("   Would you like to install poppler now via Homebrew?", default=True):
+            console.print("[cyan]Installing poppler...[/cyan]")
+            try:
+                result = subprocess.run(
+                    ["brew", "install", "poppler"],
+                    capture_output=True,
+                    text=True,
+                    timeout=300,
+                )
+
+                if result.returncode == 0:
+                    console.print("[green]✅ Poppler installed successfully![/green]")
+                    # Clear dependency cache so it gets re-checked
+                    manager.clear_cache()
+                else:
+                    console.print(f"[red]❌ Installation failed:[/red] {result.stderr}")
+                    console.print("   You can install manually with: brew install poppler")
+            except subprocess.TimeoutExpired:
+                console.print("[red]❌ Installation timed out[/red]")
+            except Exception as e:
+                console.print(f"[red]❌ Installation error:[/red] {e}")
+        else:
+            console.print("   [dim]Skipping poppler installation. PDF figures will show as placeholders.[/dim]")
+
+    elif system == "Linux":
+        # Linux
+        if not quiet:
+            console.print("[yellow]⚠️  Poppler not found[/yellow]")
+            console.print("   Install with: sudo apt install poppler-utils")
+            console.print()
+    else:
+        # Other platforms or brew not available
+        if not quiet:
+            console.print("[yellow]⚠️  Poppler not found[/yellow]")
+            console.print(f"   Install instructions: {result.resolution_hint}")
+            console.print()
+
+
 @click.command(context_settings={"help_option_names": ["-h", "--help"]})
 @click.argument(
     "manuscript_path",
@@ -86,6 +157,9 @@ def docx(
             include_footnotes=not no_footnotes,
         )
 
+        # Pre-flight check for poppler (if manuscript contains PDF figures)
+        _check_and_offer_poppler_installation(console, quiet, verbose)
+
         # Perform export
         docx_path = exporter.export()
 

rxiv_maker/core/managers/dependency_manager.py

@@ -487,6 +487,18 @@ class DependencyManager:
                 )
             )
 
+        # Poppler utilities for PDF to image conversion (DOCX export)
+        self.register_dependency(
+            DependencySpec(
+                name="pdftoppm",
+                type=DependencyType.SYSTEM_BINARY,
+                required=False,  # Only needed for DOCX export with PDF figures
+                alternatives=["pdfinfo"],
+                contexts={"docx", "export"},
+                install_hint="macOS: brew install poppler | Linux: sudo apt install poppler-utils",
+            )
+        )
+
     def register_dependency(self, spec: DependencySpec) -> None:
         """Register a dependency specification.
 

rxiv_maker/exporters/docx_exporter.py

@@ -318,9 +318,13 @@ class DocxExporter:
             # Get DOI from entry
             doi = entry.fields.get("doi")
 
-            # TODO: Implement DOI resolution if requested and DOI missing
-            # if self.resolve_dois and not doi:
-            #     doi = self._resolve_doi_from_metadata(entry)
+            # Attempt DOI resolution if requested and DOI missing
+            if self.resolve_dois and not doi:
+                doi = self._resolve_doi_from_metadata(entry)
+                if doi:
+                    # Store in entry for this export
+                    entry.fields["doi"] = doi
+                    logger.info(f"Resolved DOI for {key}: {doi}")
 
             # Format entry (full format for DOCX bibliography)
             formatted = format_bibliography_entry(entry, doi, slim=False, author_format=self.author_format)
@@ -332,6 +336,99 @@ class DocxExporter:
 
         return bibliography
 
+    def _resolve_doi_from_metadata(self, entry) -> str | None:
+        """Resolve DOI from entry metadata using CrossRef API.
+
+        Args:
+            entry: Bibliography entry to resolve DOI for
+
+        Returns:
+            Resolved DOI if found, None otherwise
+        """
+        import requests
+
+        # Try to construct a search query from available fields
+        title = entry.fields.get("title", "").strip()
+        year = entry.fields.get("year", "").strip()
+
+        if not title:
+            logger.debug(f"Cannot resolve DOI for {entry.key}: no title")
+            return None
+
+        # Clean title for search (remove LaTeX commands, braces, etc.)
+        search_title = self._clean_title_for_search(title)
+
+        # Try CrossRef search API
+        try:
+            url = "https://api.crossref.org/works"
+            params = {
+                "query.title": search_title,
+                "rows": 5,  # Get top 5 results
+            }
+
+            response = requests.get(url, params=params, timeout=10)
+
+            if response.status_code == 200:
+                data = response.json()
+                items = data.get("message", {}).get("items", [])
+
+                # Find best match
+                for item in items:
+                    item_title = item.get("title", [""])[0].lower()
+                    search_title_lower = search_title.lower()
+
+                    # Simple similarity check - titles should be very similar
+                    if item_title and (search_title_lower in item_title or item_title in search_title_lower):
+                        # Verify year matches if available
+                        if year:
+                            item_year = item.get("published", {}).get("date-parts", [[None]])[0][0]
+                            if item_year and str(item_year) != year:
+                                continue
+
+                        doi = item.get("DOI")
+                        if doi:
+                            logger.info(f"Resolved DOI for {entry.key}: {doi}")
+                            return doi
+
+            logger.debug(f"Could not resolve DOI for {entry.key} via CrossRef")
+            return None
+
+        except requests.exceptions.Timeout:
+            logger.debug(f"CrossRef API timeout resolving DOI for {entry.key}")
+            return None
+        except requests.exceptions.ConnectionError:
+            logger.debug(f"CrossRef API connection error for {entry.key}")
+            return None
+        except Exception as e:
+            logger.debug(f"Error resolving DOI for {entry.key}: {e}")
+            return None
+
+    def _clean_title_for_search(self, title: str) -> str:
+        """Clean title for CrossRef search by removing LaTeX commands.
+
+        Args:
+            title: Raw title from BibTeX entry
+
+        Returns:
+            Cleaned title suitable for search
+        """
+        import re
+
+        # Remove LaTeX commands
+        title = re.sub(r"\\[a-zA-Z]+\{([^}]*)\}", r"\1", title)  # \textit{foo} -> foo
+        title = re.sub(r"\\[a-zA-Z]+", "", title)  # \LaTeX -> LaTeX
+
+        # Remove braces
+        title = title.replace("{", "").replace("}", "")
+
+        # Remove special characters
+        title = re.sub(r"[^a-zA-Z0-9\s\-]", " ", title)
+
+        # Normalize whitespace
+        title = " ".join(title.split())
+
+        return title.strip()
+
     def _get_metadata(self) -> Dict[str, Any]:
         """Extract metadata for title page.
 

rxiv_maker/exporters/docx_writer.py

@@ -404,6 +404,19 @@ class DocxWriter:
         paragraph_format = paragraph.paragraph_format
         paragraph_format.left_indent = Pt(36)  # Indent code blocks
 
+    def _check_poppler_availability(self) -> bool:
+        """Check if poppler is available for PDF conversion.
+
+        Returns:
+            True if poppler is available, False otherwise
+        """
+        from ..core.managers.dependency_manager import DependencyStatus, get_dependency_manager
+
+        manager = get_dependency_manager()
+        result = manager.check_dependency("pdftoppm")
+
+        return result.status == DependencyStatus.AVAILABLE
+
     def _add_figure(self, doc: Document, section: Dict[str, Any], figure_number: int = None):
         """Add figure to document with caption.
 
@@ -425,9 +438,31 @@ class DocxWriter:
         if not figure_path.exists():
             logger.warning(f"Figure file not found: {figure_path}")
         elif figure_path.suffix.lower() == ".pdf":
-            # Convert PDF to image
-            img_source = convert_pdf_to_image(figure_path)
-            logger.debug(f"  PDF converted: {img_source is not None}")
+            # Check poppler availability first (cached after first check)
+            if not hasattr(self, "_poppler_checked"):
+                self._poppler_available = self._check_poppler_availability()
+                self._poppler_checked = True
+
+                if not self._poppler_available:
+                    logger.warning(
+                        "Poppler not installed - PDF figures will be shown as placeholders. "
+                        "Install with: brew install poppler (macOS) or sudo apt install poppler-utils (Linux)"
+                    )
+
+            if self._poppler_available:
+                # Convert PDF to image
+                try:
+                    from pdf2image.exceptions import PDFInfoNotInstalledError, PopplerNotInstalledError
+
+                    img_source = convert_pdf_to_image(figure_path)
+                    logger.debug(f"  PDF converted: {img_source is not None}")
+                except (PopplerNotInstalledError, PDFInfoNotInstalledError) as e:
+                    logger.error(f"Poppler utilities not found: {e}")
+                    img_source = None
+                    # Update our cached status
+                    self._poppler_available = False
+            else:
+                img_source = None
         elif figure_path.suffix.lower() in [".png", ".jpg", ".jpeg", ".gif", ".bmp"]:
             # Use image file directly
             img_source = str(figure_path)

rxiv_maker/utils/bst_generator.py

@@ -81,21 +81,41 @@ def generate_bst_file(format_type: str, output_dir: Path) -> Path:
     except IOError as e:
         raise IOError(f"Failed to read template .bst file: {e}") from e
 
-    # Replace the format string on line 222
+    # Replace the format string in the format.names function (line ~222)
     # The line looks like: s nameptr "{ff~}{vv~}{ll}{, jj}" format.name$ 't :=
-    # We need to replace the format string in quotes
-    pattern = r'(s\s+nameptr\s+")([^"]+)("\s+format\.name\$)'
+    # We need to replace ONLY in format.names, NOT in format.full.names
+    #
+    # Strategy: Match the FUNCTION {format.names} block specifically
+    # This ensures we don't modify format.full.names which is used for citation labels
+    #
+    # Pattern explanation:
+    # 1. Match "FUNCTION {format.names}" to find the start of the function
+    # 2. Use non-greedy match (.*?) to capture until we find our target line
+    # 3. Match and capture the format string in quotes
+    # 4. This avoids matching format.full.names which appears later in the file
+    pattern = r'(FUNCTION\s+\{format\.names\}.*?s\s+nameptr\s+")([^"]+)("\s+format\.name\$)'
     replacement = rf"\1{format_string}\3"
 
-    modified_content, num_subs = re.subn(pattern, replacement, bst_content)
+    modified_content, num_subs = re.subn(pattern, replacement, bst_content, flags=re.DOTALL)
 
     if num_subs == 0:
-        logger.warning("No format string pattern found in .bst file. The .bst file may have been modified.")
+        logger.warning(
+            "No format string pattern found in format.names function. "
+            "The .bst file structure may have changed. "
+            "Citation formatting may not work as expected."
+        )
         # Still write the file but log a warning
     elif num_subs > 1:
-        logger.warning(
-            f"Found {num_subs} format string patterns in .bst file. Expected only 1. All have been replaced."
+        # This should never happen with the new pattern, but keep the check
+        logger.error(
+            f"Found {num_subs} matches in .bst file. Expected exactly 1. "
+            "This indicates an unexpected .bst file structure. "
+            "Please report this issue."
         )
+        raise ValueError(f"Unexpected .bst file structure: found {num_subs} matches for format.names, expected 1")
+    else:
+        # Success - exactly one match
+        logger.debug(f"Successfully updated format.names function with format '{format_type}'")
 
     # Create output directory if it doesn't exist
     output_dir = Path(output_dir)

rxiv_maker/utils/docx_helpers.py

@@ -8,6 +8,7 @@ This module provides utility functions for DOCX generation including:
 """
 
 import io
+import logging
 import re
 from pathlib import Path
 from typing import Optional
@@ -18,6 +19,8 @@ from rxiv_maker.utils.author_name_formatter import format_author_list
 
 from ..utils.bibliography_parser import BibEntry
 
+logger = logging.getLogger(__name__)
+
 
 def remove_yaml_header(content: str) -> str:
     r"""Remove YAML frontmatter from markdown content.
@@ -395,6 +398,12 @@ def convert_pdf_to_image(pdf_path: Path, dpi: int = 150, max_width: int = 6) ->
     """
     try:
         from pdf2image import convert_from_path
+        from pdf2image.exceptions import (
+            PDFInfoNotInstalledError,
+            PDFPageCountError,
+            PDFSyntaxError,
+            PopplerNotInstalledError,
+        )
 
         # Convert first page of PDF to image
         images = convert_from_path(
@@ -427,7 +436,19 @@ def convert_pdf_to_image(pdf_path: Path, dpi: int = 150, max_width: int = 6) ->
 
         return img_bytes
 
+    except (PopplerNotInstalledError, PDFInfoNotInstalledError):
+        # Re-raise poppler errors so caller can handle them appropriately
+        # (e.g., CLI can offer to install poppler)
+        raise
+    except PDFSyntaxError as e:
+        # PDF file is malformed/corrupted
+        logger.warning(f"PDF file appears to be corrupted: {pdf_path.name} - {e}")
+        return None
+    except PDFPageCountError as e:
+        # Issue getting page count
+        logger.warning(f"Could not determine PDF page count for {pdf_path.name}: {e}")
+        return None
     except Exception as e:
-        # Log error but don't crash - return None to indicate failure
-        print(f"Warning: Failed to convert PDF to image: {e}")
+        # Other unexpected errors
+        logger.warning(f"Failed to convert {pdf_path.name} to image: {e}")
         return None

{rxiv_maker-1.16.7.dist-info → rxiv_maker-1.16.8.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rxiv-maker
-Version: 1.16.7
+Version: 1.16.8
 Summary: Write scientific preprints in Markdown. Generate publication-ready PDFs efficiently.
 Project-URL: Homepage, https://github.com/HenriquesLab/rxiv-maker
 Project-URL: Documentation, https://github.com/HenriquesLab/rxiv-maker#readme

{rxiv_maker-1.16.7.dist-info → rxiv_maker-1.16.8.dist-info}/RECORD

@@ -1,5 +1,5 @@
 rxiv_maker/__init__.py,sha256=p04JYC5ZhP6dLXkoWVlKNyiRvsDE1a4C88f9q4xO3tA,3268
-rxiv_maker/__version__.py,sha256=--L7TPRaASOQ9_Gb1AzwOD0jIisWKuGJB7fbHOHsoFs,51
+rxiv_maker/__version__.py,sha256=FDIQKkG-uf-zpYYZrGmwOD83CED6k3EcIvKFr382p-g,51
 rxiv_maker/rxiv_maker_cli.py,sha256=9Lu_mhFPXwx5jzAR6StCNxwCm_fkmP5qiOYdNuh_AwI,120
 rxiv_maker/validate.py,sha256=AIzgP59KbCQJqC9WIGfUdVv0xI6ud9g1fFznQkaGz5Q,9373
 rxiv_maker/cli/__init__.py,sha256=Jw0DTFUSofN-02xpVrt1UUzRcgH5NNd-GPNidhmNwpU,77
@@ -19,7 +19,7 @@ rxiv_maker/cli/commands/clean.py,sha256=8yQVbhHLQX0xIM7MD-0sG_agX7xVxzl1AkqPzZRR
 rxiv_maker/cli/commands/completion.py,sha256=TKc6QPEFVN8qQsu2LbPEZvsSZr_CBvyekkfTItTDI6A,789
 rxiv_maker/cli/commands/config.py,sha256=adN4ci_EB-NZsNXNY9FlFxE6CLVxblunX1dobrjNef0,33761
 rxiv_maker/cli/commands/create_repo.py,sha256=jWPwT1Ai7XBhFAi9JmSAobdFYXPlSgQCD-gx_ZUNwEo,9947
-rxiv_maker/cli/commands/docx.py,sha256=yFJxwDyQ8F6M9n4R6AUx0lq03iMQevuI_9eY2t6ke24,2849
+rxiv_maker/cli/commands/docx.py,sha256=memJ5SeSQ8rD_wwOH9gUs1TgJUpP25_gIKEu8lKn5nQ,5896
 rxiv_maker/cli/commands/figures.py,sha256=WraC0BjwxKImzCwt1A3vWs8_T4w2misP1eeW6aznpCw,3250
 rxiv_maker/cli/commands/get_rxiv_preprint.py,sha256=nSPuFpS5xZ9VaUrmwnFZ5RCAAjj0ORAj8x_EJmH0Xtg,8543
 rxiv_maker/cli/commands/init.py,sha256=2UiXtk7a5bklqwevWwhbL9lU1ASBxUwzm7JdrINHcGA,1797
@@ -80,7 +80,7 @@ rxiv_maker/core/cache/secure_cache_utils.py,sha256=EejPWvxw_mUPqO0TRBHYYTsLXWZEU
 rxiv_maker/core/managers/__init__.py,sha256=sh4ZuZH4YrAu4XTiN9ky1-tQQASKiSTY0udJJAzDRcU,950
 rxiv_maker/core/managers/cache_manager.py,sha256=8btUaRDYPOrUynHWBMz7RVeS9xcpUoyhemFNUi8NqpQ,21893
 rxiv_maker/core/managers/config_manager.py,sha256=DdM-3_mfrjHFkPQ2vOmpQnXaoSJU-ianVwUvCEIwZss,18829
-rxiv_maker/core/managers/dependency_manager.py,sha256=DwVRcvk4JcZGzYc-K6ue7aGfw8fSnne50pPI_8Arlzw,25800
+rxiv_maker/core/managers/dependency_manager.py,sha256=qtUR4sQD2x1zv4Fi77d6ThwPx9eHZ9_ZyNy0hRpIKKQ,26308
 rxiv_maker/core/managers/execution_manager.py,sha256=cEDS0KyWBHf_N74Fc8MC4VRXxmEcaz_DJtyWO5-o628,29585
 rxiv_maker/core/managers/file_manager.py,sha256=SVRnP1JQoGCAms3E7iSpOp_RG60P36Qk9HGAmJDaFvE,18641
 rxiv_maker/core/managers/install_manager.py,sha256=8HChOfbm5-uXsksKMDqmgrYNMJJtyDoL2RDNpbFwhwc,15533
@@ -106,8 +106,8 @@ rxiv_maker/engines/operations/validate_pdf.py,sha256=qyrtL752Uap3i6ntQheY570soVj
 rxiv_maker/exporters/__init__.py,sha256=NcTD1SDb8tTgsHhCS1A7TVEZncyWbDRTa6sJIdLqcsE,350
 rxiv_maker/exporters/docx_citation_mapper.py,sha256=Qp3IEqrR6lQGQPQ4JeGdOCWeg97XBbVCKdX1gtX9XfY,4584
 rxiv_maker/exporters/docx_content_processor.py,sha256=3srXfq4lC_FJpTAfu-WB930WheSm6rCy-vNUtFlsflY,23878
-rxiv_maker/exporters/docx_exporter.py,sha256=i2G_AF-Co4AOD6ZdRzDZ7VgcJLdCmxu-Fn3SykvBywQ,15152
-rxiv_maker/exporters/docx_writer.py,sha256=qI_0JklqAxF_TUHxO3wPopZpJ44O2qYjMPOptrnU0XM,41915
+rxiv_maker/exporters/docx_exporter.py,sha256=Q18TuZCbx6fzAs1f9G2A9h5N2Gw5qhCrL7a2NKXizg8,18672
+rxiv_maker/exporters/docx_writer.py,sha256=CW2Xu9-vpuEct9344bM8ofGkCiWlAYijoXVzZ7MQZ6g,43460
 rxiv_maker/install/__init__.py,sha256=kAB6P-12IKg_K1MQ-uzeC5IR11O2cNxj0t_2JMhooZs,590
 rxiv_maker/install/dependency_handlers/__init__.py,sha256=NN9dP1usXpYgLpSw0uEnJ6ugX2zefihVjdyDdm1k-cE,231
 rxiv_maker/install/dependency_handlers/latex.py,sha256=xopSJxYkg3D63rH7RoVLN-Ykl87AZqhlUrrG3m6LoWo,3304
@@ -147,11 +147,11 @@ rxiv_maker/utils/__init__.py,sha256=4ya5VR8jqRqUChlnUeMeeetOuWV-gIvjPwcE1u_1OnI,
 rxiv_maker/utils/author_name_formatter.py,sha256=UjvarbyQm89EUIYqckygx3g37o-EcNyvipBtY8GJDxs,10222
 rxiv_maker/utils/bibliography_checksum.py,sha256=Jh4VILSpGQ5KJ9UBCUb7oFy6lZ9_ncXD87vEXxw5jbY,10270
 rxiv_maker/utils/bibliography_parser.py,sha256=WZIQoEpVwdbLmbkw9FdkVgoLE5GX7itqnzPnEEb_fFU,6846
-rxiv_maker/utils/bst_generator.py,sha256=kS4k_cc2GNm3l-bwaVU7uffWbH3VDzHwgCXHn7Ro9xI,5002
+rxiv_maker/utils/bst_generator.py,sha256=m69JWMIvf9eRiHcaWB-8D3DQCDO8flVIYbOBMuzV-F0,6097
 rxiv_maker/utils/changelog_parser.py,sha256=WCDp9Iy6H6_3nC6FB7RLt6i00zuCyvU17sCU4e3pqCY,11954
 rxiv_maker/utils/citation_utils.py,sha256=spIgVxPAN6jPvoG-eOE00rVX_buUGKnUjP1Fhz31sl4,5134
 rxiv_maker/utils/dependency_checker.py,sha256=EdyIvk-W_bhC1DJCpFw5ePhjEU74C9j7RYMm06unBMA,14366
-rxiv_maker/utils/docx_helpers.py,sha256=jhxkrU80JjDJXDE3gNfsJt9PqLyByYDfymY_Jm9ZqoI,12860
+rxiv_maker/utils/docx_helpers.py,sha256=rNNnz3mhXymrTgQR4bZDnGwpUFylWVpfpJnY0bWnl30,13635
 rxiv_maker/utils/doi_resolver.py,sha256=8_oy5cTtklm1GCKXpn509yqYsu4P5gYbMjtfQ8dRgFA,10253
 rxiv_maker/utils/email_encoder.py,sha256=QMD5JbGNu68gD8SBdGHfNY8uCgbMzEcmzE1TCYDMgWY,5139
 rxiv_maker/utils/figure_checksum.py,sha256=PWgh2QAErNnnQCV-t-COACQXKICUaggAAIxhgHLCGNM,10748
@@ -188,8 +188,8 @@ rxiv_maker/validators/doi/metadata_comparator.py,sha256=euqHhKP5sHQAdZbdoAahUn6Y
 rxiv_maker/tex/template.tex,sha256=zrJ3aFfu8j9zkg1l375eE9w-j42P3rz16wMD3dSgi1I,1354
 rxiv_maker/tex/style/rxiv_maker_style.bst,sha256=jbVqrJgAm6F88cow5vtZuPBwwmlcYykclTm8RvZIo6Y,24281
 rxiv_maker/tex/style/rxiv_maker_style.cls,sha256=F2qtnS9mI6SwOIaVH76egXZkB2_GzbH4gCTG_ZcfCDQ,24253
-rxiv_maker-1.16.7.dist-info/METADATA,sha256=6O761FLD317XmFqsnlCerTogrcC1Kq4wUJW9xnz4psM,18177
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