rxiv-maker 1.15.5__py3-none-any.whl → 1.15.7__py3-none-any.whl

rxiv_maker/__version__.py

@@ -1,7 +1,7 @@
 """Version information for rxiv-maker."""
 
-__version__ = "1.15.5"
-__version_tuple__ = (1, 15, 5)
+__version__ = "1.15.7"
+__version_tuple__ = (1, 15, 7)
 
 # Note: Docker images v1.8+ use mermaid.ink API for diagram processing
 # This improves cross-platform compatibility and performance

rxiv_maker/engines/operations/track_changes.py

@@ -146,35 +146,34 @@ class TrackChangesManager:
         tag_manuscript_dir = temp_dir / "tag_manuscript"
         tag_manuscript_dir.mkdir()
 
-        # Extract each manuscript file from the tag
-        for file_name in self.manuscript_files:
-            file_path = self.manuscript_path / file_name
-            if not file_path.exists():
-                self.log(f"Skipping {file_name} (not found in current manuscript)")
-                continue
-
-            try:
-                # Try to extract file from git tag
-                result = subprocess.run(
-                    [
-                        "git",
-                        "show",
-                        f"{self.git_tag}:{self.manuscript_path.name}/{file_name}",
-                    ],
-                    capture_output=True,
-                    text=True,
-                    check=True,
-                )
-
-                # Write extracted content to temp directory
-                (tag_manuscript_dir / file_name).write_text(result.stdout, encoding="utf-8")
-                self.log(f"Extracted {file_name} from tag {self.git_tag}")
-
-            except subprocess.CalledProcessError as e:
-                self.log(f"Warning: Could not extract {file_name} from tag {self.git_tag}: {e}")
-                continue
+        try:
+            # Use git archive to extract the entire repository state at the tag
+            # This ensures all helper scripts, data files, and assets are present
+            # pipe git archive output to tar extraction
+            
+            # Note: We need to run this from the repo root or use the correct path
+            # The current working directory is expected to be the manuscript repo root
+            
+            archive_cmd = ["git", "archive", "--format=tar", self.git_tag]
+            tar_cmd = ["tar", "-x", "-C", str(tag_manuscript_dir)]
+            
+            # Create pipe
+            ps = subprocess.Popen(archive_cmd, stdout=subprocess.PIPE, cwd=self.manuscript_path.parent)
+            subprocess.check_call(tar_cmd, stdin=ps.stdout)
+            ps.wait()
+            
+            if ps.returncode != 0:
+                raise subprocess.CalledProcessError(ps.returncode, archive_cmd)
+                
+            self.log(f"Extracted full repository from tag {self.git_tag}")
+            return True
 
-        return True
+        except subprocess.CalledProcessError as e:
+            self.log(f"Error extracting files from tag {self.git_tag}: {e}", force=True)
+            return False
+        except Exception as e:
+            self.log(f"Unexpected error during extraction: {e}", force=True)
+            return False
 
     def generate_latex_files(self, manuscript_dir: Path, output_subdir: str) -> bool:
         """Generate LaTeX files from a manuscript directory.
@@ -461,12 +460,28 @@ class TrackChangesManager:
                 return False
 
             self.log("Generating LaTeX files for tag version...")
-            if not self.generate_latex_files(tag_manuscript_dir, "tag"):
+            
+            # Locate the manuscript directory within the extracted tag
+            # Try the same directory name as the current manuscript
+            target_manuscript_dir = tag_manuscript_dir / self.manuscript_path.name
+            
+            # If not found there, check the root (in case the repo IS the manuscript dir)
+            if not (target_manuscript_dir / "01_MAIN.md").exists():
+                if (tag_manuscript_dir / "01_MAIN.md").exists():
+                    target_manuscript_dir = tag_manuscript_dir
+                else:
+                    self.log(f"Warning: Could not create locate 01_MAIN.md in extracted tag files at {target_manuscript_dir} or root", force=True)
+                    # We continue with the guess, though it will likely fail in generation
+            
+            if not self.generate_latex_files(target_manuscript_dir, "tag"):
                 return False
 
             # Find the main LaTeX files
             current_tex = self.output_dir / "current" / f"{self.manuscript_path.name}.tex"
-            tag_tex = self.output_dir / "tag" / f"{tag_manuscript_dir.name}.tex"
+            
+            # The generated tex file will be named after the manuscript directory name (MANUSCRIPT -> MANUSCRIPT.tex)
+            # regardless of whether it's in the tag extraction or current
+            tag_tex = self.output_dir / "tag" / f"{self.manuscript_path.name}.tex"
 
             # Generate custom filename using the same convention as regular PDF
             # generation

{rxiv_maker-1.15.5.dist-info → rxiv_maker-1.15.7.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rxiv-maker
-Version: 1.15.5
+Version: 1.15.7
 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-1.15.5.dist-info → rxiv_maker-1.15.7.dist-info}/RECORD

@@ -1,5 +1,5 @@
 rxiv_maker/__init__.py,sha256=p04JYC5ZhP6dLXkoWVlKNyiRvsDE1a4C88f9q4xO3tA,3268
-rxiv_maker/__version__.py,sha256=hJ6I3XG0lIO85FvPwmP2npVwzzgbRuS86j79MmtBCRE,230
+rxiv_maker/__version__.py,sha256=SMokkfMA9YCiVIlBz4aeYm6SkxgNSAj_Hdbl5TCMz1E,230
 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
@@ -100,7 +100,7 @@ rxiv_maker/engines/operations/generate_figures.py,sha256=3oIuS0wryO9WpPZ3UD2qm0Y
 rxiv_maker/engines/operations/generate_preprint.py,sha256=EtWSL1-LGm8N61_CLABSswgvVw61haEx8m4727pdzgM,2650
 rxiv_maker/engines/operations/prepare_arxiv.py,sha256=cd0JN5IO-Wy9T8ab75eibyaA8_K8Gpwrz2F-95OMnx4,21551
 rxiv_maker/engines/operations/setup_environment.py,sha256=gERuThHTldH0YqgXn85995deHBP6csY1ZhCNgU6-vFg,12691
-rxiv_maker/engines/operations/track_changes.py,sha256=sGnuPr5DJOIaSdqreq5Tb9EvG3Ycg71H41Fm9RH7aQ4,21998
+rxiv_maker/engines/operations/track_changes.py,sha256=q0WTV2PNwF3f8UWFAVBvCt_uGlc6b8j4Y5RMLLuZTz4,23196
 rxiv_maker/engines/operations/validate.py,sha256=OVmtRVtG-r1hoA8IqYaNC-ijN1a5ixM3X5Z8Gda-O2M,17142
 rxiv_maker/engines/operations/validate_pdf.py,sha256=qyrtL752Uap3i6ntQheY570soVjFZRJe8ANrw5AvHFs,5899
 rxiv_maker/exporters/__init__.py,sha256=NcTD1SDb8tTgsHhCS1A7TVEZncyWbDRTa6sJIdLqcsE,350
@@ -185,8 +185,8 @@ 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-1.15.5.dist-info/METADATA,sha256=OQex7fSr5rhnQVasXA_zStz9HcD7O3PPrkZIgq1r65w,19656
-rxiv_maker-1.15.5.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
-rxiv_maker-1.15.5.dist-info/entry_points.txt,sha256=ghCN0hI9A1GlG7QY5F6E-xYPflA8CyS4B6bTQ1YLop0,97
-rxiv_maker-1.15.5.dist-info/licenses/LICENSE,sha256=GSZFoPIhWDNJEtSHTQ5dnELN38zFwRiQO2antBezGQk,1093
-rxiv_maker-1.15.5.dist-info/RECORD,,
+rxiv_maker-1.15.7.dist-info/METADATA,sha256=sqbLf9V-WQv79DaWv1DQqhiAj0Rqx_OOIVqEWxfT5k8,19656
+rxiv_maker-1.15.7.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
+rxiv_maker-1.15.7.dist-info/entry_points.txt,sha256=ghCN0hI9A1GlG7QY5F6E-xYPflA8CyS4B6bTQ1YLop0,97
+rxiv_maker-1.15.7.dist-info/licenses/LICENSE,sha256=GSZFoPIhWDNJEtSHTQ5dnELN38zFwRiQO2antBezGQk,1093
+rxiv_maker-1.15.7.dist-info/RECORD,,