rxiv-maker 1.15.7__py3-none-any.whl → 1.15.9__py3-none-any.whl

rxiv_maker/__version__.py

@@ -1,7 +1,3 @@
-"""Version information for rxiv-maker."""
+"""Version information."""
 
-__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
+__version__ = "1.15.9"

rxiv_maker/engines/operations/track_changes.py

@@ -150,21 +150,21 @@ class TrackChangesManager:
             # 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
 
@@ -200,6 +200,11 @@ class TrackChangesManager:
                 str(latex_output_dir),
             ]
 
+            # Pass config file explicitly if it exists in the manuscript directory
+            config_path = manuscript_dir / "00_CONFIG.yml"
+            if config_path.exists():
+                cmd.extend(["--config", str(config_path)])
+
             # Set environment variables like BuildManager does
             env = os.environ.copy()
             env["MANUSCRIPT_PATH"] = str(manuscript_dir)
@@ -209,6 +214,18 @@ class TrackChangesManager:
             if self.verbose:
                 self.log(f"LaTeX generation output: {result.stdout}")
 
+            # Post-process tag LaTeX to use distinct figure path
+            if output_subdir == "tag":
+                tex_file = latex_output_dir / f"{manuscript_dir.name}.tex"
+                if tex_file.exists():
+                    content = tex_file.read_text(encoding="utf-8")
+                    # Replace standard Figure path with tag specific path
+                    # Handle both Figures/ (standard) and FIGURES/ (source) just in case
+                    content = content.replace("{Figures/", "{Figures_tag/")
+                    content = content.replace("{FIGURES/", "{Figures_tag/")
+                    tex_file.write_text(content, encoding="utf-8")
+                    self.log(f"Updated figure paths in {tex_file.name} to use Figures_tag/")
+
             return True
 
         except subprocess.CalledProcessError as e:
@@ -460,25 +477,40 @@ class TrackChangesManager:
                 return False
 
             self.log("Generating LaTeX files for tag version...")
-            
+
             # 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)
+                    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
 
+            # Copy tag figures to output/Figures_tag
+            tag_figures_src = target_manuscript_dir / "FIGURES"
+            tag_figures_dst = self.output_dir / "Figures_tag"
+            
+            if tag_figures_src.exists():
+                if tag_figures_dst.exists():
+                    shutil.rmtree(tag_figures_dst)
+                shutil.copytree(tag_figures_src, tag_figures_dst)
+                self.log("Copied tag figures to Figures_tag directory")
+            else:
+                self.log("Warning: No FIGURES directory found in tag extraction", force=True)
+
             # Find the main LaTeX files
             current_tex = self.output_dir / "current" / f"{self.manuscript_path.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"

{rxiv_maker-1.15.7.dist-info → rxiv_maker-1.15.9.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rxiv-maker
-Version: 1.15.7
+Version: 1.15.9
 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-1.15.7.dist-info → rxiv_maker-1.15.9.dist-info}/RECORD

@@ -1,5 +1,5 @@
 rxiv_maker/__init__.py,sha256=p04JYC5ZhP6dLXkoWVlKNyiRvsDE1a4C88f9q4xO3tA,3268
-rxiv_maker/__version__.py,sha256=SMokkfMA9YCiVIlBz4aeYm6SkxgNSAj_Hdbl5TCMz1E,230
+rxiv_maker/__version__.py,sha256=Jie3UBhYYz9xfwQlIZS6rCw1H9FHwp9v16l4VwSxKVc,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
@@ -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=q0WTV2PNwF3f8UWFAVBvCt_uGlc6b8j4Y5RMLLuZTz4,23196
+rxiv_maker/engines/operations/track_changes.py,sha256=XMU1x31nwLIwbi1lwYJn333O7Tx9llQfBv8yY9O_Dww,24734
 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-1.15.7.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,,
+rxiv_maker-1.15.9.dist-info/METADATA,sha256=pRVBi_qnjSNaLZl3Lz7D0RsNJ4gaMp3SnFxp-4e-TA8,19656
+rxiv_maker-1.15.9.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
+rxiv_maker-1.15.9.dist-info/entry_points.txt,sha256=ghCN0hI9A1GlG7QY5F6E-xYPflA8CyS4B6bTQ1YLop0,97
+rxiv_maker-1.15.9.dist-info/licenses/LICENSE,sha256=GSZFoPIhWDNJEtSHTQ5dnELN38zFwRiQO2antBezGQk,1093
+rxiv_maker-1.15.9.dist-info/RECORD,,