rxiv-maker 1.16.1__py3-none-any.whl → 1.16.3__py3-none-any.whl

rxiv_maker/__version__.py

@@ -1,3 +1,3 @@
 """Version information."""
 
-__version__ = "1.16.1"
+__version__ = "1.16.3"

rxiv_maker/cli/commands/init.py

@@ -8,7 +8,7 @@ from ..framework import InitCommand
 @click.command(context_settings={"help_option_names": ["-h", "--help"]})
 @click.argument("manuscript_path", type=click.Path(), required=False)
 @click.option("--force", "-f", is_flag=True, help="Force overwrite existing files")
-@click.option("--no-interactive", is_flag=True, help="Skip interactive prompts and use defaults")
+@click.option("--no-interactive", is_flag=True, hidden=True, help="Deprecated (command is always non-interactive)")
 @click.option(
     "--validate", is_flag=True, help="Run validation after initialization to ensure template builds correctly"
 )
@@ -25,6 +25,9 @@ def init(
     **MANUSCRIPT_PATH**: Directory to create for your manuscript.
     Defaults to MANUSCRIPT/
 
+    This command is fully non-interactive and uses sensible defaults for all values.
+    You can customize the manuscript details by editing 00_CONFIG.yml after initialization.
+
     Creates all required files including configuration, main content, supplementary
     information, bibliography, and figure directory with example scripts.
 
@@ -45,10 +48,6 @@ def init(
     **Initialize and validate template builds correctly:**
 
         $ rxiv init --validate
-
-    **Non-interactive initialization:**
-
-        $ rxiv init --no-interactive
     """
     # Use centralized InitCommand framework - eliminates 250+ lines of boilerplate!
     command = InitCommand()

rxiv_maker/cli/commands/upgrade.py

@@ -5,12 +5,12 @@ import subprocess
 import sys
 
 import click
+from henriqueslab_updater import force_update_check
 from rich.console import Console
 
 from ... import __version__
 from ...utils.changelog_parser import fetch_and_format_changelog
 from ...utils.install_detector import detect_install_method, get_friendly_install_name, get_upgrade_command
-from ...utils.update_checker import force_update_check
 from ..interactive import prompt_confirm
 
 console = Console()

rxiv_maker/cli/framework/base.py

@@ -210,6 +210,9 @@ class BaseCommand(ABC):
             return self.execute_operation(**kwargs)
 
         except CommandExecutionError as e:
+            # Print error message to stderr before exiting
+            error_console = Console(stderr=True)
+            error_console.print(f"❌ Error: {e}", style="red")
             sys.exit(e.exit_code)
         except KeyboardInterrupt:
             self.handle_keyboard_interrupt(operation_name)

rxiv_maker/cli/framework/workflow_commands.py

@@ -50,44 +50,26 @@ class InitCommand(BaseCommand):
 
         Args:
             force: Force overwrite existing files
-            no_interactive: Skip interactive prompts
+            no_interactive: Deprecated (command is always non-interactive)
             validate: Run validation after initialization
             template: Template type to use (default, minimal, journal, preprint)
         """
-        from rich.prompt import Prompt
-
         # Get manuscript path from raw path (set during setup_common_options)
         manuscript_path = self.raw_manuscript_path
 
         manuscript_dir = Path(manuscript_path)
 
-        # Check if directory exists
+        # Check if directory exists and fail if --force not used
         if manuscript_dir.exists() and not force:
-            if not no_interactive:
-                overwrite = Prompt.ask(
-                    f"Directory '{manuscript_path}' already exists. Overwrite?", choices=["y", "n"], default="n"
-                )
-                if overwrite == "n":
-                    self.console.print("❌ Initialization cancelled", style="yellow")
-                    return
-            else:
-                raise CommandExecutionError(f"Directory '{manuscript_path}' already exists. Use --force to overwrite.")
+            raise CommandExecutionError(f"Directory '{manuscript_path}' already exists. Use --force to overwrite.")
 
-        # Get user information if interactive (BEFORE progress bar)
+        # Always use default values (non-interactive mode only)
         title = "Your Manuscript Title"
         author_name = "Your Name"
         author_email = "your.email@example.com"
         author_orcid = "0000-0000-0000-0000"
         author_affiliation = "Your Institution"
 
-        if not no_interactive:
-            self.console.print("\n📝 Enter manuscript details (press Enter for defaults):")
-            title = Prompt.ask("Title", default=title)
-            author_name = Prompt.ask("Author name", default=author_name)
-            author_email = Prompt.ask("Author email", default=author_email)
-            author_orcid = Prompt.ask("Author ORCID", default=author_orcid)
-            author_affiliation = Prompt.ask("Author affiliation", default=author_affiliation)
-
         with self.create_progress() as progress:
             task = progress.add_task(f"Initializing manuscript (template: {template})...", total=2)
 

rxiv_maker/utils/bst_generator.py

@@ -50,12 +50,29 @@ def generate_bst_file(format_type: str, output_dir: Path) -> Path:
     format_string = BST_FORMAT_MAP[format_type]
 
     # Find the template .bst file in the package
-    # The template is located at src/tex/style/rxiv_maker_style.bst
-    package_root = Path(__file__).parent.parent.parent
-    template_path = package_root / "tex" / "style" / "rxiv_maker_style.bst"
-
-    if not template_path.exists():
-        raise FileNotFoundError(f"Template .bst file not found at: {template_path}")
+    # Try multiple locations for development and installed configurations
+    possible_template_paths = [
+        # Installed package location (site-packages/rxiv_maker/tex/style/)
+        Path(__file__).parent.parent / "tex" / "style" / "rxiv_maker_style.bst",
+        # Development location (src/tex/style/)
+        Path(__file__).parent.parent.parent / "tex" / "style" / "rxiv_maker_style.bst",
+        # Alternative development location
+        Path(__file__).parent.parent.parent.parent / "src" / "tex" / "style" / "rxiv_maker_style.bst",
+    ]
+
+    template_path = None
+    for path in possible_template_paths:
+        if path.exists():
+            template_path = path
+            break
+
+    if template_path is None:
+        searched_paths = "\n".join(f"  - {p}" for p in possible_template_paths)
+        raise FileNotFoundError(
+            f"Template .bst file not found.\n"
+            f"Searched locations:\n{searched_paths}\n"
+            f"This may indicate a corrupted installation."
+        )
 
     # Read the template file
     try:

{rxiv_maker-1.16.1.dist-info → rxiv_maker-1.16.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rxiv-maker
-Version: 1.16.1
+Version: 1.16.3
 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-1.16.1.dist-info → rxiv_maker-1.16.3.dist-info}/RECORD

@@ -1,5 +1,5 @@
 rxiv_maker/__init__.py,sha256=p04JYC5ZhP6dLXkoWVlKNyiRvsDE1a4C88f9q4xO3tA,3268
-rxiv_maker/__version__.py,sha256=8DXr6AdO9lpjmX0V0QhmlTnYk_k3iaC056W7yqb_Jag,51
+rxiv_maker/__version__.py,sha256=Ee6U6W-eWQHTVnWV61WELv3p6G3PUDkO5Vt_RwLkSb0,51
 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
@@ -22,24 +22,24 @@ rxiv_maker/cli/commands/create_repo.py,sha256=jWPwT1Ai7XBhFAi9JmSAobdFYXPlSgQCD-
 rxiv_maker/cli/commands/docx.py,sha256=yFJxwDyQ8F6M9n4R6AUx0lq03iMQevuI_9eY2t6ke24,2849
 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=RLv9jLUYAZLNPjcvcVP3XzMtwl-hxVFNaf8oOD4iuEA,1680
+rxiv_maker/cli/commands/init.py,sha256=2UiXtk7a5bklqwevWwhbL9lU1ASBxUwzm7JdrINHcGA,1797
 rxiv_maker/cli/commands/install_deps.py,sha256=7gE9EKwxkWxcsG5xlyMmIOpi4f0JAUqqvDviwkSIf8s,1724
 rxiv_maker/cli/commands/repo_init.py,sha256=FlAdxYi9ST01T47LUZ7zAytR7UkyKVn6MIC6cMRCbv0,6625
 rxiv_maker/cli/commands/repos.py,sha256=SQ9nuhSkyHKFPYn_TrOxyQoGdDRI-OBOgUSGJpRu0wo,6148
 rxiv_maker/cli/commands/repos_search.py,sha256=6sUMvyHlHEX1p88hPtu0_Hf8z6JpOinJ53l9ZI-rirc,7743
 rxiv_maker/cli/commands/setup.py,sha256=9ue4bDETpSPGVkWFDfpuTDsysax5-QKGxmt42Gb7oeU,2294
 rxiv_maker/cli/commands/track_changes.py,sha256=omf_77A7htRSa8naUEPTTtUTxrSwMpzHFOuU0j1xAJw,1163
-rxiv_maker/cli/commands/upgrade.py,sha256=7wgfAZisEisCqIBBQrNhc6IqcefmaSv4f-6IIaqno-I,7304
+rxiv_maker/cli/commands/upgrade.py,sha256=5yA8Aa_zIwJ6PBE94NB_ZqRYhiQkawm-lc43u04NiYY,7301
 rxiv_maker/cli/commands/validate.py,sha256=3JghFQevJvQDQII4p_QWbQXMEUyDpM-t9-WxtaT4edo,1629
 rxiv_maker/cli/commands/version.py,sha256=VMlfSxxsrZH02d24MXLUDZfHBW39yZRpWxUpMhQ-X0Y,2737
 rxiv_maker/cli/framework/__init__.py,sha256=4FPXdP8J6v4eeEn46mwY0VtnwxjR1jnW_kTrXykQlQs,2704
-rxiv_maker/cli/framework/base.py,sha256=B9Lk8egK2rfAdD8g-EDQfrTF78fCMUBssB7FxF-AQ3I,7714
+rxiv_maker/cli/framework/base.py,sha256=GcDFFOGVrLSlRgwDPmMkEAL60TbgT-maTyiCp1g-BrA,7886
 rxiv_maker/cli/framework/cache_commands.py,sha256=J91UYLTsLTRoNdzuhAbNL2bJJovYYfX3T9jI8cNUBWU,9897
 rxiv_maker/cli/framework/config_commands.py,sha256=a1uOQkCCw3d4qlro3OwHIorcoNg03T_R4-HbfVb-hmQ,19336
 rxiv_maker/cli/framework/content_commands.py,sha256=RilxKeG2c1m2fu0CtWAvP3cGh11DGx9P-nh2kIewAg4,22596
 rxiv_maker/cli/framework/decorators.py,sha256=fh085e3k1CaLSMoZevt8hvgnEuejrf-mcNS-dwXoY_A,10365
 rxiv_maker/cli/framework/utility_commands.py,sha256=_P_KwjlyiNS-vVboU-DqkHynGPqzXyoZRWGmLMLTnOs,26214
-rxiv_maker/cli/framework/workflow_commands.py,sha256=GbK1Wv4cTQfCiOyukn_R3q3IUqKvLk8MMK1vOXW3PaE,30556
+rxiv_maker/cli/framework/workflow_commands.py,sha256=CFa3c5oJMmy9cUZxTAU97eKC6YrOljzerSAMrywjbKw,29684
 rxiv_maker/config/defaults.py,sha256=vHyLGVxe5-z9TLxu5f6NhquPvqQkER_KZv_j1I4_dHQ,3055
 rxiv_maker/config/validator.py,sha256=9XDPfo_YgasGt6NLkl6HIhaGh1fr6XsFNiXU2DSsivw,38299
 rxiv_maker/converters/__init__.py,sha256=d7WGsRwWqRQWO117IkKDP0Ap0ERiK0N2-dXHInye3_A,685
@@ -147,7 +147,7 @@ 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=EHNhMT0Tq6YXUh2TfpGwOzYaarAyjEsAeeJ4H4np7Og,4313
+rxiv_maker/utils/bst_generator.py,sha256=kS4k_cc2GNm3l-bwaVU7uffWbH3VDzHwgCXHn7Ro9xI,5002
 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
@@ -187,8 +187,8 @@ 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-1.16.1.dist-info/METADATA,sha256=A8awBHoNe4YS_8eJS9F2oNgbUoXpmy_sNgp6VsyRzXw,19818
-rxiv_maker-1.16.1.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
-rxiv_maker-1.16.1.dist-info/entry_points.txt,sha256=ghCN0hI9A1GlG7QY5F6E-xYPflA8CyS4B6bTQ1YLop0,97
-rxiv_maker-1.16.1.dist-info/licenses/LICENSE,sha256=GSZFoPIhWDNJEtSHTQ5dnELN38zFwRiQO2antBezGQk,1093
-rxiv_maker-1.16.1.dist-info/RECORD,,
+rxiv_maker-1.16.3.dist-info/METADATA,sha256=oM615ZOWCjw_f6jWA7K0rnaI9S19-C9mks2Afm9JLZ0,19818
+rxiv_maker-1.16.3.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
+rxiv_maker-1.16.3.dist-info/entry_points.txt,sha256=ghCN0hI9A1GlG7QY5F6E-xYPflA8CyS4B6bTQ1YLop0,97
+rxiv_maker-1.16.3.dist-info/licenses/LICENSE,sha256=GSZFoPIhWDNJEtSHTQ5dnELN38zFwRiQO2antBezGQk,1093
+rxiv_maker-1.16.3.dist-info/RECORD,,