scitex 2.13.0__py3-none-any.whl → 2.15.1__py3-none-any.whl

scitex/writer/dataclasses/results/_LaTeXIssue.py

@@ -1,102 +0,0 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-# Timestamp: "2025-10-29 06:08:41 (ywatanabe)"
-# File: /home/ywatanabe/proj/scitex-code/src/scitex/writer/dataclasses/_LaTeXIssue.py
-# ----------------------------------------
-from __future__ import annotations
-import os
-
-__FILE__ = "./src/scitex/writer/dataclasses/_LaTeXIssue.py"
-__DIR__ = os.path.dirname(__FILE__)
-# ----------------------------------------
-
-"""
-LaTeXIssue - dataclass for LaTeX compilation issues.
-"""
-
-from dataclasses import dataclass
-
-
-@dataclass
-class LaTeXIssue:
-    """Single LaTeX error or warning."""
-
-    type: str  # 'error' or 'warning'
-    message: str
-
-    def __str__(self) -> str:
-        """Human-readable string representation."""
-        return f"{self.type.upper()}: {self.message}"
-
-
-def run_session() -> None:
-    """Initialize scitex framework, run main function, and cleanup."""
-    global CONFIG, CC, sys, plt, rng
-    import sys
-    import matplotlib.pyplot as plt
-    import scitex as stx
-
-    args = parse_args()
-
-    CONFIG, sys.stdout, sys.stderr, plt, CC, rng = stx.session.start(
-        sys,
-        plt,
-        args=args,
-        file=__FILE__,
-        sdir_suffix=None,
-        verbose=False,
-        agg=True,
-    )
-
-    exit_status = main(args)
-
-    stx.session.close(
-        CONFIG,
-        verbose=False,
-        notify=False,
-        message="",
-        exit_status=exit_status,
-    )
-
-
-def main(args):
-    issue = LaTeXIssue(
-        type=args.type,
-        message=args.message,
-    )
-
-    print(issue)
-    print(f"\nFormatted: {issue}")
-    return 0
-
-
-def parse_args():
-    import argparse
-
-    parser = argparse.ArgumentParser(description="Demonstrate LaTeXIssue dataclass")
-    parser.add_argument(
-        "--type",
-        type=str,
-        default="error",
-        choices=["error", "warning"],
-        help="Issue type (default: error)",
-    )
-    parser.add_argument(
-        "--message",
-        type=str,
-        default="Undefined control sequence",
-        help="Issue message (default: 'Undefined control sequence')",
-    )
-
-    return parser.parse_args()
-
-
-if __name__ == "__main__":
-    run_session()
-
-
-__all__ = ["LaTeXIssue"]
-
-# python -m scitex.writer.dataclasses.results._LaTeXIssue --type warning --message "Citation not found"
-
-# EOF

scitex/writer/dataclasses/tree/MINIMUM_FILES.md

@@ -1,121 +0,0 @@
-<!-- ---
-!-- Timestamp: 2025-10-28 16:37:52
-!-- Author: ywatanabe
-!-- File: /home/ywatanabe/proj/scitex-code/src/scitex/writer/necessary_structure.md
-!-- --- -->
-
-test-writer-project/
-├── 01_manuscript
-│   ├── archive
-│   ├── base.tex
-│   ├── contents
-│   │   ├── abstract.tex
-│   │   ├── additional_info.tex
-│   │   ├── authors.tex
-│   │   ├── bibliography.bib
-│   │   ├── data_availability.tex
-│   │   ├── discussion.tex
-│   │   ├── figures
-│   │   ├── graphical_abstract.tex
-│   │   ├── highlights.tex
-│   │   ├── introduction.tex
-│   │   ├── journal_name.tex
-│   │   ├── keywords.tex
-│   │   ├── latex_styles
-│   │   ├── methods.tex
-│   │   ├── results.tex
-│   │   ├── tables
-│   │   ├── title.tex
-│   │   └── wordcount.tex
-│   └── README.md
-├── 02_supplementary
-│   ├── archive
-│   ├── base.tex
-│   ├── contents
-│   │   ├── authors.tex
-│   │   ├── bibliography.bib
-│   │   ├── figures
-│   │   ├── journal_name.tex
-│   │   ├── keywords.tex
-│   │   ├── latex_styles
-│   │   ├── methods.tex
-│   │   ├── results.tex
-│   │   ├── tables
-│   │   ├── title.tex
-│   │   └── wordcount.tex
-│   ├── README.md
-│   ├── supplementary_diff.tex
-│   └── supplementary.tex
-├── 03_revision
-│   ├── archive
-│   ├── base.tex
-│   ├── contents
-│   │   ├── authors.tex
-│   │   ├── bibliography.bib
-│   │   ├── conclusion.tex
-│   │   ├── editor
-│   │   ├── figures
-│   │   ├── introduction.tex
-│   │   ├── journal_name.tex
-│   │   ├── keywords.tex
-│   │   ├── latex_styles
-│   │   ├── README.md
-│   │   ├── references.tex
-│   │   ├── reviewer1
-│   │   ├── reviewer2
-│   │   ├── tables
-│   │   └── title.tex
-│   ├── docs
-│   │   └── email.md
-│   ├── README.md
-│   └── revision.tex
-├── compile
-├── config
-│   ├── config_manuscript.yaml
-│   ├── config_revision.yaml
-│   ├── config_supplementary.yaml
-│   └── load_config.sh
-├── Makefile
-├── README.md
-├── scripts
-│   ├── examples
-│   │   └── link_project_assets.sh
-│   ├── installation
-│   │   ├── check_requirements.sh
-│   │   ├── download_containers.sh
-│   │   └── install_on_ubuntu.sh
-│   ├── powershell
-│   │   └── pptx2tiff.ps1
-│   ├── python
-│   │   ├── crop_tif.py
-│   │   ├── csv_to_latex.py
-│   │   ├── explore_bibtex.py
-│   │   ├── generate_ai2_prompt.py
-│   │   ├── optimize_figure.py
-│   │   ├── pptx2tif.py
-│   │   └── tile_panels.py
-│   └── shell
-│       ├── compile_manuscript.sh
-│       ├── compile_revision.sh
-│       ├── compile_supplementary.sh
-│       ├── modules
-│       └── watch_compile.sh
-├── shared
-│   ├── authors.tex
-│   ├── bib_files
-│   │   ├── bibliography.bib
-│   ├── bibliography.bib
-│   ├── journal_name.tex
-│   ├── keywords.tex
-│   ├── latex_styles
-│   │   ├── bibliography.tex
-│   │   ├── columns.tex
-│   │   ├── formatting.tex
-│   │   ├── linker.tex
-│   │   └── packages.tex
-│   ├── README.md
-│   ├── templates
-│   │   └── tables
-│   └── title.tex
-
-<!-- EOF -->

scitex/writer/tests/__init__.py

@@ -1,3 +0,0 @@
-"""Tests for scitex.writer module."""
-
-__all__ = []

scitex/writer/tests/test_diff_between.py

@@ -1,451 +0,0 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-"""
-Tests for DocumentSection.diff_between() and ref resolution.
-
-Tests cover:
-- Comparing two arbitrary git references
-- Human-readable reference resolution
-- Relative time specifications (N days ago, etc.)
-- Absolute date specifications
-- Timestamp-based commit finding
-"""
-
-import shutil
-import subprocess
-import tempfile
-import time
-from datetime import datetime, timedelta
-from pathlib import Path
-
-import pytest
-
-from scitex.writer.dataclasses.core._DocumentSection import DocumentSection
-
-
-class TestDiffBetween:
-    """Test diff_between() for comparing two references."""
-
-    @pytest.fixture
-    def git_repo_with_history(self):
-        """Create git repository with multiple commits."""
-        temp_dir = tempfile.mkdtemp(prefix="scitex_diff_between_")
-        repo_path = Path(temp_dir)
-
-        # Initialize git repo
-        subprocess.run(
-            ["git", "init"],
-            cwd=repo_path,
-            capture_output=True,
-            check=True,
-        )
-
-        # Configure git
-        subprocess.run(
-            ["git", "config", "user.email", "test@example.com"],
-            cwd=repo_path,
-            capture_output=True,
-            check=True,
-        )
-        subprocess.run(
-            ["git", "config", "user.name", "Test User"],
-            cwd=repo_path,
-            capture_output=True,
-            check=True,
-        )
-
-        # Create test file with initial content
-        test_file = repo_path / "test.tex"
-        test_file.write_text("Initial content\n")
-
-        # Initial commit
-        subprocess.run(
-            ["git", "add", "test.tex"],
-            cwd=repo_path,
-            capture_output=True,
-            check=True,
-        )
-        subprocess.run(
-            ["git", "commit", "-m", "Initial commit"],
-            cwd=repo_path,
-            capture_output=True,
-            check=True,
-        )
-
-        # Commit 2: Add first section
-        test_file.write_text("Initial content\n\nSection 1\n")
-        subprocess.run(
-            ["git", "add", "test.tex"],
-            cwd=repo_path,
-            capture_output=True,
-            check=True,
-        )
-        subprocess.run(
-            ["git", "commit", "-m", "Add section 1"],
-            cwd=repo_path,
-            capture_output=True,
-            check=True,
-        )
-
-        # Commit 3: Add second section
-        test_file.write_text("Initial content\n\nSection 1\n\nSection 2\n")
-        subprocess.run(
-            ["git", "add", "test.tex"],
-            cwd=repo_path,
-            capture_output=True,
-            check=True,
-        )
-        subprocess.run(
-            ["git", "commit", "-m", "Add section 2"],
-            cwd=repo_path,
-            capture_output=True,
-            check=True,
-        )
-
-        # Create a tag
-        subprocess.run(
-            ["git", "tag", "v1.0"],
-            cwd=repo_path,
-            capture_output=True,
-            check=True,
-        )
-
-        yield test_file, repo_path
-
-        # Cleanup
-        if repo_path.exists():
-            shutil.rmtree(repo_path)
-
-    def test_diff_between_commits(self, git_repo_with_history):
-        """Test comparing two commits."""
-        test_file, repo_path = git_repo_with_history
-
-        section = DocumentSection(test_file, git_root=repo_path)
-
-        # Compare first commit to last
-        diff = section.diff_between("HEAD~2", "HEAD")
-
-        assert len(diff) > 0
-        assert "Section 1" in diff or "+" in diff
-
-    def test_diff_between_tag_and_head(self, git_repo_with_history):
-        """Test comparing tag to HEAD."""
-        test_file, repo_path = git_repo_with_history
-
-        section = DocumentSection(test_file, git_root=repo_path)
-
-        # Compare v1.0 tag to HEAD
-        diff = section.diff_between("v1.0", "HEAD")
-
-        # Should show nothing changed after tag
-        # (because we didn't add commits after creating tag in this fixture)
-        assert isinstance(diff, str)
-
-    def test_diff_between_empty_when_no_changes(self, git_repo_with_history):
-        """Test diff_between returns empty when commits are identical."""
-        test_file, repo_path = git_repo_with_history
-
-        section = DocumentSection(test_file, git_root=repo_path)
-
-        # Compare HEAD to itself
-        diff = section.diff_between("HEAD", "HEAD")
-
-        assert diff == ""
-
-    def test_diff_between_invalid_ref1(self, git_repo_with_history):
-        """Test diff_between with invalid first reference."""
-        test_file, repo_path = git_repo_with_history
-
-        section = DocumentSection(test_file, git_root=repo_path)
-
-        # Try with non-existent ref
-        diff = section.diff_between("nonexistent123", "HEAD")
-
-        assert diff == ""
-
-
-class TestRefResolution:
-    """Test _resolve_ref() for human-readable references."""
-
-    @pytest.fixture
-    def simple_git_repo(self):
-        """Create simple git repository with one file."""
-        temp_dir = tempfile.mkdtemp(prefix="scitex_ref_resolve_")
-        repo_path = Path(temp_dir)
-
-        # Initialize git repo
-        subprocess.run(
-            ["git", "init"],
-            cwd=repo_path,
-            capture_output=True,
-            check=True,
-        )
-
-        # Configure git
-        subprocess.run(
-            ["git", "config", "user.email", "test@example.com"],
-            cwd=repo_path,
-            capture_output=True,
-            check=True,
-        )
-        subprocess.run(
-            ["git", "config", "user.name", "Test User"],
-            cwd=repo_path,
-            capture_output=True,
-            check=True,
-        )
-
-        # Create and commit file
-        test_file = repo_path / "test.tex"
-        test_file.write_text("Test\n")
-
-        subprocess.run(
-            ["git", "add", "test.tex"],
-            cwd=repo_path,
-            capture_output=True,
-            check=True,
-        )
-        subprocess.run(
-            ["git", "commit", "-m", "Initial"],
-            cwd=repo_path,
-            capture_output=True,
-            check=True,
-        )
-
-        yield test_file, repo_path
-
-        # Cleanup
-        if repo_path.exists():
-            shutil.rmtree(repo_path)
-
-    def test_resolve_head(self, simple_git_repo):
-        """Test resolving HEAD reference."""
-        test_file, repo_path = simple_git_repo
-
-        section = DocumentSection(test_file, git_root=repo_path)
-        resolved = section._resolve_ref("HEAD")
-
-        assert resolved == "HEAD"
-
-    def test_resolve_now_to_head(self, simple_git_repo):
-        """Test resolving 'now' to HEAD."""
-        test_file, repo_path = simple_git_repo
-
-        section = DocumentSection(test_file, git_root=repo_path)
-        resolved = section._resolve_ref("now")
-
-        assert resolved == "HEAD"
-
-    def test_resolve_invalid_ref(self, simple_git_repo):
-        """Test resolving invalid reference returns None."""
-        test_file, repo_path = simple_git_repo
-
-        section = DocumentSection(test_file, git_root=repo_path)
-        resolved = section._resolve_ref("nonexistent_ref_xyz")
-
-        assert resolved is None
-
-
-class TestTimeResolution:
-    """Test time-based reference resolution."""
-
-    @pytest.fixture
-    def timed_git_repo(self):
-        """Create git repository with time-spaced commits."""
-        temp_dir = tempfile.mkdtemp(prefix="scitex_time_resolve_")
-        repo_path = Path(temp_dir)
-
-        # Initialize git repo
-        subprocess.run(
-            ["git", "init"],
-            cwd=repo_path,
-            capture_output=True,
-            check=True,
-        )
-
-        # Configure git
-        subprocess.run(
-            ["git", "config", "user.email", "test@example.com"],
-            cwd=repo_path,
-            capture_output=True,
-            check=True,
-        )
-        subprocess.run(
-            ["git", "config", "user.name", "Test User"],
-            cwd=repo_path,
-            capture_output=True,
-            check=True,
-        )
-
-        # Create initial commit
-        test_file = repo_path / "test.tex"
-        test_file.write_text("v1\n")
-
-        subprocess.run(
-            ["git", "add", "test.tex"],
-            cwd=repo_path,
-            capture_output=True,
-            check=True,
-        )
-        subprocess.run(
-            ["git", "commit", "-m", "v1"],
-            cwd=repo_path,
-            capture_output=True,
-            check=True,
-        )
-
-        # Wait a bit, then create second commit
-        time.sleep(1)
-        test_file.write_text("v2\n")
-        subprocess.run(
-            ["git", "add", "test.tex"],
-            cwd=repo_path,
-            capture_output=True,
-            check=True,
-        )
-        subprocess.run(
-            ["git", "commit", "-m", "v2"],
-            cwd=repo_path,
-            capture_output=True,
-            check=True,
-        )
-
-        yield test_file, repo_path
-
-        # Cleanup
-        if repo_path.exists():
-            shutil.rmtree(repo_path)
-
-    def test_parse_relative_time_days(self, timed_git_repo):
-        """Test parsing '2 days ago' specification."""
-        test_file, repo_path = timed_git_repo
-
-        section = DocumentSection(test_file, git_root=repo_path)
-        dt = section._parse_relative_time("2 days ago")
-
-        assert dt is not None
-        assert isinstance(dt, datetime)
-        # Should be about 2 days in the past
-        now = datetime.now()
-        delta = (now - dt).total_seconds()
-        assert 48 * 3600 - 60 < delta < 48 * 3600 + 60  # Within 1 minute of 2 days
-
-    def test_parse_relative_time_hours(self, timed_git_repo):
-        """Test parsing '24 hours ago' specification."""
-        test_file, repo_path = timed_git_repo
-
-        section = DocumentSection(test_file, git_root=repo_path)
-        dt = section._parse_relative_time("24 hours ago")
-
-        assert dt is not None
-        assert isinstance(dt, datetime)
-
-    def test_parse_relative_time_invalid(self, timed_git_repo):
-        """Test parsing invalid time specification."""
-        test_file, repo_path = timed_git_repo
-
-        section = DocumentSection(test_file, git_root=repo_path)
-        dt = section._parse_relative_time("invalid time spec")
-
-        assert dt is None
-
-    def test_parse_absolute_date_ymd(self):
-        """Test parsing absolute date in YYYY-MM-DD format."""
-        section = DocumentSection(Path("/tmp/test.tex"))
-        dt = section._parse_absolute_date("2025-10-28")
-
-        assert dt is not None
-        assert dt.year == 2025
-        assert dt.month == 10
-        assert dt.day == 28
-
-    def test_parse_absolute_date_ymd_hm(self):
-        """Test parsing absolute date with time in YYYY-MM-DD HH:MM format."""
-        section = DocumentSection(Path("/tmp/test.tex"))
-        dt = section._parse_absolute_date("2025-10-28 14:30")
-
-        assert dt is not None
-        assert dt.year == 2025
-        assert dt.month == 10
-        assert dt.day == 28
-        assert dt.hour == 14
-        assert dt.minute == 30
-
-    def test_parse_absolute_date_invalid(self):
-        """Test parsing invalid date specification."""
-        section = DocumentSection(Path("/tmp/test.tex"))
-        dt = section._parse_absolute_date("not a date")
-
-        assert dt is None
-
-
-class TestIsValidGitRef:
-    """Test _is_valid_git_ref() validation."""
-
-    @pytest.fixture
-    def simple_git_repo(self):
-        """Create simple git repository."""
-        temp_dir = tempfile.mkdtemp(prefix="scitex_valid_ref_")
-        repo_path = Path(temp_dir)
-
-        subprocess.run(
-            ["git", "init"],
-            cwd=repo_path,
-            capture_output=True,
-            check=True,
-        )
-        subprocess.run(
-            ["git", "config", "user.email", "test@example.com"],
-            cwd=repo_path,
-            capture_output=True,
-            check=True,
-        )
-        subprocess.run(
-            ["git", "config", "user.name", "Test User"],
-            cwd=repo_path,
-            capture_output=True,
-            check=True,
-        )
-
-        test_file = repo_path / "test.tex"
-        test_file.write_text("Test\n")
-
-        subprocess.run(
-            ["git", "add", "test.tex"],
-            cwd=repo_path,
-            capture_output=True,
-            check=True,
-        )
-        subprocess.run(
-            ["git", "commit", "-m", "Initial"],
-            cwd=repo_path,
-            capture_output=True,
-            check=True,
-        )
-
-        yield test_file, repo_path
-
-        if repo_path.exists():
-            shutil.rmtree(repo_path)
-
-    def test_valid_ref_head(self, simple_git_repo):
-        """Test that HEAD is a valid reference."""
-        test_file, repo_path = simple_git_repo
-
-        section = DocumentSection(test_file, git_root=repo_path)
-        is_valid = section._is_valid_git_ref("HEAD")
-
-        assert is_valid is True
-
-    def test_invalid_ref_nonexistent(self, simple_git_repo):
-        """Test that nonexistent reference is invalid."""
-        test_file, repo_path = simple_git_repo
-
-        section = DocumentSection(test_file, git_root=repo_path)
-        is_valid = section._is_valid_git_ref("nonexistent_xyz")
-
-        assert is_valid is False
-
-
-if __name__ == "__main__":
-    pytest.main([__file__, "-v"])