bib_optimizer 0.5.1__py3-none-any.whl

bib_optimizer/__init__.py

@@ -0,0 +1,2 @@
+# Version
+__version__ = "0.5.1"

bib_optimizer/__main__.py

@@ -0,0 +1,23 @@
+"""Version:
+--------
+
+- bib_optimizer v0.5.1
+"""
+import sys
+from bib_optimizer import helpers
+
+def main():
+    if len(sys.argv[1:]) != 3:
+        raise Exception("Sorry, please input three files: your tex filename, bib filename, and the desired new bib filename")
+    tex = sys.argv[1:][0]
+    old_bib = sys.argv[1:][1]
+    new_bib = sys.argv[1:][2]
+
+    helpers.bib_opt(tex, old_bib, new_bib)
+
+
+
+if __name__ == '__main__':
+	main()
+
+

bib_optimizer/helpers.py

@@ -0,0 +1,74 @@
+import bibtexparser
+import re
+from bibtexparser.bwriter import BibTexWriter
+
+def _augment_func(filecontent, all_keys, temp_citations):
+    for e in re.findall(r'\\cite[tp]?\{([^}]+)\}', filecontent):
+        for c in e.split(','):  
+            c = c.strip()
+            if c not in temp_citations:
+                all_keys.append(c)
+                temp_citations.add(c)
+                
+    return all_keys, temp_citations
+                
+def bib_opt(filename, input_bib, output_bib):
+    with open(filename, 'r', encoding='utf-8') as file:
+        lines = file.readlines()
+    filtered_lines = [line for line in lines if not line.lstrip().startswith('%')]
+    filecontent = ''.join(filtered_lines)
+    
+    with open(input_bib, 'r', encoding='utf-8') as bibfile:
+        bib_database = bibtexparser.load(bibfile)
+
+    allowed_keys = []
+    all_keys = []
+    temp_citations = set()
+    
+    split_pattern = r'(.*?)(\\(?:input|include)[^\n]*\n)(.*?)((?=\\(?:input|include))|\Z)'
+    matches = re.findall(split_pattern, filecontent, flags=re.DOTALL)
+    split_results = [(before, after.strip()) for before, input_line, after, _ in matches]
+    
+    input_pattern_extended = r'\\(?:input|include)\s*(?:{([^}]+)}|([^\s\n]+))'
+    matches = re.findall(input_pattern_extended, filecontent)
+    input_files_extended = [m[0] if m[0] else m[1] for m in matches]    
+
+    if not split_results:
+        all_keys, temp_citations = _augment_func(filecontent, all_keys, temp_citations)
+    else:
+        for split_result, input_file_extended in zip(split_results, input_files_extended):
+            all_keys, temp_citations = _augment_func(split_result[0], all_keys, temp_citations)
+            
+            if ".tex" not in input_file_extended:
+                input_file_extended += ".tex"
+            
+            try:
+                with open(input_file_extended, 'r', encoding='utf-8') as file:
+                    _lines = file.readlines()
+
+                _filtered_lines = [line for line in _lines if not line.lstrip().startswith('%')]
+                _filecontent = ''.join(_filtered_lines)     
+
+                all_keys, temp_citations = _augment_func(_filecontent, all_keys, temp_citations)
+            except Exception as e:
+                print(f'{e}, skipped.')
+
+            all_keys, temp_citations = _augment_func(split_result[1], all_keys, temp_citations)
+
+    for k in all_keys:
+        allowed_keys.append(k)
+    
+    entry_dict = {entry.get('ID'): entry for entry in bib_database.entries}
+    filtered_entries = [entry_dict[key] for key in allowed_keys if key in entry_dict]
+
+    writer = BibTexWriter()
+    writer.indent = '    '  
+    writer.order_entries_by = None  
+
+    new_bib_database = bibtexparser.bibdatabase.BibDatabase()
+    new_bib_database.entries = filtered_entries
+
+    with open(output_bib, 'w', encoding='utf-8') as bibfile:
+        bibfile.write(writer.write(new_bib_database))
+
+    print(f'successfully created {output_bib}')

bib_optimizer-0.5.1.dist-info/METADATA

@@ -0,0 +1,226 @@
+Metadata-Version: 2.4
+Name: bib_optimizer
+Version: 0.5.1
+Summary: Clean and optimize bib file.
+Author-email: Ka Wa Yip <yipkawa@gmail.com>
+License: MIT License
+        
+        Copyright (c) 2025 Ka Wa Yip
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy
+        of this software and associated documentation files (the "Software"), to deal
+        in the Software without restriction, including without limitation the rights
+        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+        copies of the Software, and to permit persons to whom the Software is
+        furnished to do so, subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in all
+        copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+        SOFTWARE.
+        
+Project-URL: Homepage, https://github.com/kwyip/bib_optimizer
+Project-URL: Issues, https://github.com/kwyip/bib_optimizer/issues
+Keywords: latex,bib,bibliography
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: bibtexparser<2,>=1.4.3
+Provides-Extra: build
+Requires-Dist: build; extra == "build"
+Requires-Dist: twine; extra == "build"
+Provides-Extra: dev
+Requires-Dist: black; extra == "dev"
+Requires-Dist: bumpver; extra == "dev"
+Requires-Dist: isort; extra == "dev"
+Requires-Dist: mypy; extra == "dev"
+Requires-Dist: pytest; extra == "dev"
+Dynamic: license-file
+
+  <figure>
+    <img src="https://github.com/kwyip/bib_optimizer/blob/main/logo.png?raw=True" alt="logo" height="143" />
+    <!-- <figcaption>An elephant at sunset</figcaption> -->
+  </figure>
+
+[![](https://img.shields.io/badge/License-MIT-blue.svg)](https://github.com/kwyip/bib_optimizer/blob/main/LICENSE)
+[![PyPI - Python Version](https://img.shields.io/pypi/pyversions/bib_optimizer)](https://pypi.org/project/bib-optimizer/)
+[![Static Badge](https://img.shields.io/badge/CalVer-2025.0416-ff5733)](https://pypi.org/project/bib-optimizer)
+[![Static Badge](https://img.shields.io/badge/PyPI-wheels-d8d805)](https://pypi.org/project/bib-optimizer/#files)
+[![](https://pepy.tech/badge/bib_optimizer/month)](https://pepy.tech/project/bib_optimizer)
+
+[bib-optimizer](https://bibopt.github.io/)
+==========================================
+
+Oh, sure, because who doesn't love manually cleaning up messy `.bib` files? `bib_optimizer.py` heroically steps in to remove those lazy, _unused_ citations and _reorder_ the survivors exactly as they appear in the `.tex` file—because, clearly, chaos is the default setting for bibliographies.
+
+In layman's terms, it automates bibliography management by:
+
+1.  removing unused citations,
+2.  reordering the remaining ones to match their order of appearance in the `.tex` file.
+
+**Input Files:**
+
+*   `main.tex` – The LaTeX source file.
+*   `ref.bib` – The original bibliography file.
+
+These input files will **remain unchanged**.
+
+**Output File:**
+
+*   `ref_opt.bib` – A placeholder filename for the newly generated, cleaned, and ordered bibliography file.
+
+* * *
+
+Installation
+------------
+
+### Install from PyPI with pip
+
+Create and activate a virtual environment, then install the latest release from PyPI:
+
+```bash
+python -m venv .venv
+
+# Linux/macOS
+source .venv/bin/activate
+
+# Windows
+.venv\Scripts\activate
+
+python -m pip install --upgrade bib_optimizer
+```
+
+Alternatively, install the command in an isolated environment with [uv](https://docs.astral.sh/uv/):
+
+```bash
+uv tool install bib_optimizer
+```
+
+After either installation method, the `bibopt` command is available in your terminal.
+
+### Install from source for development
+
+This repository uses uv for project and dependency management.
+
+1. **Clone the repository**
+
+   ```bash
+   git clone https://github.com/kwyip/bib_optimizer.git
+   cd bib_optimizer
+   ```
+
+2. **Install environment**
+
+   ```bash
+   # This creates the virtual environment and installs all dependencies
+   uv sync
+   ```
+
+3. **Activate environment**
+
+   ```bash
+   # Linux/MacOS
+   source .venv/bin/activate
+
+   # Windows
+   .venv\Scripts\activate
+   ```
+
+_🐍 This requires Python 3.8 or newer versions_
+
+* * *
+
+### Steps to Clean Your Bibliography
+
+1.  **Prepare the input files (e.g., by downloading them from Overleaf)**.
+2.  **Run the command to generate a new `.bib` file (for example, you may name it `ref_opt.bib`)**:  
+      
+    
+           `bibopt main.tex ref.bib ref_opt.bib`
+    
+      
+    
+3.  **Use the Cleaned Bibliography**  
+    Replace `ref.bib` with `ref_opt.bib` in your LaTeX project.
+
+* * *
+
+### Test
+
+You may test the installation using the sample input files (`sample_main.tex` and `sample_ref.bib`) located in the test folder.
+
+<img src="https://github.com/kwyip/bib_optimizer/blob/main/sample_main_shot.png?raw=True" alt="sample_main_shot"  width="34.83%"/>&nbsp;&nbsp;<img src="https://github.com/kwyip/bib_optimizer/blob/main/sample_ref_shot.png?raw=True" alt="sample_ref_shot" width="43%" />
+
+`sample_main.tex` _and_ `sample_ref.bib`
+
+<img src="https://github.com/kwyip/bib_optimizer/blob/main/sample_ref_opt_shot.png?raw=True" alt="sample_ref_opt_shot" width="43%" />
+
+_A sample_ `ref_opt.bib` _created after running_ `bibopt sample_main.tex sample_ref.bib ref_opt.bib`
+
+* * *
+
+## Code-free use with an AI agent
+
+[**Download `SKILL.md`**](./SKILL.md), then upload these files to your AI agent:
+
+- `SKILL.md`,
+- the root `.tex` file,
+- the source `.bib` file, and if any:
+- every `.tex` file referenced through `\input` or `\include`.
+
+> [!TIP]
+> Use this prompt:
+>
+> ```text
+> Use the attached `SKILL.md` to optimize the attached LaTeX and BibTeX files.
+> Return only the optimized `.bib` file.
+> ```
+
+
+https://github.com/user-attachments/assets/2b4e3224-2aee-44c1-974c-812dead72e2f
+
+
+* * *
+
+#### New feature (version 0.4.0)
+
+If the `main.tex` calls inputs from other `.tex` (e.g., with `\input{...}`), the newly generated `ref_opt.bib` will preserve the order of appearances in the `main.tex` with each inputted `.tex` as well. \
+(The dependent `.tex` files need to be placed in the same directory as `main.tex`.)
+
+---
+#### New feature (version 0.4.1)
+
+On top of version 0.4, skip any `\input` `.tex` file if not found.
+
+---
+#### New feature/Fix (version 0.4.2)
+
+Added support for the `\include{...}` command in addition to `\input{...}`, fixing missing citations when a LaTeX project uses `\include` to split its content across files.
+
+---
+#### New feature/Fix (version 0.4.3)
+
+Added Python 3.14 support and constrained `bibtexparser` to the compatible 1.x release series, fixing `ModuleNotFoundError: No module named 'bibtexparser.bwriter'` during fresh installations.
+
+---
+#### New feature/Fix (version 0.5.0)
+
+Add code-free SKILL.md
+
+♥ Lastly executed on Python `3.14` on 2026-09-29.

bib_optimizer-0.5.1.dist-info/RECORD

@@ -0,0 +1,9 @@
+bib_optimizer/__init__.py,sha256=wtNuHruEXNf66l6yJfYsYwiI1zbxaXAilx4ETNB75lw,32
+bib_optimizer/__main__.py,sha256=acTU0Czt3QFrYU-JuyyJiZEtcMAIxKEd0WEAR4dtAh0,434
+bib_optimizer/helpers.py,sha256=ml0MjhFj51T_Bjk6322Bx21KobsAI34p64fEPPOLhbo,2957
+bib_optimizer-0.5.1.dist-info/licenses/LICENSE,sha256=IzsoHjUTsM_-99MnVs-R6ndlOzyOUAMKUsPWymFOE9A,1066
+bib_optimizer-0.5.1.dist-info/METADATA,sha256=2XsLNeiuO5a5L5Louz6R9TVR9j46zh_cxgYuctoXPaU,7805
+bib_optimizer-0.5.1.dist-info/WHEEL,sha256=aeYiig01lYGDzBgS8HxWXOg3uV61G9ijOsup-k9o1sk,91
+bib_optimizer-0.5.1.dist-info/entry_points.txt,sha256=Dm0EpcwsJZNNfhnn9LYI43WLzVlgEtNFVIFL4oCSPlc,55
+bib_optimizer-0.5.1.dist-info/top_level.txt,sha256=j4x4ncmbt2X7sqnKYX_CbakLJt7NZgWLBIP1PzY8Qog,14
+bib_optimizer-0.5.1.dist-info/RECORD,,

bib_optimizer-0.5.1.dist-info/WHEEL

@@ -0,0 +1,5 @@
+Wheel-Version: 1.0
+Generator: setuptools (82.0.1)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

bib_optimizer-0.5.1.dist-info/entry_points.txt

@@ -0,0 +1,2 @@
+[console_scripts]
+bibopt = bib_optimizer.__main__:main

bib_optimizer-0.5.1.dist-info/licenses/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2025 Ka Wa Yip
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

bib_optimizer-0.5.1.dist-info/top_level.txt

@@ -0,0 +1 @@
+bib_optimizer