change parser, fix bugs

.github/workflows/bib2readme.py

@@ -1,90 +1,151 @@
 from collections import defaultdict
 from typing import Dict, List
 
-import bibtexparser
+from pybtex.database import parse_file
+from pybtex.scanner import PybtexSyntaxError
+from pylatexenc.latex2text import LatexNodes2Text
 
 # Define the categories to be printed in the README
 VALID_CATEGORIES = ["overview", "software", "paper", "uncategorized"]
 
-README_HEADER = """
+README_INTRO = """
 Welcome to the Awesome Amortized Inference repository!
 This is a curated list of resources, including overviews, software, papers, and other resources related to amortized inference.
 Feel free to explore the entries below and use the provided BibTeX information for citation purposes.
-Contributioons always welcome, this shall be a community-driven project.
-Contribution guide will follow ASAP.
+Contributions are always welcome, this is a community-driven project.
 """
 
 
 # Define Entry class
 class Entry:
-    def __init__(self, title: str, authors: str, url: str, category: str, bibtex: str):
+    def __init__(
+        self,
+        title: str,
+        authors: str,
+        url: str,
+        category: str,
+        awesome_fields: Dict[str, str],
+        bibtex: str,
+    ):
         self.title = title
         self.authors = authors
         self.url = url
         self.category = category
+        self.awesome_fields = awesome_fields
         self.bibtex = bibtex
 
     @classmethod
-    def from_bibtex(cls, entry: dict) -> "Entry":
-        title = entry.get("title", "No title").replace("{", "").replace("}", "")
-        authors = entry.get("author", "No author").replace(" and ", ", ")
-        url = entry.get("url", "")
-        category = entry.get("category", "uncategorized").lower()
+    def from_bibtex(cls, entry) -> "Entry":
+        title = entry.fields.get("title", "No title").replace("{", "").replace("}", "")
+        authors = (
+            ", ".join(
+                cls.person_to_first_last(person)
+                for person in entry.persons.get("author", [])
+            )
+            or "No author"
+        )
+        url = entry.fields.get("url", "")
+        category = entry.fields.get("category", "uncategorized").lower()
+
+        # get all fields that start with 'awesome-' and save them in a separate field
+        awesome_fields = {
+            key[len("awesome-") :]: value
+            for key, value in entry.fields.items()
+            if key.startswith("awesome-")
+        }
+
+        if category not in VALID_CATEGORIES:
+            print(
+                f"Warning: Unrecognized category '{category}' for entry '{title}'. Categorizing as 'uncategorized'."
+            )
+            category = "uncategorized"
         bibtex = cls.format_bibtex(entry)
-        return cls(title, authors, url, category, bibtex)
+        return cls(title, authors, url, category, awesome_fields, bibtex)
+
+    @staticmethod
+    def person_to_first_last(person) -> str:
+        name_parts = [
+            " ".join(part)
+            for part in [
+                person.first_names,
+                person.middle_names,
+                person.prelast_names,
+                person.last_names,
+                person.lineage_names,
+            ]
+            if part
+        ]
+        name = " ".join(name_parts)
+
+        return LatexNodes2Text().latex_to_text(name)
 
     @staticmethod
-    def format_bibtex(entry: dict) -> str:
-        bibtex_type = entry.get("ENTRYTYPE", "misc")
-        bibtex_key = entry.get("ID", "unknown")
+    def format_bibtex(entry) -> str:
+        bibtex_type = entry.type if entry.type else "misc"
+        bibtex_key = entry.key if entry.key else "unknown"
         bibtex_fields = [
-            f"  {key} = {{{value}}}"
-            for key, value in entry.items()
-            if key not in ["ENTRYTYPE", "ID"]
+            f"{key} = {{{value}}}"
+            for key, value in entry.fields.items()
+            if not key.startswith("awesome-")  # exclude awesome fields from BibTeX
         ]
+        if "author" in entry.persons:
+            bibtex_fields.append(
+                f"author = {{{' and '.join(str(person) for person in entry.persons.get('author', []))}}}"
+            )
         bibtex_str = (
-            f"@{bibtex_type}{{{bibtex_key},\n  " + ",\n  ".join(bibtex_fields) + "\n}"
+            f"@{bibtex_type}{{{bibtex_key},\n  " + ",\n  ".join(bibtex_fields) + "\n}"
         )
         return bibtex_str
 
     def to_string(self) -> str:
-        entry_str = f"- **{self.title}**. {self.authors}."
-        if self.url:
-            entry_str += f"  [[Link]]({self.url})"
-        entry_str += f"  <details><summary>Show BibTeX</summary><pre><code>{self.bibtex}</code></pre></details>"
-        entry_str += "\n"
+        entry_str = f"- **{self.title}**."
+        if self.awesome_fields:
+            entry_str += " "
+            for key, value in self.awesome_fields.items():
+                entry_str += f"[[{key.capitalize()}]]({value}) "
+        entry_str += f"<br />  {self.authors}"
+        entry_str += f"""
+  <details>
+  <summary>Show BibTeX</summary>
+  <pre><code>
+  {self.bibtex}
+  </code>
+  </pre></details>
+"""
+        # entry_str += "<br />"
         return entry_str
 
 
 def organize_entries(bib_database) -> Dict[str, List[Entry]]:
     entries_by_category: Dict[str, List[Entry]] = defaultdict(list)
-    for entry in bib_database.entries:
+    for entry_key, entry in bib_database.entries.items():
         entry_obj = Entry.from_bibtex(entry)
         entries_by_category[entry_obj.category].append(entry_obj)
     return entries_by_category
 
 
 def create_readme(entries_by_category: Dict[str, List[Entry]]) -> str:
     readme_content = "# Awesome Amortized Inference\n\n"
-    readme_content += README_HEADER
+    readme_content += README_INTRO
 
     for category in VALID_CATEGORIES:
         if category in entries_by_category:
             readme_content += f"## {category.capitalize()}\n\n"
             readme_content += "\n".join(
                 [entry.to_string() for entry in entries_by_category[category]]
             )
-            readme_content += "\n"
     return readme_content
 
 
 def main():
     try:
-        with open("data.bib") as bibtex_file:
-            bib_database = bibtexparser.load(bibtex_file)
+        bib_database = parse_file("data.bib")
     except FileNotFoundError:
         print("The data.bib file was not found.")
         exit(1)
+    except PybtexSyntaxError as e:
+        print(f"Error parsing BibTeX file: {e}")
+        exit(1)
 
     entries_by_category = organize_entries(bib_database)
     readme_content = create_readme(entries_by_category)

.github/workflows/generate_readme_from_bib.yml

@@ -25,7 +25,7 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install bibtexparser
+          pip install pybtex pylatexenc
 
       # Step 4: Run the script to generate README.md
       - name: Run README generation script