pyeasyphd 0.3.3__tar.gz → 0.3.5__tar.gz

{pyeasyphd-0.3.3 → pyeasyphd-0.3.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyeasyphd
-Version: 0.3.3
+Version: 0.3.5
 Summary: pyeasyphd
 License: GPL-3.0-or-later
 License-File: LICENSE

{pyeasyphd-0.3.3 → pyeasyphd-0.3.5}/pyeasyphd/main/__init__.py

@@ -1,9 +1,3 @@
-"""Main module for PyEasyPhD core functionality.
-
-This module contains the core classes for processing academic papers,
-managing bibliographies, and converting between different formats.
-"""
-
 __all__ = ["BasicInput", "PandocMdTo", "PythonRunMd", "PythonRunTex"]
 
 from .basic_input import BasicInput

pyeasyphd-0.3.5/pyeasyphd/scripts/__init__.py

@@ -0,0 +1,13 @@
+__all__ = [
+    "run_article_md_daily_notes",
+    "run_article_tex_submit",
+    "run_beamer_tex_weekly_reports",
+    "run_search_for_screen",
+    "run_search_for_files",
+    "run_compare_after_search",
+]
+
+from .run_article_md import run_article_md_daily_notes
+from .run_article_tex import run_article_tex_submit
+from .run_beamer_tex import run_beamer_tex_weekly_reports
+from .run_search_keywords import run_compare_after_search, run_search_for_files, run_search_for_screen

pyeasyphd-0.3.5/pyeasyphd/scripts/run_search_keywords.py

@@ -0,0 +1,262 @@
+import os
+from typing import Any, Dict, List
+
+from pyadvtools import transform_to_data_list
+from pybibtexer.tools import compare_bibs_with_zotero
+
+from pyeasyphd.tools import Searchkeywords
+
+
+def run_search_for_screen(
+    acronym: str,
+    year: int,
+    title: str,
+    path_spidered_bibs: str,
+    path_spidering_bibs: str,
+    path_conferences_journals_json: str,
+) -> None:
+    """
+    Run search for screen display with specific conference/journal parameters.
+
+    Args:
+        acronym: Conference/journal acronym to search for
+        year: Publication year to filter by
+        title: Paper title used as search keyword
+        path_spidered_bibs: Path to spidered bibliography files
+        path_spidering_bibs: Path to spidering bibliography files
+        path_conferences_journals_json: Path to conferences/journals JSON files
+    """
+    # Expand and normalize file paths
+    path_spidered_bibs = _expand_path(path_spidered_bibs)
+    path_spidering_bibs = _expand_path(path_spidering_bibs)
+    path_conferences_journals_json = _expand_path(path_conferences_journals_json)
+
+    # Configure search options
+    options = _build_search_options(
+        print_on_screen=True,
+        search_year_list=[str(year)],
+        include_publisher_list=[],
+        include_abbr_list=[acronym],
+        exclude_publisher_list=["arXiv"],
+        exclude_abbr_list=[],
+        keywords_type="Temp",
+        keywords_list_list=[[title]],
+        path_conferences_journals_json=path_conferences_journals_json,
+    )
+
+    # Execute searches across different bibliography sources
+    _execute_searches(options, "", path_spidered_bibs, path_spidering_bibs)
+
+
+def run_search_for_files(
+    keywords_type: str,
+    keywords_list_list: List[List[str]],
+    path_main_output: str,
+    path_spidered_bibs: str,
+    path_spidering_bibs: str,
+    path_conferences_journals_json: str,
+) -> None:
+    """
+    Run search and save results to files with custom keywords.
+
+    Args:
+        keywords_type: Category name for the search keywords
+        keywords_list_list: Nested list of keywords to search for
+        path_main_output: Main output directory for search results
+        path_spidered_bibs: Path to spidered bibliography files
+        path_spidering_bibs: Path to spidering bibliography files
+        path_conferences_journals_json: Path to conferences/journals JSON files
+    """
+    # Expand and normalize file paths
+    path_main_output = _expand_path(path_main_output)
+    path_spidered_bibs = _expand_path(path_spidered_bibs)
+    path_spidering_bibs = _expand_path(path_spidering_bibs)
+    path_conferences_journals_json = _expand_path(path_conferences_journals_json)
+
+    # Configure search options
+    options = _build_search_options(
+        print_on_screen=False,
+        search_year_list=[],
+        include_publisher_list=[],
+        include_abbr_list=[],
+        exclude_publisher_list=["arXiv"],
+        exclude_abbr_list=[],
+        keywords_type=keywords_type,
+        keywords_list_list=keywords_list_list,
+        path_conferences_journals_json=path_conferences_journals_json,
+    )
+
+    # Execute searches across different bibliography sources
+    _execute_searches(options, path_main_output, path_spidered_bibs, path_spidering_bibs)
+
+
+def _expand_path(path: str) -> str:
+    """Expand user home directory and environment variables in path."""
+    return os.path.expandvars(os.path.expanduser(path))
+
+
+def _build_search_options(
+    print_on_screen: bool,
+    search_year_list: List[str],
+    include_publisher_list: List[str],
+    include_abbr_list: List[str],
+    exclude_publisher_list: List[str],
+    exclude_abbr_list: List[str],
+    keywords_type: str,
+    keywords_list_list: List[List[str]],
+    path_conferences_journals_json: str,
+) -> Dict[str, Any]:
+    """
+    Build search options dictionary with common configuration.
+
+    Args:
+        print_on_screen: Whether to display results on screen
+        search_year_list: List of years to filter search results
+        include_publisher_list: List of publishers to include
+        include_abbr_list: List of conference/journal abbreviations to include
+        exclude_publisher_list: List of publishers to exclude from search
+        exclude_abbr_list: List of conference/journal abbreviations to exclude from search
+        keywords_type: Category name for search keywords
+        keywords_list_list: Nested list of search keywords
+        path_conferences_journals_json: Base path for conferences/journals JSON files
+
+    Returns:
+        Dictionary containing configured search options
+    """
+    return {
+        "print_on_screen": print_on_screen,
+        "search_year_list": search_year_list,
+        "include_publisher_list": include_publisher_list,
+        "include_abbr_list": include_abbr_list,
+        "exclude_publisher_list": exclude_publisher_list,
+        "exclude_abbr_list": exclude_abbr_list,
+        "keywords_dict": {keywords_type: keywords_list_list},
+        "keywords_type_list": [keywords_type],
+        "full_json_c": os.path.join(path_conferences_journals_json, "conferences.json"),
+        "full_json_j": os.path.join(path_conferences_journals_json, "journals.json"),
+    }
+
+
+def _execute_searches(
+    options: Dict[str, Any], path_main_output: str, path_spidered_bibs: str, path_spidering_bibs: str
+) -> None:
+    """
+    Execute searches across different bibliography sources.
+
+    Args:
+        options: Search configuration options
+        path_main_output: Base path for search results output
+        path_spidered_bibs: Path to spidered bibliography files
+        path_spidering_bibs: Path to spidering bibliography files
+    """
+    # Search in spidered bibliographies (Conferences and Journals)
+    for cj in ["Conferences", "Journals"]:
+        path_storage = os.path.join(path_spidered_bibs, cj)
+        path_output = os.path.join(path_main_output, "Search_spidered_bib", cj)
+        Searchkeywords(path_storage, path_output, options).run()
+
+    # Search in spidering bibliographies (Journals and Journals Early Access)
+    for je in ["spider_j", "spider_j_e"]:
+        path_storage = os.path.join(path_spidering_bibs, je)
+        path_output = os.path.join(path_main_output, "Search_spidering_bib", je)
+        Searchkeywords(path_storage, path_output, options).run()
+
+
+def run_compare_after_search(
+    zotero_bib: str,
+    keywords_type: str,
+    path_main_output: str,
+    path_conferences_journals_json: str,
+):
+    """
+    Compare search results with Zotero bibliography and generate comparison report.
+
+    Args:
+        zotero_bib: Path to Zotero bibliography file
+        keywords_type: Category name for the search keywords used
+        path_main_output: Main output directory for search results and comparison
+        path_conferences_journals_json: Path to conferences/journals JSON files
+    """
+    # Expand and normalize file paths
+    zotero_bib = _expand_path(zotero_bib)
+    path_main_output = _expand_path(path_main_output)
+    path_conferences_journals_json = _expand_path(path_conferences_journals_json)
+
+    # Configure search options
+    options = _build_search_options(
+        print_on_screen=False,
+        search_year_list=[],
+        include_publisher_list=[],
+        include_abbr_list=[],
+        exclude_publisher_list=["arXiv"],
+        exclude_abbr_list=[],
+        keywords_type=keywords_type,
+        keywords_list_list=[],
+        path_conferences_journals_json=path_conferences_journals_json,
+    )
+
+    # Download bibliography files from local search results
+    download_bib = _download_bib_from_local(path_main_output, keywords_type)
+
+    # Generate comparison output path and run comparison
+    path_output = os.path.join(path_main_output, "comparison_new")
+    compare_bibs_with_zotero(zotero_bib, download_bib, path_output, options)
+
+    return None
+
+
+def _generate_data_list(path_output: str, folder_name: str, keywords_type: str) -> list[str]:
+    """
+    Extract bibliography data content from files in specified folder structure.
+
+    Args:
+        path_output: Base output path for search results
+        folder_name: Specific folder name within the output structure
+        keywords_type: Category name for the search keywords used
+
+    Returns:
+        List of bibliography data content extracted from .bib files in the specified folders
+    """
+    data_list = []
+
+    # Extract data from both title and abstract bibliography folders
+    for bib_type in ["title-bib-zotero", "abstract-bib-zotero"]:
+        folder_path = os.path.join(
+            path_output,
+            f"{folder_name}-Separate",
+            "article",
+            keywords_type,
+            bib_type
+        )
+
+        # Extract bibliography data content if folder exists
+        if os.path.exists(folder_path):
+            data_list.extend(transform_to_data_list(folder_path, ".bib"))
+
+    return data_list
+
+
+def _download_bib_from_local(path_output: str, keywords_type: str) -> list[str]:
+    """
+    Collect bibliography data content from all local search result directories.
+
+    Args:
+        path_output: Base output path containing search results
+        keywords_type: Category name for the search keywords used
+
+    Returns:
+        Combined list of bibliography data content from all .bib files in search results
+    """
+    data_list = []
+
+    # Collect data from spidered bibliographies (Conferences and Journals)
+    for cj in ["Conferences", "Journals"]:
+        folder_name = os.path.join("Search_spidered_bib", cj)
+        data_list.extend(_generate_data_list(path_output, folder_name, keywords_type))
+
+    # Collect data from spidering bibliographies (journal sources)
+    for je in ["spider_j", "spider_j_e"]:
+        folder_name = os.path.join("Search_spidering_bib", je)
+        data_list.extend(_generate_data_list(path_output, folder_name, keywords_type))
+
+    return data_list

{pyeasyphd-0.3.3 → pyeasyphd-0.3.5}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pyeasyphd"
-version = "0.3.3"
+version = "0.3.5"
 description = "pyeasyphd"
 license = "GPL-3.0-or-later"
 authors = ["NextAI <nextartifintell@gmail.com>"]