pyeasyphd 0.4.1__tar.gz → 0.4.3__tar.gz

{pyeasyphd-0.4.1 → pyeasyphd-0.4.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyeasyphd
-Version: 0.4.1
+Version: 0.4.3
 Summary: pyeasyphd
 License: GPL-3.0-or-later
 License-File: LICENSE

{pyeasyphd-0.4.1 → pyeasyphd-0.4.3}/pyeasyphd/main/pandoc_md_to.py

@@ -34,6 +34,7 @@ class PandocMdTo(BasicInput):
         add_anchor_for_basic_dict (bool): Whether to add anchor for items in basic dict. Defaults to False.
         add_anchor_for_beauty_dict (bool): Whether to add anchor for items in beauty dict. Defaults to False.
         add_anchor_for_complex_dict (bool): Whether to add anchor for items in complex dict. Defaults to False.
+        details_to_bib_separator (str): Separator between <details> and bibliography content. Defaults to "\n".
     """
 
     def __init__(self, options: dict) -> None:
@@ -59,6 +60,8 @@ class PandocMdTo(BasicInput):
         self.add_anchor_for_beauty_dict: bool = options.get("add_anchor_for_beauty_dict", False)
         self.add_anchor_for_complex_dict: bool = options.get("add_anchor_for_complex_dict", False)
 
+        self.details_to_bib_separator: str = options.get("details_to_bib_separator", "\n")
+
     def pandoc_md_to_md(
         self, path_bib: str, path_md_one: str, path_md_two: str, name_md_one: Optional[str], name_md_two: Optional[str]
     ) -> List[str]:
@@ -296,7 +299,7 @@ class PandocMdTo(BasicInput):
         self, key_url_http_bib_dict: Dict[str, List[List[str]]], key_reference_dict: Dict[str, list]
     ) -> Tuple[Dict[str, List[str]], Dict[str, List[str]], Dict[str, List[str]]]:
         """Generate."""
-        header_list = ["<details>\n", "```\n"]
+        header_list = [f"<details>{self.details_to_bib_separator}", "```\n"]
         tail_list = ["```\n", "</details>\n"]
 
         key_basic_dict: Dict[str, List[str]] = {}

{pyeasyphd-0.4.1 → pyeasyphd-0.4.3}/pyeasyphd/main/python_run_md.py

@@ -20,24 +20,24 @@ def batch_convert_citations(text):
     Example: [@ref1; @ref2] -> <sup>[@ref1](#ref1)</sup><sup>[@ref2](#ref2)</sup>
     """
     # Match all citation patterns within square brackets
-    pattern = r'\[([^]]+)\]'
+    pattern = r"\[([^]]+)\]"
 
     def process_citation(match):
         citations = match.group(1)
         # Split multiple citations (support semicolon or comma separation)
-        citation_list = re.split(r'[;,]', citations)
+        citation_list = re.split(r"[;,]", citations)
 
         result = []
         for citation in citation_list:
             citation = citation.strip()
-            if citation.startswith('@'):
+            if citation.startswith("@"):
                 cite_id = citation[1:]  # Remove the @ symbol
-                result.append(f'[{citation}](#{cite_id.lower()})')
+                result.append(f"[{citation}](#{cite_id.lower()})")
             else:
                 # Keep non-citation content in original format
-                result.append(f'[{citation}]')
+                result.append(f"[{citation}]")
 
-        return ''.join(result)
+        return "".join(result)
 
     return re.sub(pattern, process_citation, text)
 
@@ -56,6 +56,7 @@ class PythonRunMd(BasicInput):
         replace_by_basic_beauty_complex_in_md (str): Replace by basic, beauty, or complex format. Defaults to "beauty".
         display_basic_beauty_complex_references_in_md (str): Display basic, beauty, or complex references. Defaults to "beauty".
         add_anchor_in_md (bool): Whether add anchor in markdown. Defaults to False.
+        details_to_bib_separator (str): Separator between <details> and bibliography content. Defaults to "\n".
     """
 
     def __init__(self, options: Dict[str, Any]) -> None:
@@ -77,6 +78,7 @@ class PythonRunMd(BasicInput):
             "display_basic_beauty_complex_references_in_md", "beauty"
         )
         self.add_anchor_in_md: bool = options.get("add_anchor_in_md", False)
+        self.details_to_bib_separator: str = options.get("details_to_bib_separator", "\n")
 
         # for md
         self._pandoc_md_to = PandocMdTo(self.options)
@@ -262,11 +264,11 @@ class PythonRunMd(BasicInput):
                 bib_in_md = combine_content_in_list(
                     [
                         ["## Bibliography\n\n"],
-                        ["<details>\n<summary>Bibliography</summary>\n\n"],
+                        [f"<details>{self.details_to_bib_separator}"],
                         ["```\n"],
                         temp_c,
                         ["```\n"],
-                        ["</details>\n"]
+                        ["</details>\n"],
                     ]
                 )
 

{pyeasyphd-0.4.1 → pyeasyphd-0.4.3}/pyeasyphd/pyeasyphd.sublime-settings

@@ -16,6 +16,8 @@
     "add_anchor_for_beauty_dict": false,
     // true, false
     "add_anchor_for_complex_dict": false,
+    // "\n" or "\n\n"
+    "details_to_bib_separator": "\n",
 
     // for md file
     // pyeasyphd/main/python_run_md.py
@@ -35,6 +37,8 @@
     "display_basic_beauty_complex_references_in_md": "beauty",
     // true, false
     "add_anchor_in_md": false,
+    // "\n" or "\n\n"
+    // "details_to_bib_separator": "\n",
 
     // for tex file
     // pyeasyphd/main/python_run_tex.py

{pyeasyphd-0.4.1 → pyeasyphd-0.4.3}/pyeasyphd/scripts/__init__.py

@@ -15,7 +15,7 @@ __all__ = [
     "run_compare_bib_with_zotero",
     "run_format_bib_to_save_by_entry_type",
     "run_format_bib_to_abbr_zotero_save",
-    "run_replace_to_standard_cite_keys"
+    "run_replace_to_standard_cite_keys",
 ]
 
 from .run_article_md import run_article_md_daily_notes

{pyeasyphd-0.4.1 → pyeasyphd-0.4.3}/pyeasyphd/scripts/run_article_md.py

@@ -9,7 +9,7 @@ def run_article_md_daily_notes(
     path_output_file: str,
     bib_path_or_file: str,
     path_conf_j_jsons: str,
-    options: dict
+    options: dict,
 ) -> None:
     """
     Run article markdown daily notes processing pipeline.
@@ -32,13 +32,11 @@ def run_article_md_daily_notes(
     _options = {
         "full_json_c": os.path.expanduser(os.path.join(path_conf_j_jsons, "conferences.json")),
         "full_json_j": os.path.expanduser(os.path.join(path_conf_j_jsons, "journals.json")),
-
         # figure options
         "includegraphics_figs_directory": "",
         "shutil_includegraphics_figs": False,
         "includegraphics_figs_in_relative_path": True,
         "figure_folder_name": "figs",  # "" or "figs" or "main"
-
         # bib options
         "abbr_index_article_for_abbr": 1,  # 0, 1, 2
         "abbr_index_inproceedings_for_abbr": 2,  # 0, 1, 2
@@ -48,34 +46,29 @@ def run_article_md_daily_notes(
         "bib_for_abbr_name": "abbr.bib",
         "bib_for_zotero_name": "zotero.bib",
         "bib_for_save_name": "save.bib",
-
         "bib_folder_name": "bibs",  # "" or "bib" or "bibs" or "main"
         "delete_original_bib_in_output_folder": True,  # default is False
         "bib_path_or_file": os.path.expanduser(bib_path_or_file),
-
         # tex options
         "handly_preamble": False,
         "final_output_main_tex_name": "main.tex",
         "run_latex": False,
         "delete_run_latex_cache": False,
-
         "input_texs_directory": "",
         "shutil_input_texs": False,  # True or False
         "input_texs_in_relative_path": True,
         "tex_folder_name": "texs",  # "" or "tex" or "texs" or "main"
         "delete_original_tex_in_output_folder": True,  # default is False
         "generate_tex": False,
-
         # md options
         # ["www", "google", "connected", "scite"]
         "display_www_google_connected_scite": ["google", "connected"],  # python_writers.py
-
         "join_flag_in_http": " | ",  # default is " | " or " |\n"
         "add_url_for_basic_dict": False,  # default is True
         "add_anchor_for_basic_dict": True,  # default is False
         "add_anchor_for_beauty_dict": False,  # default is False
         "add_anchor_for_complex_dict": False,  # default is False
-
+        "details_to_bib_separator": "\n\n",  # defulat is "\n"
         "final_output_main_md_name": "main.md",
         "delete_temp_generate_md": True,
         "add_reference_in_md": True,
@@ -84,10 +77,8 @@ def run_article_md_daily_notes(
         "replace_by_basic_beauty_complex_in_md": "beauty",  # default is "basic"
         "display_basic_beauty_complex_references_in_md": "basic",  # default is "beauty"
         "add_anchor_in_md": True,  # default is False
-
         "md_folder_name": "mds",  # "" or "md" or "main"
         "delete_original_md_in_output_folder": True,  # default is False
-
         # html options
         "generate_html": False,
     }
@@ -100,10 +91,7 @@ def run_article_md_daily_notes(
 
     # Generate output filenames based on input directory name (platform-independent)
     dir_name = os.path.basename(os.path.dirname(file_list[0]))
-    _options.update({
-        "final_output_main_tex_name": f"{dir_name}.tex",
-        "final_output_main_md_name": f"{dir_name}.md"
-    })
+    _options.update({"final_output_main_tex_name": f"{dir_name}.tex", "final_output_main_md_name": f"{dir_name}.md"})
 
     PyRunBibMdTex(path_output_file, ".md", "paper", _options).run_files(file_list, "", "current")
 

{pyeasyphd-0.4.1 → pyeasyphd-0.4.3}/pyeasyphd/scripts/run_article_tex.py

@@ -11,7 +11,7 @@ def run_article_tex_submit(
     path_output_file: str,
     bib_path_or_file: str,
     path_conf_j_jsons: str,
-    options: dict
+    options: dict,
 ) -> None:
     """
     Process academic article files (TeX, and bibliography) with automated Git version control.
@@ -39,13 +39,11 @@ def run_article_tex_submit(
     _options = {
         "full_json_c": os.path.expanduser(os.path.join(path_conf_j_jsons, "conferences.json")),
         "full_json_j": os.path.expanduser(os.path.join(path_conf_j_jsons, "journals.json")),
-
         # figure options
         "includegraphics_figs_directory": os.path.join(path_input_file, "data", "raw"),
         "shutil_includegraphics_figs": True,
         "includegraphics_figs_in_relative_path": True,
         "figure_folder_name": "figs",  # "" or "figs" or "main"
-
         # bib options
         "abbr_index_article_for_abbr": 1,  # 0, 1, 2
         "abbr_index_inproceedings_for_abbr": 0,  # 0, 1, 2
@@ -56,24 +54,20 @@ def run_article_tex_submit(
         "bib_for_zotero_name": "zotero.bib",
         "bib_for_save_name": "save.bib",
         "display_google_connected_scite": ["google", "connected", "scite"],
-
         "bib_folder_name": "bibs",  # "" or "bib" or "bibs" or "main"
         "delete_original_bib_in_output_folder": False,
         "bib_path_or_file": os.path.expanduser(bib_path_or_file),
-
         # tex options
         "handly_preamble": True,
         "final_output_main_tex_name": "main.tex",
         "run_latex": False,
         "delete_run_latex_cache": False,
-
         "input_texs_directory": os.path.join(path_input_file, "data", "raw"),
         "shutil_input_texs": True,
         "input_texs_in_relative_path": True,
         "tex_folder_name": "texs",  # "" or "tex" or "texs" or "main"
         "delete_original_tex_in_output_folder": True,
         "generate_tex": True,
-
         # html options
         "generate_html": False,
     }

{pyeasyphd-0.4.1 → pyeasyphd-0.4.3}/pyeasyphd/scripts/run_beamer_tex.py

@@ -9,7 +9,7 @@ def run_beamer_tex_weekly_reports(
     path_output_file: str,
     bib_path_or_file: str,
     path_conf_j_jsons: str,
-    options: dict
+    options: dict,
 ) -> None:
     """
     Process academic article files (TeX, and bibliography) with automated Git version control.
@@ -37,13 +37,11 @@ def run_beamer_tex_weekly_reports(
     _options = {
         "full_json_c": os.path.expanduser(os.path.join(path_conf_j_jsons, "conferences.json")),
         "full_json_j": os.path.expanduser(os.path.join(path_conf_j_jsons, "journals.json")),
-
         # figure options
         "includegraphics_figs_directory": "",
         "shutil_includegraphics_figs": True,
         "includegraphics_figs_in_relative_path": True,
         "figure_folder_name": "figs",  # "" or "figs" or "main"
-
         # bib options
         "abbr_index_article_for_abbr": 1,  # 0, 1, 2
         "abbr_index_inproceedings_for_abbr": 0,  # 0, 1, 2
@@ -54,24 +52,20 @@ def run_beamer_tex_weekly_reports(
         "bib_for_zotero_name": "zotero.bib",
         "bib_for_save_name": "save.bib",
         "display_google_connected_scite": ["google", "connected", "scite"],
-
         "bib_folder_name": "bibs",  # "" or "bib" or "bibs" or "main"
         "delete_original_bib_in_output_folder": False,
         "bib_path_or_file": os.path.expanduser(bib_path_or_file),
-
         # tex options
         "handly_preamble": True,
         "final_output_main_tex_name": "main.tex",
         "run_latex": False,
         "delete_run_latex_cache": False,
-
         "input_texs_directory": "",
         "shutil_input_texs": False,  # default is True
         "input_texs_in_relative_path": True,
         "tex_folder_name": "texs",  # "" or "tex" or "texs" or "main"
         "delete_original_tex_in_output_folder": True,  # default is False
         "generate_tex": True,
-
         # html options
         "generate_html": False,
     }

{pyeasyphd-0.4.1 → pyeasyphd-0.4.3}/pyeasyphd/scripts/run_compare.py

@@ -44,11 +44,7 @@ def run_compare_bib_with_local(
 
 
 def run_compare_bib_with_zotero(
-    options: dict,
-    need_compare_bib: str,
-    zotero_bib: str,
-    path_output: str,
-    path_conf_j_jsons: str,
+    options: dict, need_compare_bib: str, zotero_bib: str, path_output: str, path_conf_j_jsons: str
 ) -> None:
     """
     Compare a target bibliography file with Zotero bibliography data and generate comparison results.
@@ -67,9 +63,7 @@ def run_compare_bib_with_zotero(
         None: Results are written to files in the specified output directory
     """
     # Expand and normalize file paths
-    need_compare_bib, zotero_bib, path_output = expand_paths(
-        need_compare_bib, zotero_bib, path_output
-    )
+    need_compare_bib, zotero_bib, path_output = expand_paths(need_compare_bib, zotero_bib, path_output)
 
     # Update options
     options_ = build_base_options([], [], ["arXiv"], [], path_conf_j_jsons)

{pyeasyphd-0.4.1 → pyeasyphd-0.4.3}/pyeasyphd/scripts/run_format.py

@@ -6,10 +6,7 @@ from ._base import build_base_options, expand_paths
 
 
 def run_format_bib_to_save_by_entry_type(
-    options: dict,
-    need_format_bib: str,
-    path_output: str,
-    path_conf_j_jsons: str,
+    options: dict, need_format_bib: str, path_output: str, path_conf_j_jsons: str
 ) -> None:
     """
     Format a bibliography file by organizing entries according to their entry types and save the results.
@@ -38,10 +35,7 @@ def run_format_bib_to_save_by_entry_type(
 
 
 def run_format_bib_to_abbr_zotero_save(
-    options: dict,
-    need_format_bib: str,
-    path_output: str,
-    path_conf_j_jsons: str,
+    options: dict, need_format_bib: str, path_output: str, path_conf_j_jsons: str
 ) -> None:
     """
     Format a bibliography file into three different modes: abbreviated, Zotero-compatible, and cleaned source.

{pyeasyphd-0.4.1 → pyeasyphd-0.4.3}/pyeasyphd/scripts/run_replace.py

@@ -6,11 +6,7 @@ from ._base import build_base_options, expand_paths
 
 
 def run_replace_to_standard_cite_keys(
-    full_tex_md: str,
-    full_bib: str,
-    path_output: str,
-    path_conf_j_jsons: str,
-    options: Optional[dict] = None,
+    full_tex_md: str, full_bib: str, path_output: str, path_conf_j_jsons: str, options: Optional[dict] = None
 ) -> None:
     """
     Replace citation keys in LaTeX documents with standardized versions.

{pyeasyphd-0.4.1 → pyeasyphd-0.4.3}/pyeasyphd/scripts/run_search.py

@@ -10,12 +10,7 @@ from ._base import build_base_options, build_search_options, expand_path, expand
 
 
 def run_search_for_screen(
-    acronym: str,
-    year: int,
-    title: str,
-    path_spidered_bibs: str,
-    path_spidering_bibs: str,
-    path_conf_j_jsons: str,
+    acronym: str, year: int, title: str, path_spidered_bibs: str, path_spidering_bibs: str, path_conf_j_jsons: str
 ) -> None:
     """
     Run search for screen display with specific conference/journal parameters.
@@ -51,7 +46,7 @@ def run_search_for_screen(
             print_on_screen=True,
             search_year_list=search_year_list,  # Empty list for all years, otherwise specific year
             keywords_type="Temp",
-            keywords_list_list=[[title]]  # Use title as search keyword
+            keywords_list_list=[[title]],  # Use title as search keyword
         ),
     }
 
@@ -70,7 +65,7 @@ def run_search_for_files(
     path_conf_j_jsons: str,
     search_in_spidered_bibs: bool = False,
     search_in_spidering_bibs: bool = True,
-    options: Optional[dict] = None
+    options: Optional[dict] = None,
 ) -> None:
     """
     Run search and save results to files with custom keywords.
@@ -100,14 +95,14 @@ def run_search_for_files(
     options_ = {
         **build_base_options(
             include_publisher_list=[],  # No specific publishers to include
-            include_abbr_list=[],       # No specific conference/journal abbreviations to include
+            include_abbr_list=[],  # No specific conference/journal abbreviations to include
             exclude_publisher_list=["arXiv"],  # Exclude arXiv publications from search
-            exclude_abbr_list=[],       # No specific conference/journal abbreviations to exclude
+            exclude_abbr_list=[],  # No specific conference/journal abbreviations to exclude
             path_conf_j_jsons=path_conf_j_jsons,  # Path to conference/journal metadata
         ),
         **build_search_options(
-            print_on_screen=False,      # Disable screen output (results go to files only)
-            search_year_list=[],        # Empty list means search all years (no year filtering)
+            print_on_screen=False,  # Disable screen output (results go to files only)
+            search_year_list=[],  # Empty list means search all years (no year filtering)
             keywords_type=keywords_type,  # Use provided keyword category for result organization
             keywords_list_list=keywords_list_list,  # Use provided nested keyword lists for searching
         ),
@@ -121,8 +116,8 @@ def run_search_for_files(
         path_main_output,
         path_spidered_bibs,
         path_spidering_bibs,
-        search_in_spidered_bibs,   # Flag to control spidered bibliography search
-        search_in_spidering_bibs   # Flag to control spidering bibliography search
+        search_in_spidered_bibs,  # Flag to control spidered bibliography search
+        search_in_spidering_bibs,  # Flag to control spidering bibliography search
     )
 
     return None
@@ -172,9 +167,7 @@ def _execute_searches(
     return None
 
 
-def run_compare_after_search(
-    zotero_bib: str, keywords_type: str, path_main_output: str, path_conf_j_jsons: str
-):
+def run_compare_after_search(zotero_bib: str, keywords_type: str, path_main_output: str, path_conf_j_jsons: str):
     """
     Compare search results with Zotero bibliography and generate comparison report.
 

{pyeasyphd-0.4.1 → pyeasyphd-0.4.3}/pyeasyphd/tools/generate/generate_from_bibs.py

@@ -117,9 +117,7 @@ def generate_from_bibs_and_write(
                             path_abbr = os.path.join(root, files[0])
 
                 # Generate and process library
-                library = generate_library_by_filters(
-                    path_abbr, issue_or_month_flag, year_flag, new_options
-                )
+                library = generate_library_by_filters(path_abbr, issue_or_month_flag, year_flag, new_options)
 
                 # Generate md, tex, pdf, html
                 html_body = generate_html_from_bib_data(abbr, library, pp, new_options)

{pyeasyphd-0.4.1 → pyeasyphd-0.4.3}/pyeasyphd/tools/generate/generate_links.py

@@ -320,7 +320,7 @@ class PaperLinksGenerator(object):
                 for abbr in keyword_publisher_abbr[keyword][publisher]:
                     lines = []
                     for ff in folder_flags:
-                        ll = os.path.join(folder_name, cj.title(), ff, publisher.lower(), abbr, f'{abbr}.html')
+                        ll = os.path.join(folder_name, cj.title(), ff, publisher.lower(), abbr, f"{abbr}.html")
                         if os.path.exists(os.path.join(self.data_base_path, ll)):
                             lines.append(f"[Link]({ll})")
                         else:

{pyeasyphd-0.4.1 → pyeasyphd-0.4.3}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pyeasyphd"
-version = "0.4.1"
+version = "0.4.3"
 description = "pyeasyphd"
 license = "GPL-3.0-or-later"
 authors = ["NextAI <nextartifintell@gmail.com>"]