pyeasyphd 0.4.12__py3-none-any.whl → 0.4.14__py3-none-any.whl

pyeasyphd/main/basic_input.py

@@ -1,5 +1,5 @@
 import os
-from typing import Any, Dict
+from typing import Any
 
 from pyadvtools import read_list
 from pybibtexer.main import BasicInput as BasicInputInPyBibtexer
@@ -9,28 +9,28 @@ class BasicInput(BasicInputInPyBibtexer):
     """Basic input class for handling bibliography and template configurations.
 
     Args:
-        options (Dict[str, Any]): Configuration options.
+        options (dict[str, Any]): Configuration options.
 
     Attributes:
         full_csl_style_pandoc (str): Full path to CSL style for pandoc.
         full_tex_article_template_pandoc (str): Full path to tex article template for pandoc.
         full_tex_beamer_template_pandoc (str): Full path to tex beamer template for pandoc.
-        article_template_tex (List[str]): Article template for LaTeX.
-        article_template_header_tex (List[str]): Article template header for LaTeX.
-        article_template_tail_tex (List[str]): Article template tail for LaTeX.
-        beamer_template_header_tex (List[str]): Beamer template header for LaTeX.
-        beamer_template_tail_tex (List[str]): Beamer template tail for LaTeX.
-        math_commands_tex (List[str]): LaTeX math commands.
-        usepackages_tex (List[str]): LaTeX usepackages.
+        article_template_tex (list[str]): Article template for LaTeX.
+        article_template_header_tex (list[str]): Article template header for LaTeX.
+        article_template_tail_tex (list[str]): Article template tail for LaTeX.
+        beamer_template_header_tex (list[str]): Beamer template header for LaTeX.
+        beamer_template_tail_tex (list[str]): Beamer template tail for LaTeX.
+        math_commands_tex (list[str]): LaTeX math commands.
+        usepackages_tex (list[str]): LaTeX usepackages.
         handly_preamble (bool): Whether to handle preamble manually.
-        options (Dict[str, Any]): Configuration options.
+        options (dict[str, Any]): Configuration options.
     """
 
-    def __init__(self, options: Dict[str, Any]) -> None:
+    def __init__(self, options: dict[str, Any]) -> None:
         """Initialize BasicInput with configuration options.
 
         Args:
-            options (Dict[str, Any]): Configuration options dictionary.
+            options (dict[str, Any]): Configuration options dictionary.
         """
         super().__init__(options)
 
@@ -43,11 +43,11 @@ class BasicInput(BasicInputInPyBibtexer):
 
         self.options = options
 
-    def _initialize_pandoc_md_to(self, options: Dict[str, Any]) -> None:
+    def _initialize_pandoc_md_to(self, options: dict[str, Any]) -> None:
         """Initialize pandoc markdown to other formats configuration.
 
         Args:
-            options (Dict[str, Any]): Configuration options.
+            options (dict[str, Any]): Configuration options.
         """
         csl_name = options.get("csl_name", "apa-no-ampersand")
         if not isinstance(csl_name, str):
@@ -61,11 +61,11 @@ class BasicInput(BasicInputInPyBibtexer):
 
         self.article_template_tex = self._try_read_list("tex", "Article.tex")
 
-    def _initialize_python_run_tex(self, options: Dict[str, Any]) -> None:
+    def _initialize_python_run_tex(self, options: dict[str, Any]) -> None:
         """Initialize Python LaTeX processing configuration.
 
         Args:
-            options (Dict[str, Any]): Configuration options.
+            options (dict[str, Any]): Configuration options.
         """
         self.article_template_header_tex = self._try_read_list("tex", "Article_Header.tex")
         self.article_template_tail_tex = self._try_read_list("tex", "Article_Tail.tex")
@@ -89,7 +89,7 @@ class BasicInput(BasicInputInPyBibtexer):
             file_name (str): Name of the file to read.
 
         Returns:
-            List[str]: List of lines from the file, or empty list if file cannot be read.
+            list[str]: list of lines from the file, or empty list if file cannot be read.
         """
         path_file = os.path.join(self._path_templates, folder_name, file_name)
 

pyeasyphd/main/pandoc_md_to.py

@@ -3,7 +3,6 @@ import os
 import re
 import subprocess
 import time
-from typing import Dict, List, Optional, Tuple
 
 from pyadvtools import (
     combine_content_in_list,
@@ -19,7 +18,7 @@ from .basic_input import BasicInput
 
 
 class PandocMdTo(BasicInput):
-    """Pandoc markdown to various formats (md, tex, html, pdf).
+    r"""Pandoc markdown to various formats (md, tex, html, pdf).
 
     Args:
         options (dict): Configuration options.
@@ -63,8 +62,8 @@ class PandocMdTo(BasicInput):
         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]:
+        self, path_bib: str, path_md_one: str, path_md_two: str, name_md_one: str | None, name_md_two: str | None
+    ) -> list[str]:
         """Convert markdown to markdown using pandoc.
 
         Args:
@@ -75,13 +74,13 @@ class PandocMdTo(BasicInput):
             name_md_two (Optional[str]): Name of destination markdown file.
 
         Returns:
-            List[str]: List of processed markdown content lines.
+            list[str]: list of processed markdown content lines.
         """
         full_one = path_md_one if name_md_one is None else os.path.join(path_md_one, name_md_one)
         full_two = path_md_two if name_md_two is None else os.path.join(path_md_two, name_md_two)
         return self._pandoc_md_to_md(full_one, full_two, path_bib)
 
-    def _pandoc_md_to_md(self, full_md_one: str, full_md_two: str, path_bib: str) -> List[str]:
+    def _pandoc_md_to_md(self, full_md_one: str, full_md_two: str, path_bib: str) -> list[str]:
         """Internal method to convert markdown to markdown using pandoc.
 
         Args:
@@ -90,7 +89,7 @@ class PandocMdTo(BasicInput):
             path_bib (str): Path to bibliography file.
 
         Returns:
-            List[str]: List of processed markdown content lines.
+            list[str]: list of processed markdown content lines.
         """
         if not os.path.exists(path_two := os.path.dirname(full_md_two)):
             os.makedirs(path_two)
@@ -120,7 +119,7 @@ class PandocMdTo(BasicInput):
         return self._standardize_markdown_content(full_md_two)
 
     @staticmethod
-    def _standardize_markdown_content(full_md: str) -> List[str]:
+    def _standardize_markdown_content(full_md: str) -> list[str]:
         regex = re.compile(r"(\s*>*\s*[-+*]+)\s\s\s(.*)")
         for i in range(len(data_list := read_list(full_md, "r"))):
             if mch := regex.match(data_list[i]):
@@ -129,13 +128,13 @@ class PandocMdTo(BasicInput):
 
     # for pandoc markdown files to tex files
     def pandoc_md_to_tex(
-        self, template_name: str, path_md: str, path_tex: str, name_md: Optional[str], name_tex: Optional[str]
-    ) -> List[str]:
+        self, template_name: str, path_md: str, path_tex: str, name_md: str | None, name_tex: str | None
+    ) -> list[str]:
         full_one = path_md if name_md is None else os.path.join(path_md, name_md)
         full_two = path_tex if name_tex is None else os.path.join(path_tex, name_tex)
         return self._pandoc_md_to_tex(full_one, full_two, template_name)
 
-    def _pandoc_md_to_tex(self, full_md: str, full_tex: str, template_name: str) -> List[str]:
+    def _pandoc_md_to_tex(self, full_md: str, full_tex: str, template_name: str) -> list[str]:
         """Pandoc."""
         if not os.path.exists(path_tex := os.path.dirname(full_tex)):
             os.makedirs(path_tex)
@@ -156,7 +155,7 @@ class PandocMdTo(BasicInput):
 
         return self._substitute_in_tex_from_md(read_list(full_tex, "r", None))
 
-    def _substitute_in_tex_from_md(self, data_list: List[str]) -> List[str]:
+    def _substitute_in_tex_from_md(self, data_list: list[str]) -> list[str]:
         old_str_list = [r"{\[}@", r"{\[}-@", r"{\[}", r"{\]}", r"\\_"]
         new_str_list = [rf"\\{self.cite_flag_in_tex}" + "{", rf"\\{self.cite_flag_in_tex}" + "{", "{", "}", "_"]
         old_str_list.extend([r"\\footnote<.->{", r";", r"@"])
@@ -165,7 +164,7 @@ class PandocMdTo(BasicInput):
 
     # for pandoc markdown files to html files
     def pandoc_md_to_html(
-        self, path_md: str, path_html: str, name_md: Optional[str], name_html: Optional[str], operate: bool = False
+        self, path_md: str, path_html: str, name_md: str | None, name_html: str | None, operate: bool = False
     ) -> str:
         full_one = path_md if name_md is None else os.path.join(path_md, name_md)
         full_two = path_html if name_html is None else os.path.join(path_html, name_html)
@@ -192,7 +191,7 @@ class PandocMdTo(BasicInput):
         return ""
 
     # for pandoc markdown files to pdf files
-    def pandoc_md_to_pdf(self, path_md: str, path_pdf: str, name_md: Optional[str], name_pdf: Optional[str]) -> str:
+    def pandoc_md_to_pdf(self, path_md: str, path_pdf: str, name_md: str | None, name_pdf: str | None) -> str:
         full_one = path_md if name_md is None else os.path.join(path_md, name_md)
         full_two = path_pdf if name_pdf is None else os.path.join(path_pdf, name_pdf)
         return self._pandoc_md_to_pdf(full_one, full_two)
@@ -222,8 +221,8 @@ class PandocMdTo(BasicInput):
     # --------- --------- --------- --------- --------- --------- --------- --------- --------- #
     # md
     def generate_key_data_dict(
-        self, pandoc_md_data_list: List[str], key_url_http_bib_dict: Dict[str, List[List[str]]]
-    ) -> Tuple[Dict[str, List[str]], Dict[str, List[str]], Dict[str, List[str]]]:
+        self, pandoc_md_data_list: list[str], key_url_http_bib_dict: dict[str, list[list[str]]]
+    ) -> tuple[dict[str, list[str]], dict[str, list[str]], dict[str, list[str]]]:
         """Generate."""
         key_reference_dict = self._generate_citation_key_reference_dict_from_pandoc_md(pandoc_md_data_list)
         (key_basic_dict, key_beauty_dict, key_complex_dict) = self._generate_basic_beauty_complex_dict(
@@ -232,8 +231,8 @@ class PandocMdTo(BasicInput):
         return key_basic_dict, key_beauty_dict, key_complex_dict
 
     def _generate_citation_key_reference_dict_from_pandoc_md(
-        self, pandoc_md_data_list: List[str]
-    ) -> Dict[str, List[str]]:
+        self, pandoc_md_data_list: list[str]
+    ) -> dict[str, list[str]]:
         """Generate."""
         pandoc_md_data_list = self.__append_pandoc_md_reference_part(pandoc_md_data_list)
 
@@ -269,7 +268,7 @@ class PandocMdTo(BasicInput):
             key_reference_dict.update({citation_key: delete_empty_lines_last_occur_add_new_line(content)})
         return key_reference_dict
 
-    def __append_pandoc_md_reference_part(self, pandoc_md_data_list: List[str]) -> List[str]:
+    def __append_pandoc_md_reference_part(self, pandoc_md_data_list: list[str]) -> list[str]:
         """Append the line which starts with '::: {#'."""
         line_index, len_data = 0, len(pandoc_md_data_list)
         if self.markdown_name == "pandoc-markdown":
@@ -296,15 +295,15 @@ class PandocMdTo(BasicInput):
         return delete_empty_lines_last_occur_add_new_line(new_list)
 
     def _generate_basic_beauty_complex_dict(
-        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]]]:
+        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 = [f"<details>{self.details_to_bib_separator}", "```\n"]
         tail_list = ["```\n", "</details>\n"]
 
-        key_basic_dict: Dict[str, List[str]] = {}
-        key_beauty_dict: Dict[str, List[str]] = {}
-        key_complex_dict: Dict[str, List[str]] = {}
+        key_basic_dict: dict[str, list[str]] = {}
+        key_beauty_dict: dict[str, list[str]] = {}
+        key_complex_dict: dict[str, list[str]] = {}
 
         key_list_http = list(key_url_http_bib_dict.keys())
         key_list_md = list(key_reference_dict.keys())
@@ -313,10 +312,10 @@ class PandocMdTo(BasicInput):
             return key_basic_dict, key_beauty_dict, key_complex_dict
 
         for k in key_list_http:
-            a: List[str] = copy.deepcopy(key_reference_dict[k])
-            b: List[str] = copy.deepcopy(key_reference_dict[k])
-            aa: List[str] = key_url_http_bib_dict[k][0]
-            bb: List[str] = key_url_http_bib_dict[k][1]
+            a: list[str] = copy.deepcopy(key_reference_dict[k])
+            b: list[str] = copy.deepcopy(key_reference_dict[k])
+            aa: list[str] = key_url_http_bib_dict[k][0]
+            bb: list[str] = key_url_http_bib_dict[k][1]
 
             # add url
             if self.add_url_for_basic_dict:
@@ -326,9 +325,9 @@ class PandocMdTo(BasicInput):
 
             # add anchor
             if self.add_anchor_for_basic_dict:
-                a = [f'<a id="{k.lower()}"></a>\n'] + a
+                a = [f'<a id="{k.lower()}"></a>\n', *a]
             if self.add_anchor_for_beauty_dict or self.add_anchor_for_complex_dict:
-                b = [f'<a id="{k.lower()}"></a>\n'] + b
+                b = [f'<a id="{k.lower()}"></a>\n', *b]
 
             if self.display_one_line_reference_note:
                 a = ["".join(a).replace("\n", " ").strip() + "\n"]
@@ -356,7 +355,7 @@ class PandocMdTo(BasicInput):
         return None
 
     @staticmethod
-    def _generate_tex_content(file_prefix: str, add_tex_name: str, add_bib_name: str) -> Tuple[List[str], List[str]]:
+    def _generate_tex_content(file_prefix: str, add_tex_name: str, add_bib_name: str) -> tuple[list[str], list[str]]:
         if len(file_prefix) == 0:
             file_prefix = "file_prefix"
 

pyeasyphd/main/python_run_md.py

@@ -3,7 +3,7 @@ import os
 import re
 import shutil
 import time
-from typing import Any, Dict, List, Tuple
+from typing import Any
 
 from pyadvtools import combine_content_in_list, delete_empty_lines_last_occur_add_new_line, read_list, write_list
 from pybibtexer.bib.core import ConvertStrToLibrary
@@ -14,8 +14,7 @@ from .pandoc_md_to import PandocMdTo
 
 
 def batch_convert_citations(text):
-    """
-    Process all citations in the text, including multiple citations in one bracket.
+    r"""Process all citations in the text, including multiple citations in one bracket.
 
     Example: [@ref1; @ref2] -> <sup>[@ref1](#ref1)</sup><sup>[@ref2](#ref2)</sup>
     """
@@ -43,10 +42,10 @@ def batch_convert_citations(text):
 
 
 class PythonRunMd(BasicInput):
-    """Python markdown processing class.
+    r"""Python markdown processing class.
 
     Args:
-        options (Dict[str, Any]): Configuration options.
+        options (dict[str, Any]): Configuration options.
 
     Attributes:
         delete_temp_generate_md (bool): Whether to delete temporary generated markdown files. Defaults to True.
@@ -59,11 +58,11 @@ class PythonRunMd(BasicInput):
         details_to_bib_separator (str): Separator between <details> and bibliography content. Defaults to "\n".
     """
 
-    def __init__(self, options: Dict[str, Any]) -> None:
+    def __init__(self, options: dict[str, Any]) -> None:
         """Initialize PythonRunMd with configuration options.
 
         Args:
-            options (Dict[str, Any]): Configuration options.
+            options (dict[str, Any]): Configuration options.
         """
         super().__init__(options)
 
@@ -92,28 +91,28 @@ class PythonRunMd(BasicInput):
     def special_operate_for_md(
         self,
         path_output: str,
-        data_list_md: List[str],
+        data_list_md: list[str],
         output_md_name: str,
         full_bib_for_abbr: str,
         full_bib_for_zotero: str,
         template_name: str = "article",
         generate_html: bool = False,
         generate_tex: bool = True,
-    ) -> Tuple[List[str], List[str]]:
+    ) -> tuple[list[str], list[str]]:
         """Perform special operations on markdown files.
 
         Args:
             path_output (str): Path to output directory.
-            data_list_md (List[str]): List of markdown content lines.
+            data_list_md (list[str]): list of markdown content lines.
             output_md_name (str): Name of output markdown file.
             full_bib_for_abbr (str): Path to abbreviated bibliography file.
             full_bib_for_zotero (str): Path to Zotero bibliography file.
-            template_name (str, optional): Name of template to use. Defaults to "article".
-            generate_html (bool, optional): Whether to generate HTML. Defaults to False.
-            generate_tex (bool, optional): Whether to generate LaTeX. Defaults to True.
+            template_name (str): Name of template to use. Defaults to "article".
+            generate_html (bool): Whether to generate HTML. Defaults to False.
+            generate_tex (bool): Whether to generate LaTeX. Defaults to True.
 
         Returns:
-            Tuple[List[str], List[str]]: Tuple containing processed markdown and LaTeX content.
+            tuple[list[str], list[str]]: Tuple containing processed markdown and LaTeX content.
         """
         path_temp = os.path.join(path_output, "{}".format(time.strftime("%Y_%m_%d_%H_%M_%S")))
         if not os.path.exists(path_temp):
@@ -165,7 +164,7 @@ class PythonRunMd(BasicInput):
 
     def _special_operate_for_md(
         self, output_md_name: str, path_temp: str, full_bib_for_abbr: str, full_bib_for_zotero: str
-    ) -> List[str]:
+    ) -> list[str]:
         """Perform special operations for markdown processing.
 
         Args:
@@ -175,7 +174,7 @@ class PythonRunMd(BasicInput):
             full_bib_for_zotero (str): Path to Zotero bibliography file.
 
         Returns:
-            List[str]: List of processed markdown content lines.
+            list[str]: list of processed markdown content lines.
         """
         # pandoc markdown to markdown
         n1 = "1_pandoc" + ".md"
@@ -278,16 +277,16 @@ class PythonRunMd(BasicInput):
         return content_md
 
     @staticmethod
-    def _special_format(temp_list: List[str], space_one: str, space_two: str) -> List[str]:
+    def _special_format(temp_list: list[str], space_one: str, space_two: str) -> list[str]:
         """Apply special formatting for alignment.
 
         Args:
-            temp_list (List[str]): List of strings to format.
+            temp_list (list[str]): list of strings to format.
             space_one (str): First space string.
             space_two (str): Second space string.
 
         Returns:
-            List[str]: Formatted list of strings.
+            list[str]: Formatted list of strings.
         """
         for j in range(len(temp_list) - 1):
             if temp_list[j][-1] == "\n":
@@ -296,23 +295,23 @@ class PythonRunMd(BasicInput):
 
     def _generate_content_md(
         self,
-        key_basic_beauty_complex_dict: Dict[str, List[str]],
-        key_in_md_tex: List[str],
-        main_part: List[str],
-        last_part: List[str],
-        bib_in_md: List[str],
-    ) -> List[str]:
+        key_basic_beauty_complex_dict: dict[str, list[str]],
+        key_in_md_tex: list[str],
+        main_part: list[str],
+        last_part: list[str],
+        bib_in_md: list[str],
+    ) -> list[str]:
         """Generate markdown content from various components.
 
         Args:
-            key_basic_beauty_complex_dict (Dict[str, List[str]]): Dictionary of formatted references.
-            key_in_md_tex (List[str]): List of citation keys in markdown/LaTeX.
-            main_part (List[str]): Main content part.
-            last_part (List[str]): Last content part.
-            bib_in_md (List[str]): Bibliography content for markdown.
+            key_basic_beauty_complex_dict (dict[str, list[str]]): dictionary of formatted references.
+            key_in_md_tex (list[str]): list of citation keys in markdown/LaTeX.
+            main_part (list[str]): Main content part.
+            last_part (list[str]): Last content part.
+            bib_in_md (list[str]): Bibliography content for markdown.
 
         Returns:
-            List[str]: Generated markdown content.
+            list[str]: Generated markdown content.
         """
         temp_b = []
         if self.add_reference_in_md:

pyeasyphd/main/python_run_tex.py

@@ -2,7 +2,7 @@ import os
 import re
 import shutil
 import subprocess
-from typing import Any, Dict, List, Optional
+from typing import Any
 
 from pyadvtools import delete_files, insert_list_in_list, read_list, write_list
 
@@ -13,7 +13,7 @@ class PythonRunTex(BasicInput):
     """Python LaTeX processing class.
 
     Args:
-        options (Dict[str, Any]): Configuration options.
+        options (dict[str, Any]): Configuration options.
 
     Attributes:
         run_latex (bool): Whether to run LaTeX compilation. Defaults to False.
@@ -21,11 +21,11 @@ class PythonRunTex(BasicInput):
         delete_run_latex_cache (bool): Whether to delete LaTeX cache files. Defaults to True.
     """
 
-    def __init__(self, options: Dict[str, Any]) -> None:
+    def __init__(self, options: dict[str, Any]) -> None:
         """Initialize PythonRunTex with configuration options.
 
         Args:
-            options (Dict[str, Any]): Configuration options.
+            options (dict[str, Any]): Configuration options.
         """
         super().__init__(options)
 
@@ -34,11 +34,11 @@ class PythonRunTex(BasicInput):
         self.run_latex: bool = options.get("run_latex", False)
         self.pdflatex_xelatex: str = options.get("pdflatex_xelatex", "xelatex")  # pdflatex, xelatex
         self.delete_run_latex_cache: bool = options.get("delete_run_latex_cache", True)
-        self.latex_clean_file_types: Optional[List[str]] = options.get("latex_clean_file_types", None)
+        self.latex_clean_file_types: list[str] | None = options.get("latex_clean_file_types", None)
 
     def generate_standard_tex_data_list(
         self,
-        data_list_body: List[str],
+        data_list_body: list[str],
         output_tex_name: str,
         path_output: str,
         figure_folder_name: str = "figs",
@@ -46,21 +46,21 @@ class PythonRunTex(BasicInput):
         bib_folder_name: str = "bib",
         bib_name: str = "abbr.bib",
         template_name: str = "article",
-    ) -> List[str]:
+    ) -> list[str]:
         """Generate standard LaTeX data list with proper formatting.
 
         Args:
-            data_list_body (List[str]): List of body content strings.
+            data_list_body (list[str]): list of body content strings.
             output_tex_name (str): Name of output LaTeX file.
             path_output (str): Path to output directory.
-            figure_folder_name (str, optional): Name of figures folder. Defaults to "figs".
-            tex_folder_name (str, optional): Name of LaTeX folder. Defaults to "tex".
-            bib_folder_name (str, optional): Name of bibliography folder. Defaults to "bib".
-            bib_name (str, optional): Name of bibliography file. Defaults to "abbr.bib".
-            template_name (str, optional): Name of template to use. Defaults to "article".
+            figure_folder_name (str): Name of figures folder. Defaults to "figs".
+            tex_folder_name (str): Name of LaTeX folder. Defaults to "tex".
+            bib_folder_name (str): Name of bibliography folder. Defaults to "bib".
+            bib_name (str): Name of bibliography file. Defaults to "abbr.bib".
+            template_name (str): Name of template to use. Defaults to "article".
 
         Returns:
-            List[str]: List of processed LaTeX content strings.
+            list[str]: list of processed LaTeX content strings.
         """
         # for figures
         for i in range(len(data_list_body)):
@@ -78,7 +78,7 @@ class PythonRunTex(BasicInput):
 
     def _special_operate_tex(
         self,
-        data_list_body: List[str],
+        data_list_body: list[str],
         template_name: str,
         output_tex_name: str,
         path_output: str,
@@ -89,7 +89,7 @@ class PythonRunTex(BasicInput):
         """Perform special operations on LaTeX files.
 
         Args:
-            data_list_body (List[str]): List of body content strings.
+            data_list_body (list[str]): list of body content strings.
             template_name (str): Name of template to use.
             output_tex_name (str): Name of output LaTeX file.
             path_output (str): Path to output directory.
@@ -163,7 +163,7 @@ class PythonRunTex(BasicInput):
         if self.run_latex:
             if shutil.which("latexmk"):
                 os.chdir(path_output)
-                cmd = "latexmk -{} {}".format(self.pdflatex_xelatex, main_name)
+                cmd = f"latexmk -{self.pdflatex_xelatex} {main_name}"
                 try:
                     subprocess.run(cmd.split(), check=True, capture_output=True, text=True)
                 except subprocess.CalledProcessError as e:

pyeasyphd/pyeasyphd.py

@@ -12,7 +12,7 @@ def delete_files(path_storage: str, extensions) -> None:
 
     Args:
         path_storage (str): Path to the storage directory.
-        extensions: List of file extensions to delete.
+        extensions: list of file extensions to delete.
     """
     for name in os.listdir(path_storage):
         for ext in extensions:

pyeasyphd/scripts/_base.py

@@ -1,5 +1,5 @@
 import os
-from typing import Any, Dict, List
+from typing import Any
 
 
 def expand_path(path: str) -> str:
@@ -13,20 +13,19 @@ def expand_paths(*paths):
 
 
 def build_base_options(
-    include_publisher_list: List[str],
-    include_abbr_list: List[str],
-    exclude_publisher_list: List[str],
-    exclude_abbr_list: List[str],
+    include_publisher_list: list[str],
+    include_abbr_list: list[str],
+    exclude_publisher_list: list[str],
+    exclude_abbr_list: list[str],
     path_conf_j_jsons: str,
-) -> Dict[str, Any]:
-    """
-    Build options dictionary with common configuration.
+) -> dict[str, Any]:
+    """Build options dictionary with common configuration.
 
     Args:
-        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
-        exclude_abbr_list: List of conference/journal abbreviations to exclude
+        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
+        exclude_abbr_list: list of conference/journal abbreviations to exclude
         path_conf_j_jsons: Base path for conferences/journals JSON files
 
     Returns:
@@ -45,14 +44,13 @@ def build_base_options(
 
 
 def build_search_options(
-    print_on_screen: bool, search_year_list: List[str], keywords_type: str, keywords_list_list: List[List[str]]
-) -> Dict[str, Any]:
-    """
-    Build search options dictionary with common configuration.
+    print_on_screen: bool, search_year_list: list[str], keywords_type: str, keywords_list_list: list[list[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
+        search_year_list: list of years to filter search results
         keywords_type: Category name for search keywords
         keywords_list_list: Nested list of search keywords
 

pyeasyphd/scripts/run_article_md.py

@@ -2,6 +2,8 @@ import os
 
 from pyeasyphd.tools import PyRunBibMdTex
 
+from ._base import expand_path
+
 
 def run_article_md_daily_notes(
     path_input_file: str,
@@ -11,12 +13,11 @@ def run_article_md_daily_notes(
     path_conf_j_jsons: str,
     options: dict,
 ) -> None:
-    """
-    Run article markdown daily notes processing pipeline.
+    """Run article markdown daily notes processing pipeline.
 
     Args:
         path_input_file (str): Path to input files directory
-        input_file_names (list[str]): List of input file names
+        input_file_names (list[str]): list of input file names
         path_output_file (str): Path to output directory
         bib_path_or_file (str): Path to bibliography file or directory
         path_conf_j_jsons (str): Path to conferences and journals JSON files directory
@@ -25,13 +26,13 @@ def run_article_md_daily_notes(
     Returns:
         None
     """
-    path_input_file = os.path.expandvars(os.path.expanduser(path_input_file))
-    path_output_file = os.path.expandvars(os.path.expanduser(path_output_file))
+    path_input_file = expand_path(path_input_file)
+    path_output_file = expand_path(path_output_file)
 
     # Initialize default options with detailed descriptions
     _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")),
+        "full_json_c": expand_path(os.path.join(path_conf_j_jsons, "conferences.json")),
+        "full_json_j": expand_path(os.path.join(path_conf_j_jsons, "journals.json")),
         # figure options
         "includegraphics_figs_directory": "",
         "shutil_includegraphics_figs": False,
@@ -43,12 +44,12 @@ def run_article_md_daily_notes(
         "add_link_to_fields_for_abbr": ["title"],  # None, or ["title", "journal", "booktitle"]
         "maximum_authors_for_abbr": 0,  # 0, 1, 2, ...
         "add_index_to_entries": False,
-        "bib_for_abbr_name": "abbr.bib",
-        "bib_for_zotero_name": "zotero.bib",
-        "bib_for_save_name": "save.bib",
+        "bib_name_for_abbr": "abbr.bib",
+        "bib_name_for_zotero": "zotero.bib",
+        "bib_name_for_save": "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),
+        "bib_path_or_file": expand_path(bib_path_or_file),
         # tex options
         "handly_preamble": False,
         "final_output_main_tex_name": "main.tex",