2025-10-22: Automatic update

src/arxtic.py

@@ -56,22 +56,6 @@ COLOUR_INFO="\033[34m"
 COLOUR_WARNING="\033[93m"
 COLOUR_ERROR="\033[91m"
 
-ids = ["2510.06329", "2509.13163"]
-bibcodes = ["2022A&A...658A.152V", "2021A&A...649A..97L"]
-query =  "first_author:\"Voggel, K\"year:(2022)"
-
-#test1 = local_api.update_local_pdf()
-#local_api.bibtex_to_file(test1, "test1")
-#test1 = local_api.file_to_bibtex("test1")
-#test2 = bib.Library()
-#
-#utils.arxtic_comment("2022ApJ...941L..11F", test1)
-#utils.arxtic_library_add("2022ApJ...941L..11F", test1, "test1")
-#utils.arxtic_keywords_add("2022ApJ...941L..11F", test1, "kw1")
-#utils.arxtic_score("2022ApJ...941L..11F", test1, "42")
-#utils.arxtic_date_read("2022ApJ...941L..11F", test1)
-#utils.export_abstract(test1, "test1")
-
 if __name__ == "__main__":
     q = False
     s = True
@@ -79,6 +63,10 @@ if __name__ == "__main__":
                        if not f[0] == "." and ".bib" in f]
     libraries = {l: local_api.file_to_bibtex(l + ".bib") 
                  for l in libraries_names}
+
+    libraries["local"] = local_api.update_local_pdf(library=libraries["local"])
+    libraries["read"] = local_api.update_library(libraries["local"], "read")
+    libraries["unread"] = local_api.update_library(libraries["local"], "unread")
     while not q:
         print(COLOUR_INPUT + "Select an action")
         val = input("> " + COLOUR_DEFAULT)
@@ -104,6 +92,10 @@ if __name__ == "__main__":
                     lib_name = libraries_names[i]
                     lib = libraries[lib_name]
                     local_api.bibtex_to_file(lib, lib_name)
+                    for i in range(len(libraries)):
+                        lib_name = libraries_names[i]
+                        lib = libraries[lib_name]
+                        utils.export_author_year(lib, lib_name+".txt")
                     s = True
 
             elif arg0 in ["cancel", "reset", "reload"]:
@@ -117,6 +109,13 @@ if __name__ == "__main__":
                         library=libraries["local"])
                 s = False
 
+            elif arg0 in ["update"]:
+                libraries["local"] = local_api.update_local_pdf(
+                        library=libraries["local"])
+                libraries["read"] = local_api.update_library(libraries["local"], "read")
+                libraries["unread"] = local_api.update_library(libraries["local"], "unread")
+                s = False
+
             elif arg0 in ["today"]:
                 today_lib = arxiv_api.arxiv_today()
                 libraries_names.append("today")
@@ -129,10 +128,13 @@ if __name__ == "__main__":
                 elif nargs == 3:
                     if args[2] in ["abstract", "abs"]:
                         utils.print_abstract(libraries[args[1]])
-                    if args[2] in ["title", "author", "authors"]:
+                    elif args[2] in ["title"]:
                         utils.print_title_author(libraries[args[1]])
-                    if args[2] in ["reference", "references", "ref", "refs"]:
+                    elif args[2] in ["reference", "references", "ref", "refs"]:
                         utils.print_reference(libraries[args[1]])
+                    elif args[2] in ["author", "authors", "year"]:
+                        utils.print_author_year(libraries[args[1]])
+
                 else:
                     raise Exception("Not recognized")
 
@@ -141,17 +143,19 @@ if __name__ == "__main__":
                     for i in range(len(libraries)):
                         lib_name = libraries_names[i]
                         lib = libraries[lib_name]
-                        utils.export_abstract(lib, lib_name+".txt")
+                        utils.export_author_year(lib, lib_name+".txt")
 
                 elif nargs == 2:
-                    utils.export_abstract(libraries[args[1]], args[1]+".txt")
+                    utils.export_author_year(libraries[args[1]], args[1]+".txt")
                 elif nargs == 3:
                     if args[2] in ["abstract", "abs"]:
                         utils.export_abstract(libraries[args[1]], args[1]+".txt")
-                    if args[2] in ["title", "author", "authors"]:
+                    elif args[2] in ["title"]:
                         utils.export_title_author(libraries[args[1]], args[1]+".txt")
-                    if args[2] in ["reference", "references", "ref", "refs"]:
+                    elif args[2] in ["reference", "references", "ref", "refs"]:
                         utils.export_reference(libraries[args[1]], args[1]+".txt")
+                    elif args[2] in ["author", "authors", "year"]:
+                        utils.export_author_year(libraries[args[1]], args[1]+".txt")
                 else:
                     raise Exception("Not recognized")
 
@@ -181,14 +185,52 @@ if __name__ == "__main__":
                     utils.arxtic_comment(args[2], libraries[args[2]])
                     s = False
 
+            elif arg0 in ["unread", "todo"]:
+                if nargs == 2:
+                    block = utils.find(args[1], libraries["local"])
+                    known_libs = block["arxtic_library"]
+                    if not "unread" in known_libs.split(","):
+                        if "read" in known_libs.split(","):
+                            utils.arxtic_library_remove(args[1], libraries["local"], "read")
+                        utils.arxtic_library_add(args[1], libraries["local"], "unread")
+                        s = False
+
+                elif nargs == 3:
+                    block = utils.find(args[1], libraries[args[2]])
+                    known_libs = block["arxtic_library"]
+                    if not "unread" in known_libs.split(","):
+                        if "read" in known_libs.split(","):
+                            utils.arxtic_library_remove(args[1], libraries[args[2]], "read")
+                        utils.arxtic_library_add(args[1], libraries[args[2]], "unread")
+                        s = False
+                else:
+                    raise Exception("Not recognized")
+
             elif arg0 in ["read"]:
                 if nargs == 2:
                     utils.launch_reader(args[1], libraries["local"])
                     utils.arxtic_comment(args[1], libraries["local"])
+
+                    block = utils.find(args[1], libraries["local"])
+                    known_libs = block["arxtic_library"]
+                    if not "read" in known_libs.split(","):
+                        if "unread" in known_libs.split(","):
+                            utils.arxtic_library_remove(args[1], libraries["local"], "unread")
+                        utils.arxtic_library_add(args[1], libraries["local"], "read")
+                        utils.arxtic_date_read(args[1], libraries["local"])
                     s = False
+
                 elif nargs == 3:
                     utils.launch_reader(args[1], libraries[args[2]])
                     utils.arxtic_comment(args[1], libraries[args[2]])
+
+                    block = utils.find(args[1], libraries[args[2]])
+                    known_libs = block["arxtic_library"]
+                    if not "read" in known_libs.split(","):
+                        if "unread" in known_libs.split(","):
+                            utils.arxtic_library_remove(args[1], libraries[args[2]], "unread")
+                        utils.arxtic_library_add(args[1], libraries[args[2]], "read")
+                        utils.arxtic_date_read(args[1], libraries[args[2]])
                     s = False
                 else:
                     raise Exception("Not recognized")

src/legacy.py

@@ -1,194 +0,0 @@
-#!/usr/bin/env python
-#[TLP:AMBER] LIMITED DISTRIBUTION: WORK IN PROGRESS
-"""
-ArXtic: 
-
-ArXtic queries arXiv and filters the output.
-
-@ Author: Moussouni, Yaël (MSc student; yael.moussouni@etu.unistra.fr)
-@ Institution:  Université de Strasbourg, CNRS, Observatoire astronomique
-                de Strasbourg, UMR 7550, F-67000 Strasbourg, France
-@ Date: 2025-09-15
-
-Licence:
-ArXtic
-Copyright (C) 2025 Yaël Moussouni (yael.moussouni@etu.unistra.fr)
-
-legacy.py
-Copyright (C) 2025 Yaël Moussouni (yael.moussouni@etu.unistra.fr)
-
-This program is free software: you can redistribute it and/or modify 
-it under the terms of the GNU General Public License as published by 
-the Free Software Foundation; either version 3 of the License, or 
-(at your option) any later version.
-
-This program is distributed in the hope that it will be useful, 
-but WITHOUT ANY WARRANTY; without even the implied warranty of 
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License 
-along with this program. If not, see www.gnu.org/licenses/.
-"""
-import os
-import textwrap as tw
-import feedparser as fp
-import bibtexparser as bib
-import requests as rq
-import numpy as np
-from urllib.parse import urlencode, quote_plus
-
-FILTERS_DIR = os.environ.get("FILTERS_DIR")
-DB_DIR = os.environ.get("DB_DIR")
-PDF_DIR = os.environ.get("PDF_DIR")
-ARXIV_QUERY_URL = os.environ.get("ARXIV_QUERY_URL")
-ARXIV_RSS_URL = os.environ.get("ARXIV_RSS_URL")
-ADSABS_QUERY_URL = os.environ.get("ADSABS_QUERY_URL")
-ADSABS_EXPORT_URL = os.environ.get("ADSABS_EXPORT_URL")
-ADSABS_API_KEY = os.environ.get("ADSABS_API_KEY")
-
-COLOUR_DEFAULT="\033[0m"
-COLOUR_INPUT="\033[36m"
-COLOUR_OUTPUT="\033[32m"
-COLOUR_INFO="\033[34m"
-COLOUR_WARNING="\033[93m"
-COLOUR_ERROR="\033[91m"
-
-## Filters
-
-def get_filters():
-    filters = []
-    filters_list = [f for f in os.listdir(FILTERS_DIR) if not f[0] == "."]
-    for i in range(len(filters_list)):
-        path = FILTERS_DIR + filters_list[i]
-        with open(path) as filter_file:
-            dic = {"fields": [], "values": [], "score": 1}
-            for line in filter_file.readlines():
-                if "#FIELD" in line:
-                    field = line.split("=")[1].replace("\"", "").strip()
-                    dic["fields"].append(field)
-                elif "#SCORE" in line:
-                    field = line.split("=")[1].strip()
-                    dic["score"] = int(field)
-                elif line[0] == "#" or line in [" \n", "\n", ""]:
-                    continue
-                else:
-                    value = line.replace("\n", "")
-                    dic["values"].append(value)
-            filters.append(dic)
-    return filters
-
-def filter_entries(filters, entries):
-    filtered_entries = []
-    filtered_fields = []
-    filtered_keywords = []
-    filtered_score = []
-    for entry in entries:
-        added = False
-        for filter_ in filters:
-            fields = filter_["fields"]
-            values = filter_["values"]
-            score = filter_["score"]
-            for field in fields:
-                for value in values:
-                    if field in list(entry):
-                        val = entry[field]
-                    else:
-                        val = ""
-                    if not added and value.upper() in str(val).upper():
-                        filtered_entries.append(entry)
-                        filtered_fields.append([field])
-                        filtered_keywords.append([value])
-                        filtered_score.append(score)
-                        added = True
-                    elif added and value.upper() in str(val).upper():
-                        filtered_score[-1] = filtered_score[-1] + score
-                        if not field in filtered_fields[-1]:
-                            filtered_fields[-1].append(field)
-                        if not value in filtered_keywords[-1]:
-                            filtered_keywords[-1].append(value)
-    filtered_data = {"fields": filtered_fields,
-                     "keywords": filtered_keywords,
-                     "score": filtered_score}
-    return filtered_entries, filtered_data
-
-if __name__ == "__main__":
-    read = file_to_bibtex("read.bib")
-    unread = file_to_bibtex("unread.bib")
-    library = file_to_bibtex("library.bib")
-    quit_action = False
-
-    working_bibtex = bib.Library()
-
-    while not quit_action:
-        read_keys = [b.key for b in read.blocks]
-        unread_keys = [b.key for b in unread.blocks]
-        library_keys = [b.key for b in library.blocks]
-        library_keys = [b.key for b in library.blocks]
-
-
-        print(COLOUR_INPUT + "Select an action")
-        action = input("> " + COLOUR_DEFAULT)
-        if action.upper() in ["QUIT", "EXIT", "Q"]:
-            quit_action = True
-        elif action in ["", " ", "help", "h"]:
-            print(COLOUR_OUTPUT
-                  + "Available commands:\n"
-                  + "\t- quit, exit, q: exit\n"
-                  + COLOUR_DEFAULT)
-
-        # Print
-        elif action.split(" ")[0].upper() in ["PRINT", "P"]:
-            if len(action.split(" ")) == 1:
-                print_bibtex(working_bibtex)
-            elif action.split(" ")[1].upper() == "READ":
-                print_bibtex(read)
-            elif action.split(" ")[1].upper() == "UNREAD":
-                print_bibtex(unread)
-            elif action.split(" ")[1].upper() == "LIBRARY":
-                print_bibtex(library)
-            else:
-                search_key = action.split(" ")[1]
-
-                if search_key in read_keys:
-                    print_bibtex(read.blocks[read_keys.index(search_key)])
-                elif search_key in unread_keys:
-                    print_bibtex(unread.blocks[unread_keys.index(search_key)])
-                elif search_key in library_keys:
-                    print_bibtex(library.blocks[library_keys.index(search_key)])
-                else:
-                    print(COLOUR_WARNING 
-                          + f"Warning: {search_key} cannot be found"
-                          + COLOUR_DEFAULT)
-        # Clear
-        elif action.upper() in ["CLEAR", "CLEAN"]:
-            working_bibtex = bib.Library()
-        # Today
-        elif action.upper() in ["TODAY"]:
-            today_bibtex = today_arxiv()
-            working_bibtex.add(today_bibtex.blocks)
-            
-        # Library
-        elif action.upper() in ["LIBRARY"]:
-            library = list_pdf(library)
-            bibtex_to_file(library, "library.bib")
-
-        # Arxiv
-        elif action.split(" ")[0].upper() == "ARXIV":
-            arxiv_ids = action.split(" ")[1:]
-            feed = get_arxiv_from_ids(arxiv_ids)
-            entries = get_arxiv_entries(feed)
-            for entry in entries:
-                bibtex_entry = arxiv_to_bibtex(entry, 
-                                               arxtic_score=99)
-                working_bibtex.add(bibtex_entry.blocks)
-
-        # ADS
-        elif action.split(" ")[0].upper() == "ADS":
-            ads_bibcode = "".join(action.split(" ")[1:])
-            feed = get_ads_from_bibcode(ads_bibcode)
-            entries = get_ads_entries(feed)
-            for entry in entries:
-                bibtex_entry = ads_to_bibtex(entry, 
-                                             arxtic_score=99)
-                working_bibtex.add(bibtex_entry.blocks)

src/local_api.py

@@ -66,6 +66,17 @@ def bibtex_to_file(bibtex, filename, directory=DB_DIR):
     bibentry = bib.write_file(directory+filename, bibtex)
     return bibtex
 
+def update_library(source_library, lib_name):
+    new_library = bib.Library()
+    for block in source_library.blocks:
+        if isinstance(block, bib.model.Block):
+            arxtic_library = block["arxtic_library"]
+            if lib_name in arxtic_library.split(","):
+                new_library.add(block)
+    return new_library
+
+
+
 def update_local_pdf(library=None, directory=PDF_DIR):
     # TODO: delete entry in library if the PDF file is deleted. <YM, 2025-10-11>
     if library is None:

src/utils.py

@@ -61,10 +61,28 @@ COLOUR_ARXTIC = "\033[91m"
 
 ## General
 
-def wrap(txt, length=80):
+def wrap(txt, length=80, keep_line_break = False):
+    if keep_line_break:
+        wrapped_table = []
+        for line in txt.split("\n"):
+            wrapped_line = '\n'.join(tw.wrap(line, length, break_long_words=False))
+            wrapped_table += [wrapped_line]
+        wrapped_txt = "\n".join(wrapped_table)
+
+    else:
         wrapped_txt = '\n'.join(tw.wrap(txt, length, break_long_words=False))
     return wrapped_txt
 
+def parse_authors(authors):
+    author_list = authors.replace("{", "").replace("}", "").split(" and ")
+    N = len(author_list)
+    if N == 1:
+        return author_list[0]
+    elif N == 2:
+        return f"{author_list[0]} & {author_list[1]}"
+    else:
+        return f"{author_list[0]} et al."
+
 ## Prints
 
 def print_abstract(library):
@@ -72,7 +90,7 @@ def print_abstract(library):
         library = bib.Library(library)
     for block in library.blocks:
         if isinstance(block, bib.model.Block):
-            print("#"
+            print("# "
                   + COLOUR_REF 
                   + block.key + " [" + block["url"] + "]" 
                   + COLOUR_DEFAULT)
@@ -98,7 +116,7 @@ def print_abstract(library):
             if block["arxtic_comment"] != "":
                 print("Comment: "
                       + COLOUR_ARXTIC 
-                      + wrap(block["arxtic_comment"])
+                      + wrap(block["arxtic_comment"], keep_line_break=True)
                       + COLOUR_DEFAULT)
             if block["arxtic_library"] != "":
                 print("Library: " 
@@ -130,7 +148,7 @@ def print_title_author(library):
         library = bib.Library(library)
     for block in library.blocks:       
         if isinstance(block, bib.model.Block):
-            print("#"
+            print("# "
                   + COLOUR_REF 
                   + block.key + " [" + block["url"] + "]" 
                   + COLOUR_DEFAULT)
@@ -152,7 +170,7 @@ def print_title_author(library):
             if block["arxtic_comment"] != "":
                 print("Comment: "
                       + COLOUR_ARXTIC 
-                      + wrap(block["arxtic_comment"])
+                      + wrap(block["arxtic_comment"], keep_line_break=True)
                       + COLOUR_DEFAULT)
             if block["arxtic_library"] != "":
                 print("Library: " 
@@ -190,6 +208,60 @@ def print_reference(library):
             print(COLOUR_DEFAULT)
     return 0
 
+def print_author_year(library):
+    if not isinstance(library, bib.Library):
+        library = bib.Library(library)
+    for block in library.blocks:       
+        if isinstance(block, bib.model.Block):
+            print("# "
+                  + COLOUR_REF 
+                  + block.key + " [" + block["url"] + "]" 
+                  + COLOUR_DEFAULT)
+            if block["arxtic_filename"] != "":
+                print(COLOUR_REF
+                      + "("
+                      + PDF_DIR
+                      + block["arxtic_filename"]
+                      + ")"
+                      + COLOUR_DEFAULT)
+            print("Article: "
+                  + COLOUR_AUTHOR
+                  + wrap(parse_authors(block["author"]) 
+                         + " (" + block["year"] + ")")
+                  + COLOUR_DEFAULT)
+            print("Title: "
+                  + COLOUR_TITLE 
+                  + wrap(block["title"])
+                  + COLOUR_DEFAULT)
+            if block["arxtic_comment"] != "":
+                print("Comment: "
+                      + COLOUR_ARXTIC 
+                      + wrap(block["arxtic_comment"], keep_line_break=True)
+                      + COLOUR_DEFAULT)
+            if block["arxtic_library"] != "":
+                print("Library: " 
+                      + COLOUR_ARXTIC
+                      + ", ".join(block["arxtic_library"].split(","))
+                      + COLOUR_DEFAULT)
+            if block["arxtic_keywords"] != "":
+                print("Keywords: " 
+                      + COLOUR_ARXTIC
+                      + ", ".join(block["arxtic_library"].split(","))
+                      + COLOUR_DEFAULT)
+            if float(block["arxtic_score"]) >= 0:
+                print("Score: "
+                      + COLOUR_ARXTIC 
+                      + block["arxtic_score"]
+                      + COLOUR_DEFAULT)
+            if block["arxtic_date_read"] != "":
+                print("Read date: "
+                      + COLOUR_ARXTIC 
+                      + block["arxtic_date_read"]
+                      + COLOUR_DEFAULT)
+            print("")
+            print(80*"=")
+            print("")
+    return 0
 ## Exports
 
 def export_abstract(library, filename, directory=PDF_DIR):
@@ -198,14 +270,15 @@ def export_abstract(library, filename, directory=PDF_DIR):
     with open(directory + filename, "w+") as file:
         for block in library.blocks:
             if isinstance(block, bib.model.Block):
-                file.write("#" + block.key + " [" + block["url"] + "]\n")
+                file.write("# " + block.key + " [" + block["url"] + "]\n")
                 file.write(wrap("Title: " + block["title"]) + "\n")
                 file.write(wrap("Author(s): " 
                                 + ", ".join(block["author"].split(" and "))) 
                            + "\n")
                 file.write(wrap("Abstract: " + block["abstract"]) + "\n")
                 if block["arxtic_comment"] != "":
-                    file.write(wrap("Comment: " + block["arxtic_comment"])
+                    file.write(wrap("Comment: " + block["arxtic_comment"], 
+                                    keep_line_break=True)
                                + "\n")
                 if block["arxtic_library"] != "":
                     file.write("Library: " 
@@ -229,13 +302,14 @@ def export_title_author(library, filename, directory=PDF_DIR):
     with open(directory + filename, "w+") as file:
         for block in library.blocks:
             if isinstance(block, bib.model.Block):
-                file.write("#" + block.key + " [" + block["url"] + "]\n")
+                file.write("# " + block.key + " [" + block["url"] + "]\n")
                 file.write(wrap("Title: " + block["title"]) + "\n")
                 file.write(wrap("Author(s): " 
                                 + ", ".join(block["author"].split(" and "))) 
                            + "\n")
                 if block["arxtic_comment"] != "":
-                    file.write(wrap("Comment: " + block["arxtic_comment"])
+                    file.write(wrap("Comment: " + block["arxtic_comment"],
+                                    keep_line_break=True)
                                + "\n")
                 if block["arxtic_library"] != "":
                     file.write("Library: " 
@@ -259,9 +333,41 @@ def export_reference(library, filename, directory=PDF_DIR):
     with open(directory + filename, "w+") as file:
         for block in library.blocks:
             if isinstance(block, bib.model.Block):
-                file.write("#" + block.key + " [" + block["url"] + "]\n")
+                file.write("# " + block.key + " [" + block["url"] + "]\n")
     return 0
 
+def export_author_year(library, filename, directory=PDF_DIR):
+    if not isinstance(library, bib.Library):
+        library = bib.Library(library)
+    with open(directory + filename, "w+") as file:
+        for block in library.blocks:
+            if isinstance(block, bib.model.Block):
+                file.write("# " + block.key + " [" + block["url"] + "]\n")
+                file.write(wrap("Article: " 
+                                + parse_authors(block["author"]) 
+                                + " (" + block["year"] + ")")
+                           + "\n")
+                file.write(wrap("Title: " + block["title"]) + "\n")
+
+                if block["arxtic_comment"] != "":
+                    file.write(wrap("Comment: " + block["arxtic_comment"],
+                                    keep_line_break=True)
+                               + "\n")
+                if block["arxtic_library"] != "":
+                    file.write("Library: " 
+                               + ", ".join(block["arxtic_library"].split(",")) 
+                               + "\n")
+                if block["arxtic_keywords"] != "":
+                    file.write("Keywords: " 
+                               + ", ".join(block["arxtic_library"].split(",")) 
+                               + "\n")
+                if float(block["arxtic_score"]) >= 0:
+                    file.write("Score: " + block["arxtic_score"] + "\n")
+                if block["arxtic_date_read"] != "":
+                    file.write("Read date: " + block["arxtic_date_read"] + "\n")
+                file.write("\n" + 80*"=" + "\n")
+                file.write("\n")    
+    return 0
 ## Manipulation
 
 def find(key, library):