2025-10-14: Manual update, main structure done

.gitignore

@@ -1,10 +1,97 @@
-.DS_Store
+# Specific files
-*.tmp
-*.log
-tmp/
-log/
-venv/
-.venv/
 cfg/filters
 *.secret
 db/
+
+# Os generated files
+## Linux
+.Trash-*
+
+## MacOS
+.DS_Store
+.AppleDouble
+.LSOverride
+.DocumentRevisions-V100
+.fseventsd
+.Spotlight-V100
+.TemporaryItems
+.Trashes
+.VolumeIcon.icns
+.com.apple.timemachine.donotpresent
+.AppleDB
+.AppleDesktop
+Network Trash Folder
+Temporary Items
+.apdisk
+._*
+
+## Windows
+Thumbs.db
+Thumbs.db:encryptable
+ehthumbs.db
+ehthumbs_vista.db
+Desktop.ini
+desktop.ini
+$RECYCLE.BIN/
+
+# temporary or log(s) files and directories
+*.tmp
+*.log
+*.logs
+tmp/
+log/
+logs/
+
+# Python
+venv/
+.venv/
+__pycache__/
+
+# LaTeX
+Build/
+build/
+*.acn
+*.acr
+*.alg
+*.aux
+*.bak
+*.bbl
+*.bcf
+*.blg
+*.brf
+*.bst
+*.dvi
+*.fdb_latexmk
+*.fls
+*.glg
+*.glo
+*.gls
+*.idx
+*.ilg
+*.ind
+*.ist
+*.lof
+*.log
+*.lol
+*.lot
+*.maf
+*.mtc
+*.mtc1
+*.nav
+*.nlo
+*.nls
+*.out
+*.pyg
+*.run.xml
+*.snm
+*.synctex.gz
+*.tex.backup
+*.tex~
+*.thm
+*.toc
+*.vrb
+*.xdy
+*.xml
+*blx.bib
+.bak 
+.mtc

setup.sh

@@ -32,7 +32,7 @@ mkdir -p -v cfg/filters
 mkdir -p -v db
 touch db/read.bib
 touch db/unread.bib
-touch db/library.bib
+touch db/local.bib
 chmod u+x *.sh
 echo "=== Done ==="
 

src/ads_api.py

@@ -93,8 +93,8 @@ def ads_bibcode(bibcodes):
         bibentry = feed.text
         bibentry = bibentry[:-2]
         bibentry += (",\n"
-                     "\tarxtic_notes={},\n"
+                     "\tarxtic_comment={},\n"
-                     "\tarxtic_category={},\n"
+                     "\tarxtic_library={},\n"
                      "\tarxtic_keywords={},\n"
                      "\tarxtic_score={-1},\n"
                      "\tarxtic_filename={},\n"

src/arxiv_api.py

@@ -102,8 +102,8 @@ def parse_bibtex(entries,
                     f"\teprint={{{eprint}}},\n"
                     f"\turl={{{url}}},\n"
                     f"\tabstract={{{abstract}}},\n"
-                    "\tarxtic_notes={},\n"
+                    "\tarxtic_comment={},\n"
-                    "\tarxtic_category={},\n"
+                    "\tarxtic_library={},\n"
                     "\tarxtic_keywords={},\n"
                     "\tarxtic_score={-1},\n"
                     "\tarxtic_filename={},\n"

src/arxtic.py

@@ -31,6 +31,7 @@ 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 subprocess
 from urllib.parse import urlencode, quote_plus
 
 import requests as rq
@@ -59,9 +60,138 @@ ids = ["2510.06329", "2509.13163"]
 bibcodes = ["2022A&A...658A.152V", "2021A&A...649A..97L"]
 query =  "first_author:\"Voggel, K\"year:(2022)"
 
-utils.print_reference(arxiv_api.arxiv_today())
+#test1 = local_api.update_local_pdf()
-utils.print_title_author(arxiv_api.arxiv_id(ids))
+#local_api.bibtex_to_file(test1, "test1")
-print(ads_api.ads_bibcode_search(query, num=2))
+#test1 = local_api.file_to_bibtex("test1")
-utils.print_abstract(ads_api.ads_bibcode(bibcodes))
+#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
+    libraries_names = [f.replace(".bib", "") for f in os.listdir(DB_DIR)
+                       if not f[0] == "." and ".bib" in f]
+    libraries = {l: local_api.file_to_bibtex(l + ".bib") 
+                 for l in libraries_names}
+    while not q:
+        print(COLOUR_INPUT + "Select an action")
+        val = input("> " + COLOUR_DEFAULT)
+        args = val.split(" ")
+        nargs = len(args)
+
+        arg0 = args[0].lower()
+
+        try:
+
+            if arg0 in ["quit", "exit", "q"]:
+                if s == True:
+                    q = True
+                else:
+                    raise Exception(("Unsaved changes, "
+                                     "type \"save\" to update database or "
+                                     "type \"cancel\" to discard"))
+
+            elif arg0 in ["save", "write"]:
+                for i in range(len(libraries)):
+                    lib_name = libraries_names[i]
+                    lib = libraries[lib_name]
+                    local_api.bibtex_to_file(lib, lib_name)
+                    s = True
+
+            elif arg0 in ["cancel", "reset", "reload"]:
+                for i in range(len(libraries)):
+                    lib_name = libraries_names[i]
+                    libraries[lib_name] = local_api.file_to_bibtex(lib_name)
+                s = True
+
+            elif arg0 in ["local"]:
+                libraries["local"] = local_api.update_local_pdf(
+                        library=libraries["local"])
+
+            elif arg0 in ["print"]:
+                if nargs == 2:
+                    utils.print_abstract(libraries[args[1]])
+                elif nargs == 3:
+                    if args[2] in ["abstract", "abs"]:
+                        utils.print_abstract(libraries[args[1]])
+                    if args[2] in ["title", "author", "authors"]:
+                        utils.print_title_author(libraries[args[1]])
+                    if args[2] in ["reference", "references", "ref", "refs"]:
+                        utils.print_reference(libraries[args[1]])
+                else:
+                    raise Exception("Not recognized")
+
+            elif arg0 in ["export"]:
+                if nargs == 1:
+                    for i in range(len(libraries)):
+                        lib_name = libraries_names[i]
+                        lib = libraries[lib_name]
+                        utils.export_abstract(lib, lib_name+".txt")
+
+                elif nargs == 2:
+                    utils.export_abstract(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"]:
+                        utils.export_title_author(libraries[args[1]], args[1]+".txt")
+                    if args[2] in ["reference", "references", "ref", "refs"]:
+                        utils.export_reference(libraries[args[1]], args[1]+".txt")
+                else:
+                    raise Exception("Not recognized")
+
+            elif arg0 in ["mv", "move"]:
+                if nargs == 4:
+                    utils.mv(args[1], libraries[args[2]], libraries[args[3]])
+                    s = False
+                else:
+                    raise Exception("Not recognized")
+
+            elif arg0 in ["cp", "copy"]:
+                if nargs == 4:
+                    utils.cp(args[1], libraries[args[2]], libraries[args[3]])
+                    s = False
+                else:
+                    raise Exception("Not recognized")
+
+            elif arg0 in ["rm", "remove", "del", "delete"]:
+                if nargs == 3:
+                    utils.rm(args[1], libraries[args[2]])
+                    s = False
+                else:
+                    raise Exception("Not recognized")
+
+            elif arg0 in ["comment"]:
+                if nargs == 3:
+                    utils.arxtic_comment(args[2], libraries[args[2]])
+                    s = False
+
+            elif arg0 in ["read"]:
+                if nargs == 2:
+                    utils.launch_reader(args[1], libraries["local"])
+                    utils.arxtic_comment(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]])
+                    s = False
+                else:
+                    raise Exception("Not recognized")
+
+            else:
+                raise Exception("Not recognized")
+        except Exception as err:
+            msg = str(err)
+            print(COLOUR_ERROR + "Error! " + msg + COLOUR_DEFAULT)
+
+
+
+
+
 
-utils.print_reference(local_api.update_local_pdf())

src/local_api.py

@@ -76,7 +76,7 @@ def update_local_pdf(library=None, directory=PDF_DIR):
         known_pdf = [block["arxtic_filename"] for block in blocks]
     
     folder_pdf = [f for f in os.listdir(directory)
-                  if not f[0] == "." and ".pdf" if f]
+                  if not f[0] == "." and ".pdf" in f]
 
     for pdf in folder_pdf:
         fields = pdf.replace(".pdf", "").split("_")
@@ -92,6 +92,7 @@ def update_local_pdf(library=None, directory=PDF_DIR):
             arxiv_id = "/".join(fields[2:])
             arxiv_library = arxiv_api.arxiv_id(arxiv_id)
             if len(arxiv_library.blocks) == 1:
+                arxiv_library.blocks[0]["arxtic_filename"] = pdf
                 library.add(arxiv_library.blocks)
             else:
                 print(COLOUR_WARNING 
@@ -113,6 +114,7 @@ def update_local_pdf(library=None, directory=PDF_DIR):
             bibcodes = ads_api.ads_bibcode_search(query, num=2)
             if len(bibcodes) == 1:
                 ads_library = ads_api.ads_bibcode(bibcodes)
+                ads_library.blocks[0]["arxtic_filename"] = pdf
                 library.add(ads_library.blocks)
             else:
                 print(COLOUR_WARNING 

src/utils.py

@@ -31,6 +31,7 @@ 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 subprocess
 from urllib.parse import urlencode, quote_plus
 
 import requests as rq
@@ -38,39 +39,89 @@ import numpy as np
 import textwrap as tw
 import feedparser as fp
 import bibtexparser as bib
+import datetime as dt
 
 FILTERS_DIR = os.environ.get("FILTERS_DIR")
 DB_DIR = os.environ.get("DB_DIR")
 PDF_DIR = os.environ.get("PDF_DIR")
 
-COLOUR_DEFAULT="\033[0m"
+COLOUR_DEFAULT = "\033[0m"
-COLOUR_INPUT="\033[36m"
+COLOUR_INPUT = "\033[36m"
-COLOUR_OUTPUT="\033[32m"
+COLOUR_OUTPUT = "\033[32m"
-COLOUR_INFO="\033[34m"
+COLOUR_INFO = "\033[34m"
-COLOUR_WARNING="\033[93m"
+COLOUR_WARNING = "\033[93m"
-COLOUR_ERROR="\033[91m"
+COLOUR_ERROR = "\033[91m"
+
+COLOUR_REF = "\033[34m"
+COLOUR_TITLE = "\033[35m"
+COLOUR_AUTHOR = "\033[32m"
+COLOUR_ABS = "\033[36m"
+COLOUR_ARXTIC = "\033[91m"
+
+
+## General
 
 def wrap(txt, length=80):
     wrapped_txt = '\n'.join(tw.wrap(txt, length, break_long_words=False))
     return wrapped_txt
 
+## Prints
+
 def print_abstract(library):
     if not isinstance(library, bib.Library):
         library = bib.Library(library)
     for block in library.blocks:
         if isinstance(block, bib.model.Block):
-            print(COLOUR_INFO, end="")
+            print("#"
-            print(block.key, end="")
+                  + COLOUR_REF 
-            print(" [" + block["url"] + "]", end="")
+                  + block.key + " [" + block["url"] + "]" 
-            print(COLOUR_DEFAULT)
+                  + COLOUR_DEFAULT)
-
+            if block["arxtic_filename"] != "":
-            print(COLOUR_DEFAULT + wrap(block["title"]) + COLOUR_DEFAULT)
+                print(COLOUR_REF
-            print(COLOUR_OUTPUT 
+                      + "("
+                      + PDF_DIR
+                      + block["arxtic_filename"]
+                      + ")"
+                      + COLOUR_DEFAULT)
+            print("Title: "
+                  + COLOUR_TITLE 
+                  + wrap(block["title"])
+                  + COLOUR_DEFAULT)
+            print("Author(s): "
+                  + COLOUR_AUTHOR
                   + wrap(", ".join(block["author"].split(" and ")))
                   + COLOUR_DEFAULT)
-            print(COLOUR_INPUT 
+            print("Abstract: "
+                  + COLOUR_ABS
                   + wrap(block["abstract"])
                   + COLOUR_DEFAULT)
+            if block["arxtic_comment"] != "":
+                print("Comment: "
+                      + COLOUR_ARXTIC 
+                      + wrap(block["arxtic_comment"])
+                      + 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
 
@@ -79,15 +130,52 @@ def print_title_author(library):
         library = bib.Library(library)
     for block in library.blocks:       
         if isinstance(block, bib.model.Block):
-            print(COLOUR_INFO, end="")
+            print("#"
-            print(block.key, end="")
+                  + COLOUR_REF 
-            print(" [" + block["url"] + "]", end="")
+                  + block.key + " [" + block["url"] + "]" 
-            print(COLOUR_DEFAULT)
+                  + COLOUR_DEFAULT)
-
+            if block["arxtic_filename"] != "":
-            print(COLOUR_DEFAULT + wrap(block["title"]) + COLOUR_DEFAULT)
+                print(COLOUR_REF
-            print(COLOUR_OUTPUT 
+                      + "("
+                      + PDF_DIR
+                      + block["arxtic_filename"]
+                      + ")"
+                      + COLOUR_DEFAULT)
+            print("Title: "
+                  + COLOUR_TITLE 
+                  + wrap(block["title"])
+                  + COLOUR_DEFAULT)
+            print("Author(s): "
+                  + COLOUR_AUTHOR
                   + wrap(", ".join(block["author"].split(" and ")))
                   + COLOUR_DEFAULT)
+            if block["arxtic_comment"] != "":
+                print("Comment: "
+                      + COLOUR_ARXTIC 
+                      + wrap(block["arxtic_comment"])
+                      + 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
 
@@ -101,3 +189,180 @@ def print_reference(library):
             print(" [" + block["url"] + "]", end="")
             print(COLOUR_DEFAULT)
     return 0
+
+## Exports
+
+def export_abstract(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("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"])
+                               + "\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
+
+def export_title_author(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("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"])
+                               + "\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
+
+def export_reference(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")
+    return 0
+
+## Manipulation
+
+def find(key, library):
+    blocks = library.blocks
+    i = 0
+    while i < len(blocks):
+        block = blocks[i]
+        if isinstance(block, bib.model.Block):
+            if block.key == key:
+                return block
+        i += 1
+    return None
+
+def mv(key, lib_from, lib_to):
+    block = find(key, lib_from)
+    lib_to.add(block)
+    lib_from.remove(block)
+    return lib_from, lib_to
+
+def cp(key, lib_from, lib_to):
+    block = find(key, lib_from)
+    lib_to.add(block)
+    return lib_from, lib_to
+
+def rm(key, library):
+    block = find(key, library)
+    library.remove(block)
+    return library
+
+## ArXtic parameters
+
+def arxtic_comment(key, library):
+    block = find(key, library)
+    comment = block["arxtic_comment"]
+    with open("comment.tmp", "w+") as file:
+        file.write(comment)
+    subprocess.run(["nvim", "comment.tmp"])
+    with open("comment.tmp", "r") as file:
+        comment = "".join(file.readlines())
+    subprocess.run(["rm", "comment.tmp"])
+    block["arxtic_comment"] = comment
+    return library
+
+def arxtic_library_add(key, library, value):
+    block = find(key, library)
+    old_value = block["arxtic_library"]
+    new_value = old_value + "," + value
+    if new_value[0] == ",": new_value = new_value[1:]
+    if new_value[-1] == ",": new_value = new_value[:-1]
+    block["arxtic_library"] = new_value
+    return library
+
+def arxtic_library_remove(key, library, value):
+    block = find(key, library)
+    old_value = block["arxtic_library"]
+    new_value = old_value.replace(value, "").replace(",,", ",")
+    if new_value[0] == ",": new_value = new_value[1:]
+    if new_value[-1] == ",": new_value = new_value[:-1]
+    block["arxtic_library"] = new_value
+    return library
+
+def arxtic_keywords_add(key, library, value):
+    block = find(key, library)
+    old_value = block["arxtic_keywords"]
+    new_value = old_value + "," + value
+    if new_value[0] == ",": new_value = new_value[1:]
+    if new_value[-1] == ",": new_value = new_value[:-1]
+    block["arxtic_keywords"] = new_value
+    return library
+
+def arxtic_keywords_remove(key, library, value):
+    block = find(key, library)
+    old_value = block["arxtic_keywords"]
+    new_value = old_value.replace(value, "").replace(",,", ",")
+    if new_value[0] == ",": new_value = new_value[1:]
+    if new_value[-1] == ",": new_value = new_value[:-1]
+    block["arxtic_keywords"] = new_value
+    return library
+
+def arxtic_score(key, library, score):
+    block = find(key, library)
+    block["arxtic_score"] = score
+    return library
+
+def arxtic_date_read(key, library, date=None):
+    block = find(key, library)
+    if date is None:
+        date = dt.datetime.now()
+    block["arxtic_date_read"] = date.strftime("%Y-%m-%d")
+    return library
+
+def arxtic_filename(key, library, filename):
+    block = find(key, library)
+    block["arxtic_filename"] = filename
+    return library
+
+## External reader
+
+def launch_reader(key, library, directory=PDF_DIR):
+    block = find(key, library)
+    fname = block["arxtic_filename"]
+    subprocess.Popen(["/bin/flatpak", "run", "com.github.ahrm.sioyek", directory+fname],
+                   stdout = subprocess.DEVNULL,
+                   stderr = subprocess.DEVNULL)