lightkone 0.1.0__tar.gz

lightkone-0.1.0/.gitignore

@@ -0,0 +1,7 @@
+node_modules/
+dist/
+.DS_Store
+.wrangler/
+__pycache__/
+*.egg-info/
+.pytest_cache/

lightkone-0.1.0/LICENSE

@@ -0,0 +1,73 @@
+Apache License
+Version 2.0, January 2004
+http://www.apache.org/licenses/
+
+TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
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+
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+
+     You may add Your own copyright statement to Your modifications and may provide additional or different license terms and conditions for use, reproduction, or distribution of Your modifications, or for any such Derivative Works as a whole, provided Your use, reproduction, and distribution of the Work otherwise complies with the conditions stated in this License.
+
+5. Submission of Contributions. Unless You explicitly state otherwise, any Contribution intentionally submitted for inclusion in the Work by You to the Licensor shall be under the terms and conditions of this License, without any additional terms or conditions. Notwithstanding the above, nothing herein shall supersede or modify the terms of any separate license agreement you may have executed with Licensor regarding such Contributions.
+
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+
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+END OF TERMS AND CONDITIONS
+
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+
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lightkone-0.1.0/NOTICE

@@ -0,0 +1,27 @@
+Lightkone CLI
+Copyright 2026 the Lightkone authors
+
+Licensed under the Apache License, Version 2.0 (see LICENSE).
+
+Parts of this package come from Kirsche (https://github.com/kausalflow/kirsche),
+released under the MIT License:
+
+  Copyright (c) 2021 Lei Ma
+
+  Permission is hereby granted, free of charge, to any person obtaining a copy
+  of this software and associated documentation files (the "Software"), to deal
+  in the Software without restriction, including without limitation the rights
+  to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+  copies of the Software, and to permit persons to whom the Software is
+  furnished to do so, subject to the following conditions:
+
+  The above copyright notice and this permission notice shall be included in all
+  copies or substantial portions of the Software.
+
+  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+  IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+  AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+  OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+  SOFTWARE.

lightkone-0.1.0/PKG-INFO

@@ -0,0 +1,81 @@
+Metadata-Version: 2.5
+Name: lightkone
+Version: 0.1.0
+Summary: Lightkone from the command line and from Python: your papers, tags, folders, notes, BibTeX and citation map, in the same files as the web app.
+Project-URL: Homepage, https://lightkone.lab.kausalflow.com
+Project-URL: Documentation, https://lightkone.lab.kausalflow.com/docs/cli.html
+Author: KausalFlow
+License-Expression: Apache-2.0
+License-File: LICENSE
+License-File: NOTICE
+Keywords: bibtex,citations,lightkone,papers,references,research
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering
+Requires-Python: >=3.10
+Requires-Dist: click>=8.1.7
+Requires-Dist: requests>=2.26
+Requires-Dist: typer>=0.12
+Provides-Extra: all
+Requires-Dist: cryptography>=41; extra == 'all'
+Requires-Dist: networkx>=3.0; extra == 'all'
+Requires-Dist: pandas>=2.0; extra == 'all'
+Provides-Extra: crypto
+Requires-Dist: cryptography>=41; extra == 'crypto'
+Provides-Extra: data
+Requires-Dist: pandas>=2.0; extra == 'data'
+Provides-Extra: dev
+Requires-Dist: cryptography>=41; extra == 'dev'
+Requires-Dist: networkx>=3.0; extra == 'dev'
+Requires-Dist: pandas>=2.0; extra == 'dev'
+Requires-Dist: pytest>=8; extra == 'dev'
+Provides-Extra: graph
+Requires-Dist: networkx>=3.0; extra == 'graph'
+Description-Content-Type: text/markdown
+
+# Lightkone CLI
+
+The command line and Python package for [Lightkone](https://lightkone.lab.kausalflow.com),
+the web reference manager. It works on the same library as the web app: the
+plain files in your Cloudflare R2 / S3 bucket, your GitHub repository, or a
+folder on disk. Search, add, tag, file, annotate, export BibTeX and draw the
+citation map from the terminal, a script or a notebook.
+
+```bash
+pipx install lightkone               # or: pip install lightkone
+lightkone login --from-backup lightkone-settings.json   # Lightkone: Settings → Backup → Export settings
+lightkone ls author:hinton year:2010-2015
+lightkone add 2106.09685 10.1103/PhysRevLett.116.061102 -t lensing -f Physics/GR
+lightkone export in:Thesis -o thesis.bib
+lightkone map in:Thesis --open        # which of your papers cite which
+lightkone open Hinton2012-in -p 3     # read it in the web app, at page 3
+```
+
+Extras: `lightkone[data]` (pandas DataFrames), `lightkone[graph]` (networkx,
+GraphML and GEXF), `lightkone[crypto]` (encrypted settings backups), or
+`lightkone[all]`.
+
+The full guide is at <https://lightkone.lab.kausalflow.com/docs/cli.html>
+(`docs/CLI.md` in the repository).
+
+## Working on it
+
+```bash
+cd cli
+pip install -e ".[dev]"
+pytest
+```
+
+`tests/data/golden.json` holds what Lightkone's TypeScript code produces for
+the same inputs (BibTeX parsing, citation keys, `library.json` and
+`library.bib` text, search, merging, filing, the citation graph). It is
+written by `tests/cli-golden.test.ts` in the app's tests, and `npm run check`
+fails when the app's output no longer matches it. After changing one of those
+formats in the app, run `UPDATE_GOLDEN=1 npx vitest run tests/cli-golden.test.ts`
+and make the Python side pass `pytest` again.
+
+## License
+
+Apache-2.0 (see the `LICENSE` and `NOTICE` files that come with it). The Lightkone web
+app in the rest of this repository is under AGPL-3.0.

lightkone-0.1.0/README.md

@@ -0,0 +1,45 @@
+# Lightkone CLI
+
+The command line and Python package for [Lightkone](https://lightkone.lab.kausalflow.com),
+the web reference manager. It works on the same library as the web app: the
+plain files in your Cloudflare R2 / S3 bucket, your GitHub repository, or a
+folder on disk. Search, add, tag, file, annotate, export BibTeX and draw the
+citation map from the terminal, a script or a notebook.
+
+```bash
+pipx install lightkone               # or: pip install lightkone
+lightkone login --from-backup lightkone-settings.json   # Lightkone: Settings → Backup → Export settings
+lightkone ls author:hinton year:2010-2015
+lightkone add 2106.09685 10.1103/PhysRevLett.116.061102 -t lensing -f Physics/GR
+lightkone export in:Thesis -o thesis.bib
+lightkone map in:Thesis --open        # which of your papers cite which
+lightkone open Hinton2012-in -p 3     # read it in the web app, at page 3
+```
+
+Extras: `lightkone[data]` (pandas DataFrames), `lightkone[graph]` (networkx,
+GraphML and GEXF), `lightkone[crypto]` (encrypted settings backups), or
+`lightkone[all]`.
+
+The full guide is at <https://lightkone.lab.kausalflow.com/docs/cli.html>
+(`docs/CLI.md` in the repository).
+
+## Working on it
+
+```bash
+cd cli
+pip install -e ".[dev]"
+pytest
+```
+
+`tests/data/golden.json` holds what Lightkone's TypeScript code produces for
+the same inputs (BibTeX parsing, citation keys, `library.json` and
+`library.bib` text, search, merging, filing, the citation graph). It is
+written by `tests/cli-golden.test.ts` in the app's tests, and `npm run check`
+fails when the app's output no longer matches it. After changing one of those
+formats in the app, run `UPDATE_GOLDEN=1 npx vitest run tests/cli-golden.test.ts`
+and make the Python side pass `pytest` again.
+
+## License
+
+Apache-2.0 (see the `LICENSE` and `NOTICE` files that come with it). The Lightkone web
+app in the rest of this repository is under AGPL-3.0.

lightkone-0.1.0/lightkone/__init__.py

@@ -0,0 +1,23 @@
+"""Read and write a Lightkone library from Python: the same files the web app keeps in your storage."""
+
+__version__ = "0.1.0"
+
+from lightkone.library import BIB_PATH, LIBRARY_PATH, Library
+from lightkone.storage import (
+    FolderStorage,
+    GitHubStorage,
+    S3Storage,
+    Storage,
+    StorageError,
+)
+
+__all__ = [
+    "Library",
+    "Storage",
+    "FolderStorage",
+    "S3Storage",
+    "GitHubStorage",
+    "StorageError",
+    "LIBRARY_PATH",
+    "BIB_PATH",
+]

lightkone-0.1.0/lightkone/bibtex.py

@@ -0,0 +1,376 @@
+"""BibTeX reading and writing, the same way Lightkone does it.
+
+A forgiving reader (braces, quotes, nested braces, numbers, ``@string``
+macros, month names and ``#`` concatenation) and the plain writer Lightkone
+uses for ``lightkone/library.bib``. Kept in step with Lightkone's
+``src/core/bibtex.ts`` so a library saved by either tool reads the same.
+"""
+
+from __future__ import annotations
+
+import re
+import unicodedata
+from dataclasses import dataclass, field
+from typing import Any
+
+MONTHS = {
+    "jan": "January",
+    "feb": "February",
+    "mar": "March",
+    "apr": "April",
+    "may": "May",
+    "jun": "June",
+    "jul": "July",
+    "aug": "August",
+    "sep": "September",
+    "oct": "October",
+    "nov": "November",
+    "dec": "December",
+}
+
+
+@dataclass
+class BibEntry:
+    type: str
+    key: str
+    fields: dict[str, str] = field(default_factory=dict)
+
+
+_WORD_STOP = set(' \t\r\n,={}()"#')
+
+
+def parse_bibtex(text: str) -> list[BibEntry]:
+    """Every entry in a BibTeX text, with lower-cased field names and raw values."""
+    entries: list[BibEntry] = []
+    macros = dict(MONTHS)
+    n = len(text)
+    i = 0
+
+    def skip_space() -> None:
+        nonlocal i
+        while i < n and text[i].isspace():
+            i += 1
+
+    def read_word() -> str:
+        nonlocal i
+        start = i
+        while i < n and text[i] not in _WORD_STOP and not text[i].isspace():
+            i += 1
+        return text[start:i]
+
+    def read_braced() -> str:
+        nonlocal i
+        depth = 0
+        start = i + 1
+        while i < n:
+            c = text[i]
+            if c == "\\":
+                i += 2
+                continue
+            if c == "{":
+                depth += 1
+            elif c == "}":
+                depth -= 1
+                if depth == 0:
+                    i += 1
+                    return text[start : i - 1]
+            i += 1
+        return text[start:]
+
+    def read_quoted() -> str:
+        nonlocal i
+        depth = 0
+        i += 1
+        start = i
+        while i < n:
+            c = text[i]
+            if c == "\\":
+                i += 2
+                continue
+            if c == "{":
+                depth += 1
+            elif c == "}":
+                depth -= 1
+            elif c == '"' and depth == 0:
+                i += 1
+                return text[start : i - 1]
+            i += 1
+        return text[start:]
+
+    def read_value() -> str:
+        nonlocal i
+        parts: list[str] = []
+        while True:
+            skip_space()
+            c = text[i] if i < n else ""
+            if c == "{":
+                parts.append(read_braced())
+            elif c == '"':
+                parts.append(read_quoted())
+            else:
+                w = read_word()
+                if not w:
+                    break
+                parts.append(w if w.isdigit() else macros.get(w.lower(), w))
+            skip_space()
+            if i < n and text[i] == "#":
+                i += 1
+                continue
+            break
+        return "".join(parts)
+
+    while i < n:
+        at = text.find("@", i)
+        if at < 0:
+            break
+        i = at + 1
+        typ = read_word().lower()
+        skip_space()
+        opening = text[i] if i < n else ""
+        if opening not in ("{", "("):
+            continue
+        close = "}" if opening == "{" else ")"
+        i += 1
+        if typ == "comment":
+            i = at + 1
+            continue
+        if typ == "preamble":
+            read_value()
+            continue
+        if typ == "string":
+            skip_space()
+            name = read_word().lower()
+            skip_space()
+            if i < n and text[i] == "=":
+                i += 1
+                macros[name] = read_value()
+            continue
+        skip_space()
+        key_start = i
+        depth = 0
+        # Braces in a key ("Erd\H{o}s1959") are part of it, not the end of the entry.
+        while i < n and (depth > 0 or (text[i] != "," and text[i] != close)):
+            if text[i] == "{":
+                depth += 1
+            elif text[i] == "}":
+                depth -= 1
+            i += 1
+        key = text[key_start:i].strip()
+        fields: dict[str, str] = {}
+        while i < n and text[i] != close:
+            if text[i] == ",":
+                i += 1
+            skip_space()
+            if i >= n or text[i] == close:
+                break
+            name = read_word().lower()
+            skip_space()
+            if not name or i >= n or text[i] != "=":
+                # Malformed field: skip its values, then to the next comma or the end of the entry.
+                while i < n and text[i] != "," and text[i] != close:
+                    if text[i] == "{":
+                        read_braced()
+                    elif text[i] == '"':
+                        read_quoted()
+                    else:
+                        i += 1
+                continue
+            i += 1
+            fields[name] = re.sub(r"\s+", " ", read_value()).strip()
+            skip_space()
+        i += 1
+        if key or fields:
+            entries.append(BibEntry(typ, key, fields))
+    return entries
+
+
+_ACCENTS = {
+    '"': "\u0308",
+    "'": "\u0301",
+    "`": "\u0300",
+    "^": "\u0302",
+    "~": "\u0303",
+    "=": "\u0304",
+    ".": "\u0307",
+    "c": "\u0327",
+    "v": "\u030c",
+    "u": "\u0306",
+    "H": "\u030b",
+}
+_LETTERS = {
+    "ss": "ß",
+    "o": "ø",
+    "O": "Ø",
+    "ae": "æ",
+    "AE": "Æ",
+    "l": "ł",
+    "L": "Ł",
+    "i": "ı",
+}
+
+_ACCENT_RE = re.compile(
+    r"\{?\\([\"'`^~=.]|[cvuH](?=[\s{]))\s*\{?([A-Za-z]|\\[ij]\b)\}?\}?"
+)
+_LETTER_RE = re.compile(r"\{\\(ss|o|O|ae|AE|l|L|i)\}|\\(ss|o|O|ae|AE|l|L|i)\b ?")
+
+
+def plain(value: str) -> str:
+    """Remove protective braces and the most common LaTeX escapes, for display and search."""
+    v = _ACCENT_RE.sub(
+        lambda m: unicodedata.normalize(
+            "NFC", m.group(2).replace("\\", "") + _ACCENTS[m.group(1)]
+        ),
+        value,
+    )
+    v = _LETTER_RE.sub(lambda m: _LETTERS[m.group(1) or m.group(2)], v)
+    v = re.sub(r"\\(?:emph|textit|textbf|mathrm|textrm)\{([^{}]*)\}", r"\1", v)
+    v = re.sub(r"\\([&%$#_{}])", r"\1", v)
+    v = re.sub(r"(?<!\\)[{}]", "", v)
+    v = v.replace("~", " ")
+    return re.sub(r"\s+", " ", v).strip()
+
+
+_ARXIV_IN_URL = re.compile(
+    r"arxiv\.org/(?:abs|pdf|html)/([^\s?#]+?)(?:v\d+)?(?:\.pdf)?(?:[?#]|$)", re.I
+)
+_ID_KEYWORD = re.compile(r"^(doi|url|arxiv|isbn|issn|pmid|pmc):|https?://", re.I)
+
+
+def split_authors(value: str) -> list[str]:
+    """BibTeX ``author`` field to "Last, First" strings."""
+    if not value.strip():
+        return []
+    out = []
+    for raw in re.split(r"\s+and\s+", value, flags=re.I):
+        raw = raw.strip()
+        a = plain(raw)
+        if not a:
+            continue
+        # "{LIGO Scientific Collaboration}" is a corporate name: never flip it.
+        if "," in a or a.lower() == "others" or re.match(r"^\{.*\}$", raw, re.S):
+            out.append(a)
+            continue
+        parts = a.split(" ")
+        out.append(f"{parts[-1]}, {' '.join(parts[:-1])}" if len(parts) > 1 else a)
+    return out
+
+
+def entry_to_draft(entry: BibEntry) -> dict[str, Any]:
+    """A BibTeX entry as a paper draft (a paper without id and added date)."""
+    f = dict(entry.fields)
+
+    def take(name: str) -> str | None:
+        return f.pop(name, None)
+
+    title = plain(take("title") or "")
+    author = take("author")
+    editor = take("editor")
+    authors = split_authors(author if author is not None else (editor or ""))
+    year_raw = take("year")
+    m = re.search(r"\d{4}", year_raw or "")
+    year = int(m.group(0)) if m else None
+    journal = take("journal")
+    booktitle = take("booktitle")
+    venue = (
+        plain(journal or "")
+        or plain(booktitle or "")
+        or plain(f.get("publisher") or "")
+    )
+    abstract = take("abstract")
+    doi = take("doi")
+    if doi:
+        doi = re.sub(r"^https?://(dx\.)?doi\.org/", "", doi, flags=re.I)
+    url = take("url")
+    eprint = take("eprint")
+    arxivid = take("arxivid")
+    prefix = (f.get("archiveprefix") or f.get("eprinttype") or "").lower()
+    arxiv = arxivid or (eprint if prefix == "arxiv" else None)
+    if not arxiv and url:
+        mm = _ARXIV_IN_URL.search(url)
+        arxiv = mm.group(1) if mm else None
+    if not arxiv and eprint and re.match(r"^\d{4}\.\d{4,5}", eprint):
+        arxiv = eprint
+    if arxiv:
+        for k in ("archiveprefix", "eprinttype", "primaryclass"):
+            f.pop(k, None)
+    elif eprint:
+        f["eprint"] = eprint
+    tags = [plain(t) for t in re.split(r"[;,]", take("keywords") or "")]
+    tags = [t for t in tags if t and not _ID_KEYWORD.search(t)]
+    file = take("file")
+    annote = take("annote")
+    note = take("note")
+    notes = annote if annote is not None else note
+    draft: dict[str, Any] = {
+        "key": entry.key,
+        "type": entry.type,
+        "title": title,
+        "authors": authors,
+        "year": year,
+        "venue": venue or None,
+        "abstract": plain(abstract) if abstract else None,
+        "doi": doi or None,
+        "arxiv": (
+            re.sub(r"v\d+$", "", re.sub(r"^arxiv:", "", arxiv, flags=re.I))
+            if arxiv
+            else None
+        ),
+        "url": url,
+        "tags": tags,
+        "file": file,
+        "notes": notes,
+        "fields": f,
+    }
+    return {k: v for k, v in draft.items() if v is not None}
+
+
+def parse_bibtex_to_drafts(text: str) -> list[dict[str, Any]]:
+    return [entry_to_draft(e) for e in parse_bibtex(text) if e.fields.get("title")]
+
+
+def _escape(v: str) -> str:
+    return re.sub(r"\\?([&%#])", r"\\\1", v)
+
+
+def paper_to_bibtex(p: dict[str, Any]) -> str:
+    """One paper as BibTeX, exactly as Lightkone writes it."""
+    lines: list[tuple[str, str]] = []
+
+    def add(name: str, value: Any) -> None:
+        if value is not None and value != "":
+            lines.append((name, str(value)))
+
+    add("title", "{" + _escape(p.get("title", "")) + "}")
+    add(
+        "author",
+        " and ".join(
+            a if ("," in a or a == "others") else "{" + a + "}"
+            for a in p.get("authors", [])
+        ),
+    )
+    add("year", p.get("year"))
+    fields = p.get("fields") or {}
+    venue_field = (
+        "booktitle" if p.get("type") in ("inproceedings", "incollection") else "journal"
+    )
+    if p.get("venue") and not fields.get(venue_field):
+        add(venue_field, _escape(p["venue"]))
+    add("doi", p.get("doi"))
+    if p.get("arxiv"):
+        add("eprint", p["arxiv"])
+        add("archiveprefix", "arXiv")
+    add("url", p.get("url"))
+    add("abstract", _escape(p["abstract"]) if p.get("abstract") else None)
+    if p.get("tags"):
+        add("keywords", ";".join(p["tags"]))
+    add("file", p.get("file"))
+    for k, v in fields.items():
+        if not k.startswith("lightkone-"):
+            add(k, v)
+    width = max(len(k) for k, _ in lines)
+    body = ",\n".join(f"  {k.ljust(width)} = {{{v}}}" for k, v in lines)
+    return f"@{p.get('type') or 'misc'}{{{p['key']},\n{body}\n}}\n"
+
+
+def library_to_bibtex(papers: list[dict[str, Any]]) -> str:
+    return "\n".join(paper_to_bibtex(p) for p in papers)