BibexPy 2.0.0__py3-none-any.whl

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bibexpy/_web/tools/python.svg

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+<svg fill="#3776AB" role="img" viewBox="0 0 24 24" xmlns="http://www.w3.org/2000/svg"><title>Python</title><path d="M14.25.18l.9.2.73.26.59.3.45.32.34.34.25.34.16.33.1.3.04.26.02.2-.01.13V8.5l-.05.63-.13.55-.21.46-.26.38-.3.31-.33.25-.35.19-.35.14-.33.1-.3.07-.26.04-.21.02H8.77l-.69.05-.59.14-.5.22-.41.27-.33.32-.27.35-.2.36-.15.37-.1.35-.07.32-.04.27-.02.21v3.06H3.17l-.21-.03-.28-.07-.32-.12-.35-.18-.36-.26-.36-.36-.35-.46-.32-.59-.28-.73-.21-.88-.14-1.05-.05-1.23.06-1.22.16-1.04.24-.87.32-.71.36-.57.4-.44.42-.33.42-.24.4-.16.36-.1.32-.05.24-.01h.16l.06.01h8.16v-.83H6.18l-.01-2.75-.02-.37.05-.34.11-.31.17-.28.25-.26.31-.23.38-.2.44-.18.51-.15.58-.12.64-.1.71-.06.77-.04.84-.02 1.27.05zm-6.3 1.98l-.23.33-.08.41.08.41.23.34.33.22.41.09.41-.09.33-.22.23-.34.08-.41-.08-.41-.23-.33-.33-.22-.41-.09-.41.09zm13.09 3.95l.28.06.32.12.35.18.36.27.36.35.35.47.32.59.28.73.21.88.14 1.04.05 1.23-.06 1.23-.16 1.04-.24.86-.32.71-.36.57-.4.45-.42.33-.42.24-.4.16-.36.09-.32.05-.24.02-.16-.01h-8.22v.82h5.84l.01 2.76.02.36-.05.34-.11.31-.17.29-.25.25-.31.24-.38.2-.44.17-.51.15-.58.13-.64.09-.71.07-.77.04-.84.01-1.27-.04-1.07-.14-.9-.2-.73-.25-.59-.3-.45-.33-.34-.34-.25-.34-.16-.33-.1-.3-.04-.25-.02-.2.01-.13v-5.34l.05-.64.13-.54.21-.46.26-.38.3-.32.33-.24.35-.2.35-.14.33-.1.3-.06.26-.04.21-.02.13-.01h5.84l.69-.05.59-.14.5-.21.41-.28.33-.32.27-.35.2-.36.15-.36.1-.35.07-.32.04-.28.02-.21V6.07h2.09l.14.01zm-6.47 14.25l-.23.33-.08.41.08.41.23.33.33.23.41.08.41-.08.33-.23.23-.33.08-.41-.08-.41-.23-.33-.33-.23-.41-.08-.41.08z"/></svg>

bibexpy/_web/tools/r.svg

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+<svg fill="#276DC3" role="img" viewBox="0 0 24 24" xmlns="http://www.w3.org/2000/svg"><title>R</title><path d="M12 2.746c-6.627 0-12 3.599-12 8.037 0 3.897 4.144 7.144 9.64 7.88V16.26c-2.924-.915-4.925-2.755-4.925-4.877 0-3.035 4.084-5.494 9.12-5.494 5.038 0 8.757 1.683 8.757 5.494 0 1.976-.999 3.379-2.662 4.272.09.066.174.128.258.216.169.149.25.363.372.544 2.128-1.45 3.44-3.437 3.44-5.631 0-4.44-5.373-8.038-12-8.038zm-2.111 4.99v13.516l4.093-.002-.002-5.291h1.1c.225 0 .321.066.549.25.272.22.715.982.715.982l2.164 4.063 4.627-.002-2.864-4.826s-.086-.193-.265-.383a2.22 2.22 0 00-.582-.416c-.422-.214-1.149-.434-1.149-.434s3.578-.264 3.578-3.826c0-3.562-3.744-3.63-3.744-3.63zm4.127 2.93l2.478.002s1.149-.062 1.149 1.127c0 1.165-1.149 1.17-1.149 1.17h-2.478zm1.754 6.119c-.494.049-1.012.079-1.54.088v1.807a16.622 16.622 0 002.37-.473l-.471-.891s-.108-.183-.248-.394c-.039-.054-.08-.098-.111-.137z"/></svg>

bibexpy/_web/tools/refworks.svg

@@ -0,0 +1,5 @@
+<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 64 64" role="img" aria-labelledby="title">
+  <title id="title">RefWorks</title>
+  <rect width="64" height="64" rx="14" fill="#F5F3FF"/>
+  <path d="M18 17h15.6c7.1 0 11.4 3.8 11.4 10.1 0 4.2-2 7.3-5.5 8.9L47 50h-8.8l-6.5-12.4h-5.9V50H18V17Zm15 14c2.8 0 4.5-1.4 4.5-3.9s-1.7-3.9-4.5-3.9h-7.2V31H33Z" fill="#7C3AED"/>
+</svg>

bibexpy/_web/tools/scite.svg

@@ -0,0 +1,5 @@
+<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 64 64" role="img" aria-labelledby="title">
+  <title id="title">Scite</title>
+  <rect width="64" height="64" rx="14" fill="#EEF2FF"/>
+  <path d="M44 22.3c-2.5-1.4-5.7-2.3-9.4-2.3-4.1 0-6.2 1.2-6.2 3.3 0 2.2 2.5 2.8 7.2 3.8 6.3 1.3 10.7 3.6 10.7 10.2 0 6.8-5.4 10.8-14.1 10.8-5 0-9.5-1.2-12.5-3.1v-7.6c3.2 2.3 7.3 3.7 11.6 3.7 4.3 0 6.5-1.2 6.5-3.5 0-2.4-2.4-3.1-7.4-4.1-6.2-1.3-10.5-3.4-10.5-9.8 0-6.5 5.2-10.5 13.8-10.5 4.4 0 7.9.8 10.3 2.1v7Z" fill="#4F46E5"/>
+</svg>

bibexpy/_web/tools/tableau.svg

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+<svg xmlns="http://www.w3.org/2000/svg" width="1em" height="1em" viewBox="0 0 24 24"><path fill="#E97627" d="M11.654.174v2.203H9.682v.58h1.972V5.16h.696V2.957h1.97v-.58h-1.97V.174h-.348zm6.03 2.262l-.002 1.623v1.623h-2.957v.927h2.957v3.188h1.043l.011-1.582l.02-1.576l1.465-.02l1.46-.01v-.927h-2.953V2.436h-.522zm-12.407.06v3.19H2.291v.925h2.986v3.19h.985V6.61h3.013v-.925H6.262V2.496H5.77zm6.086 5.27v3.593H8.06v1.188h3.304v3.596h1.28v-3.596h3.309v-1.188h-3.31V7.766h-.637zm9.721 1.55v2.221h-2.012v.811h2.012v2.261h.887v-2.261H24v-.811h-2.029v-2.22h-.422zm-19.111.131v2.174H0v.621h1.973v2.194h.667v-2.194h2v-.62H2.609V9.446h-.318zm15.709 4.516v3.254h-3.016v.927h3.016v3.217h1.072v-3.216h2.986v-.928h-2.986v-3.254h-.533zm-12.463.008v3.246H2.262v.928h2.957v3.189H6.32v-3.189h2.955v-.928H6.32V13.97h-.55zm6.316 4.578l.002 1.103v1.1H9.566v.812h1.971v2.262h.928l.012-1.119l.017-1.143h1.969v-.812h-2v-2.203h-.465z"/></svg>

bibexpy/_web/tools/zotero.svg

@@ -0,0 +1 @@
+<svg fill="#CC2936" role="img" viewBox="0 0 24 24" xmlns="http://www.w3.org/2000/svg"><title>Zotero</title><path d="M21.231 2.462 7.18 20.923h14.564V24H2.256v-2.462L16.308 3.076H2.975V0h18.256v2.462z"/></svg>

bibexpy/cli.py

@@ -0,0 +1,242 @@
+"""BibexPy v2 — komut satırı başlatıcı.
+
+`pip install bibexpy` sonrası `bibexpy` komutu bu modülü çağırır:
+
+    bibexpy                      # ~/.bibexpy/storage, tarayıcı otomatik açılır, port 8001
+    bibexpy --port 8080          # özel port
+    bibexpy --no-browser         # sadece sunucu, tarayıcı açma
+    bibexpy --storage ./data     # bu çalıştırma için özel depolama klasörü
+    bibexpy --version            # sürüm
+
+Mimari:
+  • _web/    — Next.js static export (BIBEXPY_FRONTEND_DIST ile main.py'ye verilir)
+  • _server/ — FastAPI uygulaması; sys.path'e eklenince flat import'lar çözülür
+  • bibex_core — wheel'da ikinci top-level paket olarak kurulu
+
+Node.js / npm GEREKMEZ — UI önceden derlenmiş statik dosyalardır.
+"""
+
+from __future__ import annotations
+
+import argparse
+import os
+import re
+import socket
+import sys
+import threading
+import time
+import urllib.request
+import webbrowser
+from pathlib import Path
+
+# Wheel içindeki bu paketin kökü (cli.py'nin bulunduğu dizin).
+_PKG_DIR = Path(__file__).resolve().parent
+_WEB_DIR = _PKG_DIR / "_web"
+_SERVER_DIR = _PKG_DIR / "_server"
+
+__version__ = "2.0.0"
+__codename__ = "Helium"   # v2 surum kod adi (v1 "Hydrogen"in ardili; H -> He)
+
+
+# Ilk-calistirma .env sablonu — kullanici anahtarlari nereye gireceğini gorur.
+# Hepsi opsiyonel; anahtarsiz da calisir (enrichment/LLM graceful skip).
+_ENV_TEMPLATE = """\
+# BibexPy ayarlari — API anahtarlari (hepsi OPSIYONEL).
+# Crossref, OpenAlex ve Unpaywall UCRETSIZdir; yalniz Scopus anahtar ister.
+
+# --- Zenginlestirme kaynaklari (opsiyonel) ---
+SCOPUS_API_KEY=
+CROSSREF_EMAIL=
+UNPAYWALL_EMAIL=
+SEMANTIC_SCHOLAR_API_KEY=
+
+# --- LLM (disambiguation icin, opsiyonel) ---
+# Saglayici: deepseek | openai | openrouter | custom
+LLM_PROVIDER=deepseek
+LLM_API_KEY=
+LLM_BASE_URL=https://api.deepseek.com
+LLM_MODEL=deepseek-v4-flash
+"""
+
+
+def _write_env_template(env_file: Path) -> None:
+    """`.env` yoksa yorumlu bir sablon yaz (varsa dokunma)."""
+    if env_file.exists():
+        return
+    try:
+        env_file.write_text(_ENV_TEMPLATE, encoding="utf-8")
+    except OSError:
+        pass
+
+
+def _port_is_free(host: str, port: int) -> bool:
+    with socket.socket(socket.AF_INET, socket.SOCK_STREAM) as s:
+        s.setsockopt(socket.SOL_SOCKET, socket.SO_REUSEADDR, 1)
+        try:
+            s.bind((host, port))
+            return True
+        except OSError:
+            return False
+
+
+def _resolve_port(host: str, preferred: int) -> int:
+    """Istenen port boşsa onu; degilse sonraki 20'yi, sonra OS'tan boş port dener."""
+    if _port_is_free(host, preferred):
+        return preferred
+    for p in range(preferred + 1, preferred + 21):
+        if _port_is_free(host, p):
+            return p
+    with socket.socket(socket.AF_INET, socket.SOCK_STREAM) as s:
+        s.bind((host, 0))
+        return int(s.getsockname()[1])
+
+
+def _read_env_value(env_file: Path, key: str) -> str | None:
+    """`.env` dosyasından tek bir KEY değerini oku (yoksa None)."""
+    if not env_file.is_file():
+        return None
+    try:
+        for raw in env_file.read_text(encoding="utf-8").splitlines():
+            line = raw.strip()
+            m = re.match(rf"^{re.escape(key)}\s*=\s*(.*)$", line)
+            if m:
+                val = m.group(1).strip()
+                if (val.startswith('"') and val.endswith('"')) or (
+                    val.startswith("'") and val.endswith("'")
+                ):
+                    val = val[1:-1]
+                return val
+    except OSError:
+        return None
+    return None
+
+
+def _open_browser_when_ready(url: str, health_url: str, timeout: float = 30.0) -> None:
+    """Sunucu /api/health'e cevap verince tarayıcıyı aç.
+
+    Ayrı thread'de çalışır; sunucunun ayağa kalkmasını bekler ki tarayıcı
+    'bağlantı reddedildi' göstermesin.
+    """
+    deadline = time.monotonic() + timeout
+    while time.monotonic() < deadline:
+        try:
+            with urllib.request.urlopen(health_url, timeout=1.5) as resp:
+                if resp.status == 200:
+                    break
+        except Exception:
+            time.sleep(0.4)
+    try:
+        webbrowser.open(url)
+    except Exception:
+        pass
+
+
+def _build_parser() -> argparse.ArgumentParser:
+    p = argparse.ArgumentParser(
+        prog="bibexpy",
+        description="Self-hosted bibliometric data preparation tool "
+        "(Scopus + Web of Science).",
+    )
+    p.add_argument("--host", default="127.0.0.1", help="Bağlanılacak host (varsayılan: 127.0.0.1)")
+    p.add_argument("--port", type=int, default=6060, help="Port (varsayılan: 6060)")
+    p.add_argument(
+        "--storage",
+        default=None,
+        help="Depolama klasörü (varsayılan: ~/.bibexpy/storage veya .env'deki STORAGE_DIR)",
+    )
+    p.add_argument(
+        "--config-dir",
+        default=None,
+        help="Yapılandırma klasörü (.env burada; varsayılan: ~/.bibexpy)",
+    )
+    p.add_argument("--no-browser", action="store_true", help="Tarayıcıyı otomatik açma")
+    p.add_argument("--version", action="version", version=f"BibexPy {__version__} ({__codename__})")
+    return p
+
+
+def main(argv: list[str] | None = None) -> int:
+    # Windows konsolu (cp1254/cp850 vb.) UTF-8 olmayan codepage'lerde Türkçe
+    # karakterlerde veya ok işaretlerinde UnicodeEncodeError ile çökebilir.
+    # stdout/stderr'i UTF-8'e ayarla; errors='replace' → asla raise etmez.
+    for _stream in (sys.stdout, sys.stderr):
+        try:
+            _stream.reconfigure(encoding="utf-8", errors="replace")  # type: ignore[attr-defined]
+        except Exception:
+            pass
+
+    args = _build_parser().parse_args(argv)
+
+    # 1. Paket bütünlüğü kontrolü — build script çalışmadan kurulmuşsa anlamlı hata ver.
+    if not (_WEB_DIR / "index.html").is_file():
+        sys.stderr.write(
+            "HATA: Gömülü frontend bulunamadı (_web/index.html yok).\n"
+            "Bu wheel düzgün build edilmemiş. scripts/build_wheel.* ile yeniden üretin.\n"
+        )
+        return 2
+    if not (_SERVER_DIR / "main.py").is_file():
+        sys.stderr.write(
+            "HATA: Gömülü sunucu bulunamadı (_server/main.py yok).\n"
+            "Bu wheel düzgün build edilmemiş. scripts/build_wheel.* ile yeniden üretin.\n"
+        )
+        return 2
+
+    # 2. Yapılandırma + depolama klasörleri (yazılabilir kullanıcı konumu).
+    config_dir = Path(args.config_dir).expanduser() if args.config_dir else Path.home() / ".bibexpy"
+    config_dir.mkdir(parents=True, exist_ok=True)
+    env_file = config_dir / ".env"
+    _write_env_template(env_file)  # ilk calistirmada yorumlu sablon
+
+    # Depolama önceliği: --storage > .env'deki STORAGE_DIR > <config_dir>/storage
+    storage = (
+        args.storage
+        or _read_env_value(env_file, "STORAGE_DIR")
+        or str(config_dir / "storage")
+    )
+    storage_path = Path(storage).expanduser()
+    storage_path.mkdir(parents=True, exist_ok=True)
+
+    # 3. Ortam değişkenleri — main.py + config.py + settings router bunları okur.
+    os.environ["BIBEXPY_CONFIG_DIR"] = str(config_dir)
+    os.environ["BIBEXPY_FRONTEND_DIST"] = str(_WEB_DIR)
+    os.environ["STORAGE_DIR"] = str(storage_path)
+
+    # 4. Flat import'lar (from config import ..., from routers import ...) için
+    #    gömülü sunucu dizinini sys.path başına ekle.
+    sys.path.insert(0, str(_SERVER_DIR))
+
+    # 5. Uygulamayı import et (env var'lar set edildikten SONRA — _frontend_root()
+    #    BIBEXPY_FRONTEND_DIST'i okuyup statik UI'yi mount eder).
+    try:
+        from main import app  # type: ignore  # noqa: E402  (gömülü _server modülü)
+    except Exception as exc:  # pragma: no cover
+        sys.stderr.write(f"HATA: Sunucu uygulaması yüklenemedi: {exc}\n")
+        return 1
+
+    import uvicorn
+
+    port = _resolve_port(args.host, args.port)
+    if port != args.port:
+        print(f"  (not: {args.port} portu dolu; {port} kullaniliyor)")
+    url = f"http://{args.host}:{port}/"
+    health = f"http://{args.host}:{port}/api/health"
+
+    print(f"  BibexPy v{__version__} \"{__codename__}\"")
+    print(f"  -> Arayuz:   {url}")
+    print(f"  -> Depolama: {storage_path}")
+    print(f"  -> Ayarlar:  {env_file}")
+    print(f"  (Durdurmak icin Ctrl+C)\n")
+
+    if not args.no_browser:
+        threading.Thread(
+            target=_open_browser_when_ready, args=(url, health), daemon=True
+        ).start()
+
+    try:
+        uvicorn.run(app, host=args.host, port=port, log_level="info")
+    except KeyboardInterrupt:  # pragma: no cover
+        pass
+    return 0
+
+
+if __name__ == "__main__":  # pragma: no cover
+    raise SystemExit(main())

bibexpy-2.0.0.dist-info/METADATA

@@ -0,0 +1,105 @@
+Metadata-Version: 2.4
+Name: bibexpy
+Version: 2.0.0
+Summary: Self-hosted bibliometric data preparation tool (Scopus + Web of Science)
+Author: Burak Can Kara, Alperen Şahin, Taşkın Dirsehan
+License: GPL-3.0-or-later
+Project-URL: Homepage, https://bibexpy.com
+Project-URL: Repository, https://github.com/bcankara/BibexPy
+Project-URL: Paper, https://doi.org/10.1016/j.softx.2025.102098
+Keywords: bibliometrics,scientometrics,scopus,web of science,research
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Information Analysis
+Classifier: Framework :: FastAPI
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: fastapi>=0.110.0
+Requires-Dist: uvicorn[standard]>=0.27.0
+Requires-Dist: python-multipart>=0.0.9
+Requires-Dist: pydantic>=2.6.0
+Requires-Dist: pydantic-settings>=2.2.0
+Requires-Dist: sse-starlette>=2.0.0
+Requires-Dist: pandas>=2.0.0
+Requires-Dist: numpy>=1.24.0
+Requires-Dist: openpyxl>=3.1.2
+Requires-Dist: scikit-learn>=1.3.0
+Requires-Dist: nltk>=3.8.1
+Requires-Dist: requests>=2.31.0
+Requires-Dist: urllib3>=2.0.0
+Requires-Dist: certifi>=2023.5.7
+Requires-Dist: python-dotenv>=1.0.0
+Requires-Dist: tqdm>=4.65.0
+Requires-Dist: colorama>=0.4.6
+Requires-Dist: unidecode==1.3.6
+Requires-Dist: typing-extensions>=4.7.0
+Dynamic: license-file
+
+<p align="center">
+  <a href="https://bibexpy.com">
+    <img src="https://raw.githubusercontent.com/bcankara/BibexPy/main/apps/web/public/images/bibexpy-logo-full.png" alt="BibexPy — V2.0.0 Helium — Bibliometrics Experience with Python" width="420">
+  </a>
+</p>
+
+**Self-hosted, reproducible bibliometric data preparation for Web of Science & Scopus.**
+
+BibexPy v2.0.0 **"Helium"** merges, filters, harmonizes, enriches and exports WoS + Scopus
+records through a local web interface — with full provenance — and keeps your licensed
+exports on your own machine. It prepares analysis-ready datasets for VOSviewer, Biblioshiny,
+BibTeX, RIS, Excel and more.
+
+## Install
+
+```bash
+pip install bibexpy
+bibexpy            # launches the local web UI (browser opens automatically)
+```
+
+Requires **Python 3.10+** only — **no Node.js/npm needed** (the interface ships precompiled
+inside the package). Works on Windows, macOS and Linux.
+
+```bash
+bibexpy --port 8080          # custom port
+bibexpy --no-browser         # server only
+bibexpy --storage ./data     # custom storage folder
+bibexpy --version
+```
+
+Defaults: UI at `http://127.0.0.1:6060`, data under `~/.bibexpy/storage`, settings/API keys
+under `~/.bibexpy/.env` (managed from the in-app Settings page). Press `Ctrl+C` to stop.
+
+## Highlights (v2)
+
+- One-click **Smart Merge** — probabilistic record linkage (DOI + Jaro–Winkler), confidence
+  scoring, optional borderline review, and a copy-ready methodology paragraph.
+- **ORCID-first** author disambiguation + **address harmonization** (organization roll-up,
+  country standardization).
+- **Multi-source enrichment** (CrossRef, OpenAlex, Scopus, DataCite, Unpaywall, Europe PMC,
+  Semantic Scholar) with reverse-DOI recovery — verifiable sources only.
+- Reproducible, preset-based **filtering** and a bibliometrically weighted **quality dashboard**.
+- Full **provenance**: append-only audit log, snapshots, isolated analyses, auto-generated
+  methodology narrative.
+- Structured **export**: WoS, VOSviewer TSV, BibTeX, RIS, CSV, TSV, XLSX.
+
+## Links
+
+[Website](https://bibexpy.com) · [Docs](https://bibexpy.com/doc) ·
+[GitHub](https://github.com/bcankara/BibexPy) · [Paper (SoftwareX)](https://doi.org/10.1016/j.softx.2025.102098)
+
+## Citation
+
+> Kara, B. C., Şahin, A., & Dirsehan, T. (2025). BibexPy: Harmonizing the bibliometric symphony
+> of Scopus and Web of Science. *SoftwareX*, 30, 102098.
+> https://doi.org/10.1016/j.softx.2025.102098
+
+## License
+
+GPL-3.0-or-later