lixplore-cli 1.2.0__tar.gz → 1.2.2__tar.gz

{lixplore_cli-1.2.0 → lixplore_cli-1.2.2}/CHANGELOG.md

@@ -7,6 +7,32 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+## [1.2.2] - 2026-09-27
+
+### Changed
+- Python 3.9 or newer is required (3.8 reached end of life in October 2024; source builds on it
+  already failed). CI now tests 3.9 to 3.13
+
+### Fixed
+- Alerts `.env`: when a variable appears twice, the later line now wins (as in other `.env` tools).
+  Before, a `LIXPLORE_QUERIES` line added below the `init` template's example was silently ignored
+- Alerts `test` and `check` work before any search is set, so channels can be tested first
+  (before, both stopped with "LIXPLORE_QUERIES is empty"). `run` and `dry-run` still require it
+- PubMed: DOIs were missing for many older papers (the DOI was read only from `ELocationID`,
+  not from the article ID list), which weakened deduplication, enrichment and PDF lookup
+- PubMed: year was empty when the record only has a date range such as "2001 May 1-15"
+- PubMed: when NCBI's search backend is temporarily down, requests are retried and a clear
+  "temporarily unavailable" message is shown instead of the raw server error
+
+## [1.2.1] - 2026-09-27
+
+### Fixed
+- Journal export templates (`--template`, `--list-templates`) were missing when the package was
+  built straight from source, as the AUR and Homebrew packages do
+- Exports were written inside the installed package (`site-packages/exports/`), which fails with a
+  permission error for AUR and Homebrew installs. They now go to `exports/` in the current folder
+- `--install-man` could not find the man page in pip, AUR and Homebrew installs
+
 ## [1.2.0] - 2026-09-27
 
 ### Added
@@ -197,4 +223,4 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ---
 
-For more details, see the [README](README.md).
+For more details, see the [README](https://github.com/pryndor/Lixplore_cli#readme).

{lixplore_cli-1.2.0/lixplore_cli.egg-info → lixplore_cli-1.2.2}/PKG-INFO

@@ -1,7 +1,7 @@
 Metadata-Version: 2.4
 Name: lixplore-cli
-Version: 1.2.0
-Summary: Academic Literature Search & Export CLI Tool
+Version: 1.2.2
+Summary: Unix-inspired CLI for searching PubMed, arXiv, Crossref, DOAJ and Europe PMC, with deduplication, 8 export formats and scheduled paper alerts
 Author-email: Balasubramanian Periannan <balathepharmacist@gmail.com>
 Maintainer-email: Balasubramanian Periannan <balathepharmacist@gmail.com>
 License-Expression: MIT
@@ -18,7 +18,6 @@ Classifier: Topic :: Scientific/Engineering :: Information Analysis
 Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
 Classifier: Topic :: Text Processing :: General
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
@@ -29,7 +28,7 @@ Classifier: Operating System :: POSIX :: Linux
 Classifier: Operating System :: MacOS
 Classifier: Operating System :: Microsoft :: Windows
 Classifier: Environment :: Console
-Requires-Python: >=3.8
+Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: biopython>=1.79
@@ -37,10 +36,10 @@ Requires-Dist: requests>=2.25.0
 Requires-Dist: openpyxl>=3.0.0
 Provides-Extra: tui
 Requires-Dist: rich>=13.0.0; extra == "tui"
-Requires-Dist: textual>=4.0.0; python_version >= "3.9" and extra == "tui"
+Requires-Dist: textual>=4.0.0; extra == "tui"
 Provides-Extra: all
 Requires-Dist: rich>=13.0.0; extra == "all"
-Requires-Dist: textual>=4.0.0; python_version >= "3.9" and extra == "all"
+Requires-Dist: textual>=4.0.0; extra == "all"
 Provides-Extra: dev
 Requires-Dist: pytest>=6.0; extra == "dev"
 Requires-Dist: pytest-cov; extra == "dev"
@@ -51,9 +50,9 @@ Dynamic: license-file
 
 # Lixplore-cli
 
-> **Academic Literature Search & Export CLI Tool**
+> **A Unix-inspired command-line tool for searching scientific literature**, built for terminal users who want speed, automation and minimal interfaces.
 
-[![Python Version](https://img.shields.io/badge/python-3.7+-blue.svg)](https://www.python.org/downloads/)
+[![Python Version](https://img.shields.io/badge/python-3.9+-blue.svg)](https://www.python.org/downloads/)
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
 [![Documentation](https://img.shields.io/badge/docs-latest-blue.svg)](https://pryndor.github.io/Lixplore_cli/)
 [![GitHub](https://img.shields.io/badge/GitHub-Repository-181717?logo=github)](https://github.com/pryndor/Lixplore_cli)
@@ -62,7 +61,7 @@ Dynamic: license-file
 [![Issues](https://img.shields.io/github/issues/pryndor/Lixplore_cli)](https://github.com/pryndor/Lixplore_cli/issues)
 <a href="https://www.buymeacoffee.com/lixplore" target="_blank" rel="noopener noreferrer"><img src="https://img.shields.io/badge/Buy%20Me%20A%20Coffee-Support-40DCA5?style=flat&logo=buy-me-a-coffee" alt="Buy Me A Coffee"></a>
 
-Search across multiple academic databases (PubMed, arXiv, Crossref, DOAJ, EuropePMC) with Boolean operators, smart selection, and export to 8 formats including EndNote, Excel, and BibTeX.
+Search PubMed, arXiv, Crossref, DOAJ and Europe PMC in one command with Boolean queries, deduplicate the results, and export to 8 formats including BibTeX, RIS, EndNote and Excel. Browse and annotate papers in a full-screen TUI, and get **new-paper alerts** on email, Telegram, Slack and 14 other channels.
 
 **📚 [Complete Documentation](https://pryndor.github.io/Lixplore_cli/)** | **🐛 [Report Issues](https://github.com/pryndor/Lixplore_cli/issues)**
 
@@ -78,14 +77,15 @@ Search across multiple academic databases (PubMed, arXiv, Crossref, DOAJ, Europe
 - 💾 **8 Export Formats** - CSV, Excel, JSON, BibTeX, RIS, EndNote, XML
 - 📖 **Review Mode** - View articles in separate terminal windows
 - 🎯 **Deduplication** - Advanced duplicate removal with multiple strategies
-- 📁 **Organized Exports** - Auto-organized folders by format type
+- 📁 **Organized Exports** - Auto-organized folders by format type in `./exports/`
+- 📬 **Paper Alerts** - Scheduled digests of new papers on 17 channels, via GitHub Actions or cron
 
 ### Advanced Features
 - 📥 **PDF Downloads** - Automatic PDF downloads from PMC, arXiv, Unpaywall, and SciHub (optional)
 - 🔗 **PDF Link Display** - Show clickable PDF links for open access articles in terminal (NEW!)
 - 📚 **Reference Manager Integration** - Direct Zotero API integration and Mendeley RIS export
 - 📊 **Statistics Dashboard** - Comprehensive analytics with visualizations (publication trends, top journals, top authors)
-- 🎨 **Interactive TUI Mode** - Browse, select, and export with an interactive terminal UI
+- 🎨 **Full-screen TUI** - Search, read, rate, annotate and export in a Textual interface (`--tui`)
 - 📝 **Citation Export** - Format citations in APA, MLA, Chicago, IEEE styles
 - 🔧 **Custom API Integration** - Plugin architecture for any REST API (Springer, BASE, etc.)
 - 💡 **Metadata Enrichment** - Auto-enrich results from multiple APIs (Crossref, PubMed, arXiv)
@@ -98,7 +98,7 @@ Search across multiple academic databases (PubMed, arXiv, Crossref, DOAJ, Europe
 ### Documentation
 - 📚 **[Complete Documentation Site](https://pryndor.github.io/Lixplore_cli/)** - Comprehensive online documentation
 - 📖 **32+ Documentation Pages** - Getting started, user guides, command reference, examples
-- 🔍 **All 95 Flags Documented** - Detailed examples for every command-line flag
+- 🔍 **All 75 Flags Documented** - Detailed examples for every command-line flag
 - 🎓 **Step-by-Step Tutorials** - From installation to advanced workflows
 - 💡 **Quick Examples** - Built-in examples with `--examples` flag
 - 📄 **Man Page** - Traditional Unix man page included
@@ -149,7 +149,7 @@ lixplore --tui
 
 **Perfect for scripting, automation, and quick searches**
 
-**All 95 flags fully functional and tested!**
+**All 75 flags fully functional and tested!**
 
 ```bash
 # Quick search and export
@@ -166,7 +166,7 @@ lixplore -x -q "quantum computing" -m 25 -X csv,bibtex,ris --zip
 ```
 
 **All Features Available:**
-- ✅ 95 command-line flags fully compatible
+- ✅ 75 command-line flags
 - ✅ Multi-source search (PubMed, arXiv, Crossref, DOAJ, EuropePMC)
 - ✅ Boolean operators and advanced queries
 - ✅ 8 export formats (CSV, Excel, JSON, BibTeX, RIS, EndNote, XML)
@@ -180,9 +180,7 @@ lixplore -x -q "quantum computing" -m 25 -X csv,bibtex,ris --zip
 
 ---
 
-## 🆕 What's New in Version 2.0
-
-Lixplore has been massively upgraded with powerful new features:
+## 🆕 Feature Highlights
 
 ### 📥 PDF Download & Link Display
 **Download PDFs** automatically with smart fallback chain:
@@ -279,7 +277,7 @@ Prefer your own computer? `pip install -U lixplore-cli`, then `lixplore --alerts
 
 Before installing Lixplore, ensure you have:
 
-**Python 3.8 or higher:**
+**Python 3.9 or higher:**
 ```bash
 python3 --version
 ```
@@ -353,7 +351,7 @@ pip install -e .
 
 ### Optional: Full-screen TUI
 
-For `lixplore --tui` (Textual, Python 3.9+; older Pythons get a simpler Rich TUI):
+For `lixplore --tui` (Textual; without it you get a simpler Rich TUI):
 
 ```bash
 # With pipx (inject into existing install)
@@ -363,7 +361,7 @@ pipx inject lixplore-cli rich textual
 pip install "lixplore-cli[tui]"
 
 # Arch Linux
-sudo pacman -S python-rich
+sudo pacman -S python-textual
 ```
 
 ### ✅ Verify Installation
@@ -400,7 +398,7 @@ pip install --user lixplore-cli
 
 ### 🖥️ TUI Mode Troubleshooting (Linux)
 
-TUI mode requires the `rich` library (≥ 13.0.0). If it fails to launch, follow these steps:
+`lixplore --tui` uses [Textual](https://textual.textualize.io/) (≥ 4.0). Without Textual it falls back to a simpler TUI built on `rich` (≥ 13.0). If it fails to launch, follow these steps:
 
 #### Step 1 — Run the built-in diagnostics
 
@@ -408,18 +406,18 @@ TUI mode requires the `rich` library (≥ 13.0.0). If it fails to launch, follow
 lixplore --check-tui
 ```
 
-This prints your Python version, Rich status, and exact fix instructions.
+This prints your Python version, Textual and Rich status, and exact fix instructions.
 
-#### Step 2 — Install / inject Rich
+#### Step 2 — Install / inject Textual
 
 | Installation method | Fix command |
 |---------------------|-------------|
-| **pipx** (most common) | `pipx inject lixplore-cli rich` |
-| **pip + venv** | `pip install rich` (activate venv first) |
-| **pip install 'lixplore-cli[tui]'** | installs Rich in one step |
-| **Arch Linux** | `sudo pacman -S python-rich` |
+| **pipx** (most common) | `pipx inject lixplore-cli textual rich` |
+| **pip + venv** | `pip install "lixplore-cli[tui]"` (activate venv first) |
+| **Arch Linux (AUR)** | `sudo pacman -S python-textual` |
+| **Homebrew** | included, nothing to install |
 
-> **pipx users — common gotcha:** pipx creates an isolated environment per tool. Installing `rich` with plain `pip` or `pacman` puts it in a *different* Python environment that lixplore cannot see. Always use `pipx inject lixplore-cli rich` so Rich lands inside the same isolated env.
+> **pipx users — common gotcha:** pipx creates an isolated environment per tool. Installing `textual` with plain `pip` or `pacman` puts it in a *different* Python environment that lixplore cannot see. Always use `pipx inject lixplore-cli textual rich` so it lands inside the same isolated env.
 
 #### Step 3 — Check terminal compatibility
 
@@ -474,20 +472,20 @@ For `screen`, launch it with: `screen -T xterm-256color`
 
 #### Step 7 — Linux virtual console (tty without a desktop)
 
-If you are logged in directly on a raw Linux console (not inside GNOME Terminal, Konsole, etc.) your `TERM` will be `linux`, which does not support 256 colors. Rich's TUI will look broken or fail to render.
+If you are logged in directly on a raw Linux console (not inside GNOME Terminal, Konsole, etc.) your `TERM` will be `linux`, which does not support 256 colors. The TUI will look broken or fail to render.
 
 **Solution:** Log in via SSH from a color-capable terminal, or start a desktop session and use a terminal emulator listed in Step 3 above. Alternatively, use CLI mode (all features work without a terminal emulator).
 
 #### ✅ If TUI still doesn't work — use CLI mode
 
-All 95 flags work perfectly in CLI mode without any extra dependencies. CLI mode is fully production-ready and is what we recommend for scripting, automation, and SSH sessions:
+All flags work in CLI mode without any extra dependencies. CLI mode is fully production-ready and is what we recommend for scripting, automation, and SSH sessions:
 
 ```bash
 # CLI equivalents for common TUI workflows
 lixplore -P -q "your topic" -m 20          # search PubMed
 lixplore -A -q "your topic" -m 50 -D       # search all + deduplication
 lixplore -P -q "topic" -m 20 -X xlsx       # export to Excel
-lixplore -P -q "topic" -m 20 -i            # interactive results browser (Rich optional)
+lixplore -P -q "topic" -m 20 -i            # open the results in the TUI
 ```
 
 ### Basic Usage
@@ -512,7 +510,7 @@ lixplore -P -q "diabetes" -m 20 -X xlsx -o results.xlsx
 Visit our comprehensive documentation site for:
 - **Getting Started Guides** - Installation and first search tutorial
 - **User Guides** - Search, filtering, export, annotations, PDF management
-- **Command Reference** - All 95 flags with detailed examples
+- **Command Reference** - All 75 flags with detailed examples
 - **Advanced Features** - Automation, AI integration, Zotero, custom APIs
 - **Examples** - Common workflows, use cases, tool integrations
 
@@ -666,7 +664,7 @@ lixplore -P -q "neuroscience" -m 20 -S 2 5 8 -X enw
 
 ## 📊 Export Formats
 
-All exports are automatically organized into folders:
+All exports are automatically organized into folders under `exports/` in the folder you run `lixplore` from (use `-o FILE` to choose a path yourself):
 
 ```
 exports/
@@ -743,7 +741,7 @@ See [Quick Start](#-quick-start) above for detailed instructions.
 
 ## 🔍 Requirements
 
-- Python 3.7 or higher
+- Python 3.9 or higher
 - Internet connection for API access
 - Terminal emulator (for review feature)
 
@@ -752,9 +750,9 @@ See [Quick Start](#-quick-start) above for detailed instructions.
 - `biopython` - PubMed/NCBI API access
 - `requests` - HTTP requests
 - `openpyxl` - Excel export support
-- `rich` (optional) - Enhanced TUI with colors and formatting
+- `textual` + `rich` (optional) - Full-screen TUI
 
-All core dependencies are automatically installed. For the enhanced TUI experience, install with `pipx inject lixplore-cli rich` or `pip install "lixplore-cli[tui]"`.
+All core dependencies are automatically installed. For the TUI, install with `pip install "lixplore-cli[tui]"` or `pipx inject lixplore-cli textual rich`.
 
 ---
 
@@ -819,16 +817,15 @@ Your support enables:
 ### TUI Mode Enhancement (Active Development)
 We're actively working to bring all CLI features into the TUI mode. Upcoming updates will include:
 
-- 🔄 **All 95 Flags in TUI** - Full integration of all command-line features
+- 🔄 **All CLI Flags in TUI** - Full integration of all command-line features
 - 📊 **Advanced Filtering** - Date ranges, author search, DOI lookup in TUI
-- 🎨 **Enhanced UI** - Improved navigation and visual design
 - 📥 **PDF Integration** - Direct PDF download and viewing from TUI
 - 🔧 **Custom API Support** - GUI for adding custom data sources
 - 📋 **Profile Management** - Visual interface for export profiles
 - 🎯 **Citation Formatting** - Interactive citation style selection
 - 📈 **Advanced Statistics** - More visualization options
 
-**Current Status:** Core TUI features working (search, browse, annotate, export). CLI mode has 100% feature parity with all flags.
+**Current Status:** The Textual TUI covers search, reading, rating, annotation, library, alerts, stats and export. Enrichment, citation styles and PDF download are CLI flags for now.
 
 ---
 

{lixplore_cli-1.2.0 → lixplore_cli-1.2.2}/README.md

@@ -1,8 +1,8 @@
 # Lixplore-cli
 
-> **Academic Literature Search & Export CLI Tool**
+> **A Unix-inspired command-line tool for searching scientific literature**, built for terminal users who want speed, automation and minimal interfaces.
 
-[![Python Version](https://img.shields.io/badge/python-3.7+-blue.svg)](https://www.python.org/downloads/)
+[![Python Version](https://img.shields.io/badge/python-3.9+-blue.svg)](https://www.python.org/downloads/)
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
 [![Documentation](https://img.shields.io/badge/docs-latest-blue.svg)](https://pryndor.github.io/Lixplore_cli/)
 [![GitHub](https://img.shields.io/badge/GitHub-Repository-181717?logo=github)](https://github.com/pryndor/Lixplore_cli)
@@ -11,7 +11,7 @@
 [![Issues](https://img.shields.io/github/issues/pryndor/Lixplore_cli)](https://github.com/pryndor/Lixplore_cli/issues)
 <a href="https://www.buymeacoffee.com/lixplore" target="_blank" rel="noopener noreferrer"><img src="https://img.shields.io/badge/Buy%20Me%20A%20Coffee-Support-40DCA5?style=flat&logo=buy-me-a-coffee" alt="Buy Me A Coffee"></a>
 
-Search across multiple academic databases (PubMed, arXiv, Crossref, DOAJ, EuropePMC) with Boolean operators, smart selection, and export to 8 formats including EndNote, Excel, and BibTeX.
+Search PubMed, arXiv, Crossref, DOAJ and Europe PMC in one command with Boolean queries, deduplicate the results, and export to 8 formats including BibTeX, RIS, EndNote and Excel. Browse and annotate papers in a full-screen TUI, and get **new-paper alerts** on email, Telegram, Slack and 14 other channels.
 
 **📚 [Complete Documentation](https://pryndor.github.io/Lixplore_cli/)** | **🐛 [Report Issues](https://github.com/pryndor/Lixplore_cli/issues)**
 
@@ -27,14 +27,15 @@ Search across multiple academic databases (PubMed, arXiv, Crossref, DOAJ, Europe
 - 💾 **8 Export Formats** - CSV, Excel, JSON, BibTeX, RIS, EndNote, XML
 - 📖 **Review Mode** - View articles in separate terminal windows
 - 🎯 **Deduplication** - Advanced duplicate removal with multiple strategies
-- 📁 **Organized Exports** - Auto-organized folders by format type
+- 📁 **Organized Exports** - Auto-organized folders by format type in `./exports/`
+- 📬 **Paper Alerts** - Scheduled digests of new papers on 17 channels, via GitHub Actions or cron
 
 ### Advanced Features
 - 📥 **PDF Downloads** - Automatic PDF downloads from PMC, arXiv, Unpaywall, and SciHub (optional)
 - 🔗 **PDF Link Display** - Show clickable PDF links for open access articles in terminal (NEW!)
 - 📚 **Reference Manager Integration** - Direct Zotero API integration and Mendeley RIS export
 - 📊 **Statistics Dashboard** - Comprehensive analytics with visualizations (publication trends, top journals, top authors)
-- 🎨 **Interactive TUI Mode** - Browse, select, and export with an interactive terminal UI
+- 🎨 **Full-screen TUI** - Search, read, rate, annotate and export in a Textual interface (`--tui`)
 - 📝 **Citation Export** - Format citations in APA, MLA, Chicago, IEEE styles
 - 🔧 **Custom API Integration** - Plugin architecture for any REST API (Springer, BASE, etc.)
 - 💡 **Metadata Enrichment** - Auto-enrich results from multiple APIs (Crossref, PubMed, arXiv)
@@ -47,7 +48,7 @@ Search across multiple academic databases (PubMed, arXiv, Crossref, DOAJ, Europe
 ### Documentation
 - 📚 **[Complete Documentation Site](https://pryndor.github.io/Lixplore_cli/)** - Comprehensive online documentation
 - 📖 **32+ Documentation Pages** - Getting started, user guides, command reference, examples
-- 🔍 **All 95 Flags Documented** - Detailed examples for every command-line flag
+- 🔍 **All 75 Flags Documented** - Detailed examples for every command-line flag
 - 🎓 **Step-by-Step Tutorials** - From installation to advanced workflows
 - 💡 **Quick Examples** - Built-in examples with `--examples` flag
 - 📄 **Man Page** - Traditional Unix man page included
@@ -98,7 +99,7 @@ lixplore --tui
 
 **Perfect for scripting, automation, and quick searches**
 
-**All 95 flags fully functional and tested!**
+**All 75 flags fully functional and tested!**
 
 ```bash
 # Quick search and export
@@ -115,7 +116,7 @@ lixplore -x -q "quantum computing" -m 25 -X csv,bibtex,ris --zip
 ```
 
 **All Features Available:**
-- ✅ 95 command-line flags fully compatible
+- ✅ 75 command-line flags
 - ✅ Multi-source search (PubMed, arXiv, Crossref, DOAJ, EuropePMC)
 - ✅ Boolean operators and advanced queries
 - ✅ 8 export formats (CSV, Excel, JSON, BibTeX, RIS, EndNote, XML)
@@ -129,9 +130,7 @@ lixplore -x -q "quantum computing" -m 25 -X csv,bibtex,ris --zip
 
 ---
 
-## 🆕 What's New in Version 2.0
-
-Lixplore has been massively upgraded with powerful new features:
+## 🆕 Feature Highlights
 
 ### 📥 PDF Download & Link Display
 **Download PDFs** automatically with smart fallback chain:
@@ -228,7 +227,7 @@ Prefer your own computer? `pip install -U lixplore-cli`, then `lixplore --alerts
 
 Before installing Lixplore, ensure you have:
 
-**Python 3.8 or higher:**
+**Python 3.9 or higher:**
 ```bash
 python3 --version
 ```
@@ -302,7 +301,7 @@ pip install -e .
 
 ### Optional: Full-screen TUI
 
-For `lixplore --tui` (Textual, Python 3.9+; older Pythons get a simpler Rich TUI):
+For `lixplore --tui` (Textual; without it you get a simpler Rich TUI):
 
 ```bash
 # With pipx (inject into existing install)
@@ -312,7 +311,7 @@ pipx inject lixplore-cli rich textual
 pip install "lixplore-cli[tui]"
 
 # Arch Linux
-sudo pacman -S python-rich
+sudo pacman -S python-textual
 ```
 
 ### ✅ Verify Installation
@@ -349,7 +348,7 @@ pip install --user lixplore-cli
 
 ### 🖥️ TUI Mode Troubleshooting (Linux)
 
-TUI mode requires the `rich` library (≥ 13.0.0). If it fails to launch, follow these steps:
+`lixplore --tui` uses [Textual](https://textual.textualize.io/) (≥ 4.0). Without Textual it falls back to a simpler TUI built on `rich` (≥ 13.0). If it fails to launch, follow these steps:
 
 #### Step 1 — Run the built-in diagnostics
 
@@ -357,18 +356,18 @@ TUI mode requires the `rich` library (≥ 13.0.0). If it fails to launch, follow
 lixplore --check-tui
 ```
 
-This prints your Python version, Rich status, and exact fix instructions.
+This prints your Python version, Textual and Rich status, and exact fix instructions.
 
-#### Step 2 — Install / inject Rich
+#### Step 2 — Install / inject Textual
 
 | Installation method | Fix command |
 |---------------------|-------------|
-| **pipx** (most common) | `pipx inject lixplore-cli rich` |
-| **pip + venv** | `pip install rich` (activate venv first) |
-| **pip install 'lixplore-cli[tui]'** | installs Rich in one step |
-| **Arch Linux** | `sudo pacman -S python-rich` |
+| **pipx** (most common) | `pipx inject lixplore-cli textual rich` |
+| **pip + venv** | `pip install "lixplore-cli[tui]"` (activate venv first) |
+| **Arch Linux (AUR)** | `sudo pacman -S python-textual` |
+| **Homebrew** | included, nothing to install |
 
-> **pipx users — common gotcha:** pipx creates an isolated environment per tool. Installing `rich` with plain `pip` or `pacman` puts it in a *different* Python environment that lixplore cannot see. Always use `pipx inject lixplore-cli rich` so Rich lands inside the same isolated env.
+> **pipx users — common gotcha:** pipx creates an isolated environment per tool. Installing `textual` with plain `pip` or `pacman` puts it in a *different* Python environment that lixplore cannot see. Always use `pipx inject lixplore-cli textual rich` so it lands inside the same isolated env.
 
 #### Step 3 — Check terminal compatibility
 
@@ -423,20 +422,20 @@ For `screen`, launch it with: `screen -T xterm-256color`
 
 #### Step 7 — Linux virtual console (tty without a desktop)
 
-If you are logged in directly on a raw Linux console (not inside GNOME Terminal, Konsole, etc.) your `TERM` will be `linux`, which does not support 256 colors. Rich's TUI will look broken or fail to render.
+If you are logged in directly on a raw Linux console (not inside GNOME Terminal, Konsole, etc.) your `TERM` will be `linux`, which does not support 256 colors. The TUI will look broken or fail to render.
 
 **Solution:** Log in via SSH from a color-capable terminal, or start a desktop session and use a terminal emulator listed in Step 3 above. Alternatively, use CLI mode (all features work without a terminal emulator).
 
 #### ✅ If TUI still doesn't work — use CLI mode
 
-All 95 flags work perfectly in CLI mode without any extra dependencies. CLI mode is fully production-ready and is what we recommend for scripting, automation, and SSH sessions:
+All flags work in CLI mode without any extra dependencies. CLI mode is fully production-ready and is what we recommend for scripting, automation, and SSH sessions:
 
 ```bash
 # CLI equivalents for common TUI workflows
 lixplore -P -q "your topic" -m 20          # search PubMed
 lixplore -A -q "your topic" -m 50 -D       # search all + deduplication
 lixplore -P -q "topic" -m 20 -X xlsx       # export to Excel
-lixplore -P -q "topic" -m 20 -i            # interactive results browser (Rich optional)
+lixplore -P -q "topic" -m 20 -i            # open the results in the TUI
 ```
 
 ### Basic Usage
@@ -461,7 +460,7 @@ lixplore -P -q "diabetes" -m 20 -X xlsx -o results.xlsx
 Visit our comprehensive documentation site for:
 - **Getting Started Guides** - Installation and first search tutorial
 - **User Guides** - Search, filtering, export, annotations, PDF management
-- **Command Reference** - All 95 flags with detailed examples
+- **Command Reference** - All 75 flags with detailed examples
 - **Advanced Features** - Automation, AI integration, Zotero, custom APIs
 - **Examples** - Common workflows, use cases, tool integrations
 
@@ -615,7 +614,7 @@ lixplore -P -q "neuroscience" -m 20 -S 2 5 8 -X enw
 
 ## 📊 Export Formats
 
-All exports are automatically organized into folders:
+All exports are automatically organized into folders under `exports/` in the folder you run `lixplore` from (use `-o FILE` to choose a path yourself):
 
 ```
 exports/
@@ -692,7 +691,7 @@ See [Quick Start](#-quick-start) above for detailed instructions.
 
 ## 🔍 Requirements
 
-- Python 3.7 or higher
+- Python 3.9 or higher
 - Internet connection for API access
 - Terminal emulator (for review feature)
 
@@ -701,9 +700,9 @@ See [Quick Start](#-quick-start) above for detailed instructions.
 - `biopython` - PubMed/NCBI API access
 - `requests` - HTTP requests
 - `openpyxl` - Excel export support
-- `rich` (optional) - Enhanced TUI with colors and formatting
+- `textual` + `rich` (optional) - Full-screen TUI
 
-All core dependencies are automatically installed. For the enhanced TUI experience, install with `pipx inject lixplore-cli rich` or `pip install "lixplore-cli[tui]"`.
+All core dependencies are automatically installed. For the TUI, install with `pip install "lixplore-cli[tui]"` or `pipx inject lixplore-cli textual rich`.
 
 ---
 
@@ -768,16 +767,15 @@ Your support enables:
 ### TUI Mode Enhancement (Active Development)
 We're actively working to bring all CLI features into the TUI mode. Upcoming updates will include:
 
-- 🔄 **All 95 Flags in TUI** - Full integration of all command-line features
+- 🔄 **All CLI Flags in TUI** - Full integration of all command-line features
 - 📊 **Advanced Filtering** - Date ranges, author search, DOI lookup in TUI
-- 🎨 **Enhanced UI** - Improved navigation and visual design
 - 📥 **PDF Integration** - Direct PDF download and viewing from TUI
 - 🔧 **Custom API Support** - GUI for adding custom data sources
 - 📋 **Profile Management** - Visual interface for export profiles
 - 🎯 **Citation Formatting** - Interactive citation style selection
 - 📈 **Advanced Statistics** - More visualization options
 
-**Current Status:** Core TUI features working (search, browse, annotate, export). CLI mode has 100% feature parity with all flags.
+**Current Status:** The Textual TUI covers search, reading, rating, annotation, library, alerts, stats and export. Enrichment, citation styles and PDF download are CLI flags for now.
 
 ---
 

{lixplore_cli-1.2.0 → lixplore_cli-1.2.2}/docs/README.md

@@ -26,7 +26,7 @@ docs/
 │   ├── custom-apis.md                # Custom API integration
 │   └── zotero.md                     # Zotero integration
 ├── reference/                        # Command reference
-│   ├── flags-overview.md             # All 95 flags overview
+│   ├── flags-overview.md             # All flags overview
 │   ├── source-flags.md               # Source selection flags
 │   ├── search-flags.md               # Search parameter flags
 │   ├── filter-flags.md               # Filtering flags

lixplore_cli-1.2.2/docs/about/changelog.md

@@ -0,0 +1,3 @@
+# Changelog
+
+--8<-- "CHANGELOG.md:8:"

{lixplore_cli-1.2.0 → lixplore_cli-1.2.2}/docs/about/faq.md

@@ -18,7 +18,7 @@ No. Lixplore is purely a search and export tool. It has no machine learning depe
 
 ### What platforms does Lixplore support?
 
-Lixplore works on Linux, macOS, and Windows with Python 3.8 or higher.
+Lixplore works on Linux, macOS, and Windows with Python 3.9 or higher.
 
 ---
 
@@ -27,7 +27,7 @@ Lixplore works on Linux, macOS, and Windows with Python 3.8 or higher.
 ### How do I install Lixplore?
 
 ```bash
-pip install lixplore
+pip install lixplore-cli
 ```
 
 See the [Installation Guide](../getting-started/installation.md) for details.
@@ -45,7 +45,7 @@ Add this to your `~/.bashrc` or `~/.zshrc` to make it permanent.
 ### How do I upgrade to the latest version?
 
 ```bash
-pip install --upgrade lixplore
+pip install --upgrade lixplore-cli
 ```
 
 ---

{lixplore_cli-1.2.0 → lixplore_cli-1.2.2}/docs/examples/automation-examples.md

@@ -480,7 +480,7 @@ jobs:
           python-version: '3.10'
 
       - name: Install Lixplore
-        run: pip install lixplore
+        run: pip install lixplore-cli
 
       - name: Run literature search
         run: |
@@ -520,7 +520,7 @@ literature_search:
   stage: search
   image: python:3.10
   script:
-    - pip install lixplore
+    - pip install lixplore-cli
     - TODAY=$(date +%Y-%m-%d)
     - YESTERDAY=$(date -d "yesterday" +%Y-%m-%d)
     - lixplore -A -q "$TOPIC" -d "$YESTERDAY" "$TODAY" -m 100 -D -X json -o results.json

{lixplore_cli-1.2.0 → lixplore_cli-1.2.2}/docs/examples/integrations.md

@@ -489,7 +489,7 @@ git commit -m "Added bibliography for Chapter 2"
 # Dockerfile
 FROM python:3.10-slim
 
-RUN pip install lixplore
+RUN pip install lixplore-cli
 
 WORKDIR /workspace
 

{lixplore_cli-1.2.0 → lixplore_cli-1.2.2}/docs/getting-started/installation.md

@@ -4,7 +4,7 @@
 
 Before installing Lixplore, ensure you have:
 
-### 1. Python (Version 3.8 or Higher)
+### 1. Python (Version 3.9 or Higher)
 
 Check your Python version:
 
@@ -252,7 +252,7 @@ Check your Python version:
 python3 --version
 ```
 
-If it's below 3.8, you need to upgrade Python:
+If it's below 3.9, you need to upgrade Python:
 - **Windows**: Download from [python.org](https://www.python.org/downloads/)
 - **Mac**: `brew install python3`
 - **Linux**: `sudo apt install python3.10` (or newer)

{lixplore_cli-1.2.0 → lixplore_cli-1.2.2}/docs/getting-started/quickstart.md

@@ -7,7 +7,7 @@ Get started with Lixplore in 5 minutes!
 ## Installation
 
 ```bash
-pip install lixplore
+pip install lixplore-cli
 ```
 
 Verify installation:

{lixplore_cli-1.2.0 → lixplore_cli-1.2.2}/docs/guide/interactive.md

@@ -11,7 +11,7 @@ lixplore --tui                           # open the TUI
 lixplore -P -q "CRISPR" -m 50 -i         # run a CLI search, then browse it in the TUI
 ```
 
-On Python 3.8, or without Textual installed, these commands open the older Rich-based TUI instead. `lixplore --check-tui` reports what is installed and how to fix it.
+Without Textual installed, these commands open the older Rich-based TUI instead. `lixplore --check-tui` reports what is installed and how to fix it.
 
 ## Layout
 

{lixplore_cli-1.2.0 → lixplore_cli-1.2.2}/docs/index.md

@@ -60,7 +60,7 @@ Access open access literature:
 ### Installation
 
 ```bash
-pip install lixplore
+pip install lixplore-cli
 ```
 
 ### Basic Search
@@ -112,6 +112,6 @@ lixplore -A -q "climate change" -m 200 -D -X json -o data.json
 
 **Ready to Get Started?**
 
-Install now: `pip install lixplore`
+Install now: `pip install lixplore-cli`
 
 View all documentation in the menu above.

{lixplore_cli-1.2.0 → lixplore_cli-1.2.2}/docs/reference/flags-overview.md

@@ -1,6 +1,6 @@
 # Lixplore Command-Line Flags - Complete Reference
 
-> **Comprehensive overview of all 95+ command-line flags organized by category**
+> **Comprehensive overview of all 75 command-line flags organized by category**
 
 ## Table of Contents