lixplore-cli 1.2.2__tar.gz → 1.2.3__tar.gz

{lixplore_cli-1.2.2 → lixplore_cli-1.2.3}/CHANGELOG.md

@@ -7,6 +7,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+## [1.2.3] - 2026-09-27
+
+### Added
+- PubMed email and API key can be set in `~/.lixplore/config.json`, which also works for pip,
+  AUR and Homebrew installs (before, only `PUBMED_EMAIL` / `PUBMED_API_KEY` did)
+
 ## [1.2.2] - 2026-09-27
 
 ### Changed

{lixplore_cli-1.2.2/lixplore_cli.egg-info → lixplore_cli-1.2.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: lixplore-cli
-Version: 1.2.2
+Version: 1.2.3
 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>
@@ -364,6 +364,14 @@ pip install "lixplore-cli[tui]"
 sudo pacman -S python-textual
 ```
 
+### 🔑 Optional: PubMed email and API key
+
+An NCBI API key raises PubMed's rate limit from 3 to 10 requests per second ([get one free](https://www.ncbi.nlm.nih.gov/account/settings/)). Set `PUBMED_EMAIL` / `PUBMED_API_KEY` in your environment, or create `~/.lixplore/config.json`:
+
+```json
+{"pubmed": {"email": "you@example.org", "api_key": "your-ncbi-key"}}
+```
+
 ### ✅ Verify Installation
 
 ```bash

{lixplore_cli-1.2.2 → lixplore_cli-1.2.3}/README.md

@@ -314,6 +314,14 @@ pip install "lixplore-cli[tui]"
 sudo pacman -S python-textual
 ```
 
+### 🔑 Optional: PubMed email and API key
+
+An NCBI API key raises PubMed's rate limit from 3 to 10 requests per second ([get one free](https://www.ncbi.nlm.nih.gov/account/settings/)). Set `PUBMED_EMAIL` / `PUBMED_API_KEY` in your environment, or create `~/.lixplore/config.json`:
+
+```json
+{"pubmed": {"email": "you@example.org", "api_key": "your-ncbi-key"}}
+```
+
 ### ✅ Verify Installation
 
 ```bash

{lixplore_cli-1.2.2 → lixplore_cli-1.2.3}/docs/guide/search-sources.md

@@ -26,6 +26,32 @@
 lixplore -P -q "diabetes treatment" -m 20
 ```
 
+### Email and API key (optional)
+
+NCBI asks every tool to send a contact email, and an API key raises the rate
+limit from 3 to 10 requests per second. Get a free key under
+[NCBI account settings](https://www.ncbi.nlm.nih.gov/account/settings/). Set either:
+
+```bash
+# Environment variables (e.g. in ~/.bashrc)
+export PUBMED_EMAIL="you@example.org"
+export PUBMED_API_KEY="your-ncbi-key"
+```
+
+or `~/.lixplore/config.json`:
+
+```json
+{"pubmed": {"email": "you@example.org", "api_key": "your-ncbi-key"}}
+```
+
+The config file wins over the environment variables.
+
+### If PubMed reports "temporarily unavailable"
+
+That message comes from NCBI's own servers (for example "Cannot connect to
+SOLR"). Lixplore retries twice; if NCBI is still down, try again a few
+minutes later. Other sources keep working meanwhile.
+
 ### Advanced Search Techniques
 
 **1. MeSH Terms (Medical Subject Headings)**

{lixplore_cli-1.2.2 → lixplore_cli-1.2.3}/lixplore/sources/pubmed.py

@@ -17,17 +17,26 @@ import time
 
 # Load configuration
 def _load_config():
-    """Load email from config.json, fallback to environment or default"""
-    config_path = os.path.join(os.path.dirname(__file__), "..", "..", "config.json")
-    try:
-        with open(config_path, 'r') as f:
-            config = json.load(f)
+    """Load email from config.json, fallback to environment or default.
+
+    Looks in config.json of a source checkout first, then in
+    ~/.lixplore/config.json (works for pip, AUR and Homebrew installs):
+        {"pubmed": {"email": "you@example.org", "api_key": "..."}}
+    """
+    config_paths = [
+        os.path.join(os.path.dirname(__file__), "..", "..", "config.json"),
+        os.path.join(os.path.expanduser("~"), ".lixplore", "config.json"),
+    ]
+    for config_path in config_paths:
+        try:
+            with open(config_path, 'r') as f:
+                config = json.load(f)
             email = config.get("pubmed", {}).get("email", "")
             api_key = config.get("pubmed", {}).get("api_key", "")
             if email and email != "your_email@example.com":
                 return email, api_key
-    except (FileNotFoundError, json.JSONDecodeError):
-        pass
+        except (OSError, ValueError, AttributeError):
+            pass
 
     # Fallback to environment variable or default
     email = os.environ.get("PUBMED_EMAIL", "user@example.com")

{lixplore_cli-1.2.2 → lixplore_cli-1.2.3/lixplore_cli.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: lixplore-cli
-Version: 1.2.2
+Version: 1.2.3
 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>
@@ -364,6 +364,14 @@ pip install "lixplore-cli[tui]"
 sudo pacman -S python-textual
 ```
 
+### 🔑 Optional: PubMed email and API key
+
+An NCBI API key raises PubMed's rate limit from 3 to 10 requests per second ([get one free](https://www.ncbi.nlm.nih.gov/account/settings/)). Set `PUBMED_EMAIL` / `PUBMED_API_KEY` in your environment, or create `~/.lixplore/config.json`:
+
+```json
+{"pubmed": {"email": "you@example.org", "api_key": "your-ncbi-key"}}
+```
+
 ### ✅ Verify Installation
 
 ```bash

{lixplore_cli-1.2.2 → lixplore_cli-1.2.3}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "lixplore-cli"
-version = "1.2.2"
+version = "1.2.3"
 description = "Unix-inspired CLI for searching PubMed, arXiv, Crossref, DOAJ and Europe PMC, with deduplication, 8 export formats and scheduled paper alerts"
 readme = "README.md"
 requires-python = ">=3.9"