Update workflows with improved skills

Author: TKassis

README.md

@@ -45,30 +45,11 @@ git clone https://github.com/K-Dense-AI/k-dense-byok.git
 cd k-dense-byok
 ```
 
-### Step 2 — Add your API key
+### Step 2 — Add your API keys
 
-Create a file called `.env` inside the `kady_agent` folder with this content:
+Inside the `kady_agent` folder you'll find a file called `env.example`. Make a copy of it and rename the copy to `.env` (note the dot at the start). Then open `.env` in any text editor and paste your **OpenRouter API key** on the first line — that's the only key you need to get started.
 
-```env
-# Your OpenRouter API key (required)
-OPENROUTER_API_KEY=paste-your-key-here
-
-# Enables web search (optional)
-PARALLEL_API_KEY=paste-your-key-here
-
-# Leave these as-is — they connect internal services
-GOOGLE_GEMINI_BASE_URL=http://localhost:4000
-GEMINI_API_KEY=sk-litellm-local
-
-# The default AI model Kady uses (you can change this in the app later)
-DEFAULT_AGENT_MODEL=openrouter/google/gemini-3.1-pro-preview
-
-# Remote compute — only fill in if you have a Modal account (optional)
-MODAL_TOKEN_ID=
-MODAL_TOKEN_SECRET=
-```
-
-At minimum, you need to fill in `OPENROUTER_API_KEY`. Everything else is optional or should be left as-is.
+The file also has sections for other keys you can optionally fill in: **Parallel** for web search, **Modal** for remote compute, and a long list of scientific database and government data API keys. Just leave blank anything you don't need.
 
 ### Step 3 — Start the app
 
@@ -102,7 +83,8 @@ k-dense-byok/
 ├── start.sh              ← The one script that starts everything
 ├── server.py             ← Backend server
 ├── kady_agent/           ← Kady's brain: instructions, tools, and config
-│   ├── .env              ← Your API keys go here
+│   ├── env.example       ← Template for your API keys (copy to .env)
+│   ├── .env              ← Your API keys (created from env.example)
 │   ├── agent.py          ← Main agent definition
 │   └── tools/            ← Tools Kady can use (web search, delegation, etc.)
 ├── web/                  ← Frontend (the UI you see in your browser)

kady_agent/env.example

@@ -0,0 +1,68 @@
+## Required
+
+# LLM API keys
+OPENROUTER_API_KEY=
+
+# Gemini CLI -> LiteLLM proxy -> OpenRouter
+GOOGLE_GEMINI_BASE_URL=http://localhost:4000
+GEMINI_API_KEY=sk-litellm-local
+
+# LLMs
+DEFAULT_AGENT_MODEL="openrouter/google/gemini-3.1-pro-preview"
+
+
+## Highly Recommended (Delete if not needed and filled in correctly)
+
+# Parallel Search
+PARALLEL_API_KEY=
+
+# Modal
+MODAL_TOKEN_ID=
+MODAL_TOKEN_SECRET=
+
+
+## Optional (Delete if not needed and filled in correctly)
+
+# Scientific databases and search
+NCBI_API_KEY=
+NCBI_EMAIL=
+S2_API_KEY=
+CORE_API_KEY=
+OPENALEX_API_KEY=
+
+# Specialized scientific APIs
+ADAPTYV_API_KEY=
+ROWAN_API_KEY=
+MP_API_KEY=
+OMIM_API_KEY=
+BIOGRID_API_KEY=
+DISGENET_API_KEY=
+ADDGENE_API_KEY=
+CLUE_API_KEY=
+OPENFDA_API_KEY=
+PATENTSVIEW_API_KEY=
+DATACOMMONS_API_KEY=
+
+# Government / economic data
+FRED_API_KEY=
+BEA_API_KEY=
+BLS_API_KEY=
+CENSUS_API_KEY=
+NASA_API_KEY=
+NOAA_API_KEY=
+OPENWEATHERMAP_API_KEY=
+ALPHAVANTAGE_API_KEY=
+
+# Zotero reference manager
+ZOTERO_LIBRARY_ID=
+ZOTERO_API_KEY=
+ZOTERO_LIBRARY_TYPE=
+
+# ML / AI platforms
+HUGGINGFACE_TOKEN=
+QISKIT_IBM_TOKEN=
+
+# Other
+TILEDB_REST_TOKEN=
+GOOGLE_API_KEY=
+GOOGLE_CSE_ID=

pyproject.toml

@@ -1,13 +1,13 @@
 [project]
 name = "kady"
-version = "0.2.11"
+version = "0.2.13"
 description = "Kady — K-Dense BYOK Agent"
 readme = "README.md"
 requires-python = ">=3.13"
 dependencies = [
     "fastapi>=0.133.1",
-    "google-adk[extensions]>=1.27.5",
-    "litellm[proxy]==1.82.6",
+    "google-adk[extensions]>=1.28.0",
+    "litellm[proxy]>=1.82.6",
     "markitdown[all]>=0.1.5",
     "modal>=1.3.5",
     "openrouter>=0.7.11",