Adding test suite

.github/workflows/run_tests.yml

@@ -0,0 +1,59 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: Test Astro Web
+
+on:
+  workflow_dispatch:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+
+permissions:
+  contents: read
+
+jobs:  
+  test:
+    runs-on: ubuntu-latest
+    env:
+      ASTRO_WEB_DATABASE_URL: "sqlite:///SIMPLE.sqlite"
+      ASTRO_WEB_LOOKUP_TABLES: "Publications,Telescopes,Instruments,PhotometryFilters,Versions,RegimeList,SourceTypeList,ParameterList,AssociationList,CompanionList,Modes,Filters,Citations,References,Parameters,Regimes"
+      ASTRO_WEB_PRIMARY_TABLE: "Sources"
+      ASTRO_WEB_SOURCE_COLUMN: "source"
+      ASTRO_WEB_FOREIGN_KEY: "source"
+      ASTRO_WEB_RA_COLUMN: "ra"
+      ASTRO_WEB_DEC_COLUMN: "dec"
+      ASTRO_WEB_SPECTRA_URL_COLUMN: "access_url"
+    strategy:
+      matrix:
+        python-version: ["3.13"]
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v5
+      with:
+        enable-cache: true
+        version: "latest"
+
+    - name: Set up Python ${{ matrix.python-version }}
+      run: uv python install ${{ matrix.python-version }}
+
+    - name: Install dependencies
+      run: |
+        uv sync --all-extras --dev
+
+    - name: Download database
+      run: |
+        curl -L https://github.com/SIMPLE-AstroDB/SIMPLE-binary/raw/main/SIMPLE.sqlite -o SIMPLE.sqlite
+
+    - name: Run linter
+      run: |
+        uv run ruff check .
+
+    - name: Test with pytest
+      run: |
+        uv run pytest --cov --cov-branch --cov-report=xml

AGENTS.md

@@ -0,0 +1,21 @@
+# AGENTS.md - Astro Web
+
+## Project Overview
+Astro Web is a FastAPI-based web application for exploring astronomical databases created with the AstroDB Toolkit. It features interactive Bokeh visualizations (scatter plots, spectra), source browsing with DataTables, and both text and cone search capabilities.
+
+## Directory Structure
+- `astro_web/`: Main application package.
+    - `main.py`: FastAPI entry point.
+    - `config.py`: Configuration and environment variables.
+    - `database/`: Database interaction (astrodbkit, SQLite).
+    - `routes/`: Web page route definitions (web.py).
+    - `visualizations/`: Bokeh plot generation (scatter, spectra).
+    - `templates/`: Jinja2 HTML templates.
+    - `static/`: CSS and schema definitions.
+- `CONFIG.md`: Configuration settings guide.
+- `pyproject.toml`: Project metadata and dependencies (managed by uv).
+- `.env.example`: Template for environment variables.
+- `constitution.md`: Project constitution and development guidelines.
+
+## Guidance
+Prior to making any code changes, read the `constitution.md` file to understand the project's development guidelines and coding standards.

astro_web/config.py

@@ -55,6 +55,7 @@
     "Versions",
     "Parameters",
     "Regimes",
+    "RegimeList",
     "ParameterList",
     "AssociationList",
     "CompanionList",

astro_web/database/__init__.py

@@ -1,3 +1,39 @@
 """Database module for Astrodbkit database interactions."""
 
-__all__ = ["sources", "query"]
+from contextlib import contextmanager
+from astrodbkit.astrodb import Database
+from astro_web.config import (
+    CONNECTION_STRING,
+    FOREIGN_KEY,
+    LOOKUP_TABLES,
+    PRIMARY_TABLE,
+    SCHEMA,
+    SOURCE_COLUMN,
+)
+
+
+@contextmanager
+def get_db():
+    """
+    Context manager for astrodbkit Database connections.
+    Ensures the database session is closed and engine is disposed.
+    """
+    db = Database(
+        CONNECTION_STRING,
+        primary_table=PRIMARY_TABLE,
+        primary_table_key=SOURCE_COLUMN,
+        lookup_tables=LOOKUP_TABLES,
+        schema=SCHEMA,
+        foreign_key=FOREIGN_KEY,
+    )
+    try:
+        yield db
+    finally:
+        # Close the session and dispose the engine to release the database file
+        if hasattr(db, "session") and db.session:
+            db.session.close()
+        if hasattr(db, "engine") and db.engine:
+            db.engine.dispose()
+
+
+__all__ = ["sources", "query", "get_db"]

astro_web/database/query.py

@@ -7,20 +7,14 @@
 
 import time
 
-from astrodbkit.astrodb import Database
 from astropy.coordinates import SkyCoord
 from astropy.units import Quantity
 
 from astro_web.config import (
-    CONNECTION_STRING,
     DEC_COLUMN,
-    FOREIGN_KEY,
-    LOOKUP_TABLES,
-    PRIMARY_TABLE,
     RA_COLUMN,
-    SCHEMA,
-    SOURCE_COLUMN,
 )
+from astro_web.database import get_db
 
 
 def search_objects(query: str):
@@ -36,15 +30,8 @@ def search_objects(query: str):
                and execution_time is the time taken in seconds
     """
     start_time = time.time()
-    db = Database(
-        CONNECTION_STRING,
-        primary_table=PRIMARY_TABLE,
-        primary_table_key=SOURCE_COLUMN,
-        lookup_tables=LOOKUP_TABLES,
-        schema=SCHEMA,
-        foreign_key=FOREIGN_KEY,
-    )
-    results = db.search_object(query.strip(), resolve_simbad=True, format="pandas")
+    with get_db() as db:
+        results = db.search_object(query.strip(), resolve_simbad=True, fmt="pandas")
     execution_time = time.time() - start_time
 
     return results, execution_time
@@ -68,18 +55,20 @@ def parse_coordinates_string(coords_str):
     """
     coords_str = coords_str.strip()
 
-    # Check if the string contains sexagesimal indicators (h, m, s, d, etc.)
-    has_sexagesimal = any(char in coords_str.lower() for char in ["h", "m", "s", "d", "°", "'", '"'])
+    # Check if the string contains sexagesimal indicators or has multiple parts
+    parts = coords_str.split()
+    has_sexagesimal = (
+        any(char in coords_str.lower() for char in ["h", "m", "s", "d", "°", "'", '"', ":"]) or len(parts) > 2
+    )
 
     try:
         if has_sexagesimal:
-            # For sexagesimal format, SkyCoord can auto-detect
-            skycoord = SkyCoord(coords_str, frame="icrs")
+            # For sexagesimal format, assume hourangle for RA if not explicit
+            skycoord = SkyCoord(coords_str, frame="icrs", unit=("hour", "deg"))
             ra_decimal = skycoord.ra.deg
             dec_decimal = skycoord.dec.deg
         else:
             # For decimal format, split and parse manually
-            parts = coords_str.split()
             if len(parts) != 2:
                 raise ValueError("Expected two space-separated values for decimal coordinates (e.g., '209.30 14.48')")
 
@@ -153,17 +142,12 @@ def cone_search(ra, dec, radius_deg):
                and execution_time is the time taken in seconds
     """
     start_time = time.time()
-    db = Database(
-        CONNECTION_STRING,
-        primary_table=PRIMARY_TABLE,
-        primary_table_key=SOURCE_COLUMN,
-        lookup_tables=LOOKUP_TABLES,
-        schema=SCHEMA,
-        foreign_key=FOREIGN_KEY,
-    )
     coords = SkyCoord(ra, dec, unit="deg")
     radius = Quantity(radius_deg, "deg")
-    results = db.query_region(coords, radius=radius, fmt="pandas", ra_col=RA_COLUMN, dec_col=DEC_COLUMN)
+
+    with get_db() as db:
+        results = db.query_region(coords, radius=radius, fmt="pandas", ra_col=RA_COLUMN, dec_col=DEC_COLUMN)
+
     execution_time = time.time() - start_time
 
     # Apply 10,000 result cap if needed

astro_web/database/sources.py

@@ -2,19 +2,14 @@
 
 import logging
 
-from astrodbkit.astrodb import Database
 from specutils import Spectrum
 
 from astro_web.config import (
-    CONNECTION_STRING,
-    FOREIGN_KEY,
-    LOOKUP_TABLES,
     PRIMARY_DATATYPE,
     PRIMARY_TABLE,
-    SCHEMA,
-    SOURCE_COLUMN,
     SPECTRA_URL_COLUMN,
 )
+from astro_web.database import get_db
 
 
 def get_all_sources():
@@ -25,15 +20,8 @@ def get_all_sources():
         list: List of dictionaries representing all Sources rows, or None on error
     """
     try:
-        db = Database(
-            CONNECTION_STRING,
-            primary_table=PRIMARY_TABLE,
-            primary_table_key=SOURCE_COLUMN,
-            lookup_tables=LOOKUP_TABLES,
-            schema=SCHEMA,
-            foreign_key=FOREIGN_KEY,
-        )
-        df = db.query(db.metadata.tables[PRIMARY_TABLE]).pandas()
+        with get_db() as db:
+            df = db.query(db.metadata.tables[PRIMARY_TABLE]).pandas()
         return df.to_dict("records")
     except Exception as e:
         logging.error(f"Error getting all sources: {e}")
@@ -52,21 +40,11 @@ def get_source_inventory(source_name):
               Only tables with data are returned. Empty tables are filtered out.
     """
     try:
-        print(LOOKUP_TABLES)
-
-        # Connect to database
-        db = Database(
-            CONNECTION_STRING,
-            primary_table=PRIMARY_TABLE,
-            primary_table_key=SOURCE_COLUMN,
-            lookup_tables=LOOKUP_TABLES,
-            schema=SCHEMA,
-            foreign_key=FOREIGN_KEY,
-        )
-
         # Get inventory (returns dict of table name -> list of dicts)
         source_name = PRIMARY_DATATYPE(source_name)
-        inventory = db.inventory(source_name)
+
+        with get_db() as db:
+            inventory = db.inventory(source_name)
 
         # Filter out empty tables - only return tables that have data
         result = {}
@@ -93,20 +71,11 @@ def get_source_spectra(source_name, convert_to_spectrum=False):
                          instrument, etc.) or None on error
     """
 
-    # Connect to database
-    db = Database(
-        CONNECTION_STRING,
-        primary_table=PRIMARY_TABLE,
-        primary_table_key=SOURCE_COLUMN,
-        lookup_tables=LOOKUP_TABLES,
-        schema=SCHEMA,
-        foreign_key=FOREIGN_KEY,
-    )
-
     try:
         # Query spectra table for the source using astrodbkit's pandas method
         source_name = PRIMARY_DATATYPE(source_name)
-        spectra_df = db.query(db.Spectra).filter(db.Spectra.c.source == source_name).pandas()
+        with get_db() as db:
+            spectra_df = db.query(db.Spectra).filter(db.Spectra.c.source == source_name).pandas()
     except Exception:
         return None