fix snippets: rewrite as marimo notebooks, disable defaults

Snippets were plain Python dicts — marimo expects actual notebook
files (marimo.App with @app.cell). Rewrote all 10 as proper marimo
notebooks that load_app() can parse.

Disabled include_default_snippets — only our project snippets show.

10 snippets: duckdb, trino, bib, nessie, s3-obstore, chart-bar,
chart-line, query-demographics, query-schema, query-pmpm.

refs #75

notebooks/.marimo-config/marimo.toml

@@ -64,8 +64,8 @@ preset = "default"
 [keymap.overrides]
 
 [snippets]
-custom_paths = []
+custom_paths = ["/home/kert/notebooks/snippets"]
-include_default_snippets = true
+include_default_snippets = false
 
 [mcp]
 presets = []

notebooks/.marimo.toml

@@ -4,3 +4,4 @@ custom_css = ["/home/kert/.config/marimo/loch.css"]
 
 [snippets]
 custom_paths = ["/home/kert/notebooks/snippets"]
+include_default_snippets = false

notebooks/snippets/bib-connect.py

@@ -0,0 +1,34 @@
+import marimo
+
+__generated_with = "0.20.4"
+app = marimo.App()
+
+
+@app.cell
+def _(mo):
+    mo.md(r"""
+    # Bibliography: Connect to bib.Store
+
+    Open the bibliography store for browsing Zotero-synced references.
+    """)
+    return
+
+
+@app.cell
+def _():
+    from conf import connect
+
+    store = connect.bib()
+    items = store.list_items()
+    return connect, items, store
+
+
+@app.cell
+def _():
+    import marimo as mo
+
+    return (mo,)
+
+
+if __name__ == "__main__":
+    app.run()

notebooks/snippets/chart-bar.py

@@ -0,0 +1,51 @@
+import marimo
+
+__generated_with = "0.20.4"
+app = marimo.App()
+
+
+@app.cell
+def _(mo):
+    mo.md(r"""
+    # Chart: Horizontal bar chart
+
+    Template for a horizontal bar chart with Altair.
+    """)
+    return
+
+
+@app.cell
+def _():
+    from conf import connect
+
+    connect.theme()
+    import altair as alt
+
+    return alt, connect
+
+
+@app.cell
+def _(alt):
+    chart = (
+        alt.Chart(df.to_pandas())
+        .mark_bar()
+        .encode(
+            x=alt.X("value:Q", title="Value"),
+            y=alt.Y("category:N", sort="-x", title=None),
+            tooltip=["category:N", "value:Q"],
+        )
+        .properties(title="Title", width=600, height=300)
+    )
+    chart
+    return (chart,)
+
+
+@app.cell
+def _():
+    import marimo as mo
+
+    return (mo,)
+
+
+if __name__ == "__main__":
+    app.run()

notebooks/snippets/chart-line.py

@@ -0,0 +1,42 @@
+import marimo
+
+__generated_with = "0.20.4"
+app = marimo.App()
+
+
+@app.cell
+def _(mo):
+    mo.md(r"""
+    # Chart: Time series line chart
+
+    Template for a multi-series time series line chart with Altair.
+    """)
+    return
+
+
+@app.cell
+def _(alt):
+    chart = (
+        alt.Chart(df.to_pandas())
+        .mark_line(point=True)
+        .encode(
+            x=alt.X("date:T", title="Date"),
+            y=alt.Y("value:Q", title="Value"),
+            color=alt.Color("series:N", title="Series"),
+            tooltip=["date:T", "series:N", "value:Q"],
+        )
+        .properties(title="Title", width=800, height=350)
+    )
+    chart
+    return (chart,)
+
+
+@app.cell
+def _():
+    import marimo as mo
+
+    return (mo,)
+
+
+if __name__ == "__main__":
+    app.run()

notebooks/snippets/charts.py

@@ -1,115 +0,0 @@
-# Marimo snippets — Altair chart templates with Nature theme
-
-snippets = [
-    {
-        "title": "Chart setup — Nature theme",
-        "sections": [
-            {
-                "code": """from conf import connect
-connect.theme()
-
-import altair as alt
-""",
-            }
-        ],
-    },
-    {
-        "title": "Bar chart (horizontal)",
-        "sections": [
-            {
-                "code": """chart = (
-    alt.Chart(df.to_pandas())
-    .mark_bar()
-    .encode(
-        x=alt.X("value:Q", title="Value"),
-        y=alt.Y("category:N", sort="-x", title=None),
-        tooltip=["category:N", "value:Q"],
-    )
-    .properties(title="Title", width=600, height=300)
-)
-chart
-""",
-            }
-        ],
-    },
-    {
-        "title": "Line chart (time series)",
-        "sections": [
-            {
-                "code": """chart = (
-    alt.Chart(df.to_pandas())
-    .mark_line(point=True)
-    .encode(
-        x=alt.X("date:T", title="Date"),
-        y=alt.Y("value:Q", title="Value"),
-        color=alt.Color("series:N", title="Series"),
-        tooltip=["date:T", "series:N", "value:Q"],
-    )
-    .properties(title="Title", width=800, height=350)
-)
-chart
-""",
-            }
-        ],
-    },
-    {
-        "title": "Scatter plot",
-        "sections": [
-            {
-                "code": """chart = (
-    alt.Chart(df.to_pandas())
-    .mark_circle(opacity=0.6)
-    .encode(
-        x=alt.X("x:Q", title="X Axis"),
-        y=alt.Y("y:Q", title="Y Axis"),
-        color=alt.Color("group:N"),
-        size=alt.Size("weight:Q", legend=None),
-        tooltip=["x:Q", "y:Q", "group:N"],
-    )
-    .properties(title="Title", width=600, height=400)
-)
-chart
-""",
-            }
-        ],
-    },
-    {
-        "title": "Donut chart",
-        "sections": [
-            {
-                "code": """chart = (
-    alt.Chart(df.to_pandas())
-    .mark_arc(innerRadius=60)
-    .encode(
-        theta=alt.Theta("value:Q"),
-        color=alt.Color("category:N", title="Category"),
-        tooltip=["category:N", "value:Q"],
-    )
-    .properties(title="Title", width=350, height=350)
-)
-chart
-""",
-            }
-        ],
-    },
-    {
-        "title": "Stacked area chart",
-        "sections": [
-            {
-                "code": """chart = (
-    alt.Chart(df.to_pandas())
-    .mark_area(opacity=0.7)
-    .encode(
-        x=alt.X("date:T", title="Date"),
-        y=alt.Y("value:Q", stack=True, title="Value"),
-        color=alt.Color("category:N", title="Category"),
-        tooltip=["date:T", "category:N", "value:Q"],
-    )
-    .properties(title="Title", width=800, height=350)
-)
-chart
-""",
-            }
-        ],
-    },
-]

notebooks/snippets/connections.py

@@ -1,136 +0,0 @@
-# Marimo snippets — connection factories
-# These appear in marimo's snippet picker (Ctrl+Space or / in code cells)
-
-snippets = [
-    {
-        "title": "DuckDB — connect",
-        "sections": [
-            {
-                "code": """from conf import connect
-
-con = connect.duckdb()
-
-def q(sql):
-    \"\"\"Run SQL, return Polars DataFrame.\"\"\"
-    return con.execute(sql).pl()
-""",
-            }
-        ],
-    },
-    {
-        "title": "DuckDB — schema overview",
-        "sections": [
-            {
-                "code": """schemas = q('''
-    SELECT table_schema AS schema, count(*) AS tables
-    FROM information_schema.tables
-    WHERE table_schema != 'information_schema'
-    GROUP BY table_schema ORDER BY tables DESC
-''')
-mo.ui.table(schemas, label="Schemas")
-""",
-            }
-        ],
-    },
-    {
-        "title": "Trino — connect",
-        "sections": [
-            {
-                "code": """from conf import connect
-
-trino_con = connect.trino()
-cursor = trino_con.cursor()
-
-def tq(sql):
-    \"\"\"Run Trino SQL, return rows.\"\"\"
-    cursor.execute(sql)
-    return cursor.fetchall()
-""",
-            }
-        ],
-    },
-    {
-        "title": "Bibliography — connect",
-        "sections": [
-            {
-                "code": """from conf import connect
-
-store = connect.bib()
-items = store.list_items()
-print(f"{len(items)} bibliography items")
-""",
-            }
-        ],
-    },
-    {
-        "title": "Nessie — connect",
-        "sections": [
-            {
-                "code": """from conf import connect
-
-nessie = connect.nessie()
-refs = nessie.list_refs()
-for r in refs:
-    print(f"{r['type']}: {r['name']}")
-""",
-            }
-        ],
-    },
-    {
-        "title": "Polaris — connect",
-        "sections": [
-            {
-                "code": """from conf import connect
-
-polaris = connect.polaris()
-catalogs = polaris.list_catalogs()
-for c in catalogs:
-    print(c["name"])
-""",
-            }
-        ],
-    },
-    {
-        "title": "S3 / RustFS — connect",
-        "sections": [
-            {
-                "code": """from conf import connect
-
-s3 = connect.s3()
-objects = s3.list_objects(prefix="data/")
-for key in objects[:10]:
-    print(key)
-""",
-            }
-        ],
-    },
-    {
-        "title": "Zotero — connect",
-        "sections": [
-            {
-                "code": """from conf import connect
-
-zotero_con = connect.zotero()
-cursor = zotero_con.cursor()
-tables = cursor.execute(
-    "SELECT name FROM sqlite_master WHERE type='table' ORDER BY name"
-).fetchall()
-print(f"{len(tables)} tables")
-""",
-            }
-        ],
-    },
-    {
-        "title": "S3 / RustFS — obstore (marimo Files panel)",
-        "sections": [
-            {
-                "code": """from conf import connect
-
-# Creates an obstore S3Store that marimo auto-discovers
-# in the Files sidebar → Remote Storage panel.
-store = connect.obstore()
-""",
-            }
-        ],
-    },
-]

notebooks/snippets/duckdb-connect.py

@@ -0,0 +1,38 @@
+import marimo
+
+__generated_with = "0.20.4"
+app = marimo.App()
+
+
+@app.cell
+def _(mo):
+    mo.md(r"""
+    # DuckDB: Connect via conf.connect
+
+    Open the project DuckDB database and define a helper to run SQL queries.
+    """)
+    return
+
+
+@app.cell
+def _():
+    from conf import connect
+
+    con = connect.duckdb()
+
+    def q(sql):
+        """Run SQL and return a Polars DataFrame."""
+        return con.execute(sql).pl()
+
+    return con, connect, q
+
+
+@app.cell
+def _():
+    import marimo as mo
+
+    return (mo,)
+
+
+if __name__ == "__main__":
+    app.run()

notebooks/snippets/nessie-connect.py

@@ -0,0 +1,34 @@
+import marimo
+
+__generated_with = "0.20.4"
+app = marimo.App()
+
+
+@app.cell
+def _(mo):
+    mo.md(r"""
+    # Nessie: Git-for-Data client
+
+    Connect to Nessie for versioned Iceberg catalog operations.
+    """)
+    return
+
+
+@app.cell
+def _():
+    from conf import connect
+
+    nessie = connect.nessie()
+    refs = nessie.list_refs()
+    return connect, nessie, refs
+
+
+@app.cell
+def _():
+    import marimo as mo
+
+    return (mo,)
+
+
+if __name__ == "__main__":
+    app.run()

notebooks/snippets/queries.py

@@ -1,89 +0,0 @@
-# Marimo snippets — common healthcare analytics SQL queries
-
-snippets = [
-    {
-        "title": "Query — table profile",
-        "sections": [
-            {
-                "code": """table = "core.patient"
-profile = q(f'''
-    SELECT
-        count(*) AS rows,
-        count(*) - count(person_id) AS nulls,
-        count(DISTINCT person_id) AS distinct_ids
-    FROM {table}
-''')
-mo.ui.table(profile, label=f"Profile: {table}")
-""",
-            }
-        ],
-    },
-    {
-        "title": "Query — patient demographics",
-        "sections": [
-            {
-                "code": """demographics = q('''
-    SELECT sex, race, state, count(*) AS patients,
-           round(avg(age), 1) AS avg_age
-    FROM core.patient
-    GROUP BY sex, race, state
-    ORDER BY patients DESC
-''')
-mo.ui.table(demographics, label="Patient Demographics")
-""",
-            }
-        ],
-    },
-    {
-        "title": "Query — encounter summary",
-        "sections": [
-            {
-                "code": """encounters = q('''
-    SELECT encounter_type,
-           count(*) AS encounters,
-           count(DISTINCT person_id) AS patients
-    FROM core.encounter
-    GROUP BY encounter_type
-    ORDER BY encounters DESC
-''')
-mo.ui.table(encounters, label="Encounters by Type")
-""",
-            }
-        ],
-    },
-    {
-        "title": "Query — PMPM financial",
-        "sections": [
-            {
-                "code": """pmpm = q('''
-    SELECT year_month,
-           member_months,
-           round(total_paid / member_months, 2) AS total_pmpm,
-           round(inpatient_paid / member_months, 2) AS inpatient_pmpm,
-           round(pharmacy_paid / member_months, 2) AS pharmacy_pmpm
-    FROM financial_pmpm.pmpm_payer
-    WHERE member_months > 50
-    ORDER BY year_month
-''')
-mo.ui.table(pmpm, label="PMPM by Month")
-""",
-            }
-        ],
-    },
-    {
-        "title": "Query — chronic conditions top 20",
-        "sections": [
-            {
-                "code": """chronic = q('''
-    SELECT condition, count(DISTINCT person_id) AS patients
-    FROM chronic_conditions.cms_chronic_conditions_long
-    GROUP BY condition
-    ORDER BY patients DESC
-    LIMIT 20
-''')
-mo.ui.table(chronic, label="Top 20 Chronic Conditions")
-""",
-            }
-        ],
-    },
-]

notebooks/snippets/query-demographics.py

@@ -0,0 +1,38 @@
+import marimo
+
+__generated_with = "0.20.4"
+app = marimo.App()
+
+
+@app.cell
+def _(mo):
+    mo.md(r"""
+    # Query: Patient demographics
+
+    Summarise patient demographics by sex, race, and state.
+    """)
+    return
+
+
+@app.cell
+def _(mo, q):
+    demographics = q('''
+        SELECT sex, race, state, count(*) AS patients,
+               round(avg(age), 1) AS avg_age
+        FROM core.patient
+        GROUP BY sex, race, state
+        ORDER BY patients DESC
+    ''')
+    mo.ui.table(demographics, label="Patient Demographics")
+    return (demographics,)
+
+
+@app.cell
+def _():
+    import marimo as mo
+
+    return (mo,)
+
+
+if __name__ == "__main__":
+    app.run()

notebooks/snippets/query-pmpm.py

@@ -0,0 +1,40 @@
+import marimo
+
+__generated_with = "0.20.4"
+app = marimo.App()
+
+
+@app.cell
+def _(mo):
+    mo.md(r"""
+    # Query: PMPM financial summary
+
+    Per-member-per-month cost breakdown by service category.
+    """)
+    return
+
+
+@app.cell
+def _(mo, q):
+    pmpm = q('''
+        SELECT year_month, member_months,
+               round(total_paid / member_months, 2) AS total_pmpm,
+               round(inpatient_paid / member_months, 2) AS inpatient_pmpm,
+               round(pharmacy_paid / member_months, 2) AS pharmacy_pmpm
+        FROM financial_pmpm.pmpm_payer
+        WHERE member_months > 50
+        ORDER BY year_month
+    ''')
+    mo.ui.table(pmpm, label="PMPM by Month")
+    return (pmpm,)
+
+
+@app.cell
+def _():
+    import marimo as mo
+
+    return (mo,)
+
+
+if __name__ == "__main__":
+    app.run()

notebooks/snippets/query-schema.py

@@ -0,0 +1,38 @@
+import marimo
+
+__generated_with = "0.20.4"
+app = marimo.App()
+
+
+@app.cell
+def _(mo):
+    mo.md(r"""
+    # Query: Schema overview
+
+    List all schemas and table counts in the database.
+    """)
+    return
+
+
+@app.cell
+def _(mo, q):
+    schemas = q('''
+        SELECT table_schema AS schema, count(*) AS tables
+        FROM information_schema.tables
+        WHERE table_schema != 'information_schema'
+        GROUP BY table_schema
+        ORDER BY tables DESC
+    ''')
+    mo.ui.table(schemas, label="Schemas")
+    return (schemas,)
+
+
+@app.cell
+def _():
+    import marimo as mo
+
+    return (mo,)
+
+
+if __name__ == "__main__":
+    app.run()

notebooks/snippets/s3-obstore.py

@@ -0,0 +1,34 @@
+import marimo
+
+__generated_with = "0.20.4"
+app = marimo.App()
+
+
+@app.cell
+def _(mo):
+    mo.md(r"""
+    # S3: Remote Storage via obstore
+
+    Create an S3Store that marimo auto-discovers in Files -> Remote Storage.
+    """)
+    return
+
+
+@app.cell
+def _():
+    from conf import connect
+
+    store = connect.obstore()
+    # This S3Store is auto-discovered by marimo in Files -> Remote Storage
+    return connect, store
+
+
+@app.cell
+def _():
+    import marimo as mo
+
+    return (mo,)
+
+
+if __name__ == "__main__":
+    app.run()

notebooks/snippets/trino-connect.py

@@ -0,0 +1,34 @@
+import marimo
+
+__generated_with = "0.20.4"
+app = marimo.App()
+
+
+@app.cell
+def _(mo):
+    mo.md(r"""
+    # Trino: Connect via conf.connect
+
+    Connect to the Trino query engine for federated SQL queries.
+    """)
+    return
+
+
+@app.cell
+def _():
+    from conf import connect
+
+    trino_con = connect.trino()
+    cursor = trino_con.cursor()
+    return connect, cursor, trino_con
+
+
+@app.cell
+def _():
+    import marimo as mo
+
+    return (mo,)
+
+
+if __name__ == "__main__":
+    app.run()