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fix notebook runtime: add altair/pandas deps, fix table ref, fix sys.path
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- Add altair and pandas as dev dependencies so notebooks run as scripts
- Fix sys.path for styles/ to resolve relative to __file__, not CWD
- Fix broken table ref: chronic_conditions_long → cms_chronic_conditions_long
- Update pre-commit hook: lint only staged files, run notebooks as scripts

refs #45
This commit is contained in:
kert
2026-03-21 14:06:45 -04:00
parent 33701365be
commit cfeb09eff4
3 changed files with 154 additions and 3 deletions
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11
notebooks/acodb_explorer.py
View File

@@ -28,7 +28,12 @@ def _(mo):
@app.cell(hide_code=True) @app.cell(hide_code=True)
def _(): def _():
import sys import sys
sys.path.insert(0, "../styles") from pathlib import Path
_here = Path(__file__).resolve().parent if "__file__" in dir() else Path.cwd()
_styles = str((_here / "../styles").resolve())
if _styles not in sys.path:
sys.path.insert(0, _styles)
import altair as alt import altair as alt
import duckdb import duckdb
@@ -245,7 +250,7 @@ def _(mo):
def _(PALETTE, alt, mo, q): def _(PALETTE, alt, mo, q):
chronic = q(""" chronic = q("""
SELECT condition, count(DISTINCT person_id) AS patients SELECT condition, count(DISTINCT person_id) AS patients
FROM chronic_conditions.chronic_conditions_long FROM chronic_conditions.cms_chronic_conditions_long
GROUP BY condition GROUP BY condition
ORDER BY patients DESC ORDER BY patients DESC
LIMIT 20 LIMIT 20
@@ -273,7 +278,7 @@ def _(PALETTE, alt, mo, q):
def _(mo, q): def _(mo, q):
comorbidity = q(""" comorbidity = q("""
SELECT person_id, count(DISTINCT condition) AS condition_count SELECT person_id, count(DISTINCT condition) AS condition_count
FROM chronic_conditions.chronic_conditions_long FROM chronic_conditions.cms_chronic_conditions_long
GROUP BY person_id GROUP BY person_id
""") """)

3
pyproject.toml
View File

@@ -7,6 +7,7 @@ requires-python = ">=3.12"
dependencies = [ dependencies = [
"databricks-cli>=0.18.0", "databricks-cli>=0.18.0",
"databricks-sdk>=0.85.0", "databricks-sdk>=0.85.0",
"duckdb>=1.0.0",
"fastapi>=0.135.1", "fastapi>=0.135.1",
"fastexcel>=0.19.0", "fastexcel>=0.19.0",
"fsspec>=2024.1.0", "fsspec>=2024.1.0",
@@ -34,6 +35,8 @@ dev = [
"pytest-cov>=7.0.0", "pytest-cov>=7.0.0",
"marimo>=0.20.0", "marimo>=0.20.0",
"ruff>=0.11.0", "ruff>=0.11.0",
"altair>=6.0.0",
"pandas>=3.0.1",
] ]
[tool.ruff] [tool.ruff]
line-length = 88 line-length = 88

143
uv.lock generated
View File

@@ -1,6 +1,14 @@
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[[package]] [[package]]
name = "parsedatetime" name = "parsedatetime"
version = "2.6" version = "2.6"
@@ -1907,6 +2044,7 @@ source = { virtual = "." }
dependencies = [ dependencies = [
{ name = "databricks-cli" }, { name = "databricks-cli" },
{ name = "databricks-sdk" }, { name = "databricks-sdk" },
{ name = "duckdb" },
{ name = "fastapi" }, { name = "fastapi" },
{ name = "fastexcel" }, { name = "fastexcel" },
{ name = "fsspec" }, { name = "fsspec" },
@@ -1921,11 +2059,13 @@ dependencies = [
[package.dev-dependencies] [package.dev-dependencies]
dev = [ dev = [
{ name = "altair" },
{ name = "coverage" }, { name = "coverage" },
{ name = "dbt-core" }, { name = "dbt-core" },
{ name = "dbt-duckdb" }, { name = "dbt-duckdb" },
{ name = "marimo" }, { name = "marimo" },
{ name = "openpyxl" }, { name = "openpyxl" },
{ name = "pandas" },
{ name = "pdfplumber" }, { name = "pdfplumber" },
{ name = "polars" }, { name = "polars" },
{ name = "pytest" }, { name = "pytest" },
@@ -1937,6 +2077,7 @@ dev = [
requires-dist = [ requires-dist = [
{ name = "databricks-cli", specifier = ">=0.18.0" }, { name = "databricks-cli", specifier = ">=0.18.0" },
{ name = "databricks-sdk", specifier = ">=0.85.0" }, { name = "databricks-sdk", specifier = ">=0.85.0" },
{ name = "duckdb", specifier = ">=1.0.0" },
{ name = "fastapi", specifier = ">=0.135.1" }, { name = "fastapi", specifier = ">=0.135.1" },
{ name = "fastexcel", specifier = ">=0.19.0" }, { name = "fastexcel", specifier = ">=0.19.0" },
{ name = "fsspec", specifier = ">=2024.1.0" }, { name = "fsspec", specifier = ">=2024.1.0" },
@@ -1951,11 +2092,13 @@ requires-dist = [
[package.metadata.requires-dev] [package.metadata.requires-dev]
dev = [ dev = [
{ name = "altair", specifier = ">=6.0.0" },
{ name = "coverage", specifier = ">=7.13.4" }, { name = "coverage", specifier = ">=7.13.4" },
{ name = "dbt-core", specifier = "==1.10.15" }, { name = "dbt-core", specifier = "==1.10.15" },
{ name = "dbt-duckdb", specifier = ">=1.10,<1.11" }, { name = "dbt-duckdb", specifier = ">=1.10,<1.11" },
{ name = "marimo", specifier = ">=0.20.0" }, { name = "marimo", specifier = ">=0.20.0" },
{ name = "openpyxl", specifier = ">=3.1.5" }, { name = "openpyxl", specifier = ">=3.1.5" },
{ name = "pandas", specifier = ">=3.0.1" },
{ name = "pdfplumber", specifier = ">=0.11.9" }, { name = "pdfplumber", specifier = ">=0.11.9" },
{ name = "polars", specifier = ">=1.38.1" }, { name = "polars", specifier = ">=1.38.1" },
{ name = "pytest", specifier = ">=9.0.2" }, { name = "pytest", specifier = ">=9.0.2" },