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Merge pull request #82 from jvivian/Build-SCM-Pages
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Build scm pages
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@jvivian
jvivian authored Jun 6, 2024
2 parents 131880c + 1df008e commit b82de3d
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9 changes: 8 additions & 1 deletion .vscode/launch.json
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Expand Up @@ -10,7 +10,14 @@
"request": "launch",
"program": "${file}",
"console": "integratedTerminal",
"justMyCode": true
"justMyCode": true,
"args": [
"run",
"covid19_drdfm/data/processed/data.h5ad",
"./covid19_drdfm/data/example-data/full-global-2",
"--batch",
"State"
]
}
]
}
4 changes: 4 additions & 0 deletions Makefile
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Expand Up @@ -42,4 +42,8 @@ docs: ## Build and serve the documentation
help:
@grep -E '^[a-zA-Z_-]+:.*?## .*$$' $(MAKEFILE_LIST) | awk 'BEGIN {FS = ":.*?## "}; {printf "\033[36m%-20s\033[0m %s\n", $$1, $$2}'

.PHONY: dashboard
dashboard:
@streamlit run covid19_drdfm/streamlit/Dashboard.py

.DEFAULT_GOAL := help
87 changes: 47 additions & 40 deletions coverage.xml
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<?xml version="1.0" ?>
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<!-- Generated by coverage.py: https://coverage.readthedocs.io/en/7.4.3 -->
<!-- Based on https://raw.githubusercontent.com/cobertura/web/master/htdocs/xml/coverage-04.dtd -->
<sources>
<source>/Users/jvivian/git/covid19-drDFM/covid19_drdfm</source>
<source>/home/jvivian/covid19-drDFM/covid19_drdfm</source>
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13 changes: 10 additions & 3 deletions covid19_drdfm/cli.py
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Expand Up @@ -9,19 +9,18 @@
Process data and generate parquet DataFrame
- `c19_dfm process ./outfile.xlsx`
"""
import anndata as ann

import subprocess
from pathlib import Path
from typing import Optional

import anndata as ann
import typer
from rich import print

from covid19_drdfm.covid19 import get_project_h5ad

from covid19_drdfm.io import DataLoader
from covid19_drdfm.dfm import ModelRunner
from covid19_drdfm.io import DataLoader

app = typer.Typer()

Expand All @@ -33,10 +32,14 @@ def run_dfm(
batch: str = typer.Option(help="Name of column in h5ad.obs to use as batch variable"),
global_multiplier: int = 1,
maxiter: int = 10_000,
update_h5ad: bool = True,
):
ad = ann.read_h5ad(h5ad)
model = ModelRunner(ad, outdir, batch)
model.run(maxiter, global_multiplier)
if update_h5ad:
print(f"[bold green]:heavy_check_mark: Updating H5ad {h5ad}")
model.ad.write_h5ad(h5ad)


@app.command("create_input_data")
Expand Down Expand Up @@ -74,3 +77,7 @@ def launch_dashboard():
current_dir = Path(__file__).resolve().parent
dashboard_path = current_dir / "streamlit" / "Dashboard.py"
subprocess.run(["streamlit", "run", dashboard_path])


if __name__ == "__main__":
app()
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