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Build scm pages #82

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merged 28 commits into from
Jun 6, 2024
Merged

Build scm pages #82

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6f30be6
Basically nothing, just tinkering
AaronCooke2718 Apr 26, 2024
3be8ba2
Add run-dashboard to makefile
jvivian May 1, 2024
431f80d
John's updates
jvivian May 1, 2024
7f5c8f9
Started copying code over, need to identify if I am referring to the …
AaronCooke2718 May 1, 2024
df4752b
Update 4_SCM_Data_Selection.py
AaronCooke2718 May 3, 2024
0f7529f
Adding SCM ipynb
jvivian May 19, 2024
7f62ad5
Update data.h5ad
jvivian May 19, 2024
d8d6ee3
Add factors to output anndata object
jvivian May 19, 2024
804cf1f
Update page
jvivian May 19, 2024
8b0db49
Merge branch 'Build-SCM-Pages' of https://github.com/jvivian/covid19-…
jvivian May 19, 2024
eb1b2a2
Update notebook with working example
jvivian May 20, 2024
d6b229e
Remove buggy anndata code for now
jvivian May 20, 2024
ade8f81
Add option to parameterize dashboard inputs
jvivian May 22, 2024
8311537
Update SCM with data
jvivian May 23, 2024
78c4b1d
Update notebook
jvivian May 23, 2024
b08fb3d
shitty bugfixes, will clean up later
jvivian May 27, 2024
56454f6
Update deps
jvivian Jun 3, 2024
407db0f
Add if __name__ statement for debugger
jvivian Jun 3, 2024
86e59c3
Add data.h5ad write out
jvivian Jun 3, 2024
b649535
Swap to yaml for output
jvivian Jun 3, 2024
77c9d2b
Add failure statements to dashboard
jvivian Jun 3, 2024
96e659e
fix factor analysis page
jvivian Jun 3, 2024
bc2e038
Move work in progress pages
jvivian Jun 3, 2024
fa98b3c
Update SCM page
jvivian Jun 3, 2024
adeb704
Update launch with example
jvivian Jun 3, 2024
fb99127
Update example data
jvivian Jun 3, 2024
8c16dd9
Add SCM page
jvivian Jun 5, 2024
1df008e
FIx tests + update coverage
jvivian Jun 6, 2024
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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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@@ -1,46 +1,51 @@
<?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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Expand Down Expand Up @@ -109,7 +114,7 @@
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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 @@
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 @@
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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