remove remaining usage of typer

pyproject.toml

@@ -31,7 +31,6 @@ dependencies = [
     "sparse>=0.15.4",
     "statsmodels>=0.14.0",
     "tqdm>=4.66.1",
-    "typer>=0.12.3",
     "cyclopts",
     "vegafusion[embed]>=1.6.5",
     "xarray",

src/depiction_targeted_preproc/workflow/exp/compare_cluster_stats.py

@@ -1,9 +1,7 @@
 import altair as alt
+import cyclopts
 import polars as pl
-import typer
 from pathlib import Path
-from typer import Option
-from typing import Annotated
 
 
 def load_data(csv_paths: list[Path]) -> pl.DataFrame:
@@ -14,13 +12,15 @@ def load_data(csv_paths: list[Path]) -> pl.DataFrame:
     return pl.concat(collect)
 
 
-def compare_cluster_stats(input_csv_path: list[Path], output_pdf: Annotated[Path, Option()]) -> None:
+app = cyclopts.App()
+
+
+@app.default
+def compare_cluster_stats(input_csv_path: list[Path], output_pdf: Path) -> None:
     data = load_data(input_csv_path)
     chart = alt.Chart(data).mark_bar().encode(x="label", y="value", column="metric").resolve_scale(y="independent")
     chart.save(output_pdf)
 
 
 if __name__ == "__main__":
-    typer.run(compare_cluster_stats)
-
-# print(sys.argv)
+    app()

src/depiction_targeted_preproc/workflow/exp/plot_compare_peak_density.py

@@ -1,18 +1,18 @@
-from pathlib import Path
-from typing import Annotated
-
+import cyclopts
 import polars as pl
-import typer
 import vegafusion
-from typer import Option, Argument
+from pathlib import Path
 
 from depiction_targeted_preproc.workflow.qc.plot_peak_density import plot_density_combined_full
 
+app = cyclopts.App()
+
 
+@app.default
 def exp_plot_compare_peak_density(
-    tables_marker_distances_calib: Annotated[list[Path], Argument()],
-    table_marker_distance_uncalib: Annotated[Path, Option()],
-    output_pdf: Annotated[Path, Option()],
+    tables_marker_distances_calib: list[Path],
+    table_marker_distance_uncalib: Path,
+    output_pdf: Path,
 ) -> None:
     vegafusion.enable()
 
@@ -28,4 +28,4 @@ def exp_plot_compare_peak_density(
 
 
 if __name__ == "__main__":
-    typer.run(exp_plot_compare_peak_density)
+    app()

src/depiction_targeted_preproc/workflow/exp/plot_map_comparison.py

@@ -1,14 +1,15 @@
-import typer
+import cyclopts
 import xarray
 from matplotlib import pyplot as plt
 from pathlib import Path
-from typing import Annotated
+
+app = cyclopts.App()
 
 
 @app.default
 def exp_plot_map_comparison(
-    input_mass_shift_paths: Annotated[list[Path], typer.Argument()],
-    output_pdf_path: Annotated[Path, typer.Option()],
+    input_mass_shift_paths: list[Path],
+    output_pdf_path: Path,
 ) -> None:
     # load all the inputs
     mass_shifts = [xarray.open_dataarray(path) for path in input_mass_shift_paths]
@@ -25,4 +26,4 @@ def exp_plot_map_comparison(
 
 
 if __name__ == "__main__":
-    typer.run(exp_plot_map_comparison)
+    app()