use cyclopts

src/depiction_targeted_preproc/workflow/exp/plot_map_comparison.py

@@ -1,10 +1,11 @@
-from pathlib import Path
-from typing import Annotated
-import xarray
 import typer
+import xarray
 from matplotlib import pyplot as plt
+from pathlib import Path
+from typing import Annotated
 
 
+@app.default
 def exp_plot_map_comparison(
     input_mass_shift_paths: Annotated[list[Path], typer.Argument()],
     output_pdf_path: Annotated[Path, typer.Option()],

src/depiction_targeted_preproc/workflow/exp/plot_map_single_for_poster.py

@@ -1,14 +1,17 @@
-from pathlib import Path
-from typing import Annotated
-
-import typer
+import cyclopts
 import xarray
 from matplotlib import pyplot as plt
+from pathlib import Path
+
+# TODO delete?
+
+app = cyclopts.App()
 
 
+@app.default
 def exp_plot_map_single_for_poster(
-    input_mass_shift_path: Annotated[Path, typer.Option()],
-    output_pdf_path: Annotated[Path, typer.Option()],
+    input_mass_shift_path: Path,
+    output_pdf_path: Path,
 ) -> None:
     # load all the inputs
     shift_map = xarray.open_dataarray(input_mass_shift_path)
@@ -24,4 +27,4 @@ def exp_plot_map_single_for_poster(
 
 
 if __name__ == "__main__":
-    typer.run(exp_plot_map_single_for_poster)
+    app()

src/depiction_targeted_preproc/workflow/qc/plot_peak_counts_per_spectrum.py

@@ -1,11 +1,8 @@
-from pathlib import Path
-from typing import Annotated
-
 import altair as alt
+import cyclopts
 import polars as pl
-import typer
 from loguru import logger
-from typer import Option
+from pathlib import Path
 
 from depiction.parallel_ops import ReadSpectraParallel, ParallelConfig
 from depiction.persistence import ImzmlReadFile, ImzmlReader
@@ -35,10 +32,14 @@ def get_peak_counts(read_peaks: ImzmlReadFile, mass_groups: pl.DataFrame, n_jobs
     )
 
 
+app = cyclopts.App()
+
+
+@app.default
 def qc_plot_peak_counts_per_spectrum(
-    imzml_peaks: Annotated[Path, Option()],
-    output_pdf: Annotated[Path, Option()],
-    config_path: Annotated[Path, Option()],
+    imzml_peaks: Path,
+    output_pdf: Path,
+    config_path: Path,
 ) -> None:
     config = PipelineParameters.parse_yaml(config_path)
     read_peaks = ImzmlReadFile(imzml_peaks)
@@ -63,4 +64,4 @@ def qc_plot_peak_counts_per_spectrum(
 
 
 if __name__ == "__main__":
-    typer.run(qc_plot_peak_counts_per_spectrum)
+    app()

src/depiction_targeted_preproc/workflow/qc/plot_sample_spectra_before_after.py

@@ -1,8 +1,6 @@
 import cyclopts
 import polars as pl
 from pathlib import Path
-from typer import Option
-from typing import Annotated
 
 from depiction.persistence import ImzmlReadFile
 from depiction.visualize.plot_mass_spectrum import PlotMassSpectrum

src/depiction_targeted_preproc/workflow/qc/table_marker_surroundings.py

@@ -1,10 +1,8 @@
-from collections.abc import Sequence
-from pathlib import Path
-from typing import Annotated
-
+import cyclopts
 import numpy as np
 import polars as pl
-import typer
+from collections.abc import Sequence
+from pathlib import Path
 
 from depiction.parallel_ops import ParallelConfig, ReadSpectraParallel
 from depiction.persistence import ImzmlReadFile, ImzmlReader
@@ -51,12 +49,16 @@ def get_marker_surroundings(
     )
 
 
+app = cyclopts.App()
+
+
+@app.default
 def qc_table_marker_surroundings(
-    imzml_peaks: Annotated[Path, typer.Option()],
-    mass_list: Annotated[Path, typer.Option()],
-    config_path: Annotated[Path, typer.Option()],
-    output_table: Annotated[Path, typer.Option()],
-    mz_max_dist: Annotated[float, typer.Option()] = 3.0,
+    imzml_peaks: Path,
+    mass_list: Path,
+    config_path: Path,
+    output_table: Path,
+    mz_max_dist: float = 3.0,
 ) -> None:
     config = PipelineParameters.parse_yaml(config_path)
     n_jobs = config.n_jobs
@@ -73,10 +75,5 @@ def qc_table_marker_surroundings(
     dist_df.write_parquet(output_table)
 
 
-def main() -> None:
-    """Parses CLI args and calls `qc_table_marker_distances`."""
-    typer.run(qc_table_marker_surroundings)
-
-
 if __name__ == "__main__":
-    main()
+    app()