Coda plots docs with dict

scverse · Sep 6, 2024 · fce6249 · fce6249
1 parent 378121d
commit fce6249
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Showing 2 changed files with 7 additions and 11 deletions.
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -27,9 +27,9 @@ jobs:
  - os: ubuntu-latest
  python: "3.12"
  run_mode: "slow"
-# - os: ubuntu-latest
-# python: "3.12"
-# run_mode: "fast"
+ # - os: ubuntu-latest
+ # python: "3.12"
+ # run_mode: "fast"
  - os: ubuntu-latest
  python: "3.12"
  run_mode: slow

diff --git a/pertpy/tools/_coda/_base_coda.py b/pertpy/tools/_coda/_base_coda.py
@@ -1025,7 +1025,7 @@ def get_node_df(self, data: AnnData | MuData, modality_key: str = "coda"):
  >>> key_added="lineage", add_level_name=True
  >>> )
  >>> mdata = tasccoda.prepare(
- >>> mdata, formula="Health", reference_cell_type="automatic", tree_key="lineage", pen_args={"phi": 0}
+ >>> mdata, formula="Health", reference_cell_type="automatic", tree_key="lineage", pen_args={"phi" : 0}
  >>> )
  >>> tasccoda.run_nuts(mdata, num_samples=1000, num_warmup=100, rng_key=42)
  >>> node_effects = tasccoda.get_node_df(mdata)
@@ -1843,9 +1843,6 @@ def plot_draw_tree( # pragma: no cover
  tight_text: When False, boundaries of the text are approximated according to general font metrics,
  producing slightly worse aligned text faces but improving the performance of tree visualization in scenes with a lot of text faces.
  show_scale: Include the scale legend in the tree image or not.
- show: If True, plot the tree inline. If false, return tree and tree_style objects.
- file_name: Path to the output image file. Valid extensions are .SVG, .PDF, .PNG.
- Output image can be saved whether show is True or not.
  units: Unit of image sizes. “px”: pixels, “mm”: millimeters, “in”: inches.
  figsize: Figure size.
  dpi: Dots per inches.
@@ -1864,7 +1861,7 @@ def plot_draw_tree( # pragma: no cover
  >>> key_added="lineage", add_level_name=True
  >>> )
  >>> mdata = tasccoda.prepare(
- >>> mdata, formula="Health", reference_cell_type="automatic", tree_key="lineage", pen_args={"phi": 0}
+ >>> mdata, formula="Health", reference_cell_type="automatic", tree_key="lineage", pen_args=dict(phi=0)
  >>> )
  >>> tasccoda.run_nuts(mdata, num_samples=1000, num_warmup=100, rng_key=42)
  >>> tasccoda.plot_draw_tree(mdata, tree="lineage")
@@ -1934,7 +1931,6 @@ def plot_draw_effects( # pragma: no cover
  tight_text: When False, boundaries of the text are approximated according to general font metrics,
  producing slightly worse aligned text faces but improving the performance of tree visualization in scenes with a lot of text faces.
  show_scale: Include the scale legend in the tree image or not.
- file_name: Path to the output image file. valid extensions are .SVG, .PDF, .PNG. Output image can be saved whether show is True or not.
  units: Unit of image sizes. “px”: pixels, “mm”: millimeters, “in”: inches.
  figsize: Figure size.
  dpi: Dots per inches.
@@ -1954,7 +1950,7 @@ def plot_draw_effects( # pragma: no cover
  >>> key_added="lineage", add_level_name=True
  >>> )
  >>> mdata = tasccoda.prepare(
- >>> mdata, formula="Health", reference_cell_type="automatic", tree_key="lineage", pen_args={"phi": 0}
+ >>> mdata, formula="Health", reference_cell_type="automatic", tree_key="lineage", pen_args=dict(phi=0)
  >>> )
  >>> tasccoda.run_nuts(mdata, num_samples=1000, num_warmup=100, rng_key=42)
  >>> tasccoda.plot_draw_effects(mdata, covariate="Health[T.Inflamed]", tree="lineage")
@@ -2151,7 +2147,7 @@ def plot_effects_umap( # pragma: no cover
  >>> modality_key="coda",
  >>> reference_cell_type="18",
  >>> formula="condition",
- >>> pen_args={"phi": 0, "lambda_1": 3.5},
+ >>> pen_args=dict(phi=0, lambda_1=3.5),
  >>> tree_key="tree"
  >>> )
  >>> tasccoda_model.run_nuts(