Merge branch 'main' into feature/docs_examples

# Conflicts:
#	pertpy/tools/_distances/_distances.py

.pre-commit-config.yaml

@@ -25,7 +25,7 @@ repos:
             # https://github.com/jupyterlab/jupyterlab/issues/12675
             language_version: "17.9.1"
     - repo: https://github.com/astral-sh/ruff-pre-commit
-      rev: v0.0.288
+      rev: v0.0.292
       hooks:
           - id: ruff
             args: [--fix, --exit-non-zero-on-fix]

docs/usage/usage.md

@@ -428,6 +428,48 @@ pred.obs["condition"] = "pred"
 
 See [scgen tutorial](https://pertpy.readthedocs.io/en/latest/tutorials/notebooks/scgen_perturbation_prediction.html) for a more elaborate tutorial.
 
+#### CINEMA-OT
+
+An implementation of [CINEMA-OT](https://github.com/vandijklab/CINEMA-OT) with the ott-jax library.
+CINEMA-OT is a causal framework for perturbation effect analysis to identify individual treatment effects and synergy at the single cell level.
+CINEMA-OT separates confounding sources of variation from perturbation effects to obtain an optimal transport matching that reflects counterfactual cell pairs.
+These cell pairs represent causal perturbation responses permitting a number of novel analyses, such as individual treatment effect analysis, response clustering, attribution analysis, and synergy analysis.
+See [Causal identification of single-cell experimental perturbation effects with CINEMA-OT](https://www.biorxiv.org/content/10.1101/2022.07.31.502173v3.abstract) for more details.
+
+```{eval-rst}
+.. currentmodule:: pertpy
+```
+
+```{eval-rst}
+.. autosummary::
+    :toctree: tools
+
+    tools.Cinemaot
+```
+
+Example implementation:
+
+```python
+import pertpy as pt
+
+adata = pt.dt.cinemaot_example()
+
+model = pt.tl.Cinemaot()
+de = model.causaleffect(
+    adata,
+    pert_key="perturbation",
+    control="No stimulation",
+    return_matching=True,
+    thres=0.5,
+    smoothness=1e-5,
+    eps=1e-3,
+    solver="Sinkhorn",
+    preweight_label="cell_type0528",
+)
+```
+
+See [CINEMA-OT tutorial](https://pertpy.readthedocs.io/en/latest/tutorials/notebooks/cinemaot.html) for a more elaborate tutorial.
+
 ### Perturbation space
 
 Various modules for calculating and evaluating perturbation spaces.
@@ -559,3 +601,12 @@ See [perturbation space tutorial](https://pertpy.readthedocs.io/en/latest/tutori
     plot.scg.reg_var_plot
     plot.scg.binary_classifier
 ```
+
+#### CINEMA-OT
+
+```{eval-rst}
+.. autosummary::
+    :toctree: plot
+
+    plot.cot.vis_matching
+```

pertpy/data/__init__.py

@@ -6,6 +6,7 @@
     bhattacherjee,
     burczynski_crohn,
     chang_2021,
+    cinemaot_example,
     datlinger_2017,
     datlinger_2021,
     dialogue_example,

pertpy/data/_dataloader.py

@@ -49,7 +49,7 @@ def _download(  # pragma: no cover
     response = requests.get(url, stream=True)
     total = int(response.headers.get("content-length", 0))
 
-    with Progress(refresh_per_second=1500) as progress:
+    with Progress(refresh_per_second=100) as progress:
         task = progress.add_task("[red]Downloading...", total=total)
         Path(output_path).mkdir(parents=True, exist_ok=True)
         with Path(download_to_path).open("wb") as file: