From c049ea1a6d7c7a7a33cf8d9246351c9680f26219 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Sat, 19 Oct 2024 07:14:30 +0000
Subject: [PATCH] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/scvi/external/sysvi/_base_components.py | 4 +++-
 src/scvi/external/sysvi/_model.py           | 8 +++++---
 src/scvi/external/sysvi/_module.py          | 3 ++-
 src/scvi/external/sysvi/_utils.py           | 2 +-
 4 files changed, 11 insertions(+), 6 deletions(-)

diff --git a/src/scvi/external/sysvi/_base_components.py b/src/scvi/external/sysvi/_base_components.py
index ed4cfe214e..09c0569f45 100644
--- a/src/scvi/external/sysvi/_base_components.py
+++ b/src/scvi/external/sysvi/_base_components.py
@@ -197,7 +197,9 @@ def __init__(
                             Dropout(p=dropout_rate) if dropout_rate > 0 else None,
                         ),
                     )
-                    for i, (n_in, n_out) in enumerate(zip(layers_dim[:-1], layers_dim[1:]))
+                    for i, (n_in, n_out) in enumerate(
+                        zip(layers_dim[:-1], layers_dim[1:], strict=False)
+                    )
                 ]
             )
         )
diff --git a/src/scvi/external/sysvi/_model.py b/src/scvi/external/sysvi/_model.py
index 0da03933fe..7277a76b64 100644
--- a/src/scvi/external/sysvi/_model.py
+++ b/src/scvi/external/sysvi/_model.py
@@ -2,7 +2,7 @@
 
 import logging
 from collections.abc import Sequence
-from typing import Literal, Tuple
+from typing import Literal
 
 import numpy as np
 import pandas as pd
@@ -118,7 +118,7 @@ def get_latent_representation(
         give_mean: bool = True,
         batch_size: int | None = None,
         return_dist: bool = False,
-    ) -> np.ndarray | Tuple[np.ndarray, np.ndarray]:
+    ) -> np.ndarray | tuple[np.ndarray, np.ndarray]:
         """Return the latent representation for each cell.
 
         Parameters
@@ -300,7 +300,9 @@ def setup_anndata(
             )
 
         # Make one-hot embedding with specified order
-        systems_dict = dict(zip(batch_order, ([float(i) for i in range(0, len(batch_order))])))
+        systems_dict = dict(
+            zip(batch_order, ([float(i) for i in range(0, len(batch_order))]), strict=False)
+        )
         adata.uns["batch_order"] = batch_order
         system_cat = pd.Series(
             pd.Categorical(values=adata.obs[batch_key], categories=batch_order, ordered=True),
diff --git a/src/scvi/external/sysvi/_module.py b/src/scvi/external/sysvi/_module.py
index bec63c9fb3..92ebfde80e 100644
--- a/src/scvi/external/sysvi/_module.py
+++ b/src/scvi/external/sysvi/_module.py
@@ -1,7 +1,8 @@
 from __future__ import annotations
 
+from typing import Literal
+
 import torch
-from typing_extensions import Literal
 
 from scvi import REGISTRY_KEYS
 from scvi.module.base import BaseModuleClass, LossOutput, auto_move_data
diff --git a/src/scvi/external/sysvi/_utils.py b/src/scvi/external/sysvi/_utils.py
index 5eadcb8819..ad2e8bcab0 100644
--- a/src/scvi/external/sysvi/_utils.py
+++ b/src/scvi/external/sysvi/_utils.py
@@ -140,7 +140,7 @@ def dummies_categories(values: pd.Series, categories: list):
         cov_embed_data = []
         for cov_cat_embed_key in cov_cat_embed_keys:
             cat_order = categ_orders[cov_cat_embed_key]
-            cat_map = dict(zip(cat_order, range(len(cat_order))))
+            cat_map = dict(zip(cat_order, range(len(cat_order)), strict=False))
             cov_embed_data.append(meta_data[cov_cat_embed_key].map(cat_map))
         cov_embed_data = pd.concat(cov_embed_data, axis=1)
     else: