Merge branch 'theislab:main' into fix/get_df-with-default-args

.github/workflows/release.yml

@@ -20,7 +20,7 @@ jobs:
             - name: Install dependencies
               run: |
                   python -m pip install --upgrade pip
-                  python -m pip build
+                  python -m pip install --upgrade build
 
             - name: Build package
               run: |

pyproject.toml

@@ -1,11 +1,10 @@
 [build-system]
-build-backend = "hatchling.build"
-requires = ["hatchling"]
-
+requires = ["setuptools>=61", "setuptools-scm[toml]>=6.2"]
+build-backend = "setuptools.build_meta"
 
 [project]
 name = "scvelo"
-version = "0.3.1"
+dynamic = ["version"]
 description = "RNA velocity generalized through dynamical modeling"
 readme = {file = "README.md", content-type="text/markdown"}
 requires-python = ">=3.8"
@@ -98,8 +97,10 @@ docs = [
     "nbsphinx>=0.7,<0.8.7"
 ]
 
-[tool.hatch.build.targets.wheel]
-packages = ["scvelo"]
+[tool.setuptools]
+include-package-data = true
+
+[tool.setuptools_scm]
 
 [tool.coverage.run]
 source = ["scvelo"]

scvelo/plotting/utils.py

@@ -1460,6 +1460,7 @@ def hist(
     ax=None,
     dpi=None,
     show=True,
+    save=None,
     **kwargs,
 ):
     """Plot a histogram.
@@ -1530,6 +1531,9 @@ def hist(
         Figure dpi.
     show: `bool`, optional (default: `None`)
         Show the plot, do not return axis.
+    save: `bool` or `str`, optional (default: `None`)
+        If `True` or a `str`, save the figure. A string is appended to the default filename.
+        Infer the filetype if ending on {'.pdf', '.png', '.svg'}.
 
     Returns
     -------
@@ -1658,10 +1662,9 @@ def log_fmt(x, pos):
     if rcParams["savefig.transparent"]:
         ax.patch.set_alpha(0)
 
-    if not show:
+    savefig_or_show(dpi=dpi, save=save, show=show)
+    if show is False:
         return ax
-    else:
-        pl.show()
 
 
 # TODO: Add docstrings

scvelo/tools/_vi_model.py

@@ -127,7 +127,6 @@ def train(
         max_epochs: Optional[int] = 500,
         lr: float = 1e-2,
         weight_decay: float = 1e-2,
-        use_gpu: Optional[Union[str, int, bool]] = None,
         accelerator: str = "auto",
         devices: Union[int, List[int], str] = "auto",
         train_size: float = 0.9,
@@ -149,9 +148,14 @@ def train(
             Learning rate for optimization
         weight_decay
             Weight decay for optimization
-        use_gpu
-            Use default GPU if available (if None or True), or index of GPU to use (if int),
-            or name of GPU (if str, e.g., `'cuda:0'`), or use CPU (if False).
+        accelerator
+            Supports passing different accelerator types `("cpu", "gpu", "tpu", "ipu", "hpu", "mps, "auto")` as well as
+            custom accelerator instances.
+        devices
+            The devices to use. Can be set to a non-negative index (`int` or `str`), a sequence of device indices
+            (`list` or comma-separated `str`), the value `-1` to indicate all available devices, or `"auto"` for
+            automatic selection based on the chosen `accelerator`. If set to `"auto"` and `accelerator` is not
+            determined to be `"cpu"`, then `devices` will be set to the first available device.
         train_size
             Size of training set in the range [0.0, 1.0].
         validation_size
@@ -195,7 +199,8 @@ def train(
             training_plan=training_plan,
             data_splitter=data_splitter,
             max_epochs=max_epochs,
-            use_gpu=use_gpu,
+            accelerator=accelerator,
+            devices=devices,
             **trainer_kwargs,
         )
         return runner()