fix: Updated with pre-commit errors fix

.editorconfig

@@ -3,7 +3,7 @@ import logging
 from rich.console import Console
 from rich.logging import RichHandler
 
-from ._destvi_utils import 
+from ._destvi_utils import
 
 try:
     import importlib.metadata as importlib_metadata
@@ -29,4 +29,4 @@ logger.addHandler(ch)
 # this prevents double outputs
 logger.propagate = False
 
-__all__ = ["destvi_utils"]
+__all__ = ["destvi_utils"]

.flake8

@@ -2,4 +2,3 @@
 ignore = E203, E266, E501, W503, W605, N812
 exclude = .git,docs
 max-line-length = 119
-

.github/workflows/test.yml

@@ -11,35 +11,34 @@ on:
 
 jobs:
   build:
-
     runs-on: ubuntu-latest
     strategy:
       matrix:
         python-version: [3.11, 3.12, 3.13]
 
     steps:
-    - uses: actions/checkout@v4
+      - uses: actions/checkout@v4
 
-    - uses: actions/setup-python@v5
-      with:
-        python-version: ${{ matrix.python }}
-        cache: "pip"
-        cache-dependency-path: "**/pyproject.toml"
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python }}
+          cache: "pip"
+          cache-dependency-path: "**/pyproject.toml"
 
-    - name: Install dependencies
-      run: |
-        pip install pytest-cov
-        pip install .[dev]
-    - name: Lint with flake8
-      run: |
-        flake8
-    - name: Format with black
-      run: |
-        black --check .
-    - name: Test with pytest
-      run: |
-        pytest --cov-report=xml --cov=destvi_utils
-    - name: After success
-      run: |
-        bash <(curl -s https://codecov.io/bash)
-        pip list
+      - name: Install dependencies
+        run: |
+          pip install pytest-cov
+          pip install .[dev]
+      - name: Lint with flake8
+        run: |
+          flake8
+      - name: Format with black
+        run: |
+          black --check .
+      - name: Test with pytest
+        run: |
+          pytest --cov-report=xml --cov=destvi_utils
+      - name: After success
+        run: |
+          bash <(curl -s https://codecov.io/bash)
+          pip list

README.md

@@ -6,18 +6,25 @@
 [![codecov](https://codecov.io/gh/YosefLab/destvi_utils/branch/main/graph/badge.svg?token=BGI9Z8R11R)](https://codecov.io/gh/YosefLab/destvi_utils)
 [![Code Style](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/python/black)
 
-Implementation of the automatic pipeline for downstream analysis of DestVI's results. This small package will help generate scientific hypotheses via similar visualization techniques as in the original publication, [destVI](https://www.biorxiv.org/content/10.1101/2021.05.10.443517v1).
+Implementation of the automatic pipeline for downstream analysis of DestVI's
+results. This small package will help generate scientific hypotheses via similar
+visualization techniques as in the original publication,
+[destVI](https://www.biorxiv.org/content/10.1101/2021.05.10.443517v1).
 
-# Basic installation
+## Basic installation
 
-```
+```bash
 pip install git+https://github.com/yoseflab/destvi_utils.git
 ```
-Please be sure to install a version of [PyTorch](https://pytorch.org/) that is compatible with your GPU (if applicable).
 
+Please be sure to install a version of
+[PyTorch](https://pytorch.org/) that is compatible with your GPU (if
+applicable).
 
-# Resources
+## Resources
 
--   API reference, and installation guides are available in
+- API reference, and installation guides are available in
     the [documentation](https://destvi-utils.readthedocs.io/en/latest/).
--   Please use the [issues](https://github.com/yoseflab/destvi_utils_/issues) to submit bug reports.
+- Please use the
+    [issues](https://github.com/yoseflab/destvi_utils_/issues) to submit
+    bug reports.

docs/api/index.rst

@@ -14,4 +14,4 @@ destvi_utils
    automatic_proportion_threshold
    explore_gamma_space
    de_genes
-   plot_de_genes
+   plot_de_genes

docs/extensions/typed_returns.py

@@ -11,7 +11,7 @@ def process_return(lines):
         m = re.fullmatch(r"(?P<param>\w+)\s+:\s+(?P<type>[\w.]+)", line)
         if m:
             # Once this is in scanpydoc, we can use the fancy hover stuff
-            yield f'-{m["param"]} (:class:`~{m["type"]}`)'
+            yield f"-{m['param']} (:class:`~{m['type']}`)"
         else:
             yield line
 

docs/release_notes/index.rst

@@ -9,4 +9,4 @@ Version 0.1
 .. toctree::
    :maxdepth: 2
 
-   v0.1.0
+   v0.1.0

docs/release_notes/v0.1.0.rst

@@ -1,3 +1,3 @@
 New in 0.1.0 (2022-04-02)
 -------------------------
-Initial release of the utilities functions. Complies with `scvi-tools>=0.15.0`.
+Initial release of the utilities functions. Complies with `scvi-tools>=0.15.0`.

pyproject.toml

@@ -33,11 +33,11 @@ version = "0.2.0"
 adjustText = ">=0.7.1"
 anndata = ">=0.7.5"
 black = {version = ">=20.8b1", optional = true}
-cmap2d = {git = "https://github.com/cane11/cmap2d", tag = "v1.0"}
+cmap2d = {git = "https://github.com/cane11/cmap2d", tag = "master"}
 codecov = {version = ">=2.0.8", optional = true}
 flake8 = {version = ">=3.7.7", optional = true}
 gseapy = {version = ">=0.10.2"}
-hotspot = {git = "https://github.com/YosefLab/Hotspot", tag = "v1.0"}
+hotspotsc = {version = ">=1.0"}
 importlib-metadata = {version = "^1.0", python = "<3.8"}
 ipython = ">=7.1.1"
 isort = {version = ">=5.7", optional = true}
@@ -55,7 +55,7 @@ python = ">=3.11.0,<4.0"
 igraph = {version = "*"}
 scanpy = ">=1.6,<2.0"
 scanpydoc = {version = ">=0.5", optional = true}
-scvi-tools  = {git = "https://github.com/scverse/scvi-tools", tag = "Ori-destvi_v2_2"}
+scvi-tools  = {version = ">=1.4.1"}
 sphinx = {version = ">=4.1,<4.4", optional = true}
 sphinx-autodoc-typehints = {version = "*", optional = true}
 sphinx-rtd-theme = {version = "*", optional = true}