Merge pull request #409 from jo-mueller/fix-precommit

Fix precommit and update python versions

Author: jo-mueller

.github/workflows/build_book.yml

@@ -1,3 +1,4 @@
+# pre-commit: disable
 name: deploy-book
 
 # Run this when the master or main branch changes
@@ -57,4 +58,4 @@ jobs:
     # Deploy the book's HTML to GitHub Pages
     - name: Deploy to GitHub Pages
       id: deployment
-      uses: actions/deploy-pages@v4
+      uses: actions/deploy-pages@v4

.github/workflows/test_and_deploy.yml

@@ -21,7 +21,7 @@ jobs:
     strategy:
       matrix:
         platform: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12"]
 
     steps:
       - uses: actions/checkout@v4

.pre-commit-config.yaml

@@ -19,9 +19,3 @@ repos:
     rev: v0.3.0
     hooks:
       - id: napari-plugin-checks
-  # https://mypy.readthedocs.io/en/stable/
-  # you may wish to add this as well!
-  # - repo: https://github.com/pre-commit/mirrors-mypy
-  #   rev: v1.9.0
-  #   hooks:
-  #     - id: mypy

docs/04_FAQ/Installation.md

@@ -8,12 +8,15 @@ Depending on how you have your Python set up on your machine, different preparat
 - [Getting started with Python and Anaconda](https://biapol.github.io/blog/mara_lampert/getting_started_with_mambaforge_and_python/readme.html): If you have not yet installed Python or Anaconda on your computer **at all**, this explains how to set it up and create an environment that contain the most basic functionality ([napari](https://napari.org/stable/) & [Jupyterlab](https://jupyter.org/))
 - Setting up a new environment: If you already have Python installed and want to create a new environment for napari-stress, follow these steps to create a new environment and install napari-stress into it.
 
+```{important}
+Please note that napari-stress is not compatible with Python 3.9 or lower. You need to use Python 3.10 or higher.
+```
+
 ```bash
-conda create -n stress Python=3.9
+conda create -n stress Python=3.10
 conda acticate stress
-conda install mamba -c conda-forge
 
-mamba install napari pyqt devbio-napari
+conda install napari pyqt devbio-napari
 pip install napari-stress
 ```
 

docs/conf.py

@@ -13,7 +13,6 @@
 autosummary_generate = True
 bibtex_bibfiles = ["references.bib"]
 comments_config = {"hypothesis": False, "utterances": False}
-copyright = "2022"
 exclude_patterns = ["**.ipynb_checkpoints", ".DS_Store", "Thumbs.db", "_build"]
 extensions = [
     "sphinx_togglebutton",

docs/intro.md

@@ -22,13 +22,13 @@ Welcome to the documentation for napari-stress! This ressource provides informat
 
 ## Installation
 
-To install nappari-STRESS in your environment (provided you have Python and napari already installed), simply type this in your command:
+To install nappari-STRESS in your environment (provided you have Python>=3.10 and napari already installed), simply type this in your command:
 
 ```
 pip install napari-stress
 ```
 
-For more detailed installation instructions,, hints and some known issues, please refer to the [installation section](FAQ:installation).
+For more detailed installation instructions, hints and some known issues, please refer to the [installation section](FAQ:installation).
 
 ### Other useful packages
 

docs/requirements.txt

@@ -1,4 +1,4 @@
-jupyter-book>=0.7.0b
+jupyter-book>=1.0.4
 napari
 QtPy
 napari-stress>=0.3.9

src/napari_stress/_approximation/expansion.py

@@ -1,6 +1,7 @@
-import numpy as np
 from typing import TYPE_CHECKING
 
+import numpy as np
+
 if TYPE_CHECKING:
     import napari
 

src/napari_stress/_approximation/expansion_base.py

@@ -1,5 +1,6 @@
 from abc import ABC, abstractmethod
 from typing import TYPE_CHECKING
+
 if TYPE_CHECKING:
     import napari
 

src/napari_stress/_approximation/expansion_napari.py

@@ -1,5 +1,7 @@
-from napari_tools_menu import register_function
 from typing import TYPE_CHECKING
+
+from napari_tools_menu import register_function
+
 if TYPE_CHECKING:
     import napari