Apply new templates

.copier-answers.yml

@@ -1,6 +1,6 @@
 # WARNING: Do not edit this file manually.
 # Any changes will be overwritten by Copier.
-_commit: 185e6d8
+_commit: v0.3.1
 _src_path: gh:easyscience/templates
 app_docs_url: https://easyscience.github.io/peasy-app
 app_doi: 10.5281/zenodo.18163581

.gitignore

@@ -3,6 +3,11 @@ __pycache__/
 .venv/
 .coverage
 
+# PyInstaller
+dist/
+build/
+*.spec
+
 # MkDocs
 docs/site/
 

.pre-commit-config.yaml

@@ -11,32 +11,35 @@ repos:
         pass_filenames: false
         stages: [pre-commit]
 
-      - id: pixi-py-lint-check-staged
-        name: pixi run py-lint-check-staged
+      - id: pixi-py-lint-check
+        name: pixi run py-lint-check-pre STAGED_FILES
         entry: pixi run py-lint-check-pre
         language: system
-        pass_filenames: false
+        pass_filenames: true
+        files: ^(src/|tests/|docs/docs/tutorials/).*\.py$
         stages: [pre-commit]
 
-      - id: pixi-py-format-check-staged
-        name: pixi run py-format-check-staged
+      - id: pixi-py-format-check
+        name: pixi run py-format-check-pre STAGED_FILES
         entry: pixi run py-format-check-pre
         language: system
-        pass_filenames: false
+        pass_filenames: true
+        files: ^(src/|tests/|docs/docs/tutorials/).*\.py$
         stages: [pre-commit]
 
-      - id: pixi-nonpy-format-check-modified
-        name: pixi run nonpy-format-check-modified
-        entry: pixi run nonpy-format-check-modified
+      - id: pixi-nonpy-format-check
+        name: pixi run nonpy-format-check-pre STAGED_FILES
+        entry: pixi run nonpy-format-check-pre
         language: system
-        pass_filenames: false
+        pass_filenames: true
         stages: [pre-commit]
 
       - id: pixi-docs-format-check
-        name: pixi run docs-format-check
-        entry: pixi run docs-format-check
+        name: pixi run docs-format-check-pre STAGED_FILES
+        entry: pixi run docs-format-check-pre
         language: system
-        pass_filenames: false
+        pass_filenames: true
+        files: ^(src/|docs/docs/tutorials/).*\.py$
         stages: [pre-commit]
 
       # ----------------

README.md

@@ -13,6 +13,8 @@
 calculations based on a theoretical model and refining its parameters
 against experimental data.
 
+<!-- HOME REPOSITORY SECTION -->
+
 **EasyPeasy** is available both as a Python library and as a
 cross-platform desktop application.
 

codecov.yml

@@ -0,0 +1,13 @@
+# Codecov configuration
+# https://docs.codecov.com/docs/codecovyml-reference
+
+coverage:
+  status:
+    project:
+      default:
+        # Make project coverage informational (won't block PR)
+        informational: true
+    patch:
+      default:
+        # Require patch coverage but with threshold
+        threshold: 1%

docs/docs/assets/stylesheets/extra.css

@@ -222,9 +222,27 @@ Adjust the margins and paddings to fit the defaults in MkDocs Material and do no
   width: 100% !important;
   display: flex !important;
 }
+
 .jp-Notebook {
   padding: 0 !important;
   margin-top: -3em !important;
+
+  /* Ensure notebook content stretches across the page */
+  width: 100% !important;
+  max-width: 100% !important;
+
+  /* mkdocs-material + some notebook HTML end up as flex */
+  align-items: stretch !important;
+}
+
+.jp-Notebook .jp-Cell {
+  /* Key: flex children often need min-width: 0 to prevent weird shrink */
+  width: 100% !important;
+  max-width: 100% !important;
+  min-width: 0 !important;
+
+  /* Removes jupyter cell paddings */
+  padding-left: 0 !important;
 }
 
 /* Removes jupyter cell prefixes, like In[123]: */
@@ -234,11 +252,6 @@ Adjust the margins and paddings to fit the defaults in MkDocs Material and do no
   display: none !important;
 }
 
-/* Removes jupyter cell paddings */
-.jp-Cell {
-  padding-left: 0 !important;
-}
-
 /* Removes jupyter output cell padding to align with input cell text */
 .jp-RenderedText {
   padding-left: 0.85em !important;

docs/docs/installation-and-setup/index.md

@@ -8,8 +8,8 @@ icon: material/cog-box
 **Python 3.11** through **3.13**.
 
 To install and set up EasyPeasy, we recommend using
-[**Pixi**](https://prefix.dev), a modern package manager for Windows,
-macOS, and Linux.
+[**Pixi**](https://pixi.prefix.dev), a modern package manager for
+Windows, macOS, and Linux.
 
 !!! note "Main benefits of using Pixi"
 
@@ -46,16 +46,9 @@ This section describes the simplest way to set up EasyPeasy using
   ```txt
   pixi add python=3.13
   ```
-- Add the GNU Scientific Library (GSL) dependency:
+- Add EasyPeasy to the Pixi environment from PyPI:
   ```txt
-  pixi add gsl
-  ```
-- Add EasyPeasy with the `visualization` extras, which include optional
-  dependencies used for simplified visualization of charts and tables.
-  This can be especially useful for running the Jupyter Notebook
-  examples:
-  ```txt
-  pixi add --pypi "easypeasy[visualization]"
+  pixi add --pypi easypeasy
   ```
 - Add a Pixi task to run EasyPeasy commands easily:
   ```txt
@@ -159,20 +152,7 @@ simply delete and recreate the environment.
 ### Installing from PyPI { #from-pypi }
 
 EasyPeasy is available on **PyPI (Python Package Index)** and can be
-installed using `pip`.
-
-We recommend installing the latest release of EasyPeasy with the
-`visualization` extras, which include optional dependencies used for
-simplified visualization of charts and tables. This can be especially
-useful for running the Jupyter Notebook examples. To do so, use the
-following command:
-
-```txt
-pip install 'easypeasy[visualization]'
-```
-
-If only the core functionality is needed, the library can be installed
-simply with:
+installed using `pip`. To do so, use the following command:
 
 ```txt
 pip install easypeasy
@@ -214,10 +194,10 @@ To install EasyPeasy from the `develop` branch of GitHub, for example:
 pip install git+https://github.com/easyscience/peasy-lib@develop
 ```
 
-To include extra dependencies (e.g., visualization):
+To include extra dependencies (e.g., dev):
 
 ```txt
-pip install 'easypeasy[visualization] @ git+https://github.com/easyscience/peasy-lib@develop'
+pip install 'easypeasy[dev] @ git+https://github.com/easyscience/peasy-lib@develop'
 ```
 
 ## How to Run Tutorials

docs/docs/tutorials/tutorial.ipynb

@@ -0,0 +1,63 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "0",
+   "metadata": {},
+   "source": [
+    "# Dummy Tutorial\n",
+    "\n",
+    "This is a dummy tutorial file to ensure that the tutorials section is\n",
+    "not empty. You can replace this file with actual tutorial content as\n",
+    "needed."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "1",
+   "metadata": {},
+   "source": [
+    "## Import Library"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "2",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import easypeasy"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "3",
+   "metadata": {},
+   "source": [
+    "## Step 1: Blah Blah Blah"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "4",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# This is a placeholder for tutorial content.\n",
+    "print('This is a dummy tutorial.')\n",
+    "print('Imported library:', easypeasy)"
+   ]
+  }
+ ],
+ "metadata": {
+  "jupytext": {
+   "cell_metadata_filter": "-all",
+   "main_language": "python",
+   "notebook_metadata_filter": "-all"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}