Update to v4.1.0

Author: fmind

.github/workflows/assign.yml

@@ -12,7 +12,7 @@ jobs:
       pull-requests: write
     steps:
     - name: 'Auto-assign issue'
-      uses: pozil/auto-assign-issue@v1
+      uses: pozil/auto-assign-issue@v2
       with:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
           assignees: fmind

.github/workflows/publish.yml

@@ -15,11 +15,11 @@ jobs:
     - name: Checkout
       uses: actions/checkout@v4
     - name: Install uv
-      uses: astral-sh/setup-uv@v4
+      uses: astral-sh/setup-uv@v5
       with:
         enable-cache: true
     - name: Setup Python
       uses: actions/setup-python@v5
       with:
         python-version-file: .python-version
-    - run: uv run invoke deploy
+    - run: uv run just deploy

.python-version

@@ -1 +1 @@
-3.12
+3.13

README.md

@@ -41,13 +41,13 @@ To start contributing , you will need to set up your development environment:
 2. In the cloned repository directory, install dependencies using [uv](https://docs.astral.sh/uv/):
 
 ```bash
-invoke install
+uv run just install
 ```
 
 3. Serve the documentation locally (from that directory) to see course material in your browser:
 
 ```bash
-invoke serve
+uv run just serve
 ```
 
 You can then access the course at this URL from your computer: http://localhost:8000/

docs/1. Initializing/1.2. uv.md

@@ -130,10 +130,10 @@ uv tool run ruff --version
 - **Installing a specific Python version**:
 
 ```bash
-uv python install 3.12
+uv python install 3.13
 ```
 
-This command downloads and installs Python 3.12. You can then use this version to create virtual environments or run scripts.
+This command downloads and installs Python 3.13. You can then use this version to create virtual environments or run scripts.
 
 - **Listing available Python versions**:
 
@@ -150,7 +150,7 @@ uv python list --only-installed
 - **Removing a specific Python version**:
 
 ```bash
-uv python remove 3.12
+uv python remove 3.13
 ```
 
 ## uv additional resources

docs/1. Initializing/1.3. uv (project).md

@@ -61,29 +61,58 @@ Integrating uv into your MLOps project involves several key steps designed to co
 The `pyproject.toml` file plays a central role in defining your project’s dependencies and settings.
 
 ```toml
-# https://docs.astral.sh/uv/reference/pyproject-toml/
+# https://docs.astral.sh/uv/reference/settings/
+# https://packaging.python.org/en/latest/guides/writing-pyproject-toml/
+
+# PROJECT
 
 [project]
 name = "bikes"
-version = "1.0.0"
+version = "4.1.0"
 description = "Predict the number of bikes available."
-authors = [{ name = "Your Name", email = "Your Email" }]
+authors = [{ name = "Médéric HURIER", email = "[email protected]" }]
 readme = "README.md"
-requires-python = ">=3.12"
-dependencies = []
 license = { file = "LICENSE.txt" }
 keywords = ["mlops", "python", "package"]
+requires-python = ">=3.13"
+dependencies = [
+    "loguru>=0.7.3",
+    "matplotlib>=3.10.1",
+    "mlflow>=2.20.3",
+    "numba>=0.61.0",
+    "numpy>=2.1.3",
+    "omegaconf>=2.3.0",
+    "pandas>=2.2.3",
+    "pandera>=0.23.0",
+    "plotly>=6.0.0",
+    "plyer>=2.1.0",
+    "psutil>=7.0.0",
+    "pyarrow>=19.0.1",
+    "pydantic-settings>=2.8.1",
+    "pydantic>=2.10.6",
+    "pynvml>=12.0.0",
+    "scikit-learn>=1.6.1",
+    "setuptools>=75.8.2",
+    "shap>=0.46.0",
+    "hatchling>=1.27.0",
+]
+
+# LINKS
 
 [project.urls]
-Homepage = "https://github.com/fmind/bikes"
-Documentation = "https://fmind.github.io/bikes/"
-Repository = "https://github.com/fmind/bikes"
-"Bug Tracker" = "https://github.com/fmind/bikes/issues"
-Changelog = "https://github.com/fmind/bikes/blob/main/CHANGELOG.md"
+Homepage = "https://github.com/fmind/mlops-python-package"
+Documentation = "https://fmind.github.io/mlops-python-package/bikes.html"
+Repository = "https://github.com/fmind/mlops-python-package"
+"Bug Tracker" = "https://github.com/fmind/mlops-python-package/issues"
+Changelog = "https://github.com/fmind/mlops-python-package/blob/main/CHANGELOG.md"
+
+# SCRIPTS
 
 [project.scripts]
 bikes = 'bikes.scripts:main'
 
+# SYSTEMS
+
 [build-system]
 requires = ["hatchling"]
 build-backend = "hatchling.build"

docs/1. Initializing/1.6. VS Code.md

@@ -79,7 +79,6 @@ This section lists the extensions you can install from [VS Code Marketplace](htt
 - [**aaron-bond.better-comments**](https://marketplace.visualstudio.com/items?itemName=aaron-bond.better-comments): highlight comments based on a prefix (e.g., \*, !, ?, TODO, …).
 - [**bierner.markdown-mermaid**](https://marketplace.visualstudio.com/items?itemName=bierner.markdown-mermaid): display [Mermaid](https://mermaid.js.org/) diagrams in Markdown. Great to share and visualize complex concepts and design decisions.
 - [**christian-kohler.path-intellisense**](https://marketplace.visualstudio.com/items?itemName=christian-kohler.path-intellisense): autocomplete file paths on your system.
-- [**dchanco.vsc-invoke**](https://marketplace.visualstudio.com/items?itemName=dchanco.vsc-invoke): execute [Invoke](https://www.pyinvoke.org/) tasks from VS Code (alternative to [GNU Make](https://www.gnu.org/software/make/manual/make.html)).
 - [**donjayamanne.githistory**](https://marketplace.visualstudio.com/items?itemName=donjayamanne.githistory): visualize your Git history (files, branches, commits, …).
 - [**eamodio.gitlens**](https://marketplace.visualstudio.com/items?itemName=eamodio.gitlens): enhanced your git experience (e.g., git blame, code lens, …).
 - [**GitHub.remotehub**](https://marketplace.visualstudio.com/items?itemName=GitHub.remotehub): remotely browse and edit GitHub repositories.

docs/1. Initializing/1.7. pyenv (ARCHIVE).md renamed to docs/1. Initializing/archives/1.2. pyenv.md

@@ -2,7 +2,7 @@
 description: Learn how to use pyenv to manage Python versions in MLOps projects and ensure that each project uses the correct Python version.
 ---
 
-# 1.7. pyenv (ARCHIVE)
+# 1.2. pyenv
 
 ## What is pyenv?
 
@@ -26,27 +26,27 @@ When setting up pyenv for MLOps projects, the key consideration is to select a P
 
 ## How to install the required version of Python for your project?
 
-To install a particular Python version, like Python 3.12, use the command below with pyenv:
+To install a particular Python version, like Python 3.13, use the command below with pyenv:
 
 ```bash
-pyenv install 3.12
+pyenv install 3.13
 ```
 
 You can select the global version of Python to use on your system with this command:
 
 ```bash
-pyenv global 3.12
+pyenv global 3.13
 ```
 
 ## How can you select the version of Python for your project?
 
 To set a Python version for your project, proceed as follows:
 
 1. Go to your project's root directory.
-2. Create a `.python-version` file, adding the desired Python version (e.g., `3.12`) to it:
+2. Create a `.python-version` file, adding the desired Python version (e.g., `3.13`) to it:
 
 ```text
-3.12
+3.13
 ```
 
 3. Once pyenv is configured and active, it will automatically switch to the version specified in the `.python-version` file upon entering the project directory. You can verify the active Python version with:

docs/1. Initializing/1.8. Poetry (ARCHIVE).md renamed to docs/1. Initializing/archives/1.3. Poetry.md

@@ -2,7 +2,7 @@
 description: Discover how to use Poetry to manage project dependencies and build Python packages, streamlining the process of creating production-ready artifacts.
 ---
 
-# 1.8 Poetry (ARCHIVE)
+# 1.3 Poetry
 
 ## What is Poetry?
 
@@ -33,7 +33,7 @@ requests = "^2.25.1"
 pytest = "^5.2"
 ```
 
-You will learn more on how to construct and publish Python Package in the [Package section of this course](../3. Productionizing/3.0. Package.md).
+You will learn more on how to construct and publish Python Package in the [Package section of this course](../../3. Productionizing/3.0. Package.md).
 
 ## Why do you need a package manager?
 
@@ -95,7 +95,7 @@ packages = [{ include = "bikes", from = "src" }]
 bikes = 'bikes.scripts:main'
 
 [tool.poetry.dependencies]
-python = "^3.12"
+python = "^3.13"
 
 [build-system]
 requires = ["poetry-core"]

docs/1. Initializing/index.md

@@ -13,5 +13,3 @@ The initialization phase is crucial in setting the stage for efficient and strea
 - **[1.4. git](./1.4. git.md)**: Focuses on `git`, the cornerstone version control system integral to GitHub. You'll learn how to initiate and manage repositories effectively, a critical skill for collaborative development.
 - **[1.5. GitHub](./1.5. GitHub.md)**: Discusses how to leverage GitHub for project hosting, version control, and collaboration. It's a pivotal component in modern development workflows, facilitating teamwork and project management.
 - **[1.6. VS Code](./1.6. VS Code.md)**: Highlights the setup of Visual Studio Code (VS Code), showing how to adapt this versatile editor into an integrated development environment (IDE) customized for Python and MLOps projects.
-- **[1.7. pyenv (ARCHIVE)](./1.7. pyenv (ARCHIVE).md)**: Explores `pyenv`, a Python version management tool that simplifies handling multiple Python versions on a single machine. It ensures each project uses the correct Python version, preventing conflicts and compatibility issues.
-- **[1.8. Poetry (ARCHIVE)](./1.8. Poetry (ARCHIVE).md)**: Introduces `Poetry`, a Python dependency management tool that simplifies package installation and project configuration. You'll learn how to create, manage, and publish Python packages using Poetry.

docs/3. Productionizing/3.0. Package.md

@@ -67,7 +67,7 @@ version = "3.0.0"
 description = "Predict the number of bikes available."
 authors = [{ name = "Médéric HURIER", email = "[email protected]" }]
 readme = "README.md"
-requires-python = ">=3.12"
+requires-python = ">=3.13"
 dependencies = []
 license = { file = "LICENSE.txt" }
 keywords = ["mlops", "python", "package"]
@@ -88,7 +88,6 @@ default-groups = ["checks", "commits", "dev", "docs", "notebooks"]
 [build-system]
 requires = ["hatchling"]
 build-backend = "hatchling.build"
-
 ```
 
 This information not only aids users in understanding what your package does but also facilitates its discovery and integration into other projects.

docs/3. Productionizing/3.6. VS Code Workspace.md

@@ -52,7 +52,6 @@ VS Code Workspace configurations support [the same settings as user settings](ht
 	"extensions": {
 		"recommendations": [
 			"charliermarsh.ruff",
-			"dchanco.vsc-invoke",
 			"ms-python.mypy-type-checker",
 			"ms-python.python",
 			"ms-python.vscode-pylance",

docs/4. Validating/4.0. Typing.md

@@ -135,7 +135,7 @@ class GridCVSearcher(pdt.BaseModel):
 [Mypy](https://mypy-lang.org/) is the primary tool for type checking in Python, providing [command-line](https://pypi.org/project/mypy/) and [IDE integration](https://marketplace.visualstudio.com/items?itemName=ms-python.mypy-type-checker) options.
 
 ```bash
-uv add --group checkers mypy
+uv add --group check mypy
 uv run mypy src/ tests/
 ```
 
@@ -158,7 +158,7 @@ Example mypy configuration in `pyproject.toml`:
 # improve error messages
 pretty = true
 # specify the python version
-python_version = "3.12"
+python_version = "3.13"
 # check untyped definitions
 check_untyped_defs = true
 # all missing imports in code

docs/4. Validating/4.1. Linting.md

@@ -23,7 +23,7 @@ Linters are indispensable in Python development due to several key reasons:
 
 ```bash
 # ruff installation (one shot)
-uv add --group checkers ruff
+uv add --group check ruff
 # ruff code base linting
 uv run ruff src/ tests/
 ```

docs/4. Validating/4.4. Security.md

@@ -34,7 +34,7 @@ To mitigate security risks in Python, tools like [Bandit](https://bandit.readthe
 
 ```bash
 # Bandit installation
-uv add --group checkers bandit
+uv add --group check bandit
 # Running Bandit to lint the codebase
 uv run bandit src/
 ```
@@ -52,7 +52,18 @@ For detailed configuration options and best practices, the [Bandit documentation
 
 Reducing security risks on GitHub involves leveraging its tools for dependency management and vulnerability scanning. [GitHub's Dependabot](https://docs.github.com/en/code-security/dependabot) is an automated tool that monitors your repositories for known vulnerabilities in dependencies and provides updates or patches. Configuring Dependabot and regular code audits can significantly enhance your project's security posture.
 
-To set up Dependabot in your GitHub repository, you can add a `.github/dependabot.yml` file with configurations tailored to your project's specific needs, specifying the frequency of checks, the directories to monitor, and the package managers to use.
+To set up Dependabot in your GitHub repository, you can add a [`.github/dependabot.yml`](https://github.com/fmind/mlops-python-package/blob/main/.github/dependabot.yml) file with configurations tailored to your project's specific needs, specifying the frequency of checks, the directories to monitor, and the package managers to use.
+
+```yaml
+# https://docs.github.com/en/code-security/dependabot/working-with-dependabot/dependabot-options-reference
+
+version: 2
+updates:
+  - package-ecosystem: "pip"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+```
 
 By staying vigilant with updates, practicing secure coding standards, and utilizing available tools, developers can significantly reduce the security risks associated with Python and MLOps projects.
 

docs/4. Validating/4.5. Formatting.md

@@ -30,7 +30,7 @@ You can format your codebase as follows:
 
 ```bash
 # ruff installation (one-time)
-uv add --group checkers ruff
+uv add --group check ruff
 # format the imports
 uv run ruff check --select you --fix src/ tests/
 # format the sources