Merge pull request #11 from project-delphi/dependencies

build(dependencies): refactor package dependencies out of requirement…

.pre-commit-config.yaml

@@ -19,7 +19,6 @@ repos:
       - id: debug-statements
       - id: name-tests-test
       - id: requirements-txt-fixer
-        filenames: "./requirements/requirements_dev.txt ./requirements/requirements_test.txt ./requirements/requirements_run.txt"
   - repo: https://github.com/asottile/add-trailing-comma
     rev: v3.1.0
     hooks:
@@ -30,20 +29,20 @@ repos:
       - id: pyupgrade
         args: [--py38-plus]
   - repo: https://github.com/psf/black
-    rev: 23.10.0
+    rev: 24.2.0
     hooks:
       - id: black
   - repo: https://github.com/commitizen-tools/commitizen
-    rev: 3.12.0
+    rev: v3.14.1
     hooks:
       - id: commitizen
         stages: [commit-msg]
   - repo: https://github.com/abravalheri/validate-pyproject
-    rev: v0.15
+    rev: v0.16
     hooks:
       - id: validate-pyproject
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.6.1
+    rev: v1.8.0
     hooks:
       - id: mypy
         args: ["--config-file", "pyproject.toml"]
@@ -53,16 +52,12 @@ repos:
           - types-chardet
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.1.1
+    rev: v0.2.1
     hooks:
       - id: ruff
         types_or: [python, pyi, jupyter]
         args: ["--fix"]
   - repo: https://github.com/kynan/nbstripout
-    rev: 0.6.1
+    rev: 0.7.1
     hooks:
       - id: nbstripout
-  - repo: https://github.com/hadolint/hadolint
-    rev: v2.12.1-beta
-    hooks:
-      - id: hadolint

Makefile

@@ -52,27 +52,27 @@ install-upgrade-pip:# Upgrade pip version
 .PHONY: install-dev
 install-dev:# Install developer dependencies (formatting, linting)
 	source ./.venv/bin/activate
-	pip install -r requirements_dev.txt
+	pip install -e ".[dev]"
 
 
 
 .PHONY: install-run
 install-run:# Install application only dependencies
 	source ./.venv/bin/activate
-	pip install -r requirements.txt
+	pip install -e .
 
 .PHONY: install
 install: install-upgrade-pip install-dev install-run# Upgrade pip and install developer, test & application dependencies
 
 .PHONY: uninstall-dev
 uninstall-dev:# Uninstall developer dependencies
 	source ./.venv/bin/activate
-	pip uninstall -r requirements_dev.txt
+	pip uninstall ".[dev]"
 
 .PHONY: uninstall-run
 uninstall-run:# Uninstall application only dependencies
 	source ./.venv/bin/activate
-	pip uninstall -r requirements.txt
+	pip uninstall .
 
 .PHONY: uninstall
 uninstall:# Uninstall all dependencies

experimental/.gitkeep

@@ -1 +0,0 @@
-

notebooks/notebooks_intro.ipynb

@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "id": "a35eeb9f-df70-4ab1-a243-2d2025888eb0",
+   "id": "0",
    "metadata": {},
    "source": [
     "# Introduction to the JupyterLab and Jupyter Notebooks\n",
@@ -39,7 +39,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "fe55883a-6887-43dd-9498-5333a51799e2",
+   "id": "1",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -58,7 +58,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "b9670d85-ef29-4dfd-b4b5-e76d279c1f1a",
+   "id": "2",
    "metadata": {},
    "source": [
     "## Next steps 🏃\n",

pyproject.toml

@@ -1,3 +1,61 @@
+[build-system]
+requires = [
+    "flit_core >=3.2,<4",
+]
+build-backend = "flit_core.buildapi"
+
+[project]
+name = "project-scaffold"
+version = "0.1.0"
+description = "Scaffold to start DS/ML projects"
+readme = "README.md"
+requires-python = ">=3.8"
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "License :: OSI Approved :: MIT License",
+    "Natural Language :: English",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+]
+dependencies = [
+"click",
+"fastapi",
+"flax",
+"jax",
+"keras",
+"matplotlib",
+"numpy",
+"pandas",
+"pytorch-tabnet",
+"scikit-learn",
+"tensorflow",
+"torch",
+"torchaudio",
+"torchvision",
+"uvicorn[standard]",
+]
+
+[project.optional-dependencies]
+dev = [
+"black[jupyter]",
+"commitizen",
+"coverage",
+"ipython",
+"isort",
+"jupytext",
+"mypy",
+"nbstripout",
+"pre-commit",
+"pydoclint",
+"pytest",
+"pytest-cov",
+"pyupgrade",
+"ruff",
+"tqdm",
+]
+
 [tool.ruff]
 # Enable pycodestyle (`E`) and Pyflakes (`F`) codes by default.
 select = ["D", "E", "F", "I"]
@@ -62,6 +120,9 @@ dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
 # Assume Python 3.10.
 target-version = "py310"
 
+[tool.flit.module]
+name="src"
+
 [tool.ruff.per-file-ignores]
 "*test*.py" = ["D"] # ignore all docstring lints in tests
 

src/__init__.py

@@ -0,0 +1,8 @@
+"""
+The __init__ module.
+
+It serves as the entry point for the package and contains the initialization logic.
+
+Author: Ravi Kalia
+Date: 02/13/2024
+"""

src/tests/module_2_test.py

@@ -1,4 +1,5 @@
 """Placeholder for module 2 tests docstring."""
+
 from utils.module_2 import bye