Merge pull request #357 from coding-for-reproducible-research/data_science_best_practice_short_course

[WIP] Data Science Best Practice Short Course

Author: FinleyGibson

_toc.yml

@@ -343,6 +343,9 @@ parts:
           - file: short_courses/r_environments
           - file: short_courses/r_functions
           - file: short_courses/r_unit_testing
+      - file: short_courses/best_practices
+        sections:
+          - file: short_courses/data_science_best_practices
   - caption: Join Us!
     chapters: 
       - file: contributing/community

short_courses/best_practices.md

@@ -0,0 +1,13 @@
+# Best Practices 
+
+This section contains our short, focused Best Practices courses designed to help you quickly develop specific skills without committing to a full workshop series.
+
+## Included modules
+- **Data Science Best Practices** – Learn how to set up and manage Python environments for reproducible workflows. [Clickable Link to Self Study Notes](data_science_best_practices.md)
+
+
+## Who is this for?
+Learners who want to quickly enhance their skills in targeted areas, or refresh their knowledge on specific topics.
+
+## How to use these notes
+Work through the materials in sequence or jump directly to the topic you need. Each module is self-contained and can be completed independently.

short_courses/data_science_best_practices.md

@@ -0,0 +1,33 @@
+[tool.poetry]
+name = "{project-name}"
+version = "1.0.0"
+description = "A brief description of your project."
+authors = ["Your Name <[email protected]>"]
+license = "MIT"
+readme = "README.md"
+packages = [
+    { include = "{project-name}", from = "src" }
+]
+
+# Main project dependencies
+[tool.poetry.dependencies]
+python = "^3.8"
+# Example dependencies (add your specific requirements)
+numpy = "^1.21"
+pandas = "^1.3"
+
+# Development dependencies
+[tool.poetry.dev-dependencies]
+pytest = "^6.2"             # for testing
+jupyter = "^1.0.0"          # for running notebooks in the examples folder
+
+# Scripts can also be specified here if necessary
+# Defining a script
+[tool.poetry.scripts]
+example-script = "scripts.example_module:main_function"
+# can be run with: poetry run example-script
+
+
+[build-system]
+requires = ["poetry-core>=1.0.0"]
+build-backend = "poetry.core.masonry.api"

short_courses/files/example_pyproject.toml

@@ -0,0 +1,19 @@
+{
+    "python.pythonPath": ".venv/bin/python",   // Ensure VSCode uses Poetry's virtual environment
+    "python.linting.enabled": true,            // Enable linting
+    "python.linting.ruffEnabled": true,        // Enable Ruff as the linter
+    "python.linting.ruffPath": ".venv/bin/ruff", // Point to Ruff inside Poetry's virtual environment
+    "python.formatting.provider": "black",     // Use black for auto-formatting
+    "python.formatting.blackPath": ".venv/bin/black", // Ensure black from Poetry's virtual environment is used
+    "python.testing.pytestEnabled": true,      // Enable pytest for testing
+    "python.testing.pytestArgs": [
+        "tests"                               // Specify the test folder for pytest
+    ],
+    "files.exclude": {
+        "**/.venv": true,                      // Exclude .venv folder from the file explorer
+        "**/__pycache__": true                 // Exclude __pycache__ from the file explorer
+    },
+    "editor.formatOnSave": true,               // Automatically format on save
+    "editor.defaultFormatter": "ms-python.black", // Set black as the default formatter
+    "python.testing.autoTestDiscoverOnSaveEnabled": true // Automatically discover tests on file save
+}

short_courses/files/example_settings.json

@@ -0,0 +1,33 @@
+# tests/test_advanced.py
+
+import pytest
+
+class ExampleTestClass:
+    # Class-level setup and teardown (executed once for the entire class)
+    @classmethod
+    def setup_class(cls):
+        print("\nClass-level setup")
+        cls.class_resource = "Class resource setup"
+
+    @classmethod
+    def teardown_class(cls):
+        print("\nClass-level teardown")
+        cls.class_resource = None
+
+    # Object-level setup and teardown (executed before each test method)
+    def setup_method(self):
+        print("\nObject-level setup")
+        self.test_resource = "Test resource setup"
+
+    def teardown_method(self):
+        print("\nObject-level teardown")
+        self.test_resource = None
+
+    def test_addition(self):
+        assert 1 + 1 == 2
+        print(f"Using {self.test_resource}")
+
+    def test_subtraction(self):
+        assert 2 - 1 == 1
+        print(f"Using {self.test_resource}")
+

short_courses/files/example_test_advanced.py

@@ -0,0 +1,7 @@
+# tests/test_simple.py
+
+def test_addition():
+    assert 1 + 1 == 2
+
+def test_subtraction():
+    assert 2 - 1 == 1