Setup template

Author: ghurault

.gitignore

@@ -1,3 +1,5 @@
+#### Python
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
@@ -160,3 +162,7 @@ cython_debug/
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 #.idea/
+
+#### Custom
+
+/data/

.vscode/settings.json

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+{
+    "python.testing.unittestArgs": [
+        "-v",
+        "-s",
+        "./tests",
+        "-p",
+        "test_*.py"
+    ],
+    "python.testing.pytestEnabled": false,
+    "python.testing.unittestEnabled": true,
+    "[python]": {
+        "editor.rulers": [88],
+        "editor.defaultFormatter": "ms-python.black-formatter",
+    },
+    "flake8.args": [
+        "--exclude=analysis/*py",
+        "--max-line-length=88",
+        "--ignore=D100, D202, E203, D412, W503",
+    ]
+}

README.md

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+# Python analysis template
+
+This repository can be used as a template for data science projects.
+After cloning the repository, you can change:
+
+- The repository name
+- The name of the VS code workspace file
+- Project information in [`pyproject.toml`](pyproject.toml)
+
+## File structure
+
+- Analysis scripts and notebooks should go to [`analysis/`](analysis/)
+- Data files should go to [`data/`](data/). By default, files in `data/` are ignored by Git.
+- Results/output files (e.g. figures, output data) should go to [`results/`](results/). These files are ignored by Git.
+- Reusable functions and modules are stored in the local package [`src/`](src/). The package can be installed in development mode with `pip install -e .`
+- Tests for functions in [`src/`](src/) should go to [`tests/`](tests/) and follow the convention `test_*.py`.
+
+
+## Setup computational environment
+
+To set up the environment with conda, navigate to the repository directory and run the following in the command line:
+
+```
+conda create -n myenv python=3.11
+conda activate myenv
+pip install -e .
+```
+
+## Development environment
+
+I usually work with Visual Studio code, and I have predefined some settings.
+In particular, I use:
+
+- [Black](https://black.readthedocs.io/en/stable/index.html) for formatting.
+- Flake8 for linting.
+- [Google docstring format](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html) to document functions and classes, with the help of the autoDocstring extension. 

analysis/.gitkeep

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+{
+	"folders": [
+		{
+			"path": "."
+		}
+	],
+	"settings": {
+		"autoDocstring.docstringFormat": "google",
+	}
+}

myproject.code-workspace

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+[build-system]
+requires = ["setuptools >= 64"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "src"
+version = "0.0.1"
+description = ""
+authors = [
+  {name = "Guillem Hurault", email = "guillem.hurault@hotmail.fr"}
+]
+readme = "README.md"
+license = {file = "LICENSE"}
+classifiers = [
+  "Programming Language :: Python :: 3",
+]
+# dependencies = []
+requires-python = ">=3.8"
+
+[project.urls]
+# Homepage = ""
+# Documentation = ""
+# Repository = ""
+# Issues = ""

pyproject.toml

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+# Ignore everything except this file
+!.gitignote

results/.gitignore

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+# Keep setup.py to facilitate local package installation in editable mode
+
+from setuptools import find_packages, setup
+
+setup(name="src", packages=find_packages())