add dev tools an unittests

environment.yml

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+name: eo-datascience
+channels:
+  - conda-forge
+dependencies:
+  - python=3.10
+  - pip
+  - mamba
+  - jupyter
+  - nbformat

pyproject.toml

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+[build-system]
+requires = ["setuptools"]
+build-backend = "setuptools.build_meta"

setup.cfg

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+[metadata]
+name = eo_datascience
+version = attr: eo_datascience.__version__
+description = Examples of TUWien Jupyter notebooks for education
+author = TU Wien GEO MRS group
+author_email = [email protected]
+long_description = file: README.md
+url = https://github.com/TUW-GEO/eo-datascience
+platforms = any
+classifiers =
+    Intended Audience :: Science/Research
+    Topic :: Scientific/Engineering
+    Topic :: Scientific/Engineering :: GIS
+    Topic :: Software Development :: Libraries
+    Programming Language :: Python :: 3
+    Programming Language :: Python :: 3.8
+    Programming Language :: Python :: 3.9
+    Operating System :: POSIX
+    Natural Language :: English
+
+[options]
+package_dir =
+    = src
+packages = find:
+install_requires =
+    nbformat
+
+[options.packages.find]
+where = src
+
+[options.extras_require]
+test =
+    pytest
+    pytest-cov

setup.py

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+from setuptools import setup
+
+setup()

src/eo_datascience/__init__.py

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+from eo_datascience._version import __commit__
+from eo_datascience._version import __version__
+
+name = "eo_datascience"

src/eo_datascience/_version.py

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+__version__ = "v0.0.0"
+__commit__ = "0000000"

src/eo_datascience/clean_nb.py

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+import os
+import nbformat
+from pathlib import Path
+
+def clean_up_frontmatter(dir = './notebooks', save=False):
+    # Define the path to the notebooks
+    nb_paths = find_ipynb(dir)
+
+    # Iterate over the notebooks
+    for nb_path in nb_paths:
+        # Load the notebook
+        nb = nbformat.read(nb_path, as_version=4)
+        if nb.cells[0].source.startswith('---'):
+            #Load frontmatter
+            fm = nb.cells[0].source.split('\n')
+
+            # Extract the title and the subtitle
+            title, subtitle = '', ''
+            for line in fm:
+                if line.startswith('title'):
+                    title = line.split(': ')[1]
+                if line.startswith('subtitle'):
+                    subtitle = line.split(': ')[1]
+
+            # Update the cell
+            nb.cells[0].source = f'# {title}\n{subtitle}\n'
+
+            # Save the notebook
+            if save:
+                nbformat.write(nb, nb_path)
+            else:
+                return nb
+
+def convert_refs(dir="./notebooks", save=True):
+    nb_paths = find_ipynb(dir)
+
+    # Iterate over the notebooks
+    for nb_path in nb_paths:
+        # Load the notebook
+        nb = nbformat.read(nb_path, as_version=4)
+        for i in range(len(nb.cells)):
+            if i != 0:
+                nb.cells[i].source = nb.cells[i].source.replace(r"[@", r"{cite}`").replace(r"]", r"`")
+
+        # Save the notebook
+        if save:
+            nbformat.write(nb, nb_path)
+        else:
+            return nb
+
+def find_ipynb(dir):
+    root = Path(dir).resolve()
+    nb_paths = [root / file for file in os.listdir(root) if file.endswith('.ipynb')]
+    return nb_paths
+
+def main():
+    clean_up_frontmatter()
+
+if __name__ == '__main__':
+    main()

tests/mock.ipynb

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+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "---\n",
+    "title: This a mock Jupyter file\n",
+    "subtitle: We use it for testing\n",
+    "author: anonymous\n",
+    "---"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "[@ref1] "
+   ]
+  }
+ ],
+ "metadata": {
+  "language_info": {
+   "name": "python"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

tests/test_quarto_nb_conversions.py

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+import nbformat
+from pathlib import Path
+import pytest
+from eo_datascience.clean_nb import clean_up_frontmatter, convert_refs
+
+def test_remove_front_matter():
+    assert clean_up_frontmatter("./tests", False)["cells"][0]["source"] == "# This a mock Jupyter file\nWe use it for testing\n"
+
+def test_conversion_of_refs():
+    assert convert_refs("./tests", False)["cells"][1]["source"] == r'{cite}`ref1` '