pratical first part

Makefile

+README.html: README.md
+	pandoc -s --highlight-style pygments --mathjax README.md -o REAME.html

README.md

+---
+title: Packaging with Python
+---
+
+## Python `pip`
+
+[![cc_by_sa](./img/cc_by_sa.png)](http://creativecommons.org/licenses/by-sa/4.0/)
+
+![pipy](https://pypi.org/static/images/logo-large.72ad8bf1.svg)
+
+The Python Package Index (PyPI) is a repository of software for the Python programming language.
+
+You can install the python `pip` manager with the following command
+
+**Some outdated distributions still have python2 as default python, use python3 command**
+
+On Ubuntu
+
+```bash
+apt install python3-pip
+```
+
+On OSX
+
+```bash
+brew install python3
+```
+
+With docker:
+```bash
+docker run -it python:3.8-alpine sh
+```
+
+## installing packages with `pip`
+
+And then you can install any packages you want on [https://pypi.org/](https://pypi.org/)
+
+```bash
+sudo pip3 install setuptools==50.0.2 # system wide install
+sudo pip3 install setuptools==50.0.2 --user # user install
+pip3 install twine wheel --user
+```
+
+`pip` is just another python module
+
+```bash
+python3 -m pip install --user --upgrade pip
+```
+
+## Packaging python projects
+
+You can follow the official guide ([https://packaging.python.org/tutorials/packaging-projects/](https://packaging.python.org/tutorials/packaging-projects/))
+
+### Creating the package files
+
+This is the recommended basic structure your project should have to easily build a pip packages:
+
+```
+your_project/
+├── LICENSE
+├── README.md
+├── example_pkg/
+│   └── __init__.py
+├── setup.py
+└── tests/
+```
+
+But we can adapt it to follow the [LBMC guide of good practices](http://www.ens-lyon.fr/LBMC/intranet/services-communs/pole-bioinformatique/ressources/good_practice_LBMC)
+
+
+```
+your_project/
+├── LICENSE
+├── README.md
+├── src/
+│   └── example_pkg/
+│      └── __init__.py
+│   └── setup.py
+│   └── tests/
+```
+
+All you python code goes in the `example_pkg/` folder. The most important file for the packaging is the `setup.py` file.
+
+Here is a basic `setup.py` file:
+
+```python
+import setuptools
+
+with open("../README.md", "r") as fh:
+    long_description = fh.read()
+
+setuptools.setup(
+    name="example-pkg-YOUR-USERNAME-HERE", # Replace with your own username
+    version="0.0.1",
+    author="Example Author",
+    author_email="author@example.com",
+    description="A small example package",
+    long_description=long_description,
+    long_description_content_type="text/markdown",
+    url="https://github.com/pypa/sampleproject",
+    packages=setuptools.find_packages(),
+    classifiers=[
+········"Programming·Language·::·Python·::·3",
+········"License·::·OSI·Approved·::·CEA·CNRS·Inria·Logiciel·Libre·License,·\
+ version·2.1·(CeCILL-2.1)",
+········"Operating·System·::·OS·Independent"
+····],
+    python_requires='>=3.6',
+)
+```
+
+- `name` is the distribution name of your package. This can be any name as long as only contains letters, numbers, _ , and -. It also must not already be taken on [pypi.org](https://pypi.org/). Be sure to update this with your username, as this ensures you won’t try to upload a package with the same name as one which already exists when you upload the package.
+- `version` is the package version see PEP 440 for more details on versions.
+- `author` and `author_email` are used to identify the author of the package.
+- `description` is a short, one-sentence summary of the package.
+- `long_description` is a detailed description of the package. This is shown on the package detail package on the Python Package Index. In this case, the long description is loaded from `README.md` which is a common pattern.
+- `long_description_content_type` tells the index what type of markup is used for the long description. In this case, it’s Markdown.
+- `url` is the URL for the homepage of the project. For many projects, this will just be a link to GitHub, GitLab, Bitbucket, or similar code hosting service.
+- `packages` is a list of all Python import packages that should be included in the Distribution Package. Instead of listing each package manually, we can use find_packages() to automatically discover all packages and subpackages. In this case, the list of packages will be example_pkg as that’s the only package present.
+- `classifiers` gives the index and pip some additional metadata about your package. In this case, the package is only compatible with Python 3, is licensed under the MIT license, and is OS-independent. You should always include at least which version(s) of Python your package works on, which license your package is available under, and which operating systems your package will work on. For a complete list of classifiers, see [https://pypi.org/classifiers/](https://pypi.org/classifiers/).
+
+## Creating distribution archives
+
+Now you just have to run the following command in the same directory as the `setup.py` file:
+
+```bash
+python3 setup.py sdist bdist_wheel
+```
+
+It will create files in the `dist/` directory
+
+```
+dist/
+  example_pkg_YOUR_USERNAME_HERE-0.0.1-py3-none-any.whl
+  example_pkg_YOUR_USERNAME_HERE-0.0.1.tar.gz
+```
+
+The `tar.gz` file is a Source Archive whereas the `.whl` file is a Built Distribution. Newer pip versions preferentially install built distributions, but will fall back to source archives if needed.
+**You should always upload a source archive and provide built archives for the platforms your project is compatible with.**
+
+
+