add dependecies section

README.md

@@ -2,9 +2,15 @@
 title: Packaging with Python
 ---
 
-## Python `pip`
+# Packaging with Python
+
+## 
+
+![cc](https://creativecommons.org/images/deed/cc_icon_white_x2.png)![by](https://creativecommons.org/images/deed/attribution_icon_white_x2.png)![sa](https://creativecommons.org/images/deed/sa_white_x2.png)
+
 
-[![cc_by_sa](./img/cc_by_sa.png)](http://creativecommons.org/licenses/by-sa/4.0/)
+
+## Python `pip`
 
 ![pipy](https://pypi.org/static/images/logo-large.72ad8bf1.svg)
 
@@ -138,5 +144,111 @@ dist/
 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.**
 
+What can you do with those two file ?
+
+### Install them:
+
+You can use the `.whl` or the `.tar.gz` file to install your package
+
+```bash
+pip3 install dist/example_pkg_YOUR_USERNAME_HERE-0.0.1.tar.gz --user
+```
+
+### Upload them
+
+You can upload your package to [pypi](https://pypi.org), but first you can run test on [https://test.pypi.org/](https://test.pypi.org/). As https://pypi.org is an archive, if you upload broken packages, they will stay there.
+
+You first need to create an account https://test.pypi.org/account/register/
+
+Then we use the `twine` tools that we installed before
+
+```bash
+twine upload --skip-existing --repository testpypi dist/*
+```
+
+The output should look like that:
+
+```bash
+Uploading distributions to https://test.pypi.org/legacy/
+Enter your username: [your username]
+Enter your password:
+Uploading example_pkg_YOUR_USERNAME_HERE-0.0.1-py3-none-any.whl
+100%|█████████████████████| 4.65k/4.65k [00:01<00:00, 2.88kB/s]
+Uploading example_pkg_YOUR_USERNAME_HERE-0.0.1.tar.gz
+100%|█████████████████████| 4.25k/4.25k [00:01<00:00, 3.05kB/s]
+```
+
+To install your package from https://test.pypi.org you can use the following `pip` options:
+
+```bash
+pip install --index-url https://test.pypi.org/simple/ --no-deps example-pkg-YOUR-USERNAME-HERE --user
+```
+
+You should be able to open a python console anywhere and run:
+
+```python
+>>> import example_pkg
+```
+
+When everything is OK, you can create an account on https://pypi.org and use the `twine`command without the `--repository testpypi` option.
+
+## Creating executable software
+
+You can also use `pip` to distribute executable software. To do that, you have to specify the `__main__` function to execute when calling your software in the `setup.py` file.
+
+```python
+setuptools.setup(
+  	...
+		entry_points={
+        'console_scripts': ['example_pkg=example_pkg.__main__:main'],
+    },
+  	...
+)
+```
+
+You can have different executable in this list with the format `EXECUTABLE_NAME=LIBRARY.FILE:FUNCTION`
+
+After the installation, calling `example_pkg`will run your software if your `$PATH` is correctly configured.
+
+## Adding dependencies to your package
+
+As your project will grow more complex, you will split it into different file for code clarity.
+
+Your `__init__.py` file will need to contain a list of all the `.py` files in the `example_pkg` repository:
+
+```python
+#!/usr/bin/env python3
+# -*-coding:Utf-8 -*
+
+"""
+idr library
+"""
+
+name = "midr"
+__all__ = ["__main__",
+    "idr", "samic", "archimedean", "archimedean_plots",
+    "log", "narrowpeak", "raw_matrix", "auxiliary"]
+```
+
+As you don't want to reinvente the wheel, you may also import other python library (which could be installed with `pip`). You can specify a list of these library in the `setup.py`file:
+
+```python
+setuptools.setup(
+  	...
+		install_requires=[
+        'cmake>=3.18'
+        'scipy>=1.3',
+        'numpy>=1.16',
+        'pynverse>=0.1',
+        'pandas>=0.25.0',
+        'mpmath>=1.1.0',
+        'matplotlib>=3.0.0'
+    ],
+  	...
+)
+```
+
+**Don't forget to specify the version of each dependency to ensure that the function you use are present in the installed library.**
 
+If, some package are required for the installation of your package (for example here `cmake`), you should also add them to the `install_requires`list.