@@ -68,145 +68,7 @@ machine. Here are some instructions for you to follow *after* this course, to se
6868up Python on your machine.
6969
7070Although one can install a plain-vanilla Python and all required libraries by hand,
71- we recommend installing [ Anaconda] [ anaconda-website ] ,
72- a Python distribution that comes with everything we need for the lesson.
73- Detailed installation instructions for various operating systems can be found
74- on The Carpentries [ template website for workshops] [ anaconda-instructions ]
75- and in [ Anaconda documentation] [ anaconda-install ] .
76-
77- ### Launch Python interface
78-
79- To start working with Python, we need to launch a program that will interpret and execute our
80- Python commands. Below we list several options. If you don't have a preference, proceed with the
81- top option in the list that is available on your machine. Otherwise, you may use any interface
82- you like.
83-
84- ### Option A: Jupyter Notebook
85-
86- A Jupyter Notebook provides a browser-based interface for working with Python.
87- If you installed Anaconda, you can launch a notebook in two ways:
88-
89- ::::::::::::::::: spoiler
90-
91- ### Anaconda Navigator
92-
93- 1 . Launch Anaconda Navigator.
94- It might ask you if you'd like to send anonymized usage information to Anaconda developers:
95- ![ ] ( fig/anaconda-navigator-first-launch.png ) {alt='Anaconda Navigator first launch'}
96- Make your choice and click "Ok, and don't show again" button.
97- 2 . Find the "Notebook" tab and click on the "Launch" button:
98- ![ ] ( fig/anaconda-navigator-notebook-launch.png ) {alt='Anaconda Navigator Notebook launch'}
99- Anaconda will open a new browser window or tab with a Notebook Dashboard showing you the
100- contents of your Home (or User) folder.
101- 3 . Navigate to the ` data ` directory by clicking on the directory names leading to it:
102- ` Desktop ` , ` swc-python ` , then ` data ` :
103- ![ ] ( fig/jupyter-notebook-data-directory.png ) {alt='Anaconda Navigator Notebook directory'}
104- 4 . Launch the notebook by clicking on the "New" button and then selecting "Python 3":
105- ![ ] ( fig/jupyter-notebook-launch-notebook.png ) {alt='Anaconda Navigator Notebook directory'}
106-
107- :::::::::::::::::::::::::
108-
109-
110- ::::::::::::::::: spoiler
111-
112- ### Command line (Terminal)
113-
114- 1\. Navigate to the ` data ` directory:
115-
116- ::::::::::::::::: spoiler
117-
118- ### Unix shell
119-
120- If you're using a Unix shell application, such as Terminal app in macOS, Console or Terminal
121- in Linux, or [ Git Bash] [ gitbash ] on Windows, execute the following command:
122-
123- ``` bash
124- cd ~ /Desktop/swc-python/data
125- ```
126-
127- :::::::::::::::::::::::::
128-
129- ::::::::::::::::: spoiler
130-
131- ### Command Prompt (Windows)
132-
133- On Windows, you can use its native Command Prompt program. The easiest way to start it up is
134- pressing <kbd >Windows Logo Key</kbd >\+ <kbd >R</kbd >, entering ` cmd ` , and hitting
135- <kbd >Return</kbd >. In the Command Prompt, use the following command to navigate to
136- the ` data ` folder:
137-
138- ``` source
139- cd /D %userprofile%\Desktop\swc-python\data
140- ```
141-
142- :::::::::::::::::::::::::
143-
144- 2\. Start Jupyter server
145-
146- ::::::::::::::::: spoiler
147-
148- ### Unix shell
149-
150- ``` bash
151- jupyter notebook
152- ```
153-
154- :::::::::::::::::::::::::
155-
156-
157- ::::::::::::::::: spoiler
158-
159- ### Command Prompt (Windows)
160-
161- ``` source
162- python -m notebook
163- ```
164-
165- :::::::::::::::::::::::::
166-
167- 3\. Launch the notebook by clicking on the "New" button on the right and selecting "Python 3"
168- from the drop-down menu:
169- ![ ] ( fig/jupyter-notebook-launch-notebook2.png ) {alt='Anaconda Navigator Notebook directory'}
170-
171- :::::::::::::::::::::::::
172-
173- <!-- vertical spacer -->
174-
175- ### Option B: IPython interpreter
176-
177- IPython is an alternative solution situated somewhere in between the plain-vanilla Python
178- interpreter and Jupyter Notebook. It provides an interactive command-line based interpreter with
179- various convenience features and commands. You should have IPython on your system if you installed
180- [ Anaconda] [ anaconda-instructions ] .
181-
182- To start using IPython, execute:
183-
184- ``` source
185- ipython
186- ```
187-
188- <!-- vertical spacer -->
189-
190- ### Option C: plain-vanilla Python interpreter
191-
192- To launch a plain-vanilla Python interpreter, execute:
193-
194- ``` source
195- python
196- ```
197-
198- If you are using [ Git Bash on Windows] [ gitbash ] , you have to call Python * via* ` winpty ` :
199-
200- ``` source
201- winpty python
202- ```
203-
204- [ anaconda-website ] : https://www.anaconda.com/
205- [ anaconda-instructions ] : https://carpentries.github.io/workshop-template/install_instructions/#python
206- [ anaconda-install ] : https://docs.anaconda.com/anaconda/install
207- [ zipfile1 ] : data/python-novice-inflammation-data.zip
208- [ zipfile2 ] : ../episodes/files/code/python-novice-inflammation-code.zip
209- [ gitbash ] : https://gitforwindows.org
210-
211-
212-
71+ we recommend installing [ Miniforge] ( https://conda-forge.org/download/ ) , an open-source
72+ installer. You can see a [ quick start guide] ( https://kirenz.github.io/codelabs/codelabs/miniforge-setup/#0 )
73+ for using ` conda ` to run Python scripts. You can see the [ Python docs] ( https://www.python.org/about/gettingstarted/ )
74+ here for more information.
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