README.md 3.54 KB
Newer Older
Paul McCarthy's avatar
readme  
Paul McCarthy committed
1
2
3
4
# 2018 WIN PyTreat


This repository contains Jupyter notebooks and data for the 2018 WIN PyTreat.
Paul McCarthy's avatar
Paul McCarthy committed
5
6
7
8
It contains the following:

- The `talks` directory contains some (but not all) of the _Topyc_ talks that
  will be given throughout the week.
9
10
11
12
13
14
15
16
17
18
19

- The `getting_started` directory contains a series of practicals intended
  for those of you who are new to the Python programming language, or need
  a refresher.

- The `advanced_topics` directory contains a series of practicals on various
  aspects of the Python programming language - these are intended for those
  of you who are familiar with the basics of Python, and want to learn more
  about the language.


Paul McCarthy's avatar
Paul McCarthy committed
20
The practicals have been written under the assumption that FSL 5.0.10 is
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
installed.


## For attendees


To run these notebooks in the `fslpython` environment, you must first install
jupyter:


```
# If your FSL installation requires administrative privileges to modify, then
# you MUST run these commands as root - don't just prefix each individual
# command with sudo, or you will probably install jupyter into the wrong
# location!
#
# One further complication - once you have become root, $FSLDIR may not be set,
Paul McCarthy's avatar
Paul McCarthy committed
38
# so either set it as we have done below, or make sure that it is set, before
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
# proceeding.
sudo su
export FSLDIR=/usr/local/fsl
source $FSLDIR/fslpython/bin/activate fslpython
conda install jupyter
source deactivate
ln -s $FSLDIR/fslpython/envs/fslpython/bin/jupyter $FSLDIR/bin/fsljupyter
```


Then, clone this repository on your local machine, and run
`fsljupyter notebook`:


```
git clone git@git.fmrib.ox.ac.uk:fsl/pytreat-2018-practicals.git
cd pytreat-2018-practicals
fsljupyter notebook
```


Paul McCarthy's avatar
Paul McCarthy committed
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
Throughout the week we might make changes to this repository. When this
happens, we will ask you to update your local clone of the repository with the
following command:


```
git reset --hard HEAD
git pull origin master
```


> Note that this will overwrite any changes that you have made to the
> files in your repository!


75
76
77
78
Have fun!


## For contributors
Paul McCarthy's avatar
readme  
Paul McCarthy committed
79
80


Paul McCarthy's avatar
Paul McCarthy committed
81
The upstream repository can be found at:
Paul McCarthy's avatar
Paul McCarthy committed
82
83

https://git.fmrib.ox.ac.uk/fsl/pytreat-2018-practicals
Paul McCarthy's avatar
readme  
Paul McCarthy committed
84
85
86
87


To contribute to the practicals:

Paul McCarthy's avatar
Paul McCarthy committed
88
1. Fork the upstream repository on gitlab
Paul McCarthy's avatar
readme  
Paul McCarthy committed
89

Paul McCarthy's avatar
Paul McCarthy committed
90
2. Make a local clone of your fork:
Paul McCarthy's avatar
readme  
Paul McCarthy committed
91

Paul McCarthy's avatar
Paul McCarthy committed
92
93
94
    ```
    git clone git@git.fmrib.ox.ac.uk:<username>/pytreat-2018-practicals
    ```
Paul McCarthy's avatar
Paul McCarthy committed
95
96
97

3. Add the upstream repository as a remote:

Paul McCarthy's avatar
Paul McCarthy committed
98
99
100
    ```
    git remote add upstream git@git.fmrib.ox.ac.uk:fsl/pytreat-2018-practicals.git
    ```
Paul McCarthy's avatar
Paul McCarthy committed
101
102
103
104
105

4. Make your changes on your local repository

5. Rebase onto the upstream repository, and push your changes to your fork:

Paul McCarthy's avatar
Paul McCarthy committed
106
107
    ```
    git fetch --all
Paul McCarthy's avatar
Paul McCarthy committed
108
109
    git rebase upstream/master
    git push --force origin master
Paul McCarthy's avatar
Paul McCarthy committed
110
    ```
Paul McCarthy's avatar
Paul McCarthy committed
111
112
113

6. In gitlab, submit a merge request from your fork back to the upstream
   repository.
Paul McCarthy's avatar
Paul McCarthy committed
114
115


116
117
When you install `jupyter` above, you may also wish to install
[`notedown`](https://github.com/aaren/notedown):
Paul McCarthy's avatar
Paul McCarthy committed
118

Paul McCarthy's avatar
Paul McCarthy committed
119
```
120
121
122
# .
# see instructions above
# .
Paul McCarthy's avatar
Paul McCarthy committed
123
124
125
conda install jupyter
pip install notedown
source deactivate
126
ln -s $FSLDIR/fslpython/envs/fslpython/bin/jupyter  $FSLDIR/bin/fsljupyter
Paul McCarthy's avatar
Paul McCarthy committed
127
128
129
ln -s $FSLDIR/fslpython/envs/fslpython/bin/notedown $FSLDIR/bin/fslnotedown
```

130
131
132
133
134
`notedown` is a handy tool which allows you to convert a markdown (`.md`) file
to a Jupyter notebook (`.ipynb`) file. So you can write your practical in your
text editor of choice, and then convert it into a notebook, instead of writing
the practical in the web browser interface. If you install notedown as
suggested in the code block above, you can run it on a markdown file like so:
Paul McCarthy's avatar
Paul McCarthy committed
135
136
137


```
138
fslnotedown my_markdown_file.md > my_notebook.ipynb
Paul McCarthy's avatar
Paul McCarthy committed
139
```