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ivadomed documentation modifications (#851)
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* update installation step in doc for linux and mac users

* update do with add git clone step

* minor change with spacing

* update git command and add clone step

* added source installaton step and CC link

* fixes neuropoly reference and CC link

* removed canada compute reference
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copperwiring committed Aug 31, 2021
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22 changes: 17 additions & 5 deletions docs/source/installation.rst
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Expand Up @@ -39,30 +39,42 @@ There are fundamentally two different approaches to install ``IvadoMed``:
Approach 1: Conda
------------------

Step 1: Create new Conda Env called IvadoMedEnv (may taken 5 to 15 minutes)
Step 1: Clone the `ivadomed <https://github.com/ivadomed/ivadomed>`_ repository.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

::

git clone https://github.com/neuropoly/ivadomed.git
cd ivadomed

Step 2: Create new Conda Env called IvadoMedEnv (may take 5 to 15 minutes)
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

::

conda env create --file environment.yml

Step 2 : Activate environment and use
Step 3 : Activate environment and use
++++++++++++++++++++++++++++++++++++++

::

conda activate IvadoMedEnv

Note that this is NOT compatible with ComputeCanada because of their no anaconda policy: https://docs.computecanada.ca/wiki/Anaconda/en
Step 4 : Install from source
++++++++++++++++++++++++++++++++++++++

::

pip install -e .

Approach 2: Venv
-----------------

Step 1: Setup Python Virtual Environment.
+++++++++++++++++++++++++++++++++++++++++

``ivadomed`` requires Python >= 3.6 and <3.9. We recommend
``ivadomed`` requires Python >= 3.6 and <3.9 (If you are using `Compute Canada <https://www.computecanada.ca/>`_, you can load modules (e.g. python 3.9) as mentioned `here <https://intranet.neuro.polymtl.ca/computing-resources/compute-canada#modules>`_ and `also here <https://docs.computecanada.ca/wiki/Utiliser_des_modules/en#Loading_modules_automatically>`_ ). We recommend
working under a virtual environment, which could be set as follows:

::
Expand All @@ -84,7 +96,7 @@ Step 2: Clone the `ivadomed <https://github.com/ivadomed/ivadomed>`_ repository.

::

git clone git@github.com:ivadomed/ivadomed.git
git clone https://github.com/ivadomed/ivadomed.git
cd ivadomed

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