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Merge pull request #1 from RayStick/int/setup
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Int/setup
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Stefano Moia authored Apr 28, 2020
2 parents 3a95163 + c588dda commit 496b45b
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14 changes: 7 additions & 7 deletions docs/contributing.rst
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Expand Up @@ -9,12 +9,12 @@ First of all: thank you!
Contributions can be made in different ways, not only code!
As we follow the `all-contributors`_ specification, any contribution will be recognised accordingly.

The first thing you might want to do, is having a look at the `contributor guide <contributorfile.html>`_ page as well as the `code of conduct <conduct.html>`_.
The first thing you might want to do, is have a look at the `contributor guide <contributorfile.html>`_ page as well as the `code of conduct <conduct.html>`_.

The second thing is to be sure you have ``git`` and ``pip`` installed in your system.
The second thing is to check you have ``git`` and ``pip`` installed in your system.

The third thing is to install ``phys2bids`` as a developer.
This will let you run the program with the latest modification, without requiring to re-install it every time.
This will let you run the program with the latest modification, without requiring you to re-install it every time.

.. _`all-contributors`: https://github.com/all-contributors/all-contributors

Expand All @@ -32,7 +32,7 @@ Basic installation
If you use python frequently, or you are a python developer, chances are that all the necessary dependencies
are already installed in your system.

Move in the ``phy2bids`` folder and execute the command::
Move into the ``phys2bids`` folder and execute the command::

``pip3 install -e .``

Expand All @@ -44,10 +44,10 @@ Full developer installation
^^^^^^^^^^^^^^^^^^^^^^^^^^^

If it's your first experience as a python developer, or you just want to be sure that you have everything you need
to collaborate with us, you can install ``phy2bids`` and all the other packages that we frequently use during development
to collaborate with us, you can install ``phy2bids`` with all the other packages that we frequently use during development
in one step.

Move in the ``phy2bids`` folder and execute the command::
Move into the ``phys2bids`` folder and execute the command::

``pip3 install -e .[all]``

Expand All @@ -58,4 +58,4 @@ This will install:
- All the **interface** modules, that deal with the interfaces for all the file formats.
- All the **style** modules, such as ``flake8``, to help you linter the code!
- All the **documentation** modules, like ``sphinx``, so that you can build the docs locally before submitting them.
- All the **test** modules, like ``pytest``, in order for you to test your code locally before committing it!
- All the **test** modules, like ``pytest``, in order for you to test your code locally before committing it!
6 changes: 3 additions & 3 deletions docs/howto.rst
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Expand Up @@ -18,7 +18,7 @@ Setup
In order to follow the tutorial, you need a very quick setup: download or clone the `github repository <https://github.com/physiopy/phys2bids>`_ and install either the latest stable or development release as described `here <installation.html#install-with-pip>`_.

.. warning::
Before starting using ``phy2bids``, check that you have installed all the extra modules that you need, depending on the files you will work with.
Before starting to use ``phy2bids``, check that you have installed all the extra modules that you need, depending on the files you will work with.

For instance, if you are planning to process AcqKnowledge files, install the interface dependencies as described `here <installation.html#>`_.

Expand Down Expand Up @@ -209,8 +209,8 @@ If for some reason ``-ntp`` and the number of timepoints found by ``phys2bids``
3. The file doesn't have all the trigger pulses you expect because the recording started later than the MRI recording (e.g. by mistake).

.. note::
``phys2bids`` was created to deal with little sampling errors - such as distracted researchers that started sampling a bit too late than expected. For this reason, if it finds less trigger pulses than the amount specified, it will assume that the missing ones are at the beginning and anticipate the starting time consequently.
``phys2bids`` was created to deal with little sampling errors - such as distracted researchers that started sampling a bit too late than expected. For this reason, if it finds less trigger pulses than the amount specified, it will assume that the missing ones are at the beginning and anticipate the starting time consequently.


Let's go through an example where the number of timepoints automatically found is not correct. For that, will we use tutorial_file_v2.txt (in the same location as tutorial_file.txt):

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5 changes: 3 additions & 2 deletions docs/installation.rst
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Expand Up @@ -28,7 +28,7 @@ Install with ``pip``
^^^^^^^^^^^^^^^^^^^^

.. note::
The following instruction are provided assuming that python 3 is **not** your default version of python.
The following instructions are provided assuming that python 3 is **not** your default version of python.
If it is, remember to use ``pip`` instead of ``pip3``.
If you want to check, type ``python --version`` in a terminal.

Expand All @@ -51,7 +51,7 @@ Open a terminal in the ``phy2bids`` folder and execute the command::
Install extra modules
~~~~~~~~~~~~~~~~~~~~~

If you are planning to use other file formats than plain ``txt``, you need to install extra modules to have the right interface.
If you are planning to use file formats other than plain ``txt``, you need to install extra modules to have the right interface.
Extra modules installation can be done with the sintax::

pip3 install <package>[<extra>]
Expand All @@ -62,6 +62,7 @@ Where ``<package>>`` is either ``phys2bids`` or ``.``, depending on how you inst
- ``interfaces``: for all the interfaces above.

For instance, if you plan to install phys2bids and use all the interfaces, run::

pip3 install phys2bids[interfaces]

Install without ``pip``
Expand Down

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