DOCS: add brief neurodocker tutorial #2464

kaczmarj · 2018-02-23T21:35:28Z

Changes proposed in this pull request

Add a brief Neurodocker tutorial to the documentation (would be available at https://nipype.readthedocs.io/en/latest/users/neurodocker.html)
Add links to Neurodocker tutorial in https://nipype.readthedocs.io/en/latest/users/install.html.
Add links to Singularity and Neurodocker in link_names.txt.

satra · 2018-02-23T21:43:24Z

doc/users/install.rst

@@ -14,7 +14,7 @@ You can follow the `Nipype tutorial <https://miykael.github.io/nipype_tutorial/>
 or use this docker container: `docker pull nipype/nipype`

 or if you want to build custom docker containers with specific versions of
-software see `Neurodocker <https://github.com/kaczmarj/neurodocker>`_
+software see Neurodocker_. Read the `brief tutorial <neurodocker.html>`_.


@kaczmarj - i don't think the html is necessary.

just: brief tutorial <neurodocker_tutorial>_.

@satra - i could not get that to render properly, so i used :doc:neurodocker instead.

satra · 2018-02-23T21:43:32Z

doc/users/install.rst

@@ -108,7 +108,7 @@ Interface Dependencies
 Nipype provides wrappers around many neuroimaging tools and contains some
 algorithms. These tools will need to be installed for Nipype to run. You can
 create containers with different versions of these tools installed using
-`Neurodocker <https://github.com/kaczmarj/neurodocker>`_
+Neurodocker_. Read the `brief tutorial <neurodocker.html>`_.


mgxd

LGTM - minor comments

mgxd · 2018-02-23T21:41:35Z

doc/users/neurodocker.rst

+   image. The package manager is ``apt`` or ``yum``, depending on the base
+   image.
+2. Next, users should configure the container to fit their needs. This includes
+   installing neuroimaing software, installing packages from the chosen package


neuroimaging

mgxd · 2018-02-23T21:42:49Z

doc/users/neurodocker.rst

+Use NeuroDebian
+---------------
+
+This example install AFNI and ANTs from the NeuoDebian repositories. It also


satra · 2018-02-23T21:44:29Z

doc/users/neurodocker.rst

+This example install AFNI and ANTs from the NeuoDebian repositories. It also
+installs ``git`` and ``vim``.
+::
+  $ docker run --rm kaczmarj/neurodocker:v0.3.2 generate --base neurodebian:stretch --pkg-manager apt --install afni ants git vim


perhaps break this line with a backslash

djarecka · 2018-02-23T22:04:34Z

@kaczmarj - don't forget to add the new tutorial to index.rst

djarecka · 2018-02-23T22:07:45Z

just noticed that this is part of install.rst, so ignore my previous comment

effigies · 2018-02-23T22:30:49Z

You should be able to link with the text of the section header. On Feb 23, 2018 5:27 PM, "Jakub Kaczmarzyk" <notifications@github.com> wrote: *@kaczmarj* commented on this pull request. ------------------------------ In doc/users/install.rst <#2464 (comment)>:

@@ -14,7 +14,7 @@ You can follow the `Nipype tutorial <https://miykael.github.io/nipype_tutorial/>

or use this docker container: `docker pull nipype/nipype` or if you want to build custom docker containers with specific versions of -software see `Neurodocker <https://github.com/kaczmarj/neurodocker

`_

+software see Neurodocker_. Read the `brief tutorial <neurodocker.html>`_. @satra <https://github.com/satra> - i could not get that to render properly, so i used :doc:neurodocker instead. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#2464 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAFF8mVMRY-RwNqCygri4Wiq9svmKrDuks5tXzs_gaJpZM4SRgpj> .

codecov-io · 2018-02-23T23:27:45Z

Codecov Report

Merging #2464 into master will decrease coverage by <.01%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##           master    #2464      +/-   ##
==========================================
- Coverage   66.67%   66.66%   -0.01%     
==========================================
  Files         328      328              
  Lines       42551    42551              
  Branches     5276     5276              
==========================================
- Hits        28370    28366       -4     
- Misses      13501    13505       +4     
  Partials      680      680

Flag	Coverage Δ
#smoketests	`50.76% <ø> (ø)`	⬆️
#unittests	`63.98% <ø> (-0.01%)`	⬇️

Impacted Files	Coverage Δ
nipype/pipeline/plugins/multiproc.py	`79.76% <0%> (-2.39%)`	⬇️

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 1ecd0ff...25697ad. Read the comment docs.

kaczmarj · 2018-02-24T01:49:39Z

Should I update the links to the tutorial? I got the syntax from https://github.com/nipy/nipype/blob/master/doc/users/joinnode_and_itersource.rst.

effigies

A couple stylistic comments. Overall this looks great.

effigies · 2018-02-24T14:06:51Z

doc/users/install.rst

@@ -14,7 +14,7 @@ You can follow the `Nipype tutorial <https://miykael.github.io/nipype_tutorial/>
 or use this docker container: `docker pull nipype/nipype`

 or if you want to build custom docker containers with specific versions of
-software see `Neurodocker <https://github.com/kaczmarj/neurodocker>`_
+software see Neurodocker_. Read the brief :doc:`neurodocker`.


I don't like the way this whole section ends up looking, with blank lines followed by sentence fragments.

What about:

To get started using Docker, you can follow the `Nipype tutorial <https://miykael.github.io/nipype_tutorial/>`_, or pull the `nipype/nipype` image from Docker hub:: docker pull nipype/nipype You may also build custom docker containers with specific versions of software using Neurodocker_ (see `Neurodocker tutorial`_).

(:doc: works, so go ahead and do that if you want. I'm just demonstrating what I meant earlier.)

I added this, but the Neurodocker tutorial link still does not render properly for me when written this way. I kept the :doc: syntax.

effigies · 2018-02-24T14:08:08Z

doc/users/install.rst

-`Neurodocker <https://github.com/kaczmarj/neurodocker>`_
+Neurodocker_. Read the brief :doc:`neurodocker`.
+
+


Too many blank lines.

effigies · 2018-02-24T14:08:44Z

doc/users/install.rst

@@ -108,7 +108,9 @@ Interface Dependencies
 Nipype provides wrappers around many neuroimaging tools and contains some
 algorithms. These tools will need to be installed for Nipype to run. You can
 create containers with different versions of these tools installed using
-`Neurodocker <https://github.com/kaczmarj/neurodocker>`_
+Neurodocker_. Read the brief :doc:`neurodocker`.


I would prefer that this be parenthetical, rather than a sentence. See above suggestion.

Jakub Kaczmarzyk added 2 commits February 23, 2018 16:19

add singularity and neurodocker links

dca8f56

add brief neurodocker tutorial

a1531a8

mgxd added this to the 1.0.1 milestone Feb 23, 2018

satra reviewed Feb 23, 2018

View reviewed changes

mgxd approved these changes Feb 23, 2018

View reviewed changes

satra reviewed Feb 23, 2018

View reviewed changes

Jakub Kaczmarzyk added 2 commits February 23, 2018 17:20

fix links to neurodocker

34b5b20

fix spelling errors + formatting

ba605e1

effigies reviewed Feb 24, 2018

View reviewed changes

Jakub Kaczmarzyk added 2 commits February 24, 2018 11:16

Merge remote-tracking branch 'upstream/master' into docs/neurodocker

133b461

fix style

25697ad

effigies merged commit 81bcf41 into nipy:master Feb 24, 2018

kaczmarj deleted the docs/neurodocker branch February 26, 2018 14:39

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

DOCS: add brief neurodocker tutorial #2464

DOCS: add brief neurodocker tutorial #2464

kaczmarj commented Feb 23, 2018

satra Feb 23, 2018

kaczmarj Feb 23, 2018

satra Feb 23, 2018

mgxd left a comment

mgxd Feb 23, 2018

mgxd Feb 23, 2018

satra Feb 23, 2018

djarecka commented Feb 23, 2018

djarecka commented Feb 23, 2018

effigies commented Feb 23, 2018 via email

codecov-io commented Feb 23, 2018 •

edited

Loading

kaczmarj commented Feb 24, 2018

effigies left a comment

effigies Feb 24, 2018

kaczmarj Feb 24, 2018

effigies Feb 24, 2018

effigies Feb 24, 2018

		`Neurodocker <https://github.com/kaczmarj/neurodocker>`_
		Neurodocker_. Read the brief :doc:`neurodocker`.

DOCS: add brief neurodocker tutorial #2464

DOCS: add brief neurodocker tutorial #2464

Conversation

kaczmarj commented Feb 23, 2018

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

mgxd left a comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

djarecka commented Feb 23, 2018

djarecka commented Feb 23, 2018

effigies commented Feb 23, 2018 via email

codecov-io commented Feb 23, 2018 • edited Loading

Codecov Report

kaczmarj commented Feb 24, 2018

effigies left a comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

codecov-io commented Feb 23, 2018 •

edited

Loading