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DOC: Some more details in installation instructions. #305

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@arokem
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arokem commented Jan 3, 2014

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Then from any python console or script try ::
easy_install nibabel

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@Garyfallidis

Garyfallidis Jan 4, 2014

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Ariel? Why to suggest easy_install and not pip install here? We don't recommend easy_install anywhere else in the installation instructions.

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@arokem

arokem Jan 4, 2014

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Following this:

http://mail.scipy.org/pipermail/nipy-devel/2013-November/009585.html

On Sat, Jan 4, 2014 at 7:20 AM, Eleftherios Garyfallidis <
notifications@github.com> wrote:

In doc/installation.rst:

-Then from any python console or script try ::

  • easy_install nibabel

Ariel? Why to suggest easy_install and not pip install here? We don't
recommend easy_install anywhere else in the installation instructions.


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Garyfallidis Jan 4, 2014

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Let me try to install it in a windows machine. I think this e-mail is irrelevant from if you are going to use pip or easy_install.

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@arokem

arokem Jan 4, 2014

Member

You're probably right, but this is the only method that has been tested so
far. So we know this works for sure. That's why I rewrote it that way.

On Sat, Jan 4, 2014 at 7:52 AM, Eleftherios Garyfallidis <
notifications@github.com> wrote:

In doc/installation.rst:

-Then from any python console or script try ::

  • easy_install nibabel

Let me try to install it in a windows machine. I think this e-mail is
irrelevant from if you are going to use pip or easy_install.


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arokem Jan 4, 2014

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Let me know how your tests on the Windows machine go, and I will change
accordingly.

On Sat, Jan 4, 2014 at 7:54 AM, Ariel Rokem arokem@gmail.com wrote:

You're probably right, but this is the only method that has been tested so
far. So we know this works for sure. That's why I rewrote it that way.

On Sat, Jan 4, 2014 at 7:52 AM, Eleftherios Garyfallidis <
notifications@github.com> wrote:

In doc/installation.rst:

-Then from any python console or script try ::

  • easy_install nibabel

Let me try to install it in a windows machine. I think this e-mail is
irrelevant from if you are going to use pip or easy_install.


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#. Similarly, you can install dipy_ itself, by opening a Canopy Command Prompt
and typing ::
easy_install dipy

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@Garyfallidis

Garyfallidis Jan 4, 2014

Member

Same as above

pip install dipy
When this is all said and done, we can try to see if the installation

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@Garyfallidis

Garyfallidis Jan 4, 2014

Member

"When this is all said and done" doesn't read nicely (maybe too informal). Can you changed it to something else? Perhaps, "When the installation has finished we can check if it is successful in the following way. From a Python console ... ".

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@arokem

arokem Jan 4, 2014

Member

OK

On Sat, Jan 4, 2014 at 7:33 AM, Eleftherios Garyfallidis <
notifications@github.com> wrote:

In doc/installation.rst:

-Then from any python console or script try ::
+#. Even with Canopy installed, you will still need to install the nibabel_

  • library, which supports reading and writing of neuroimaging data formats.
  • As of November 2013, nibabel is included in the Canopy Package Manager only
  • as a "Community Package" (i.e. without dependencies provided), and
  • attempting to install it generates an error. Instead, open a terminal shell and type
  • at the command line the following command ::
  •   pip install nibabel
    
    +#. Finally, we are ready to install dipy itself. Same as with nibabel
  • above, we will type at the terminal shell command line ::
  •    pip install dipy
    
    +When this is all said and done, we can try to see if the installation

"When this is all said and done" doesn't read nicely (maybe too informal).
Can you changed it to something else? Perhaps, "When the installation has
finished we can check if it is successful in the following way. From a
Python console ... ".


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Linux
-----
For Debian, Ubuntu and Mint set up the NeuroDebian_ repositories - see `NeuroDebian how to`_. Then::
First of all, let us say: thank god for NeuroDebian_. This wonderful project

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@Garyfallidis

Garyfallidis Jan 4, 2014

Member

Okay here it is too informal!!! Remove all all godliness and praise please. I personally prefer it as it was before.

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@arokem

arokem Jan 4, 2014

Member

OK. But you gotta love what they do.

On Sat, Jan 4, 2014 at 7:36 AM, Eleftherios Garyfallidis <
notifications@github.com> wrote:

In doc/installation.rst:

Linux


-For Debian, Ubuntu and Mint set up the NeuroDebian_ repositories - see NeuroDebian how to. Then::
+First of all, let us say: thank god for NeuroDebian
. This wonderful project

Okay here it is too informal!!! Remove all all godliness and praise
please. I personally prefer it as it was before.


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@@ -78,7 +78,9 @@
.. _ETS: http://code.enthought.com/projects/tool-suite.php
.. _`Enthought Tool Suite`: http://code.enthought.com/projects/tool-suite.php
.. _canopy: https://www.enthought.com/products/canopy
.. _Canopy: https://www.enthought.com/products/canopy

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@Garyfallidis

Garyfallidis Jan 4, 2014

Member

As far as I know it doesn't make a difference for rst if you call something with capital letters or not. What I mean is that you can write

.. _canopy: https://www.enthought.com/products/canopy

but then call Canopy_ or canopy_ and it will be the same exact result.

So, maybe there is no reason to change the first letter for _canopy and _anaconda.

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@arokem

arokem Jan 4, 2014

Member

OK

On Sat, Jan 4, 2014 at 7:40 AM, Eleftherios Garyfallidis <
notifications@github.com> wrote:

In doc/links_names.inc:

@@ -78,7 +78,9 @@
.. _ETS: http://code.enthought.com/projects/tool-suite.php
.. _Enthought Tool Suite: http://code.enthought.com/projects/tool-suite.php
.. _canopy: https://www.enthought.com/products/canopy
+.. _Canopy: https://www.enthought.com/products/canopy

As far as I know it doesn't make a difference for rst if you call
something with capital letters or not. What I mean is that you can write

.. _canopy: https://www.enthought.com/products/canopy

but then call Canopy_ or canopy_ and it will be the same exact result.

So, maybe there is no reason to change the first letter for _canopy and
_anaconda.


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@matthew-brett

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matthew-brett commented Jan 4, 2014

Guys - I'm pretty confident that the windows double-click installer will work - and that easy_install is picking that up anyway.

So - Eleftherios - maybe install canopy and double click install nibabel and dipy from downloading the .exe installers from dipy. I still think that links to the .exe installers are the best and most general way for windows.

@arokem

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arokem commented Jan 4, 2014

How about this:

arokem@2296e38

On Sat, Jan 4, 2014 at 7:59 AM, Matthew Brett notifications@github.comwrote:

Guys - I'm pretty confident that the windows double-click installer will
work - and that easy_install is picking that up anyway.

So - Eleftherios - maybe install canopy and double click install nibabel
and dipy from downloading the .exe installers from dipy. I still think that
links to the .exe installers are the best and most general way for windows.


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@matthew-brett

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matthew-brett commented Jan 4, 2014

Fine with me - Eletherios - can you check if that works for you?

@Garyfallidis

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Garyfallidis commented Jan 4, 2014

I 'll try different things. I am on an slow windows machine. But will have an answer soon.

@arokem

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arokem commented Jan 4, 2014

Excellent. I'm going to leave my desk soon (and go to the gym!), but I will
be back at noon or so and will check in on this then.

On Sat, Jan 4, 2014 at 8:30 AM, Eleftherios Garyfallidis <
notifications@github.com> wrote:

I 'll try different things. I am on an slow windows machine. But will have
an answer soon.


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@Garyfallidis

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Garyfallidis commented Jan 4, 2014

Wow! Here is a surprise!!! For the free version of Canopy you need to subscribe to get Cython (Cython is not included in the free version). This is super annoying. I will uninstall Canopy and try with Anaconda.

But first I will run the executables.

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Garyfallidis commented Jan 4, 2014

Okay when I use the windows executables (for dipy and nibabel) with Canopy (free version) it works.

@arokem

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arokem commented Jan 4, 2014

OK - sounds good. This is probably because the executables already have the
cython stuff compiled.

So - the last version of this PR is good? Merge?

On Sat, Jan 4, 2014 at 9:00 AM, Eleftherios Garyfallidis <
notifications@github.com> wrote:

Okay when I use the windows executables (for dipy and nibabel) with Canopy
(free version) it works.


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@Garyfallidis

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Garyfallidis commented Jan 4, 2014

Not yet but we are getting there. I replaced Canopy with Anaconda in a Windows machine and Anaconda's installation was much easier and more FOSS if you know what I mean. In Anaconda you don't need install specific packages and all important packages are installed by default with the free version. This is a big advantage against Canopy. Also in Anaconda you can just do

pip install nibabel
pip install dipy

and it will compile and install dipy in Windows with no problem which is awesome! Which means that we don't need necessary to create executables. The same pip commands didn't work in Canopy - neither easy_install dipy worked (probably because we don't have executables for 0.7.0 in pypi)

Also in Anaconda's installation using executables worked as well.

In summary, I see Anaconda as more advantageous than Canopy as Anaconda can be used with pip install/remove and with executables. Also it is easier to install and it supports all standard and optional packages. Furthermore, when we tested Anaconda in Macosx it was similarly very easy to use. So, I vote to replace Canopy with Anaconda in the installation instructions.

Finally, Anaconda has a command prompt as Canopy which could be handy for some Windows' users.

@arokem

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arokem commented Jan 4, 2014

OK. Could you rewrite those instructions for Windows, following what you
did and put in a PR against my branch? Try to be as detailed as possible.
For example, saying to a Windows user : "open a terminal and run pip
install" will not cut it. They will have no idea what you are talking
about. At least initially, so you have to say things like: "In your Start
menu, go to applications and launch the Anaconda Terminal Application"
(assuming there is such a thing).

Following the previous discussion with Matthew, I think that we settled on
suggesting to use the binary installers as the first thing to do and 'pip
install' is going to be in that 'notes' box after it.

On Sat, Jan 4, 2014 at 12:39 PM, Eleftherios Garyfallidis <
notifications@github.com> wrote:

Not yet but we are getting there. I replaced Canopy with Anaconda in a
Windows machine and Anaconda's installation was much easier and more FOSS
if you know what I mean. In Anaconda you don't need install specific
packages and all important packages are installed by default with the free
version. This is a big advantage against Canopy. Also in Anaconda you can
just do

pip install nibabel
pip install dipy

and it will compile and install dipy in Windows with no problem which is
awesome! Which means that we don't need necessary to create executables.
The same pip commands didn't work in Canopy - neither easy_install dipy
worked (probably because we don't have executables for 0.7.0 in pypi)

Also in Anaconda's installation using executables worked as well.

In summary, I see Anaconda as more advantageous than Canopy as Anaconda
can be used with pip install/remove and with executables. Also it is easier
to install and it supports all standard and optional packages. Furthermore,
when we tested Anaconda in Macosx it was similarly very easy to use. So, I
vote to replace Canopy with Anaconda in the installation instructions.

Finally, Anaconda has a command prompt as Canopy which could be handy for
some Windows' users.


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@Garyfallidis

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Garyfallidis commented Jan 4, 2014

Sure, I 'll do that asap.

dipy_ is in active development at the moment. You can install it from our latest release, but you may find that the release has gotten well behind the current development - at least - we hope so - if we're developing fast enough!
dipy_ is in active development at the moment. You can install it from our
latest release, but you may find that the release has gotten well behind the
current development - at least - we hope so - if we're developing fast enough!

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@stefanv

stefanv Jan 4, 2014

Contributor

Surely we hope to change this!

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@arokem

arokem Jan 5, 2014

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Sure

On Sat, Jan 4, 2014 at 3:56 PM, Stefan van der Walt <
notifications@github.com> wrote:

In doc/installation.rst:

@@ -4,7 +4,13 @@
Installation
############

-dipy_ is in active development at the moment. You can install it from our latest release, but you may find that the release has gotten well behind the current development - at least - we hope so - if we're developing fast enough!
+dipy_ is in active development at the moment. You can install it from our
+latest release, but you may find that the release has gotten well behind the
+current development - at least - we hope so - if we're developing fast enough!

Surely we hope to change this!


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@@ -4,7 +4,13 @@
Installation
############
dipy_ is in active development at the moment. You can install it from our latest release, but you may find that the release has gotten well behind the current development - at least - we hope so - if we're developing fast enough!

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@stefanv

stefanv Jan 4, 2014

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Scratch "at the moment"

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@arokem

arokem Jan 5, 2014

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OK

On Sat, Jan 4, 2014 at 3:56 PM, Stefan van der Walt <
notifications@github.com> wrote:

In doc/installation.rst:

@@ -4,7 +4,13 @@
Installation
############

-dipy_ is in active development at the moment. You can install it from our latest release, but you may find that the release has gotten well behind the current development - at least - we hope so - if we're developing fast enough!

Scratch "at the moment"


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pip install nibabel
pip install dipy
#. You will still need to install the nibabel_ library, which supports reading
and writing of neuroimaging data formats. As of November 2013, nibabel is

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@stefanv

stefanv Jan 4, 2014

Contributor

Why do we give an explanation of the path that does not work? At least, first give a short explanation of what to do to get it to work, and then perhaps mention routes to be avoided.

and double-click it to launch the installation.
Now, you should be able to start using dipy_ Then from any python console or

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@stefanv

stefanv Jan 5, 2014

Contributor

Full stop missing

>>> import dipy
.. note::
There are other alternatives than the one we have outlined above to

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@stefanv

stefanv Jan 5, 2014

Contributor

We can perhaps "refactor" this text by explaining once that "nibabel" is a dependency of "dipy", then proceed to show how to install both on all platforms. These easy_install / pip instructions can be given for all platforms.

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@arokem

arokem Jan 5, 2014

Member

I am over-explaining this here, because I assume that people are like me and will not read instructions that are not meant for their platform. Also, I would not bother to read the 'dependencies' section if I were in their shoes, so I was trying to make the explanation be complete here.

attempting to install it generates an error. Instead, open a terminal shell and type
at the command line the following command ::
pip install nibabel

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@stefanv

stefanv Jan 5, 2014

Contributor

See note about refactoring above.

Linux
-----
For Debian, Ubuntu and Mint set up the NeuroDebian_ repositories - see `NeuroDebian how to`_. Then::
For Debian, Ubuntu and Mint set up the NeuroDebian_ repositories - see
`NeuroDebian how to`_. Then::

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@stefanv

stefanv Jan 5, 2014

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"how-to"

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arokem Jan 5, 2014

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I think it's fine as is. I am not sure how the quotes would work with the Sphinx link. It's quite finicky!

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arokem commented Jan 11, 2014

Anyone have anything else to say here, or do y'all wanna merge this?

@Garyfallidis

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Garyfallidis commented Jan 11, 2014

Sorry for not being responsive, I am on my way back to Sherbrooke, I
haven't yet updated the anaconda parts except if you did that already.
On Jan 10, 2014 8:19 PM, "Ariel Rokem" notifications@github.com wrote:

Anyone have anything else to say here, or do y'all wanna merge this?


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@arokem

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arokem commented Jan 11, 2014

Sorry - I see now that we've had this discussion already. I got a little
antsy.

Safe travels!

On Fri, Jan 10, 2014 at 5:26 PM, Eleftherios Garyfallidis <
notifications@github.com> wrote:

Sorry for not being responsive, I am on my way back to Sherbrooke, I
haven't yet updated the anaconda parts except if you did that already.
On Jan 10, 2014 8:19 PM, "Ariel Rokem" notifications@github.com wrote:

Anyone have anything else to say here, or do y'all wanna merge this?


Reply to this email directly or view it on GitHub<
https://github.com/nipy/dipy/pull/305#issuecomment-32082328>
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arokem commented Jan 14, 2014

OK - I think this is ready to go now, with @Garyfallidis recent edits.

Garyfallidis added a commit that referenced this pull request Jan 14, 2014

Merge pull request #305 from arokem/installation-instructions
DOC: Some more details in installation instructions.

@Garyfallidis Garyfallidis merged commit d1e29f1 into nipy:master Jan 14, 2014

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Details
@@ -52,7 +52,7 @@
because we've already applied a white matter mask.
"""
seeds = utils.seeds_from_mask(white_matter, density=1)
seeds = utils.seeds_from_mask(white_matter, density=2)

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@stefanv

stefanv Jan 14, 2014

Contributor

"DOC: Some more details in installation instructions." Hrmm :)

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arokem Jan 14, 2014

Member

Yeah. We snuck that one in :-)

I think it also got in with bagos bf. either way, no harm

On Tuesday, January 14, 2014, Stefan van der Walt wrote:

In doc/examples/streamline_tools.py:

@@ -52,7 +52,7 @@
because we've already applied a white matter mask.
"""

-seeds = utils.seeds_from_mask(white_matter, density=1)
+seeds = utils.seeds_from_mask(white_matter, density=2)

"DOC: Some more details in installation instructions." Hrmm :)


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