DOC: Some more details in installation instructions. #305

arokem · 2014-01-03T20:17:36Z

No description provided.

Garyfallidis · 2014-01-04T15:20:52Z

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.

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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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.

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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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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matthew-brett · 2014-01-04T15:59:04Z

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 · 2014-01-04T16:18:10Z

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 · 2014-01-04T16:30:29Z

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

Garyfallidis · 2014-01-04T16:30:51Z

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

arokem · 2014-01-04T16:32:20Z

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 · 2014-01-04T16:48:30Z

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.

Garyfallidis · 2014-01-04T17:00:45Z

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

arokem · 2014-01-04T19:29:40Z

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 · 2014-01-04T20:39:44Z

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 · 2014-01-04T20:44:26Z

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 · 2014-01-04T21:04:48Z

Sure, I 'll do that asap.

stefanv · 2014-01-04T23:56:23Z

doc/installation.rst

-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!

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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arokem · 2014-01-11T01:19:24Z

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

Garyfallidis · 2014-01-11T01:26:45Z

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 · 2014-01-11T01:38:59Z

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?

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arokem · 2014-01-14T01:30:01Z

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

DOC: Some more details in installation instructions.

stefanv · 2014-01-14T15:18:04Z

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 :)

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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Garyfallidis reviewed Jan 4, 2014
View reviewed changes

stefanv reviewed Jan 4, 2014
View reviewed changes

arokem added 4 commits January 13, 2014 17:29

DOC: Some more details in installation instructions.

dd24824

DOC: Formulation.

249c3e7

DOC: Be little less gushing.

6256f0a

DOC: we don't need dual targets. Caps taken care by the Sphinx.

9453f6b

arokem and others added 4 commits January 13, 2014 17:29

DOC: Suggest using .exe installers instead.

7edda7a

DOC: Link to easy_install.

d84c83c

DOC: Fixes following comments from Stefan.

926636a

DOC: replaced Canopy with Anaconda in installation instructions

a428406

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

Merge pull request #305 from arokem/installation-instructions

d1e29f1

DOC: Some more details in installation instructions.

Garyfallidis merged commit d1e29f1 into dipy:master Jan 14, 2014

stefanv reviewed Jan 14, 2014
View reviewed changes

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DOC: Some more details in installation instructions. #305

DOC: Some more details in installation instructions. #305

arokem commented Jan 3, 2014

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

DOC: Some more details in installation instructions. #305

DOC: Some more details in installation instructions. #305

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