From a95c5de1f651607f3112caa8a9cc76cb04f6118f Mon Sep 17 00:00:00 2001 From: Shoshana Berleant Date: Tue, 17 May 2016 15:05:50 -0700 Subject: [PATCH 1/3] add instructions to install; fix doc build for python 3 --- doc/sphinxext/numpy_ext/numpydoc.py | 6 +++--- doc/users/install.rst | 4 ++++ 2 files changed, 7 insertions(+), 3 deletions(-) diff --git a/doc/sphinxext/numpy_ext/numpydoc.py b/doc/sphinxext/numpy_ext/numpydoc.py index ab375c112f..e27a4a6184 100644 --- a/doc/sphinxext/numpy_ext/numpydoc.py +++ b/doc/sphinxext/numpy_ext/numpydoc.py @@ -40,7 +40,7 @@ def mangle_docstrings(app, what, name, obj, options, lines, if what == 'module': # Strip top title - title_re = re.compile(ur'^\s*[#*=]{4,}\n[a-z0-9 -]+\n[#*=]{4,}\s*', + title_re = re.compile(r'^\s*[#*=]{4,}\n[a-z0-9 -]+\n[#*=]{4,}\s*', re.I | re.S) lines[:] = title_re.sub(u'', u"\n".join(lines)).split(u"\n") else: @@ -61,7 +61,7 @@ def mangle_docstrings(app, what, name, obj, options, lines, references = [] for line in lines: line = line.strip() - m = re.match(ur'^.. \[([a-z0-9_.-])\]', line, re.I) + m = re.match(r'^.. \[([a-z0-9_.-])\]', line, re.I) if m: references.append(m.group(1)) @@ -70,7 +70,7 @@ def mangle_docstrings(app, what, name, obj, options, lines, if references: for i, line in enumerate(lines): for r in references: - if re.match(ur'^\d+$', r): + if re.match(r'^\d+$', r): new_r = u"R%d" % (reference_offset[0] + int(r)) else: new_r = u"%s%d" % (r, reference_offset[0]) diff --git a/doc/users/install.rst b/doc/users/install.rst index 3b4c1e162c..5384fdea7b 100644 --- a/doc/users/install.rst +++ b/doc/users/install.rst @@ -21,6 +21,10 @@ To check out the latest development version:: git clone git://github.com/nipy/nipype.git +or:: + + git clone https://github.com/nipy/nipype.git + Install ------- From 7c25f3eab3576a3c1f54272fa8921969c1a2afd4 Mon Sep 17 00:00:00 2001 From: Shoshana Berleant Date: Tue, 17 May 2016 17:39:49 -0700 Subject: [PATCH 2/3] more installation instructions; fix link to nose --- doc/links_names.txt | 2 +- doc/users/install.rst | 27 +++++++++++++++++---------- 2 files changed, 18 insertions(+), 11 deletions(-) diff --git a/doc/links_names.txt b/doc/links_names.txt index cadf37825b..4964805551 100644 --- a/doc/links_names.txt +++ b/doc/links_names.txt @@ -56,7 +56,7 @@ .. _doctest-mode: http://www.cis.upenn.edu/~edloper/projects/doctestmode/ .. _bazaar: http://bazaar-vcs.org/ .. _subversion: http://subversion.tigris.org/ -.. _nose: http://somethingaboutorange.com/mrl/projects/nose +.. _nose: http://nose.readthedocs.io/en/latest/ .. _`python coverage tester`: http://nedbatchelder.com/code/modules/coverage.html .. Other python projects diff --git a/doc/users/install.rst b/doc/users/install.rst index 5384fdea7b..88f5451ee5 100644 --- a/doc/users/install.rst +++ b/doc/users/install.rst @@ -62,6 +62,8 @@ If you downloaded the source distribution named something like ``nipype-x.y.tar.gz``, then unpack the tarball, change into the ``nipype-x.y`` directory and install nipype using:: + easy_install nibabel + pip install -r requirements.txt python setup.py install **Note:** Depending on permissions you may need to use ``sudo``. @@ -111,10 +113,15 @@ recommendations. Must Have ~~~~~~~~~ -Python_ 2.7 - Nibabel_ 1.0 - 1.4 - Neuroimaging file i/o library + Neuroimaging file i/o library. + +.. note:: + + Full distributions of Nipype, such as the ones in Anaconda_ or Canopy_, provide + the following packages automatically. + +Python_ 2.7 NetworkX_ 1.0 - 1.8 Python package for working with complex networks. @@ -128,10 +135,6 @@ Enthought_ Traits_ 4.0.0 - 4.3.0 Dateutil 1.5 - -.. note:: - - Full distributions such as Anaconda_ or Canopy_ provide the above packages, - except Nibabel_. Strong Recommendations ~~~~~~~~~~~~~~~~~~~~~~ @@ -144,18 +147,22 @@ Matplotlib_ 1.0 - 1.2 Plotting library `RDFLib `_ 4.1 -RDFLibrary required for provenance export as RDF + RDFLibrary required for provenance export as RDF Sphinx_ 1.1 Required for building the documentation `Graphviz `_ - Required for building the documentation + Required for building the documentation. The python wrapper package (``graphviz``) + and the program itself both need to be installed. Interface Dependencies ~~~~~~~~~~~~~~~~~~~~~~ -These are the software packages that nipype.interfaces wraps: +You might not need some of the following packages, depending on what exactly you +want to use nipype for. If you do need any of them, install nipype's wrapper package +(``nipype.interfaces``), then install the programs separately onto your computer, just +like you would install any other app. FSL_ 4.1.0 or later From 542f681921aae9bcd44fe8771b73d832094fa8d0 Mon Sep 17 00:00:00 2001 From: Shoshana Berleant Date: Tue, 17 May 2016 17:50:13 -0700 Subject: [PATCH 3/3] remove confusing references to nibabel in install instructions --- doc/users/install.rst | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/doc/users/install.rst b/doc/users/install.rst index 88f5451ee5..c46865ff19 100644 --- a/doc/users/install.rst +++ b/doc/users/install.rst @@ -50,9 +50,8 @@ Mac OS X ~~~~~~~~ The easiest way to get nipype running on Mac OS X is to install Anaconda_ or -Canopy_ and then add nibabel and nipype by executing:: +Canopy_ and then add nipype by executing:: - easy_install nibabel easy_install nipype From source @@ -62,7 +61,6 @@ If you downloaded the source distribution named something like ``nipype-x.y.tar.gz``, then unpack the tarball, change into the ``nipype-x.y`` directory and install nipype using:: - easy_install nibabel pip install -r requirements.txt python setup.py install @@ -113,14 +111,14 @@ recommendations. Must Have ~~~~~~~~~ -Nibabel_ 1.0 - 1.4 - Neuroimaging file i/o library. - .. note:: Full distributions of Nipype, such as the ones in Anaconda_ or Canopy_, provide the following packages automatically. +Nibabel_ 1.0 - 1.4 + Neuroimaging file i/o library. + Python_ 2.7 NetworkX_ 1.0 - 1.8