Updates to install information (#247)

* Updates to install information Closes #246 * FIX: pip command * FIX: install_requires * DOC: Anaconda * FIX: no-deps * FIX: Reorder * FIX: CircleCI * FIX: export * FIX: Deps
nipy · Jul 12, 2018 · cdb4ffe · cdb4ffe
1 parent d79a650
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diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -2,7 +2,7 @@ version: 2
 jobs:
     build:
       docker:
-        - image: circleci/python:3.6-stretch
+        - image: circleci/python:3.6-jessie
       steps:
         # Get our data and merge with upstream
         - checkout
@@ -19,32 +19,28 @@ jobs:
         - restore_cache:
             keys:
               - data-cache
+              - pip-cache
 
-        - run: echo "export SUBJECTS_DIR=$HOME/subjects" >> $BASH_ENV
+        # Fix libgcc_s.so.1 pthread_cancel bug:
+        # https://github.com/ContinuumIO/anaconda-issues/issues/9190#issuecomment-386508136
+        # https://github.com/golemfactory/golem/issues/1019
+        - run: sudo apt-get install libgl1-mesa-glx libegl1-mesa libxrandr2 libxrandr2 libxss1 libxcursor1 libxcomposite1 libasound2 libxi6 libxtst6 qt5-default
+        - run: echo "export SUBJECTS_DIR=~/subjects" >> $BASH_ENV
+        - run: echo "export PATH=~/.local/bin:$PATH" >> $BASH_ENV
+        - run: echo "export LD_PRELOAD=/usr/lib/x86_64-linux-gnu/libgobject-2.0.so.0.4200.1" >> $BASH_ENV
+        # Spin up Xvfb
         - run: echo "export DISPLAY=:99" >> $BASH_ENV
         - run: /sbin/start-stop-daemon --start --quiet --pidfile /tmp/custom_xvfb_99.pid --make-pidfile --background --exec /usr/bin/Xvfb -- :99 -screen 0 1400x900x24 -ac +extension GLX +render -noreset;
-        # Get latest Anaconda running
-        - run: echo "export PATH=~/miniconda/envs/mne/bin:~/miniconda/bin:$PATH" >> $BASH_ENV
-        - run:
-            command: |
-              wget -q http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O ~/miniconda.sh;
-              chmod +x ~/miniconda.sh;
-              ~/miniconda.sh -b -p ~/miniconda;
-        - run:
-            command: |
-              conda update --yes --quiet conda;
-              conda env create --quiet -f environment.yml;
-
-        - run: pip install sphinx numpydoc https://api.github.com/repos/sphinx-gallery/sphinx-gallery/zipball/master
-        # This is a CircleCI-specific fix -- for some reason 5.9.2 is problematic
-        # here but not on Travis, we get:
-        #
-        #     libgcc_s.so.1 must be installed for pthread_cancel to work
-        #     Aborted
-        #
-        - run: pip install --upgrade --no-deps pyqt5>=5.10
-        - run: python -c "from mayavi import mlab; import matplotlib.pyplot as plt; mlab.figure(); plt.figure()"
-        - run: python setup.py develop
+        # Python env
+        - run: pip install -U --user --progress-bar off numpy scipy matplotlib vtk PyQt5 sip PyQt5-sip nibabel sphinx numpydoc pillow imageio https://api.github.com/repos/sphinx-gallery/sphinx-gallery/zipball/master
+        - run: pip install -U --user --progress-bar off mayavi
+        - save_cache:
+            key: pip-cache
+            paths:
+              - "~/.cache/pip"
+        - run: python setup.py develop --user
+        # Check libs
+        - run: LIBGL_DEBUG=verbose python -c "from mayavi import mlab; import matplotlib.pyplot as plt; mlab.figure(); plt.figure()"
         - run: echo $SUBJECTS_DIR
         - run:
             command: |
@@ -56,11 +52,6 @@ jobs:
                 rm fsaverage_min.zip;
               fi;
         - run: ls $SUBJECTS_DIR
-        - run:
-            command: |
-              if [[ $(cat build.txt) == "html_dev" ]] || [[ $(cat build.txt) == "html_stable" ]]; then
-                SUBJECTS_DIR=~/mne_data/MNE-sample-data/subjects python -c "import mne; mne.datasets._download_all_example_data()";
-              fi;
         - run: cd doc && sphinx-build -D plot_gallery=1 -D sphinx_gallery_conf.filename_pattern=^\(\(?\!plot_fmri_activation_volume\|plot_morphometry\|plot_label\.py\|plot_probabilistic_label\|plot_resting_correlations\|plot_transparent_brain\|rotate_animation\|save_movie\|save_views\).\)*\$ -b html -d _build/doctrees . _build/html
 
         - store_artifacts:

diff --git a/doc/install.rst b/doc/install.rst
@@ -5,36 +5,33 @@
 Installing and Getting Started
 ==============================
 
-Installing PySurfer is quite simple with pip_::
+PySurfer can be installed with pip_. Note that the package name on PyPi is different from the library name that you import::
 
     pip install pysurfer
 
 If you already have PySurfer installed, you can also use pip to update it::
 
-    pip install -U pysurfer
+    pip install -U --no-deps pysurfer
 
-If you would like to save movies of time course data, also include the
-optional dependency `imageio` with::
+If you would like to save movies of time course data, it is necessary to include the optional dependency ``imageio`` with::
 
-    pip install -U pysurfer[save_movie]
+    pip install pysurfer[save_movie]
 
 If you'd like to install the development version, you have two options. You can
-use pip::
+install straight from github::
 
-    pip install git+git://github.com/nipy/pysurfer.git#egg=pysurfer
+    pip install https://api.github.com/repos/nipy/PySurfer/zipball/master
 
 Or you can clone the `git repository <https://github.com/nipy/PySurfer>`_ and
-install from the source directory::
+install from your local source directory::
 
-    python setup.py install
-
-If you don't have pip, you can also install PySurfer with easy_install_, or use
-easy_install to get pip.
+    pip install .
 
 Dependencies
 ~~~~~~~~~~~~
 
-PySurfer requires Python 2.7, and it does not work on Python 3.
+PySurfer works on Python 2.7 and 3.6+.
+(Older Python 3 versions will probably work, but are not tested.)
 
 To use PySurfer, you will need to have the following Python packages:
 
@@ -44,39 +41,36 @@ To use PySurfer, you will need to have the following Python packages:
 * mayavi_
 * matplotlib_
 
-Some functions also make use of the Python Imaging Library (PIL_), although
-it's not mandatory.
-
-An easy option to set up this environment is the Anaconda_ distribution, which
-is free and ships with many of the required packages. If you use Anaconda,
-you'll need to install Mayavi separately. This can be done using the ``conda``
-command::
-
-    conda install mayavi
-
-You'll also need to install nibabel, which can be done using ``pip`` as above.
-
-Another option for getting set up is the Enthough Canopy_ environment, which is
-similar to Anaconda and free for academic use.
+Some input/output functions also make use of the Python Imaging Library (PIL_)
+and ``imageio``, although they are not mandatory.
 
 Getting started
 ~~~~~~~~~~~~~~~
 
+Because PySurfer relies on some complicated dependencies (Mayavi, VTK and a GUI
+library), it can be more difficult to get started with than is the case with
+other Python libraries. Consider using the Anaconda_ distribution
+or Enthough Canopy_ environment. The difficulty on these
+platforms is generally getting Mayavi and VTK installed; see their
+installation instructions for information.
+
 PySurfer generally works out of the box on Linux systems. Getting started on
-OSX can be a bit more difficult. We have had success using the Anaconda
-distribution with the additional step of setting the environment variable
-``QT_API`` to ``pyqt``::
+OSX may be trickier. We have had success using the Anaconda distribution with
+the additional step of setting the environment variables ``QT_API`` and ``ETS_TOOLKIT``, e.g.::
 
     export QT_API=pyqt
+    export ETS_TOOLKIT=qt4
 
-If you're using Canopy, you need to do something similar with the
-``ETS_TOOLKIT`` variable::
+The values you set should match the GUI library you are using.
 
-    export ETS_TOOLKIT=qt4
+You may wish to consult the `Mayavi installation docs
+<http://docs.enthought.com/mayavi/mayavi/installation.html>`_ if you are having
+trouble getting things working.
 
-If you want to use PySurfer interactively, you should do so in ipython_. After
-starting ipython (either in the terminal, qtconsole, or notebook), you have to
-activate the correct GUI backend, which is probably qt::
+If you are using PySurfer interactively in IPython_/Jupyter, you should
+activate one of the GUI event loops so that the Mayavi window runs in a
+separate process. After starting IPython (either in the terminal, qtconsole, or
+notebook), you have to activate the correct GUI backend, which is probably qt::
 
     %gui qt
 

diff --git a/setup.py b/setup.py
@@ -35,33 +35,9 @@
 VERSION = version
 
 
-def check_dependencies():
-    # nibabel and mayavi are in install_requires
-    needed_deps = ["numpy", "scipy", "matplotlib"]
-    missing_deps = []
-    for dep in needed_deps:
-        try:
-            __import__(dep)
-        except ImportError:
-            missing_deps.append(dep)
-
-    if missing_deps:
-        missing = ", ".join(missing_deps)
-        raise ImportError("Missing dependencies: %s" % missing)
-
-
 if __name__ == "__main__":
     if os.path.exists('MANIFEST'):
         os.remove('MANIFEST')
-
-    import sys
-    if not (len(sys.argv) >= 2 and ('--help' in sys.argv[1:] or
-            sys.argv[1] in ('--help-commands',
-                            '--version',
-                            'egg_info',
-                            'clean'))):
-        check_dependencies()
-
     setup(name=DISTNAME,
           maintainer=MAINTAINER,
           include_package_data=True,
@@ -76,9 +52,8 @@ def check_dependencies():
           classifiers=['Intended Audience :: Science/Research',
                        'Intended Audience :: Developers',
                        'Programming Language :: Python :: 2.7',
-                       'Programming Language :: Python :: 3.3',
-                       'Programming Language :: Python :: 3.4',
-                       'Programming Language :: Python :: 3.5',
+                       'Programming Language :: Python :: 3.6',
+                       'Programming Language :: Python :: 3.7',
                        'License :: OSI Approved',
                        'Programming Language :: Python',
                        'Topic :: Software Development',
@@ -91,6 +66,6 @@ def check_dependencies():
           platforms='any',
           packages=['surfer', 'surfer.tests'],
           scripts=['bin/pysurfer'],
-          install_requires=['nibabel >= 1.2', 'mayavi'],
+          install_requires=['numpy', 'scipy', 'matplotlib', 'nibabel >= 1.2', 'mayavi'],
           extras_require={'save_movie': ['imageio >= 1.5']},
           )