Add Conda packaging

.conda/bin/build

@@ -0,0 +1,15 @@
+#!/usr/bin/env bash
+
+DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+
+export BRAINIAK_HOME=$DIR/../../
+
+# See run-tests.sh
+export MKL_THREADING_LAYER=GNU
+
+if [ -z ${CONDA_HOME+dummy} ]
+then
+    CONDA_HOME="$HOME"/miniconda3
+fi
+
+"$CONDA_HOME"/bin/conda build "$DIR"/..

.conda/bin/docker

@@ -0,0 +1,6 @@
+#!/usr/bin/env bash
+
+DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+
+# Need to run apt update && apt install -y build-essential curl git
+docker run --rm -w /src -v $DIR/../..:/src -ti ubuntu:trusty /bin/bash

.conda/bin/install-miniconda

@@ -0,0 +1,28 @@
+#!/usr/bin/env bash
+
+# Install Miniconda.
+echo ""
+echo "Installing a fresh version of Miniconda."
+MINICONDA_URL="https://repo.continuum.io/miniconda"
+
+MINICONDA_FILE="Miniconda3-latest-Linux-x86_64.sh"
+if [[ "$OSTYPE" == "darwin"* ]]; then
+  MINICONDA_FILE="Miniconda3-latest-MacOSX-x86_64.sh"
+fi
+
+curl -L "${MINICONDA_URL}/${MINICONDA_FILE}" -o ~/${MINICONDA_FILE}
+
+# Update an existing miniconda installation, if it exists
+bash ~/$MINICONDA_FILE -b -u
+
+# Clean up
+rm -f ~/${MINICONDA_FILE}
+
+# Configure conda.
+echo ""
+echo "Configuring conda."
+source ~/miniconda3/bin/activate root
+conda config --add channels conda-forge --add channels defaults
+conda config --set show_channel_urls true
+conda install --yes --quiet conda-build
+source deactivate

.conda/build.sh

@@ -0,0 +1,15 @@
+#!/bin/bash
+
+if [[ "$OSTYPE" == "darwin"* ]]; then
+  export MACOSX_DEPLOYMENT_TARGET=10.9
+  export CC=$(which clang)
+  export CXX=$(which clang++)
+fi
+
+echo $PREFIX
+
+# Install pymanopt via pip because there isn't a conda package
+$PYTHON -m pip install pymanopt
+
+# NOTE: This is the recommended way to install packages
+$PYTHON setup.py install --single-version-externally-managed --record=record.txt

.conda/meta.yaml

@@ -0,0 +1,67 @@
+{% set conda_package_nonexistent = (
+    "pymanopt",
+) %}
+{% set data = load_setup_py_data() %}
+
+package:
+  # Repeating name because of the following issue:
+  # https://github.com/conda/conda-build/issues/2475
+  name: brainiak
+  version: {{ GIT_DESCRIBE_TAG[1:] }}
+
+about:
+  home: {{ data.get('url') }}
+  license: {{ data.get('license') }}
+  summary: {{ data.get('description') }}
+
+source:
+  path: ../
+
+build:
+  number: {{ GIT_DESCRIBE_NUMBER }}
+  script_env:
+
+    # We need the source directory because conda removes source / working
+    # directories by the time we reach the test phase. We can optionally pass in
+    # the --keep-old-work flag later on to use the $PREFIX/work directory
+    - BRAINIAK_HOME
+    - MKL_THREADING_LAYER
+
+requirements:
+  build:
+    - {{ compiler('cxx') }}
+
+  host:
+    - python
+    - setuptools
+    - pip
+    - openmp
+    {% for req in data.get('setup_requires', [])
+        if req not in conda_package_nonexistent -%}
+    - {{req}}
+    {% endfor %}
+    {% for req in data.get('install_requires', [])
+        if req not in conda_package_nonexistent -%}
+    - {{req}}
+    {% endfor %}
+
+  run:
+    - python
+    - openmp
+    {% for req in data.get('install_requires', [])
+        if req not in conda_package_nonexistent -%}
+    - {{req}}
+    {% endfor %}
+
+test:
+  commands:
+    - find $BRAINIAK_HOME/tests | grep pycache | xargs rm -rf
+    - mpiexec -n 2 pytest $BRAINIAK_HOME
+
+      # Known issue: https://github.com/travis-ci/travis-ci/issues/4704#issuecomment-348435959
+    - python -c 'import os,sys,fcntl; flags = fcntl.fcntl(sys.stdout, fcntl.F_GETFL); fcntl.fcntl(sys.stdout, fcntl.F_SETFL, flags&~os.O_NONBLOCK);'
+    - conda inspect linkages -p $PREFIX brainiak  # [not win]
+    - conda inspect objects -p $PREFIX brainiak  # [osx]
+  requires:
+    - pytest
+    - numdifftools

.travis.yml

@@ -40,6 +40,17 @@ matrix:
       env: *macos_env
       before_install: *macos_before_install
 
+    # Build and test conda packages
+    - os: linux
+      dist: trusty
+      install: ./.conda/bin/install-miniconda
+      script: ./.conda/bin/build
+
+    - os: osx
+      osx_image: xcode8
+      install: ./.conda/bin/install-miniconda
+      script: ./.conda/bin/build
+
 install:
     - python3 -m pip install -U pip codecov
 

CONTRIBUTING.rst

@@ -281,6 +281,22 @@ Making a release
 This information is only of interest to the core contributors who have the
 right to make releases.
 
+Before making a release, ensure that:
+
+1. The following environment variables are set::
+
+    export $CONDA_HOME=/path/to/miniconda3
+
+2. The following Conda channels are enabled::
+
+    conda config --add channels conda-forge --add channels defaults
+
+3. The following Conda packages are installed::
+
+    conda install conda-build anaconda-client
+
+To make a release:
+
 1. Choose a release number, ``v``. We follow `Semantic Versioning
    <http://semver.org>`_, although we omit the patch number when it is 0.
 
@@ -300,7 +316,7 @@ right to make releases.
 
        git tag v<v>
 
-4. Create and test the distribution package::
+4. Create and test the source distribution package::
 
        python3 setup.py sdist
        tar -xf dist/brainiak-<v>.tar.gz
@@ -313,3 +329,15 @@ right to make releases.
 
        git tag --push
        twine upload dist/brainiak-<v>.tar.gz
+
+
+7. Create and test Conda packages (repeat command for all OSes and Python
+   versions); requires the ``conda-build`` Conda package::
+
+       .conda/bin/build
+
+8. Upload the built Conda package (repeat command for all OSes and Python
+   versions); requires the ``anaconda-client`` Conda package::
+
+       anaconda upload -u brainiak \
+       $CONDA_HOME/conda-bld/<OS>/brainiak-<v>-<python_version>.tar.bz2

README.rst

@@ -23,93 +23,19 @@ To reduce verbosity, we may refer to the Brain Imaging Analysis Kit using the
 package name), we use ``brainiak``.
 
 
-Requirements
-============
-
-We support Linux and MacOS with Python version 3.4 or higher. Most of the
-dependencies will be installed automatically. However, a few need to be
-installed manually.
-
-
-Linux
------
-
-Install the following packages (Ubuntu 16.04 is used in these instructions)::
-
-    apt install build-essential libgomp1 libmpich-dev mpich python3-dev \
-        python3-pip python3-venv
-
-Install updated version of the following Python packages::
-
-    python3 -m pip install --user -U pip
-
-Note the ``--user`` flag, which instructs Pip to not overwrite system
-files. You must add ``$HOME/.local/bin`` to your ``$PATH`` to be able to run
-the updated Pip, e.g., by adding the following line to ``$HOME/.profile``
-and launching a new login shell (e.g., logout or execute ``bash -l``)::
-
-    PATH="$HOME/.local/bin:$PATH"
-
-
-MacOS
------
-
-Install the Xcode Command Line Tools::
-
-    xcode-select --install
-
-Install ``brew`` from https://brew.sh. If you already have ``brew``, examine
-the output of the following command to make sure it is working::
-
-    brew doctor
-
-Then install the following::
-
-    brew install llvm cmake mpich python3
-
-Note that if your MacOS does not have ``gcc`` (a prerequisite of ``mpich``), 
-it will take a long time (perhaps over an hour) to install ``gcc`` from source for you.
-
-You must instruct programs to use this ``clang`` version at ``/usr/local/opt/llvm/bin``.
-One way to do this, which
-works for most programs, is setting the ``CC`` environment variable. You can
-add the following lines to ``$HOME/.profile`` (or ``$HOME/.bash_profile``, if
-you have one). For them to take effect, you must logout or launch a new login
-shell, e.g., ``bash -l``::
-
-    export CC=/usr/local/opt/llvm/bin/clang
-    export CXX=/usr/local/opt/llvm/bin/clang++
-
-In addition, you also need to specify the directories that the newly installed `clang`
-will seek for compiling and linking::
-
-    export LDFLAGS="-L/usr/local/opt/llvm/lib "\
-    "-Wl,-rpath,/usr/local/opt/llvm/lib $LDFLAGS"
-    export CPPFLAGS="-I/usr/local/opt/llvm/include $CPPFLAGS"
-
-Install updated versions of the following Python packages::
-
-    python3 -m pip install -U pip
-
-
-Installing and upgrading
-========================
+Quickstart
+==========
 
-The Brain Imaging Analysis Kit is available on PyPI. You can install it (or
-upgrade to the latest version) using the following command::
+If you have `Conda <conda.io>`_::
 
-    python3 -m pip install -U brainiak
+    conda install -c brainiak -c defaults -c conda-forge brainiak
 
-Note that you may see a ``Failed building wheel for brainiak`` message (`issue
-#61`_). Installation will proceed despite this failure. You can safely ignore it
-as long as you see ``Successfully installed`` at the end.
+Otherwise, or if you want to compile from source, install the requirements (see
+`docs/installation`) and then install from PyPI::
 
-.. _issue #61:
-   https://github.com/brainiak/brainiak/issues/61
+    python3 -m pip install brainiak
 
-Until we reach version 1.0, we will only support the latest released version.
-Therefore, if you have a problem with an older version, please upgrade to the
-latest version before creating an issue on GitHub.
+Note that we do not support Windows.
 
 
 Docker
@@ -179,4 +105,4 @@ http://brainiak.org." Additionally, if you use `RRIDs
 <https://scicrunch.org/resolver>`_ to identify resources, please mention
 BrainIAK as "Brain Imaging Analysis Kit, RRID:SCR_014824". Finally, please cite
 the publications referenced in the documentation of the BrainIAK modules you
-use, e.g., `SRM <http://pythonhosted.org/brainiak/brainiak.funcalign.html>`_.
+use, e.g., `SRM <http://brainiak.org/docs/brainiak.funcalign.html>`_.

docs/index.rst

@@ -10,6 +10,7 @@ Table of contents
 
 .. toctree::
 
+   installation
    release_notes
    api
    contributing