mihaic · May 25, 2021 · May 19, 2021 · May 25, 2021
diff --git a/.conda/bin/jenkins-server-customization b/.conda/bin/jenkins-server-customization
diff --git a/.conda/meta.yaml b/.conda/meta.yaml
@@ -7,7 +7,7 @@ package:
   # Repeating name because of the following issue:
   # https://github.com/conda/conda-build/issues/2475
   name: brainiak
-  version: {{ GIT_DESCRIBE_TAG[1:] }}
+  version: {{ environ.get('GIT_DESCRIBE_TAG', 'v0.1.dev1')[1:] }}
 
 about:
   home: {{ data.get('url') }}
@@ -18,7 +18,7 @@ source:
   path: ../
 
 build:
-  number: {{ GIT_DESCRIBE_NUMBER }}
+  number: {{ environ.get('GIT_DESCRIBE_NUMBER', 0) }}
   script_env:
 
     # We need the source directory because conda removes source / working

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -0,0 +1,46 @@
+on: [pull_request]
+jobs:
+  pypi:
+    env:
+      IGNORE_CONDA: true
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-20.04, macos-latest]
+        python-version: [3.8]
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - uses: mpi4py/setup-mpi@v1
+      - run: |
+          python3 -m pip install -U pip
+      - if: ${{ contains(matrix.os, 'ubuntu') }}
+        run: |
+          ./pr-check.sh
+      - if: ${{ contains(matrix.os, 'macos') }}
+        run: |
+          export CC=$(brew --prefix)/opt/llvm/bin/clang
+          export CXX=$(brew --prefix)/opt/llvm/bin/clang++
+          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"
+          ./pr-check.sh
+      - uses: codecov/codecov-action@v1
+  conda:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-20.04, macos-latest]
+        python-version: [3.8]
+    steps:
+      - uses: actions/checkout@v2
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          channels: conda-forge
+          python-version: ${{ matrix.python-version }}
+      - run: |
+          export CONDA_HOME=$CONDA
+          conda install conda-build
+          .conda/bin/build ${{ matrix.python-version }}
diff --git a/.travis.yml b/.travis.yml
diff --git a/README.rst b/README.rst
@@ -1,8 +1,9 @@
 Brain Imaging Analysis Kit
 ==========================
 
-.. image:: https://travis-ci.org/brainiak/brainiak.svg?branch=master
-    :target: https://travis-ci.org/brainiak/brainiak
+.. image:: https://github.com/brainiak/brainiak/actions/workflows/main.yml/badge.svg
+    :alt: Status of GitHub Actions workflow
+    :target: https://github.com/brainiak/brainiak/actions
 
 .. image:: https://codecov.io/gh/brainiak/brainiak/branch/master/graph/badge.svg
     :target: https://codecov.io/gh/brainiak/brainiak

diff --git a/pr-check.sh b/pr-check.sh
@@ -73,7 +73,7 @@ function exit_with_error_and_venv {
     exit_with_error "$1"
 }
 
-if [ $(which conda) ]
+if [ -z $IGNORE_CONDA ] && [ $(which conda) ]
 then
     export PYTHONNOUSERSITE=True
     create_venv=create_conda_venv
@@ -113,27 +113,13 @@ python3 -m pip install -U pip || \
 # brainiak will also be installed together with the developer dependencies, but
 # we install it first here to check that installation succeeds without the
 # developer dependencies.
-python3 -m pip install $ignore_installed -U -e . || \
+python3 -m pip install $ignore_installed -U -e .[matnormal] || \
     exit_with_error_and_venv "Failed to install BrainIAK."
 
 # install developer dependencies
 python3 -m pip install $ignore_installed -U -r requirements-dev.txt || \
     exit_with_error_and_venv "Failed to install development requirements."
 
-# Source a user-specified Bash script to customize the installation.
-# This option is not supported and should not be documented in user docs.
-# In particular we use it on our CentOS 6 Jenkins server with .conda/bin/
-customization_script_flag=$1
-if [ ${customization_script_flag:-default} = "--customization-script" ]
-then
-    customization_script=$2
-    if [ ${customization_script:-default} = "default" ]
-    then
-        exit_with_error_and_venv "Must specify customization script"
-    else
-        source $customization_script
-    fi
-fi
 
 # static analysis
 ./run-checks.sh || \

diff --git a/requirements-dev.txt b/requirements-dev.txt
@@ -1,4 +1,3 @@
--e .[matnormal]  # Installing BrainIAK here ensures no requirement conflict.
 coverage
 flake8
 flake8-print

diff --git a/run-tests.sh b/run-tests.sh
@@ -37,7 +37,7 @@ if [ -z $mpi_command ]
 then
     mpi_command=mpiexec
 fi
-$mpi_command -n 2 coverage run -m pytest
+$mpi_command -n 2 coverage run -m mpi4py -m pytest
 
 # Coverage produces empty files which trigger warnings on combine
 find . -name ".coverage.*" -size 0 -print0 | xargs -0 rm -f

diff --git a/setup.cfg b/setup.cfg
@@ -1,16 +1,8 @@
 [flake8]
 max-complexity = 10
-ignore =
-    # Defaults
-    # https://gitlab.com/pycqa/flake8/blob/master/src/flake8/defaults.py
-    E121,
-    E123,
-    E126,
-    E226,
-    E24,
-    E704,
-    W503,
-    W504,
+extend-ignore =
+    # Docstrings
+    D,
 
 [coverage:run]
 source = brainiak

diff --git a/setup.py b/setup.py
@@ -3,6 +3,7 @@
 from setuptools import setup, Extension, find_packages
 from setuptools.command.build_ext import build_ext
 import os
+import site
 import sys
 import setuptools
 from copy import deepcopy
@@ -12,6 +13,9 @@
     "lower versions are not supported"
 )
 
+# https://github.com/pypa/pip/issues/7953#issuecomment-645133255
+site.ENABLE_USER_SITE = "--user" in sys.argv[1:]
+
 here = os.path.abspath(os.path.dirname(__file__))
 
 # Get the long description from the README file

diff --git a/tests/.flake8 b/tests/.flake8
@@ -1,16 +1,8 @@
 [flake8]
 max-complexity = 10
-ignore =
-    # Defaults
-    # https://gitlab.com/pycqa/flake8/blob/master/src/flake8/defaults.py
-    E121,
-    E123,
-    E126,
-    E226,
-    E24,
-    E704,
-    W503,
-    W504,
+extend-ignore =
     # Print restriction only applies to libraries
     T001,
-    T003
+    T003,
+    # Docstrings
+    D,
diff --git a/tests/conftest.py b/tests/conftest.py
@@ -1,3 +1,5 @@
+import multiprocessing
+
 from mpi4py import MPI
 import pytest
 import numpy
@@ -14,3 +16,10 @@ def seeded_rng():
     random.seed(0)
     numpy.random.seed(0)
     tensorflow.random.set_seed(0)
+
+
+skip_non_fork = pytest.mark.skipif(
+    multiprocessing.get_start_method() != "fork"
+    and MPI.COMM_WORLD.Get_attr(MPI.APPNUM) is not None,
+    reason="MPI only works with multiprocessing fork start method.",
+)
diff --git a/tests/fcma/test_mvpa_voxel_selection.py b/tests/fcma/test_mvpa_voxel_selection.py
@@ -12,6 +12,8 @@
 #  See the License for the specific language governing permissions and
 #  limitations under the License.
 
+import conftest
+
 from brainiak.fcma.mvpa_voxelselector import MVPAVoxelSelector
 from brainiak.searchlight.searchlight import Searchlight
 from sklearn import svm
@@ -23,6 +25,7 @@
 prng = RandomState(1234567890)
 
 
+@conftest.skip_non_fork
 def test_mvpa_voxel_selection():
     data = prng.rand(5, 5, 5, 8).astype(np.float32)
     # all MPI processes read the mask; the mask file is small

diff --git a/tests/fcma/test_voxel_selection.py b/tests/fcma/test_voxel_selection.py
@@ -12,6 +12,8 @@
 #  See the License for the specific language governing permissions and
 #  limitations under the License.
 
+import conftest
+
 from brainiak.fcma.voxelselector import VoxelSelector
 from scipy.stats.mstats import zscore
 from sklearn import svm
@@ -37,6 +39,7 @@ def create_epoch():
     return mat
 
 
+@conftest.skip_non_fork
 def test_voxel_selection():
     fake_raw_data = [create_epoch() for i in range(8)]
     labels = [0, 1, 0, 1, 0, 1, 0, 1]
@@ -80,6 +83,7 @@ def test_voxel_selection():
             "results")
 
 
+@conftest.skip_non_fork
 def test_voxel_selection_with_two_masks():
     fake_raw_data1 = [create_epoch() for i in range(8)]
     fake_raw_data2 = [create_epoch() for i in range(8)]

diff --git a/tests/searchlight/test_searchlight.py b/tests/searchlight/test_searchlight.py
@@ -16,6 +16,7 @@
 
 import numpy as np
 from mpi4py import MPI
+import conftest
 
 from brainiak.searchlight.searchlight import Searchlight
 from brainiak.searchlight.searchlight import Diamond, Ball
@@ -30,6 +31,7 @@ def cube_sfn(data, msk, myrad, bcast_var):
     return None
 
 
+@conftest.skip_non_fork
 def test_searchlight_with_cube():
     sl = Searchlight(sl_rad=3)
     comm = MPI.COMM_WORLD
@@ -97,6 +99,7 @@ def diamond_sfn(data, msk, myrad, bcast_var):
     return None
 
 
+@conftest.skip_non_fork
 def test_searchlight_with_diamond():
     sl = Searchlight(sl_rad=3, shape=Diamond)
     comm = MPI.COMM_WORLD
@@ -136,6 +139,7 @@ def ball_sfn(data, msk, myrad, bcast_var):
     return None
 
 
+@conftest.skip_non_fork
 def test_searchlight_with_ball():
     sl = Searchlight(sl_rad=3, shape=Ball)
     comm = MPI.COMM_WORLD
@@ -212,6 +216,7 @@ def block_test_sfn(data, msk, myrad, bcast_var, extra_params):
         return outmat[myrad:-myrad, myrad:-myrad, myrad:-myrad]
 
 
+@conftest.skip_non_fork
 def test_correctness():  # noqa: C901
     def voxel_test(data, mask, max_blk_edge, rad):