diff --git a/Makefile b/Makefile
index 2190f815fc..af060fcad1 100644
--- a/Makefile
+++ b/Makefile
@@ -8,7 +8,7 @@ PROJECT=nibabel
# The Python executable to be used
#
PYTHON ?= python
-NOSETESTS = $(PYTHON) $(shell which nosetests)
+TEST_RUNNER ?= pytest
#
# Determine details on the Python/system
@@ -66,7 +66,6 @@ distclean: clean
-o -iname '#*#' | xargs -L10 rm -f
-rm -r dist
-rm build-stamp
- -rm -r .tox
# -rm tests/data/*.hdr.* tests/data/*.img.* tests/data/something.nii \
# tests/data/noise* tests/data/None.nii
@@ -83,22 +82,23 @@ $(WWW_DIR):
# Tests
#
-test: unittest testmanual
+test: test-style unittest testmanual
-
-ut-%: build
- @PYTHONPATH=.:$(PYTHONPATH) $(NOSETESTS) nibabel/tests/test_$*.py
-
-
-unittest: build
- @PYTHONPATH=.:$(PYTHONPATH) $(NOSETESTS) nibabel --with-doctest
+unittest: build test-clean
+ export CHECK_TYPE=test; ./tools/ci/check.sh
testmanual: build
- @cd doc/source && PYTHONPATH=../..:$(PYTHONPATH) $(NOSETESTS) --with-doctest --doctest-extension=.rst . dicom
+ export CHECK_TYPE=doc; ./tools/ci/check.sh
+coverage: unittest
-coverage: build
- @PYTHONPATH=.:$(PYTHONPATH) $(NOSETESTS) --with-coverage --cover-package=nibabel
+.PHONY: test-style
+test-style:
+ export CHECK_TYPE=style; ./tools/ci/check.sh
+
+.PHONY: test-clean
+test-clean:
+ rm -rf for_testing
#
@@ -252,11 +252,13 @@ sdist-venv: clean
rm -rf dist venv
unset PYTHONPATH && $(PYTHON) setup.py sdist --formats=zip
virtualenv --system-site-packages --python=$(PYTHON) venv
- . venv/bin/activate && pip install --ignore-installed nose
+ . venv/bin/activate && pip install -r dev-requirements.txt
mkdir venv/tmp
cd venv/tmp && unzip ../../dist/*.zip
. venv/bin/activate && cd venv/tmp/nibabel* && python setup.py install
- unset PYTHONPATH && . venv/bin/activate && cd venv && nosetests --with-doctest nibabel nisext
+ unset PYTHONPATH && . \
+ venv/bin/activate && \
+ cd venv && $(TEST_RUNNER) --doctest-modules --doctest-plus nibabel nisext
source-release: distclean
$(PYTHON) -m compileall .
@@ -269,17 +271,7 @@ venv-tests:
make distclean
- rm -rf $(VIRTUAL_ENV)/lib/python$(PYVER)/site-packages/nibabel
$(PYTHON) setup.py install
- cd .. && nosetests $(VIRTUAL_ENV)/lib/python$(PYVER)/site-packages/nibabel
-
-tox-fresh:
- # tox tests with fresh-installed virtualenvs. Needs network. And
- # pytox, obviously.
- tox -c tox.ini
-
-tox-stale:
- # tox tests with MB's already-installed virtualenvs (numpy and nose
- # installed)
- tox -e python25,python26,python27,python32,np-1.2.1
+ cd .. && $(TEST_RUNNER) $(VIRTUAL_ENV)/lib/python$(PYVER)/site-packages/nibabel
refresh-readme:
$(PYTHON) tools/refresh_readme.py
diff --git a/dev-requirements.txt b/dev-requirements.txt
index 69302061bc..a6485b1706 100644
--- a/dev-requirements.txt
+++ b/dev-requirements.txt
@@ -1,3 +1,5 @@
# Requirements for running tests
-r requirements.txt
pytest
+pytest-doctestplus
+flake8
diff --git a/doc-requirements.txt b/doc-requirements.txt
index c934d76e6b..517bde85e9 100644
--- a/doc-requirements.txt
+++ b/doc-requirements.txt
@@ -1,6 +1,8 @@
# Requirements for building docs
-r requirements.txt
sphinx<3
-numpydoc
+jinja2<3
+numpydoc<1.3
+MarkupSafe<2.1
texext
matplotlib >=1.3.1
diff --git a/doc/source/dicom/derivations/spm_dicom_orient.py b/doc/source/dicom/derivations/spm_dicom_orient.py
index 936e807ce1..033abc486e 100644
--- a/doc/source/dicom/derivations/spm_dicom_orient.py
+++ b/doc/source/dicom/derivations/spm_dicom_orient.py
@@ -46,7 +46,7 @@ def numbered_vector(nrows, symbol_prefix):
R = zeros(4, 2)
R[:3, :] = R3
-# The following is specific to the SPM algorithm.
+# The following is specific to the SPM algorithm.
x1 = ones(4, 1)
y1 = ones(4, 1)
y1[:3, :] = pos_pat_0
diff --git a/doc/source/scripts/make_coord_examples.py b/doc/source/scripts/make_coord_examples.py
index f763b28c28..d54650eb6f 100644
--- a/doc/source/scripts/make_coord_examples.py
+++ b/doc/source/scripts/make_coord_examples.py
@@ -68,6 +68,7 @@
x, y = 0, 1
# Make a rectangular box with these sides
+
def make_ortho_box(bl, x_len, y_len):
""" Make a box with sides parallel to the axes
"""
@@ -76,6 +77,7 @@ def make_ortho_box(bl, x_len, y_len):
[bl[x], bl[y] + y_len],
[bl[x] + x_len, bl[y] + y_len]))
+
orth_epi_box = make_ortho_box(epi_bl, epi_x_len, epi_y_len)
# Structural bounding box
@@ -126,6 +128,7 @@ def plot_localizer():
def save_plot():
# Plot using global variables
plot_localizer()
+
def vx2mm(pts):
return pts - iso_center
plot_box(vx2mm(rot_box), label='EPI bounding box')
diff --git a/doc/tools/build_modref_templates.py b/doc/tools/build_modref_templates.py
index 6ec6848579..d19ea12081 100755
--- a/doc/tools/build_modref_templates.py
+++ b/doc/tools/build_modref_templates.py
@@ -37,7 +37,7 @@ def abort(error):
try:
__import__(package)
- except ImportError as e:
+ except ImportError:
abort("Can not import " + package)
module = sys.modules[package]
@@ -71,7 +71,11 @@ def abort(error):
print('***', source_version)
if source_version != installed_version:
- abort("Installed version does not match source version")
+ abort(
+ "Installed version does not match source version. "
+ "source_version=" + str(source_version) +
+ "installed_version=" + str(installed_version)
+ )
docwriter = ApiDocWriter(package, rst_extension='.rst',
other_defines=other_defines)
diff --git a/setup.cfg b/setup.cfg
index e81b1db10b..d7f4d730eb 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -96,10 +96,17 @@ nibabel =
max-line-length = 100
ignore = D100,D101,D102,D103,D104,D105,D200,D201,D202,D204,D205,D208,D209,D210,D300,D301,D400,D401,D403,E24,E121,E123,E126,E226,E266,E402,E704,E731,F821,I100,I101,I201,N802,N803,N804,N806,W503,W504,W605
exclude =
+ venv
+ build
*test*
*sphinx*
nibabel/externals/*
*/__init__.py
+ # temporary -- should be removed in another PR
+ ./doc/source/conf.py
+ ./doc/tools/apigen.py
+ ./nisext
+ ./tools
[versioneer]
VCS = git
diff --git a/tools/ci/activate.sh b/tools/ci/activate.sh
index ebef3b650b..6dbde8294e 100644
--- a/tools/ci/activate.sh
+++ b/tools/ci/activate.sh
@@ -1,10 +1,10 @@
-if [ -e virtenv/bin/activate ]; then
- source virtenv/bin/activate
-elif [ -e virtenv/Scripts/activate ]; then
- source virtenv/Scripts/activate
+if [ -e venv/bin/activate ]; then
+ source venv/bin/activate
+elif [ -e venv/Scripts/activate ]; then
+ source venv/Scripts/activate
else
echo Cannot activate virtual environment
- ls -R virtenv
+ ls -R venv
false
fi
diff --git a/tools/ci/check.sh b/tools/ci/check.sh
index e497833521..f40052bc0c 100755
--- a/tools/ci/check.sh
+++ b/tools/ci/check.sh
@@ -14,8 +14,7 @@ set -x
export NIBABEL_DATA_DIR="$PWD/nibabel-data"
if [ "${CHECK_TYPE}" == "style" ]; then
- # Run styles only on core nibabel code.
- flake8 nibabel
+ flake8
elif [ "${CHECK_TYPE}" == "doc" ]; then
cd doc
make html && make doctest
diff --git a/tools/ci/create_venv.sh b/tools/ci/create_venv.sh
index 7a28767396..b3441af010 100755
--- a/tools/ci/create_venv.sh
+++ b/tools/ci/create_venv.sh
@@ -12,7 +12,7 @@ echo SETUP_REQUIRES = $SETUP_REQUIRES
set -x
python -m pip install --upgrade pip virtualenv
-virtualenv --python=python virtenv
+virtualenv --python=python venv
source tools/ci/activate.sh
python --version
python -m pip install -U $SETUP_REQUIRES
diff --git a/tox.ini b/tox.ini
deleted file mode 100644
index a0002e12b6..0000000000
--- a/tox.ini
+++ /dev/null
@@ -1,20 +0,0 @@
-[tox]
-# From-scratch tox-default-name virtualenvs
-envlist = py25,py26,py27,py32
-[testenv]
-deps =
- nose
- numpy
-commands=nosetests --with-doctest
-# MBs virtualenvs; numpy, nose already installed. Run these with:
-# tox -e python25,python26,python27,python32,np-1.2.1
-[testenv:python25]
-deps =
-[testenv:python26]
-deps =
-[testenv:python27]
-deps =
-[testenv:python32]
-deps =
-[testenv:np-1.2.1]
-deps =