Don't use matplotlib in a GUI-dependent fashion

[TheChymera]

On my headless data analysis servers, on which I do not need and have disabled GUI support, I get this error from nipype. It seems matplotlib's default behaviour here is to use tkinter (a GUI package) for plotting.

Since from what I can tell we only use plt.show in tools/make_examples.py I suggest prepending all other matplotlib.pyplot imports with:

import matplotlib
matplotlib.use('Cairo')

As shown here. I can implement this easily enough myself.

This will indeed add cairo as a dependency, but we already depend on pygraphviz, which already depends on graphviz, which already depends on cairo. Also, we will no longer depend on tkinter support for the python core package.

What do you guys think?

[satra]

matplotlib.use('agg') should be imported before anything in the nipype library and when used through plugins. and since matplotlib is not a dependency of nipype as a whole, interfaces which need it import it specifically.

perhaps the error that you are seeing is outside of the typical use case and should be handled separately.

do you get the same error if you try one of the interfaces that uses matplotlib.

[TheChymera]

ah, I believe this is a nipy issue.

[bartoli]

I will comment here to avoid opening something potentially useless. I'd rather not have to add matplotlib.use('agg') at some place matplotlib can be imported.

I had no issue with mpl 1.5.1, but i now do in 1.5.3. I am actually building matplotlib myself so i figured i would disable tkagg backend at build time.
So i modified setup.cfg from

#agg=auto
#tkagg=auto
#backend=Agg

to

agg=True
tkagg=False
backend=Agg

And yet, setup.py is still saying
tkagg: yes [installing; run-time loading from Python Tcl / Tk]
and trying to load it (and failing)

Is there no way anymore to use 'just agg' without having to specify anything in each script?

[TheChymera]

Maybe something is wrong with your matplotlib build?

I also build it myself (seeing as I am using Gentoo, I build all packages), and I have successfully and very easily deactivted the tk backend, as seen here (eix reports with what features the package was built):

chymera@zenbookhost ~ $ eix -e matplotlib
[I] dev-python/matplotlib
     Available versions:  1.4.3 (~)1.5.0 (~)1.5.1 (~)1.5.3 **9999 {cairo doc examples excel fltk gtk gtk2 gtk3 latex pyside qt4 qt5 test tk wxwidgets PYTHON_TARGETS="python2_7 python3_4 python3_5"}
     Installed versions:  1.5.3(02:29:53 30.10.2016)(cairo gtk3 latex wxwidgets -doc -examples -excel -fltk -gtk2 -pyside -qt4 -qt5 -test -tk PYTHON_TARGETS="python2_7 python3_4 -python3_5")
     Homepage:            http://matplotlib.org/
     Description:         Pure python plotting library with matlab like syntax

chymera@zenbookhost ~ $ ipython
Python 2.7.12 (default, Oct  1 2016, 05:21:18) 
Type "copyright", "credits" or "license" for more information.

IPython 5.1.0 -- An enhanced Interactive Python.
?         -> Introduction and overview of IPython's features.
%quickref -> Quick reference.
help      -> Python's own help system.
object?   -> Details about 'object', use 'object??' for extra details.

In [1]: import matplotlib

In [2]: matplotlib.get_backend()
Out[2]: u'GTK3Agg'

There's even a live pakage for matplotlib in Gentoo, so if you want to build matplotlib yourself and work in a highly customized environment and/or on the cutting edge, I would really recommend Gentoo. However, it seems the Gentoo package (below) is doing exactly what you described you were doing manually (the relevant section is under python_configure()), so maybe something else on your system is out of place and interfering?

# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$

EAPI=6

PYTHON_COMPAT=( python2_7 python3_{4,5} )
PYTHON_REQ_USE='tk?,threads(+)'

inherit distutils-r1 eutils flag-o-matic multiprocessing virtualx toolchain-funcs

DESCRIPTION="Pure python plotting library with matlab like syntax"
HOMEPAGE="http://matplotlib.org/"
SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"

SLOT="0"
# Main license: matplotlib
# Some modules: BSD
# matplotlib/backends/qt4_editor: MIT
# Fonts: BitstreamVera, OFL-1.1
LICENSE="BitstreamVera BSD matplotlib MIT OFL-1.1"
KEYWORDS="~amd64 ~arm ~ppc ~ppc64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~x64-macos ~x86-macos"
IUSE="cairo doc excel examples fltk gtk2 gtk3 latex pyside qt4 qt5 test tk wxwidgets"

PY2_FLAGS="|| ( $(python_gen_useflags python2_7) )"
REQUIRED_USE="
	doc? ( ${PY2_FLAGS} )
	excel? ( ${PY2_FLAGS} )
	fltk? ( ${PY2_FLAGS} )
	gtk2? ( ${PY2_FLAGS} )
	wxwidgets? ( ${PY2_FLAGS} )
	test? (
		cairo fltk latex pyside qt5 qt4 tk wxwidgets
		|| ( gtk2 gtk3 )
		)"

# #456704 -- a lot of py2-only deps
PY2_USEDEP=$(python_gen_usedep python2_7)
COMMON_DEPEND="
	dev-python/cycler[${PYTHON_USEDEP}]
	>=dev-python/numpy-1.6[${PYTHON_USEDEP}]
	dev-python/python-dateutil:0[${PYTHON_USEDEP}]
	dev-python/pytz[${PYTHON_USEDEP}]
	>=dev-python/six-1.4[${PYTHON_USEDEP}]
	media-fonts/stix-fonts
	media-libs/freetype:2
	media-libs/libpng:0
	media-libs/qhull
	cairo? (
		|| (
			dev-python/pycairo[${PYTHON_USEDEP}]
			dev-python/cairocffi[${PYTHON_USEDEP}]
			)
		)
	gtk2? (
		dev-libs/glib:2=
		x11-libs/gdk-pixbuf
		x11-libs/gtk+:2
		dev-python/pygtk[${PY2_USEDEP}] )
	wxwidgets? ( >=dev-python/wxpython-2.8:*[${PY2_USEDEP}] )"

# internal copy of pycxx highly patched
#	dev-python/pycxx

DEPEND="${COMMON_DEPEND}
	dev-python/versioneer[${PYTHON_USEDEP}]
	dev-python/setuptools[${PYTHON_USEDEP}]
	virtual/pkgconfig
	doc? (
		app-text/dvipng
		dev-python/pillow[${PYTHON_USEDEP}]
		dev-python/ipython[${PYTHON_USEDEP}]
		dev-python/mock[${PY2_USEDEP}]
		dev-python/numpydoc[${PYTHON_USEDEP}]
		dev-python/sphinx[${PYTHON_USEDEP}]
		dev-python/xlwt[${PYTHON_USEDEP}]
		dev-texlive/texlive-latexextra
		dev-texlive/texlive-fontsrecommended
		dev-texlive/texlive-latexrecommended
		media-gfx/graphviz[cairo]
	)
	test? (
		dev-python/mock[${PYTHON_USEDEP}]
		>=dev-python/nose-0.11.1[${PYTHON_USEDEP}]
		)"

RDEPEND="${COMMON_DEPEND}
	>=dev-python/pyparsing-1.5.6[${PYTHON_USEDEP}]
	excel? ( dev-python/xlwt[${PYTHON_USEDEP}] )
	fltk? ( dev-python/pyfltk[${PYTHON_USEDEP}] )
	gtk3? (
		dev-python/pygobject:3[${PYTHON_USEDEP}]
		x11-libs/gtk+:3[introspection] )
	latex? (
		virtual/latex-base
		app-text/ghostscript-gpl
		app-text/dvipng
		app-text/poppler[utils]
		dev-texlive/texlive-fontsrecommended
		dev-texlive/texlive-latexextra
		dev-texlive/texlive-xetex
	)
	pyside? ( dev-python/pyside[X,${PYTHON_USEDEP}] )
	qt4? ( dev-python/PyQt4[X,${PYTHON_USEDEP}] )
	qt5? ( dev-python/PyQt5[gui,widgets,${PYTHON_USEDEP}] )
	"

# A few C++ source files are written to srcdir.
# Other than that, the ebuild shall be fit for out-of-source build.
DISTUTILS_IN_SOURCE_BUILD=1

PATCHES=( "${FILESDIR}/${PN}-1.5.3-freetype-spurious-failure.patch" )

pkg_setup() {
	unset DISPLAY # bug #278524
	use doc && DISTUTILS_ALL_SUBPHASE_IMPLS=( python2.7 )
}

use_setup() {
	local uword="${2:-${1}}"
	if use ${1}; then
		echo "${uword} = True"
		echo "${uword}agg = True"
	else
		echo "${uword} = False"
		echo "${uword}agg = False"
	fi
}

python_prepare_all() {
# Generates test failures, but fedora does it
#	local PATCHES=(
#		"${FILESDIR}"/${P}-unbundle-pycxx.patch
#		"${FILESDIR}"/${P}-unbundle-agg.patch
#	)
#	rm -r agg24 CXX || die
#	rm -r agg24 || die

#	cat > lib/${PN}/externals/six.py <<-EOF
#	from __future__ import absolute_import
#	from six import *
#	EOF

	sed \
		-e 's/matplotlib.pyparsing_py[23]/pyparsing/g' \
		-i lib/matplotlib/{mathtext,fontconfig_pattern}.py \
		|| die "sed pyparsing failed"

	# suggested by upstream
#	sed \
#		-e '/tol/s:32:35:g' \
#		-i lib/matplotlib/tests/test_mathtext.py || die

	sed \
		-e "s:/usr/:${EPREFIX}/usr/:g" \
		-i setupext.py || die

	export XDG_RUNTIME_DIR="${T}/runtime-dir"
	mkdir "${XDG_RUNTIME_DIR}" || die
	chmod 0700 "${XDG_RUNTIME_DIR}" || die

	distutils-r1_python_prepare_all
}

python_configure_all() {
	append-flags -fno-strict-aliasing
	append-cppflags -DNDEBUG  # or get old trying to do triangulation
	tc-export PKG_CONFIG
}

python_configure() {
	mkdir -p "${BUILD_DIR}" || die

	# create setup.cfg (see setup.cfg.template for any changes).

	# common switches.
	cat > "${BUILD_DIR}"/setup.cfg <<- EOF || die
		[directories]
		basedirlist = "${EPREFIX}/usr"
		[provide_packages]
		pytz = False
		dateutil = False
		[gui_support]
		agg = True
		$(use_setup cairo)
		$(use_setup pyside)
		$(use_setup qt4)
		$(use_setup qt5)
		$(use_setup tk)
	EOF

	if use gtk3 && use cairo; then
		echo "gtk3cairo = True" >> "${BUILD_DIR}"/setup.cfg || die
	else
		echo "gtk3cairo = False" >> "${BUILD_DIR}"/setup.cfg || die
	fi

	if $(python_is_python3); then
		cat >> "${BUILD_DIR}"/setup.cfg <<- EOF || die
			six = True
			fltk = False
			fltkagg = False
			gtk = False
			gtkagg = False
			wx = False
			wxagg = False
		EOF
	else
		cat >> "${BUILD_DIR}"/setup.cfg <<-EOF || die
			six = False
			$(use_setup fltk)
			$(use_setup gtk2 gtk)
			$(use_setup gtk3)
			$(use_setup wxwidgets wx)
		EOF
	fi
}

wrap_setup() {
	local MPLSETUPCFG=${BUILD_DIR}/setup.cfg
	export MPLSETUPCFG
	unset DISPLAY

	# Note: remove build... if switching to out-of-source build
	"${@}" build --build-lib="${BUILD_DIR}"/build/lib
}

python_compile() {
	wrap_setup distutils-r1_python_compile
}

python_compile_all() {
	if use doc; then
		cd doc || die

		# necessary for in-source build
		local -x PYTHONPATH="${BUILD_DIR}"/build/lib:${PYTHONPATH}

		VARTEXFONTS="${T}"/fonts \
		"${EPYTHON}" ./make.py --small html || die
	fi
}

python_test() {
	wrap_setup distutils_install_for_testing

#	virtx ${EPYTHON} tests.py \
#		--no-pep8 \
#		--no-network \
#		--verbose \
#		--processes=$(makeopts_jobs)

	virtx "${EPYTHON}" -c "import sys, matplotlib as m; sys.exit(0 if m.test(verbosity=2) else 1)"
}

python_install() {
	wrap_setup distutils-r1_python_install
}

python_install_all() {
	use doc && local HTML_DOCS=( doc/build/html/. )

	distutils-r1_python_install_all

	if use examples; then
		dodoc -r examples
		docompress -x /usr/share/doc/${PF}/examples
	fi
}