Test case failure with test_visium_default not having any visible data points

[detrout]

• I have checked that this issue has not already been reported.
• I have confirmed this bug exists on the latest version of scanpy. (Well released version)
• (optional) I have confirmed this bug exists on the master branch of scanpy.

Hello, I was trying to build a Debian package for scanpy 1.8.2, and unsurprisingly ran into problems with the plot tests. Most of the problems were just slight plot layout differences, but the test_embedding_plots::test_visium_default test ends up generating a blank plot.

I can get something where the dots are visible by setting a color, but the color bar doesn't match the default.

I also tried add_outline=True which got me closer but is still not right, and still pretty hard to see.

I tried adjusting the marker size but didn't get very far. do you have any guesses what might be wrong?

Thanks

anndata 0.7.5+ds
scanpy 1.8.2
sinfo 0.3.1

PIL 8.3.2
anndata 0.7.5+ds
asciitree NA
beta_ufunc NA
binom_ufunc NA
cycler 0.10.0
cython_runtime NA
dateutil 2.8.1
fasteners NA
h5py 3.3.0
igraph 0.9.6
joblib 0.17.0
kiwisolver 1.3.2
leidenalg 0.8.8
llvmlite 0.35.0
matplotlib 3.3.4
monotonic NA
mpl_toolkits NA
natsort 7.1.0
nbinom_ufunc NA
numba 0.52.0
numcodecs 0.8.1+ds
numexpr 2.7.3
numpy 1.19.5
packaging 21.0
pandas 1.1.5
pkg_resources NA
pyexpat NA
pyparsing 2.4.7
pytoml NA
pytz 2021.3
scanpy 1.8.2
scipy 1.7.1
setuptools_scm NA
sinfo 0.3.1
sitecustomize NA
six 1.16.0
sklearn 0.23.2
tables 3.6.1
texttable 1.6.3
zarr 2.10.2+ds

Python 3.9.8 (main, Nov 7 2021, 15:47:09) [GCC 11.2.0]
Linux-5.14.0-2-amd64-x86_64-with-glibc2.32
4 logical CPU cores

Session information updated at 2021-11-10 22:03

[ivirshup]

How are you building the package and running the tests? Are you working with a clone of the repo?

[detrout]

I downloaded the github source archive at the 1.8.2 tag. The build process applies a few patches viewable here.

One is a small change to some R code, and the other is I marked several more tests as needs internet because the Debian builds in an environment without network access and those ultimately tried to download something. (And it's really unclear if we can legally redistributed the 10x pbmc3k dataset.)

The Debian build file is (here)[https://salsa.debian.org/med-team/python-scanpy/-/blob/master/debian/rules] though mostly it lets you see what tests I was skipping because of missing dependencies.

Also if I set a color like in_tissue, or array_row the data shows up.

I can paste the full build log if you'd like but this is the dependencies installed and the environment variables.

Build-Origin: Debian
Build-Architecture: amd64
Build-Date: Sun, 14 Nov 2021 20:11:26 +0000
Build-Path: /<<PKGBUILDDIR>>
Installed-Build-Depends:
 adduser (= 3.118),
 adwaita-icon-theme (= 41.0-1),
 autoconf (= 2.71-2),
 automake (= 1:1.16.5-1),
 autopoint (= 0.21-4),
 autotools-dev (= 20180224.1+nmu1),
 base-files (= 12),
 base-passwd (= 3.5.52),
 bash (= 5.1-3.1),
 binutils (= 2.37-8),
 binutils-common (= 2.37-8),
 binutils-x86-64-linux-gnu (= 2.37-8),
 blt (= 2.5.3+dfsg-4.1),
 bsdextrautils (= 2.37.2-4),
 bsdutils (= 1:2.37.2-4),
 build-essential (= 12.9),
 bzip2 (= 1.0.8-4),
 ca-certificates (= 20211016),
 coreutils (= 8.32-4.1),
 cpp (= 4:11.2.0-2),
 cpp-11 (= 11.2.0-10),
 dash (= 0.5.11+git20210903+057cd650a4ed-3),
 dbus (= 1.12.20-3),
 dbus-bin (= 1.12.20-3),
 dbus-daemon (= 1.12.20-3),
 dbus-session-bus-common (= 1.12.20-3),
 dbus-system-bus-common (= 1.12.20-3),
 dbus-user-session (= 1.12.20-3),
 dconf-gsettings-backend (= 0.40.0-2),
 dconf-service (= 0.40.0-2),
 debconf (= 1.5.79),
 debhelper (= 13.5.2),
 debianutils (= 5.5-1),
 dh-autoreconf (= 20),
 dh-python (= 5.20211105),
 dh-strip-nondeterminism (= 1.12.0-2),
 diffutils (= 1:3.7-5),
 dmsetup (= 2:1.02.175-2.1),
 docutils-common (= 0.17.1+dfsg-2),
 dpkg (= 1.20.9),
 dpkg-dev (= 1.20.9),
 dwz (= 0.14-1),
 file (= 1:5.39-3),
 findutils (= 4.8.0-1),
 flit (= 3.0.0-1),
 fontconfig (= 2.13.1-4.2),
 fontconfig-config (= 2.13.1-4.2),
 fonts-font-awesome (= 5.0.10+really4.7.0~dfsg-4.1),
 fonts-lato (= 2.0-2.1),
 fonts-lyx (= 2.3.6-1),
 g++ (= 4:11.2.0-2),
 g++-11 (= 11.2.0-10),
 gcc (= 4:11.2.0-2),
 gcc-11 (= 11.2.0-10),
 gcc-11-base (= 11.2.0-10),
 gettext (= 0.21-4),
 gettext-base (= 0.21-4),
 gir1.2-atk-1.0 (= 2.36.0-2),
 gir1.2-freedesktop (= 1.70.0-2),
 gir1.2-gdkpixbuf-2.0 (= 2.42.6+dfsg-2),
 gir1.2-glib-2.0 (= 1.70.0-2),
 gir1.2-gtk-3.0 (= 3.24.30-3),
 gir1.2-harfbuzz-0.0 (= 2.7.4-1),
 gir1.2-pango-1.0 (= 1.48.10+ds1-1),
 grep (= 3.7-1),
 groff-base (= 1.22.4-7),
 gtk-update-icon-cache (= 3.24.30-3),
 gzip (= 1.10-4),
 hicolor-icon-theme (= 0.17-2),
 hostname (= 3.23),
 imagemagick (= 8:6.9.11.60+dfsg-1.3),
 imagemagick-6-common (= 8:6.9.11.60+dfsg-1.3),
 imagemagick-6.q16 (= 8:6.9.11.60+dfsg-1.3),
 init-system-helpers (= 1.60),
 intltool-debian (= 0.35.0+20060710.5),
 libacl1 (= 2.3.1-1),
 libaec0 (= 1.0.6-1),
 libamd2 (= 1:5.10.1+dfsg-2),
 libaom3 (= 3.2.0-1),
 libapparmor1 (= 3.0.3-5),
 libarchive-zip-perl (= 1.68-1),
 libargon2-1 (= 0~20171227-0.2),
 libarpack2 (= 3.8.0-1),
 libasan6 (= 11.2.0-10),
 libatk-bridge2.0-0 (= 2.38.0-2),
 libatk1.0-0 (= 2.36.0-2),
 libatk1.0-data (= 2.36.0-2),
 libatlas3-base (= 3.10.3-11),
 libatomic1 (= 11.2.0-10),
 libatspi2.0-0 (= 2.42.0-2),
 libattr1 (= 1:2.5.1-1),
 libaudit-common (= 1:3.0.6-1),
 libaudit1 (= 1:3.0.6-1),
 libavahi-client3 (= 0.8-5),
 libavahi-common-data (= 0.8-5),
 libavahi-common3 (= 0.8-5),
 libbinutils (= 2.37-8),
 libblas3 (= 3.10.0-1),
 libblkid1 (= 2.37.2-4),
 libblosc1 (= 1.21.1+ds1-1),
 libbrotli1 (= 1.0.9-2+b2),
 libbsd0 (= 0.11.3-1),
 libbz2-1.0 (= 1.0.8-4),
 libc-bin (= 2.32-4),
 libc-dev-bin (= 2.32-4),
 libc6 (= 2.32-4),
 libc6-dev (= 2.32-4),
 libcairo-gobject2 (= 1.16.0-5),
 libcairo2 (= 1.16.0-5),
 libcap-ng0 (= 0.7.9-2.2+b1),
 libcap2 (= 1:2.44-1),
 libcc1-0 (= 11.2.0-10),
 libcolamd2 (= 1:5.10.1+dfsg-2),
 libcolord2 (= 1.4.5-3),
 libcom-err2 (= 1.46.4-1),
 libcrypt-dev (= 1:4.4.26-1),
 libcrypt1 (= 1:4.4.26-1),
 libcryptsetup12 (= 2:2.4.1-1),
 libctf-nobfd0 (= 2.37-8),
 libctf0 (= 2.37-8),
 libcups2 (= 2.3.3op2-7),
 libcurl4 (= 7.79.1-2),
 libcxsparse3 (= 1:5.10.1+dfsg-2),
 libdatrie1 (= 0.2.13-2),
 libdav1d5 (= 0.9.2-1+b1),
 libdb5.3 (= 5.3.28+dfsg1-0.8),
 libdbus-1-3 (= 1.12.20-3),
 libdconf1 (= 0.40.0-2),
 libde265-0 (= 1.0.8-1),
 libdebconfclient0 (= 0.261),
 libdebhelper-perl (= 13.5.2),
 libdeflate0 (= 1.8-1),
 libdevmapper1.02.1 (= 2:1.02.175-2.1),
 libdpkg-perl (= 1.20.9),
 libedit2 (= 3.1-20210910-1),
 libelf1 (= 0.185-2),
 libepoxy0 (= 1.5.9-2),
 libexpat1 (= 2.4.1-3),
 libffi8 (= 3.4.2-3),
 libfftw3-double3 (= 3.3.8-2),
 libfile-stripnondeterminism-perl (= 1.12.0-2),
 libfontconfig1 (= 2.13.1-4.2),
 libfreetype6 (= 2.11.0+dfsg-1),
 libfribidi0 (= 1.0.8-2),
 libgcc-11-dev (= 11.2.0-10),
 libgcc-s1 (= 11.2.0-10),
 libgcrypt20 (= 1.9.4-3+b1),
 libgdbm-compat4 (= 1.22-1),
 libgdbm6 (= 1.22-1),
 libgdk-pixbuf-2.0-0 (= 2.42.6+dfsg-2),
 libgdk-pixbuf2.0-common (= 2.42.6+dfsg-2),
 libgfortran5 (= 11.2.0-10),
 libgirepository-1.0-1 (= 1.70.0-2),
 libglib2.0-0 (= 2.70.1-1),
 libglpk40 (= 5.0-1),
 libgmp10 (= 2:6.2.1+dfsg-2),
 libgnutls30 (= 3.7.2-2),
 libgomp1 (= 11.2.0-10),
 libgpg-error0 (= 1.42-3),
 libgraphite2-3 (= 1.3.14-1),
 libgssapi-krb5-2 (= 1.18.3-7),
 libgtk-3-0 (= 3.24.30-3),
 libgtk-3-common (= 3.24.30-3),
 libharfbuzz0b (= 2.7.4-1),
 libhdf5-103-1 (= 1.10.7+repack-4),
 libhdf5-hl-100 (= 1.10.7+repack-4),
 libheif1 (= 1.12.0-2+b3),
 libhogweed6 (= 3.7.3-1),
 libicu67 (= 67.1-7),
 libidn2-0 (= 2.3.2-2),
 libigraph1 (= 0.8.5+ds1-1),
 libimagequant0 (= 2.12.2-1.1),
 libip4tc2 (= 1.8.7-1),
 libisl23 (= 0.24-2),
 libitm1 (= 11.2.0-10),
 libjbig0 (= 2.1-3.1+b2),
 libjpeg62-turbo (= 1:2.1.1-1),
 libjs-jquery (= 3.5.1+dfsg+~3.5.5-8),
 libjs-jquery-hotkeys (= 0~20130707+git2d51e3a9+dfsg-2.1),
 libjs-jquery-isonscreen (= 1.2.0-1.1),
 libjs-jquery-metadata (= 12-3),
 libjs-jquery-tablesorter (= 1:2.31.3+dfsg1-2),
 libjs-jquery-throttle-debounce (= 1.1+dfsg.1-1.1),
 libjs-jquery-ui (= 1.13.0+dfsg-1),
 libjs-sphinxdoc (= 4.2.0-5),
 libjs-underscore (= 1.9.1~dfsg-4),
 libjson-c5 (= 0.15-2),
 libk5crypto3 (= 1.18.3-7),
 libkeyutils1 (= 1.6.1-2),
 libkmod2 (= 29-1),
 libkrb5-3 (= 1.18.3-7),
 libkrb5support0 (= 1.18.3-7),
 liblapack3 (= 3.10.0-1),
 liblbfgsb0 (= 3.0+dfsg.3-9),
 liblcms2-2 (= 2.12~rc1-2),
 libldap-2.4-2 (= 2.4.59+dfsg-1),
 libllvm11 (= 1:11.1.0-4),
 liblqr-1-0 (= 0.4.2-2.1),
 liblsan0 (= 11.2.0-10),
 libltdl7 (= 2.4.6-15),
 liblz4-1 (= 1.9.3-2),
 liblzf1 (= 3.6-3),
 liblzma5 (= 5.2.5-2),
 liblzo2-2 (= 2.10-2),
 libmagic-mgc (= 1:5.39-3),
 libmagic1 (= 1:5.39-3),
 libmagickcore-6.q16-6 (= 8:6.9.11.60+dfsg-1.3),
 libmagickwand-6.q16-6 (= 8:6.9.11.60+dfsg-1.3),
 libmd0 (= 1.0.4-1),
 libmount1 (= 2.37.2-4),
 libmpc3 (= 1.2.1-1),
 libmpdec3 (= 2.5.1-2),
 libmpfr6 (= 4.1.0-3),
 libncurses6 (= 6.2+20210905-1),
 libncursesw6 (= 6.2+20210905-1),
 libnettle8 (= 3.7.3-1),
 libnghttp2-14 (= 1.43.0-1),
 libnsl-dev (= 1.3.0-2),
 libnsl2 (= 1.3.0-2),
 libnuma1 (= 2.0.14-3),
 libopenjp2-7 (= 2.4.0-3),
 libp11-kit0 (= 0.24.0-5),
 libpam-modules (= 1.4.0-10),
 libpam-modules-bin (= 1.4.0-10),
 libpam-runtime (= 1.4.0-10),
 libpam-systemd (= 249.6-2),
 libpam0g (= 1.4.0-10),
 libpango-1.0-0 (= 1.48.10+ds1-1),
 libpangocairo-1.0-0 (= 1.48.10+ds1-1),
 libpangoft2-1.0-0 (= 1.48.10+ds1-1),
 libpangoxft-1.0-0 (= 1.48.10+ds1-1),
 libpcre2-8-0 (= 10.39-2),
 libpcre3 (= 2:8.39-13),
 libperl5.32 (= 5.32.1-6),
 libpfm4 (= 4.11.1+git32-gd0b85fb-1),
 libpipeline1 (= 1.5.4-1),
 libpixman-1-0 (= 0.40.0-1),
 libpng16-16 (= 1.6.37-3),
 libprocps8 (= 2:3.3.17-5),
 libpsl5 (= 0.21.0-1.2),
 libpython3-stdlib (= 3.9.7-1),
 libpython3.9-minimal (= 3.9.8-2),
 libpython3.9-stdlib (= 3.9.8-2),
 libquadmath0 (= 11.2.0-10),
 libraqm0 (= 0.7.0-4),
 libreadline8 (= 8.1-2),
 librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b2),
 libsasl2-2 (= 2.1.27+dfsg-2.3),
 libsasl2-modules-db (= 2.1.27+dfsg-2.3),
 libseccomp2 (= 2.5.2-2),
 libselinux1 (= 3.3-1),
 libsemanage-common (= 3.3-1),
 libsemanage2 (= 3.3-1),
 libsepol2 (= 3.3-1),
 libsigsegv2 (= 2.13-1),
 libsmartcols1 (= 2.37.2-4),
 libsnappy1v5 (= 1.1.8-1),
 libsqlite3-0 (= 3.36.0-2),
 libssh2-1 (= 1.10.0-2),
 libssl1.1 (= 1.1.1l-1),
 libstdc++-11-dev (= 11.2.0-10),
 libstdc++6 (= 11.2.0-10),
 libsub-override-perl (= 0.09-2),
 libsuitesparseconfig5 (= 1:5.10.1+dfsg-2),
 libsystemd0 (= 249.6-2),
 libsz2 (= 1.0.6-1),
 libtasn1-6 (= 4.18.0-3),
 libtbb2 (= 2020.3-1),
 libtcl8.6 (= 8.6.12+dfsg-1),
 libthai-data (= 0.1.28-4.1),
 libthai0 (= 0.1.28-4.1),
 libtiff5 (= 4.3.0-2),
 libtinfo6 (= 6.2+20210905-1),
 libtirpc-common (= 1.3.2-2),
 libtirpc-dev (= 1.3.2-2),
 libtirpc3 (= 1.3.2-2),
 libtk8.6 (= 8.6.12-1),
 libtool (= 2.4.6-15),
 libtsan0 (= 11.2.0-10),
 libubsan1 (= 11.2.0-10),
 libuchardet0 (= 0.0.7-1),
 libudev1 (= 249.6-2),
 libunistring2 (= 0.9.10-6),
 libuuid1 (= 2.37.2-4),
 libwayland-client0 (= 1.19.0-2+b1),
 libwayland-cursor0 (= 1.19.0-2+b1),
 libwayland-egl1 (= 1.19.0-2+b1),
 libwebp6 (= 0.6.1-2.1),
 libwebpdemux2 (= 0.6.1-2.1),
 libwebpmux3 (= 0.6.1-2.1),
 libx11-6 (= 2:1.7.2-2+b1),
 libx11-data (= 2:1.7.2-2),
 libx265-199 (= 3.5-2),
 libxau6 (= 1:1.0.9-1),
 libxcb-render0 (= 1.14-3),
 libxcb-shm0 (= 1.14-3),
 libxcb1 (= 1.14-3),
 libxcomposite1 (= 1:0.4.5-1),
 libxcursor1 (= 1:1.2.0-2),
 libxdamage1 (= 1:1.1.5-2),
 libxdmcp6 (= 1:1.1.2-3),
 libxext6 (= 2:1.3.4-1),
 libxfixes3 (= 1:5.0.3-2),
 libxft2 (= 2.3.2-2),
 libxi6 (= 2:1.8-1),
 libxinerama1 (= 2:1.1.4-2),
 libxkbcommon0 (= 1.3.1-1),
 libxml2 (= 2.9.12+dfsg-5),
 libxrandr2 (= 2:1.5.2-1),
 libxrender1 (= 1:0.9.10-1),
 libxss1 (= 1:1.2.3-1),
 libz3-4 (= 4.8.12-1+b1),
 libzstd1 (= 1.4.8+dfsg-3),
 linux-libc-dev (= 5.14.16-1),
 llvm-11 (= 1:11.1.0-4),
 llvm-11-linker-tools (= 1:11.1.0-4),
 llvm-11-runtime (= 1:11.1.0-4),
 login (= 1:4.8.1-2),
 lsb-base (= 11.1.0),
 m4 (= 1.4.18-5),
 mailcap (= 3.70),
 make (= 4.3-4.1),
 man-db (= 2.9.4-2),
 mawk (= 1.3.4.20200120-2),
 media-types (= 4.0.0),
 mime-support (= 3.66),
 mount (= 2.37.2-4),
 ncurses-base (= 6.2+20210905-1),
 ncurses-bin (= 6.2+20210905-1),
 openssl (= 1.1.1l-1),
 passwd (= 1:4.8.1-2),
 patch (= 2.7.6-7),
 perl (= 5.32.1-6),
 perl-base (= 5.32.1-6),
 perl-modules-5.32 (= 5.32.1-6),
 po-debconf (= 1.0.21+nmu1),
 procps (= 2:3.3.17-5),
 python-matplotlib-data (= 3.3.4-2),
 python-tables-data (= 3.6.1-5),
 python3 (= 3.9.7-1),
 python3-all (= 3.9.7-1),
 python3-anndata (= 0.7.5+ds-3),
 python3-asciitree (= 0.3.3-3),
 python3-attr (= 20.3.0-1),
 python3-certifi (= 2020.6.20-1),
 python3-cffi-backend (= 1.15.0-1),
 python3-chardet (= 4.0.0-1),
 python3-cov-core (= 1.15.0-3),
 python3-coverage (= 5.1+dfsg.1-2+b2),
 python3-cryptography (= 3.3.2-1),
 python3-cycler (= 0.11.0-1),
 python3-dateutil (= 2.8.1-6),
 python3-decorator (= 4.4.2-2),
 python3-distutils (= 3.9.8-1),
 python3-docutils (= 0.17.1+dfsg-2),
 python3-fasteners (= 0.14.1-2),
 python3-gi (= 3.42.0-1+b1),
 python3-h5py (= 3.3.0-5),
 python3-h5py-serial (= 3.3.0-5),
 python3-harmony (= 0.7.1-1),
 python3-idna (= 2.10-1),
 python3-igraph (= 0.9.6-1),
 python3-importlib-metadata (= 4.6.4-1),
 python3-iniconfig (= 1.1.1-1),
 python3-jeepney (= 0.6.0-1),
 python3-joblib (= 0.17.0-4),
 python3-keyring (= 23.2.0-1),
 python3-kiwisolver (= 1.3.2-1),
 python3-leidenalg (= 0.8.8-1),
 python3-lib2to3 (= 3.9.8-1),
 python3-librecaptcha (= 0.7.3-1),
 python3-llvmlite (= 0.37.0-1),
 python3-louvain (= 0.0+20181013git3fc1f575-2),
 python3-matplotlib (= 3.3.4-2),
 python3-minimal (= 3.9.7-1),
 python3-monotonic (= 1.6-2),
 python3-more-itertools (= 8.10.0-2),
 python3-natsort (= 7.1.0-1),
 python3-networkx (= 2.5+ds-2),
 python3-nose2 (= 0.9.2-1),
 python3-numba (= 0.52.0-5),
 python3-numcodecs (= 0.8.1+ds-3),
 python3-numexpr (= 2.7.3-2),
 python3-numpy (= 1:1.19.5-1),
 python3-packaging (= 21.0-1),
 python3-pandas (= 1.1.5+dfsg-2),
 python3-pandas-lib (= 1.1.5+dfsg-2),
 python3-patsy (= 0.5.2-2),
 python3-pil (= 8.3.2-1),
 python3-pkg-resources (= 58.2.0-1),
 python3-pluggy (= 0.13.0-7.1),
 python3-ply (= 3.11-5),
 python3-py (= 1.10.0-1),
 python3-pygments (= 2.7.1+dfsg-2.1),
 python3-pyparsing (= 2.4.7-1),
 python3-pytest (= 6.2.5-1),
 python3-pytest-cov (= 3.0.0-1),
 python3-pytoml (= 0.1.21-1),
 python3-requests (= 2.25.1+dfsg-2),
 python3-roman (= 3.3-1),
 python3-scipy (= 1.7.1-2),
 python3-seaborn (= 0.11.2-2),
 python3-secretstorage (= 3.3.1-1),
 python3-setuptools (= 58.2.0-1),
 python3-setuptools-scm (= 6.0.1-1),
 python3-sinfo (= 0.3.1-2),
 python3-six (= 1.16.0-2),
 python3-sklearn (= 0.23.2-5),
 python3-sklearn-lib (= 0.23.2-5),
 python3-skmisc (= 0.1.4+dfsg-1),
 python3-slimit (= 0.8.1-4),
 python3-statsmodels (= 0.12.2-2),
 python3-statsmodels-lib (= 0.12.2-2),
 python3-stdlib-list (= 0.8.0-4),
 python3-tables (= 3.6.1-5),
 python3-tables-lib (= 3.6.1-5),
 python3-texttable (= 1.6.3-2),
 python3-threadpoolctl (= 2.1.0-1),
 python3-tk (= 3.9.8-1),
 python3-toml (= 0.10.2-1),
 python3-tqdm (= 4.57.0-2),
 python3-tz (= 2021.3-1),
 python3-urllib3 (= 1.26.5-1~exp1),
 python3-wheel (= 0.34.2-1),
 python3-zarr (= 2.10.2+ds-2),
 python3-zipp (= 1.0.0-3),
 python3.9 (= 3.9.8-2),
 python3.9-minimal (= 3.9.8-2),
 readline-common (= 8.1-2),
 rpcsvc-proto (= 1.4.2-4),
 sed (= 4.8-1),
 sensible-utils (= 0.0.17),
 sgml-base (= 1.30),
 shared-mime-info (= 2.0-1),
 sphinx-rtd-theme-common (= 1.0.0+dfsg-1),
 systemd (= 249.6-2),
 systemd-sysv (= 249.6-2),
 sysvinit-utils (= 3.00-1),
 tar (= 1.34+dfsg-1),
 tk8.6-blt2.5 (= 2.5.3+dfsg-4.1),
 ttf-bitstream-vera (= 1.10-8.1),
 tzdata (= 2021e-1),
 ucf (= 3.0043),
 umap-learn (= 0.4.5+dfsg-2),
 util-linux (= 2.37.2-4),
 x11-common (= 1:7.7+23),
 xkb-data (= 2.33-1),
 xml-core (= 0.18+nmu1),
 xz-utils (= 5.2.5-2),
 zlib1g (= 1:1.2.11.dfsg-2)
Environment:
 DEB_BUILD_OPTIONS="parallel=4"
 LANG="en_US.UTF-8"
 LC_ALL="C.UTF-8"
 LC_COLLATE="C.UTF-8"
 LC_CTYPE="en_US.UTF-8"
 LC_MESSAGES="en_US.UTF-8"
 LD_LIBRARY_PATH="/usr/lib/libeatmydata"
 SOURCE_DATE_EPOCH="1625592742"

[detrout]

I can get the data by skipping the spatial plot.

If I run this in a fresh IPython session I get the attached plot.

import scanpy
from matplotlib import pyplot
from scanpy.tests.test_embedding_plots import HERE
from scanpy.plotting._tools import scatterplots
adata = scanpy.read_visium(HERE / "_data" / "visium_data" / "1.0.0")
adata.obs = adata.obs.astype({'array_row': 'str'})
data_points, components = scatterplots._get_data_points(adata, "spatial", None, None, None)
pyplot.scatter(data_points[0][:, 0], data_points[0][:, 1])
pyplot.savefig("visium.png")

If I call scanpy.pl.spatial before I call pyplot.scatter I get the black plot, so it's probably some default isn't right.