UPDATE
I finally figured out where this is coming from, and it's because of the Anaconda environment.
git-gui and gitk use Tcl/Tk and tkinter as a GUI library, and as mentionned in this answer:
tkinter works linking to a Tk/Tcl interpreter that, loosely
speaking, is contained in a couple of DLL, in particular the graphical
library is libtk6.0.so.
Most of the extra fonts not seen by tkinter are managed by the
Freetype library and Anaconda's libtk6.0.so is not built against
Freetype...
I have made the test, and I can conclude that it is very well coming from this :
$ conda deactivate
$ gitk # fonts are okay
$ conda activate base
$ (base) gitk # fonts are weird
$ (base) conda deactivate
$ gitk # fonts are okay again
One workaround is the one mentionned here:
I resolved this issue by removing wish files in ANACONDA_PATH/bin and
related virtual environments
Except that I renamed the files instead of removing them, e.g. wish -> wish-i-renamed-it.
Sources :
Make Anaconda's tkinter aware of system fonts or install new fonts for Anaconda
https://github.com/ContinuumIO/anaconda-issues/issues/6833
This old answer doesn't apply anymore
I just restarted my computer this morning, and the fonts are back !
They are all here !
I really don't know why though...
Here is my update log :
$ less /var/log/apt/history.log
Start-Date: 2018-06-05 09:36:17
Commandline: aptdaemon role='role-commit-packages' sender=':1.127'
Upgrade: liblouis9:amd64 (2.6.4-2ubuntu0.1, 2.6.4-2ubuntu0.2), snapd:amd64 (2.32.3.2, 2.32.9), python3-louis:amd64 (2.6.4-2ubuntu0.1, 2.6.4-2ubuntu0.2), libexempi3:amd64 (2.2.2-2, 2.2.2-2ubuntu0.1), liblouis-data:amd64 (2.6.4-2ubuntu0.1, 2.6.4-2ubuntu0.2)
End-Date: 2018-06-05 09:36:36
Start-Date: 2018-06-06 08:31:53
Commandline: aptdaemon role='role-commit-packages' sender=':1.100'
Upgrade: libelf1:amd64 (0.165-3ubuntu1, 0.165-3ubuntu1.1), libelf1:i386 (0.165-3ubuntu1, 0.165-3ubuntu1.1)
End-Date: 2018-06-06 08:31:57
Start-Date: 2018-06-06 08:32:51
Commandline: aptdaemon role='role-commit-packages' sender=':1.100'
Upgrade: git-gui:amd64 (1:2.7.4-0ubuntu1.3, 1:2.7.4-0ubuntu1.4), git-man:amd64 (1:2.7.4-0ubuntu1.3, 1:2.7.4-0ubuntu1.4), git:amd64 (1:2.7.4-0ubuntu1.3, 1:2.7.4-0ubuntu1.4), gitk:amd64 (1:2.7.4-0ubuntu1.3, 1:2.7.4-0ubuntu1.4)
End-Date: 2018-06-06 08:33:03
Start-Date: 2018-06-07 10:39:47
Commandline: aptdaemon role='role-commit-packages' sender=':1.124'
Upgrade: liblouis9:amd64 (2.6.4-2ubuntu0.2, 2.6.4-2ubuntu0.3), google-chrome-stable:amd64 (67.0.3396.62-1, 67.0.3396.79-1), python3-louis:amd64 (2.6.4-2ubuntu0.2, 2.6.4-2ubuntu0.3), liblouis-data:amd64 (2.6.4-2ubuntu0.2, 2.6.4-2ubuntu0.3)
End-Date: 2018-06-07 10:40:04
Start-Date: 2018-06-13 08:46:19
Commandline: aptdaemon role='role-commit-packages' sender=':1.107'
Install: linux-headers-4.4.0-128:amd64 (4.4.0-128.154, automatic), linux-headers-4.4.0-128-generic:amd64 (4.4.0-128.154, automatic), linux-image-4.4.0-128-generic:amd64 (4.4.0-128.154, automatic), linux-signed-image-4.4.0-128-generic:amd64 (4.4.0-128.154, automatic), linux-image-extra-4.4.0-128-generic:amd64 (4.4.0-128.154, automatic)
Upgrade: libimage-magick-perl:amd64 (8:6.8.9.9-7ubuntu5.9, 8:6.8.9.9-7ubuntu5.11), linux-headers-generic:amd64 (4.4.0.127.133, 4.4.0.128.134), linux-libc-dev:amd64 (4.4.0-127.153, 4.4.0-128.154), libldap-2.4-2:amd64 (2.4.42+dfsg-2ubuntu3.2, 2.4.42+dfsg-2ubuntu3.3), libldap-2.4-2:i386 (2.4.42+dfsg-2ubuntu3.2, 2.4.42+dfsg-2ubuntu3.3), libimage-magick-q16-perl:amd64 (8:6.8.9.9-7ubuntu5.9, 8:6.8.9.9-7ubuntu5.11), imagemagick:amd64 (8:6.8.9.9-7ubuntu5.9, 8:6.8.9.9-7ubuntu5.11), adobe-flash-properties-gtk:amd64 (1:20180508.1-0ubuntu0.16.04.1, 1:20180607.1-0ubuntu0.16.04.1), linux-image-generic:amd64 (4.4.0.127.133, 4.4.0.128.134), libmagickwand-6.q16-2:amd64 (8:6.8.9.9-7ubuntu5.9, 8:6.8.9.9-7ubuntu5.11), linux-signed-image-generic:amd64 (4.4.0.127.133, 4.4.0.128.134), slack-desktop:amd64 (3.2.0-beta25a7a50e, 3.2.1), google-chrome-stable:amd64 (67.0.3396.79-1, 67.0.3396.87-1), linux-signed-generic:amd64 (4.4.0.127.133, 4.4.0.128.134), adobe-flashplugin:amd64 (1:20180508.1-0ubuntu0.16.04.1, 1:20180607.1-0ubuntu0.16.04.1), imagemagick-6.q16:amd64 (8:6.8.9.9-7ubuntu5.9, 8:6.8.9.9-7ubuntu5.11), libmagickcore-6.q16-2-extra:amd64 (8:6.8.9.9-7ubuntu5.9, 8:6.8.9.9-7ubuntu5.11), firefox-locale-en:amd64 (60.0.1+build2-0ubuntu0.16.04.1, 60.0.2+build1-0ubuntu0.16.04.1), firefox-locale-fr:amd64 (60.0.1+build2-0ubuntu0.16.04.1, 60.0.2+build1-0ubuntu0.16.04.1), gpgv:amd64 (1.4.20-1ubuntu3.1, 1.4.20-1ubuntu3.2), libmagickcore-6.q16-2:amd64 (8:6.8.9.9-7ubuntu5.9, 8:6.8.9.9-7ubuntu5.11), firefox:amd64 (60.0.1+build2-0ubuntu0.16.04.1, 60.0.2+build1-0ubuntu0.16.04.1), imagemagick-common:amd64 (8:6.8.9.9-7ubuntu5.9, 8:6.8.9.9-7ubuntu5.11), libmagick++-6.q16-5v5:amd64 (8:6.8.9.9-7ubuntu5.9, 8:6.8.9.9-7ubuntu5.11), gnupg:amd64 (1.4.20-1ubuntu3.1, 1.4.20-1ubuntu3.2), linux-generic:amd64 (4.4.0.127.133, 4.4.0.128.134), spotify-client:amd64 (1:1.0.77.338.g758ebd78-41, 1:1.0.80.480.g51b03ac3-13)
End-Date: 2018-06-13 08:49:26
Start-Date: 2018-06-14 15:36:26
Commandline: aptdaemon role='role-commit-packages' sender=':1.128'
Upgrade: perl-base:amd64 (5.22.1-9ubuntu0.3, 5.22.1-9ubuntu0.5), perl-modules-5.22:amd64 (5.22.1-9ubuntu0.3, 5.22.1-9ubuntu0.5), console-setup-linux:amd64 (1.108ubuntu15.3, 1.108ubuntu15.4), console-setup:amd64 (1.108ubuntu15.3, 1.108ubuntu15.4), libperl5.22:amd64 (5.22.1-9ubuntu0.3, 5.22.1-9ubuntu0.5), keyboard-configuration:amd64 (1.108ubuntu15.3, 1.108ubuntu15.4), perl:amd64 (5.22.1-9ubuntu0.3, 5.22.1-9ubuntu0.5)
End-Date: 2018-06-14 15:37:04
Start-Date: 2018-06-15 10:36:50
Commandline: aptdaemon role='role-commit-packages' sender=':1.152'
Upgrade: gnupg-agent:amd64 (2.1.11-6ubuntu2, 2.1.11-6ubuntu2.1), ruby2.3:amd64 (2.3.1-2~16.04.9, 2.3.1-2~16.04.10), libmagic1:amd64 (1:5.25-2ubuntu1, 1:5.25-2ubuntu1.1), ruby2.3-dev:amd64 (2.3.1-2~16.04.9, 2.3.1-2~16.04.10), dirmngr:amd64 (2.1.11-6ubuntu2, 2.1.11-6ubuntu2.1), libruby2.3:amd64 (2.3.1-2~16.04.9, 2.3.1-2~16.04.10), gnupg2:amd64 (2.1.11-6ubuntu2, 2.1.11-6ubuntu2.1), file:amd64 (1:5.25-2ubuntu1, 1:5.25-2ubuntu1.1)
End-Date: 2018-06-15 10:37:08
Start-Date: 2018-06-19 09:04:17
Commandline: aptdaemon role='role-commit-packages' sender=':1.168'
Upgrade: libwebkit2gtk-4.0-37:amd64 (2.20.2-0ubuntu0.16.04.1, 2.20.3-0ubuntu0.16.04.1), gir1.2-webkit2-4.0:amd64 (2.20.2-0ubuntu0.16.04.1, 2.20.3-0ubuntu0.16.04.1), desktop-file-utils:amd64 (0.22-1ubuntu5.1, 0.22-1ubuntu5.2), libjavascriptcoregtk-4.0-18:amd64 (2.20.2-0ubuntu0.16.04.1, 2.20.3-0ubuntu0.16.04.1), wireless-regdb:amd64 (2015.07.20-1ubuntu1, 2018.05.09-0ubuntu1~16.04.1), libwebkit2gtk-4.0-37-gtk2:amd64 (2.20.2-0ubuntu0.16.04.1, 2.20.3-0ubuntu0.16.04.1), gir1.2-javascriptcoregtk-4.0:amd64 (2.20.2-0ubuntu0.16.04.1, 2.20.3-0ubuntu0.16.04.1)
End-Date: 2018-06-19 09:04:32
Start-Date: 2018-06-20 10:39:10
Commandline: aptdaemon role='role-commit-packages' sender=':1.182'
Upgrade: libgcrypt20:amd64 (1.6.5-2ubuntu0.4, 1.6.5-2ubuntu0.5), libgcrypt20:i386 (1.6.5-2ubuntu0.4, 1.6.5-2ubuntu0.5)
End-Date: 2018-06-20 10:39:15
Start-Date: 2018-06-21 16:30:24
Commandline: aptdaemon role='role-commit-packages' sender=':1.214'
Upgrade: amd64-microcode:amd64 (2.20160316.1, 3.20180524.1~ubuntu0.16.04.1)
End-Date: 2018-06-21 16:30:48
And this is my reboot log :
$ last -x | grep reboot
reboot system boot 4.4.0-128-generi Tue Jun 26 09:08 still running
reboot system boot 4.4.0-128-generi Fri Jun 15 10:38 - 18:33 (10+07:55)
reboot system boot 4.4.0-127-generi Tue Jun 12 09:26 - 18:33 (13+09:06)
reboot system boot 4.4.0-127-generi Tue Jun 12 09:21 - 09:25 (00:03)
reboot system boot 4.4.0-127-generi Tue Jun 5 16:43 - 09:20 (6+16:37)
reboot system boot 4.4.0-127-generi Mon Jun 4 12:54 - 09:20 (7+20:26)
The only way I could see why is the fact that I upgraded git-gui and gitk on June 6th.
But why did only work when rebooting on the 26th ?
There is no Tcl/Tk upgrade, but there are gtk upgrades, so I don't know if that has something to do with it...
Maybe someone can figure it out ?