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Initialization font issue in MacOS Sonoma 14.4.1
Hello Dr. Wu,
Thank you for developing this toolkit. It looks cool! I'm trying OGU and encounter the following font failures when initializing OGU:
$ python -m OGU init
21:48:12 INFO Failed to extract font properties from /System/Library/Fonts/Apple Color Emoji.ttc: In FT2Font: Could not set the fontsize (invalid pixel size; error code 0x17)
21:48:12 INFO Failed to extract font properties from /System/Library/Fonts/LastResort.otf: tuple indices must be integers or slices, not str
21:48:13 INFO Failed to extract font properties from /System/Library/Fonts/Supplemental/NISC18030.ttf: In FT2Font: Could not set the fontsize (invalid pixel size; error code 0x17)
21:48:13 INFO generated new fontManager
21:48:13 INFO Try to locate or install all third-party software.
21:48:13 WARNING Cannot find mafft.bat, try to install. May cost minutes
21:48:13 WARNING Cannot find iqtree2, try to install. May cost minutes
21:48:14 INFO Downloading iqtree-2.2.2.2-MacOSX.zip from https://ogu2023.s3.ap-east-1.amazonaws.com/iqtree-2.2.2.2-MacOSX.zip
21:48:14 INFO Downloading mafft-7.511-mac.zip from https://ogu2023.s3.ap-east-1.amazonaws.com/mafft-7.511-mac.zip
21:48:18 INFO iqtree-2.2.2.2-MacOSX.zip got. Installing...
21:48:18 INFO iqtree2 installed successfully.
21:48:20 INFO mafft-7.511-mac.zip got. Installing...
21:48:21 INFO mafft.bat installed successfully.
21:48:21 INFO Got IQTREE.
21:48:21 INFO Got MAFFT.
I don't believe these errors are fatal, but I wanted to report them in case they can be resolved. Please let me know if you need more information from me.
Best, JianJun
Dear JianJun,
Sorry for late response. I haven't receive email notification from GitHub (guess there are some repo settings need change).
The failed logs is from matplotlib, which will check and register all fonts in your operating systems during the first time running. It said that three fonts in macOS cannot be recognized. Since that the software only use Times New Roman and Arial or other limited fonts to draw visualization result, such fonts (emoji, special-purpose font and a long-time problematic font) missing have no effect for the program's function, as you said, they are not fatal.
However, they are indeed annoying. I will try to find out solution from matplotlib community. Once the problem is fixed, I will build a new release and let you know.
Thanks again for using the software and give valuable feedback.
Sincerely Ping Wu
Hello Dr. Wu,
Thank you for developing this toolkit. It looks cool! I'm trying OGU and encounter the following font failures when initializing OGU:
$ python -m OGU init 21:48:12 INFO Failed to extract font properties from /System/Library/Fonts/Apple Color Emoji.ttc: In FT2Font: Could not set the fontsize (invalid pixel size; error code 0x17) 21:48:12 INFO Failed to extract font properties from /System/Library/Fonts/LastResort.otf: tuple indices must be integers or slices, not str 21:48:13 INFO Failed to extract font properties from /System/Library/Fonts/Supplemental/NISC18030.ttf: In FT2Font: Could not set the fontsize (invalid pixel size; error code 0x17) 21:48:13 INFO generated new fontManager 21:48:13 INFO Try to locate or install all third-party software. 21:48:13 WARNING Cannot find mafft.bat, try to install. May cost minutes 21:48:13 WARNING Cannot find iqtree2, try to install. May cost minutes 21:48:14 INFO Downloading iqtree-2.2.2.2-MacOSX.zip from https://ogu2023.s3.ap-east-1.amazonaws.com/iqtree-2.2.2.2-MacOSX.zip 21:48:14 INFO Downloading mafft-7.511-mac.zip from https://ogu2023.s3.ap-east-1.amazonaws.com/mafft-7.511-mac.zip 21:48:18 INFO iqtree-2.2.2.2-MacOSX.zip got. Installing... 21:48:18 INFO iqtree2 installed successfully. 21:48:20 INFO mafft-7.511-mac.zip got. Installing... 21:48:21 INFO mafft.bat installed successfully. 21:48:21 INFO Got IQTREE. 21:48:21 INFO Got MAFFT.I don't believe these errors are fatal, but I wanted to report them in case they can be resolved. Please let me know if you need more information from me.
Best, JianJun
Dear Jianjun,
After several tries, I found that the core of the problem is from matplotlib's font manager. Since matplotlib decided to ignore this problem, and it is hard to build a blacklist of fonts and push the code to them, I tried to hide such harmless logs.
Maybe you can try the new version, OGU v1.52, by running:
pip install -U OGU
# remove old font cache
rm -rf ~/.matplotlib
rm -rf ~/.config/matplotlib
and then reinitialize the program.
If the problem remains unsolved on your computer, please let me know.
Currently, it's just a naive work-around. Given that OGU just draws simple figures, in the future, a light-weight drawing library may be used to replace matplotlib in OGU.
Sincerely, Ping Wu