Dot cannot be run in Pycharm with Sphinx and Graphviz - path

I am trying to create a class diagram with sphinx. For this I created a virtual environment in Pycharm and added this to conf.py:
extensions = ['sphinx.ext.autodoc','sphinx.ext.inheritance_diagram']
In my spamfilter.rst file I added the following lines:
Diagrams
=================
.. inheritance-diagram:: spamfilter
The output is not a diagram and looks like this.
The following warning is displayed:
WARNING: dot command 'dot' cannot be run (needed for graphviz output), check the graphviz_dot setting
When I look into the folder C:\Users\Name\PycharmProjects\documentation\venv\Lib\site-packages\graphviz, there is a dot.py file, so I do not understand what is wrong. A similar question for Mac OS has been asked here. I tried the solution but it seems like it only works for Mac, because when I paste export PATH=$PATH:~/opt/bin to the Pycharm Terminal, it tells me that the command export could not be found. Honestly I have problems understanding why sometimes you can just use packages and other times they cannot be found even when they are installed, I am self-taught and a beginner.

The "pip install graphviz" command installs a Python package that provides an interface to Graphviz (https://pypi.org/project/graphviz). This package is not required by Sphinx.
In order to create inheritance diagrams with Sphinx, the actual Graphviz toolkit (including dot.exe) must be installed. See https://www.graphviz.org.
If dot.exe is not in the PATH, you can use the graphviz_dot configuration option.

I had the same problem where rendering a C4 model with PlantUML didn't work in the IDE (PyCharm 2022.2.1 Pro) on a newer M1 MacOS Monterey. I had it working on a Big Sur intel Mac prior to the upgrade with no extra effort, so the chip change caused me to go down a lot of paths with Rosetta and so on that were all unsuccessful.
The error was:
Dot Executable: /opt/local/bin/dot
File does not exist
Cannot find Graphviz.
Graphviz was installed correctly, and dot was on my path, but it wasn't in /opt/local/bin/dot. Since it was in /opt/homebrew/bin/dot, all I needed to do was link the actual file with the path it was searching for:
cd /opt
sudo ln -s homebrew local
et voilà, PyCharm is now correctly rendering the puml in the IDE.

Related

Fixing pkg-config using Apple silicon and homebrew

I am working with C++ on an M1 Mac, and I used Time Machine to get my old laptop's data on the new one once I got it. The old laptop was not an Apple silicon MacBook. The problem is that I think this screwed up my homebrew installation, since it changed the default location from /usr/local/Cellar/ to /opt/homebrew/Cellar/ and so now I have two homebrew versions since I installed it again on my new laptop after I got it (since nothing was working with homebrew at first and thought it didn't carry over using Time Machine, oops)
I didn't use homebrew much until recently so I didn't notice, but it has made compiling C++ programs with external libraries very difficult since everything I need is on my new homebrew installation in /opt/homebrew/Cellar/ except pkg-config, which when I call it in a bash script or on the command line points to my old homebrew installation.
For example, I have pugixml in my new installation of homebrew and when I enter pkg-config --libs --cflags pugixml
Package pugixml was not found in the pkg-config search path.
Perhaps you should add the directory containing `pugixml.pc'
to the PKG_CONFIG_PATH environment variable
No package 'pugixml' found
pkg-config finds the libraries in the older homebrew installation just fine
My only alternative is to manually inspect the .pc files in the new homebrew installation and enter the flags in my Makefile. I would prefer not to do this. What's the best way to make sure that pkg-config works correctly? If someone knows how to get the new installation of pkg-config to be used at the command line that would solve all my problems I have right now
edit: I forgot to mention this - when I use the which command and ask which pkg-config it outputs /opt/homebrew/bin/pkg-config. This is sort of confusing since this is the new location
Remove the old (Intel) installation with the official uninstall script.
You have to make it executable with:
chmod +x uninstall.sh
And run it with
./uninstall.sh --path=/usr/local
Then reinstall everything you need on the new M1 version under /opt/homebrew.

Export flutter PATH makes docker cli and/or npm not working

I have the following problem.
I noticed that, once i installed flutter and added its path to my .zshrc file, like this
export PATH={$PATH}:/Users/matteo/Documents/flutter/bin
I have problems with docker and/or npm. (E.G. I get the error docker: command not found)
I tried moving my line of code in different places in my .zshrc file, and it seems like depending on where my line of code is placed, sometimes only docker is not found, sometimes only npm, sometimes both of them.
Are there any connection, maybe under the hood, between those 3 application?
My computer is a Macbook Pro with Big Sur 11.4 and M1 chip.
Thanks for help,
Matteo.
you are exporting the path the wrong way, you should add it as follows:
export PATH="$PATH:/Users/matteo/Documents/flutter/bin"
After you have updated the ".zshrc" file, run this command to ensure changes have been notified to OS
source ~/.zshrc
Reference: https://flutter.dev/docs/get-started/install/macos

Installing Wine on Mac OS Catalina. Error: No available formula with the name "wine"

I'm trying to install Wine on my Mac via Brew. I'm using Catalina and just updated brew, installed XQuartz and have Xcode installed. When I type the command "Brew install wine" it returns the following:
Error: No available formula with the name "wine"
==> Searching for a previously deleted formula (in the last month)...
Warning: homebrew/core is shallow clone. To get complete history run:
git -C "$(brew --repo homebrew/core)" fetch --unshallow
wine was deleted from homebrew/core in commit 82bd38bc:
wine: delete
To show the formula before removal run:
git -C "$(brew --repo homebrew/core)" show 82bd38bc^:Formula/wine.rb
If you still use this formula consider creating your own tap:
https://docs.brew.sh/How-to-Create-and-Maintain-a-Tap
I'm following this tutorial: https://www.davidbaumgold.com/tutorials/wine-mac/
When I run Brew doctor I get the following:
Please note that these warnings are just used to help the Homebrew maintainers
with debugging if you file an issue. If everything you use Homebrew for is
working fine: please don't worry or file an issue; just ignore this. Thanks!
Warning: "config" scripts exist outside your system or Homebrew directories.
`./configure` scripts often look for *-config scripts to determine if
software packages are installed, and which additional flags to use when
compiling and linking.
Having additional scripts in your path can confuse software installed via
Homebrew if the config script overrides a system or Homebrew-provided
script of the same name. We found the following "config" scripts:
/Library/Frameworks/Python.framework/Versions/3.7/bin/python3.7-config
/Library/Frameworks/Python.framework/Versions/3.7/bin/python3.7m-config
/Library/Frameworks/Python.framework/Versions/3.7/bin/python3-config
Warning: Unbrewed dylibs were found in /usr/local/lib.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.
Unexpected dylibs:
/usr/local/lib/libtcl8.6.dylib
/usr/local/lib/libtk8.6.dylib
Warning: Unbrewed header files were found in /usr/local/include.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.
Unexpected header files:
/usr/local/include/fakemysql.h
/usr/local/include/fakepq.h
/usr/local/include/fakesql.h
/usr/local/include/itcl.h
/usr/local/include/itcl2TclOO.h
/usr/local/include/itclDecls.h
/usr/local/include/itclInt.h
/usr/local/include/itclIntDecls.h
/usr/local/include/itclMigrate2TclCore.h
/usr/local/include/itclTclIntStubsFcn.h
/usr/local/include/mysqlStubs.h
/usr/local/include/odbcStubs.h
/usr/local/include/pqStubs.h
/usr/local/include/tcl.h
/usr/local/include/tclDecls.h
/usr/local/include/tclOO.h
/usr/local/include/tclOODecls.h
/usr/local/include/tclPlatDecls.h
/usr/local/include/tclThread.h
/usr/local/include/tclTomMath.h
/usr/local/include/tclTomMathDecls.h
/usr/local/include/tdbc.h
/usr/local/include/tdbcDecls.h
/usr/local/include/tdbcInt.h
/usr/local/include/tk.h
/usr/local/include/tkDecls.h
/usr/local/include/tkPlatDecls.h
Warning: Unbrewed .pc files were found in /usr/local/lib/pkgconfig.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.
Unexpected .pc files:
/usr/local/lib/pkgconfig/tcl.pc
/usr/local/lib/pkgconfig/tk.pc
Warning: Unbrewed static libraries were found in /usr/local/lib.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.
Unexpected static libraries:
/usr/local/lib/libtclstub8.6.a
/usr/local/lib/libtkstub8.6.a
I'm not sure these warnings has something to do with it.
Thanks in advance!
I was able to build Wine 64 bit from source on macOS Catalina and successfully run Notepad++ 64 bit on it.
My steps were more or less something like that:
Download Wine 4.20 from https://dl.winehq.org/wine/source/4.x/wine-4.20.tar.xz
Extract it
In terminal go to extracted directory
Run: ./configure --enable-win64
It showed that it cannot find some library (I do not remember what exactly) so I installed it with macports (sudo port install name_of_missing_package reported by ./configure)
After I was able to run ./configure --enable-win64 succesfully without errors in terminal run: make
It compiled after more than 30 minutes.
I run it with: ./wine start
It opened windows console and here I was able to cd to Notepad++ 64 bit directory (downloaded from https://notepad-plus-plus.org/repository/7.x/7.0/npp.7.bin.x64.zip note that newest version did not work and throwed some errors about some dll's)
I typed notepad++ to run exe file
It showed some errors about freetype fonts so I installed them with macports and I had to copy them from /opt/X11/lib to /usr/local/lib before wine detected them
After fixing freetype fonts problem I was able to run notepad++
Also you might want to run: sudo spctl --master-disable to disable gatekeeper if you will see some system alerts about loading app from unknown developer.
Also note that instead of ./wine start you can run ./wine explorer for graphical file manager instead of console
Those steps might not be exactly precise, as I'm not sure if I did not miss something but hope it will help someone.
Also note that obviously wine on macOS Catalina will be able to run only some 64 bit windows apps and all 32 bit windows app will not work. I also tested it with IrfanView 64 bit (https://www.fosshub.com/IrfanView.html?dwl=iview453_x64_setup.exe) and it also works fine.
In case you wanted to get wine working for purpose of running 32 bit games then unfortunately it will not work with wine but you can try with virtualbox. You can check https://www.youtube.com/watch?v=3AO8dF0vviQ for some performance improvements tips.
Wine hast been removed from homebrew due to the incompatibility to Macos Catalina
https://discourse.brew.sh/t/issue-with-wine/6188/3
Try using wine64 to run your .exe files after installing wine. The manuals and references don't seem to mention this explicitly.
More Info
I followed the guidance in the wine manual to install using home-brew. After install, I got an error when trying to test the installation like it says in the quickstart.
Install wine-stable using homebrew
brew tap homebrew/cask-versions
brew install --cask --no-quarantine wine-stable
After install, test by opening notepad
wine notepad
zsh: bad CPU type in executable: wine
While uninstalling wine, I noticed one of the linked libraries was called wine64. I immediately reinstalled and tried again using wine64 as the call, as I am using wine on an M1 Mac. This was successful!
You can also use winehelp to get access to more commands that will work with 64bit processor.
Based on https://github.com/Homebrew/homebrew-core/pull/46556#issuecomment-559938873 you can do brew cask install wine-stable on newer version of OS X. And works with recent versions of homebrew since the source version was moved :(
How to install wine on Mac OS Catalina with brew
install homebrew with
/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install.sh)"
install xquartz to install wine using brew
brew cask install xquartz
install wine using brew
brew install homebrew/cask-versions/wine-devel
run wine and check the version
wine64 --version
As of Wine 5.0 there is no 32bit support on mac in the official version, but you are able to achieve it via the
Unofficial Wineskin Winery
You can download it from github releases here. And then create a Wineskin with WS11WineCX[64/32]bit19.0.[0/1]. All WS11 versions support Catalina. To use it you also need to turn off the no32exec boot argument. You theoretically can do it by typing:
sudo nvram boot-args="no32exec=0"
into the Terminal while you're logged in but it didn't work out for me, so if you'll have the same problem, reboot into the Recovery mode, in the menubar pick Utilities -> Terminal and type just:
nvram boot-args="no32exec=0"
(without sudo).
Example
To be more exact, to install eg. Steam 32bit, you would:
Install the Unofficiall Wineskin Winery from the provided link
Turn on the 32bit execution boot argument by going into Recovery Mode and entering nvram boot-args="no32exec=0" into the terminal
Open Wineskin, click the '+' sign and scroll down to find the WS11WineCX64bit19.0.1 (the newest version with 64 and 32 bit support, at the time of writing)
Click update/install under the Wrapper Version.
Click Create New Blank Wrapper, name it and click through installation of mono and gecko.
Launch the Wrapper App from Finder. Click Install Software, choose setup executable, and proceed through installation. Then pick the executable from a menu. (In case of steam, Steam.exe)
Note: If you get the "No windows app to open the file"(Like I did) error, click advanced -> configuration and set the Windows EXE to the path to the installer. Then find the place that it has installed in and set that as Windows EXE. Then you can run by clicking Test Run.
Enjoy your windows app, as an .app file!
Hope I helped!

ghostview no longer works after homebrew upgrade of ghostscript

I recently did an update/upgrade with homebrew, and now gv no longer opens any of my .ps files. The Ghostscript error window that comes up says "Unknown device: x11 Error: PostScript interpreter failed in main window".
If I try gs --help, it doesn't list x11 under available devices, and the Default output device is "bbox". I tried uninstalling and reinstalling through homebrew. I tried to reinstall adding "--with-x11" but that throws the error "invalid option: --with-x11" - apparently that's no longer allowed. I've upgraded my command line code through the app store, and tried all of this again - nothing changed. I'm on High Sierra 10.13.3, using Homebrew 2.0.6, ghostscript 9.26_1, and gv 3.7.4.
I'm not a Mac developer so I'm not completely familiar with Homebrew, but it does sound like the package has been built wiithout X11 support. The fact that --help doesn't list the device is pretty clear.
I do notice from the website that in the last 30 days there have been 2 downloads of --with-x11. So possibly they've removed X11 support recently.
The only other thing I can suggest (assuming you are comfortable with compiling yourself) is to get the sources from www.ghostscript.com, untar the source tarball, then in a terminal window, from the 'ghostpdl' directory, execute ./autogen.sh, then when that is complete, execute 'make'.
Assuming you have autotools, gcc and the X11 development package, that should build a version of Ghostscript which includes X support. Looking at the Homebrew forumla, and assuming this has worked for you in the past, I think you should be able to build Ghostscript that way.
You might want to add --disable-cups --disable-compile-inits --disable-gtk --disablefontconfig --without-libidn to the ./autogen.sh command line to mimic the Homebrew formula. I'm not sure why they disable CUPS, but whatever.
Other than that, this isn't really a Ghostscript question as such, you would need to contact whoever handles the Homebrew Ghostscript distribution, which isn't any of the Ghostscript development team.
For those searching for a solution, I've put together a custom Homebrew tap that allows you to easily install GV (commonly called Ghostview, but really a derivative of it):
brew install johnhcc/gs-x11/gv
This will automatically install a version of Ghostscript with X11 enabled in the process (it is a dependency). You can optionally install the dependency by itself, it you want:
brew install johnhcc/gs-x11/ghostscript-x11
The main page is here:
https://github.com/johnhcc/homebrew-gs-x11

Opencv installation problems

I am trying to follow a guide to install Opencv however I am having problems.
I am following this guide:
https://www.pyimagesearch.com/2016/12/19/install-opencv-3-on-macos-with-homebrew-the-easy-way/
However there is an addendum when it reaches this point:
Update — 15 May 2017:
Which then sends you to this page:
This Page
As stated in this guide I installed OpenCV3 using this command:
brew install opencv3 --with-contrib --with-python3
I then stepped back to the original install guide here
However when checking my site packages using this line:
ls -l /usr/local/opt/opencv3/lib/python3.7/site-packages/
The directory is not found.
I then tried to cd to this directory one step at a time and found in my 'opt' directory that some of the folders were names incorrectly or at least different than to be expected.
I have two opencv folders:
opencv
opencv#3
I also have three python folders:
python3
python#2
python#3
Should I rename the opencv and python folders? If so how?
Mac OS High Sierra

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