I am using Protege-5.0.0-beta-23 on Windows machine. I have created an ontology. I would like to visualize my ontology with OWLViz. I have installed Graphviz and from Protege -> preferences I have setup Dot Application Path (C:\Program Files (x86)\Graphviz2.30\bin\dot.exe) properly. However still in Protege GUI, I do not see OWLViz tab. Please let me know how to fix it.
I am using protege5.0 on Ubuntu.But the setting is the same.You can modify tools menu item to show OWLViz. [Window]->[Tabs]->[OWLViz].
reference picture
Download instructions can be found in the link below but I've summarised the key steps to make it easier:
http://www.graphviz.org/download/
STEPS FOR MAC:
If you're on Mac, it's a pretty straightforward install - just open a terminal window and run one of these:
$ sudo port install graphviz
or
$ brew install graphviz
STEPS FOR WINDOWS:
Just head to the address below to download Graphviz and unzip and store the Graphviz folder within the Plugins folder in the Protege directory. Then make sure the Path to DOT application is referenced properly in Preferences > OWLViz tab > Path to DOT. Browse to where the dot.exe file is in the Graphviz folder that was unzipped to the Plugins folder
https://www2.graphviz.org/Packages/stable/windows/10/msbuild/Release/Win32/
Related
In PyCharm, I've added the Python environment /usr/bin/python. However,
from gnuradio import gr
fails as an undefined reference. However, it works fine in the Python interpreter from the command line.
GNURadio works fine with python outside of Pycharm. Everything is installed and configured how I want it.
Gnuradio is located at /usr/local/lib/python2.7/site-packages/gnuradio
Also:
PYTHONPATH=/usr/local/lib/python2.7/site-packages:/usr/local/lib/python2.7/site-packages/gnuradio
Adding a Path
Go into File → Settings → Project Settings → Project Interpreter.
Then press configure interpreter, and navigate to the "Paths" tab.
Press the + button in the Paths area. You can put the path to the module you'd like it to recognize.
But I don't know the path..
Open the python interpreter where you can import the module.
>> import gnuradio
>> gnuradio.__file__
"path/to/gnuradio"
Most commonly you'll have a folder structure like this:
foobarbaz/
gnuradio/
__init__.py
other_file.py
You want to add foobarbaz to the path here.
You should never need to modify the path directly, either through environment variables or sys.path. Whether you use the os (ex. apt-get), or pip in a virtualenv, packages will be installed to a location already on the path.
In your example, GNU Radio is installed to the system Python 2's standard site-packages location, which is already in the path. Pointing PyCharm at the correct interpreter is enough; if it isn't there is something else wrong that isn't apparent. It may be that /usr/bin/python does not point to the same interpreter that GNU Radio was installed in; try pointing specifically at the python2.7 binary. Or, PyCharm used to be somewhat bad at detecting packages; File > Invalidate Caches > Invalidate and Restart would tell it to rescan.
This answer will cover how you should set up a project environment, install packages in different scenarios, and configure PyCharm. I refer multiple times to the Python Packaging User Guide, written by the same group that maintains the official Python packaging tools.
The correct way to develop a Python application is with a virtualenv. Packages and version are installed without affecting the system or other projects. PyCharm has a built-in interface to create a virtualenv and install packages. Or you can create it from the command line and then point PyCharm at it.
$ cd MyProject
$ python2 -m virtualenv env
$ . env/bin/activate
$ pip install -U pip setuptools # get the latest versions
$ pip install flask # install other packages
In your PyCharm project, go to File > Settings > Project > Project Interpreter. If you used virtualenvwrapper or PyCharm to create the env, then it should show up in the menu. If not, click the gear, choose Add Local, and locate the Python binary in the env. PyCharm will display all the packages in the selected env.
In some cases, such as with GNU Radio, there is no package to install with pip, the package was installed system-wide when you install the rest of GNU Radio (ex. apt-get install gnuradio). In this case, you should still use a virtualenv, but you'll need to make it aware of this system package.
$ python2 -m virtualenv --system-site-packages env
Unfortunately it looks a little messy, because all system packages will now appear in your env, but they are just links, you can still safely install or upgrade packages without affecting the system.
In some cases, you will have multiple local packages you're developing, and will want one project to use the other package. In this case you might think you have to add the local package to the other project's path, but this is not the case. You should install your package in development mode. All this requires is adding a setup.py file to your package, which will be required anyway to properly distribute and deploy the package later.
Minimal setup.py for your first project:
from setuptools import setup, find_packages
setup(
name='mypackage',
version='0.1',
packages=find_packages(),
)
Then install it in your second project's env:
$ pip install -e /path/to/first/project
For me, it was just a matter of marking the directory as a source root.
Add path in PyCharm 2017
File -> Settings (or Ctrl+Alt+S) -> Project -> Project Interpreter
Show all
Select bottom icon on the right side
Click on the plus button to add new path to your module
My version is PyCharm Professional edition 3.4, and the Adding a Path part is different.
You can go to "Preferences" --> "Project Interpreter". Choose the tool button at the right top corner.
Then choose "More..." --> "Show path for the selected interpreter" --> "Add". Then you can add a path.
DON'T change the interpreter path.
Change the project structure instead:
File -> Settings -> Project -> Project structure -> Add content root
In PyCharm 2020.1 CE and Professional, you can add a path to your project's Python interpreter by doing the following:
1) Click the interpreter in the bottom right corner of the project and select 'Interpreter Settings'
2) Click the settings button to the right of the interpreter name and select 'Show All':
3) Make sure your project's interpreter is selected and click the fifth button in the bottom toolbar, 'show paths for the selected interpreter':
4) Click the '+' button in the bottom toolbar and add a path to the folder containing your module:
For PyCharm Community Edition 2016.3.2 it is:
"Project Interpreter" -> Top right settings icon -> "More".
Then on the right side there should be a packages icon. When hovering over it it should say "Show paths for selected interpreter". Click it.
Then click the "Add" button or press "alt+insert" to add a new path.
As quick n dirty fix, this worked for me:
Adding this 2 lines before the problematic import:
import sys
sys.path.append('C:\\Python27\\Lib\site-packages')
On Project Explorer, you can right click on the folder where the module is contained and set as 'Source'.
It will be parsed in the Index for code completion as well as other items.
I'm new to PyCharm (using 2018.3.4 CE) and Python so I rotely tried to follow each of the above suggestions to access the PIL (Pillow) package which I knew was in system-site-packages. None worked. I was about to give up for the night when I happened to notice the venv/pyvenv.cfg file under my project in the Project Explorer window. I found the line "include-system-site-packages = false" in that file and so I changed it to "true". Problem solved.
In my PyCharm 2019.3, select the project, then File ---> Settings, then Project: YourProjectName, in 'Project Interpreter', click the interpreter or settings, ---> Show all... ---> Select the current interpreter ---> Show paths for the selected interpreter ---> then click 'Add' to add your library, in my case, it is a wheel package
For me there is also another issue. If you try to add a folder that in the past had a .idea folder, but your current project has it's own .idea folder your pycharm might get confused for some reason -- even if you have the right python/conda env. For me deleting the .idea folder of the other project fixed the confusion that it could find the obviously correctly installed pkgs. Then it was it was able to find them in the pycharm editor GUI snf stopped underlyinging them in red.
Download anaconda
https://anaconda.org/
once done installing anaconda...
Go into Settings -> Project Settings -> Project Interpreter.
Then navigate to the "Paths" tab and search for /anaconda/bin/python
click apply
I am working on documentation for a software. And i have used graphviz directive inside my rest file.
.. graphviz::
:align: center
However when i run
make html
i get an error for dot command even though graphviz is installed in my virtenv (OS - mac). I have updated the conf.py to have the extension 'sphinx.ext.graphviz'
WARNING: dot command ‘dot’ cannot be run (needed for graphviz output), check the graphviz_dot setting
The problem could be referred to an incorrect configuration of "dot" executable from GraphViz PATH.
See: https://github.com/IQSS/dataverse/pull/7230
On my windows machine, I solved it following these steps:
Check if the dot installation has been performed, going in the installation path (the default installation path is: C:\Program Files (x86)\GraphvizX.XX\bin) and running here the command dot.exe
Go to Control Panel > System and Security > System, and on the right side navigation panel, click the Advanced systems settings link.
In Advance settings, a dialogue box opens that shows the Environment Variables button. Click the button.
Select the entry Path in the system variables section and add C:\Program Files (x86)\GraphvizX.XX\bin to the existing path.
I think the problem could be solved on your OS machine just adding the PATH using the export command, such as:
export PATH=$PATH:~/opt/bin
Ref: https://bobswift.atlassian.net/wiki/spaces/GVIZ/pages/20971549/How+to+install+Graphviz+software
https://osxdaily.com/2014/08/14/add-new-path-to-path-command-line/
It looks like Sphinx can't find dot executable. Make sure it's in your path.
I failed to understand the INSTALL.md file. I know few programming knowledge. I appreciate anyone can give me a thorough explanation or instruction.
The software I wanna install is https://sourceforge.net/projects/scidavis/
Information in INSTALL.md
Mac OS X - MacPorts instructions
These notes refer to use MacPorts. Using other build environments such
as HomeBrew is presumably equally as viable, but you may need to hack
the config files a bit.
Install MacPorts.
Install XCode and XCode command line
tools
If you want to be able to run your build on an earlier version of
MacOSX than your build machine, see How to build a Macintosh
executable that will run on older versions of
MacOSX.
Install the prerequisites for scidavis.
port install qt4-mac qwt52 qwtplot3d boost gsl py27-pyqt4 py-pyqwt py27-sip muparser
Sadly, you may need to do this step multiple times before eveything
is installed
link sip-2.7 share directory to where sip expects it to be:
ln -sf /opt/local/Library/Frameworks/Python.framework/Versions/2.7/share/sip /opt/local/share/py27-sip
Add qt's bin directory to your PATH
PATH=/opt/local/bin:/opt/local/libexec/qt4/bin:$PATH
Configure scidavis
qmake CONFIG+=osx_dist
Build scidavis
make qmake
make
Create the installable package
sh mkMacDist.sh
Thanks in advance
If you are trying to install a tar.gz files you must first run gunzip on the file. gunzip filename. This should give you a .tar file. To open the tar file run: tar -x filename.tar.
NOTE: if you're trying to install a unix executable, it's sometimes easier to use homebrew. Search the internet for the application you're trying to install and the term homebrew, and it might bring up a page on homebrew and give you a simple install command which you can run in the mac terminal.
Steps to install tar.gz on macOS
Double click it the tar.gz file open it
Its contents (e.g. directories/files it contained) should appear in the same directory the tar.gz file is in (to prevent clutter, consider placing the tar.gz file in a new, empty directory before double clicking on it)
One of the new files might be a unix executable that looks like this:
Open another finder window (command + n), navigate to this location /usr/local/bin, and place the executable file you found in the previous step in this new location (you can do this using the mac terminal if you prefer - here's a random example showing show)
At this point, open a new terminal tab, and type the name of the program (the file you moved in steps 4), terminal should recognise the program. However, if you see this there is one more step:
Go to System Preferences -> Security & Privacy -> General tab. Click the lock icon, type password if it asks for it, and then click on 'Allow'.
I'm trying to create a php documentation on my local XAMPP host (on Windows 7) with phpDocumentor.phar (v2.). It gives me (after parsing all the files) this error:
Unable to find the dot command of the GraphViz package. Is GraphViz correctly installed and present in your path?
I searched a lot, but nothing helps. What does 'path' means? If I open a command box at any location I can start the dot.exe (which gives me no output but waiting prompt). In my environment path variable the bin folders is added. GraphViz is installed correct in Program Files and runs standalone.
What could I do or check?
In order to get GraphViz running properly with a Windows based phpdoc installation, just put the GraphViz program directory (c:\some\path\graphviz\release\bin) to the Windows Path system variable.
In order to do this, follow these steps (Win7, please provide your OS version if this doesn't apply to your situation):
From the desktop, right-click My Computer and click Properties.
In the System Properties window, click on the Advanced tab.
In the Advanced section, click the Environment Variables button.
In the Environment Variables window, highlight the Path variable in the Systems Variable section and click the Edit button.
Different directories are separated with a semicolon:
C:\Program Files;C:\Winnt;C:\Winnt\System32
It will most likely look a bit different in your enviroment, so please just take this for an example. Just add the GraphViz Path at the end like this:
C:\Program Files;C:\Winnt;C:\Winnt\System32;C:\somefolder\graphviz\release\bin
I'm not too sure if you have to reboot your system after changing this value. You had to do this in the old days of Win2k, and I just don't know if this still applies to modern Windows versions. It surely doesn't hurt!
After this, phpdoc should be able to find the dot command.
The steps to resolve this error are:
download Windows Packages from
https://graphviz.gitlab.io/_pages/Download/Download_windows.html
Just install it
add c:\Program Files\Graphviz*\dot.exe or c:\Program Files (x86)\Graphviz*\dot.exe to your environment variable PATH
run phpdoc
Re-start your machine & run phpdoc (if still shows the same error message)
I am trying to do it, but all I can get is some source code that I don't know how to do deal with I downloaded from http://pkgconfig.freedesktop.org/releases/.
This is a step-by-step procedure to get pkg-config working on Windows, based on my experience, using the info from Oliver Zendel's comment.
I assume here that MinGW was installed to C:\MinGW. There were multiple versions of the packages available, and in each case I just downloaded the latest version.
go to http://ftp.gnome.org/pub/gnome/binaries/win32/dependencies/
download the file pkg-config_0.26-1_win32.zip
extract the file bin/pkg-config.exe to C:\MinGW\bin
download the file gettext-runtime_0.18.1.1-2_win32.zip
extract the file bin/intl.dll to C:\MinGW\bin
go to http://ftp.gnome.org/pub/gnome/binaries/win32/glib/2.28
download the file glib_2.28.8-1_win32.zip
extract the file bin/libglib-2.0-0.dll to C:\MinGW\bin
Now CMake will be able to use pkg-config if it is configured to use MinGW.
Get the precompiled binaries from http://ftp.gnome.org/pub/gnome/binaries/win32/dependencies/
Download pkg-config and its depend libraries :
pkg-config_0.26-1_win32.zip
glib_2.28.8-1_win32.zip
gettext-runtime_0.18.1.1-2_win32.zip
A alternative without glib dependency is pkg-config-lite.
Extract pkg-config.exe from the archive and put it in your path.
Nowdays this package is available using chocolatey, then it could be installed with
choco install pkgconfiglite
I did this by installing Cygwin64 from this link https://www.cygwin.com/
Then - View Full, Search gcc and scroll down to find pkg-config.
Click on icon to select latest version.
This worked for me well.
I would like to extend the answer of #dzintars about the Cygwin version of pkg-config in that focus how should one use it properly with CMake, because I see various comments about CMake in this topic.
I have experienced many troubles with CMake + Cygwin's pkg-config and I want to share my experience how to avoid them.
1. The symlink C:/Cygwin64/bin/pkg-config -> pkgconf.exe does not work in Windows console.
It is not a native Windows .lnk symlink and it won't be callable in Windows console cmd.exe even if you add ".;" to your %PATHEXT% (see https://www.mail-archive.com/cygwin#cygwin.com/msg104088.html).
It won't work from CMake, because CMake calls pkg-config with the method execute_process() (FindPkgConfig.cmake) which opens a new cmd.exe.
Solution: Add -DPKG_CONFIG_EXECUTABLE=C:/Cygwin64/bin/pkgconf.exe to the CMake command line (or set it in CMakeLists.txt).
2. Cygwin's pkg-config recognizes only Cygwin paths in PKG_CONFIG_PATH (no Windows paths).
For example, on my system the .pc files are located in C:\Cygwin64\usr\x86_64-w64-mingw32\sys-root\mingw\lib\pkgconfig. The following three paths are valid, but only path C works in PKG_CONFIG_PATH:
A) c:/Cygwin64/usr/x86_64-w64-mingw32/sys-root/mingw/lib/pkgconfig -
does not work.
B) /c/cygdrive/usr/x86_64-w64-mingw32/sys-root/mingw/lib/pkgconfig -
does not work.
C) /usr/x86_64-w64-mingw32/sys-root/mingw/lib/pkgconfig - works.
Solution: add .pc files location always as a Cygwin path into PKG_CONFIG_PATH.
3) CMake converts forward slashes to backslashes in PKG_CONFIG_PATH on Cygwin.
It happens due to the bug https://gitlab.kitware.com/cmake/cmake/-/issues/21629. It prevents using the workaround described in [2].
Solution: manually update the function _pkg_set_path_internal() in the file C:/Program Files/CMake/share/cmake-3.x/Modules/FindPkgConfig.cmake. Comment/remove the line:
file(TO_NATIVE_PATH "${_pkgconfig_path}" _pkgconfig_path)
4) CMAKE_PREFIX_PATH, CMAKE_FRAMEWORK_PATH, CMAKE_APPBUNDLE_PATH have no effect on pkg-config in Cygwin.
Reason: the bug https://gitlab.kitware.com/cmake/cmake/-/issues/21775.
Solution: Use only PKG_CONFIG_PATH as an environment variable if you run CMake builds on Cygwin. Forget about CMAKE_PREFIX_PATH, CMAKE_FRAMEWORK_PATH, CMAKE_APPBUNDLE_PATH.
Install mingw64 from https://sourceforge.net/projects/mingw-w64/. Avoid program files/(x86) folder for installation. Ex. c:/mingw-w64
Download pkg-config__win64.zip from here
Extract above zip file and copy paste all the files from pkg-config/bin folder to mingw-w64. In my case its 'C:\mingw-w64\i686-8.1.0-posix-dwarf-rt_v6-rev0\mingw32\bin'
Now set path = C:\mingw-w64\i686-8.1.0-posix-dwarf-rt_v6-rev0\mingw32\bin
taddaaa you are done.
If you find any security issue then follow steps as well
Search for windows defender security center in system
Navigate to apps & browser control> Exploit protection settings> Program setting> Click on '+add program customize'
Select add program by name
Enter program name: pkgconf.exe
OK
Now check all the settings and set it all the settings to off and apply.
Thats DONE!
Another place where you can get more updated binaries can be found at Fedora Build System site. Direct link to mingw-pkg-config package is: http://koji.fedoraproject.org/koji/buildinfo?buildID=354619
for w64-based computers you have to install mingw64. If pkg-config.exe is missing then, you can refer to http://ftp.acc.umu.se/pub/gnome/binaries/win64/dependencies/
Unzip and copy/merge pkg-config.exe into your C:\mingw-w64 installation, eg. into on my pc into C:\mingw-w64\x86_64-8.1.0-posix-seh-rt_v6-rev0\mingw64\bin
In 2022 VS Code works with CMake & pkgconfig out of the box (add pkgconf && vcpkg-pkgconfig-get-modules to your vcpkg.json)
From: https://github.com/JoinMarket-Org/joinmarket/wiki/Installing-JoinMarket-on-Windows
This guide describes how to install JoinMarket and its dependencies (python, libsodium, secp256k1) on Windows.
Some or all of this may or may not work for all versions of Windows. Reports appreciated. It is not claimed to be in any way comprehensive. Verification of downloads are your own responsibility.
Install JoinMarket - go to https://github.com/JoinMarket-Org/joinmarket/releases and download the most recent release. Unzip it into any location you choose.
You will need to install MinGW from here or go to their website. After a few introductory screens, you will be shown a windows with some optional components that you have to choose; this basic setup is sufficient:
From "Basic Setup" in the left menu:
mingw-developer-toolkit
mingw32-base
mingw32-gcc-g++
msys-base
Once you have chosen these, choose "Update" from the main menu first item. These components will be installed into C:\MinGW\bin. Once that is complete, you should have this dll: libgcc_s_dw2-1.dll in that folder C:\MinGW\bin, along with a lot of other files; I'm mentioning this file explicitly, since it's needed specifically for libsecp256k1 to operate in this setup.
Next, you must make sure C:\MinGW\bin is added to your PATH variable. Here's one guide to how to do that; you must append ;C:\MinGW\bin to the end of the path before continuing.
Install Python from https://www.python.org/ftp/python/2.7.11/python-2.7.11.msi. Run the executable. Choose to install the feature Add python.exe to Path (it's the last option in the installer, off by default - switch it on) on local hard drive during installation; Python should then be installed in C:\Python27 (EXTRA NOTE: the most recent 2.7 installation linked here seems to install pip automatically, which is very useful for step 4)
Check that Python runs. Open a new command prompt as administrator by typing cmd.exe into the Start menu and pressing Ctrl+Shift+Enter. Type python and you should see something like:
Python 2.7.11 (default....
....
>>>
Exit the Python console with exit() or by pressing Ctrl+C. Now, make sure your version of pip is up to date: run the command: python -m pip install --upgrade pip.
Go to the directory C:\Python27\Lib\distutils and add a new file, called distutils.cfg. Inside it, put:
[build]
compiler=mingw32
Close and save the file.
Next, you need to install the dll for libnacl. First go to https://download.libsodium.org/libsodium/releases/ and choose the file libsodium-1.0.4-msvc.zip to download. Unzip anywhere, and then copy the file libsodium.dll from the directory \Win32\Release\v120\dynamic (do not use v140), and paste it into root joinmarket directory (the same directory where README.md lives). Then you need to address the Visual C++ 2013 runtime dependency. Do so by going to www.microsoft.com/en-us/download/details.aspx?id=40784 and clicking Download. Choose x86 even on a 64-bit system, and run the executable.
Note that after doing this, you must run pip install -r requirements-windows.txt from the Joinmarket root directory (where the README.md file is) and should not get an error message (this will install/check the python packages libnacl and secp256k1(-transient)).