I want to use RDkit with python3 in windows OS
But here are something I got confused
Besides the author said the most recommend way is anaconda(I don't want this),the other way is to install RDkit with release binary package. But as I follow the document as BELLOW:
Get the appropriate windows binary build from: https://github.com/rdkit/rdkit/releases
Extract the zip file somewhere without a space in the name, i.e. C:\
The rest of this will assume that the installation is in C:\RDKit_2015_09_2
Set the following environment variables:
RDBASE: C:\RDKit_2015_09_2
PYTHONPATH: %RDBASE% if there is already a PYTHONPATH, put ;%RDBASE% at the end.
PATH: add ;%RDBASE%\lib to the end
I do got the latest releases
I unzip the package
But the directory doesn't have the sub dir name "lib" in last step: PATH: add ;%RDBASE%\lib to the end
What can I do? do I mkdir named lib at there? Or just the binary package is not full?
besides, if i want to use compile source code way,the example enviroment is python2.7,can i compile it with python3?
i have fix this problem
the result i put on my github
Related
condensed version of what I want to achieve:
Create .rpm and .deb packages from my source.py source code and make sure all dependencies get resolved when installing them on an deb/rpm based linux distribution.
More details:
Let's assume I have created a piece of software which is located in a folder structure like this:
---MyProgram Folder
---MyProgram Folder
---img Folder
---logo.ico File
---media Folder
---head.txt File
---__init__.py File
---source.py File
---a.py File
---LICENSE File
---README.md File
---setup.py File
The file setup.py contains the following:
import setuptools
with open("README.md", "r") as fh:
long_description = fh.read()
setuptools.setup(
name="MyProgram",
version="0.0.1",
author="First Last",
author_email="email#memore.com",
description="A tool to create nice things",
long_description=long_description,
long_description_content_type="text/markdown",
url="https://google.com",
packages=setuptools.find_packages(),
classifiers=[
"Programming Language :: Python :: 3",
"License :: OSI Approved :: MIT License",
"Operating System :: OS Independent",
],
python_requires='>=3.7',
data_files=[
('.../MyProgram/img/logo.ico'),
('.../MyProgram/media/head.txt'),
],
)
I now run
python setup.py sdist bdist_rpm
from a cmd line under '.../MyProgram'. Two folders 'dist' and 'build' are created as well as 'MyProgram.tar.gz' and two rpm's 'MyProgram-noarch.rpm' and 'MyProgram-src.rpm'.
When i try to install 'noarch.rpm' under fedora 31 the process end successfully but no "shortcut" is created, and when i type MyProgram in a cmd line it is not found.
rpm -ql MyFilter
does find it and outputs a bunch of paths:
/usr/lib/python3.7/site-packages/MyProgram/...
/usr/lib/python3.7/site-packages/MyProgram/source.py
/usr/lib/python3.7/site-packages/MyProgram/a.py
....
Which tells me that my installation at least has copied the basic filesystem. But i also see that all the original .py files are still .py files.
My questions:
How can i 'make' the rpm so that all dependencies are contained inside the rpm, or at least get resolved by dnf/apt/yum when installing the rpm? In other wording: Is it possible to bundle all dependencies into a rpm/deb like in an .exe for example?
How can i specify a path like '/usr/bin' or 'usr/share' as installation target
dir?
How can i add a launcher app bundled into the rpm/deb?
Is the above a good way of doing this at all?
If the solution to this is trivial and i just overlooked it i am really sorry to bother you but atm i just can't see it. Sites that have relevant information and that i already reviewed:
https://docs.python.org/2.0/dist/creating-rpms.html
https://github.com/AppImage/AppImageKit/wiki/Bundling-Python-apps
Python 3.5 create .rpm with pyinstaller generated executable
https://github.com/junaruga/rpm-py-installer
https://www.pyinstaller.org/
https://packaging.python.org/overview/#python-source-distributions
https://packaging.python.org/overview/
https://pyinstaller.readthedocs.io/en/stable/usage.html
https://pyinstaller.readthedocs.io/en/stable/installation.html
https://python-packaging-tutorial.readthedocs.io/en/latest/setup_py.html
Just my two cents, rather than a complete answer. Will mostly touch on RPM packaging.
The bdist_rpm option seems easy, but you have little control of the logic of the .spec file it generates/uses and cannot do fancy stuff like scriplets, etc.
That is, unless you take the approach of having it generate the .spec file and quit (instead of building final RPM). From the docs:
If you wish, you can separate these three steps. You can use the --spec-only option to make bdist_rpm just create the .spec file and exit; in this case, the .spec file will be written to the “distribution directory”—normally dist/, but customizable with the --dist-dir option. (Normally, the .spec file winds up deep in the “build tree,” in a temporary directory created by bdist_rpm.)
But as a matter of preference and consistency, I would advise on following distro-specific guidelines for packaging Python apps.
In that way, you will be more in line with the distro's you are building for.
It is not the easiest way though. You will have to shift through some docs. Basically, if you're building for anything CentOS/RHEL, Fedora guidelines for packaging should be observed.
You can find the extra reference here, with the example .spec file for building both Python 2 and 3 versions of the same app.
For this whole 'build like a distro' thing, you would definitely want to look into using mock for the job, to build your package in a chroot.
As for the "shortcut" issue, you have to have your setup.py declare some console scripts for it to create one when you install your package. E.g. from lastversion's setup.py:
entry_points={"console_scripts": ["lastversion = lastversion:main"]},
This entry will result in a "binary" lastversion created/installed (which runs the defined function) when you install your Python package.
Subsequently, in the spec files, the macro %py2_install will make use of setup.py to create the same launcher program.
And you will then be able to ensure that launcher is packaged by placing it in the files section of the spec file:
%files -n python3-myapp
%license COPYING
%doc README.rst
%{python3_sitelib}/%{srcname}/
%{python3_sitelib}/%{srcname}-*.egg-info/
%{_bindir}/myapp
I just installed Cmake from git clone wget http://www.cmake.org/files/v2.8/cmake-2.8.3.tar.gz in a new folder on a Linux server. The compilation worked but cmake command is not recognized from other paths. Should I copy the entire contents of cmake-2.8.0 folder to usr/local/bin? Or is the contents of bin folder that need to be copied?
Thanks
On Linux and other Unix-based systems, a common arrangement is to install packages to /opt and add relevant entries to the PATH environment variable to make them available. This is intended for packages not provided by the native package manager or distribution. By choosing an appropriate directory structure, this can be done in a way which also allows different versions to be installed simultaneously and the user can pick which one they want by adding the relevant directory to the PATH.
For the specific case of CMake asked about in the question, you can use a directory structure like /opt/cmake/<version> and then add the relevant /opt/cmake/<version>/bin directory to your PATH (e.g. /opt/cmake/3.8.2/bin for the 3.8.2 CMake release). You can even just download the official pre-built CMake tarballs, unpack them and move the top level directory into the /opt/cmake area as the particular version you downloaded. I've used this successfully on Linux, MacOS and Solaris, as I'm sure have many others.
Note that once you've run CMake on a particular source tree, the cmake executable doesn't need to be on the PATH any more. If cmake needs to be re-run, the build will do so itself and it records the full path to the cmake executable in its own cache, so the PATH isn't even consulted (this is essential in ensuring the same version of CMake continues to be used for all builds regardless of the PATH, since PATH can change between login sessions, etc.). You would only need cmake on your PATH if you intend to invoke cmake manually or for the first time you run it on a source tree, but in both of these cases you can always just use the full path to the cmake executable if you preferred.
I should also add that the entire set of files provided in the CMake package are required, not just the bin directory. CMake makes extensive use of files in its other directories, such as the various modules it comes with. If you are building CMake from source, you may want to build the package target so you get a relocatable tarball or similar which will contain everything that should be included when you provide a CMake package on your system.
After the build, use 'sudo make install'. This will make sure the correct libraries and binaries are copied to their proper places.
Usually this will install the binary to /usr/local/bin.
Make sure the PATH variable has this included.
sudo make install did not copy to /usr/local/bin/ for some reason, so I copied the content of CMAKE /bin. to usr/local/bin an it worked.
cp –a bin/. /usr/local/bin/
I'm trying to use wxHaskell to modify wxAsteroids. Every time I try to change something within the wxAsteroids1.1.0.1.tar.gz folder it does not affect the program. Is there a way to update the wxAsteroids.exe in order to use the code? Unzipping the .tar.gz gives me this error when trying to run Asteroids.lhs:
could not find module 'Paths_wxAsteroids'
Use -v to see a list of the files searched for.
tar xzf wxAstroids*
This will get your the package in a wxAstroids-<version> directory. Change to that directory and...
vi xAstroids.cabal
-- Edit the file, add Paths_wxAstroids to the other-modules: list.
Now the package should be fixed, so reinstall this fixed version
cabal install
Yay!
I am trying to build a dev package out of some .so files - i.e libraries.
dh_make -f ../ mylibs.tar.gz
then I choose
-l
since I want a library package.
A debian folder is created which consists of among others the controlfile and the install file.
When I finally create the package with
dpkg-buildpackage
I get the following error message:
dh_install: mylibs-dev missing files (usr/include/*), aborting
I dont understand what is missing since the headers are copied to
usr/include
I have checked the directory and the headers are copied there. So why do I get this error message?
the install-file look like this:
usr/lib/lib*.so.*
So - may the path to usr/include be missing here? I've tried with
usr/include/h.*
but it does not work
The debian install files are most often used for source packages that produce several binary packages. In that case, dh_auto_install installs to the directory debian/tmp/ and dh_install moves the files from there to each package. However, when there is a single package, dh_auto_install takes a shortcut and installs directly to debian/package-name/. In that case, you only need to list in the install file the files that make install missed (usually none). If you list the regular, installed files, dh_install will get confused because it is still looking for them in debian/tmp/.
It is possible to override either the directory where dh_auto_install installs, or the directory where dh_install is looking, but you probably don't need either.
I installed tcl to learn it, however, I installed all the files in the wrong location. I am trying to uninstall it, But the uninstall file does not work. I am trying to carry out the instructions form their website:
To uninstall ActiveTcl, run the "uninstall.tcl" script that is located in the directory where you extracted the ActiveTcl archive. Note that you must use the "wish" in the distribution you wish to uninstall. For example:
% /path/Tcl/bin/wish /path/Tcl/lib/ppm/log/ActiveTcl/uninstall_ActiveTcl.tcl
stored, by default, in the directory /lib/ppm/log/ActiveTcl. You must use the wish interpreter from the distribution you wish to uninstall. Ensure that you do not run the uninstall script from a directory that will be removed during the uninstallation.
For example:
% /path/Tcl/bin/wish /path/Tcl/lib/ppm/log/ActiveTcl/uninstall_ActiveTcl.tcl
Note: if you are uninstalling both ActiveTcl and Tcl Dev Kit, uninstall Tcl Dev Kit before uninstalling ActiveTcl.
There is no uninstall_ActiveTcl.tcl. I do see an "uninstall" file but it does not have an extension, and I do not know how to run it.
Any help is appreciated
Thank you
Try editing the file to a uninstall.tcl file and see if that works. Take a back-up first though. Because we might need that file later
I re-installed it in a new location, compared the files that were installed between the old and the new location and deleted the file sin the old location. Unfortunately I could not delete many of the hidden files, as I did not know if they were there originally or if they belonged to Tcl. I am really surprised and disappointed there is no easy way to uninstall tcl properly.
I strongly suspect that you should uninstall ActiveTcl as follows:
Open a command prompt
Change directory to where you found the install file - e.g.
$ cd path_to_Tcl_installation/bin
Run the file
$ ./uninstall
On linux systems, you don't need any particular file extension in order to be able to run a file.
I don't know CentOS but a little googling led me to a forum thread that describes how to open a command prompt.
Good luck