I had some troubles installing vmd-python into VirtualEnv (sorry, not a big fan of Conda) on Ubuntu 18.04:
$ python3 -m venv test_venv # Create empty environment
$ . test_venv/bin/activate
$ pip install numpy
Successfully installed numpy-1.16.2
$ python setup.py install
running install
running build
Finding libraries...
Newer libtcl8.6 used
LIB: libtcl8.6.so -> /usr/lib/x86_64-linux-gnu/
INC: tcl.h -> /usr/include/tcl8.6/
LIB: libsqlite3.so -> /usr/lib/x86_64-linux-gnu/
INC: sqlite3.h -> /usr/include/
LIB: libexpat.so -> /usr/lib/x86_64-linux-gnu/
INC: expat.h -> /usr/include/
LIB: libnetcdf.so -> /usr/lib/x86_64-linux-gnu/
INC: netcdf.h -> /usr/include/
Finding python location via fallback method...
Traceback (most recent call last):
File "setup.py", line 458, in <module>
'test': VMDTest,
File "/tmp/test_venv/lib/python3.6/site-packages/setuptools/__init__.py", line 129, in setup
return distutils.core.setup(**attrs)
File "/usr/lib/python3.6/distutils/core.py", line 148, in setup
dist.run_commands()
File "/usr/lib/python3.6/distutils/dist.py", line 955, in run_commands
self.run_command(cmd)
File "/usr/lib/python3.6/distutils/dist.py", line 974, in run_command
cmd_obj.run()
File "setup.py", line 424, in run
self.run_command("build")
File "/usr/lib/python3.6/distutils/cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "/usr/lib/python3.6/distutils/dist.py", line 974, in run_command
cmd_obj.run()
File "setup.py", line 71, in run
self.compile_vmd()
File "setup.py", line 85, in compile_vmd
self.set_environment_variables(pydir)
File "setup.py", line 327, in set_environment_variables
pythonldflag = self._get_python_ldflag(pydir)
File "setup.py", line 251, in _get_python_ldflag
candidate_libs = self._find_library_dir(pylibname)
File "setup.py", line 216, in _find_library_dir
libfile);
RuntimeError: Could not find library 'libpython3.6*.so' in standard library directories. Update $LD_LIBRARY_PATH to include the directory containing this file, or make sure it is present on your system
The problem is that in case of VirtualEnv (and, I guess, system-wide Python), sysconfig.get_config_var("LIBDIR") does not return the directory where libpythonX.Y.so is stored.
Unable to find a more robust way to deal with this issue, I've adapted this StackOverflow answer to check both LIBDIR and LIBPL paths. It works with both VirtualEnv (Python 3.6) and Anaconda (Python 3.7) for me.
I'm not sure you want this additional complexity if you're not planning to support VirtualEnv as an installation method, but IMHO it's nice to have.
Hi!
I had some troubles installing vmd-python into VirtualEnv (sorry, not a big fan of Conda) on Ubuntu 18.04:
The problem is that in case of VirtualEnv (and, I guess, system-wide Python),
sysconfig.get_config_var("LIBDIR")does not return the directory where libpythonX.Y.so is stored.Unable to find a more robust way to deal with this issue, I've adapted this StackOverflow answer to check both
LIBDIRandLIBPLpaths. It works with both VirtualEnv (Python 3.6) and Anaconda (Python 3.7) for me.I'm not sure you want this additional complexity if you're not planning to support VirtualEnv as an installation method, but IMHO it's nice to have.