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9.0 3.0 3.0 1.12 MB

Library for coarse-grained simulations of probes flexibly coupled to biomolecules.

License: Mozilla Public License 2.0

CMake 21.68% C++ 57.60% Python 17.53% Shell 3.18%

pymol fluorescence fret science-research simulation-toolkit accessible-volumes

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mayeshh fdsteffen felixerichson

labellib's Issues

Deploy pip/conda releases by Travis and Appveyor

The pypi and the conda releases are currently maintained manually. I suggest to modify both CI build process to automatically deploy conda and pypi packages for all supported platforms whenever either there is a new release or there is a push to the master branch.

Opinions?

Task list:

Failing osx continous integration build

The master branch CI builds on macOS is failing (see: https://travis-ci.org/Fluorescence-Tools/LabelLib/jobs/659682332).

PyBind11 build issue

There is still a PyBind11 build issue.

This error seems only to occur if there are multiple versions of the same "Python". In the Travis build environment, the path variables are all properly set. Hence, if set(PYTHONLIBS_FOUND TRUE) is set, the Python.h include is still found.

TravisCI output:

CMake Error at thirdparty/pybind11/tools/FindPythonLibsNew.cmake:95 (message):
Python config failure:
pyenv: python3.6: command not found

The `python3.6' command exists in these Python versions:
3.6
3.6.3

I tried to "fix" it by changeing FlexLabel/CMakeList.txt
(see: pybind/pybind11#236)

set(PYTHONLIBS_FOUND TRUE) set(PYTHON_MODULE_EXTENSION .so) set(PYTHON_MODULE_PREFIX "") find_package(pybind11 2.2 QUIET) if(NOT pybind11_FOUND) message(STATUS "Using thirdparty/pybind11") add_subdirectory(${CMAKE_SOURCE_DIR}/thirdparty/pybind11 pybind11_bin) endif(NOT pybind11_FOUND)
However, of course if set(PYTHONLIBS_FOUND TRUE) is used find_package(pybind11 2.2 QUIET) does not initilaize all paths to include Python.h and you get build problems on platforms where the python libraries are not in the paths.

Version naming.

Build
The automated way of naming the python versions is incompatible with source distributions on PyPi. When a source distribution is downloaded there is no Git version. Hence, by default, the installation will have the version "unknown_version"

pip install LabelLib==2019.10.9 install version from 2018

Hi,
I am using the LabelLib package in my code with the new feature of using the points from the AV cloud (av.points()), which was added to the 2019 version of LabelLib (#10)

However, I cannot install the new version via pip on Windows: The command pip install LabelLib==2019.10.9 still installs the old version from 2018. It only works with conda conda install -c tpeulen labellib.

Since I want to add LabelLib to the dependencies of a package, it should work with pip as well. Otherwise it will install the wrong version of LabelLib.

I have seen that the tar.gz file is not provided for the latest versions. But even for the version 2019.3.17, pip installs the 2018.12.14 instead. Do you know, where this might come from? Can you update PyPI to support Windows installations of the latest version. Thank you!

Switch from LGPL to less copyleft MPL

Unlike LGPL, MPL does not require that derived closed software is linked dynamically. Otherwise they are similar. This will allow to make LabelLib header-only.
http://www.mozilla.org/MPL/2.0/FAQ.html

Function that calculates for a given Grid3D a list of cartesian points

This is a very trivial enhancement suggestion, that however may improve the performance of LabelLib, particularly when Python is used

Right now, to create a list of the valid labeling positions, we loop over the density array.

  MP=np.array([0.0,0.0,0.0])
  vol=0.0
  iat = 0
  for iz in range(nz):
    for iy in range(ny):
      for ix in range(nx):
        val = g[ix, iy, iz]
        if val <= 0.0:
          continue

It would be more efficient, if this loop would be implemented in C/C++, meaning if there would be a function that converts a Grid3D object to a list of (Cartesian) points optionally with density values.

Zenodo release and conda-forge

The source code is now tight to Zenodo releases. However, the Zenodo release does not do a git clone --submodule.

Hence, due to the dependency on thirdparty submodules LabelLib cannot be built with the Zenodo release alone.

I know, this is not very elegant, however, to make it possible to build LabelLib using the Zenodo release alone and to address the issue that conda-forge wants releases to be build from tarballs as opposed to git repositories, we should consider coping the dependencies instead of using submodules.

This would solve issues with conda-forge and zenodo alike.

For the next release we could/should link labellib to Zenodo (see: link). This way, LabelLib gets a DOI and could be cited.

Originally posted by @tpeulen in #11 (comment)

pubby-flat issue MacOS

LabelLib does not compile on MacOS. I nailed down the problem to the newly introduced library pubby-flat. In the file 'flat_map.hpp' std::void_t is used. This only became a part of the std library in C++17, which is not supported by clang / LLVM - the standard MacOS compiler.

take a look at line 184 flat_map.hpp

Mirate pybin11 to swig

I would like to make the LabelLib compatible with the integrative modeling (IMP) toolkit. The IMP approach of wrapping C/C++ functions and classes is through SWIG. Hence, I'd like to migrate the pybind11 bindings to SWIG.

Documentation and examples

Could you please provide documentation and some test cases so that I can try using the tool?

LabelLib fails

Hello,

I have had a persistent problem with LabelLib. Upon running the code in pymol

_genAV('ins_sub_2_test0', '/ins_sub_2_test0//F/60/CB', allowed_sphere_radius=1.5, linker_diameter=4.5, linker_length=20.5)_

I get the following error

Traceback (most recent call last):
  File "C:\Users\fbsmawadmin\Anaconda3_\Lib\site-packages\LabelLib\FlexLabel\python\LabelLib_pymol.py", line 40, in genAV
    av1=ll.dyeDensityAV1(xyzRT.T,source,linker_length, linker_diameter, dye_radius, disc_step)
AttributeError: module 'LabelLib' has no attribute 'dyeDensityAV1'

might there be some python script or a line missing that defines the attribute dyeDensityAV1 ??

Opinions on next release

Since the last release in 2018 the the calculation of distance distributions among other features has been added to LabelLib.

If there are no new features planned in the near future, it may be time for a new release.

Contribute LabelLib to conda forge

We should consider to add LabelLib to conda forge. This way, LabelLib could be used with less hassle by more people. I already created a conda-recipe that builds on macOS, Windows, and Linux.

https://github.com/Fluorescence-Tools/conda-recipes/

Only Python 2.7 is a bit tricky to build on Windows because stdint.h is missing in VS 2008 (the standard compiler for Python 2.7 on Windows). If it is okay to drop python 2.7 support for conda-forge contributing LabelLib to conda-forge should be straightforward.

https://conda-forge.org/docs/maintainer/adding_pkgs.html#dev-contribute-pkgs

The question is if we fell that LabelLib is mature enough to be submitted to conda-forge.

Semantic versioning

LabelLib reached a level of maturity where others may start to use it, either by incorporating its code or by linking against it. Still, we may want to change the library. Hence, I suggest to use for future releases semantic versioning. This way, others can easily track if a new release breaks their code.
In semantic versioning:

Given a version number MAJOR.MINOR.PATCH, increment the:

MAJOR version when you make incompatible API changes,
MINOR version when you add functionality in a backwards compatible manner, and
PATCH version when you make backwards compatible bug fixes.

Installation of LabelLib with pip fails

Dear all

A user from us want to use LabelLib with Pymol.

But it fails:

C:\Windows\system32>pip install LabelLib
Collecting LabelLib
  Using cached LabelLib-2019.4.29.tar.gz (3.1 MB)
Requirement already satisfied: numpy in c:\program files\python37\lib\site-packages (from LabelLib) (1.16.4+mkl)
Building wheels for collected packages: LabelLib
  Building wheel for LabelLib (setup.py) ... error
  ERROR: Command errored out with exit status 1:
   command: 'c:\program files\python37\python.exe' -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\\Users\\CRONAD~1\\AppData\\Local\\Temp\\pip-install-yntdocqw\\labellib\\setup.py'"'"'; __file__='"'"'C:\\Users\\CRONAD~1\\AppData\\Local\\Temp\\pip-install-yntdocqw\\labellib\\setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d 'C:\Users\CRONAD~1\AppData\Local\Temp\pip-wheel-xmeh667a'
       cwd: C:\Users\CRONAD~1\AppData\Local\Temp\pip-install-yntdocqw\labellib\
  Complete output (64 lines):
  running bdist_wheel
  running build
  running build_ext
  -- Building for: NMake Makefiles
  CMake Warning (dev) in CMakeLists.txt:
    No project() command is present.  The top-level CMakeLists.txt file must
    contain a literal, direct call to the project() command.  Add a line of
    code such as

      project(ProjectName)

    near the top of the file, but after cmake_minimum_required().

    CMake is pretending there is a "project(Project)" command on the first
    line.
  This warning is for project developers.  Use -Wno-dev to suppress it.

  CMake Error in CMakeLists.txt:
    Generator

      NMake Makefiles

    does not support platform specification, but platform

      x64

    was specified.


  CMake Error: CMAKE_C_COMPILER not set, after EnableLanguage
  CMake Error: CMAKE_CXX_COMPILER not set, after EnableLanguage
  -- Configuring incomplete, errors occurred!
  See also "C:/Users/CronAdmin/AppData/Local/Temp/pip-install-yntdocqw/labellib/build/temp.win-amd64-3.7/Release/CMakeFiles/CMakeOutput.log".
  Traceback (most recent call last):
    File "<string>", line 1, in <module>
    File "C:\Users\CRONAD~1\AppData\Local\Temp\pip-install-yntdocqw\labellib\setup.py", line 85, in <module>
      install_requires=['numpy'],
    File "c:\program files\python37\lib\site-packages\setuptools\__init__.py", line 145, in setup
      return distutils.core.setup(**attrs)
    File "c:\program files\python37\lib\distutils\core.py", line 148, in setup
      dist.run_commands()
    File "c:\program files\python37\lib\distutils\dist.py", line 966, in run_commands
      self.run_command(cmd)
    File "c:\program files\python37\lib\distutils\dist.py", line 985, in run_command
      cmd_obj.run()
    File "c:\program files\python37\lib\site-packages\wheel\bdist_wheel.py", line 290, in run
      self.run_command('build')
    File "c:\program files\python37\lib\distutils\cmd.py", line 313, in run_command
      self.distribution.run_command(command)
    File "c:\program files\python37\lib\distutils\dist.py", line 985, in run_command
      cmd_obj.run()
    File "c:\program files\python37\lib\distutils\command\build.py", line 135, in run
      self.run_command(cmd_name)
    File "c:\program files\python37\lib\distutils\cmd.py", line 313, in run_command
      self.distribution.run_command(command)
    File "c:\program files\python37\lib\distutils\dist.py", line 985, in run_command
      cmd_obj.run()
    File "C:\Users\CRONAD~1\AppData\Local\Temp\pip-install-yntdocqw\labellib\setup.py", line 32, in run
      self.build_extension(ext)
    File "C:\Users\CRONAD~1\AppData\Local\Temp\pip-install-yntdocqw\labellib\setup.py", line 56, in build_extension
      subprocess.check_call(['cmake', ext.sourcedir] + cmake_args, cwd=self.build_temp, env=env)
    File "c:\program files\python37\lib\subprocess.py", line 347, in check_call
      raise CalledProcessError(retcode, cmd)
  subprocess.CalledProcessError: Command '['cmake', 'C:\\Users\\CRONAD~1\\AppData\\Local\\Temp\\pip-install-yntdocqw\\labellib', '-DPYTHON_LIBRARY_OUTPUT_DIRECTORY=C:\\Users\\CRONAD~1\\AppData\\Local\\Temp\\pip-install-yntdocqw\\labellib\\build\\lib.win-amd64-3.7', '-DPYTHON_EXECUTABLE=c:\\program files\\python37\\python.exe', '-DCMAKE_LIBRARY_OUTPUT_DIRECTORY_RELEASE=C:\\Users\\CRONAD~1\\AppData\\Local\\Temp\\pip-install-yntdocqw\\labellib\\build\\lib.win-amd64-3.7', '-A', 'x64']' returned non-zero exit status 1.
  ----------------------------------------
  ERROR: Failed building wheel for LabelLib
  Running setup.py clean for LabelLib
Failed to build LabelLib
Installing collected packages: LabelLib
    Running setup.py install for LabelLib ... error
    ERROR: Command errored out with exit status 1:
     command: 'c:\program files\python37\python.exe' -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\\Users\\CRONAD~1\\AppData\\Local\\Temp\\pip-install-yntdocqw\\labellib\\setup.py'"'"'; __file__='"'"'C:\\Users\\CRONAD~1\\AppData\\Local\\Temp\\pip-install-yntdocqw\\labellib\\setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record 'C:\Users\CRONAD~1\AppData\Local\Temp\pip-record-tig9e8wa\install-record.txt' --single-version-externally-managed --compile --install-headers 'c:\program files\python37\Include\LabelLib'
         cwd: C:\Users\CRONAD~1\AppData\Local\Temp\pip-install-yntdocqw\labellib\
    Complete output (66 lines):
    running install
    running build
    running build_ext
    -- Building for: NMake Makefiles
    CMake Warning (dev) in CMakeLists.txt:
      No project() command is present.  The top-level CMakeLists.txt file must
      contain a literal, direct call to the project() command.  Add a line of
      code such as

        project(ProjectName)

      near the top of the file, but after cmake_minimum_required().

      CMake is pretending there is a "project(Project)" command on the first
      line.
    This warning is for project developers.  Use -Wno-dev to suppress it.

    CMake Error in CMakeLists.txt:
      Generator

        NMake Makefiles

      does not support platform specification, but platform

        x64

      was specified.


    CMake Error: CMAKE_C_COMPILER not set, after EnableLanguage
    CMake Error: CMAKE_CXX_COMPILER not set, after EnableLanguage
    -- Configuring incomplete, errors occurred!
    See also "C:/Users/CronAdmin/AppData/Local/Temp/pip-install-yntdocqw/labellib/build/temp.win-amd64-3.7/Release/CMakeFiles/CMakeOutput.log".
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "C:\Users\CRONAD~1\AppData\Local\Temp\pip-install-yntdocqw\labellib\setup.py", line 85, in <module>
        install_requires=['numpy'],
      File "c:\program files\python37\lib\site-packages\setuptools\__init__.py", line 145, in setup
        return distutils.core.setup(**attrs)
      File "c:\program files\python37\lib\distutils\core.py", line 148, in setup
        dist.run_commands()
      File "c:\program files\python37\lib\distutils\dist.py", line 966, in run_commands
        self.run_command(cmd)
      File "c:\program files\python37\lib\distutils\dist.py", line 985, in run_command
        cmd_obj.run()
      File "c:\program files\python37\lib\site-packages\setuptools\command\install.py", line 61, in run
        return orig.install.run(self)
      File "c:\program files\python37\lib\distutils\command\install.py", line 545, in run
        self.run_command('build')
      File "c:\program files\python37\lib\distutils\cmd.py", line 313, in run_command
        self.distribution.run_command(command)
      File "c:\program files\python37\lib\distutils\dist.py", line 985, in run_command
        cmd_obj.run()
      File "c:\program files\python37\lib\distutils\command\build.py", line 135, in run
        self.run_command(cmd_name)
      File "c:\program files\python37\lib\distutils\cmd.py", line 313, in run_command
        self.distribution.run_command(command)
      File "c:\program files\python37\lib\distutils\dist.py", line 985, in run_command
        cmd_obj.run()
      File "C:\Users\CRONAD~1\AppData\Local\Temp\pip-install-yntdocqw\labellib\setup.py", line 32, in run
        self.build_extension(ext)
      File "C:\Users\CRONAD~1\AppData\Local\Temp\pip-install-yntdocqw\labellib\setup.py", line 56, in build_extension
        subprocess.check_call(['cmake', ext.sourcedir] + cmake_args, cwd=self.build_temp, env=env)
      File "c:\program files\python37\lib\subprocess.py", line 347, in check_call
        raise CalledProcessError(retcode, cmd)
    subprocess.CalledProcessError: Command '['cmake', 'C:\\Users\\CRONAD~1\\AppData\\Local\\Temp\\pip-install-yntdocqw\\labellib', '-DPYTHON_LIBRARY_OUTPUT_DIRECTORY=C:\\Users\\CRONAD~1\\AppData\\Local\\Temp\\pip-install-yntdocqw\\labellib\\build\\lib.win-amd64-3.7', '-DPYTHON_EXECUTABLE=c:\\program files\\python37\\python.exe', '-DCMAKE_LIBRARY_OUTPUT_DIRECTORY_RELEASE=C:\\Users\\CRONAD~1\\AppData\\Local\\Temp\\pip-install-yntdocqw\\labellib\\build\\lib.win-amd64-3.7', '-A', 'x64']' returned non-zero exit status 1.
    ----------------------------------------
ERROR: Command errored out with exit status 1: 'c:\program files\python37\python.exe' -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\\Users\\CRONAD~1\\AppData\\Local\\Temp\\pip-install-yntdocqw\\labellib\\setup.py'"'"'; __file__='"'"'C:\\Users\\CRONAD~1\\AppData\\Local\\Temp\\pip-install-yntdocqw\\labellib\\setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record 'C:\Users\CRONAD~1\AppData\Local\Temp\pip-record-tig9e8wa\install-record.txt' --single-version-externally-managed --compile --install-headers 'c:\program files\python37\Include\LabelLib' Check the logs for full command output.

Any idea why?

Thanks

Continous integration

We should consider continuous integration, e.g., with TravisCI.

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