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December 7, 2015 16:59
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| ====================================================================== | |
| ERROR: test_coordinates (MDAnalysisTests.coordinates.test_dcd.TestNCDF2DCD) | |
| ---------------------------------------------------------------------- | |
| Traceback (most recent call last): | |
| File "/users/ardita/MDAPCAvenv2/lib/python2.7/site-packages/MDAnalysisTests-0.13.0_dev0-py2.7.egg/MDAnalysisTests/coordinates/test_dcd.py", line 373, in setUp | |
| self.u = mda.Universe(PRMncdf, NCDF) | |
| File "/users/ardita/MDAPCAvenv2/lib/python2.7/site-packages/MDAnalysis-0.13.0_dev0-py2.7-linux-x86_64.egg/MDAnalysis/core/AtomGroup.py", line 3801, in __init__ | |
| self.load_new(coordinatefile, **kwargs) | |
| File "/users/ardita/MDAPCAvenv2/lib/python2.7/site-packages/MDAnalysis-0.13.0_dev0-py2.7-linux-x86_64.egg/MDAnalysis/core/AtomGroup.py", line 4341, in load_new | |
| self.trajectory = reader(filename, **kwargs) # unified trajectory API | |
| File "/users/ardita/MDAPCAvenv2/lib/python2.7/site-packages/MDAnalysis-0.13.0_dev0-py2.7-linux-x86_64.egg/MDAnalysis/coordinates/TRJ.py", line 421, in __init__ | |
| raise ImportError("netCDF4 package missing.\n" | |
| ImportError: netCDF4 package missing. | |
| netcdf4-python with the netCDF and HDF5 libraries must be installed for the AMBER ncdf Reader. | |
| See installation instructions at https://github.com/MDAnalysis/mdanalysis/wiki/netcdf | |
| -------------------- >> begin captured logging << -------------------- | |
| MDAnalysis.core.AtomGroup: DEBUG: Universe.load_new(): loading /users/ardita/MDAPCAvenv2/lib/python2.7/site-packages/MDAnalysisTests-0.13.0_dev0-py2.7.egg/MDAnalysisTests/data/Amber/bala.ncdf... | |
| MDAnalysis.coordinates.AMBER: CRITICAL: netcdf4-python with the netCDF and HDF5 libraries must be installed for the AMBER ncdf Reader. | |
| MDAnalysis.coordinates.AMBER: CRITICAL: See installation instructions at https://github.com/MDAnalysis/mdanalysis/wiki/netcdf | |
| --------------------- >> end captured logging << --------------------- | |
| ====================================================================== | |
| ERROR: NCDFReader: Test that DCDWriter correctly writes the CHARMM | |
| ---------------------------------------------------------------------- | |
| Traceback (most recent call last): | |
| File "/users/ardita/MDAPCAvenv2/lib/python2.7/site-packages/MDAnalysisTests-0.13.0_dev0-py2.7.egg/MDAnalysisTests/coordinates/test_dcd.py", line 373, in setUp | |
| self.u = mda.Universe(PRMncdf, NCDF) | |
| File "/users/ardita/MDAPCAvenv2/lib/python2.7/site-packages/MDAnalysis-0.13.0_dev0-py2.7-linux-x86_64.egg/MDAnalysis/core/AtomGroup.py", line 3801, in __init__ | |
| self.load_new(coordinatefile, **kwargs) | |
| File "/users/ardita/MDAPCAvenv2/lib/python2.7/site-packages/MDAnalysis-0.13.0_dev0-py2.7-linux-x86_64.egg/MDAnalysis/core/AtomGroup.py", line 4341, in load_new | |
| self.trajectory = reader(filename, **kwargs) # unified trajectory API | |
| File "/users/ardita/MDAPCAvenv2/lib/python2.7/site-packages/MDAnalysis-0.13.0_dev0-py2.7-linux-x86_64.egg/MDAnalysis/coordinates/TRJ.py", line 421, in __init__ | |
| raise ImportError("netCDF4 package missing.\n" | |
| ImportError: netCDF4 package missing. | |
| netcdf4-python with the netCDF and HDF5 libraries must be installed for the AMBER ncdf Reader. | |
| See installation instructions at https://github.com/MDAnalysis/mdanalysis/wiki/netcdf | |
| -------------------- >> begin captured logging << -------------------- | |
| MDAnalysis.core.AtomGroup: DEBUG: Universe.load_new(): loading /users/ardita/MDAPCAvenv2/lib/python2.7/site-packages/MDAnalysisTests-0.13.0_dev0-py2.7.egg/MDAnalysisTests/data/Amber/bala.ncdf... | |
| MDAnalysis.coordinates.AMBER: CRITICAL: netcdf4-python with the netCDF and HDF5 libraries must be installed for the AMBER ncdf Reader. | |
| MDAnalysis.coordinates.AMBER: CRITICAL: See installation instructions at https://github.com/MDAnalysis/mdanalysis/wiki/netcdf | |
| --------------------- >> end captured logging << --------------------- | |
| ====================================================================== | |
| ERROR: test_hausdorff_bound (MDAnalysisTests.analysis.test_psa.TestPSAnalysis) | |
| ---------------------------------------------------------------------- | |
| Traceback (most recent call last): | |
| File "/users/ardita/MDAPCAvenv2/lib/python2.7/site-packages/MDAnalysisTests-0.13.0_dev0-py2.7.egg/MDAnalysisTests/analysis/test_psa.py", line 57, in tearDown | |
| shutil.rmtree('psadata') # remove psa data directory | |
| File "/usr/remote/python/2.7.8/lib/python2.7/shutil.py", line 247, in rmtree | |
| rmtree(fullname, ignore_errors, onerror) | |
| File "/usr/remote/python/2.7.8/lib/python2.7/shutil.py", line 256, in rmtree | |
| onerror(os.rmdir, path, sys.exc_info()) | |
| File "/usr/remote/python/2.7.8/lib/python2.7/shutil.py", line 254, in rmtree | |
| os.rmdir(path) | |
| OSError: [Errno 39] Directory not empty: 'psadata/fitted_trajs' | |
| -------------------- >> begin captured stderr << --------------------- | |
| Fitted frame 90/98 [ 91.8%]] | |
| --------------------- >> end captured stderr << ---------------------- | |
| -------------------- >> begin captured logging << -------------------- | |
| MDAnalysis.topology.PSF: DEBUG: PSF file /users/ardita/MDAPCAvenv2/lib/python2.7/site-packages/MDAnalysisTests-0.13.0_dev0-py2.7.egg/MDAnalysisTests/data/adk.psf: format STANDARD | |
| MDAnalysis.core.AtomGroup: DEBUG: Universe.load_new(): loading /users/ardita/MDAPCAvenv2/lib/python2.7/site-packages/MDAnalysisTests-0.13.0_dev0-py2.7.egg/MDAnalysisTests/data/adk_dims.dcd... | |
| MDAnalysis.topology.PSF: DEBUG: PSF file /users/ardita/MDAPCAvenv2/lib/python2.7/site-packages/MDAnalysisTests-0.13.0_dev0-py2.7.egg/MDAnalysisTests/data/adk.psf: format STANDARD | |
| MDAnalysis.core.AtomGroup: DEBUG: Universe.load_new(): loading /users/ardita/MDAPCAvenv2/lib/python2.7/site-packages/MDAnalysisTests-0.13.0_dev0-py2.7.egg/MDAnalysisTests/data/adk_dims2.dcd... | |
| MDAnalysis.topology.PSF: DEBUG: PSF file /users/ardita/MDAPCAvenv2/lib/python2.7/site-packages/MDAnalysisTests-0.13.0_dev0-py2.7.egg/MDAnalysisTests/data/adk.psf: format STANDARD | |
| MDAnalysis.core.AtomGroup: DEBUG: Universe.load_new(): loading /users/ardita/MDAPCAvenv2/lib/python2.7/site-packages/MDAnalysisTests-0.13.0_dev0-py2.7.egg/MDAnalysisTests/data/adk_dims.dcd... | |
| MDAnalysis.analysis.align: INFO: RMS-fitting on 214 atoms. | |
| MDAnalysis.analysis.align: INFO: Wrote 98 RMS-fitted coordinate frames to file '/users/ardita/MDAPCA2/mdanalysis/testsuite/MDAnalysisTests/psadata/fitted_trajs/fitted_psa001.dcd' | |
| MDAnalysis.topology.PSF: DEBUG: PSF file /users/ardita/MDAPCAvenv2/lib/python2.7/site-packages/MDAnalysisTests-0.13.0_dev0-py2.7.egg/MDAnalysisTests/data/adk.psf: format STANDARD | |
| MDAnalysis.core.AtomGroup: DEBUG: Universe.load_new(): loading /users/ardita/MDAPCA2/mdanalysis/testsuite/MDAnalysisTests/psadata/fitted_trajs/fitted_psa001.dcd... | |
| MDAnalysis.analysis.align: INFO: RMS-fitting on 214 atoms. | |
| MDAnalysis.analysis.align: INFO: Wrote 102 RMS-fitted coordinate frames to file '/users/ardita/MDAPCA2/mdanalysis/testsuite/MDAnalysisTests/psadata/fitted_trajs/fitted_psa002.dcd' | |
| MDAnalysis.topology.PSF: DEBUG: PSF file /users/ardita/MDAPCAvenv2/lib/python2.7/site-packages/MDAnalysisTests-0.13.0_dev0-py2.7.egg/MDAnalysisTests/data/adk.psf: format STANDARD | |
| MDAnalysis.core.AtomGroup: DEBUG: Universe.load_new(): loading /users/ardita/MDAPCA2/mdanalysis/testsuite/MDAnalysisTests/psadata/fitted_trajs/fitted_psa002.dcd... | |
| MDAnalysis.analysis.align: INFO: RMS-fitting on 214 atoms. | |
| MDAnalysis.analysis.align: INFO: Wrote 98 RMS-fitted coordinate frames to file '/users/ardita/MDAPCA2/mdanalysis/testsuite/MDAnalysisTests/psadata/fitted_trajs/fitted_psa003.dcd' | |
| MDAnalysis.topology.PSF: DEBUG: PSF file /users/ardita/MDAPCAvenv2/lib/python2.7/site-packages/MDAnalysisTests-0.13.0_dev0-py2.7.egg/MDAnalysisTests/data/adk.psf: format STANDARD | |
| MDAnalysis.core.AtomGroup: DEBUG: Universe.load_new(): loading /users/ardita/MDAPCA2/mdanalysis/testsuite/MDAnalysisTests/psadata/fitted_trajs/fitted_psa003.dcd... | |
| MDAnalysis.analysis.psa: INFO: Wrote distance matrix to file '/users/ardita/MDAPCA2/mdanalysis/testsuite/MDAnalysisTests/psadata/distance_matrices/hausdorff'.npz | |
| MDAnalysis.analysis.psa: INFO: Wrote distance matrix to file '/users/ardita/MDAPCA2/mdanalysis/testsuite/MDAnalysisTests/psadata/distance_matrices/hausdorff'.dat | |
| MDAnalysis.analysis.psa: INFO: Wrote distance matrix to file '/users/ardita/MDAPCA2/mdanalysis/testsuite/MDAnalysisTests/psadata/distance_matrices/discrete_frechet'.npz | |
| MDAnalysis.analysis.psa: INFO: Wrote distance matrix to file '/users/ardita/MDAPCA2/mdanalysis/testsuite/MDAnalysisTests/psadata/distance_matrices/discrete_frechet'.dat | |
| --------------------- >> end captured logging << --------------------- | |
| ====================================================================== | |
| ERROR: test_reversal_frechet (MDAnalysisTests.analysis.test_psa.TestPSAnalysis) | |
| ---------------------------------------------------------------------- | |
| Traceback (most recent call last): | |
| File "/users/ardita/MDAPCAvenv2/lib/python2.7/site-packages/MDAnalysisTests-0.13.0_dev0-py2.7.egg/MDAnalysisTests/analysis/test_psa.py", line 57, in tearDown | |
| shutil.rmtree('psadata') # remove psa data directory | |
| File "/usr/remote/python/2.7.8/lib/python2.7/shutil.py", line 247, in rmtree | |
| rmtree(fullname, ignore_errors, onerror) | |
| File "/usr/remote/python/2.7.8/lib/python2.7/shutil.py", line 256, in rmtree | |
| onerror(os.rmdir, path, sys.exc_info()) | |
| File "/usr/remote/python/2.7.8/lib/python2.7/shutil.py", line 254, in rmtree | |
| os.rmdir(path) | |
| OSError: [Errno 39] Directory not empty: 'psadata/fitted_trajs' | |
| -------------------- >> begin captured stderr << --------------------- | |
| Fitted frame 90/98 [ 91.8%]] | |
| --------------------- >> end captured stderr << ---------------------- | |
| -------------------- >> begin captured logging << -------------------- | |
| MDAnalysis.topology.PSF: DEBUG: PSF file /users/ardita/MDAPCAvenv2/lib/python2.7/site-packages/MDAnalysisTests-0.13.0_dev0-py2.7.egg/MDAnalysisTests/data/adk.psf: format STANDARD | |
| MDAnalysis.core.AtomGroup: DEBUG: Universe.load_new(): loading /users/ardita/MDAPCAvenv2/lib/python2.7/site-packages/MDAnalysisTests-0.13.0_dev0-py2.7.egg/MDAnalysisTests/data/adk_dims.dcd... | |
| MDAnalysis.topology.PSF: DEBUG: PSF file /users/ardita/MDAPCAvenv2/lib/python2.7/site-packages/MDAnalysisTests-0.13.0_dev0-py2.7.egg/MDAnalysisTests/data/adk.psf: format STANDARD | |
| MDAnalysis.core.AtomGroup: DEBUG: Universe.load_new(): loading /users/ardita/MDAPCAvenv2/lib/python2.7/site-packages/MDAnalysisTests-0.13.0_dev0-py2.7.egg/MDAnalysisTests/data/adk_dims2.dcd... | |
| MDAnalysis.topology.PSF: DEBUG: PSF file /users/ardita/MDAPCAvenv2/lib/python2.7/site-packages/MDAnalysisTests-0.13.0_dev0-py2.7.egg/MDAnalysisTests/data/adk.psf: format STANDARD | |
| MDAnalysis.core.AtomGroup: DEBUG: Universe.load_new(): loading /users/ardita/MDAPCAvenv2/lib/python2.7/site-packages/MDAnalysisTests-0.13.0_dev0-py2.7.egg/MDAnalysisTests/data/adk_dims.dcd... | |
| MDAnalysis.analysis.align: INFO: RMS-fitting on 214 atoms. | |
| MDAnalysis.analysis.align: INFO: Wrote 98 RMS-fitted coordinate frames to file '/users/ardita/MDAPCA2/mdanalysis/testsuite/MDAnalysisTests/psadata/fitted_trajs/fitted_psa001.dcd' | |
| MDAnalysis.topology.PSF: DEBUG: PSF file /users/ardita/MDAPCAvenv2/lib/python2.7/site-packages/MDAnalysisTests-0.13.0_dev0-py2.7.egg/MDAnalysisTests/data/adk.psf: format STANDARD | |
| MDAnalysis.core.AtomGroup: DEBUG: Universe.load_new(): loading /users/ardita/MDAPCA2/mdanalysis/testsuite/MDAnalysisTests/psadata/fitted_trajs/fitted_psa001.dcd... | |
| MDAnalysis.analysis.align: INFO: RMS-fitting on 214 atoms. | |
| MDAnalysis.analysis.align: INFO: Wrote 102 RMS-fitted coordinate frames to file '/users/ardita/MDAPCA2/mdanalysis/testsuite/MDAnalysisTests/psadata/fitted_trajs/fitted_psa002.dcd' | |
| MDAnalysis.topology.PSF: DEBUG: PSF file /users/ardita/MDAPCAvenv2/lib/python2.7/site-packages/MDAnalysisTests-0.13.0_dev0-py2.7.egg/MDAnalysisTests/data/adk.psf: format STANDARD | |
| MDAnalysis.core.AtomGroup: DEBUG: Universe.load_new(): loading /users/ardita/MDAPCA2/mdanalysis/testsuite/MDAnalysisTests/psadata/fitted_trajs/fitted_psa002.dcd... | |
| MDAnalysis.analysis.align: INFO: RMS-fitting on 214 atoms. | |
| MDAnalysis.analysis.align: INFO: Wrote 98 RMS-fitted coordinate frames to file '/users/ardita/MDAPCA2/mdanalysis/testsuite/MDAnalysisTests/psadata/fitted_trajs/fitted_psa003.dcd' | |
| MDAnalysis.topology.PSF: DEBUG: PSF file /users/ardita/MDAPCAvenv2/lib/python2.7/site-packages/MDAnalysisTests-0.13.0_dev0-py2.7.egg/MDAnalysisTests/data/adk.psf: format STANDARD | |
| MDAnalysis.core.AtomGroup: DEBUG: Universe.load_new(): loading /users/ardita/MDAPCA2/mdanalysis/testsuite/MDAnalysisTests/psadata/fitted_trajs/fitted_psa003.dcd... | |
| MDAnalysis.analysis.psa: INFO: Wrote distance matrix to file '/users/ardita/MDAPCA2/mdanalysis/testsuite/MDAnalysisTests/psadata/distance_matrices/hausdorff'.npz | |
| MDAnalysis.analysis.psa: INFO: Wrote distance matrix to file '/users/ardita/MDAPCA2/mdanalysis/testsuite/MDAnalysisTests/psadata/distance_matrices/hausdorff'.dat | |
| MDAnalysis.analysis.psa: INFO: Wrote distance matrix to file '/users/ardita/MDAPCA2/mdanalysis/testsuite/MDAnalysisTests/psadata/distance_matrices/discrete_frechet'.npz | |
| MDAnalysis.analysis.psa: INFO: Wrote distance matrix to file '/users/ardita/MDAPCA2/mdanalysis/testsuite/MDAnalysisTests/psadata/distance_matrices/discrete_frechet'.dat | |
| --------------------- >> end captured logging << --------------------- | |
| ====================================================================== | |
| ERROR: test_reversal_hausdorff (MDAnalysisTests.analysis.test_psa.TestPSAnalysis) | |
| ---------------------------------------------------------------------- | |
| Traceback (most recent call last): | |
| File "/users/ardita/MDAPCAvenv2/lib/python2.7/site-packages/MDAnalysisTests-0.13.0_dev0-py2.7.egg/MDAnalysisTests/analysis/test_psa.py", line 57, in tearDown | |
| shutil.rmtree('psadata') # remove psa data directory | |
| File "/usr/remote/python/2.7.8/lib/python2.7/shutil.py", line 247, in rmtree | |
| rmtree(fullname, ignore_errors, onerror) | |
| File "/usr/remote/python/2.7.8/lib/python2.7/shutil.py", line 256, in rmtree | |
| onerror(os.rmdir, path, sys.exc_info()) | |
| File "/usr/remote/python/2.7.8/lib/python2.7/shutil.py", line 254, in rmtree | |
| os.rmdir(path) | |
| OSError: [Errno 39] Directory not empty: 'psadata/fitted_trajs' | |
| -------------------- >> begin captured stderr << --------------------- | |
| Fitted frame 90/98 [ 91.8%]] | |
| --------------------- >> end captured stderr << ---------------------- | |
| -------------------- >> begin captured logging << -------------------- | |
| MDAnalysis.topology.PSF: DEBUG: PSF file /users/ardita/MDAPCAvenv2/lib/python2.7/site-packages/MDAnalysisTests-0.13.0_dev0-py2.7.egg/MDAnalysisTests/data/adk.psf: format STANDARD | |
| MDAnalysis.core.AtomGroup: DEBUG: Universe.load_new(): loading /users/ardita/MDAPCAvenv2/lib/python2.7/site-packages/MDAnalysisTests-0.13.0_dev0-py2.7.egg/MDAnalysisTests/data/adk_dims.dcd... | |
| MDAnalysis.topology.PSF: DEBUG: PSF file /users/ardita/MDAPCAvenv2/lib/python2.7/site-packages/MDAnalysisTests-0.13.0_dev0-py2.7.egg/MDAnalysisTests/data/adk.psf: format STANDARD | |
| MDAnalysis.core.AtomGroup: DEBUG: Universe.load_new(): loading /users/ardita/MDAPCAvenv2/lib/python2.7/site-packages/MDAnalysisTests-0.13.0_dev0-py2.7.egg/MDAnalysisTests/data/adk_dims2.dcd... | |
| MDAnalysis.topology.PSF: DEBUG: PSF file /users/ardita/MDAPCAvenv2/lib/python2.7/site-packages/MDAnalysisTests-0.13.0_dev0-py2.7.egg/MDAnalysisTests/data/adk.psf: format STANDARD | |
| MDAnalysis.core.AtomGroup: DEBUG: Universe.load_new(): loading /users/ardita/MDAPCAvenv2/lib/python2.7/site-packages/MDAnalysisTests-0.13.0_dev0-py2.7.egg/MDAnalysisTests/data/adk_dims.dcd... | |
| MDAnalysis.analysis.align: INFO: RMS-fitting on 214 atoms. | |
| MDAnalysis.analysis.align: INFO: Wrote 98 RMS-fitted coordinate frames to file '/users/ardita/MDAPCA2/mdanalysis/testsuite/MDAnalysisTests/psadata/fitted_trajs/fitted_psa001.dcd' | |
| MDAnalysis.topology.PSF: DEBUG: PSF file /users/ardita/MDAPCAvenv2/lib/python2.7/site-packages/MDAnalysisTests-0.13.0_dev0-py2.7.egg/MDAnalysisTests/data/adk.psf: format STANDARD | |
| MDAnalysis.core.AtomGroup: DEBUG: Universe.load_new(): loading /users/ardita/MDAPCA2/mdanalysis/testsuite/MDAnalysisTests/psadata/fitted_trajs/fitted_psa001.dcd... | |
| MDAnalysis.analysis.align: INFO: RMS-fitting on 214 atoms. | |
| MDAnalysis.analysis.align: INFO: Wrote 102 RMS-fitted coordinate frames to file '/users/ardita/MDAPCA2/mdanalysis/testsuite/MDAnalysisTests/psadata/fitted_trajs/fitted_psa002.dcd' | |
| MDAnalysis.topology.PSF: DEBUG: PSF file /users/ardita/MDAPCAvenv2/lib/python2.7/site-packages/MDAnalysisTests-0.13.0_dev0-py2.7.egg/MDAnalysisTests/data/adk.psf: format STANDARD | |
| MDAnalysis.core.AtomGroup: DEBUG: Universe.load_new(): loading /users/ardita/MDAPCA2/mdanalysis/testsuite/MDAnalysisTests/psadata/fitted_trajs/fitted_psa002.dcd... | |
| MDAnalysis.analysis.align: INFO: RMS-fitting on 214 atoms. | |
| MDAnalysis.analysis.align: INFO: Wrote 98 RMS-fitted coordinate frames to file '/users/ardita/MDAPCA2/mdanalysis/testsuite/MDAnalysisTests/psadata/fitted_trajs/fitted_psa003.dcd' | |
| MDAnalysis.topology.PSF: DEBUG: PSF file /users/ardita/MDAPCAvenv2/lib/python2.7/site-packages/MDAnalysisTests-0.13.0_dev0-py2.7.egg/MDAnalysisTests/data/adk.psf: format STANDARD | |
| MDAnalysis.core.AtomGroup: DEBUG: Universe.load_new(): loading /users/ardita/MDAPCA2/mdanalysis/testsuite/MDAnalysisTests/psadata/fitted_trajs/fitted_psa003.dcd... | |
| MDAnalysis.analysis.psa: INFO: Wrote distance matrix to file '/users/ardita/MDAPCA2/mdanalysis/testsuite/MDAnalysisTests/psadata/distance_matrices/hausdorff'.npz | |
| MDAnalysis.analysis.psa: INFO: Wrote distance matrix to file '/users/ardita/MDAPCA2/mdanalysis/testsuite/MDAnalysisTests/psadata/distance_matrices/hausdorff'.dat | |
| MDAnalysis.analysis.psa: INFO: Wrote distance matrix to file '/users/ardita/MDAPCA2/mdanalysis/testsuite/MDAnalysisTests/psadata/distance_matrices/discrete_frechet'.npz | |
| MDAnalysis.analysis.psa: INFO: Wrote distance matrix to file '/users/ardita/MDAPCA2/mdanalysis/testsuite/MDAnalysisTests/psadata/distance_matrices/discrete_frechet'.dat | |
| --------------------- >> end captured logging << --------------------- | |
| ---------------------------------------------------------------------- | |
| Ran 3360 tests in 209.631s | |
| FAILED (KNOWNFAIL=3, SKIP=48, errors=5) |
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