id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2664 Session save fails for numpy array of strings Tristan Croll Greg Couch "{{{ The following bug report has been submitted: Platform: Linux-3.10.0-957.12.2.el7.x86_64-x86_64-with-centos-7.6.1810-Core ChimeraX Version: 0.91 (2019-12-03) Description This is a little weird... as per #2589, last night saving a session with a `take_snapshot()` method that includes a Numpy array of strings was raising an exception about not being able to create a 1000-odd dimensional array. This morning I added the follwing at line 203 of state.py: {{{ items = [_copy(o) for o in data] print(data.__class__) return data.__class__(items) }}} ... to get a better understanding of what's going on. For reasons unfathomable to me, that changed the traceback to this (much more informative) one - even after I reverted state.py to remove the `print` call. Anyway, the root cause of the traceback is that the session save code doesn't know what to do with a Numpy array of strings - if I convert it to a list, everything is fine. Log: Startup Messages --- warning | 'clip' is a prefix of an existing command 'clipper' UCSF ChimeraX version: 0.91 (2019-12-03) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX Successfully installed 'ChimeraX_ISOLDE-1.0b3.dev9-cp37-cp37m-linux_x86_64.whl' Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ Processing /home/tic20/.cache/ChimeraX/0.91/installers/ChimeraX_ISOLDE-1.0b3.dev9-cp37-cp37m-linux_x86_64.whl Requirement already satisfied, skipping upgrade: ChimeraX-Clipper>=0.9.13 in /home/tic20/.local/share/ChimeraX/0.91/site-packages (from ChimeraX- ISOLDE==1.0b3.dev9) (0.9.13) Requirement already satisfied, skipping upgrade: ChimeraX-Atomic>=1.0 in /opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages (from ChimeraX- ISOLDE==1.0b3.dev9) (1.0) Requirement already satisfied, skipping upgrade: ChimeraX-Core==0.91 in /opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages (from ChimeraX- ISOLDE==1.0b3.dev9) (0.91) Installing collected packages: ChimeraX-ISOLDE Found existing installation: ChimeraX-ISOLDE 1.0b3.dev9 Uninstalling ChimeraX-ISOLDE-1.0b3.dev9: Successfully uninstalled ChimeraX-ISOLDE-1.0b3.dev9 Successfully installed ChimeraX-ISOLDE-1.0b3.dev9 Lock 140266156042576 acquired on /home/tic20/.cache/ChimeraX/0.91/toolshed/bundle_info.cache.lock Lock 140266156042576 released on /home/tic20/.cache/ChimeraX/0.91/toolshed/bundle_info.cache.lock > open test_save_restore.py > open 3io0 structureFactors true Summary of feedback from opening 3io0 fetched from pdb --- warning | WARNING: multiple experimental reflection datasets found: F_meas_au, F_meas_sigma_au, pdbx_F_plus, pdbx_F_plus_sigma, pdbx_F_minus, pdbx_F_minus_sigma, pdbx_anom_difference, pdbx_anom_difference_sigma, intensity_meas, intensity_sigma, pdbx_I_plus, pdbx_I_plus_sigma, pdbx_I_minus, pdbx_I_minus_sigma Automatically choosing ""intensity_meas, intensity_sigma"". note | Reflection data provided as intensities. Performing French & Wilson scaling to convert to amplitudes... 3io0 title: Crystal structure of EtuB from Clostridium kluyveri [more info...] Chain information for 3io0 --- Chain | Description 1.1/A | EtuB protein 3io0 mmCIF Assemblies --- 1| author_and_software_defined_assembly > isolde restrain distances #1 > addh Summary of feedback from adding hydrogens to 3io0 #1.1 --- notes | Termini for 3io0 (#1.1) chain A determined from SEQRES records Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: /A PRO 76 Chain-final residues that are actual C termini: /A PHE 304 Chain-final residues that are not actual C termini: Missing OXT added to C-terminal residue /A PHE 304 198 hydrogen bonds 1692 hydrogens added > isolde start > set selectionWidth 4 executed test_save_restore.py Done loading forcefield > select clear > save test.cxs Session saving is not yet implemented for ISOLDE. Custom restraints will not be saved. Traceback (most recent call last): File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/session.py"", line 796, in save session.save(output, version=version, include_maps=include_maps) File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/session.py"", line 556, in save mgr.discovery(self._state_containers) File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/session.py"", line 255, in discovery self.processed[key] = self.process(obj, parents) File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/session.py"", line 288, in process return copy_state(data, convert=convert) File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/state.py"", line 208, in copy_state return _copy(data) File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/state.py"", line 195, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/state.py"", line 195, in items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/state.py"", line 203, in _copy return data.__class__(items) TypeError: 'str' object cannot be interpreted as an integer TypeError: 'str' object cannot be interpreted as an integer File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/state.py"", line 203, in _copy return data.__class__(items) See log for complete Python traceback. Traceback (most recent call last): File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/cmd_line/tool.py"", line 258, in execute cmd.run(cmd_text) File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2837, in run result = ci.function(session, **kw_args) File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/commands/save.py"", line 64, in save _handle_unexpected_keyword_error(e, 5) File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/commands/save.py"", line 61, in save fmt.export(session, filename, fmt.nicknames[0], **kw) File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/io.py"", line 220, in export result = self.export_func(session, path, **kw) File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/session.py"", line 796, in save session.save(output, version=version, include_maps=include_maps) File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/session.py"", line 556, in save mgr.discovery(self._state_containers) File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/session.py"", line 255, in discovery self.processed[key] = self.process(obj, parents) File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/session.py"", line 288, in process return copy_state(data, convert=convert) File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/state.py"", line 208, in copy_state return _copy(data) File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/state.py"", line 195, in _copy items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/state.py"", line 195, in items = [(_copy(k), _copy(v)) for k, v in data.items()] File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/state.py"", line 203, in _copy return data.__class__(items) TypeError: 'str' object cannot be interpreted as an integer TypeError: 'str' object cannot be interpreted as an integer File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/state.py"", line 203, in _copy return data.__class__(items) See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 418.87.01 OpenGL renderer: TITAN Xp/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation }}} " defect closed normal 0.91 Sessions wontfix all ChimeraX