panda update==>relion starfile read error

[FlorianBeckOle]

Hi,

after reinstalling ArtiaX I get the error pasted below when reading a relion star file:
(os: SLELS15 sp7 ldd (GNU libc) 2.38)
I guess the plugin Installation pulls a new version of starfile and resulting in a new pandas,
which causes the error.
I could fix it by installing an older version of pandas and starfile in ChimeraX command line.
pip install pandas==1.5.3
pip install starfile==0.4.1

But I guess its better to fix ether the packaging or the code upstream.

best

Florian

File "/fs/pool/pool-bmapps/hpcl5S15/app/soft/CHIMERAX/1.9.1/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/fs/pool/pool-bmapps/hpcl5S15/app/soft/CHIMERAX/1.9.1/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 132, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/fs/pool/pool-bmapps/hpcl5S15/app/soft/CHIMERAX/1.9.1/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/fs/pool/pool-bmapps/hpcl5S15/app/soft/CHIMERAX/1.9.1/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 215, in provider_open
models, status = collated_open(session, None, [data], data_format, _add_models,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/fs/pool/pool-bmapps/hpcl5S15/app/soft/CHIMERAX/1.9.1/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 526, in collated_open
return remember_data_format()
^^^^^^^^^^^^^^^^^^^^^^
File "/fs/pool/pool-bmapps/hpcl5S15/app/soft/CHIMERAX/1.9.1/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 497, in remember_data_format
models, status = func(*func_args, **func_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/fs/home/fbecktest/.local/share/ChimeraX/1.9/lib/python3.11/site-packages/chimerax/artiax/io/formats.py", line 25, in open
return open_particle_list(session, data, file_name, format_name=self.name, from_chimx=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/fs/home/fbecktest/.local/share/ChimeraX/1.9/lib/python3.11/site-packages/chimerax/artiax/io/io.py", line 104, in open_particle_list
data = formats[format_name].particle_data(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/fs/home/fbecktest/.local/share/ChimeraX/1.9/lib/python3.11/site-packages/chimerax/artiax/io/RELION/RELIONParticleData.py", line 126, in init
super().init(
File "/fs/home/fbecktest/.local/share/ChimeraX/1.9/lib/python3.11/site-packages/chimerax/artiax/io/ParticleData.py", line 507, in init
self.read_file()
File "/fs/home/fbecktest/.local/share/ChimeraX/1.9/lib/python3.11/site-packages/chimerax/artiax/io/RELION/RELIONParticleData.py", line 252, in read_file
if np.issubdtype(df.dtypes[key], np.number):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/fs/pool/pool-bmapps/hpcl5S15/app/soft/CHIMERAX/1.9.1/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/numpy/core/numerictypes.py", line 417, in issubdtype
arg1 = dtype(arg1).type
^^^^^^^^^^^
TypeError: Cannot interpret '<StringDtype(na_value=nan)>' as a data type

TypeError: Cannot interpret '' as a data type

File "/fs/pool/pool-bmapps/hpcl5S15/app/soft/CHIMERAX/1.9.1/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/numpy/core/numerictypes.py", line 417, in issubdtype
arg1 = dtype(arg1).type
^^^^^^^^^^^

See log for complete Python traceback.
got this error from ArtiaX ChimeraX after rinstalling.
Version evrything the same
Traceback (most recent call last):
File "/fs/home/fbecktest/.local/share/ChimeraX/1.9/lib/python3.11/site-packages/chimerax/artiax/widgets/ArtiaxOpenDialog.py", line 66, in _qt_safe
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""
File "/fs/pool/pool-bmapps/hpcl5S15/app/soft/CHIMERAX/1.9.1/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/fs/pool/pool-bmapps/hpcl5S15/app/soft/CHIMERAX/1.9.1/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/fs/pool/pool-bmapps/hpcl5S15/app/soft/CHIMERAX/1.9.1/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 132, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/fs/pool/pool-bmapps/hpcl5S15/app/soft/CHIMERAX/1.9.1/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/fs/pool/pool-bmapps/hpcl5S15/app/soft/CHIMERAX/1.9.1/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 215, in provider_open
models, status = collated_open(session, None, [data], data_format, _add_models,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/fs/pool/pool-bmapps/hpcl5S15/app/soft/CHIMERAX/1.9.1/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 526, in collated_open
return remember_data_format()
^^^^^^^^^^^^^^^^^^^^^^
File "/fs/pool/pool-bmapps/hpcl5S15/app/soft/CHIMERAX/1.9.1/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 497, in remember_data_format
models, status = func(*func_args, **func_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/fs/home/fbecktest/.local/share/ChimeraX/1.9/lib/python3.11/site-packages/chimerax/artiax/io/formats.py", line 25, in open
return open_particle_list(session, data, file_name, format_name=self.name, from_chimx=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/fs/home/fbecktest/.local/share/ChimeraX/1.9/lib/python3.11/site-packages/chimerax/artiax/io/io.py", line 104, in open_particle_list
data = formats[format_name].particle_data(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/fs/home/fbecktest/.local/share/ChimeraX/1.9/lib/python3.11/site-packages/chimerax/artiax/io/RELION/RELIONParticleData.py", line 126, in init
super().init(
File "/fs/home/fbecktest/.local/share/ChimeraX/1.9/lib/python3.11/site-packages/chimerax/artiax/io/ParticleData.py", line 507, in init
self.read_file()
File "/fs/home/fbecktest/.local/share/ChimeraX/1.9/lib/python3.11/site-packages/chimerax/artiax/io/RELION/RELIONParticleData.py", line 252, in read_file
if np.issubdtype(df.dtypes[key], np.number):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/fs/pool/pool-bmapps/hpcl5S15/app/soft/CHIMERAX/1.9.1/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/numpy/core/numerictypes.py", line 417, in issubdtype
arg1 = dtype(arg1).type
^^^^^^^^^^^
TypeError: Cannot interpret '<StringDtype(na_value=nan)>' as a data type

TypeError: Cannot interpret '' as a data type

File "/fs/pool/pool-bmapps/hpcl5S15/app/soft/CHIMERAX/1.9.1/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/numpy/core/numerictypes.py", line 417, in issubdtype
arg1 = dtype(arg1).type
^^^^^^^^^^^

[uermel]

Hi @FlorianBeckOle , thanks for reporting this. This should be addressed by #53 thanks to @bwmr, and is part of the 0.7.0 release. Please try updating to 0.7.0 and let me know if you encounter any issue.