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Opened 10 months ago
Closed 6 months ago
#16558 closed defect (fixed)
Cannot 'pip install pyKVFinger'
| Reported by: | Owned by: | Zach Pearson | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | chimera-programmers | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.26100
ChimeraX Version: 1.10.dev202412280203 (2024-12-28 02:03:40 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
UCSF ChimeraX version: 1.10.dev202412280203 (2024-12-28)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "C:/Users/taher/Desktop/4i23 prepared protein.cxs"
Log from Mon Jan 6 13:04:30 2025 Startup Messages
---
warning | Your computer has Intel graphics driver 7810 with a known bug that causes all Qt user interface panels to be blank. ChimeraX can partially fix this but may make some panel titlebars and edges black. Hopefully newer Intel graphics drivers will fix this.
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.10.dev202412280203 (2024-12-28)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 4i23 fromDatabase pdbe_bio format mmcif
Summary of feedback from opening 4i23 fetched from pdbe_bio
---
warning | Missing or incomplete sequence information. Inferred polymer connectivity.
4i23 bioassembly 1 title:
Crystal structure of the wild-type EGFR kinase domain in complex with
dacomitinib (soaked) [more info...]
Chain information for 4i23 bioassembly 1 #1
---
Chain | Description
A | Epidermal growth factor receptor
Non-standard residues in 4i23 bioassembly 1 #1
---
1C9 — (1C9)
Computing secondary structure
Opened 1 biological assemblies for 4i23
> select protein
2429 atoms, 2479 bonds, 3 pseudobonds, 304 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> save "C:/Users/taher/Desktop/4i23 ligand.cxs"
> close session
> open 4i23 format mmcif fromDatabase pdbe_bio
Summary of feedback from opening 4i23 fetched from pdbe_bio
---
warning | Missing or incomplete sequence information. Inferred polymer connectivity.
4i23 bioassembly 1 title:
Crystal structure of the wild-type EGFR kinase domain in complex with
dacomitinib (soaked) [more info...]
Chain information for 4i23 bioassembly 1 #1
---
Chain | Description
A | Epidermal growth factor receptor
Non-standard residues in 4i23 bioassembly 1 #1
---
1C9 — (1C9)
Computing secondary structure
Opened 1 biological assemblies for 4i23
> open 4i23 format mmcif fromDatabase pdbe_bio
Summary of feedback from opening 4i23 fetched from pdbe_bio
---
warning | Missing or incomplete sequence information. Inferred polymer connectivity.
4i23 bioassembly 1 title:
Crystal structure of the wild-type EGFR kinase domain in complex with
dacomitinib (soaked) [more info...]
Chain information for 4i23 bioassembly 1 #2
---
Chain | Description
A | Epidermal growth factor receptor
Non-standard residues in 4i23 bioassembly 1 #2
---
1C9 — (1C9)
Opened 1 biological assemblies for 4i23
Computing secondary structure
> select ligand
44 atoms, 48 bonds, 2 residues, 2 models selected
> delete atoms sel
> delete bonds sel
> select #2/A
2429 atoms, 2479 bonds, 3 pseudobonds, 304 residues, 2 models selected
> select clear
> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"
4858 atoms, 4958 bonds, 6 pseudobonds, 608 residues, 4 models selected
> select ions
Nothing selected
> select solvent
Nothing selected
> ui tool show "Dock Prep"
Starting dock prep
Deleting solvent
Deleting non-metal-complex ions
Deleting non-current alt locs
Filling out missing side chains
4i23 bioassembly 1 #1/A ILE 1018: phi -117.4, psi none trans
4i23 bioassembly 1 #2/A ILE 1018: phi -117.4, psi none trans
Applying ILE rotamer (chi angles: 61.7 -80.0) to 4i23 bioassembly 1 #1/A ILE
1018
Applying ILE rotamer (chi angles: 61.7 -80.0) to 4i23 bioassembly 1 #2/A ILE
1018
Summary of feedback from adding hydrogens to multiple structures
---
notes | No usable SEQRES records for 4i23 bioassembly 1 (#1) chain A; guessing termini instead
Chain-initial residues that are actual N termini: 4i23 bioassembly 1 #1/A SER
695
Chain-initial residues that are not actual N termini: 4i23 bioassembly 1 #1/A
GLY 724, 4i23 bioassembly 1 #1/A ALA 750, 4i23 bioassembly 1 #1/A ASP 1006
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: 4i23 bioassembly 1 #1/A
ILE 1018, 4i23 bioassembly 1 #1/A SER 720, 4i23 bioassembly 1 #1/A LEU 747,
4i23 bioassembly 1 #1/A PRO 990
Adding 'H' to 4i23 bioassembly 1 #1/A GLY 724
Adding 'H' to 4i23 bioassembly 1 #1/A ALA 750
Adding 'H' to 4i23 bioassembly 1 #1/A ASP 1006
4i23 bioassembly 1 #1/A ILE 1018 is not terminus, removing H atom from 'C'
No usable SEQRES records for 4i23 bioassembly 1 (#2) chain A; guessing termini
instead
Chain-initial residues that are actual N termini: 4i23 bioassembly 1 #2/A SER
695
Chain-initial residues that are not actual N termini: 4i23 bioassembly 1 #2/A
GLY 724, 4i23 bioassembly 1 #2/A ALA 750, 4i23 bioassembly 1 #2/A ASP 1006
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: 4i23 bioassembly 1 #2/A
ILE 1018, 4i23 bioassembly 1 #2/A SER 720, 4i23 bioassembly 1 #2/A LEU 747,
4i23 bioassembly 1 #2/A PRO 990
Adding 'H' to 4i23 bioassembly 1 #2/A GLY 724
Adding 'H' to 4i23 bioassembly 1 #2/A ALA 750
Adding 'H' to 4i23 bioassembly 1 #2/A ASP 1006
4i23 bioassembly 1 #2/A ILE 1018 is not terminus, removing H atom from 'C'
4966 hydrogens added
Closest equivalent command: addcharge standardizeResidues none
Using Amber 20 recommended default charges and atom types for standard
residues
Dock prep finished
> select ligand
Nothing selected
> save "C:/Users/taher/Desktop/4i23 prepared protein.cxs"
——— End of log from Mon Jan 6 13:04:30 2025 ———
> view name session-start
opened ChimeraX session
> ui tool show "Find Cavities"
pyKVFinder module not installed; fetching from PyPi repository...
'pip install pyKVFinder' failed. Error from pip: WARNING: Retrying
(Retry(total=4, connect=None, read=None, redirect=None, status=None)) after
connection broken by
'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at
0x00000226E5955ED0>: Failed to establish a new connection: [Errno 11001]
getaddrinfo failed')': /simple/pykvfinder/
WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None,
status=None)) after connection broken by
'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at
0x00000226E5956E50>: Failed to establish a new connection: [Errno 11001]
getaddrinfo failed')': /simple/pykvfinder/
WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None,
status=None)) after connection broken by
'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at
0x00000226E5957A90>: Failed to establish a new connection: [Errno 11001]
getaddrinfo failed')': /simple/pykvfinder/
WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None,
status=None)) after connection broken by
'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at
0x00000226E5964150>: Failed to establish a new connection: [Errno 11001]
getaddrinfo failed')': /simple/pykvfinder/
WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None,
status=None)) after connection broken by
'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at
0x00000226E5965210>: Failed to establish a new connection: [Errno 11001]
getaddrinfo failed')': /simple/pykvfinder/
ERROR: Could not find a version that satisfies the requirement pyKVFinder
(from versions: none)
ERROR: No matching distribution found for pyKVFinder
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\kvfinder\\__init__.py", line 48, in check_pyKVFinder
import pyKVFinder
ModuleNotFoundError: No module named 'pyKVFinder'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 571, in start_tool
ti = api._api_caller.start_tool(api, session, self, tool_info)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1399, in start_tool
return cls._get_func(api, "start_tool")(session, ti.name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\kvfinder\\__init__.py", line 42, in start_tool
check_pyKVFinder(session.logger)
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\kvfinder\\__init__.py", line 54, in check_pyKVFinder
run(logger.session, pip_cmd, log=False)
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\core\commands\pip.py", line 88, in pip
run_logged_pip(pip_cmd, session.logger)
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\core\python_utils.py", line 143, in run_logged_pip
raise RuntimeError(s)
RuntimeError: WARNING: Retrying (Retry(total=4, connect=None, read=None,
redirect=None, status=None)) after connection broken by
'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at
0x00000226E5955ED0>: Failed to establish a new connection: [Errno 11001]
getaddrinfo failed')': /simple/pykvfinder/
WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None,
status=None)) after connection broken by
'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at
0x00000226E5956E50>: Failed to establish a new connection: [Errno 11001]
getaddrinfo failed')': /simple/pykvfinder/
WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None,
status=None)) after connection broken by
'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at
0x00000226E5957A90>: Failed to establish a new connection: [Errno 11001]
getaddrinfo failed')': /simple/pykvfinder/
WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None,
status=None)) after connection broken by
'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at
0x00000226E5964150>: Failed to establish a new connection: [Errno 11001]
getaddrinfo failed')': /simple/pykvfinder/
WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None,
status=None)) after connection broken by
'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at
0x00000226E5965210>: Failed to establish a new connection: [Errno 11001]
getaddrinfo failed')': /simple/pykvfinder/
ERROR: Could not find a version that satisfies the requirement pyKVFinder
(from versions: none)
ERROR: No matching distribution found for pyKVFinder
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\ui\gui.py", line 1863, in <lambda>
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\ui\cmd.py", line 219, in ui_tool_show
return bi.start_tool(session, name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 578, in start_tool
raise ToolshedError(
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Find
Cavities in bundle ChimeraX-KVFinder:
WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None,
status=None)) after connection broken by
'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at
0x00000226E5955ED0>: Failed to establish a new connection: [Errno 11001]
getaddrinfo failed')': /simple/pykvfinder/
WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None,
status=None)) after connection broken by
'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at
0x00000226E5956E50>: Failed to establish a new connection: [Errno 11001]
getaddrinfo failed')': /simple/pykvfinder/
WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None,
status=None)) after connection broken by
'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at
0x00000226E5957A90>: Failed to establish a new connection: [Errno 11001]
getaddrinfo failed')': /simple/pykvfinder/
WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None,
status=None)) after connection broken by
'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at
0x00000226E5964150>: Failed to establish a new connection: [Errno 11001]
getaddrinfo failed')': /simple/pykvfinder/
WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None,
status=None)) after connection broken by
'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at
0x00000226E5965210>: Failed to establish a new connection: [Errno 11001]
getaddrinfo failed')': /simple/pykvfinder/
ERROR: Could not find a version that satisfies the requirement pyKVFinder
(from versions: none)
ERROR: No matching distribution found for pyKVFinder
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Find
Cavities in bundle ChimeraX-KVFinder:
WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None,
status=None)) after connection broken by 'NewConnectionError(': Failed to
establish a new connection: [Errno 11001] getaddrinfo failed')':
/simple/pykvfinder/
WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None,
status=None)) after connection broken by 'NewConnectionError(': Failed to
establish a new connection: [Errno 11001] getaddrinfo failed')':
/simple/pykvfinder/
WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None,
status=None)) after connection broken by 'NewConnectionError(': Failed to
establish a new connection: [Errno 11001] getaddrinfo failed')':
/simple/pykvfinder/
WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None,
status=None)) after connection broken by 'NewConnectionError(': Failed to
establish a new connection: [Errno 11001] getaddrinfo failed')':
/simple/pykvfinder/
WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None,
status=None)) after connection broken by 'NewConnectionError(': Failed to
establish a new connection: [Errno 11001] getaddrinfo failed')':
/simple/pykvfinder/
ERROR: Could not find a version that satisfies the requirement pyKVFinder
(from versions: none)
ERROR: No matching distribution found for pyKVFinder
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 578, in start_tool
raise ToolshedError(
See log for complete Python traceback.
> ui tool show "Find Cavities"
pyKVFinder module not installed; fetching from PyPi repository...
'pip install pyKVFinder' failed. Error from pip: WARNING: Retrying
(Retry(total=4, connect=None, read=None, redirect=None, status=None)) after
connection broken by
'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at
0x000001A14A505ED0>: Failed to establish a new connection: [Errno 11001]
getaddrinfo failed')': /simple/pykvfinder/
WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None,
status=None)) after connection broken by
'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at
0x000001A14A506E90>: Failed to establish a new connection: [Errno 11001]
getaddrinfo failed')': /simple/pykvfinder/
WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None,
status=None)) after connection broken by
'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at
0x000001A14A507990>: Failed to establish a new connection: [Errno 11001]
getaddrinfo failed')': /simple/pykvfinder/
WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None,
status=None)) after connection broken by
'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at
0x000001A14A514150>: Failed to establish a new connection: [Errno 11001]
getaddrinfo failed')': /simple/pykvfinder/
WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None,
status=None)) after connection broken by
'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at
0x000001A14A515250>: Failed to establish a new connection: [Errno 11001]
getaddrinfo failed')': /simple/pykvfinder/
ERROR: Could not find a version that satisfies the requirement pyKVFinder
(from versions: none)
ERROR: No matching distribution found for pyKVFinder
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\kvfinder\\__init__.py", line 48, in check_pyKVFinder
import pyKVFinder
ModuleNotFoundError: No module named 'pyKVFinder'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 571, in start_tool
ti = api._api_caller.start_tool(api, session, self, tool_info)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1399, in start_tool
return cls._get_func(api, "start_tool")(session, ti.name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\kvfinder\\__init__.py", line 42, in start_tool
check_pyKVFinder(session.logger)
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\kvfinder\\__init__.py", line 54, in check_pyKVFinder
run(logger.session, pip_cmd, log=False)
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\core\commands\pip.py", line 88, in pip
run_logged_pip(pip_cmd, session.logger)
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\core\python_utils.py", line 143, in run_logged_pip
raise RuntimeError(s)
RuntimeError: WARNING: Retrying (Retry(total=4, connect=None, read=None,
redirect=None, status=None)) after connection broken by
'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at
0x000001A14A505ED0>: Failed to establish a new connection: [Errno 11001]
getaddrinfo failed')': /simple/pykvfinder/
WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None,
status=None)) after connection broken by
'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at
0x000001A14A506E90>: Failed to establish a new connection: [Errno 11001]
getaddrinfo failed')': /simple/pykvfinder/
WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None,
status=None)) after connection broken by
'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at
0x000001A14A507990>: Failed to establish a new connection: [Errno 11001]
getaddrinfo failed')': /simple/pykvfinder/
WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None,
status=None)) after connection broken by
'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at
0x000001A14A514150>: Failed to establish a new connection: [Errno 11001]
getaddrinfo failed')': /simple/pykvfinder/
WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None,
status=None)) after connection broken by
'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at
0x000001A14A515250>: Failed to establish a new connection: [Errno 11001]
getaddrinfo failed')': /simple/pykvfinder/
ERROR: Could not find a version that satisfies the requirement pyKVFinder
(from versions: none)
ERROR: No matching distribution found for pyKVFinder
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\ui\gui.py", line 1863, in <lambda>
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\ui\cmd.py", line 219, in ui_tool_show
return bi.start_tool(session, name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 578, in start_tool
raise ToolshedError(
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Find
Cavities in bundle ChimeraX-KVFinder:
WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None,
status=None)) after connection broken by
'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at
0x000001A14A505ED0>: Failed to establish a new connection: [Errno 11001]
getaddrinfo failed')': /simple/pykvfinder/
WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None,
status=None)) after connection broken by
'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at
0x000001A14A506E90>: Failed to establish a new connection: [Errno 11001]
getaddrinfo failed')': /simple/pykvfinder/
WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None,
status=None)) after connection broken by
'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at
0x000001A14A507990>: Failed to establish a new connection: [Errno 11001]
getaddrinfo failed')': /simple/pykvfinder/
WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None,
status=None)) after connection broken by
'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at
0x000001A14A514150>: Failed to establish a new connection: [Errno 11001]
getaddrinfo failed')': /simple/pykvfinder/
WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None,
status=None)) after connection broken by
'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at
0x000001A14A515250>: Failed to establish a new connection: [Errno 11001]
getaddrinfo failed')': /simple/pykvfinder/
ERROR: Could not find a version that satisfies the requirement pyKVFinder
(from versions: none)
ERROR: No matching distribution found for pyKVFinder
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Find
Cavities in bundle ChimeraX-KVFinder:
WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None,
status=None)) after connection broken by 'NewConnectionError(': Failed to
establish a new connection: [Errno 11001] getaddrinfo failed')':
/simple/pykvfinder/
WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None,
status=None)) after connection broken by 'NewConnectionError(': Failed to
establish a new connection: [Errno 11001] getaddrinfo failed')':
/simple/pykvfinder/
WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None,
status=None)) after connection broken by 'NewConnectionError(': Failed to
establish a new connection: [Errno 11001] getaddrinfo failed')':
/simple/pykvfinder/
WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None,
status=None)) after connection broken by 'NewConnectionError(': Failed to
establish a new connection: [Errno 11001] getaddrinfo failed')':
/simple/pykvfinder/
WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None,
status=None)) after connection broken by 'NewConnectionError(': Failed to
establish a new connection: [Errno 11001] getaddrinfo failed')':
/simple/pykvfinder/
ERROR: Could not find a version that satisfies the requirement pyKVFinder
(from versions: none)
ERROR: No matching distribution found for pyKVFinder
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 578, in start_tool
raise ToolshedError(
See log for complete Python traceback.
> ui tool show "Find Cavities"
pyKVFinder module not installed; fetching from PyPi repository...
'pip install pyKVFinder' failed. Error from pip:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\kvfinder\\__init__.py", line 48, in check_pyKVFinder
import pyKVFinder
ModuleNotFoundError: No module named 'pyKVFinder'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 571, in start_tool
ti = api._api_caller.start_tool(api, session, self, tool_info)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1399, in start_tool
return cls._get_func(api, "start_tool")(session, ti.name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\kvfinder\\__init__.py", line 42, in start_tool
check_pyKVFinder(session.logger)
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\kvfinder\\__init__.py", line 54, in check_pyKVFinder
run(logger.session, pip_cmd, log=False)
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\core\commands\pip.py", line 88, in pip
run_logged_pip(pip_cmd, session.logger)
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\core\python_utils.py", line 143, in run_logged_pip
raise RuntimeError(s)
RuntimeError
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\ui\gui.py", line 1863, in <lambda>
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\ui\cmd.py", line 219, in ui_tool_show
return bi.start_tool(session, name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 578, in start_tool
raise ToolshedError(
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Find
Cavities in bundle ChimeraX-KVFinder:
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Find
Cavities in bundle ChimeraX-KVFinder:
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 578, in start_tool
raise ToolshedError(
See log for complete Python traceback.
> ui tool show "Find Cavities"
pyKVFinder module not installed; fetching from PyPi repository...
'pip install pyKVFinder' failed. Error from pip: ERROR: Exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_vendor\urllib3\response.py", line 438, in _error_catcher
yield
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_vendor\urllib3\response.py", line 561, in read
data = self._fp_read(amt) if not fp_closed else b""
^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_vendor\urllib3\response.py", line 527, in _fp_read
return self._fp.read(amt) if amt is not None else self._fp.read()
^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_vendor\cachecontrol\filewrapper.py", line 98, in read
data: bytes = self.__fp.read(amt)
^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\http\client.py",
line 466, in read
s = self.fp.read(amt)
^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\socket.py", line
706, in readinto
return self._sock.recv_into(b)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\ssl.py", line
1278, in recv_into
return self.read(nbytes, buffer)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\ssl.py", line
1134, in read
return self._sslobj.read(len, buffer)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ssl.SSLError: [SSL: DECRYPTION_FAILED_OR_BAD_RECORD_MAC] decryption failed or
bad record mac (_ssl.c:2576)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\cli\base_command.py", line 105, in _run_wrapper
status = _inner_run()
^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\cli\base_command.py", line 96, in _inner_run
return self.run(options, args)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\cli\req_command.py", line 67, in wrapper
return func(self, options, args)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\commands\install.py", line 379, in run
requirement_set = resolver.resolve(
^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\resolution\resolvelib\resolver.py", line 179, in
resolve
self.factory.preparer.prepare_linked_requirements_more(reqs)
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\operations\prepare.py", line 554, in
prepare_linked_requirements_more
self._complete_partial_requirements(
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\operations\prepare.py", line 469, in
_complete_partial_requirements
for link, (filepath, _) in batch_download:
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\network\download.py", line 184, in __call__
for chunk in chunks:
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\network\utils.py", line 65, in response_chunks
for chunk in response.raw.stream(
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_vendor\urllib3\response.py", line 622, in stream
data = self.read(amt=amt, decode_content=decode_content)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_vendor\urllib3\response.py", line 560, in read
with self._error_catcher():
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\contextlib.py",
line 155, in __exit__
self.gen.throw(typ, value, traceback)
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_vendor\urllib3\response.py", line 449, in _error_catcher
raise SSLError(e)
pip._vendor.urllib3.exceptions.SSLError: [SSL:
DECRYPTION_FAILED_OR_BAD_RECORD_MAC] decryption failed or bad record mac
(_ssl.c:2576)
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\kvfinder\\__init__.py", line 48, in check_pyKVFinder
import pyKVFinder
ModuleNotFoundError: No module named 'pyKVFinder'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 571, in start_tool
ti = api._api_caller.start_tool(api, session, self, tool_info)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1399, in start_tool
return cls._get_func(api, "start_tool")(session, ti.name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\kvfinder\\__init__.py", line 42, in start_tool
check_pyKVFinder(session.logger)
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\kvfinder\\__init__.py", line 54, in check_pyKVFinder
run(logger.session, pip_cmd, log=False)
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\core\commands\pip.py", line 88, in pip
run_logged_pip(pip_cmd, session.logger)
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\core\python_utils.py", line 143, in run_logged_pip
raise RuntimeError(s)
RuntimeError: ERROR: Exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_vendor\urllib3\response.py", line 438, in _error_catcher
yield
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_vendor\urllib3\response.py", line 561, in read
data = self._fp_read(amt) if not fp_closed else b""
^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_vendor\urllib3\response.py", line 527, in _fp_read
return self._fp.read(amt) if amt is not None else self._fp.read()
^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_vendor\cachecontrol\filewrapper.py", line 98, in read
data: bytes = self.__fp.read(amt)
^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\http\client.py",
line 466, in read
s = self.fp.read(amt)
^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\socket.py", line
706, in readinto
return self._sock.recv_into(b)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\ssl.py", line
1278, in recv_into
return self.read(nbytes, buffer)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\ssl.py", line
1134, in read
return self._sslobj.read(len, buffer)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ssl.SSLError: [SSL: DECRYPTION_FAILED_OR_BAD_RECORD_MAC] decryption failed or
bad record mac (_ssl.c:2576)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\cli\base_command.py", line 105, in _run_wrapper
status = _inner_run()
^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\cli\base_command.py", line 96, in _inner_run
return self.run(options, args)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\cli\req_command.py", line 67, in wrapper
return func(self, options, args)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\commands\install.py", line 379, in run
requirement_set = resolver.resolve(
^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\resolution\resolvelib\resolver.py", line 179, in
resolve
self.factory.preparer.prepare_linked_requirements_more(reqs)
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\operations\prepare.py", line 554, in
prepare_linked_requirements_more
self._complete_partial_requirements(
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\operations\prepare.py", line 469, in
_complete_partial_requirements
for link, (filepath, _) in batch_download:
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\network\download.py", line 184, in __call__
for chunk in chunks:
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\network\utils.py", line 65, in response_chunks
for chunk in response.raw.stream(
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_vendor\urllib3\response.py", line 622, in stream
data = self.read(amt=amt, decode_content=decode_content)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_vendor\urllib3\response.py", line 560, in read
with self._error_catcher():
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\contextlib.py",
line 155, in __exit__
self.gen.throw(typ, value, traceback)
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_vendor\urllib3\response.py", line 449, in _error_catcher
raise SSLError(e)
pip._vendor.urllib3.exceptions.SSLError: [SSL:
DECRYPTION_FAILED_OR_BAD_RECORD_MAC] decryption failed or bad record mac
(_ssl.c:2576)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\ui\gui.py", line 1863, in <lambda>
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\ui\cmd.py", line 219, in ui_tool_show
return bi.start_tool(session, name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 578, in start_tool
raise ToolshedError(
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Find
Cavities in bundle ChimeraX-KVFinder:
ERROR: Exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_vendor\urllib3\response.py", line 438, in _error_catcher
yield
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_vendor\urllib3\response.py", line 561, in read
data = self._fp_read(amt) if not fp_closed else b""
^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_vendor\urllib3\response.py", line 527, in _fp_read
return self._fp.read(amt) if amt is not None else self._fp.read()
^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_vendor\cachecontrol\filewrapper.py", line 98, in read
data: bytes = self.__fp.read(amt)
^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\http\client.py",
line 466, in read
s = self.fp.read(amt)
^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\socket.py", line
706, in readinto
return self._sock.recv_into(b)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\ssl.py", line
1278, in recv_into
return self.read(nbytes, buffer)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\ssl.py", line
1134, in read
return self._sslobj.read(len, buffer)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ssl.SSLError: [SSL: DECRYPTION_FAILED_OR_BAD_RECORD_MAC] decryption failed or
bad record mac (_ssl.c:2576)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\cli\base_command.py", line 105, in _run_wrapper
status = _inner_run()
^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\cli\base_command.py", line 96, in _inner_run
return self.run(options, args)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\cli\req_command.py", line 67, in wrapper
return func(self, options, args)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\commands\install.py", line 379, in run
requirement_set = resolver.resolve(
^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\resolution\resolvelib\resolver.py", line 179, in
resolve
self.factory.preparer.prepare_linked_requirements_more(reqs)
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\operations\prepare.py", line 554, in
prepare_linked_requirements_more
self._complete_partial_requirements(
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\operations\prepare.py", line 469, in
_complete_partial_requirements
for link, (filepath, _) in batch_download:
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\network\download.py", line 184, in __call__
for chunk in chunks:
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\network\utils.py", line 65, in response_chunks
for chunk in response.raw.stream(
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_vendor\urllib3\response.py", line 622, in stream
data = self.read(amt=amt, decode_content=decode_content)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_vendor\urllib3\response.py", line 560, in read
with self._error_catcher():
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\contextlib.py",
line 155, in __exit__
self.gen.throw(typ, value, traceback)
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_vendor\urllib3\response.py", line 449, in _error_catcher
raise SSLError(e)
pip._vendor.urllib3.exceptions.SSLError: [SSL:
DECRYPTION_FAILED_OR_BAD_RECORD_MAC] decryption failed or bad record mac
(_ssl.c:2576)
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Find
Cavities in bundle ChimeraX-KVFinder:
ERROR: Exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_vendor\urllib3\response.py", line 438, in _error_catcher
yield
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_vendor\urllib3\response.py", line 561, in read
data = self._fp_read(amt) if not fp_closed else b""
^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_vendor\urllib3\response.py", line 527, in _fp_read
return self._fp.read(amt) if amt is not None else self._fp.read()
^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_vendor\cachecontrol\filewrapper.py", line 98, in read
data: bytes = self.__fp.read(amt)
^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\http\client.py",
line 466, in read
s = self.fp.read(amt)
^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\socket.py", line
706, in readinto
return self._sock.recv_into(b)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\ssl.py", line
1278, in recv_into
return self.read(nbytes, buffer)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\ssl.py", line
1134, in read
return self._sslobj.read(len, buffer)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ssl.SSLError: [SSL: DECRYPTION_FAILED_OR_BAD_RECORD_MAC] decryption failed or
bad record mac (_ssl.c:2576)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\cli\base_command.py", line 105, in _run_wrapper
status = _inner_run()
^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\cli\base_command.py", line 96, in _inner_run
return self.run(options, args)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\cli\req_command.py", line 67, in wrapper
return func(self, options, args)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\commands\install.py", line 379, in run
requirement_set = resolver.resolve(
^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\resolution\resolvelib\resolver.py", line 179, in
resolve
self.factory.preparer.prepare_linked_requirements_more(reqs)
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\operations\prepare.py", line 554, in
prepare_linked_requirements_more
self._complete_partial_requirements(
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\operations\prepare.py", line 469, in
_complete_partial_requirements
for link, (filepath, _) in batch_download:
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\network\download.py", line 184, in __call__
for chunk in chunks:
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\network\utils.py", line 65, in response_chunks
for chunk in response.raw.stream(
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_vendor\urllib3\response.py", line 622, in stream
data = self.read(amt=amt, decode_content=decode_content)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_vendor\urllib3\response.py", line 560, in read
with self._error_catcher():
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\contextlib.py",
line 155, in __exit__
self.gen.throw(typ, value, traceback)
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_vendor\urllib3\response.py", line 449, in _error_catcher
raise SSLError(e)
pip._vendor.urllib3.exceptions.SSLError: [SSL:
DECRYPTION_FAILED_OR_BAD_RECORD_MAC] decryption failed or bad record mac
(_ssl.c:2576)
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 578, in start_tool
raise ToolshedError(
See log for complete Python traceback.
> select protein
9824 atoms, 9924 bonds, 6 pseudobonds, 608 residues, 4 models selected
> ui tool show "Find Cavities"
pyKVFinder module not installed; fetching from PyPi repository...
'pip install pyKVFinder' failed. Error from pip:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\kvfinder\\__init__.py", line 48, in check_pyKVFinder
import pyKVFinder
ModuleNotFoundError: No module named 'pyKVFinder'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 571, in start_tool
ti = api._api_caller.start_tool(api, session, self, tool_info)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1399, in start_tool
return cls._get_func(api, "start_tool")(session, ti.name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\kvfinder\\__init__.py", line 42, in start_tool
check_pyKVFinder(session.logger)
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\kvfinder\\__init__.py", line 54, in check_pyKVFinder
run(logger.session, pip_cmd, log=False)
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\core\commands\pip.py", line 88, in pip
run_logged_pip(pip_cmd, session.logger)
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\core\python_utils.py", line 143, in run_logged_pip
raise RuntimeError(s)
RuntimeError
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\ui\gui.py", line 1863, in <lambda>
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\ui\cmd.py", line 219, in ui_tool_show
return bi.start_tool(session, name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 578, in start_tool
raise ToolshedError(
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Find
Cavities in bundle ChimeraX-KVFinder:
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Find
Cavities in bundle ChimeraX-KVFinder:
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 578, in start_tool
raise ToolshedError(
See log for complete Python traceback.
> ui tool show "Find Cavities"
pyKVFinder module not installed; fetching from PyPi repository...
'pip install pyKVFinder' failed. Error from pip: ERROR: Exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_vendor\urllib3\response.py", line 438, in _error_catcher
yield
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_vendor\urllib3\response.py", line 561, in read
data = self._fp_read(amt) if not fp_closed else b""
^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_vendor\urllib3\response.py", line 527, in _fp_read
return self._fp.read(amt) if amt is not None else self._fp.read()
^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_vendor\cachecontrol\filewrapper.py", line 98, in read
data: bytes = self.__fp.read(amt)
^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\http\client.py",
line 466, in read
s = self.fp.read(amt)
^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\socket.py", line
706, in readinto
return self._sock.recv_into(b)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\ssl.py", line
1278, in recv_into
return self.read(nbytes, buffer)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\ssl.py", line
1134, in read
return self._sslobj.read(len, buffer)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ssl.SSLError: [SSL: DECRYPTION_FAILED_OR_BAD_RECORD_MAC] decryption failed or
bad record mac (_ssl.c:2576)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\cli\base_command.py", line 105, in _run_wrapper
status = _inner_run()
^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\cli\base_command.py", line 96, in _inner_run
return self.run(options, args)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\cli\req_command.py", line 67, in wrapper
return func(self, options, args)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\commands\install.py", line 379, in run
requirement_set = resolver.resolve(
^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\resolution\resolvelib\resolver.py", line 179, in
resolve
self.factory.preparer.prepare_linked_requirements_more(reqs)
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\operations\prepare.py", line 554, in
prepare_linked_requirements_more
self._complete_partial_requirements(
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\operations\prepare.py", line 469, in
_complete_partial_requirements
for link, (filepath, _) in batch_download:
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\network\download.py", line 184, in __call__
for chunk in chunks:
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\network\utils.py", line 65, in response_chunks
for chunk in response.raw.stream(
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_vendor\urllib3\response.py", line 622, in stream
data = self.read(amt=amt, decode_content=decode_content)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_vendor\urllib3\response.py", line 560, in read
with self._error_catcher():
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\contextlib.py",
line 155, in __exit__
self.gen.throw(typ, value, traceback)
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_vendor\urllib3\response.py", line 449, in _error_catcher
raise SSLError(e)
pip._vendor.urllib3.exceptions.SSLError: [SSL:
DECRYPTION_FAILED_OR_BAD_RECORD_MAC] decryption failed or bad record mac
(_ssl.c:2576)
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\kvfinder\\__init__.py", line 48, in check_pyKVFinder
import pyKVFinder
ModuleNotFoundError: No module named 'pyKVFinder'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 571, in start_tool
ti = api._api_caller.start_tool(api, session, self, tool_info)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1399, in start_tool
return cls._get_func(api, "start_tool")(session, ti.name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\kvfinder\\__init__.py", line 42, in start_tool
check_pyKVFinder(session.logger)
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\kvfinder\\__init__.py", line 54, in check_pyKVFinder
run(logger.session, pip_cmd, log=False)
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\core\commands\pip.py", line 88, in pip
run_logged_pip(pip_cmd, session.logger)
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\core\python_utils.py", line 143, in run_logged_pip
raise RuntimeError(s)
RuntimeError: ERROR: Exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_vendor\urllib3\response.py", line 438, in _error_catcher
yield
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_vendor\urllib3\response.py", line 561, in read
data = self._fp_read(amt) if not fp_closed else b""
^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_vendor\urllib3\response.py", line 527, in _fp_read
return self._fp.read(amt) if amt is not None else self._fp.read()
^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_vendor\cachecontrol\filewrapper.py", line 98, in read
data: bytes = self.__fp.read(amt)
^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\http\client.py",
line 466, in read
s = self.fp.read(amt)
^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\socket.py", line
706, in readinto
return self._sock.recv_into(b)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\ssl.py", line
1278, in recv_into
return self.read(nbytes, buffer)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\ssl.py", line
1134, in read
return self._sslobj.read(len, buffer)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ssl.SSLError: [SSL: DECRYPTION_FAILED_OR_BAD_RECORD_MAC] decryption failed or
bad record mac (_ssl.c:2576)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\cli\base_command.py", line 105, in _run_wrapper
status = _inner_run()
^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\cli\base_command.py", line 96, in _inner_run
return self.run(options, args)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\cli\req_command.py", line 67, in wrapper
return func(self, options, args)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\commands\install.py", line 379, in run
requirement_set = resolver.resolve(
^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\resolution\resolvelib\resolver.py", line 179, in
resolve
self.factory.preparer.prepare_linked_requirements_more(reqs)
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\operations\prepare.py", line 554, in
prepare_linked_requirements_more
self._complete_partial_requirements(
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\operations\prepare.py", line 469, in
_complete_partial_requirements
for link, (filepath, _) in batch_download:
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\network\download.py", line 184, in __call__
for chunk in chunks:
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\network\utils.py", line 65, in response_chunks
for chunk in response.raw.stream(
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_vendor\urllib3\response.py", line 622, in stream
data = self.read(amt=amt, decode_content=decode_content)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_vendor\urllib3\response.py", line 560, in read
with self._error_catcher():
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\contextlib.py",
line 155, in __exit__
self.gen.throw(typ, value, traceback)
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_vendor\urllib3\response.py", line 449, in _error_catcher
raise SSLError(e)
pip._vendor.urllib3.exceptions.SSLError: [SSL:
DECRYPTION_FAILED_OR_BAD_RECORD_MAC] decryption failed or bad record mac
(_ssl.c:2576)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\ui\gui.py", line 1863, in <lambda>
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\ui\cmd.py", line 219, in ui_tool_show
return bi.start_tool(session, name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 578, in start_tool
raise ToolshedError(
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Find
Cavities in bundle ChimeraX-KVFinder:
ERROR: Exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_vendor\urllib3\response.py", line 438, in _error_catcher
yield
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_vendor\urllib3\response.py", line 561, in read
data = self._fp_read(amt) if not fp_closed else b""
^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_vendor\urllib3\response.py", line 527, in _fp_read
return self._fp.read(amt) if amt is not None else self._fp.read()
^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_vendor\cachecontrol\filewrapper.py", line 98, in read
data: bytes = self.__fp.read(amt)
^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\http\client.py",
line 466, in read
s = self.fp.read(amt)
^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\socket.py", line
706, in readinto
return self._sock.recv_into(b)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\ssl.py", line
1278, in recv_into
return self.read(nbytes, buffer)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\ssl.py", line
1134, in read
return self._sslobj.read(len, buffer)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ssl.SSLError: [SSL: DECRYPTION_FAILED_OR_BAD_RECORD_MAC] decryption failed or
bad record mac (_ssl.c:2576)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\cli\base_command.py", line 105, in _run_wrapper
status = _inner_run()
^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\cli\base_command.py", line 96, in _inner_run
return self.run(options, args)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\cli\req_command.py", line 67, in wrapper
return func(self, options, args)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\commands\install.py", line 379, in run
requirement_set = resolver.resolve(
^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\resolution\resolvelib\resolver.py", line 179, in
resolve
self.factory.preparer.prepare_linked_requirements_more(reqs)
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\operations\prepare.py", line 554, in
prepare_linked_requirements_more
self._complete_partial_requirements(
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\operations\prepare.py", line 469, in
_complete_partial_requirements
for link, (filepath, _) in batch_download:
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\network\download.py", line 184, in __call__
for chunk in chunks:
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\network\utils.py", line 65, in response_chunks
for chunk in response.raw.stream(
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_vendor\urllib3\response.py", line 622, in stream
data = self.read(amt=amt, decode_content=decode_content)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_vendor\urllib3\response.py", line 560, in read
with self._error_catcher():
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\contextlib.py",
line 155, in __exit__
self.gen.throw(typ, value, traceback)
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_vendor\urllib3\response.py", line 449, in _error_catcher
raise SSLError(e)
pip._vendor.urllib3.exceptions.SSLError: [SSL:
DECRYPTION_FAILED_OR_BAD_RECORD_MAC] decryption failed or bad record mac
(_ssl.c:2576)
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Find
Cavities in bundle ChimeraX-KVFinder:
ERROR: Exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_vendor\urllib3\response.py", line 438, in _error_catcher
yield
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_vendor\urllib3\response.py", line 561, in read
data = self._fp_read(amt) if not fp_closed else b""
^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_vendor\urllib3\response.py", line 527, in _fp_read
return self._fp.read(amt) if amt is not None else self._fp.read()
^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_vendor\cachecontrol\filewrapper.py", line 98, in read
data: bytes = self.__fp.read(amt)
^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\http\client.py",
line 466, in read
s = self.fp.read(amt)
^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\socket.py", line
706, in readinto
return self._sock.recv_into(b)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\ssl.py", line
1278, in recv_into
return self.read(nbytes, buffer)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\ssl.py", line
1134, in read
return self._sslobj.read(len, buffer)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ssl.SSLError: [SSL: DECRYPTION_FAILED_OR_BAD_RECORD_MAC] decryption failed or
bad record mac (_ssl.c:2576)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\cli\base_command.py", line 105, in _run_wrapper
status = _inner_run()
^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\cli\base_command.py", line 96, in _inner_run
return self.run(options, args)
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\cli\req_command.py", line 67, in wrapper
return func(self, options, args)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\commands\install.py", line 379, in run
requirement_set = resolver.resolve(
^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\resolution\resolvelib\resolver.py", line 179, in
resolve
self.factory.preparer.prepare_linked_requirements_more(reqs)
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\operations\prepare.py", line 554, in
prepare_linked_requirements_more
self._complete_partial_requirements(
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\operations\prepare.py", line 469, in
_complete_partial_requirements
for link, (filepath, _) in batch_download:
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\network\download.py", line 184, in __call__
for chunk in chunks:
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_internal\network\utils.py", line 65, in response_chunks
for chunk in response.raw.stream(
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_vendor\urllib3\response.py", line 622, in stream
data = self.read(amt=amt, decode_content=decode_content)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_vendor\urllib3\response.py", line 560, in read
with self._error_catcher():
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\contextlib.py",
line 155, in __exit__
self.gen.throw(typ, value, traceback)
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\pip\\_vendor\urllib3\response.py", line 449, in _error_catcher
raise SSLError(e)
pip._vendor.urllib3.exceptions.SSLError: [SSL:
DECRYPTION_FAILED_OR_BAD_RECORD_MAC] decryption failed or bad record mac
(_ssl.c:2576)
File "C:\Program Files\ChimeraX 1.10.dev202412280203\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 578, in start_tool
raise ToolshedError(
See log for complete Python traceback.
OpenGL version: 3.3.0 - Build 26.20.100.7810
OpenGL renderer: Intel(R) UHD Graphics 620
OpenGL vendor: Intel
Python: 3.11.4
Locale: en_IN.cp1252
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: windows
Manufacturer: LENOVO
Model: 81HN
OS: Microsoft Windows 11 Enterprise (Build 26100)
Memory: 7,981,445,120
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i3-8130U CPU @ 2.20GHz
OSLanguage: en-US
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2024.12.14
cftime: 1.6.4.post1
charset-normalizer: 3.4.1
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.59
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10.dev202412280203
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.5.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.7
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-ProfileGrids: 1.0.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.15
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.42.2
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
comtypes: 1.4.5
contourpy: 1.3.1
coverage: 7.6.10
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.11
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.0.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.8
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
pluggy: 1.5.0
prompt_toolkit: 3.0.48
psutil: 6.0.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
pytest: 8.3.4
pytest-cov: 6.0.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pywin32: 306
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.3.0
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
WMI: 1.5.1
Change History (13)
comment:1 by , 10 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Cannot 'pip install pyKVFinger' |
comment:2 by , 9 months ago
comment:4 by , 9 months ago
As we've discussed before updating from numpy 1 to 2 is a large change that may effect many ChimeraX capabilities. It would be good to learn what all will break, but don't put that in the daily build until we understand all the ramifications.
comment:6 by , 9 months ago
Tom: Of course, I'll take notes on the roadblocks I encounter on my local build.
Eric: Neither, yet, I was just trying it out locally to see what it would take to resolve the ticket.
comment:7 by , 9 months ago
Even before putting numpy 2 in a tech preview some careful study should be done to the changes from numpy 1 to numpy 2 since our C++ code heavily uses the numpy 1 C API. In December we put out a build I think just one that had numpy 2 and got bug reports such as #16520 where ribbons did not work correctly. Almost every ChimeraX C++ module I have written to optimize anything (e.g. ribbons) uses numpy 1 C API so we need to understand the numpy 2 API changes and compare against our numpy C++ use.
comment:8 by , 9 months ago
I agree, I was just able to reproduce that actually. The changelog for numpy 2 is here:
https://numpy.org/devdocs/release/2.0.0-notes.html#numpy-2-0-python-api-removals
I plan to just grep the codebase for what's removed, deprecated, etc, then for anything in the compatibility section or C API change section so I can see what is/isn't already OK.
Then obviously it would be good to write tests for every failure a person encounters during testing, like that non-numeric array ticket.
comment:9 by , 9 months ago
I made a numpy 1 to numpy 2 ticket #16848 to keep track of the issues in moving ChimeraX from numpy 1 to 2.
comment:10 by , 9 months ago
The PyKVFinder PyPi package lists numpy dependency
"numpy>=1.21.5",
in its pyproject.toml file
https://github.com/LBC-LNBio/pyKVFinder/blob/master/pyproject.toml
The ChimeraX numpy (1.26.4) satisfies that so I'm not sure why installing PyKVFinder would install numpy 2. Also that dependency seems certainly like an error. It is absurd for a dependency to say it is compatible with all future major version changes since a major version can change any API. Probably that dependency was created before numpy 2 existed and there may be many PyPi packages that have similar numpy dependencies that didn't realize there might be a new major version.
comment:11 by , 9 months ago
Well, in its "requires" section it's got numpy>=1.21.5, but in its "dependencies" section it's got numpy~=2.2.1!
comment:12 by , 9 months ago
Right! The requires numpy>=1.21.5 is in the [build-system] section of the pyproject.toml file while the dependency numpy~=2.2.1 is in the [project] section and is the one that gets installed as a dependency.
This is exactly the situation that puzzles me with numpy 1 vs 2 compatibility. pyKVFinder requires numpy 2 and ChimeraX requires numpy 1. They cannot operate in the same Python since only one numpy module can be installed. This is a basic problem of pinning constraints in Python that I never thought about. If two modules say they require different versions (even just a different patch version) then the pip dependency resolver should say they can't coexist.
comment:13 by , 6 months ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
Works as of some updates from the kvfinder team.
Note:
See TracTickets
for help on using tickets.
Well, I find that I can install pyKVFinder on a daily build I just downloaded for Windows. There is an error, but it's not this long traceback, just a warning about clashing numpys:
{{{Errors may have occurred when running pip:
pip standard error:
---
ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
chimerax-bundlebuilder 1.4.0 requires numpy==1.26.4, but you have numpy 2.2.2 which is incompatible.
nptyping 2.5.0 requires numpy<2.0.0,>=1.20.0; python_version >= "3.8", but you have numpy 2.2.2 which is incompatible.
---
pip standard output:
---
---}}}
nptyping (in the ccore distribution) is the main issue.