clics / clics3 Goto Github PK

While this may be a bit stressful, I think it's worth it. Otherwise we'd release something that's basically not dead, but EOL on arrival.

The headers still have repeated labels, like "Subgraph Subgraph FIREWOOD" at
https://clics.clld.org/graphs/subgraph_10

README.md should describe the requirements

• pyclics>=2.0
• pyclics-clustering>=1.0
• installing the data running pip install -r datasets.txt

and the processing workflow, i.e. the sequence of clics commands.

rewrite the docs accordingly

This involves:

• updated pyclics, pylexibank and dependencies
• update datasets

• the network (see #39 )
• the lexical data - augmented with CLICS value - as CLDF Wordlist
• the sqlite database - since its use is described in the cookbook?

... and in release description, once paper is published ...

Due to changes in gcd and our pinning of networkx the workflow doesn't work with Python versions >=3.9.x.

What is the terminal command that allows me to download all the colexifications, containing:

| ID A | Concept A | ID B | Concept B | Families | Languages | Words |                                                                                                                                      
|-------:|:-------------------------|-------:|:---------------------------|-----------:|------------:|--------:|
| 906 | TREE | 1803 | WOOD | 59 | 348 | 361 |
...

Add a reminder to the README that the analysis should ideally be run inside a virtual environment.

When I ran the command pip install -r datasets.txt, I received the following error:

ERROR: File "setup.py" not found. Directory cannot be installed in editable mode: /Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages

Thanks for looking into it!

Here's the full stack trace when I included --log:

--- Logging error ---
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/logging/handlers.py", line 73, in emit
if self.shouldRollover(record):
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/logging/handlers.py", line 189, in shouldRollover
self.stream = self._open()
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/utils/logging.py", line 217, in _open
return logging.handlers.RotatingFileHandler._open(self)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/logging/init.py", line 1171, in _open
return open(self.baseFilename, self.mode, encoding=self.encoding,
IsADirectoryError: [Errno 21] Is a directory: '/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages'
Call stack:
File "/Library/Frameworks/Python.framework/Versions/3.9/bin/pip", line 8, in
sys.exit(main())
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/cli/main.py", line 73, in main
return command.main(cmd_args)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/cli/base_command.py", line 111, in main
return self._main(args)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/cli/base_command.py", line 189, in _main
status = self.run(options, args)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/cli/req_command.py", line 178, in wrapper
return func(self, options, args)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/commands/install.py", line 239, in run
logger.debug("Using %s", get_pip_version())
Message: 'Using %s'
Arguments: ('pip 21.0.1 from /Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip (python 3.9)',)
--- Logging error ---
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/logging/handlers.py", line 73, in emit
if self.shouldRollover(record):
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/logging/handlers.py", line 189, in shouldRollover
self.stream = self._open()
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/utils/logging.py", line 217, in _open
return logging.handlers.RotatingFileHandler._open(self)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/logging/init.py", line 1171, in _open
return open(self.baseFilename, self.mode, encoding=self.encoding,
IsADirectoryError: [Errno 21] Is a directory: '/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages'
Call stack:
File "/Library/Frameworks/Python.framework/Versions/3.9/bin/pip", line 8, in
sys.exit(main())
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/cli/main.py", line 73, in main
return command.main(cmd_args)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/cli/base_command.py", line 111, in main
return self._main(args)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/cli/base_command.py", line 189, in _main
status = self.run(options, args)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/cli/req_command.py", line 178, in wrapper
return func(self, options, args)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/commands/install.py", line 240, in run
options.use_user_site = decide_user_install(
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/commands/install.py", line 649, in decide_user_install
logger.debug("Non-user install because site-packages writeable")
Message: 'Non-user install because site-packages writeable'
Arguments: ()
--- Logging error ---
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/logging/handlers.py", line 73, in emit
if self.shouldRollover(record):
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/logging/handlers.py", line 189, in shouldRollover
self.stream = self._open()
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/utils/logging.py", line 217, in _open
return logging.handlers.RotatingFileHandler._open(self)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/logging/init.py", line 1171, in _open
return open(self.baseFilename, self.mode, encoding=self.encoding,
IsADirectoryError: [Errno 21] Is a directory: '/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages'
Call stack:
File "/Library/Frameworks/Python.framework/Versions/3.9/bin/pip", line 8, in
sys.exit(main())
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/cli/main.py", line 73, in main
return command.main(cmd_args)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/cli/base_command.py", line 111, in main
return self._main(args)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/cli/base_command.py", line 189, in _main
status = self.run(options, args)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/cli/req_command.py", line 178, in wrapper
return func(self, options, args)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/commands/install.py", line 276, in run
wheel_cache = WheelCache(options.cache_dir, options.format_control)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/cache.py", line 244, in init
self._ephem_cache = EphemWheelCache(format_control)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/cache.py", line 215, in init
self._temp_dir = TempDirectory(
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/utils/temp_dir.py", line 139, in init
path = self._create(kind)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/utils/temp_dir.py", line 189, in _create
logger.debug("Created temporary directory: %s", path)
Message: 'Created temporary directory: %s'
Arguments: ('/private/var/folders/mj/tpq_f8ms4hx8g02sm2t9p_4h0000gp/T/pip-ephem-wheel-cache-ebstlo3v',)
--- Logging error ---
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/logging/handlers.py", line 73, in emit
if self.shouldRollover(record):
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/logging/handlers.py", line 189, in shouldRollover
self.stream = self._open()
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/utils/logging.py", line 217, in _open
return logging.handlers.RotatingFileHandler._open(self)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/logging/init.py", line 1171, in _open
return open(self.baseFilename, self.mode, encoding=self.encoding,
IsADirectoryError: [Errno 21] Is a directory: '/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages'
Call stack:
File "/Library/Frameworks/Python.framework/Versions/3.9/bin/pip", line 8, in
sys.exit(main())
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/cli/main.py", line 73, in main
return command.main(cmd_args)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/cli/base_command.py", line 111, in main
return self._main(args)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/cli/base_command.py", line 189, in _main
status = self.run(options, args)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/cli/req_command.py", line 178, in wrapper
return func(self, options, args)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/commands/install.py", line 278, in run
req_tracker = self.enter_context(get_requirement_tracker())
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/cli/command_context.py", line 36, in enter_context
return self._main_context.enter_context(context_provider)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_vendor/contextlib2.py", line 442, in enter_context
result = _cm_type.enter(cm)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/contextlib.py", line 117, in enter
return next(self.gen)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/req/req_tracker.py", line 55, in get_requirement_tracker
TempDirectory(kind='req-tracker')
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/utils/temp_dir.py", line 139, in init
path = self._create(kind)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/utils/temp_dir.py", line 189, in _create
logger.debug("Created temporary directory: %s", path)
Message: 'Created temporary directory: %s'
Arguments: ('/private/var/folders/mj/tpq_f8ms4hx8g02sm2t9p_4h0000gp/T/pip-req-tracker-yx4lccxm',)
--- Logging error ---
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/logging/handlers.py", line 73, in emit
if self.shouldRollover(record):
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/logging/handlers.py", line 189, in shouldRollover
self.stream = self._open()
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/utils/logging.py", line 217, in _open
return logging.handlers.RotatingFileHandler._open(self)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/logging/init.py", line 1171, in _open
return open(self.baseFilename, self.mode, encoding=self.encoding,
IsADirectoryError: [Errno 21] Is a directory: '/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages'
Call stack:
File "/Library/Frameworks/Python.framework/Versions/3.9/bin/pip", line 8, in
sys.exit(main())
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/cli/main.py", line 73, in main
return command.main(cmd_args)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/cli/base_command.py", line 111, in main
return self._main(args)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/cli/base_command.py", line 189, in _main
status = self.run(options, args)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/cli/req_command.py", line 178, in wrapper
return func(self, options, args)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/commands/install.py", line 278, in run
req_tracker = self.enter_context(get_requirement_tracker())
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/cli/command_context.py", line 36, in enter_context
return self._main_context.enter_context(context_provider)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_vendor/contextlib2.py", line 442, in enter_context
result = _cm_type.enter(cm)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/contextlib.py", line 117, in enter
return next(self.gen)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/req/req_tracker.py", line 58, in get_requirement_tracker
logger.debug("Initialized build tracking at %s", root)
Message: 'Initialized build tracking at %s'
Arguments: ('/private/var/folders/mj/tpq_f8ms4hx8g02sm2t9p_4h0000gp/T/pip-req-tracker-yx4lccxm',)
--- Logging error ---
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/logging/handlers.py", line 73, in emit
if self.shouldRollover(record):
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/logging/handlers.py", line 189, in shouldRollover
self.stream = self._open()
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/utils/logging.py", line 217, in _open
return logging.handlers.RotatingFileHandler._open(self)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/logging/init.py", line 1171, in _open
return open(self.baseFilename, self.mode, encoding=self.encoding,
IsADirectoryError: [Errno 21] Is a directory: '/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages'
Call stack:
File "/Library/Frameworks/Python.framework/Versions/3.9/bin/pip", line 8, in
sys.exit(main())
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/cli/main.py", line 73, in main
return command.main(cmd_args)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/cli/base_command.py", line 111, in main
return self._main(args)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/cli/base_command.py", line 189, in _main
status = self.run(options, args)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/cli/req_command.py", line 178, in wrapper
return func(self, options, args)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/commands/install.py", line 278, in run
req_tracker = self.enter_context(get_requirement_tracker())
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/cli/command_context.py", line 36, in enter_context
return self._main_context.enter_context(context_provider)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_vendor/contextlib2.py", line 442, in enter_context
result = _cm_type.enter(cm)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/contextlib.py", line 117, in enter
return next(self.gen)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/req/req_tracker.py", line 60, in get_requirement_tracker
with RequirementTracker(root) as tracker:
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/req/req_tracker.py", line 70, in init
logger.debug("Created build tracker: %s", self._root)
Message: 'Created build tracker: %s'
Arguments: ('/private/var/folders/mj/tpq_f8ms4hx8g02sm2t9p_4h0000gp/T/pip-req-tracker-yx4lccxm',)
--- Logging error ---
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/logging/handlers.py", line 73, in emit
if self.shouldRollover(record):
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/logging/handlers.py", line 189, in shouldRollover
self.stream = self._open()
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/utils/logging.py", line 217, in _open
return logging.handlers.RotatingFileHandler._open(self)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/logging/init.py", line 1171, in _open
return open(self.baseFilename, self.mode, encoding=self.encoding,
IsADirectoryError: [Errno 21] Is a directory: '/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages'
Call stack:
File "/Library/Frameworks/Python.framework/Versions/3.9/bin/pip", line 8, in
sys.exit(main())
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/cli/main.py", line 73, in main
return command.main(cmd_args)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/cli/base_command.py", line 111, in main
return self._main(args)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/cli/base_command.py", line 189, in _main
status = self.run(options, args)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/cli/req_command.py", line 178, in wrapper
return func(self, options, args)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/commands/install.py", line 278, in run
req_tracker = self.enter_context(get_requirement_tracker())
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/cli/command_context.py", line 36, in enter_context
return self._main_context.enter_context(context_provider)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_vendor/contextlib2.py", line 442, in enter_context
result = _cm_type.enter(cm)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/contextlib.py", line 117, in enter
return next(self.gen)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/req/req_tracker.py", line 60, in get_requirement_tracker
with RequirementTracker(root) as tracker:
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/req/req_tracker.py", line 74, in enter
logger.debug("Entered build tracker: %s", self._root)
Message: 'Entered build tracker: %s'
Arguments: ('/private/var/folders/mj/tpq_f8ms4hx8g02sm2t9p_4h0000gp/T/pip-req-tracker-yx4lccxm',)
--- Logging error ---
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/logging/handlers.py", line 73, in emit
if self.shouldRollover(record):
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/logging/handlers.py", line 189, in shouldRollover
self.stream = self._open()
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/utils/logging.py", line 217, in _open
return logging.handlers.RotatingFileHandler._open(self)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/logging/init.py", line 1171, in _open
return open(self.baseFilename, self.mode, encoding=self.encoding,
IsADirectoryError: [Errno 21] Is a directory: '/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages'
Call stack:
File "/Library/Frameworks/Python.framework/Versions/3.9/bin/pip", line 8, in
sys.exit(main())
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/cli/main.py", line 73, in main
return command.main(cmd_args)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/cli/base_command.py", line 111, in main
return self._main(args)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/cli/base_command.py", line 189, in _main
status = self.run(options, args)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/cli/req_command.py", line 178, in wrapper
return func(self, options, args)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/commands/install.py", line 280, in run
directory = TempDirectory(
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/utils/temp_dir.py", line 139, in init
path = self._create(kind)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/utils/temp_dir.py", line 189, in _create
logger.debug("Created temporary directory: %s", path)
Message: 'Created temporary directory: %s'
Arguments: ('/private/var/folders/mj/tpq_f8ms4hx8g02sm2t9p_4h0000gp/T/pip-install-6qwuucrd',)
ERROR: File "setup.py" not found. Directory cannot be installed in editable mode: /Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages
--- Logging error ---
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/cli/base_command.py", line 189, in _main
status = self.run(options, args)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/cli/req_command.py", line 178, in wrapper
return func(self, options, args)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/commands/install.py", line 287, in run
reqs = self.get_requirements(args, options, finder, session)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/cli/req_command.py", line 361, in get_requirements
req_to_add = install_req_from_parsed_requirement(
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/req/constructors.py", line 448, in install_req_from_parsed_requirement
req = install_req_from_editable(
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/req/constructors.py", line 212, in install_req_from_editable
parts = parse_req_from_editable(editable_req)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/req/constructors.py", line 183, in parse_req_from_editable
name, url, extras_override = parse_editable(editable_req)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/req/constructors.py", line 96, in parse_editable
raise InstallationError(msg)
pip._internal.exceptions.InstallationError: File "setup.py" not found. Directory cannot be installed in editable mode: /Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/logging/handlers.py", line 73, in emit
if self.shouldRollover(record):
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/logging/handlers.py", line 189, in shouldRollover
self.stream = self._open()
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/utils/logging.py", line 217, in _open
return logging.handlers.RotatingFileHandler._open(self)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/logging/init.py", line 1171, in _open
return open(self.baseFilename, self.mode, encoding=self.encoding,
IsADirectoryError: [Errno 21] Is a directory: '/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages'
Call stack:
File "/Library/Frameworks/Python.framework/Versions/3.9/bin/pip", line 8, in
sys.exit(main())
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/cli/main.py", line 73, in main
return command.main(cmd_args)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/cli/base_command.py", line 111, in main
return self._main(args)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/cli/base_command.py", line 199, in _main
logger.critical(str(exc))
Message: 'File "setup.py" not found. Directory cannot be installed in editable mode: /Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages'
Arguments: ()
--- Logging error ---
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/cli/base_command.py", line 189, in _main
status = self.run(options, args)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/cli/req_command.py", line 178, in wrapper
return func(self, options, args)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/commands/install.py", line 287, in run
reqs = self.get_requirements(args, options, finder, session)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/cli/req_command.py", line 361, in get_requirements
req_to_add = install_req_from_parsed_requirement(
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/req/constructors.py", line 448, in install_req_from_parsed_requirement
req = install_req_from_editable(
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/req/constructors.py", line 212, in install_req_from_editable
parts = parse_req_from_editable(editable_req)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/req/constructors.py", line 183, in parse_req_from_editable
name, url, extras_override = parse_editable(editable_req)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/req/constructors.py", line 96, in parse_editable
raise InstallationError(msg)
pip._internal.exceptions.InstallationError: File "setup.py" not found. Directory cannot be installed in editable mode: /Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/logging/handlers.py", line 73, in emit
if self.shouldRollover(record):
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/logging/handlers.py", line 189, in shouldRollover
self.stream = self._open()
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/utils/logging.py", line 217, in _open
return logging.handlers.RotatingFileHandler._open(self)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/logging/init.py", line 1171, in _open
return open(self.baseFilename, self.mode, encoding=self.encoding,
IsADirectoryError: [Errno 21] Is a directory: '/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages'
Call stack:
File "/Library/Frameworks/Python.framework/Versions/3.9/bin/pip", line 8, in
sys.exit(main())
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/cli/main.py", line 73, in main
return command.main(cmd_args)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/cli/base_command.py", line 111, in main
return self._main(args)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/cli/base_command.py", line 200, in _main
logger.debug('Exception information:', exc_info=True)
Message: 'Exception information:'
Arguments: ()
--- Logging error ---
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/logging/handlers.py", line 73, in emit
if self.shouldRollover(record):
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/logging/handlers.py", line 189, in shouldRollover
self.stream = self._open()
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/utils/logging.py", line 217, in _open
return logging.handlers.RotatingFileHandler._open(self)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/logging/init.py", line 1171, in _open
return open(self.baseFilename, self.mode, encoding=self.encoding,
IsADirectoryError: [Errno 21] Is a directory: '/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages'
Call stack:
File "/Library/Frameworks/Python.framework/Versions/3.9/bin/pip", line 8, in
sys.exit(main())
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/cli/main.py", line 73, in main
return command.main(cmd_args)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/cli/base_command.py", line 111, in main
return self._main(args)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/contextlib.py", line 124, in exit
next(self.gen)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/cli/command_context.py", line 28, in main_context
yield
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_vendor/contextlib2.py", line 468, in exit
if cb(*exc_details):
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_vendor/contextlib2.py", line 396, in _exit_wrapper
return cm_exit(cm, *exc_details)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/contextlib.py", line 124, in exit
next(self.gen)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/req/req_tracker.py", line 61, in get_requirement_tracker
yield tracker
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/req/req_tracker.py", line 84, in exit
self.cleanup()
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pip/_internal/req/req_tracker.py", line 139, in cleanup
logger.debug("Removed build tracker: %r", self._root)
Message: 'Removed build tracker: %r'
Arguments: ('/private/var/folders/mj/tpq_f8ms4hx8g02sm2t9p_4h0000gp/T/pip-req-tracker-yx4lccxm',)

In the sqlite database that is obtained after the CLICS install, what seems to be the same concept (parameter) is represented multiple times with different numeric identifiers. For example, consider the types for Friday:
478_friday
993_friday
218_friday
350_friday

Is there a reason that such a distinction is made? What leads to the classification? Or is it safe to collapse these multiple parameters into a single concept? Some documentation would really help this in regard, especially to weed out potential mistakes in future research using CLICS3.

Hi there,

I thought I would have a go building this project and running the web app in docker, and so far the result looks like this:

Is this what it's supposed to look like? Or am I doing something wrong. I am running it in firefox, but it seems to be missing something.