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License: GNU General Public License v3.0
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Get user info from config.yaml
now user info is found in the python configuration file. This info should be obtained from the expipe config.yaml file or the cinpla_config.yaml file
expipe crash/AttributeError
Hi @lepmik, @alejoe91 and others.
I've had a pretty frustrating day after updating to the latest commit d75ff89 (as the wiki documentation was no longer in sync with the version I had before).
First, after running python setup.py develop --extra browser I'm getting for any expipe execution the error:
$ expipe
Error when loading plugin `<class 'expipe_plugin_cinpla.main.CinplaPlugin'>`
Traceback (most recent call last):
File "/Users/ehagen/COBRA/expipe-dev/expipe-cli/expipecli/utils/misc.py", line 56, in __getattribute__
return object.__getattribute__(self, attr)
AttributeError: '_LazyImport' object has no attribute 'POSSIBLE_TAGS'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/Users/ehagen/anaconda3/envs/expipe/bin/expipe", line 11, in <module>
load_entry_point('expipe-cli', 'console_scripts', 'expipe')()
File "/Users/ehagen/anaconda3/envs/expipe/lib/python3.6/site-packages/pkg_resources/__init__.py", line 570, in load_entry_point
return get_distribution(dist).load_entry_point(group, name)
File "/Users/ehagen/anaconda3/envs/expipe/lib/python3.6/site-packages/pkg_resources/__init__.py", line 2687, in load_entry_point
return ep.load()
File "/Users/ehagen/anaconda3/envs/expipe/lib/python3.6/site-packages/pkg_resources/__init__.py", line 2341, in load
return self.resolve()
File "/Users/ehagen/anaconda3/envs/expipe/lib/python3.6/site-packages/pkg_resources/__init__.py", line 2347, in resolve
module = __import__(self.module_name, fromlist=['__name__'], level=0)
File "/Users/ehagen/COBRA/expipe-dev/expipe-cli/expipecli/main.py", line 85, in <module>
load_cli_plugins(expipe)
File "/Users/ehagen/COBRA/expipe-dev/expipe-cli/expipecli/main.py", line 81, in load_cli_plugins
raise e
File "/Users/ehagen/COBRA/expipe-dev/expipe-cli/expipecli/main.py", line 78, in load_cli_plugins
plugin().attach_to_cli(cli)
File "/Users/ehagen/COBRA/expipe-dev/expipe-plugin-cinpla/expipe_plugin_cinpla/main.py", line 68, in attach_to_cli
cli_misc.attach_to_cli(cli)
File "/Users/ehagen/COBRA/expipe-dev/expipe-plugin-cinpla/expipe_plugin_cinpla/cli_misc.py", line 24, in attach_to_cli
envvar=PAR.POSSIBLE_TAGS,
File "/Users/ehagen/COBRA/expipe-dev/expipe-cli/expipecli/utils/misc.py", line 59, in __getattribute__
self._esky_lazy_load()
File "/Users/ehagen/COBRA/expipe-dev/expipe-cli/expipecli/utils/misc.py", line 45, in _esky_lazy_load
self._esky_lazy_target = self._esky_lazy_loader()
File "/Users/ehagen/COBRA/expipe-dev/expipe-plugin-cinpla/expipe_plugin_cinpla/imports.py", line 179, in PAR
return load_parameters()
File "/Users/ehagen/COBRA/expipe-dev/expipe-plugin-cinpla/expipe_plugin_cinpla/config.py", line 149, in load_parameters
PAR = load_python_module(settings['current']['params'])
KeyError: 'params'
Second, you have to consider adapting to a workflow using issues, bugfix/feature branches, pull requests, and merges that also squash the commit history for individual issues. Right now mostly everything is done using a ton of incremental commits on branch:master and there is no way to tell what was the last good commit as there are no travisCI testing with this repository, and the revision history is a incomprehensible mess. There are reasons why commit messages should be descriptive ;-)
merge with pyopenephys
Now that changes are done locally in this repo on pyopenephys, these changes must be merged with the pyopenephys repo.
Old utils files in expipe-plugin-cinpla
In master branch the config files in expipe-dev/expipe-plugin-cinpla/utils are not updated. They are different than the one described in wiki. Not so important, but it looks cleaner if they are updated.
expipe env remove crashes
expipe env remove mros
Traceback (most recent call last):
File "/media/milad/ssd-scratch/apps/anaconda3/envs/expipe/bin/expipe", line 11, in <module>
load_entry_point('expipe-cli', 'console_scripts', 'expipe')()
File "/media/milad/ssd-scratch/apps/anaconda3/envs/expipe/lib/python3.6/site-packages/click/core.py", line 722, in __call__
return self.main(*args, **kwargs)
File "/media/milad/ssd-scratch/apps/anaconda3/envs/expipe/lib/python3.6/site-packages/click/core.py", line 697, in main
rv = self.invoke(ctx)
File "/media/milad/ssd-scratch/apps/anaconda3/envs/expipe/lib/python3.6/site-packages/click/core.py", line 1066, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/media/milad/ssd-scratch/apps/anaconda3/envs/expipe/lib/python3.6/site-packages/click/core.py", line 1066, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/media/milad/ssd-scratch/apps/anaconda3/envs/expipe/lib/python3.6/site-packages/click/core.py", line 895, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/media/milad/ssd-scratch/apps/anaconda3/envs/expipe/lib/python3.6/site-packages/click/core.py", line 535, in invoke
return callback(*args, **kwargs)
File "/home/milad/Dropbox/repos/neuroscience/expipe-dev/expipe-plugin-cinpla/expipe_plugin_cinpla/cli_environment.py", line 85, in remove
' ' + current_settings[project_id])
TypeError: must be str, not dict
Move template rules to project modules
Now the template rules (which templates that are to be registered to each action etc.) are specified in a python configuration file. This info can be moved to project modules
support for git < 1.8
in git 1.7 (e.g. some rh6 machines) the command git rev-list HEAD --count is not supported.
Adding a version check on git --version and manually counting the number of revisions is a solution.
consider dismantling expipe-plugin-cinpla and current repo into project specific repositories
With the new filesystem based expipe we have the opportunity to have data, metadata and analysis scripts collected in one project on github or similar. Then cli plugins can be loaded upon discovery when you are in an expipe project (project specific directory). Completely generic code should of course be added to packages installable with conda or pypi.
messages error
Traceback (most recent call last):
File "C:\Users\torkelh\AppData\Local\conda\conda\envs\phy\Scripts\expipe-scrip
t.py", line 11, in <module>
load_entry_point('expipe-cli', 'console_scripts', 'expipe')()
File "C:\Users\torkelh\AppData\Local\conda\conda\envs\phy\lib\site-packages\cl
ick\core.py", line 722, in __call__
return self.main(*args, **kwargs)
File "C:\Users\torkelh\AppData\Local\conda\conda\envs\phy\lib\site-packages\cl
ick\core.py", line 697, in main
rv = self.invoke(ctx)
File "C:\Users\torkelh\AppData\Local\conda\conda\envs\phy\lib\site-packages\cl
ick\core.py", line 1066, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "C:\Users\torkelh\AppData\Local\conda\conda\envs\phy\lib\site-packages\cl
ick\core.py", line 1066, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "C:\Users\torkelh\AppData\Local\conda\conda\envs\phy\lib\site-packages\cl
ick\core.py", line 895, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "C:\Users\torkelh\AppData\Local\conda\conda\envs\phy\lib\site-packages\cl
ick\core.py", line 535, in invoke
return callback(*args, **kwargs)
File "c:\apps\expipe-cinpla\expipe-plugin-cinpla\expipe_plugin_cinpla\cli\open
ephys.py", line 155, in generate_openephys_action
action.create_message(text=m, user=user, datetime=datetime.now())
File "c:\apps\expipe-cinpla\expipe\expipe\core.py", line 641, in create_messag
e
result = self._db_messages.push(message)
File "c:\apps\expipe-cinpla\expipe\expipe\core.py", line 1055, in push
url = self.build_url(name)
File "c:\apps\expipe-cinpla\expipe\expipe\core.py", line 1005, in build_url
full_path = "/".join([self.path, name])
TypeError: sequence item 1: expected str instance, dict found
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