lukassnoek / ni-edu Goto Github PK

Hi Lukas,
thanks for sharing this great resource.

I am having problems with the installation on a Mac following the instructions on the website.
Opening one of your notebooks or trying to create a new notebook yields a 500 : Internal Server Error

The same error occurs when trying to open a tutorial on Binder.
I have the feeling that nbgrader is the culprit. Can you help?

Best,
Jens

1. Created environment
   conda create -n ni-edu anaconda python=3.8.5

2 cloned git repository
git clone https://github.com/lukassnoek/NI-edu.git

3. activated environment
   conda activate ni-edu

4. more installation:
   cd NI-edu
   pip install .

error messages:
...
Attempting uninstall: sqlalchemy
Found existing installation: SQLAlchemy 1.3.20
Uninstalling SQLAlchemy-1.3.20:
Successfully uninstalled SQLAlchemy-1.3.20
ERROR: After October 2020 you may experience errors when installing or updating packages. This is because pip will change the way that it resolves dependency conflicts.

We recommend you use --use-feature=2020-resolver to test your packages with the new resolver before it becomes the default.

nbconvert 6.0.7 requires nbclient<0.6.0,>=0.5.0, but you'll have nbclient 0.7.0 which is incompatible.
nbclient 0.7.0 requires traitlets>=5.2.2, but you'll have traitlets 5.0.5 which is incompatible.
jinja2 3.1.2 requires MarkupSafe>=2.0, but you'll have markupsafe 1.1.1 which is incompatible.
reportlab 3.6.11 requires pillow>=9.0.0, but you'll have pillow 8.0.1 which is incompatible.
jupyter-server 1.21.0 requires jupyter-client>=6.1.12, but you'll have jupyter-client 6.1.7 which is incompatible.
jupyter-server 1.21.0 requires jupyter-core>=4.7.0, but you'll have jupyter-core 4.6.3 which is incompatible.
jupyter-server 1.21.0 requires nbconvert>=6.4.4, but you'll have nbconvert 6.0.7 which is incompatible.
jupyter-server 1.21.0 requires nbformat>=5.2.0, but you'll have nbformat 5.0.8 which is incompatible.
jupyter-server 1.21.0 requires tornado>=6.1.0, but you'll have tornado 6.0.4 which is incompatible.
jupyter-server 1.21.0 requires traitlets>=5.1, but you'll have traitlets 5.0.5 which is incompatible.
nbgrader 0.8.1 requires ipywidgets>=7.6, but you'll have ipywidgets 7.5.1 which is incompatible.
nbgrader 0.8.1 requires notebook<7,>=6.4, but you'll have notebook 6.1.4 which is incompatible.
nbgrader 0.8.1 requires requests>=2.26, but you'll have requests 2.24.0 which is incompatible.
Successfully installed Mako-1.2.3 alembic-1.8.1 anyio-3.6.1 awscli-1.25.93 botocore-1.27.92 greenlet-1.1.3.post0 importlib-resources-5.10.0 jinja2-3.1.2 jmespath-1.0.1 jupyter-contrib-core-0.4.0 jupyter-contrib-nbextensions-0.5.1 jupyter-highlight-selected-word-0.2.0 jupyter-latex-envs-1.4.6 jupyter-nbextensions-configurator-0.5.0 jupyter-server-1.21.0 nbclassic-0.3.7 nbclient-0.7.0 nbgrader-0.8.1 neurodesign-0.2.2 nibabel-4.0.2 niedu-0.1.dev0 nilearn-0.9.2 notebook-shim-0.2.0 pdfrw-0.4 progressbar-2.5 pyasn1-0.4.8 rapidfuzz-2.11.1 reportlab-3.6.11 rsa-4.7.2 s3transfer-0.6.0 sklearn-

5. Recommended test works
   (ni-edu) jens@jvsmac NI-edu % python test_course_environment.py
   Checking Python version ... OK!
   Checking anaconda installation ... OK!
   Checking niedu installation ... OK!
   Checking FSL installation ... OK!
   (ni-edu) jens@jvsmac NI-edu %

6. opening a notebook, e.g. week1\python_for_mri.ipynb (with safari) leads to display
   500 : internal server error

7,. opening a notebook in binder also fails with
500 : internal server error

(ni-edu) jens@jvsmac NI-edu % jupyter notebook
[I 14:53:23.848 NotebookApp] [jupyter_nbextensions_configurator] enabled 0.4.1
[I 14:53:23.912 NotebookApp] JupyterLab extension loaded from /Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/site-packages/jupyterlab
[I 14:53:23.912 NotebookApp] JupyterLab application directory is /Users/jens/opt/anaconda3/envs/ni-edu/share/jupyter/lab
[W 14:53:26.225 NotebookApp] Error loading server extension nbgrader.server_extensions.assignment_list
Traceback (most recent call last):
File "/Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/site-packages/notebook/notebookapp.py", line 1942, in init_server_extensions
mod = importlib.import_module(modulename)
File "/Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/importlib/init.py", line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "", line 1014, in _gcd_import
File "", line 991, in _find_and_load
File "", line 961, in _find_and_load_unlocked
File "", line 219, in _call_with_frames_removed
File "", line 1014, in _gcd_import
File "", line 991, in _find_and_load
File "", line 961, in _find_and_load_unlocked
File "", line 219, in _call_with_frames_removed
File "", line 1014, in _gcd_import
File "", line 991, in _find_and_load
File "", line 975, in _find_and_load_unlocked
File "", line 671, in _load_unlocked
File "", line 783, in exec_module
File "", line 219, in _call_with_frames_removed
File "/Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/site-packages/nbgrader/init.py", line 11, in
from .server_extensions.assignment_list import load_jupyter_server_extension as load_assignments
File "/Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/site-packages/nbgrader/server_extensions/assignment_list/init.py", line 1, in
from .handlers import load_jupyter_server_extension
File "/Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/site-packages/nbgrader/server_extensions/assignment_list/handlers.py", line 18, in
from ...apps import NbGrader
File "/Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/site-packages/nbgrader/apps/init.py", line 1, in
from .baseapp import NbGrader
File "/Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/site-packages/nbgrader/apps/baseapp.py", line 22, in
from .. import preprocessors
File "/Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/site-packages/nbgrader/preprocessors/init.py", line 1, in
from .base import NbGraderPreprocessor
File "/Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/site-packages/nbgrader/preprocessors/base.py", line 1, in
from nbconvert.preprocessors import Preprocessor
File "/Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/site-packages/nbconvert/init.py", line 4, in
from .exporters import *
File "/Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/site-packages/nbconvert/exporters/init.py", line 3, in
from .html import HTMLExporter
File "/Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/site-packages/nbconvert/exporters/html.py", line 14, in
from jinja2 import contextfilter
ImportError: cannot import name 'contextfilter' from 'jinja2' (/Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/site-packages/jinja2/init.py)
[W 14:53:26.230 NotebookApp] Error loading server extension nbgrader.server_extensions.course_list
Traceback (most recent call last):
File "/Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/site-packages/notebook/notebookapp.py", line 1942, in init_server_extensions
mod = importlib.import_module(modulename)
File "/Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/importlib/init.py", line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "", line 1014, in _gcd_import
File "", line 991, in _find_and_load
File "", line 975, in _find_and_load_unlocked
File "", line 671, in _load_unlocked
File "", line 783, in exec_module
File "", line 219, in _call_with_frames_removed
File "/Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/site-packages/nbgrader/server_extensions/course_list/init.py", line 1, in
from .handlers import load_jupyter_server_extension
File "/Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/site-packages/nbgrader/server_extensions/course_list/handlers.py", line 18, in
from ...apps import NbGrader
File "/Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/site-packages/nbgrader/init.py", line 11, in
from .server_extensions.assignment_list import load_jupyter_server_extension as load_assignments
File "/Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/site-packages/nbgrader/server_extensions/assignment_list/init.py", line 1, in
from .handlers import load_jupyter_server_extension
File "/Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/site-packages/nbgrader/server_extensions/assignment_list/handlers.py", line 18, in
from ...apps import NbGrader
File "/Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/site-packages/nbgrader/apps/init.py", line 1, in
from .baseapp import NbGrader
File "/Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/site-packages/nbgrader/apps/baseapp.py", line 22, in
from .. import preprocessors
File "/Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/site-packages/nbgrader/preprocessors/init.py", line 1, in
from .base import NbGraderPreprocessor
File "/Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/site-packages/nbgrader/preprocessors/base.py", line 1, in
from nbconvert.preprocessors import Preprocessor
File "/Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/site-packages/nbconvert/init.py", line 4, in
from .exporters import *
File "/Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/site-packages/nbconvert/exporters/init.py", line 3, in
from .html import HTMLExporter
File "/Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/site-packages/nbconvert/exporters/html.py", line 14, in
from jinja2 import contextfilter
ImportError: cannot import name 'contextfilter' from 'jinja2' (/Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/site-packages/jinja2/init.py)
[W 14:53:26.231 NotebookApp] Error loading server extension nbgrader.server_extensions.formgrader
Traceback (most recent call last):
File "/Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/site-packages/notebook/notebookapp.py", line 1942, in init_server_extensions
mod = importlib.import_module(modulename)
File "/Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/importlib/init.py", line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "", line 1014, in _gcd_import
File "", line 991, in _find_and_load
File "", line 975, in _find_and_load_unlocked
File "", line 671, in _load_unlocked
File "", line 783, in exec_module
File "", line 219, in _call_with_frames_removed
File "/Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/site-packages/nbgrader/server_extensions/formgrader/init.py", line 1, in
from .formgrader import load_jupyter_server_extension
File "/Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/site-packages/nbgrader/server_extensions/formgrader/formgrader.py", line 5, in
from nbconvert.exporters import HTMLExporter
File "/Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/site-packages/nbconvert/init.py", line 4, in
from .exporters import *
File "/Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/site-packages/nbconvert/exporters/init.py", line 3, in
from .html import HTMLExporter
File "/Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/site-packages/nbconvert/exporters/html.py", line 14, in
from jinja2 import contextfilter
ImportError: cannot import name 'contextfilter' from 'jinja2' (/Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/site-packages/jinja2/init.py)
[W 14:53:26.233 NotebookApp] Error loading server extension nbgrader.server_extensions.validate_assignment
Traceback (most recent call last):
File "/Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/site-packages/notebook/notebookapp.py", line 1942, in init_server_extensions
mod = importlib.import_module(modulename)
File "/Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/importlib/init.py", line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "", line 1014, in _gcd_import
File "", line 991, in _find_and_load
File "", line 975, in _find_and_load_unlocked
File "", line 671, in _load_unlocked
File "", line 783, in exec_module
File "", line 219, in _call_with_frames_removed
File "/Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/site-packages/nbgrader/server_extensions/validate_assignment/init.py", line 1, in
from .handlers import load_jupyter_server_extension
File "/Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/site-packages/nbgrader/server_extensions/validate_assignment/handlers.py", line 15, in
from ...apps import NbGrader
File "/Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/site-packages/nbgrader/init.py", line 11, in
from .server_extensions.assignment_list import load_jupyter_server_extension as load_assignments
File "/Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/site-packages/nbgrader/server_extensions/assignment_list/init.py", line 1, in
from .handlers import load_jupyter_server_extension
File "/Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/site-packages/nbgrader/server_extensions/assignment_list/handlers.py", line 18, in
from ...apps import NbGrader
File "/Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/site-packages/nbgrader/apps/init.py", line 1, in
from .baseapp import NbGrader
File "/Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/site-packages/nbgrader/apps/baseapp.py", line 22, in
from .. import preprocessors
File "/Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/site-packages/nbgrader/preprocessors/init.py", line 1, in
from .base import NbGraderPreprocessor
File "/Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/site-packages/nbgrader/preprocessors/base.py", line 1, in
from nbconvert.preprocessors import Preprocessor
File "/Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/site-packages/nbconvert/init.py", line 4, in
from .exporters import *
File "/Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/site-packages/nbconvert/exporters/init.py", line 3, in
from .html import HTMLExporter
File "/Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/site-packages/nbconvert/exporters/html.py", line 14, in
from jinja2 import contextfilter
ImportError: cannot import name 'contextfilter' from 'jinja2' (/Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/site-packages/jinja2/init.py)
[I 14:53:26.234 NotebookApp] Serving notebooks from local directory: /Users/jens/NI-edu
[I 14:53:26.234 NotebookApp] Jupyter Notebook 6.1.4 is running at:
[I 14:53:26.234 NotebookApp] http://localhost:8888/?token=49b5faa45abc25ee8383eddf6e89be07092fcfef30939b1e
[I 14:53:26.234 NotebookApp] or http://127.0.0.1:8888/?token=49b5faa45abc25ee8383eddf6e89be07092fcfef30939b1e
[I 14:53:26.234 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[C 14:53:26.245 NotebookApp]

To access the notebook, open this file in a browser:
    file:///Users/jens/Library/Jupyter/runtime/nbserver-51294-open.html
Or copy and paste one of these URLs:
    http://localhost:8888/?token=49b5faa45abc25ee8383eddf6e89be07092fcfef30939b1e
 or http://127.0.0.1:8888/?token=49b5faa45abc25ee8383eddf6e89be07092fcfef30939b1e

[E 14:54:41.102 NotebookApp] Uncaught exception GET /notebooks/NI-edu/fMRI-introduction/week_1/python_for_mri.ipynb (::1)
HTTPServerRequest(protocol='http', host='localhost:8888', method='GET', uri='/notebooks/NI-edu/fMRI-introduction/week_1/python_for_mri.ipynb', version='HTTP/1.1', remote_ip='::1')
Traceback (most recent call last):
File "/Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/site-packages/tornado/web.py", line 1703, in _execute
result = await result
File "/Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/site-packages/tornado/gen.py", line 748, in run
yielded = self.gen.send(value)
File "/Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/site-packages/notebook/notebook/handlers.py", line 95, in get
self.write(self.render_template('notebook.html',
File "/Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/site-packages/notebook/base/handlers.py", line 512, in render_template
return template.render(**ns)
File "/Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/site-packages/jinja2/environment.py", line 1301, in render
self.environment.handle_exception()
File "/Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/site-packages/jinja2/environment.py", line 936, in handle_exception
raise rewrite_traceback_stack(source=source)
File "/Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/site-packages/notebook/templates/notebook.html", line 1, in top-level template code
{% extends "page.html" %}
File "/Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/site-packages/notebook/templates/page.html", line 154, in top-level template code
{% block header %}
File "/Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/site-packages/notebook/templates/notebook.html", line 115, in block 'header'
{% for exporter in get_frontend_exporters() %}
File "/Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/site-packages/notebook/notebook/handlers.py", line 40, in get_frontend_exporters
for name in get_export_names():
File "/Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/site-packages/nbconvert/exporters/base.py", line 141, in get_export_names
e = get_exporter(exporter_name)(config=config)
File "/Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/site-packages/nbconvert/exporters/base.py", line 101, in get_exporter
exporter = entrypoints.get_single('nbconvert.exporters', name).load()
File "/Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/site-packages/entrypoints.py", line 82, in load
mod = import_module(self.module_name)
File "/Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/importlib/init.py", line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "", line 1014, in _gcd_import
File "", line 991, in _find_and_load
File "", line 961, in _find_and_load_unlocked
File "", line 219, in _call_with_frames_removed
File "", line 1014, in _gcd_import
File "", line 991, in _find_and_load
File "", line 975, in _find_and_load_unlocked
File "", line 671, in _load_unlocked
File "", line 783, in exec_module
File "", line 219, in _call_with_frames_removed
File "/Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/site-packages/nbconvert/init.py", line 4, in
from .exporters import *
File "/Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/site-packages/nbconvert/exporters/init.py", line 3, in
from .html import HTMLExporter
File "/Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/site-packages/nbconvert/exporters/html.py", line 14, in
from jinja2 import contextfilter
ImportError: cannot import name 'contextfilter' from 'jinja2' (/Users/jens/opt/anaconda3/envs/ni-edu/lib/python3.8/site-packages/jinja2/init.py)
[E 14:54:41.109 NotebookApp] {
"Host": "localhost:8888",
"Cookie": "username-localhost-8888="2|1:0|10:1666097607|23:username-localhost-8888|44:ZjM1NmNjMTA2ZTUxNDk1OWE4ZWI5NGQ3ZTFlMTFjYTE=|f9ff5f79e8648d7f0fc01c4f331fe4f283151c259cece5f2e9c93ed27044819b"; username-localhost-8890="2|1:0|10:1665248858|23:username-localhost-8890|44:Y2VhNjkwZjA5M2Y4NGE4OTlkZDExNjAzNTdkMGVjZDI=|ccf16ca6402429d11e74321db90c3c466f81a55a62238b6c3f4228906b9126f6"; username-localhost-8889="2|1:0|10:1664455795|23:username-localhost-8889|44:Y2RjZDE0N2E0NDRjNGFmNGI5MDEwNDhjZTc2YmNhMDY=|790dd05319b962c95bdfe4f7dc1f4facb9d5df53e832badcf7c350d25045977c"; _xsrf=2|ff6872c7|262934dc8620594ba202db17a6b2745d|1664454299",
"Connection": "keep-alive",
"Upgrade-Insecure-Requests": "1",
"Accept": "text/html,application/xhtml+xml,application/xml;q=0.9,/;q=0.8",
"User-Agent": "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_15_7) AppleWebKit/605.1.15 (KHTML, like Gecko) Version/15.4 Safari/605.1.15",
"Referer": "http://localhost:8888/tree/NI-edu/fMRI-introduction/week_1",
"Accept-Language": "en-GB,en;q=0.9",
"Accept-Encoding": "gzip, deflate"
}
[E 14:54:41.109 NotebookApp] 500 GET /notebooks/NI-edu/fMRI-introduction/week_1/python_for_mri.ipynb (::1) 116.95ms referer=http://localhost:8888/tree/NI-edu/fMRI-introduction/week_1