MetaCell / MetaCell/nwb-explorer
(with --dev): Missing icon in menu-list
- Dominant language
- JavaScript
- Stars
- 27
- Forks
- 16
- PR merge metrics
- No merged PRs in 30d
Description
This isn't urgent, but filing it as an FYI.
Building nwb-explorer from source using `python utilities/install.py --dev` results in an icon missing from the menu list. If the `--dev` flag is not used, the icon shows up correctly. So, perhaps this indicates some change/bug in the newer/development versions of some underlying components/deps.
= How to reproduce:
Install and run NWBE:
```
$ git clone git@github.com:MetaCell/nwb-explorer.git
$ cd nwb-explorer
$ git checkout development # or master
$ python3.7 -m venv .venv
$ source .venv/bin/activate
$ python --version
Python 3.7.10
$ python utilities/install.py --dev
...
...
$ NWBE
```
Click on an NWBE file on the landing page, for example Lanore et al.
Notice the missing icon (in the list, under "controls"):

The inspector shows that the fontawesome icon is not correctly included in a class for it to show:

This is what we get on live, for comparison:

This is the difference in Python packages with and without using `--dev`:
``` diff
--- withoutdev.txt 2021-04-22 11:53:58.416409778 +0100
+++ withdev.txt 2021-04-22 11:48:45.014457164 +0100
@@ -7,24 +7,33 @@
attrs==20.3.0
backcall==0.2.0
bleach==3.3.0
-cached-property==1.5.2
+bokeh==2.3.1
cachetools==4.2.1
+ccfwidget==0.5.3
certifi==2020.12.5
cffi==1.14.5
chardet==4.0.0
+cloudpickle==1.6.0
+colorcet==2.0.6
coverage==5.5
cycler==0.10.0
+dask==2021.4.0
decorator==4.4.2
defusedxml==0.7.1
Deprecated==1.2.12
distlib==0.3.1
+-e git+git@github.com:sanjayankur31/nwb-explorer.git@b06988eceaaf14e8ef30281a8e7751dde01f1b38#egg=nwb_explorer
+-e git+https://github.com/openworm/org.geppetto.frontend.jupyter.git@6742c22070d0cdc3cb370ebb12d8b2f4a103d7ff#egg=jupyter_geppetto
+-e git+https://github.com/openworm/pygeppetto.git@f357319f9bfc751d79837d2cf6d8306432438472#egg=pygeppetto
entrypoints==0.3
fasteners==0.16
filelock==3.0.12
-h5py==3.2.1
-hdmf==1.6.4
+fsspec==2021.4.0
+h5py==2.10.0
+hdmf==2.4.0
+holoviews==1.14.3
idna==2.10
-imageio==2.5.0
+imageio==2.9.0
importlib-metadata==4.0.1
ipydatawidgets==4.2.0
ipykernel==5.5.3
@@ -32,9 +41,15 @@
ipysheet==0.4.4
ipython==7.22.0
ipython-genutils==0.2.0
+ipytree==0.2.1
ipyvolume==0.5.2
ipywebrtc==0.6.0
ipywidgets==7.6.3
+itk-core==5.2.0
+itk-filtering==5.2.0
+itk-meshtopolydata==0.7.0
+itk-numerics==5.2.0
+itkwidgets==0.32.0
jedi==0.18.0
Jinja2==2.11.3
jsonschema==3.2.0
@@ -42,37 +57,42 @@
jupyter-client==6.1.12
jupyter-console==6.4.0
jupyter-core==4.7.1
-jupyter-geppetto==1.1.1
jupyterlab-pygments==0.1.2
jupyterlab-widgets==1.0.0
kiwisolver==1.3.1
+locket==0.2.1
lxml==4.6.3
+Markdown==3.3.4
MarkupSafe==1.1.1
matplotlib==3.4.1
mistune==0.8.4
more-itertools==8.7.0
+msgpack-python==0.5.6
multimethod==1.5
nbclient==0.5.3
nbconvert==6.0.7
nbformat==5.1.3
ndx-grayscalevolume==0.0.2
ndx-icephys-meta==0.1.0
+ndx-spectrum==0.2.2
nest-asyncio==1.5.1
networkx==2.5.1
nose==1.3.7
notebook==6.3.0
numcodecs==0.7.3
-numpy==1.20.2
-nwb-explorer==0.6.0
-nwbwidgets==0.4.0
+numpy==1.19.3
+nwbwidgets==0.6.0
ordered-set==4.0.2
packaging==20.9
pandas==1.2.4
pandocfilters==1.4.3
+panel==0.11.3
+param==1.10.1
parso==0.8.2
+partd==1.2.0
pexpect==4.8.0
pickleshare==0.7.5
-Pillow==7.0.0
+Pillow==8.2.0
plotly==4.14.3
pluggy==0.13.1
prometheus-client==0.10.1
@@ -80,10 +100,10 @@
ptyprocess==0.7.0
py==1.10.0
pycparser==2.20
-pyecore==0.11.6
-pygeppetto==0.8.0
+pyct==0.4.8
+pyecore==0.12.0
Pygments==2.8.1
-pynwb==1.3.0
+pynwb==1.4.0
pyparsing==2.4.7
pyrsistent==0.17.3
pytest==4.6.2
@@ -91,12 +111,14 @@
python-dateutil==2.8.1
pythreejs==2.3.0
pytz==2021.1
+pyviz-comms==2.0.1
PyWavelets==1.1.1
+PyYAML==5.4.1
pyzmq==22.0.3
qtconsole==5.0.3
QtPy==1.9.0
-quantities==0.12.3
-redis==2.10.6
+quantities==0.12.4
+redis==3.5.3
requests==2.25.1
RestrictedPython==5.1
retrying==1.3.3
@@ -104,18 +126,20 @@
ruamel.yaml.clib==0.2.2
scikit-image==0.18.1
scipy==1.6.2
-seaborn==0.8.1
+seaborn==0.11.1
Send2Trash==1.5.0
six==1.15.0
terminado==0.9.4
testpath==0.4.4
tifffile==2021.4.8
toml==0.10.2
+toolz==0.11.1
tornado==6.1
tox==3.12.1
tqdm==4.60.0
traitlets==5.0.5
traittypes==0.2.1
+trimesh==3.9.14
typing-extensions==3.7.4.3
urllib3==1.26.4
uuid==1.30
@@ -124,5 +148,7 @@
webencodings==0.5.1
widgetsnbextension==3.5.1
wrapt==1.12.1
+xarray==0.17.0
zarr==2.7.1
zipp==3.4.1
+zstandard==0.15.2
```
Contributor guide
No contributing guide indexed for this repository
Research direction
Start by reproducing the missing icon with `python utilities/install.py --dev`, then compare the development and non-development package sets shown in the issue. Inspect the menu list and its Font Awesome class in the running NWBE application; done means the controls icon appears in the development installation as it does on live.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- javascript, python
- Domain
- build-system, frontend
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100