MetaCell / MetaCell/nwb-explorer

(with --dev): Missing icon in menu-list

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PRIORITY: Medium
Dominant language
JavaScript
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27
Forks
16
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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"):

![202104221144-nwbe-missing-icon](https://user-images.githubusercontent.com/102575/115702076-657fe300-a360-11eb-9449-8a79fa6c8c2a.png)

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

![202104221145-nwbe-inspector](https://user-images.githubusercontent.com/102575/115702140-76c8ef80-a360-11eb-9011-917b3625c1ba.png)

This is what we get on live, for comparison:
![202104221148-nwbe-live-inspector](https://user-images.githubusercontent.com/102575/115702276-a2e47080-a360-11eb-9a69-fe3e8fadd60f.png)

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

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