ipycytoscape not displaying correctly

[cmutel]

@tngTUDOR Want to take a crack at this? Our infrastructure instructions are here: https://github.com/Depart-de-Sentier/brightcon-2023-talks/blob/main/Infrastructure.md

The notebook from eaternity should work but instead we get:

[cmutel]

jupyter --version

Selected Jupyter core packages...
IPython          : 8.5.0
ipykernel        : 6.15.3
ipywidgets       : not installed
jupyter_client   : 7.3.5
jupyter_core     : 4.11.1
jupyter_server   : not installed
jupyterlab       : not installed
nbclient         : not installed
nbconvert        : not installed
nbformat         : 5.6.1
notebook         : not installed
qtconsole        : not installed
traitlets        : 5.4.0

[cmutel]

I am working on spring.brightway.dev for now with the notebook kernel bw25.

[cmutel]

Not sure this is relevant, but see https://github.com/cytoscape/ipycytoscape#for-jupyterlab-users

[cmutel]

OK, plenty of Javascript errors in the inspector, including Module jupyter-cytoscape, semver range ^1.3.3 is not registered as a widget module.

[tngTUDOR]

Isn't ipywidgets missing?

---

From: Chris Mutel @.> Sent: Thursday, September 14, 2023 15:10 To: Depart-de-Sentier/brightcon-2023-talks @.> Cc: Tomas NAVARRETE @.>; Mention @.> Subject: Re: [Depart-de-Sentier/brightcon-2023-talks] ipycytoscape not displaying correctly (Issue #2)

OK, plenty of Javascript errors in the inspector, including Module jupyter-cytoscape, semver range ^1.3.3 is not registered as a widget module.

— Reply to this email directly, view it on GitHubhttps://github.com/Depart-de-Sentier/brightcon-2023-talks/issues/2#issuecomment-1719423309, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ACPXT62WCBIPWZOYERSSJX3X2L627ANCNFSM6AAAAAA4YCMDAU. You are receiving this because you were mentioned.Message ID: @.***>

[cmutel]

Not in bw25 - this is now (always) installed by default.

[tngTUDOR]

OK. I can reproduce the bug with the bw25 env.

---

From: Chris Mutel @.> Sent: Thursday, September 14, 2023 15:36 To: Depart-de-Sentier/brightcon-2023-talks @.> Cc: Tomas NAVARRETE @.>; Mention @.> Subject: Re: [Depart-de-Sentier/brightcon-2023-talks] ipycytoscape not displaying correctly (Issue #2)

Not in bw25 - this is now (always) installed by default.

— Reply to this email directly, view it on GitHubhttps://github.com/Depart-de-Sentier/brightcon-2023-talks/issues/2#issuecomment-1719469109, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ACPXT64ZGUHMSPOH4MWKCNTX2MB57ANCNFSM6AAAAAA4YCMDAU. You are receiving this because you were mentioned.Message ID: @.***>

[tngTUDOR]

a local fresh with the following seems to work fine: (the diff first)

8d7
<   - anyio=4.0.0=pyhd8ed1ab_0
10,12d8
<   - argon2-cffi=23.1.0=pyhd8ed1ab_0
<   - argon2-cffi-bindings=21.2.0=py311hd4cff14_3
<   - arrow=1.2.3=pyhd8ed1ab_0
16,18d11
<   - async-lru=2.0.4=pyhd8ed1ab_0
<   - attrs=23.1.0=pyh71513ae_1
<   - babel=2.12.1=pyhd8ed1ab_1
22,23d14
<   - beautifulsoup4=4.12.2=pyha770c72_0
<   - bleach=6.0.0=pyhd8ed1ab_0
37,38d27
<   - cached-property=1.5.2=hd8ed1ab_1
<   - cached_property=1.5.2=pyha770c72_1
40d28
<   - cffi=1.15.1=py311h409f033_3
48,49d35
<   - defusedxml=0.7.1=pyhd8ed1ab_0
<   - entrypoints=0.4=pyhd8ed1ab_0
54d39
<   - fqdn=1.5.1=pyhd8ed1ab_0
61d45
<   - importlib_resources=6.0.1=pyhd8ed1ab_0
66d49
<   - isoduration=20.11.0=pyhd8ed1ab_0
68,74d50
<   - jinja2=3.1.2=pyhd8ed1ab_1
<   - json5=0.9.14=pyhd8ed1ab_0
<   - jsonpointer=2.4=py311h38be061_2
<   - jsonschema=4.19.0=pyhd8ed1ab_1
<   - jsonschema-specifications=2023.7.1=pyhd8ed1ab_0
<   - jsonschema-with-format-nongpl=4.19.0=pyhd8ed1ab_1
<   - jupyter-lsp=2.2.0=pyhd8ed1ab_0
77,82d52
<   - jupyter_events=0.7.0=pyhd8ed1ab_2
<   - jupyter_server=2.7.3=pyhd8ed1ab_0
<   - jupyter_server_terminals=0.4.4=pyhd8ed1ab_1
<   - jupyterlab=4.0.5=pyhd8ed1ab_0
<   - jupyterlab_pygments=0.2.2=pyhd8ed1ab_0
<   - jupyterlab_server=2.25.0=pyhd8ed1ab_0
99d68
<   - libgomp=13.2.0=h807b86a_0
118d86
<   - markupsafe=2.1.3=py311h459d7ec_0
122d89
<   - mistune=3.0.1=pyhd8ed1ab_0
126,128d92
<   - nbclient=0.8.0=pyhd8ed1ab_0
<   - nbconvert-core=7.8.0=pyhd8ed1ab_0
<   - nbformat=5.9.2=pyhd8ed1ab_0
131d94
<   - notebook-shim=0.2.3=pyhd8ed1ab_0
136d98
<   - overrides=7.4.0=pyhd8ed1ab_0
139d100
<   - pandocfilters=1.5.0=pyhd8ed1ab_0
147d107
<   - pkgutil-resolve-name=1.3.10=pyhd8ed1ab_1
149d108
<   - prometheus_client=0.17.1=pyhd8ed1ab_0
156d114
<   - pycparser=2.21=pyhd8ed1ab_0
163,164d120
<   - python-fastjsonschema=2.18.0=pyhd8ed1ab_0
<   - python-json-logger=2.0.7=pyhd8ed1ab_0
169d124
<   - pyyaml=6.0.1=py311h459d7ec_0
172d126
<   - referencing=0.30.2=pyhd8ed1ab_0
174,176d127
<   - rfc3339-validator=0.1.4=pyhd8ed1ab_0
<   - rfc3986-validator=0.1.1=pyh9f0ad1d_0
<   - rpds-py=0.10.3=py311h46250e7_0
178d128
<   - send2trash=1.8.2=pyh41d4057_0
182,183d131
<   - sniffio=1.3.0=pyhd8ed1ab_0
<   - soupsieve=2.5=pyhd8ed1ab_1
189,190d136
<   - terminado=0.17.1=pyh41d4057_0
<   - tinycss2=1.2.1=pyhd8ed1ab_0
198d143
<   - typing_utils=0.1.0=pyhd8ed1ab_0
201d145
<   - uri-template=1.3.0=pyhd8ed1ab_0
205,207d148
<   - webcolors=1.13=pyhd8ed1ab_0
<   - webencodings=0.5.1=pyhd8ed1ab_2
<   - websocket-client=1.6.3=pyhd8ed1ab_0
217d157
<   - yaml=0.2.5=h7f98852_2

name: bc23talks
channels:
  - cmutel
  - conda-forge
dependencies:
  - _libgcc_mutex=0.1=conda_forge
  - _openmp_mutex=4.5=2_kmp_llvm
  - anyio=4.0.0=pyhd8ed1ab_0
  - appdirs=1.4.4=pyh9f0ad1d_0
  - argon2-cffi=23.1.0=pyhd8ed1ab_0
  - argon2-cffi-bindings=21.2.0=py311hd4cff14_3
  - arrow=1.2.3=pyhd8ed1ab_0
  - asteval=0.9.31=pyhd8ed1ab_0
  - asttokens=2.4.0=pyhd8ed1ab_0
  - astunparse=1.6.3=pyhd8ed1ab_0
  - async-lru=2.0.4=pyhd8ed1ab_0
  - attrs=23.1.0=pyh71513ae_1
  - babel=2.12.1=pyhd8ed1ab_1
  - backcall=0.2.0=pyh9f0ad1d_0
  - backports=1.0=pyhd8ed1ab_3
  - backports.functools_lru_cache=1.6.5=pyhd8ed1ab_0
  - beautifulsoup4=4.12.2=pyha770c72_0
  - bleach=6.0.0=pyhd8ed1ab_0
  - brightway25=1.0.6=py_10
  - brotli=1.1.0=hd590300_0
  - brotli-bin=1.1.0=hd590300_0
  - brotli-python=1.1.0=py311hb755f60_0
  - bw2analyzer=0.11.7=pyhd8ed1ab_0
  - bw2calc=2.0.dev13=py_0
  - bw2data=4.0.dev21=py_0
  - bw2io=0.9.dev21=py_0
  - bw2parameters=1.1.0=pyhd8ed1ab_0
  - bw_migrations=0.2=pyhd8ed1ab_0
  - bw_processing=0.8.5=pyhd8ed1ab_0
  - bzip2=1.0.8=h7f98852_4
  - ca-certificates=2023.7.22=hbcca054_0
  - cached-property=1.5.2=hd8ed1ab_1
  - cached_property=1.5.2=pyha770c72_1
  - certifi=2023.7.22=pyhd8ed1ab_0
  - cffi=1.15.1=py311h409f033_3
  - charset-normalizer=3.2.0=pyhd8ed1ab_0
  - colorama=0.4.6=pyhd8ed1ab_0
  - comm=0.1.4=pyhd8ed1ab_0
  - contourpy=1.1.0=py311h9547e67_0
  - cycler=0.11.0=pyhd8ed1ab_0
  - debugpy=1.8.0=py311hb755f60_0
  - decorator=5.1.1=pyhd8ed1ab_0
  - defusedxml=0.7.1=pyhd8ed1ab_0
  - entrypoints=0.4=pyhd8ed1ab_0
  - et_xmlfile=1.1.0=pyhd8ed1ab_0
  - exceptiongroup=1.1.3=pyhd8ed1ab_0
  - executing=1.2.0=pyhd8ed1ab_0
  - fonttools=4.42.1=py311h459d7ec_0
  - fqdn=1.5.1=pyhd8ed1ab_0
  - freetype=2.12.1=h267a509_2
  - fs=2.4.16=pyhd8ed1ab_0
  - icu=73.2=h59595ed_0
  - idna=3.4=pyhd8ed1ab_0
  - importlib-metadata=6.8.0=pyha770c72_0
  - importlib_metadata=6.8.0=hd8ed1ab_0
  - importlib_resources=6.0.1=pyhd8ed1ab_0
  - ipycytoscape=1.3.3=pyhd8ed1ab_1
  - ipykernel=6.25.2=pyh2140261_0
  - ipython=8.15.0=pyh0d859eb_0
  - ipywidgets=8.1.1=pyhd8ed1ab_0
  - isoduration=20.11.0=pyhd8ed1ab_0
  - jedi=0.19.0=pyhd8ed1ab_0
  - jinja2=3.1.2=pyhd8ed1ab_1
  - json5=0.9.14=pyhd8ed1ab_0
  - jsonpointer=2.4=py311h38be061_2
  - jsonschema=4.19.0=pyhd8ed1ab_1
  - jsonschema-specifications=2023.7.1=pyhd8ed1ab_0
  - jsonschema-with-format-nongpl=4.19.0=pyhd8ed1ab_1
  - jupyter-lsp=2.2.0=pyhd8ed1ab_0
  - jupyter_client=8.3.1=pyhd8ed1ab_0
  - jupyter_core=5.3.1=py311h38be061_0
  - jupyter_events=0.7.0=pyhd8ed1ab_2
  - jupyter_server=2.7.3=pyhd8ed1ab_0
  - jupyter_server_terminals=0.4.4=pyhd8ed1ab_1
  - jupyterlab=4.0.5=pyhd8ed1ab_0
  - jupyterlab_pygments=0.2.2=pyhd8ed1ab_0
  - jupyterlab_server=2.25.0=pyhd8ed1ab_0
  - jupyterlab_widgets=3.0.9=pyhd8ed1ab_0
  - kiwisolver=1.4.5=py311h9547e67_0
  - lcms2=2.15=haa2dc70_1
  - ld_impl_linux-64=2.40=h41732ed_0
  - lerc=4.0.0=h27087fc_0
  - libblas=3.9.0=16_linux64_mkl
  - libbrotlicommon=1.1.0=hd590300_0
  - libbrotlidec=1.1.0=hd590300_0
  - libbrotlienc=1.1.0=hd590300_0
  - libcblas=3.9.0=16_linux64_mkl
  - libdeflate=1.18=h0b41bf4_0
  - libexpat=2.5.0=hcb278e6_1
  - libffi=3.4.2=h7f98852_5
  - libgcc-ng=13.2.0=h807b86a_0
  - libgfortran-ng=13.2.0=h69a702a_0
  - libgfortran5=13.2.0=ha4646dd_0
  - libgomp=13.2.0=h807b86a_0
  - libhwloc=2.9.2=default_h554bfaf_1009
  - libiconv=1.17=h166bdaf_0
  - libjpeg-turbo=2.1.5.1=hd590300_1
  - liblapack=3.9.0=16_linux64_mkl
  - libnsl=2.0.0=h7f98852_0
  - libpng=1.6.39=h753d276_0
  - libsodium=1.0.18=h36c2ea0_1
  - libsqlite=3.43.0=h2797004_0
  - libstdcxx-ng=13.2.0=h7e041cc_0
  - libtiff=4.5.1=h8b53f26_1
  - libuuid=2.38.1=h0b41bf4_0
  - libwebp-base=1.3.1=hd590300_0
  - libxcb=1.15=h0b41bf4_0
  - libxml2=2.11.5=h232c23b_1
  - libxslt=1.1.37=h0054252_1
  - libzlib=1.2.13=hd590300_5
  - llvm-openmp=16.0.6=h4dfa4b3_0
  - lxml=4.9.3=py311h1a07684_0
  - markupsafe=2.1.3=py311h459d7ec_0
  - matplotlib-base=3.7.2=py311h54ef318_0
  - matplotlib-inline=0.1.6=pyhd8ed1ab_0
  - matrix_utils=0.2.5=pyhd8ed1ab_0
  - mistune=3.0.1=pyhd8ed1ab_0
  - mkl=2022.2.1=h84fe81f_16997
  - mrio_common_metadata=0.2.1=pyhd8ed1ab_0
  - munkres=1.1.4=pyh9f0ad1d_0
  - nbclient=0.8.0=pyhd8ed1ab_0
  - nbconvert-core=7.8.0=pyhd8ed1ab_0
  - nbformat=5.9.2=pyhd8ed1ab_0
  - ncurses=6.4=hcb278e6_0
  - nest-asyncio=1.5.6=pyhd8ed1ab_0
  - notebook-shim=0.2.3=pyhd8ed1ab_0
  - numpy=1.25.2=py311h64a7726_0
  - openjpeg=2.5.0=hfec8fc6_2
  - openpyxl=3.1.2=py311h459d7ec_0
  - openssl=3.1.2=hd590300_0
  - overrides=7.4.0=pyhd8ed1ab_0
  - packaging=23.1=pyhd8ed1ab_0
  - pandas=2.1.0=py311h320fe9a_0
  - pandocfilters=1.5.0=pyhd8ed1ab_0
  - parso=0.8.3=pyhd8ed1ab_0
  - peewee=3.16.3=py311h65c2ff9_0
  - pexpect=4.8.0=pyh1a96a4e_2
  - pickleshare=0.7.5=py_1003
  - pillow=10.0.0=py311h0b84326_0
  - pint=0.22=pyhd8ed1ab_1
  - pip=23.2.1=pyhd8ed1ab_0
  - pkgutil-resolve-name=1.3.10=pyhd8ed1ab_1
  - platformdirs=3.10.0=pyhd8ed1ab_0
  - prometheus_client=0.17.1=pyhd8ed1ab_0
  - prompt-toolkit=3.0.39=pyha770c72_0
  - prompt_toolkit=3.0.39=hd8ed1ab_0
  - psutil=5.9.5=py311h2582759_0
  - pthread-stubs=0.4=h36c2ea0_1001
  - ptyprocess=0.7.0=pyhd3deb0d_0
  - pure_eval=0.2.2=pyhd8ed1ab_0
  - pycparser=2.21=pyhd8ed1ab_0
  - pygments=2.16.1=pyhd8ed1ab_0
  - pypardiso=0.4.2=pyhd8ed1ab_1
  - pyparsing=3.0.9=pyhd8ed1ab_0
  - pysocks=1.7.1=pyha2e5f31_6
  - python=3.11.5=hab00c5b_0_cpython
  - python-dateutil=2.8.2=pyhd8ed1ab_0
  - python-fastjsonschema=2.18.0=pyhd8ed1ab_0
  - python-json-logger=2.0.7=pyhd8ed1ab_0
  - python-tzdata=2023.3=pyhd8ed1ab_0
  - python_abi=3.11=3_cp311
  - pytz=2023.3.post1=pyhd8ed1ab_0
  - pyxlsb=1.0.10=pyhd8ed1ab_0
  - pyyaml=6.0.1=py311h459d7ec_0
  - pyzmq=25.1.1=py311h75c88c4_0
  - readline=8.2=h8228510_1
  - referencing=0.30.2=pyhd8ed1ab_0
  - requests=2.31.0=pyhd8ed1ab_0
  - rfc3339-validator=0.1.4=pyhd8ed1ab_0
  - rfc3986-validator=0.1.1=pyh9f0ad1d_0
  - rpds-py=0.10.3=py311h46250e7_0
  - scipy=1.11.2=py311h64a7726_1
  - send2trash=1.8.2=pyh41d4057_0
  - setuptools=68.2.2=pyhd8ed1ab_0
  - setuptools-scm=7.1.0=pyhd8ed1ab_0
  - six=1.16.0=pyh6c4a22f_0
  - sniffio=1.3.0=pyhd8ed1ab_0
  - soupsieve=2.5=pyhd8ed1ab_1
  - spectate=1.0.1=pyhd8ed1ab_0
  - stack_data=0.6.2=pyhd8ed1ab_0
  - stats_arrays=0.6.5=pyhd8ed1ab_0
  - tabulate=0.9.0=pyhd8ed1ab_1
  - tbb=2021.10.0=h00ab1b0_0
  - terminado=0.17.1=pyh41d4057_0
  - tinycss2=1.2.1=pyhd8ed1ab_0
  - tk=8.6.12=h27826a3_0
  - tomli=2.0.1=pyhd8ed1ab_0
  - tornado=6.3.3=py311h459d7ec_0
  - tqdm=4.66.1=pyhd8ed1ab_0
  - traitlets=5.9.0=pyhd8ed1ab_0
  - typing-extensions=4.7.1=hd8ed1ab_0
  - typing_extensions=4.7.1=pyha770c72_0
  - typing_utils=0.1.0=pyhd8ed1ab_0
  - tzdata=2023c=h71feb2d_0
  - unidecode=1.3.6=pyhd8ed1ab_0
  - uri-template=1.3.0=pyhd8ed1ab_0
  - urllib3=2.0.4=pyhd8ed1ab_0
  - voluptuous=0.13.1=pyhd8ed1ab_0
  - wcwidth=0.2.6=pyhd8ed1ab_0
  - webcolors=1.13=pyhd8ed1ab_0
  - webencodings=0.5.1=pyhd8ed1ab_2
  - websocket-client=1.6.3=pyhd8ed1ab_0
  - wheel=0.41.2=pyhd8ed1ab_0
  - whoosh=2.7.4=py311h38be061_7
  - widgetsnbextension=4.0.9=pyhd8ed1ab_0
  - wrapt=1.15.0=py311h2582759_0
  - xlrd=2.0.1=pyhd8ed1ab_3
  - xlsxwriter=3.1.3=pyhd8ed1ab_0
  - xorg-libxau=1.0.11=hd590300_0
  - xorg-libxdmcp=1.1.3=h7f98852_0
  - xz=5.2.6=h166bdaf_0
  - yaml=0.2.5=h7f98852_2
  - zeromq=4.3.4=h9c3ff4c_1
  - zipp=3.16.2=pyhd8ed1ab_0
  - zstd=1.5.5=hfc55251_0
prefix: /home/jempepresidente/mambaforge/envs/bc23talks

[tngTUDOR]

Fixed. Ipycitoscape needs to be installed ALSO in the base env of Jupiter hub