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Update env Jupyter extensions, Python 3.11, QGIS 3.34 + others second try #106

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merged 2 commits into from
Jan 26, 2024
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Update env Jupyter extensions, Python 3.11, QGIS 3.34 + others second try #106

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2949447
update env with new ext and software
tsnow03 Jan 26, 2024
e6d395d
remove one space
tsnow03 Jan 26, 2024
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50 changes: 28 additions & 22 deletions environment.yml
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Original file line number Diff line number Diff line change
@@ -1,15 +1,11 @@
name: cryocloud

channels:
- conda-forge
- nodefaults

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Best to add these lines back...

dependencies:
- python~=3.10.10
- python~=3.11.0
# Required until https://github.com/jupyterhub/repo2docker/pull/1196 is merged
- jupyterhub-singleuser>=3.0,<4.0
- jupyterhub-singleuser~=4.0.1
# nbgitpuller is very helpful when distributing user content
- nbgitpuller==1.1.1
- nbgitpuller~=1.2.0
# Specify major version of jupyterlab to use. Manually bump it when you want to upgrade
# jupyterlab version
- jupyterlab>=4.0,<4.1
Expand All @@ -18,22 +14,32 @@ dependencies:
# https://syncthing.net/ provides a dropbox-like interface for syncing directories across users,
# hubs and machines. Used along with `jupyter-syncthing-proxy`.
- jupyter-syncthing-proxy==1.0.3
- syncthing==1.22.1
- syncthing~=1.22.1
# gh-scoped-creds allows users to securely push to GitHub from their repo.
# https://blog.jupyter.org/securely-pushing-to-github-from-a-jupyterhub-3ee42dfdc54f has
# some more information
- gh-scoped-creds==4.1
# More git tools from github-cli
- gh~=2.32.1

# VS Code support
- jupyter-vscode-proxy~=0.5
- code-server~=4.16.1

# Jupyter tools
- ipython~=8.20.0
- ipywidgets~=8.1.1
- jupyterlab-favorites==3.1.0
- jupyter-ai~=2.9.1
- jupyter-book~=0.15.1
# - jupyter-offlinenotebook~=0.2.2 # Outdated according to jupyterlab
# - jupyter-collaboration~=2.0.1 # Causing save issues
- jupyterlab-favorites~=3.2.1
- jupyterlab-geojson~=3.4.0
- jupyterlab-git~=0.50.0
- jupyterlab-h5web~=11.1.0
- jupyterlab-myst~=2.1.0
- jupyter-book~=0.15.1
# - jupyterlab-plotly~=5.18.0 # Outdated accoring to jupyterlab
- jupyterlab_pygments~=0.3.0 # To bring extension uptodate
- jupytext~=1.16.1
- nbconvert==6.5.3
- nbdime~=4.0.1
Expand All @@ -42,23 +48,23 @@ dependencies:
- cython==0.29.32 # optimization, C API access
- hypothesis==6.58.0 # needed by numpy testing tools
- networkx==2.8.8
- numba==0.56.4 # high-performance numerics
- numba~=0.58.1 # high-performance numerics
- numpy==1.23.5
- pandas~=1.5.1
- pandas>=2.0.1,<3.0
- scikit-image==0.19.3
- scikit-learn==1.1.3
- scikit-learn>=1.2.2,<2.0.0
- scipy==1.9.3
- statsmodels==0.13.5
- sympy==1.11.1
- sympy~=1.12
- xarray>=2023.05.0

# Visualization packages
- bokeh~=3.2.2
- cartopy~=0.21.1 # geospatial plotting with matplotlib
- cartopy~=0.22.0 # geospatial plotting with matplotlib
- geoviews~=1.10.1
- hvplot~=0.8.4
- ipyleaflet~=0.17.3
- ipympl==0.9.3 # This enables matplotlib interaction with jupyter widgets
- ipympl~=0.9.3 # This enables matplotlib interaction with jupyter widgets
- matplotlib~=3.8.0
- plotly~=5.18.0
- seaborn==0.12.1 # statistical plotting with matplotlib
Expand Down Expand Up @@ -96,11 +102,11 @@ dependencies:

# Distributed computing
- dask>=2023.12.1
- dask-labextension==6.0.0
- dask-labextension~=7.0.0
- dask-geopandas~=0.3.1

# Other useful generic python packages
- pillow~=9.5 # Python imaging library, useful for many image-related tasks
- pillow~=10.2.0 # Python imaging library, useful for many image-related tasks
- pytest==7.2.0
- pytest-cov==4.0.0
- pep8==1.7.1
Expand All @@ -114,12 +120,12 @@ dependencies:
# Packages specific to cryo work
- h5coro~=0.0.6
- icepyx~=0.8.1
- itslive~=0.3.0
- itslive~=0.3.2
- is2view~=0.0.5
- sliderule~=4.0.0

# Desktop tools whose versions are more recent on conda-forge than ubuntu
- qgis~=3.28.6
- qgis~=3.34.0
# Maybe needed for qgis? https://github.com/conda-forge/qgis-feedstock/issues/263
- pyopencl
# Resolves warning "No ICDs were found": https://github.com/CryoInTheCloud/hub-image/issues/50
Expand All @@ -128,10 +134,10 @@ dependencies:
- websockify>=0.10
# Includes new subcommands (`switch` & `restore`) and vulnerability fixes
# over the version available via ubuntu sources
- git >=2.39
- git>=2.39

# Not all packages will be available from conda-forge, we install from pip when we need to.
- pip==22.3.1
- pip~=23.3.2
- pip:
# Access linux desktop from inside JupyterHub
- jupyter-desktop-server==0.1.3