From 4e1367d495d8b7a97a879f7dd52664448e3cfde2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E2=80=9Ctsnow03=E2=80=9D?= Date: Mon, 22 Jan 2024 00:19:14 -0700 Subject: [PATCH 01/57] update env to JupyterLab4 and others --- environment.yml | 72 +++++++++++++++++++++++++++---------------------- 1 file changed, 40 insertions(+), 32 deletions(-) diff --git a/environment.yml b/environment.yml index e93b192..ad92b0c 100644 --- a/environment.yml +++ b/environment.yml @@ -5,70 +5,78 @@ channels: - nodefaults 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 # 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>=3.0,<4.0 + - jupyterlab>=4.0 # This provides memory usage stats on JupyterLab and classic notebook - - jupyter-resource-usage==0.7.1 + - jupyter-resource-usage~=1.0.0 # 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 +# - jupyter-vscode-server==0.0.10 +# - code-server==4.20.0 # Jupyter tools - - ipython==8.6.0 + - ipython~=8.17.0 # Warning: There's a bug in ipykernel 6.18 that crashes hvplot. # See https://github.com/ipython/ipykernel/pull/1037. Restriction # can be relaxed once that's fixed. - ipykernel=6.16.0 - - ipywidgets==7.7.2 - - jupyterlab-favorites==3.1.0 - - jupyterlab-geojson==3.3.1 - - jupyterlab-git==0.41.0 - - jupyterlab-myst==1.1.0 + - ipywidgets~=8.0.0 + - jupyterlab-favorites==3.2.0 + - jupyterlab-geojson==3.4.0 + - jupyter-collaboration~=2.0.1 + - jupyterlab-git==0.50.0 +# - jupyter-ai==2.9.1 # Requires pandas>=2.0.1 + - jupyterlab-myst==2.1.0 + - jupyterlab-h5web~=11.1.0 - jupyter-book~=0.15.1 - jupytext==1.14.1 - nbconvert==6.5.3 - - nbdime==3.1.1 + - nbdime==4.0.1 # Core scientific python stack - 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 - - numpy==1.23.5 - - pandas~=1.5.1 - - scikit-image==0.19.3 - - scikit-learn==1.1.3 + - numba==0.58.1 # high-performance numerics + - numpy~=1.26.0 + - pandas==1.5.1 + - scikit-image==0.22.0 + - scikit-learn==1.4.0 - scipy==1.9.3 - statsmodels==0.13.5 - - sympy==1.11.1 + - sympy~=1.12.0 - 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 - matplotlib~=3.8.0 - - plotly==5.11.0 + - plotly==5.18.0 - seaborn==0.12.1 # statistical plotting with matplotlib - - geemap~=0.24.4 + - geemap~=0.30.0 # Geospatial data packages - geopandas~=0.13.2 @@ -100,13 +108,13 @@ dependencies: - intake-xarray==0.6.1 - gcsfs>=2023.5.0 - # Distributed computing - - dask==2022.11.0 - - dask-labextension==6.0.0 + # Distributed computing * + - dask==2024.1.0 + - 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 @@ -117,7 +125,7 @@ dependencies: - esmpy~=8.4.2 - xmip~=0.7.1 - # Packages specific to cryo work + # Packages specific to cryo work * - h5coro~=0.0.6 - icepyx~=0.8.1 - itslive~=0.3.0 @@ -125,19 +133,19 @@ dependencies: - 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 - - ocl-icd-system + # - ocl-icd-system # needed for Linux desktop to work - 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 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https://conda.anaconda.org/conda-forge/noarch/sphinx-copybutton-0.5.2-pyhd8ed1ab_0.conda#ac832cc43adc79118cf6e23f1f9b8995 @@ -657,13 +699,12 @@ https://conda.anaconda.org/conda-forge/noarch/sphinx-jupyterbook-latex-0.5.2-pyh https://conda.anaconda.org/conda-forge/noarch/sphinx-multitoc-numbering-0.1.3-pyhd8ed1ab_0.tar.bz2#40749a4d0f0d2e11c65fb26c1cd16a90 https://conda.anaconda.org/conda-forge/noarch/sphinx-thebe-0.2.1-pyhd8ed1ab_0.conda#8a4151bde2af98c6cbc42ee12b48eb7f https://conda.anaconda.org/conda-forge/noarch/sphinx-togglebutton-0.3.2-pyhd8ed1ab_0.tar.bz2#382738101934261ea7931d1460e64868 -https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-applehelp-1.0.7-pyhd8ed1ab_0.conda#aebfabcb60c33a89c1f9290cab49bc93 +https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-applehelp-1.0.8-pyhd8ed1ab_0.conda#611a35a27914fac3aa37611a6fe40bb5 https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-bibtex-2.5.0-pyhd8ed1ab_0.tar.bz2#b2e5c9aece936ebf9f26abdf71ddd74b https://conda.anaconda.org/conda-forge/noarch/jupyter-book-0.15.1-pyhd8ed1ab_0.conda#f10d556d3b3dc0aeae6aee37c412ea60 -https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-devhelp-1.0.5-pyhd8ed1ab_0.conda#ebf08f5184d8eaa486697bc060031953 -https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-htmlhelp-2.0.4-pyhd8ed1ab_0.conda#a9a89000dfd19656ad004b937eeb6828 -https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-qthelp-1.0.6-pyhd8ed1ab_0.conda#cf5c9649272c677a964a7313279e3a9b +https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-devhelp-1.0.6-pyhd8ed1ab_0.conda#d7e4954df0d3aea2eacc7835ad12671d +https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-htmlhelp-2.0.5-pyhd8ed1ab_0.conda#7e1e7437273682ada2ed5e9e9714b140 +https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-qthelp-1.0.7-pyhd8ed1ab_0.conda#26acae54b06f178681bfb551760f5dd1 https://conda.anaconda.org/conda-forge/noarch/sphinx-5.0.2-pyh6c4a22f_0.tar.bz2#d4eaa1f50733a377480ce1d5aac556c7 -https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-serializinghtml-1.1.9-pyhd8ed1ab_0.conda#0612e497d7860728f2cda421ea2aec09 -# pip py @ https://files.pythonhosted.org/packages/f6/f0/10642828a8dfb741e5f3fbaac830550a518a775c7fff6f04a007259b0548/py-1.11.0-py2.py3-none-any.whl#sha256=607c53218732647dff4acdfcd50cb62615cedf612e72d1724fb1a0cc6405b378 +https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-serializinghtml-1.1.10-pyhd8ed1ab_0.conda#e507335cb4ca9cff4c3d0fa9cdab255e # pip jupyter-desktop-server @ https://files.pythonhosted.org/packages/15/df/6f249cd3c3db684c8f9e67bc5470c4b593f882fbb03b1649f72ae7a26566/jupyter-desktop-server-0.1.3.tar.gz#sha256=5915a2dbbe250f59b3cc01859297b26b2e1836e03a5db4bfbfd438005649d7e4 From 3cfae23bee8bd68575412a824a8e81eadc602346 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E2=80=9Ctsnow03=E2=80=9D?= Date: Mon, 22 Jan 2024 01:03:21 -0700 Subject: [PATCH 03/57] update env adding a few edits --- environment.yml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/environment.yml b/environment.yml index ad92b0c..e0a254c 100644 --- a/environment.yml +++ b/environment.yml @@ -12,9 +12,9 @@ dependencies: - nbgitpuller==1.2.0 # Specify major version of jupyterlab to use. Manually bump it when you want to upgrade # jupyterlab version - - jupyterlab>=4.0 + - jupyterlab>=4.0,<4.1 # This provides memory usage stats on JupyterLab and classic notebook - - jupyter-resource-usage~=1.0.0 + - jupyter-resource-usage~=1.0.1 # 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 @@ -41,16 +41,16 @@ dependencies: - ipywidgets~=8.0.0 - jupyterlab-favorites==3.2.0 - - jupyterlab-geojson==3.4.0 + - jupyterlab-geojson~=3.4.0 - jupyter-collaboration~=2.0.1 - - jupyterlab-git==0.50.0 + - jupyterlab-git~=0.50.0 # - jupyter-ai==2.9.1 # Requires pandas>=2.0.1 - - jupyterlab-myst==2.1.0 + - jupyterlab-myst~=2.1.0 - jupyterlab-h5web~=11.1.0 - jupyter-book~=0.15.1 - jupytext==1.14.1 - nbconvert==6.5.3 - - nbdime==4.0.1 + - nbdime~=4.0.1 # Core scientific python stack - cython==0.29.32 # optimization, C API access From a84b839eb35ec39162ceb916b5ec7aa43bc75d24 Mon Sep 17 00:00:00 2001 From: actions-bot <58130806+actions-bot@users.noreply.github.com> Date: Mon, 22 Jan 2024 08:15:48 +0000 Subject: [PATCH 04/57] [condalock-command] autogenerated conda-lock files --- conda-linux-64.lock | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conda-linux-64.lock b/conda-linux-64.lock index f36a597..23cbe83 100644 --- a/conda-linux-64.lock +++ b/conda-linux-64.lock @@ -1,6 +1,6 @@ # Generated by conda-lock. # platform: linux-64 -# input_hash: b4ca4a9b51f7d1335bc925c6943786fde36051f5f5ed5a157efc1495f559775c +# input_hash: 48c4c420a07aac8bdf9d709383854c30ab3c896bf5e491e59ac7d7d611c2e329 @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2023.11.17-hbcca054_0.conda#01ffc8d36f9eba0ce0b3c1955fa780ee From b60b633c86e545d50ed0ad742c1656c0fa9e4d2a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E2=80=9Ctsnow03=E2=80=9D?= Date: Mon, 22 Jan 2024 01:36:30 -0700 Subject: [PATCH 05/57] removing updgrades of a couple packages not required --- environment.yml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/environment.yml b/environment.yml index e0a254c..31c4784 100644 --- a/environment.yml +++ b/environment.yml @@ -57,13 +57,13 @@ dependencies: - hypothesis==6.58.0 # needed by numpy testing tools - networkx==2.8.8 - numba==0.58.1 # high-performance numerics - - numpy~=1.26.0 - - pandas==1.5.1 - - scikit-image==0.22.0 - - scikit-learn==1.4.0 + - numpy==1.23.5 + - pandas~=1.5.1 + - scikit-image==0.19.3 + - scikit-learn==1.1.3 - scipy==1.9.3 - statsmodels==0.13.5 - - sympy~=1.12.0 + - sympy~=1.11.0 - xarray>=2023.05.0 # Visualization packages @@ -137,7 +137,7 @@ dependencies: # 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 - # - ocl-icd-system +# - ocl-icd-system # needed for Linux desktop to work - websockify>=0.10 # Includes new subcommands (`switch` & `restore`) and vulnerability fixes From cebae27f313fc2aa60ea9782ef8c69e68f8255cc Mon Sep 17 00:00:00 2001 From: actions-bot <58130806+actions-bot@users.noreply.github.com> Date: Mon, 22 Jan 2024 08:39:00 +0000 Subject: [PATCH 06/57] [condalock-command] autogenerated conda-lock files --- conda-linux-64.lock | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/conda-linux-64.lock b/conda-linux-64.lock index 23cbe83..abebf0f 100644 --- a/conda-linux-64.lock +++ b/conda-linux-64.lock @@ -1,6 +1,6 @@ # Generated by conda-lock. # platform: linux-64 -# input_hash: 48c4c420a07aac8bdf9d709383854c30ab3c896bf5e491e59ac7d7d611c2e329 +# input_hash: e4db5a4ac2e3c45483ca6ce1c9088ce4fe880b36dc14b94f428f4d803ae39766 @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2023.11.17-hbcca054_0.conda#01ffc8d36f9eba0ce0b3c1955fa780ee @@ -248,7 +248,6 @@ https://conda.anaconda.org/conda-forge/noarch/jupyterlab-geojson-3.4.0-pyhd8ed1a https://conda.anaconda.org/conda-forge/noarch/jupyterlab-myst-2.1.0-pyhd8ed1ab_0.conda#01b3067af472c554a7b5f756fda53224 https://conda.anaconda.org/conda-forge/noarch/jupyterlab_widgets-3.0.9-pyhd8ed1ab_0.conda#8370e0a9dc443f9b45a23fd30e7a6b3b https://conda.anaconda.org/conda-forge/linux-64/kiwisolver-1.4.5-py311h9547e67_1.conda#2c65bdf442b0d37aad080c8a4e0d452f -https://conda.anaconda.org/conda-forge/noarch/lazy_loader-0.3-pyhd8ed1ab_0.conda#69ea1d0fa7ab33b48c88394ad1dead65 https://conda.anaconda.org/conda-forge/linux-64/lcms2-2.16-hb7c19ff_0.conda#51bb7010fc86f70eee639b4bb7a894f5 https://conda.anaconda.org/conda-forge/linux-64/libblas-3.9.0-20_linux64_openblas.conda#2b7bb4f7562c8cf334fc2e20c2d28abc https://conda.anaconda.org/conda-forge/linux-64/libclang13-15.0.7-default_ha2b6cf4_4.conda#898e0dd993afbed0d871b60c2eb33b83 @@ -433,7 +432,7 @@ https://conda.anaconda.org/conda-forge/noarch/rfc3339-validator-0.1.4-pyhd8ed1ab https://conda.anaconda.org/conda-forge/noarch/rsa-4.7.2-pyh44b312d_0.tar.bz2#3452ab3790dbb1df9508b3fa4ea2f806 https://conda.anaconda.org/conda-forge/linux-64/ruamel.yaml-0.18.5-py311h459d7ec_0.conda#1101ec27377f8e45d8431a5f21d744f1 https://conda.anaconda.org/conda-forge/linux-64/sip-6.7.12-py311hb755f60_0.conda#02336abab4cb5dd794010ef53c54bd09 -https://conda.anaconda.org/conda-forge/noarch/sympy-1.12-pypyh9d50eac_103.conda#2f7d6347d7acf6edf1ac7f2189f44c8f +https://conda.anaconda.org/conda-forge/noarch/sympy-1.11.1-pypyh9d50eac_103.conda#3893579a690fcd781c3dcedfd019bb9f https://conda.anaconda.org/conda-forge/noarch/terminado-0.18.0-pyh0d859eb_0.conda#e463f348b8b0eb62c9f7c6fbc780286c https://conda.anaconda.org/conda-forge/noarch/tinycss2-1.2.1-pyhd8ed1ab_0.tar.bz2#7234c9eefff659501cd2fe0d2ede4d48 https://conda.anaconda.org/conda-forge/noarch/tqdm-4.64.1-pyhd8ed1ab_0.tar.bz2#5526ff3f88f9db87bb0924b9ce575345 @@ -485,7 +484,7 @@ https://conda.anaconda.org/conda-forge/noarch/mako-1.3.0-pyhd8ed1ab_0.conda#92ca https://conda.anaconda.org/conda-forge/noarch/markdown-3.5.2-pyhd8ed1ab_0.conda#db7b48fa4eeb0c21b2f3f5b1f7d9ebcf https://conda.anaconda.org/conda-forge/noarch/mdit-py-plugins-0.4.0-pyhd8ed1ab_0.conda#6c5358a10873a15398b6f15f60cb5e1f https://conda.anaconda.org/conda-forge/noarch/nose2-0.9.2-py_0.tar.bz2#6016c166523ee4955697bccbde8700bf -https://conda.anaconda.org/conda-forge/linux-64/numpy-1.26.3-py311h64a7726_0.conda#231eef4f33640338f64ef9ab690ba08d +https://conda.anaconda.org/conda-forge/linux-64/numpy-1.23.5-py311h7d28db0_0.conda#de8cf17747d9efed488cafea2c39c9a1 https://conda.anaconda.org/conda-forge/linux-64/poppler-23.12.0-h590f24d_0.conda#480189ac126a8c6c61e14476c8ba7c9a https://conda.anaconda.org/conda-forge/noarch/pqdm-0.2.0-pyhd8ed1ab_0.conda#d97731e8c7b51823b977f9fd42fb0b1a https://conda.anaconda.org/conda-forge/noarch/prompt_toolkit-3.0.42-hd8ed1ab_0.conda#85a2189ecd2fcdd86e92b2d4ea8fe461 @@ -547,7 +546,7 @@ https://conda.anaconda.org/conda-forge/linux-64/pywavelets-1.4.1-py311h1f0f07a_1 https://conda.anaconda.org/conda-forge/noarch/redis-py-5.0.1-pyhd8ed1ab_0.conda#7d6dc4cc2415d0df21f6a4a369db4932 https://conda.anaconda.org/conda-forge/noarch/rich-click-1.7.3-pyhd8ed1ab_0.conda#dc858795a3dcc70135ae2c61b75a251a https://conda.anaconda.org/conda-forge/noarch/s3transfer-0.6.2-pyhd8ed1ab_0.conda#f57096b122c78f7d8bd6885f52db1077 -https://conda.anaconda.org/conda-forge/linux-64/scipy-1.9.3-py311h69910c8_1.tar.bz2#d50e2928da16d11d3cdfe498eae4965d +https://conda.anaconda.org/conda-forge/linux-64/scipy-1.9.3-py311h69910c8_2.tar.bz2#bb44baf80c9e22d4581dea2c030adb1c https://conda.anaconda.org/conda-forge/noarch/setuptools_scm-8.0.4-hd8ed1ab_0.conda#2a6b1e6a1a0c301e4bfff82d7672437a https://conda.anaconda.org/conda-forge/linux-64/shapely-2.0.2-py311h2032efe_1.conda#4ba860ff851768615b1a25b788022750 https://conda.anaconda.org/conda-forge/noarch/snuggs-1.4.7-py_0.tar.bz2#cb83a3d6ecf73f50117635192414426a @@ -573,7 +572,7 @@ https://conda.anaconda.org/conda-forge/linux-64/netcdf4-1.6.5-nompi_py311he8ad70 https://conda.anaconda.org/conda-forge/linux-64/qt-main-5.15.8-h450f30e_18.conda#ef0430f8df5dcdedcaaab340b228f30c https://conda.anaconda.org/conda-forge/noarch/requests-oauthlib-1.3.1-pyhd8ed1ab_0.tar.bz2#61b279f051eef9c89d58f4d813e75e04 https://conda.anaconda.org/conda-forge/noarch/s3fs-2023.6.0-pyhd8ed1ab_0.conda#6c06cee0c302aca34978d8e0ae617880 -https://conda.anaconda.org/conda-forge/linux-64/scikit-learn-1.4.0-py311hc009520_0.conda#00dddf34e32a268242365329d51fb0f7 +https://conda.anaconda.org/conda-forge/linux-64/scikit-learn-1.1.3-py311h3b52e38_1.tar.bz2#65547502b7a454f9f1a1451b30217aca https://conda.anaconda.org/conda-forge/linux-64/statsmodels-0.13.5-py311h4c7f6c3_2.tar.bz2#90433f3ada9b209351a6cb42d2f5ca7f https://conda.anaconda.org/conda-forge/noarch/tifffile-2023.12.9-pyhd8ed1ab_0.conda#454bc0aff84f35fa53ba9e0369737a9b https://conda.anaconda.org/conda-forge/linux-64/tiledb-2.19.0-hc1131af_0.conda#51f6de9ca86bdeeb92e89e4abccd03e8 @@ -608,7 +607,7 @@ https://conda.anaconda.org/conda-forge/linux-64/qjson-0.9.0-h0c700ba_1009.conda# https://conda.anaconda.org/conda-forge/linux-64/qtkeychain-0.14.2-hbc31b07_0.conda#a70f152003f91bbbd1321a3ad4c27f93 https://conda.anaconda.org/conda-forge/linux-64/qtwebkit-5.212-h60108c6_16.conda#1e2785758dc448d977c48a0bd684a02f https://conda.anaconda.org/conda-forge/linux-64/qwt-6.2.0-h1a478b3_6.conda#675b4dd9357b5245b654f5f136d39b09 -https://conda.anaconda.org/conda-forge/linux-64/scikit-image-0.22.0-py311h320fe9a_2.conda#e94b7f09b52628b89e66cdbd8c3029dd +https://conda.anaconda.org/conda-forge/linux-64/scikit-image-0.19.3-py311h8b32b4d_2.tar.bz2#2100881f52d5ca36fd7f511e1a3f8652 https://conda.anaconda.org/conda-forge/noarch/seaborn-base-0.12.1-pyhd8ed1ab_0.tar.bz2#f87b94dc53178574eedd09c317c2318f https://conda.anaconda.org/conda-forge/noarch/xarray-datatree-0.0.13-pyhd8ed1ab_0.conda#df8242aef902cb65736d5d01cc18a664 https://conda.anaconda.org/conda-forge/noarch/bqplot-0.12.42-pyhd8ed1ab_0.conda#2eac77cc02664018a2491363da2b74f6 From fead1a75da10d1e830389be61c4dc3281b1661c4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E2=80=9Ctsnow03=E2=80=9D?= Date: Mon, 22 Jan 2024 01:39:40 -0700 Subject: [PATCH 07/57] minor fix to uncomment ocl --- environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/environment.yml b/environment.yml index 31c4784..5b2a2f1 100644 --- a/environment.yml +++ b/environment.yml @@ -137,7 +137,7 @@ dependencies: # 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 -# - ocl-icd-system + - ocl-icd-system # needed for Linux desktop to work - websockify>=0.10 # Includes new subcommands (`switch` & `restore`) and vulnerability fixes From 174dcfef47765cdc554449d7cf5ca5e25bada3fb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E2=80=9Ctsnow03=E2=80=9D?= Date: Mon, 22 Jan 2024 02:08:57 -0700 Subject: [PATCH 08/57] minor fix to comments --- environment.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/environment.yml b/environment.yml index 5b2a2f1..ebe8746 100644 --- a/environment.yml +++ b/environment.yml @@ -108,7 +108,7 @@ dependencies: - intake-xarray==0.6.1 - gcsfs>=2023.5.0 - # Distributed computing * + # Distributed computing - dask==2024.1.0 - dask-labextension==7.0.0 - dask-geopandas~=0.3.1 @@ -125,7 +125,7 @@ dependencies: - esmpy~=8.4.2 - xmip~=0.7.1 - # Packages specific to cryo work * + # Packages specific to cryo work - h5coro~=0.0.6 - icepyx~=0.8.1 - itslive~=0.3.0 From f88bf3bafed5c34d2188d53ab363a3b34bc753ee Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E2=80=9Ctsnow03=E2=80=9D?= Date: Mon, 22 Jan 2024 02:34:49 -0700 Subject: [PATCH 09/57] added code-server for vscode --- environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/environment.yml b/environment.yml index ebe8746..1738a14 100644 --- a/environment.yml +++ b/environment.yml @@ -29,7 +29,7 @@ dependencies: # VS Code support - jupyter-vscode-proxy==0.5 # - jupyter-vscode-server==0.0.10 -# - code-server==4.20.0 + - code-server~=4.16.1 # Jupyter tools - ipython~=8.17.0 From fbf1a7fd290a83bbf9f90fca496c25dfd9c3ecc3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E2=80=9Ctsnow03=E2=80=9D?= Date: Mon, 22 Jan 2024 10:15:06 -0700 Subject: [PATCH 10/57] scaling back env for testing --- environment.yml | 23 ++++++++++++----------- 1 file changed, 12 insertions(+), 11 deletions(-) diff --git a/environment.yml b/environment.yml index 1738a14..1cd310e 100644 --- a/environment.yml +++ b/environment.yml @@ -5,16 +5,16 @@ channels: - nodefaults dependencies: - - python~=3.11.0 + - python~=3.10.10 # Required until https://github.com/jupyterhub/repo2docker/pull/1196 is merged - - jupyterhub-singleuser>=4.0 + - jupyterhub==4.0.2 # nbgitpuller is very helpful when distributing user content - - nbgitpuller==1.2.0 + - nbgitpuller==1.1.1 # Specify major version of jupyterlab to use. Manually bump it when you want to upgrade # jupyterlab version - jupyterlab>=4.0,<4.1 # This provides memory usage stats on JupyterLab and classic notebook - - jupyter-resource-usage~=1.0.1 + - jupyter-resource-usage~=0.7.1 # 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 @@ -32,21 +32,22 @@ dependencies: - code-server~=4.16.1 # Jupyter tools - - ipython~=8.17.0 + - ipython~=8.6.0 # Warning: There's a bug in ipykernel 6.18 that crashes hvplot. # See https://github.com/ipython/ipykernel/pull/1037. Restriction # can be relaxed once that's fixed. - ipykernel=6.16.0 - - ipywidgets~=8.0.0 - - jupyterlab-favorites==3.2.0 + - ipywidgets~=7.7.2 +# - jupyterlab-favorites~=3.2.0 + - jupyterlab-favorites==3.1.1 - jupyterlab-geojson~=3.4.0 - - jupyter-collaboration~=2.0.1 +# - jupyter-collaboration~=2.0.1 - jupyterlab-git~=0.50.0 # - jupyter-ai==2.9.1 # Requires pandas>=2.0.1 - jupyterlab-myst~=2.1.0 - - jupyterlab-h5web~=11.1.0 +# - jupyterlab-h5web~=11.1.0 - jupyter-book~=0.15.1 - jupytext==1.14.1 - nbconvert==6.5.3 @@ -72,7 +73,7 @@ dependencies: - geoviews~=1.10.1 - hvplot~=0.8.4 - ipyleaflet~=0.17.3 - - ipympl==0.9.3 # This enables matplotlib interaction with jupyter widgets + - ipympl==0.9.2 # This enables matplotlib interaction with jupyter widgets - matplotlib~=3.8.0 - plotly==5.18.0 - seaborn==0.12.1 # statistical plotting with matplotlib @@ -110,7 +111,7 @@ dependencies: # Distributed computing - dask==2024.1.0 - - dask-labextension==7.0.0 + - dask-labextension==6.0.0 - dask-geopandas~=0.3.1 # Other useful generic python packages From 861bc2252b5a2d9f3ac975a74d010f8201586c14 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E2=80=9Ctsnow03=E2=80=9D?= Date: Mon, 22 Jan 2024 12:33:54 -0700 Subject: [PATCH 11/57] removing extensions for testing --- environment.yml | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/environment.yml b/environment.yml index 1cd310e..337a72a 100644 --- a/environment.yml +++ b/environment.yml @@ -28,7 +28,6 @@ dependencies: # VS Code support - jupyter-vscode-proxy==0.5 -# - jupyter-vscode-server==0.0.10 - code-server~=4.16.1 # Jupyter tools @@ -41,17 +40,17 @@ dependencies: - ipywidgets~=7.7.2 # - jupyterlab-favorites~=3.2.0 - - jupyterlab-favorites==3.1.1 - - jupyterlab-geojson~=3.4.0 +# - jupyterlab-favorites==3.1.1 +# - jupyterlab-geojson~=3.4.0 # - jupyter-collaboration~=2.0.1 - - jupyterlab-git~=0.50.0 +# - jupyterlab-git~=0.50.0 # - jupyter-ai==2.9.1 # Requires pandas>=2.0.1 - jupyterlab-myst~=2.1.0 # - jupyterlab-h5web~=11.1.0 - jupyter-book~=0.15.1 - jupytext==1.14.1 - nbconvert==6.5.3 - - nbdime~=4.0.1 +# - nbdime~=4.0.1 # Core scientific python stack - cython==0.29.32 # optimization, C API access From cf826e48b03e22deb1f7917a468c081913ba44e9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E2=80=9Ctsnow03=E2=80=9D?= Date: Mon, 22 Jan 2024 13:19:27 -0700 Subject: [PATCH 12/57] downgrading for testing --- environment.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/environment.yml b/environment.yml index 337a72a..3460565 100644 --- a/environment.yml +++ b/environment.yml @@ -7,7 +7,7 @@ channels: dependencies: - python~=3.10.10 # Required until https://github.com/jupyterhub/repo2docker/pull/1196 is merged - - jupyterhub==4.0.2 + - jupyterhub-singleuser>=3.0,<4.0 # nbgitpuller is very helpful when distributing user content - nbgitpuller==1.1.1 # Specify major version of jupyterlab to use. Manually bump it when you want to upgrade @@ -137,7 +137,7 @@ dependencies: # 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 - - ocl-icd-system +# - ocl-icd-system # needed for Linux desktop to work - websockify>=0.10 # Includes new subcommands (`switch` & `restore`) and vulnerability fixes From dae529a56d9f6d3494dee4b9d44a7da936199800 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E2=80=9Ctsnow03=E2=80=9D?= Date: Mon, 22 Jan 2024 14:30:54 -0700 Subject: [PATCH 13/57] upgrading nbconvert --- environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/environment.yml b/environment.yml index 3460565..1e83790 100644 --- a/environment.yml +++ b/environment.yml @@ -49,7 +49,7 @@ dependencies: # - jupyterlab-h5web~=11.1.0 - jupyter-book~=0.15.1 - jupytext==1.14.1 - - nbconvert==6.5.3 + - nbconvert==7.14.2 # - nbdime~=4.0.1 # Core scientific python stack From 36ee1d7d05ccee3ab6e12e4f29dbdd48e2554244 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E2=80=9Ctsnow03=E2=80=9D?= Date: Mon, 22 Jan 2024 23:11:04 -0700 Subject: [PATCH 14/57] back to the full env upgrade --- environment.yml | 39 +++++++++++++++++++-------------------- 1 file changed, 19 insertions(+), 20 deletions(-) diff --git a/environment.yml b/environment.yml index 1e83790..212eb55 100644 --- a/environment.yml +++ b/environment.yml @@ -5,16 +5,16 @@ channels: - nodefaults 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 # This provides memory usage stats on JupyterLab and classic notebook - - jupyter-resource-usage~=0.7.1 + - jupyter-resource-usage~=1.0.1 # 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 @@ -31,26 +31,25 @@ dependencies: - code-server~=4.16.1 # Jupyter tools - - ipython~=8.6.0 + - ipython~=8.20.0 # Warning: There's a bug in ipykernel 6.18 that crashes hvplot. # See https://github.com/ipython/ipykernel/pull/1037. Restriction # can be relaxed once that's fixed. - - ipykernel=6.16.0 + - ipykernel~=6.29.0 - - ipywidgets~=7.7.2 -# - jupyterlab-favorites~=3.2.0 -# - jupyterlab-favorites==3.1.1 -# - jupyterlab-geojson~=3.4.0 -# - jupyter-collaboration~=2.0.1 -# - jupyterlab-git~=0.50.0 + - ipywidgets~=8.1.1 + - jupyterlab-favorites~=3.2.0 + - jupyterlab-geojson~=3.4.0 + - jupyter-collaboration~=2.0.1 + - jupyterlab-git~=0.50.0 # - jupyter-ai==2.9.1 # Requires pandas>=2.0.1 - jupyterlab-myst~=2.1.0 -# - jupyterlab-h5web~=11.1.0 + - jupyterlab-h5web~=11.1.0 - jupyter-book~=0.15.1 - - jupytext==1.14.1 - - nbconvert==7.14.2 -# - nbdime~=4.0.1 + - jupytext==1.16.1 + - nbconvert==6.5.3 + - nbdime~=4.0.1 # Core scientific python stack - cython==0.29.32 # optimization, C API access @@ -58,9 +57,9 @@ dependencies: - networkx==2.8.8 - numba==0.58.1 # high-performance numerics - numpy==1.23.5 - - pandas~=1.5.1 + - pandas>=1.5.1 - 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~=1.11.0 @@ -110,7 +109,7 @@ dependencies: # Distributed computing - dask==2024.1.0 - - dask-labextension==6.0.0 + - dask-labextension==7.0.0 - dask-geopandas~=0.3.1 # Other useful generic python packages @@ -137,7 +136,7 @@ dependencies: # 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 -# - ocl-icd-system + - ocl-icd-system # needed for Linux desktop to work - websockify>=0.10 # Includes new subcommands (`switch` & `restore`) and vulnerability fixes From 35661d42803377f934721c856344798c6b80846e Mon Sep 17 00:00:00 2001 From: actions-bot <58130806+actions-bot@users.noreply.github.com> Date: Tue, 23 Jan 2024 07:21:26 +0000 Subject: [PATCH 15/57] [condalock-command] autogenerated conda-lock files --- conda-linux-64.lock | 49 ++++++++++++++++++++++++--------------------- 1 file changed, 26 insertions(+), 23 deletions(-) diff --git a/conda-linux-64.lock b/conda-linux-64.lock index abebf0f..671edb4 100644 --- a/conda-linux-64.lock +++ b/conda-linux-64.lock @@ -1,6 +1,6 @@ # Generated by conda-lock. # platform: linux-64 -# input_hash: e4db5a4ac2e3c45483ca6ce1c9088ce4fe880b36dc14b94f428f4d803ae39766 +# input_hash: 069528b5179316cbbaa497966a83b9926edd8c00cda7b882b558b0dc791990dc @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2023.11.17-hbcca054_0.conda#01ffc8d36f9eba0ce0b3c1955fa780ee @@ -71,6 +71,7 @@ https://conda.anaconda.org/conda-forge/linux-64/libtasn1-4.19.0-h166bdaf_0.tar.b https://conda.anaconda.org/conda-forge/linux-64/libunistring-0.9.10-h7f98852_0.tar.bz2#7245a044b4a1980ed83196176b78b73a https://conda.anaconda.org/conda-forge/linux-64/libutf8proc-2.8.0-h166bdaf_0.tar.bz2#ede4266dc02e875fe1ea77b25dd43747 https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b +https://conda.anaconda.org/conda-forge/linux-64/libuv-1.46.0-hd590300_0.conda#d23c76f7e6dcd6243d1b6ef5e62d17d2 https://conda.anaconda.org/conda-forge/linux-64/libvpx-1.13.1-h59595ed_0.conda#0974a6d3432e10bae02bcab0cce1b308 https://conda.anaconda.org/conda-forge/linux-64/libwebp-base-1.3.2-hd590300_0.conda#30de3fd9b3b602f7473f30e684eeea8c https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc @@ -172,7 +173,7 @@ https://conda.anaconda.org/conda-forge/linux-64/libgcrypt-1.10.3-hd590300_0.cond https://conda.anaconda.org/conda-forge/linux-64/libglib-2.78.3-h783c2da_0.conda#9bd06b12bbfa6fd1740fd23af4b0f0c7 https://conda.anaconda.org/conda-forge/linux-64/libhwloc-2.9.3-default_h554bfaf_1009.conda#f36ddc11ca46958197a45effdd286e45 https://conda.anaconda.org/conda-forge/linux-64/libllvm15-15.0.7-hb3ce162_4.conda#8a35df3cbc0c8b12cc8af9473ae75eef -https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.25-pthreads_h413a1c8_0.conda#d172b34a443b95f86089e8229ddc9a17 +https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.26-pthreads_h413a1c8_0.conda#760ae35415f5ba8b15d09df5afe8b23a https://conda.anaconda.org/conda-forge/linux-64/libsndfile-1.2.2-hc60ed4a_1.conda#ef1910918dd895516a769ed36b5b3a4e https://conda.anaconda.org/conda-forge/linux-64/libthrift-0.19.0-hb90f79a_1.conda#8cdb7d41faa0260875ba92414c487e2d https://conda.anaconda.org/conda-forge/linux-64/libtiff-4.6.0-ha9c0a0a_2.conda#55ed21669b2015f77c180feb1dd41930 @@ -180,12 +181,13 @@ https://conda.anaconda.org/conda-forge/linux-64/libxslt-1.1.39-h76b75d6_0.conda# https://conda.anaconda.org/conda-forge/linux-64/minizip-4.0.4-h0ab5242_0.conda#813bc75d9c33ddd9c9d5b8d9c560e152 https://conda.anaconda.org/conda-forge/linux-64/mpc-1.3.1-hfe3b2da_0.conda#289c71e83dc0daa7d4c81f04180778ca https://conda.anaconda.org/conda-forge/linux-64/mysql-libs-8.0.33-hca2cd23_6.conda#e87530d1b12dd7f4e0f856dc07358d60 -https://conda.anaconda.org/conda-forge/linux-64/nss-3.96-h1d7d5a4_0.conda#1c8f8b8eb041ecd54053fc4b6ad57957 +https://conda.anaconda.org/conda-forge/linux-64/nodejs-16.20.2-h1990674_2.conda#d2d03f9273e6a735dce8e957767d2dca +https://conda.anaconda.org/conda-forge/linux-64/nss-3.97-h1d7d5a4_0.conda#b916d71a3032416e3f9136090d814472 https://conda.anaconda.org/conda-forge/linux-64/orc-1.9.2-h4b38347_0.conda#6e6f990b097d3e237e18a8e321d08484 https://conda.anaconda.org/conda-forge/linux-64/python-3.11.7-hab00c5b_1_cpython.conda#27cf681282c11dba7b0b1fd266e8f289 https://conda.anaconda.org/conda-forge/linux-64/re2-2023.06.02-h2873b5e_0.conda#bb2d5e593ef13fe4aff0bc9440f945ae https://conda.anaconda.org/conda-forge/linux-64/sqlite-3.44.2-h2c6b66d_0.conda#4f2892c672829693fd978d065db4e8be -https://conda.anaconda.org/conda-forge/linux-64/ucx-1.15.0-h75e419f_2.conda#5798de4587dc70fa6db81663e79f176a +https://conda.anaconda.org/conda-forge/linux-64/ucx-1.15.0-h75e419f_3.conda#5baf4efbca923cdf73490c62cc7de1e2 https://conda.anaconda.org/conda-forge/linux-64/xcb-util-0.4.0-hd590300_1.conda#9bfac7ccd94d54fd21a0501296d60424 https://conda.anaconda.org/conda-forge/linux-64/xcb-util-keysyms-0.4.0-h8ee46fc_1.conda#632413adcd8bc16b515cab87a2932913 https://conda.anaconda.org/conda-forge/linux-64/xcb-util-renderutil-0.3.9-hd590300_1.conda#e995b155d938b6779da6ace6c6b13816 @@ -211,6 +213,7 @@ https://conda.anaconda.org/conda-forge/noarch/certifi-2023.11.17-pyhd8ed1ab_0.co https://conda.anaconda.org/conda-forge/noarch/charset-normalizer-3.3.2-pyhd8ed1ab_0.conda#7f4a9e3fcff3f6356ae99244a014da6a https://conda.anaconda.org/conda-forge/noarch/click-8.1.7-unix_pyh707e725_0.conda#f3ad426304898027fc619827ff428eca https://conda.anaconda.org/conda-forge/noarch/cloudpickle-3.0.0-pyhd8ed1ab_0.conda#753d29fe41bb881e4b9c004f0abf973f +https://conda.anaconda.org/conda-forge/linux-64/code-server-4.16.1-h424e19c_0.conda#c276b7d42d2b90a490b6a89d1c77d0dc https://conda.anaconda.org/conda-forge/noarch/colorama-0.4.4-pyh9f0ad1d_0.tar.bz2#c08b4c1326b880ed44f3ffb04803332f https://conda.anaconda.org/conda-forge/noarch/colour-0.1.5-pyhd8ed1ab_1.conda#de5ef3b303f625ac94939665ab85e996 https://conda.anaconda.org/conda-forge/noarch/cycler-0.12.1-pyhd8ed1ab_0.conda#5cd86562580f274031ede6aa6aa24441 @@ -243,13 +246,13 @@ https://conda.anaconda.org/conda-forge/noarch/ipython_genutils-0.2.0-py_1.tar.bz https://conda.anaconda.org/conda-forge/noarch/jmespath-1.0.1-pyhd8ed1ab_0.tar.bz2#2cfa3e1cf3fb51bb9b17acc5b5e9ea11 https://conda.anaconda.org/conda-forge/noarch/json5-0.9.14-pyhd8ed1ab_0.conda#dac1dabba2b5a9d1aee175c5fcc7b436 https://conda.anaconda.org/conda-forge/linux-64/jsonpointer-2.4-py311h38be061_3.conda#41d52d822edf991bf0e6b08c1921a8ec -https://conda.anaconda.org/conda-forge/noarch/jupyterlab-favorites-3.2.0-pyhd8ed1ab_0.conda#dd2961fb46d6ee750289ea809488560e +https://conda.anaconda.org/conda-forge/noarch/jupyterlab-favorites-3.2.1-pyhd8ed1ab_0.conda#d1eebb9c9d3662ec1697b2bf0ce451c7 https://conda.anaconda.org/conda-forge/noarch/jupyterlab-geojson-3.4.0-pyhd8ed1ab_0.conda#a98e9b2a8648b246b9aec4a67cfea5f7 https://conda.anaconda.org/conda-forge/noarch/jupyterlab-myst-2.1.0-pyhd8ed1ab_0.conda#01b3067af472c554a7b5f756fda53224 https://conda.anaconda.org/conda-forge/noarch/jupyterlab_widgets-3.0.9-pyhd8ed1ab_0.conda#8370e0a9dc443f9b45a23fd30e7a6b3b https://conda.anaconda.org/conda-forge/linux-64/kiwisolver-1.4.5-py311h9547e67_1.conda#2c65bdf442b0d37aad080c8a4e0d452f https://conda.anaconda.org/conda-forge/linux-64/lcms2-2.16-hb7c19ff_0.conda#51bb7010fc86f70eee639b4bb7a894f5 -https://conda.anaconda.org/conda-forge/linux-64/libblas-3.9.0-20_linux64_openblas.conda#2b7bb4f7562c8cf334fc2e20c2d28abc +https://conda.anaconda.org/conda-forge/linux-64/libblas-3.9.0-21_linux64_openblas.conda#0ac9f44fc096772b0aa092119b00c3ca https://conda.anaconda.org/conda-forge/linux-64/libclang13-15.0.7-default_ha2b6cf4_4.conda#898e0dd993afbed0d871b60c2eb33b83 https://conda.anaconda.org/conda-forge/linux-64/libcups-2.3.3-h4637d8d_4.conda#d4529f4dff3057982a7617c7ac58fde3 https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.5.0-hca28451_0.conda#7144d5a828e2cae218e0e3c98d8a0aeb @@ -296,7 +299,7 @@ https://conda.anaconda.org/conda-forge/noarch/pure_eval-0.2.2-pyhd8ed1ab_0.tar.b https://conda.anaconda.org/conda-forge/noarch/pyasn1-0.5.1-pyhd8ed1ab_0.conda#fb1a800972b072aa4d16450983c81418 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https://conda.anaconda.org/conda-forge/noarch/geopandas-0.13.2-pyhd8ed1ab_1.conda#47226a55e4ae3bc9feb3a17925874817 From 0be9509c287db7c8f3bd982aaff912fbe6a62922 Mon Sep 17 00:00:00 2001 From: actions-bot <58130806+actions-bot@users.noreply.github.com> Date: Tue, 23 Jan 2024 07:36:23 +0000 Subject: [PATCH 16/57] [condalock-command] autogenerated conda-lock files --- conda-linux-64.lock | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/conda-linux-64.lock b/conda-linux-64.lock index 671edb4..e16ba00 100644 --- a/conda-linux-64.lock +++ b/conda-linux-64.lock @@ -1,6 +1,6 @@ # Generated by conda-lock. # platform: linux-64 -# input_hash: 069528b5179316cbbaa497966a83b9926edd8c00cda7b882b558b0dc791990dc +# input_hash: 5aff8f730a848ff23e728abf1ffe021e04a3661a9eea7aff3dd11e3decbee435 @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2023.11.17-hbcca054_0.conda#01ffc8d36f9eba0ce0b3c1955fa780ee @@ -675,7 +675,7 @@ https://conda.anaconda.org/conda-forge/noarch/jupyterlab-4.0.11-pyhd8ed1ab_0.con https://conda.anaconda.org/conda-forge/noarch/nbdime-4.0.1-pyhd8ed1ab_0.conda#dd76d44a144499f8ff3254fd20cdb7a2 https://conda.anaconda.org/conda-forge/linux-64/pyarrow-14.0.2-py311h39c9aba_2_cpu.conda#07fb7193fa96aab8e61c4483b9e61e51 https://conda.anaconda.org/conda-forge/noarch/sankee-0.2.4-pyhd8ed1ab_0.conda#5cddf4d134860b0e13d2709e0a8201ce -https://conda.anaconda.org/conda-forge/noarch/dask-labextension-7.0.0-pyhd8ed1ab_0.conda#bccfda61b2c35a3cec53bd3417e3d783 +https://conda.anaconda.org/conda-forge/noarch/dask-labextension-6.0.0-pyhd8ed1ab_0.tar.bz2#32a0ba2d4b9ed598d90463d0032aace3 https://conda.anaconda.org/conda-forge/noarch/geemap-0.30.4-pyhd8ed1ab_1.conda#c8aaa5c4cc5aa50606b03575fa6d6ce3 https://conda.anaconda.org/conda-forge/noarch/jupyterhub-singleuser-4.0.2-pyh31011fe_0.conda#9eb773051ad8ecc804ed3bdec84ecce5 https://conda.anaconda.org/conda-forge/noarch/jupyterlab-git-0.50.0-pyhd8ed1ab_0.conda#42b7b173793e526df16894baed8661a5 From 6a423577e2a1400d3ec8cdfabc5fe578e64502a7 Mon Sep 17 00:00:00 2001 From: Tasha Snow Date: Tue, 23 Jan 2024 23:46:11 -0700 Subject: [PATCH 17/57] Update environment.yml Co-authored-by: Wei Ji <23487320+weiji14@users.noreply.github.com> --- environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/environment.yml b/environment.yml index 4137e16..c4df3e0 100644 --- a/environment.yml +++ b/environment.yml @@ -9,7 +9,7 @@ dependencies: # Required until https://github.com/jupyterhub/repo2docker/pull/1196 is merged - jupyterhub-singleuser~=4.0.1 # nbgitpuller is very helpful when distributing user content - - nbgitpuller==1.2.0 + - 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 From 97fdfe04dc30e3aa6f3b69f180bf0eee4dd88b50 Mon Sep 17 00:00:00 2001 From: Tasha Snow Date: Tue, 23 Jan 2024 23:46:21 -0700 Subject: [PATCH 18/57] Update environment.yml Co-authored-by: Wei Ji <23487320+weiji14@users.noreply.github.com> --- environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/environment.yml b/environment.yml index c4df3e0..ba5f011 100644 --- a/environment.yml +++ b/environment.yml @@ -27,7 +27,7 @@ dependencies: - gh~=2.32.1 # VS Code support - - jupyter-vscode-proxy==0.5 + - jupyter-vscode-proxy~=0.5 - code-server~=4.16.1 # Jupyter tools From 68335cdc2c297c416d3ed421c653f3a470b8b013 Mon Sep 17 00:00:00 2001 From: Tasha Snow Date: Tue, 23 Jan 2024 23:46:28 -0700 Subject: [PATCH 19/57] Update environment.yml Co-authored-by: Wei Ji <23487320+weiji14@users.noreply.github.com> --- environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/environment.yml b/environment.yml index ba5f011..39f6548 100644 --- a/environment.yml +++ b/environment.yml @@ -36,7 +36,7 @@ dependencies: - ipykernel~=6.29.0 - ipywidgets~=8.1.1 - - jupyterlab-favorites~=3.2.0 + - jupyterlab-favorites~=3.2.1 - jupyterlab-geojson~=3.4.0 - jupyter-collaboration~=2.0.1 - jupyterlab-git~=0.50.0 From 533cd3abf44156b7ea05f4cdfcfd7d3a8805577a Mon Sep 17 00:00:00 2001 From: Tasha Snow Date: Tue, 23 Jan 2024 23:46:42 -0700 Subject: [PATCH 20/57] Update environment.yml Co-authored-by: Wei Ji <23487320+weiji14@users.noreply.github.com> --- environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/environment.yml b/environment.yml index 39f6548..cd8e9b2 100644 --- a/environment.yml +++ b/environment.yml @@ -40,7 +40,7 @@ dependencies: - jupyterlab-geojson~=3.4.0 - jupyter-collaboration~=2.0.1 - jupyterlab-git~=0.50.0 -# - jupyter-ai==2.9.1 # Requires pandas>=2.0.1 + - jupyter-ai~=2.9.1 - jupyterlab-myst~=2.1.0 - jupyterlab-h5web~=11.1.0 - jupyter-book~=0.15.1 From e83624f5259f8e43892b7facfb4651ea3b0a6c52 Mon Sep 17 00:00:00 2001 From: Tasha Snow Date: Tue, 23 Jan 2024 23:46:59 -0700 Subject: [PATCH 21/57] Update environment.yml Co-authored-by: Wei Ji <23487320+weiji14@users.noreply.github.com> --- environment.yml | 3 --- 1 file changed, 3 deletions(-) diff --git a/environment.yml b/environment.yml index cd8e9b2..2554323 100644 --- a/environment.yml +++ b/environment.yml @@ -32,9 +32,6 @@ dependencies: # Jupyter tools - ipython~=8.20.0 - - - ipykernel~=6.29.0 - - ipywidgets~=8.1.1 - jupyterlab-favorites~=3.2.1 - jupyterlab-geojson~=3.4.0 From dc68a7b8f064c98f22bc6c36fa3f2305acf5e828 Mon Sep 17 00:00:00 2001 From: Tasha Snow Date: Tue, 23 Jan 2024 23:47:11 -0700 Subject: [PATCH 22/57] Update environment.yml Co-authored-by: Wei Ji <23487320+weiji14@users.noreply.github.com> --- environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/environment.yml b/environment.yml index 2554323..d9f2c67 100644 --- a/environment.yml +++ b/environment.yml @@ -49,7 +49,7 @@ dependencies: - cython==0.29.32 # optimization, C API access - hypothesis==6.58.0 # needed by numpy testing tools - networkx==2.8.8 - - numba==0.58.1 # high-performance numerics + - numba~=0.58.1 # high-performance numerics - numpy==1.23.5 - pandas>=1.5.1 - scikit-image==0.19.3 From e11032e199210bb95c6637097bec62975f287881 Mon Sep 17 00:00:00 2001 From: Tasha Snow Date: Tue, 23 Jan 2024 23:47:35 -0700 Subject: [PATCH 23/57] Update environment.yml Co-authored-by: Wei Ji <23487320+weiji14@users.noreply.github.com> --- environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/environment.yml b/environment.yml index d9f2c67..5d429c3 100644 --- a/environment.yml +++ b/environment.yml @@ -65,7 +65,7 @@ dependencies: - geoviews~=1.10.1 - hvplot~=0.8.4 - ipyleaflet~=0.17.3 - - ipympl==0.9.2 # 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 From 582b468b004d045f6b192731c958ea84f753b2e0 Mon Sep 17 00:00:00 2001 From: Tasha Snow Date: Tue, 23 Jan 2024 23:47:44 -0700 Subject: [PATCH 24/57] Update environment.yml Co-authored-by: Wei Ji <23487320+weiji14@users.noreply.github.com> --- environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/environment.yml b/environment.yml index 5d429c3..b7b8298 100644 --- a/environment.yml +++ b/environment.yml @@ -138,7 +138,7 @@ dependencies: - git>=2.39 # Not all packages will be available from conda-forge, we install from pip when we need to. - - pip==23.3.2 + - pip~=23.3.2 - pip: # Access linux desktop from inside JupyterHub - jupyter-desktop-server==0.1.3 From 7f4c834d3a12bcf6e8ea29a3462cbe64747ef956 Mon Sep 17 00:00:00 2001 From: Tasha Snow Date: Tue, 23 Jan 2024 23:47:57 -0700 Subject: [PATCH 25/57] Update environment.yml Co-authored-by: Wei Ji <23487320+weiji14@users.noreply.github.com> --- environment.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/environment.yml b/environment.yml index b7b8298..47641f2 100644 --- a/environment.yml +++ b/environment.yml @@ -105,7 +105,6 @@ dependencies: - dask>=2023.12.1 - dask-labextension==6.0.0 - dask-geopandas~=0.3.1 - # Other useful generic python packages - pillow~=10.2.0 # Python imaging library, useful for many image-related tasks - pytest==7.2.0 From f8e296bc821220074bd1fbd0b056a26983a18e6c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E2=80=9Ctsnow03=E2=80=9D?= Date: Tue, 23 Jan 2024 23:58:09 -0700 Subject: [PATCH 26/57] update itslive in pip install in env --- environment.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/environment.yml b/environment.yml index 47641f2..c2ebc72 100644 --- a/environment.yml +++ b/environment.yml @@ -51,12 +51,12 @@ dependencies: - networkx==2.8.8 - 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>=1.2.2,<2.0.0 - scipy==1.9.3 - statsmodels==0.13.5 - - sympy~=1.11.0 + - sympy~=1.12 - xarray>=2023.05.0 # Visualization packages @@ -120,7 +120,6 @@ dependencies: # Packages specific to cryo work - h5coro~=0.0.6 - icepyx~=0.8.1 - - itslive~=0.3.0 - is2view~=0.0.5 - sliderule~=4.0.0 @@ -141,3 +140,4 @@ dependencies: - pip: # Access linux desktop from inside JupyterHub - jupyter-desktop-server==0.1.3 + - itslive~=0.3.2 # Move above once updates are in mamba From 9608dbc9f95c5567eb2e3603a771487cb608c90d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E2=80=9Ctsnow03=E2=80=9D?= Date: Wed, 24 Jan 2024 13:35:38 -0700 Subject: [PATCH 27/57] add offlinenotebook ext to env --- environment.yml | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/environment.yml b/environment.yml index c2ebc72..ffbbf7f 100644 --- a/environment.yml +++ b/environment.yml @@ -9,7 +9,7 @@ dependencies: # Required until https://github.com/jupyterhub/repo2docker/pull/1196 is merged - jupyterhub-singleuser~=4.0.1 # nbgitpuller is very helpful when distributing user content - - nbgitpuller~=1.2.0 + - nbgitpuller~=1.1.0 # Specify major version of jupyterlab to use. Manually bump it when you want to upgrade # jupyterlab version - jupyterlab>=4.0,<4.1 @@ -33,14 +33,15 @@ dependencies: # Jupyter tools - ipython~=8.20.0 - ipywidgets~=8.1.1 + - jupyter-ai~=2.9.1 + - jupyter-book~=0.15.1 + - jupyter-offlinenotebook~=0.2.2 + - jupyter-collaboration~=2.0.1 - jupyterlab-favorites~=3.2.1 - jupyterlab-geojson~=3.4.0 - - jupyter-collaboration~=2.0.1 - jupyterlab-git~=0.50.0 - - jupyter-ai~=2.9.1 - - jupyterlab-myst~=2.1.0 - jupyterlab-h5web~=11.1.0 - - jupyter-book~=0.15.1 + - jupyterlab-myst~=2.1.0 - jupytext~=1.16.1 - nbconvert==6.5.3 - nbdime~=4.0.1 @@ -103,7 +104,7 @@ 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~=10.2.0 # Python imaging library, useful for many image-related tasks From 2e45899731b55f589ecba9974b1ac93dd45a74a2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E2=80=9Ctsnow03=E2=80=9D?= Date: Wed, 24 Jan 2024 14:17:15 -0700 Subject: [PATCH 28/57] remove some extensions for testing env --- environment.yml | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) diff --git a/environment.yml b/environment.yml index ffbbf7f..9a35bee 100644 --- a/environment.yml +++ b/environment.yml @@ -9,7 +9,7 @@ dependencies: # Required until https://github.com/jupyterhub/repo2docker/pull/1196 is merged - jupyterhub-singleuser~=4.0.1 # nbgitpuller is very helpful when distributing user content - - nbgitpuller~=1.1.0 + - 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 @@ -31,19 +31,22 @@ dependencies: - code-server~=4.16.1 # Jupyter tools +# - bqplot~=0.12.1 - ipython~=8.20.0 - ipywidgets~=8.1.1 - jupyter-ai~=2.9.1 - jupyter-book~=0.15.1 - - jupyter-offlinenotebook~=0.2.2 - - jupyter-collaboration~=2.0.1 - - jupyterlab-favorites~=3.2.1 +# - jupyter-offlinenotebook~=0.2.2 +# - jupyter-collaboration~=2.0.1 +# - jupyterlab-favorites~=3.2.1 - jupyterlab-geojson~=3.4.0 - jupyterlab-git~=0.50.0 - - jupyterlab-h5web~=11.1.0 +# - jupyterlab-h5web~=11.1.0 - jupyterlab-myst~=2.1.0 +# - jupyterlab-plotly~=5.18.0 +# - jupyterlab-pygments~=0.3.0 - jupytext~=1.16.1 - - nbconvert==6.5.3 + - nbconvert==6.5.3 #7.14.2 - nbdime~=4.0.1 # Core scientific python stack From d4ea6e17bdc7eb12c1a12e1f1af61d476c8764e5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E2=80=9Ctsnow03=E2=80=9D?= Date: Wed, 24 Jan 2024 14:56:43 -0700 Subject: [PATCH 29/57] add back h5web for testing env --- environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/environment.yml b/environment.yml index 9a35bee..3df9a75 100644 --- a/environment.yml +++ b/environment.yml @@ -41,7 +41,7 @@ dependencies: # - jupyterlab-favorites~=3.2.1 - jupyterlab-geojson~=3.4.0 - jupyterlab-git~=0.50.0 -# - jupyterlab-h5web~=11.1.0 + - jupyterlab-h5web~=11.1.0 - jupyterlab-myst~=2.1.0 # - jupyterlab-plotly~=5.18.0 # - jupyterlab-pygments~=0.3.0 From c20cbcb970542e191e1cb94bc6c6c9cd514e237f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E2=80=9Ctsnow03=E2=80=9D?= Date: Wed, 24 Jan 2024 16:43:42 -0700 Subject: [PATCH 30/57] add back favs for testing env --- environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/environment.yml b/environment.yml index 3df9a75..5b0a23c 100644 --- a/environment.yml +++ b/environment.yml @@ -38,7 +38,7 @@ dependencies: - jupyter-book~=0.15.1 # - jupyter-offlinenotebook~=0.2.2 # - jupyter-collaboration~=2.0.1 -# - jupyterlab-favorites~=3.2.1 + - jupyterlab-favorites~=3.2.1 - jupyterlab-geojson~=3.4.0 - jupyterlab-git~=0.50.0 - jupyterlab-h5web~=11.1.0 From 3de9ca1556a036ad56f450b0b90971fc658b8deb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E2=80=9Ctsnow03=E2=80=9D?= Date: Wed, 24 Jan 2024 22:03:44 -0700 Subject: [PATCH 31/57] add back collaboration for testing env --- environment.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/environment.yml b/environment.yml index 5b0a23c..1fbffb6 100644 --- a/environment.yml +++ b/environment.yml @@ -37,8 +37,8 @@ dependencies: - jupyter-ai~=2.9.1 - jupyter-book~=0.15.1 # - jupyter-offlinenotebook~=0.2.2 -# - jupyter-collaboration~=2.0.1 - - jupyterlab-favorites~=3.2.1 + - jupyter-collaboration~=2.0.1 +# - jupyterlab-favorites~=3.2.1 - jupyterlab-geojson~=3.4.0 - jupyterlab-git~=0.50.0 - jupyterlab-h5web~=11.1.0 From cfd17a53b7f794a85fbb736a6381233aed5bcf54 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E2=80=9Ctsnow03=E2=80=9D?= Date: Thu, 25 Jan 2024 08:35:34 -0700 Subject: [PATCH 32/57] adding back all jupyter extensions except collaboration --- environment.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/environment.yml b/environment.yml index 1fbffb6..15c4331 100644 --- a/environment.yml +++ b/environment.yml @@ -31,20 +31,20 @@ dependencies: - code-server~=4.16.1 # Jupyter tools -# - bqplot~=0.12.1 + - bqplot~=0.12.1 - ipython~=8.20.0 - ipywidgets~=8.1.1 - jupyter-ai~=2.9.1 - jupyter-book~=0.15.1 # - jupyter-offlinenotebook~=0.2.2 - - jupyter-collaboration~=2.0.1 -# - jupyterlab-favorites~=3.2.1 +# - jupyter-collaboration~=2.0.1 + - 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 # - jupyterlab-plotly~=5.18.0 -# - jupyterlab-pygments~=0.3.0 + - jupyterlab_pygments~=0.3.0 - jupytext~=1.16.1 - nbconvert==6.5.3 #7.14.2 - nbdime~=4.0.1 From 8c4666cd6b9a26f5a35d545cbf08f2baebea0c13 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E2=80=9Ctsnow03=E2=80=9D?= Date: Thu, 25 Jan 2024 10:16:16 -0700 Subject: [PATCH 33/57] added some documentation to env --- environment.yml | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/environment.yml b/environment.yml index 15c4331..df614f3 100644 --- a/environment.yml +++ b/environment.yml @@ -31,20 +31,20 @@ dependencies: - code-server~=4.16.1 # Jupyter tools - - bqplot~=0.12.1 + - bqplot~=0.12.41 # Not helpful at the moment - ipython~=8.20.0 - ipywidgets~=8.1.1 - jupyter-ai~=2.9.1 - jupyter-book~=0.15.1 -# - jupyter-offlinenotebook~=0.2.2 -# - jupyter-collaboration~=2.0.1 +# - jupyter-offlinenotebook~=0.2.2 # Outdated accoring 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 -# - jupyterlab-plotly~=5.18.0 - - jupyterlab_pygments~=0.3.0 +# - 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 #7.14.2 - nbdime~=4.0.1 @@ -109,6 +109,7 @@ dependencies: - dask>=2023.12.1 - dask-labextension~=7.0.0 - dask-geopandas~=0.3.1 + # Other useful generic python packages - pillow~=10.2.0 # Python imaging library, useful for many image-related tasks - pytest==7.2.0 From 287810a3d927f311f6acabb8cdf294487edb8488 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E2=80=9Ctsnow03=E2=80=9D?= Date: Thu, 25 Jan 2024 15:00:49 -0700 Subject: [PATCH 34/57] moved itslive out of pip install --- environment.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/environment.yml b/environment.yml index df614f3..b254c16 100644 --- a/environment.yml +++ b/environment.yml @@ -31,12 +31,11 @@ dependencies: - code-server~=4.16.1 # Jupyter tools - - bqplot~=0.12.41 # Not helpful at the moment - ipython~=8.20.0 - ipywidgets~=8.1.1 - jupyter-ai~=2.9.1 - jupyter-book~=0.15.1 -# - jupyter-offlinenotebook~=0.2.2 # Outdated accoring to jupyterlab +# - 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 @@ -46,7 +45,7 @@ dependencies: # - 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 #7.14.2 + - nbconvert==6.5.3 - nbdime~=4.0.1 # Core scientific python stack @@ -125,6 +124,7 @@ dependencies: # Packages specific to cryo work - h5coro~=0.0.6 - icepyx~=0.8.1 + - itslive~=0.3.2 - is2view~=0.0.5 - sliderule~=4.0.0 @@ -145,4 +145,4 @@ dependencies: - pip: # Access linux desktop from inside JupyterHub - jupyter-desktop-server==0.1.3 - - itslive~=0.3.2 # Move above once updates are in mamba +# - itslive~=0.3.2 # Move above once updates are in mamba From e83bbf1d33aa72ab76a4cc6a2e6b0c0349492a53 Mon Sep 17 00:00:00 2001 From: actions-bot <58130806+actions-bot@users.noreply.github.com> Date: Thu, 25 Jan 2024 22:02:54 +0000 Subject: [PATCH 35/57] [condalock-command] autogenerated conda-lock files --- conda-linux-64.lock | 104 +++++++++++++++++++++++++++----------------- 1 file changed, 65 insertions(+), 39 deletions(-) diff --git a/conda-linux-64.lock b/conda-linux-64.lock index e16ba00..48a12f6 100644 --- a/conda-linux-64.lock +++ b/conda-linux-64.lock @@ -1,6 +1,6 @@ # Generated by conda-lock. # platform: linux-64 -# input_hash: 5aff8f730a848ff23e728abf1ffe021e04a3661a9eea7aff3dd11e3decbee435 +# input_hash: 27b38d1e9ce01d74be4f17e1944107afed232cfd2ad85d719fd512c40a9ceabd @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2023.11.17-hbcca054_0.conda#01ffc8d36f9eba0ce0b3c1955fa780ee @@ -26,7 +26,7 @@ https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_3.cond 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https://conda.anaconda.org/conda-forge/linux-64/dbus-1.13.6-h5008d03_3.tar.bz2#ecfff944ba3960ecb334b9a2663d708d https://conda.anaconda.org/conda-forge/linux-64/debugpy-1.8.0-py311hb755f60_1.conda#2c241533b8eafe8028442d46ef41eb13 https://conda.anaconda.org/conda-forge/noarch/decorator-5.1.1-pyhd8ed1ab_0.tar.bz2#43afe5ab04e35e17ba28649471dd7364 +https://conda.anaconda.org/conda-forge/noarch/deepmerge-1.1.1-pyhd8ed1ab_0.conda#d91c3d8ac3f2ab36ca4ea32ac42f731e https://conda.anaconda.org/conda-forge/noarch/defusedxml-0.7.1-pyhd8ed1ab_0.tar.bz2#961b3a227b437d82ad7054484cfa71b2 https://conda.anaconda.org/conda-forge/linux-64/docutils-0.15.2-py311h38be061_6.tar.bz2#0571e4aa0f435cee39033065d28501f2 https://conda.anaconda.org/conda-forge/noarch/entrypoints-0.4-pyhd8ed1ab_0.tar.bz2#3cf04868fee0a029769bd41f4b2fbf2d +https://conda.anaconda.org/conda-forge/noarch/et_xmlfile-1.1.0-pyhd8ed1ab_0.conda#a2f2138597905eaa72e561d8efb42cf3 https://conda.anaconda.org/conda-forge/noarch/exceptiongroup-1.2.0-pyhd8ed1ab_2.conda#8d652ea2ee8eaee02ed8dc820bc794aa https://conda.anaconda.org/conda-forge/noarch/executing-2.0.1-pyhd8ed1ab_0.conda#e16be50e378d8a4533b989035b196ab8 https://conda.anaconda.org/conda-forge/noarch/fasteners-0.17.3-pyhd8ed1ab_0.tar.bz2#348e27e78a5e39090031448c72f66d5e @@ -264,7 +266,7 @@ https://conda.anaconda.org/conda-forge/linux-64/libwebp-1.3.2-h658648e_1.conda#0 https://conda.anaconda.org/conda-forge/linux-64/llvmlite-0.41.1-py311ha6695c7_0.conda#60fa8c1f3fb0d99dd10a9af2aff9c400 https://conda.anaconda.org/conda-forge/noarch/locket-1.0.0-pyhd8ed1ab_0.tar.bz2#91e27ef3d05cc772ce627e51cff111c4 https://conda.anaconda.org/conda-forge/linux-64/logzero-1.7.0-py311h38be061_5.conda#7b807bdb2a7e4aa9ccbc1870cb292cf6 -https://conda.anaconda.org/conda-forge/linux-64/lxml-5.1.0-py311h9691dec_0.conda#cee803b62c62e5f3326be31e57161ff5 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https://conda.anaconda.org/conda-forge/noarch/jupyter-server-mathjax-0.2.6-pyh5bfe37b_1.conda#11ca195fc8a16770661a387bcce27c36 https://conda.anaconda.org/conda-forge/noarch/jupyter-server-proxy-4.1.0-pyhd8ed1ab_0.conda#b404b1dc6ca2bbb66663507150cb6927 -https://conda.anaconda.org/conda-forge/noarch/jupyter_server_fileid-0.9.1-pyhd8ed1ab_0.conda#6ce5585ef1f70cfa16352b9c03ddbfc5 https://conda.anaconda.org/conda-forge/noarch/jupyterlab-h5web-11.1.0-pyhd8ed1ab_0.conda#7a24c2d8f78dcb2edf72ac3405637308 https://conda.anaconda.org/conda-forge/noarch/jupyterlab_server-2.25.2-pyhd8ed1ab_0.conda#f45557d5551b54dc2a74133a310bc1ba https://conda.anaconda.org/conda-forge/linux-64/libarrow-substrait-14.0.2-h61ff412_2_cpu.conda#838d3d33c458225578f64e59c4410a9f @@ -668,15 +694,15 @@ https://conda.anaconda.org/conda-forge/noarch/ee_extra-0.0.15-pyhd8ed1ab_0.conda https://conda.anaconda.org/conda-forge/noarch/eerepr-0.0.4-pyhd8ed1ab_0.conda#79fa01f350230710f970400598b905b7 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https://conda.anaconda.org/conda-forge/noarch/dask-2024.1.0-pyhd8ed1ab_0.conda#9 https://conda.anaconda.org/conda-forge/noarch/nbgitpuller-1.2.0-pyhd8ed1ab_0.conda#e74db5ccfcf794e3d67ec7c9c125a39a https://conda.anaconda.org/conda-forge/noarch/intake-0.6.6-pyhd8ed1ab_0.tar.bz2#1dc29fb9182b0f3ce935a8bd4c341ed5 https://conda.anaconda.org/conda-forge/noarch/is2view-0.0.5-pyhd8ed1ab_0.conda#a47538fd9bb7cf7d6c35716cccae1ddc -https://conda.anaconda.org/conda-forge/noarch/intake-esm-2023.10.27-pyhd8ed1ab_0.conda#33c61707d49697391beaa86b4eaf109e +https://conda.anaconda.org/conda-forge/noarch/intake-esm-2023.11.10-pyhd8ed1ab_0.conda#e0c73b7dc6419a243c5fe104ec241a48 https://conda.anaconda.org/conda-forge/noarch/intake-xarray-0.6.1-pyhd8ed1ab_0.tar.bz2#6cc318952c249b55ae83f8a994342672 https://conda.anaconda.org/conda-forge/noarch/intake-stac-0.4.0-pyhd8ed1ab_0.tar.bz2#d9a48c97623dc88751dbd266b89497e3 https://conda.anaconda.org/conda-forge/noarch/myst-parser-0.18.1-pyhd8ed1ab_0.tar.bz2#bcfdf5c7d8bf5c6f6be7b4c66fff2eca From 0e40ef3c2bbce5f8ce0f79bb8328b8fb8b6fafd5 Mon Sep 17 00:00:00 2001 From: Tasha Snow Date: Thu, 25 Jan 2024 17:13:13 -0700 Subject: [PATCH 36/57] Remove whitespace in env Co-authored-by: Wei Ji <23487320+weiji14@users.noreply.github.com> --- environment.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/environment.yml b/environment.yml index b254c16..7e4d0ce 100644 --- a/environment.yml +++ b/environment.yml @@ -108,7 +108,6 @@ dependencies: - dask>=2023.12.1 - dask-labextension~=7.0.0 - dask-geopandas~=0.3.1 - # Other useful generic python packages - pillow~=10.2.0 # Python imaging library, useful for many image-related tasks - pytest==7.2.0 From d7cf3c95c7438e763678c08fc998f117631c8c1d Mon Sep 17 00:00:00 2001 From: Tasha Snow Date: Thu, 25 Jan 2024 17:13:38 -0700 Subject: [PATCH 37/57] Remove itslive comment Co-authored-by: Wei Ji <23487320+weiji14@users.noreply.github.com> --- environment.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/environment.yml b/environment.yml index 7e4d0ce..3d1ca6a 100644 --- a/environment.yml +++ b/environment.yml @@ -144,4 +144,3 @@ dependencies: - pip: # Access linux desktop from inside JupyterHub - jupyter-desktop-server==0.1.3 -# - itslive~=0.3.2 # Move above once updates are in mamba From eacd4eb513cc026e238255d9c16d49dd5249d349 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E2=80=9Ctsnow03=E2=80=9D?= Date: Thu, 25 Jan 2024 18:50:51 -0700 Subject: [PATCH 38/57] fix conflicts --- environment.yml | 69 ++++++++++++++++++++++++++----------------------- 1 file changed, 37 insertions(+), 32 deletions(-) diff --git a/environment.yml b/environment.yml index 3d1ca6a..c7bad14 100644 --- a/environment.yml +++ b/environment.yml @@ -7,14 +7,14 @@ channels: dependencies: - python~=3.11.0 # Required until https://github.com/jupyterhub/repo2docker/pull/1196 is merged - - jupyterhub-singleuser~=4.0.1 + - jupyterhub-singleuser>=4.0 # nbgitpuller is very helpful when distributing user content - - nbgitpuller~=1.2.0 + - 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 + - jupyterlab>=4.0 # This provides memory usage stats on JupyterLab and classic notebook - - jupyter-resource-usage~=1.0.1 + - jupyter-resource-usage~=1.0.0 # 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 @@ -27,39 +27,43 @@ dependencies: - gh~=2.32.1 # VS Code support - - jupyter-vscode-proxy~=0.5 - - code-server~=4.16.1 + - jupyter-vscode-proxy==0.5 +# - jupyter-vscode-server==0.0.10 +# - code-server==4.20.0 # Jupyter tools - - ipython~=8.20.0 - - ipywidgets~=8.1.1 - - 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 + - ipython~=8.17.0 + + # Warning: There's a bug in ipykernel 6.18 that crashes hvplot. + # See https://github.com/ipython/ipykernel/pull/1037. Restriction + # can be relaxed once that's fixed. + - ipykernel=6.16.0 + + - ipywidgets~=8.0.0 + - jupyterlab-favorites==3.2.0 + - jupyterlab-geojson==3.4.0 + - jupyter-collaboration~=2.0.1 + - jupyterlab-git==0.50.0 +# - jupyter-ai==2.9.1 # Requires pandas>=2.0.1 + - jupyterlab-myst==2.1.0 - jupyterlab-h5web~=11.1.0 - - jupyterlab-myst~=2.1.0 -# - jupyterlab-plotly~=5.18.0 # Outdated accoring to jupyterlab - - jupyterlab_pygments~=0.3.0 # To bring extension uptodate + - jupyter-book~=0.15.1 - jupytext~=1.16.1 - nbconvert==6.5.3 - - nbdime~=4.0.1 + - nbdime==4.0.1 # Core scientific python stack - cython==0.29.32 # optimization, C API access - hypothesis==6.58.0 # needed by numpy testing tools - networkx==2.8.8 - - numba~=0.58.1 # high-performance numerics - - numpy==1.23.5 - - pandas>=2.0.1,<3.0 - - scikit-image==0.19.3 - - scikit-learn>=1.2.2,<2.0.0 + - numba==0.58.1 # high-performance numerics + - numpy~=1.26.0 + - pandas==1.5.1 + - scikit-image==0.22.0 + - scikit-learn==1.4.0 - scipy==1.9.3 - statsmodels==0.13.5 - - sympy~=1.12 + - sympy~=1.12.0 - xarray>=2023.05.0 # Visualization packages @@ -70,7 +74,7 @@ dependencies: - ipyleaflet~=0.17.3 - ipympl~=0.9.3 # This enables matplotlib interaction with jupyter widgets - matplotlib~=3.8.0 - - plotly~=5.18.0 + - plotly==5.18.0 - seaborn==0.12.1 # statistical plotting with matplotlib - geemap~=0.30.0 @@ -104,10 +108,11 @@ dependencies: - intake-xarray==0.6.1 - gcsfs>=2023.5.0 - # Distributed computing - - dask>=2023.12.1 - - dask-labextension~=7.0.0 + # Distributed computing * + - dask==2024.1.0 + - dask-labextension==7.0.0 - dask-geopandas~=0.3.1 + # Other useful generic python packages - pillow~=10.2.0 # Python imaging library, useful for many image-related tasks - pytest==7.2.0 @@ -120,7 +125,7 @@ dependencies: - esmpy~=8.4.2 - xmip~=0.7.1 - # Packages specific to cryo work + # Packages specific to cryo work * - h5coro~=0.0.6 - icepyx~=0.8.1 - itslive~=0.3.2 @@ -132,7 +137,7 @@ dependencies: # 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 - - ocl-icd-system + # - ocl-icd-system # needed for Linux desktop to work - websockify>=0.10 # Includes new subcommands (`switch` & `restore`) and vulnerability fixes @@ -140,7 +145,7 @@ dependencies: - git>=2.39 # Not all packages will be available from conda-forge, we install from pip when we need to. - - pip~=23.3.2 + - pip==23.3.2 - pip: # Access linux desktop from inside JupyterHub - jupyter-desktop-server==0.1.3 From 36cf52c72c9070dea3eed5550faeb05ec348b32b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E2=80=9Ctsnow03=E2=80=9D?= Date: Thu, 25 Jan 2024 18:52:15 -0700 Subject: [PATCH 39/57] fix conflicts --- conda-linux-64.lock | 152 ++++++++++++++++++-------------------------- 1 file changed, 63 insertions(+), 89 deletions(-) diff --git a/conda-linux-64.lock b/conda-linux-64.lock index 48a12f6..3d1f925 100644 --- a/conda-linux-64.lock +++ b/conda-linux-64.lock @@ -1,6 +1,6 @@ # Generated by conda-lock. # platform: linux-64 -# input_hash: 27b38d1e9ce01d74be4f17e1944107afed232cfd2ad85d719fd512c40a9ceabd +# input_hash: b4ca4a9b51f7d1335bc925c6943786fde36051f5f5ed5a157efc1495f559775c @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2023.11.17-hbcca054_0.conda#01ffc8d36f9eba0ce0b3c1955fa780ee @@ -26,7 +26,7 @@ https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_3.cond https://conda.anaconda.org/conda-forge/linux-64/alsa-lib-1.2.10-hd590300_0.conda#75dae9a4201732aa78a530b826ee5fe0 https://conda.anaconda.org/conda-forge/linux-64/aom-3.7.1-h59595ed_0.conda#504e70332b8322cda93b7bceb5925fca https://conda.anaconda.org/conda-forge/linux-64/attr-2.5.1-h166bdaf_1.tar.bz2#d9c69a24ad678ffce24c6543a0176b00 -https://conda.anaconda.org/conda-forge/linux-64/aws-c-common-0.9.12-hd590300_0.conda#7dbb94ffb9df66406f3101625807cac1 +https://conda.anaconda.org/conda-forge/linux-64/aws-c-common-0.9.10-hd590300_0.conda#93729f7a54b25cb135ac2b67ea3a7603 https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4 https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.25.0-hd590300_0.conda#89e40af02dd3a0846c0c1131c5126706 https://conda.anaconda.org/conda-forge/linux-64/charls-2.4.2-h59595ed_0.conda#4336bd67920dd504cd8c6761d6a99645 @@ -71,7 +71,6 @@ https://conda.anaconda.org/conda-forge/linux-64/libtasn1-4.19.0-h166bdaf_0.tar.b https://conda.anaconda.org/conda-forge/linux-64/libunistring-0.9.10-h7f98852_0.tar.bz2#7245a044b4a1980ed83196176b78b73a https://conda.anaconda.org/conda-forge/linux-64/libutf8proc-2.8.0-h166bdaf_0.tar.bz2#ede4266dc02e875fe1ea77b25dd43747 https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b -https://conda.anaconda.org/conda-forge/linux-64/libuv-1.46.0-hd590300_0.conda#d23c76f7e6dcd6243d1b6ef5e62d17d2 https://conda.anaconda.org/conda-forge/linux-64/libvpx-1.13.1-h59595ed_0.conda#0974a6d3432e10bae02bcab0cce1b308 https://conda.anaconda.org/conda-forge/linux-64/libwebp-base-1.3.2-hd590300_0.conda#30de3fd9b3b602f7473f30e684eeea8c https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc @@ -111,10 +110,10 @@ https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161 https://conda.anaconda.org/conda-forge/linux-64/yaml-0.2.5-h7f98852_2.tar.bz2#4cb3ad778ec2d5a7acbdf254eb1c42ae https://conda.anaconda.org/conda-forge/linux-64/zfp-1.0.1-h59595ed_0.conda#fd486bffbf0d6841cf1456a8f2e3a995 https://conda.anaconda.org/conda-forge/linux-64/zlib-ng-2.0.7-h0b41bf4_0.conda#49e8329110001f04923fe7e864990b0c -https://conda.anaconda.org/conda-forge/linux-64/aws-c-cal-0.6.9-h14ec70c_3.conda#7da4b84275e63f56d158d6250727a70f -https://conda.anaconda.org/conda-forge/linux-64/aws-c-compression-0.2.17-h572eabf_8.conda#cc6630010cb1211cc15fb348f7c7eb70 -https://conda.anaconda.org/conda-forge/linux-64/aws-c-sdkutils-0.1.13-h572eabf_1.conda#7c56e8a2c4e8729443217e62e0bf65ba -https://conda.anaconda.org/conda-forge/linux-64/aws-checksums-0.1.17-h572eabf_7.conda#f7323eedc2685a24661cd6b57d7ed321 +https://conda.anaconda.org/conda-forge/linux-64/aws-c-cal-0.6.9-h5d48c4d_2.conda#9e51dfd5da37c1817d2a850188861987 +https://conda.anaconda.org/conda-forge/linux-64/aws-c-compression-0.2.17-h7f92143_7.conda#c55a1a0c1419fcdfce6d21c41b0f92ab +https://conda.anaconda.org/conda-forge/linux-64/aws-c-sdkutils-0.1.13-h7f92143_0.conda#a4a83424ad4eab023c6e5b4adf264006 +https://conda.anaconda.org/conda-forge/linux-64/aws-checksums-0.1.17-h7f92143_6.conda#46bd4e9c2fd10de83bae22f0bb71139b https://conda.anaconda.org/conda-forge/linux-64/expat-2.5.0-hcb278e6_1.conda#8b9b5aca60558d02ddaa09d599e55920 https://conda.anaconda.org/conda-forge/linux-64/glog-0.6.0-h6f12383_0.tar.bz2#b31f3565cb84435407594e548a2fb7b2 https://conda.anaconda.org/conda-forge/linux-64/hdf4-4.2.15-h2a13503_7.conda#bd77f8da987968ec3927990495dc22e4 @@ -159,10 +158,10 @@ https://conda.anaconda.org/conda-forge/linux-64/xorg-libsm-1.2.4-h7391055_0.cond https://conda.anaconda.org/conda-forge/linux-64/zeromq-4.3.5-h59595ed_0.conda#8851084c192dbc56215ac4e3c9aa30fa https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.13-hd590300_5.conda#68c34ec6149623be41a1933ab996a209 https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.5-hfc55251_0.conda#04b88013080254850d6c01ed54810589 -https://conda.anaconda.org/conda-forge/linux-64/aws-c-io-0.14.0-hf8f278a_1.conda#30ebacf5b5fd61294851301887dc7518 +https://conda.anaconda.org/conda-forge/linux-64/aws-c-io-0.13.36-hb3b01f7_3.conda#e699c37931ecbb452a6d074c1c738b07 https://conda.anaconda.org/conda-forge/linux-64/blosc-1.21.5-h0f2a231_0.conda#009521b7ed97cca25f8f997f9e745976 https://conda.anaconda.org/conda-forge/linux-64/brotli-bin-1.1.0-hd590300_1.conda#39f910d205726805a958da408ca194ba -https://conda.anaconda.org/conda-forge/linux-64/c-blosc2-2.13.1-hb4ffafa_0.conda#44c240217db28e1b3e1428625b4b4bbd +https://conda.anaconda.org/conda-forge/linux-64/c-blosc2-2.12.0-hb4ffafa_0.conda#1a9b16afb84d734a1bb2d196c308d477 https://conda.anaconda.org/conda-forge/linux-64/exiv2-0.27.6-hb9a316c_1.conda#1ab9f607cdc93a3ab793f4e87df115d2 https://conda.anaconda.org/conda-forge/linux-64/fftw-3.3.10-nompi_hc118613_108.conda#6fa90698000b05dfe8ce6515794fe71a https://conda.anaconda.org/conda-forge/linux-64/freetype-2.12.1-h267a509_2.conda#9ae35c3d96db2c94ce0cef86efdfa2cb @@ -173,7 +172,7 @@ https://conda.anaconda.org/conda-forge/linux-64/libgcrypt-1.10.3-hd590300_0.cond https://conda.anaconda.org/conda-forge/linux-64/libglib-2.78.3-h783c2da_0.conda#9bd06b12bbfa6fd1740fd23af4b0f0c7 https://conda.anaconda.org/conda-forge/linux-64/libhwloc-2.9.3-default_h554bfaf_1009.conda#f36ddc11ca46958197a45effdd286e45 https://conda.anaconda.org/conda-forge/linux-64/libllvm15-15.0.7-hb3ce162_4.conda#8a35df3cbc0c8b12cc8af9473ae75eef -https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.26-pthreads_h413a1c8_0.conda#760ae35415f5ba8b15d09df5afe8b23a +https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.25-pthreads_h413a1c8_0.conda#d172b34a443b95f86089e8229ddc9a17 https://conda.anaconda.org/conda-forge/linux-64/libsndfile-1.2.2-hc60ed4a_1.conda#ef1910918dd895516a769ed36b5b3a4e https://conda.anaconda.org/conda-forge/linux-64/libthrift-0.19.0-hb90f79a_1.conda#8cdb7d41faa0260875ba92414c487e2d https://conda.anaconda.org/conda-forge/linux-64/libtiff-4.6.0-ha9c0a0a_2.conda#55ed21669b2015f77c180feb1dd41930 @@ -181,13 +180,12 @@ https://conda.anaconda.org/conda-forge/linux-64/libxslt-1.1.39-h76b75d6_0.conda# https://conda.anaconda.org/conda-forge/linux-64/minizip-4.0.4-h0ab5242_0.conda#813bc75d9c33ddd9c9d5b8d9c560e152 https://conda.anaconda.org/conda-forge/linux-64/mpc-1.3.1-hfe3b2da_0.conda#289c71e83dc0daa7d4c81f04180778ca https://conda.anaconda.org/conda-forge/linux-64/mysql-libs-8.0.33-hca2cd23_6.conda#e87530d1b12dd7f4e0f856dc07358d60 -https://conda.anaconda.org/conda-forge/linux-64/nodejs-16.20.2-h1990674_2.conda#d2d03f9273e6a735dce8e957767d2dca -https://conda.anaconda.org/conda-forge/linux-64/nss-3.97-h1d7d5a4_0.conda#b916d71a3032416e3f9136090d814472 +https://conda.anaconda.org/conda-forge/linux-64/nss-3.96-h1d7d5a4_0.conda#1c8f8b8eb041ecd54053fc4b6ad57957 https://conda.anaconda.org/conda-forge/linux-64/orc-1.9.2-h4b38347_0.conda#6e6f990b097d3e237e18a8e321d08484 https://conda.anaconda.org/conda-forge/linux-64/python-3.11.7-hab00c5b_1_cpython.conda#27cf681282c11dba7b0b1fd266e8f289 https://conda.anaconda.org/conda-forge/linux-64/re2-2023.06.02-h2873b5e_0.conda#bb2d5e593ef13fe4aff0bc9440f945ae https://conda.anaconda.org/conda-forge/linux-64/sqlite-3.44.2-h2c6b66d_0.conda#4f2892c672829693fd978d065db4e8be -https://conda.anaconda.org/conda-forge/linux-64/ucx-1.15.0-h75e419f_3.conda#5baf4efbca923cdf73490c62cc7de1e2 +https://conda.anaconda.org/conda-forge/linux-64/ucx-1.15.0-h75e419f_2.conda#5798de4587dc70fa6db81663e79f176a https://conda.anaconda.org/conda-forge/linux-64/xcb-util-0.4.0-hd590300_1.conda#9bfac7ccd94d54fd21a0501296d60424 https://conda.anaconda.org/conda-forge/linux-64/xcb-util-keysyms-0.4.0-h8ee46fc_1.conda#632413adcd8bc16b515cab87a2932913 https://conda.anaconda.org/conda-forge/linux-64/xcb-util-renderutil-0.3.9-hd590300_1.conda#e995b155d938b6779da6ace6c6b13816 @@ -199,8 +197,8 @@ https://conda.anaconda.org/conda-forge/noarch/appdirs-1.4.4-pyh9f0ad1d_0.tar.bz2 https://conda.anaconda.org/conda-forge/noarch/asciitree-0.3.3-py_2.tar.bz2#c0481c9de49f040272556e2cedf42816 https://conda.anaconda.org/conda-forge/noarch/async_generator-1.10-py_0.tar.bz2#d56c596e61b1c4952acf0a9920856c12 https://conda.anaconda.org/conda-forge/noarch/attrs-23.2.0-pyh71513ae_0.conda#5e4c0743c70186509d1412e03c2d8dfa -https://conda.anaconda.org/conda-forge/linux-64/aws-c-event-stream-0.4.1-h97bb272_2.conda#5a16088be732d54b50c134203f712d24 -https://conda.anaconda.org/conda-forge/linux-64/aws-c-http-0.8.0-h9129f04_2.conda#ec632590307b47ac47d22ebcf91f4043 +https://conda.anaconda.org/conda-forge/linux-64/aws-c-event-stream-0.4.1-h0bcb0bb_1.conda#a0ea3a72521dc6aa29299df56f9ce530 +https://conda.anaconda.org/conda-forge/linux-64/aws-c-http-0.8.0-hd268abd_1.conda#1300bac362cf5f8b6d0abd777b70d5a8 https://conda.anaconda.org/conda-forge/noarch/backoff-2.2.1-pyhd8ed1ab_0.tar.bz2#4600709bd85664d8606ae0c76642f8db https://conda.anaconda.org/conda-forge/linux-64/backports.zoneinfo-0.2.1-py311h38be061_8.conda#5384590f14dfe6ccd02811236afc9f8e https://conda.anaconda.org/conda-forge/noarch/blinker-1.7.0-pyhd8ed1ab_0.conda#550da20b2c2e38be9cc44bb819fda5d5 @@ -213,7 +211,6 @@ https://conda.anaconda.org/conda-forge/noarch/certifi-2023.11.17-pyhd8ed1ab_0.co https://conda.anaconda.org/conda-forge/noarch/charset-normalizer-3.3.2-pyhd8ed1ab_0.conda#7f4a9e3fcff3f6356ae99244a014da6a https://conda.anaconda.org/conda-forge/noarch/click-8.1.7-unix_pyh707e725_0.conda#f3ad426304898027fc619827ff428eca https://conda.anaconda.org/conda-forge/noarch/cloudpickle-3.0.0-pyhd8ed1ab_0.conda#753d29fe41bb881e4b9c004f0abf973f -https://conda.anaconda.org/conda-forge/linux-64/code-server-4.16.1-h424e19c_0.conda#c276b7d42d2b90a490b6a89d1c77d0dc 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https://conda.anaconda.org/conda-forge/linux-64/qgis-3.34.3-py311ha16602e_0.conda#51cae087c4e6cdb5c905075b42a2dbcf https://conda.anaconda.org/conda-forge/noarch/rioxarray-0.14.1-pyhd8ed1ab_0.conda#5156f4c96119e2832419a9b17cb82cab +https://conda.anaconda.org/conda-forge/noarch/whiteboxgui-2.3.0-pyhd8ed1ab_0.conda#96916399e481bbf4cc727ab14d539359 https://conda.anaconda.org/conda-forge/noarch/earthengine-api-0.1.386-pyhd8ed1ab_0.conda#eb3e671f004390c6168a2aa9ed9148e0 https://conda.anaconda.org/conda-forge/noarch/gcsfs-2023.6.0-pyhd8ed1ab_0.conda#6369d600f32e61f19bcee2ae4ad19694 https://conda.anaconda.org/conda-forge/noarch/geopandas-0.13.2-pyhd8ed1ab_1.conda#47226a55e4ae3bc9feb3a17925874817 https://conda.anaconda.org/conda-forge/noarch/geoviews-1.10.1-pyhd8ed1ab_0.conda#08f49562f35d932cb35047016c46bde3 -https://conda.anaconda.org/conda-forge/noarch/jupyter-ai-magics-2.9.1-pyhd8ed1ab_0.conda#e0b8784a64c2ef4fcf1c51976ec857e9 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-694,6 +666,7 @@ https://conda.anaconda.org/conda-forge/noarch/ee_extra-0.0.15-pyhd8ed1ab_0.conda https://conda.anaconda.org/conda-forge/noarch/eerepr-0.0.4-pyhd8ed1ab_0.conda#79fa01f350230710f970400598b905b7 https://conda.anaconda.org/conda-forge/noarch/geeadd-0.5.6-pyhd8ed1ab_0.tar.bz2#a5cf57778f34bb5e81779393176bb5c5 https://conda.anaconda.org/conda-forge/noarch/icepyx-0.8.1-pyhd8ed1ab_0.conda#ea2517cb1e6fdc1749b9e1f806480a38 +https://conda.anaconda.org/conda-forge/noarch/jupyter-collaboration-2.0.1-pyhd8ed1ab_0.conda#0573928fe6b08ad71c795af0889b8a93 https://conda.anaconda.org/conda-forge/noarch/jupyter-syncthing-proxy-1.0.3-pyhd8ed1ab_0.conda#85c9949446d54c1b80c83e0357703174 https://conda.anaconda.org/conda-forge/noarch/jupyter-vscode-proxy-0.5-pyhd8ed1ab_0.conda#97e6ff376f730a316fb9d74c5c54c5a1 https://conda.anaconda.org/conda-forge/noarch/jupyterlab-4.0.11-pyhd8ed1ab_0.conda#42370604825af7396ef4317b67b22e2c @@ -702,7 +675,6 @@ https://conda.anaconda.org/conda-forge/linux-64/pyarrow-14.0.2-py311h39c9aba_2_c https://conda.anaconda.org/conda-forge/noarch/sankee-0.2.4-pyhd8ed1ab_0.conda#5cddf4d134860b0e13d2709e0a8201ce https://conda.anaconda.org/conda-forge/noarch/dask-labextension-7.0.0-pyhd8ed1ab_0.conda#bccfda61b2c35a3cec53bd3417e3d783 https://conda.anaconda.org/conda-forge/noarch/geemap-0.30.4-pyhd8ed1ab_1.conda#c8aaa5c4cc5aa50606b03575fa6d6ce3 -https://conda.anaconda.org/conda-forge/noarch/jupyter-ai-2.9.1-pyhd8ed1ab_0.conda#4444eecc5dac55aeded238685aca2dc7 https://conda.anaconda.org/conda-forge/noarch/jupyterhub-singleuser-4.0.2-pyh31011fe_0.conda#9eb773051ad8ecc804ed3bdec84ecce5 https://conda.anaconda.org/conda-forge/noarch/jupyterlab-git-0.50.0-pyhd8ed1ab_0.conda#42b7b173793e526df16894baed8661a5 https://conda.anaconda.org/conda-forge/noarch/notebook-7.0.7-pyhd8ed1ab_0.conda#ce3e06227eb2d96b11e685b2cabcf9aa @@ -712,7 +684,7 @@ https://conda.anaconda.org/conda-forge/noarch/dask-2024.1.0-pyhd8ed1ab_0.conda#9 https://conda.anaconda.org/conda-forge/noarch/nbgitpuller-1.2.0-pyhd8ed1ab_0.conda#e74db5ccfcf794e3d67ec7c9c125a39a https://conda.anaconda.org/conda-forge/noarch/intake-0.6.6-pyhd8ed1ab_0.tar.bz2#1dc29fb9182b0f3ce935a8bd4c341ed5 https://conda.anaconda.org/conda-forge/noarch/is2view-0.0.5-pyhd8ed1ab_0.conda#a47538fd9bb7cf7d6c35716cccae1ddc -https://conda.anaconda.org/conda-forge/noarch/intake-esm-2023.11.10-pyhd8ed1ab_0.conda#e0c73b7dc6419a243c5fe104ec241a48 +https://conda.anaconda.org/conda-forge/noarch/intake-esm-2023.10.27-pyhd8ed1ab_0.conda#33c61707d49697391beaa86b4eaf109e https://conda.anaconda.org/conda-forge/noarch/intake-xarray-0.6.1-pyhd8ed1ab_0.tar.bz2#6cc318952c249b55ae83f8a994342672 https://conda.anaconda.org/conda-forge/noarch/intake-stac-0.4.0-pyhd8ed1ab_0.tar.bz2#d9a48c97623dc88751dbd266b89497e3 https://conda.anaconda.org/conda-forge/noarch/myst-parser-0.18.1-pyhd8ed1ab_0.tar.bz2#bcfdf5c7d8bf5c6f6be7b4c66fff2eca @@ -736,3 +708,5 @@ https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-qthelp-1.0.7-pyhd8ed https://conda.anaconda.org/conda-forge/noarch/sphinx-5.0.2-pyh6c4a22f_0.tar.bz2#d4eaa1f50733a377480ce1d5aac556c7 https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-serializinghtml-1.1.10-pyhd8ed1ab_0.conda#e507335cb4ca9cff4c3d0fa9cdab255e # pip jupyter-desktop-server @ https://files.pythonhosted.org/packages/15/df/6f249cd3c3db684c8f9e67bc5470c4b593f882fbb03b1649f72ae7a26566/jupyter-desktop-server-0.1.3.tar.gz#sha256=5915a2dbbe250f59b3cc01859297b26b2e1836e03a5db4bfbfd438005649d7e4 + + From fbe4f440a9e171104c3960b14edbc11554167c6d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E2=80=9Ctsnow03=E2=80=9D?= Date: Mon, 22 Jan 2024 01:03:21 -0700 Subject: [PATCH 40/57] update env adding a few edits --- environment.yml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/environment.yml b/environment.yml index c7bad14..5a12a62 100644 --- a/environment.yml +++ b/environment.yml @@ -12,9 +12,9 @@ dependencies: - nbgitpuller==1.2.0 # Specify major version of jupyterlab to use. Manually bump it when you want to upgrade # jupyterlab version - - jupyterlab>=4.0 + - jupyterlab>=4.0,<4.1 # This provides memory usage stats on JupyterLab and classic notebook - - jupyter-resource-usage~=1.0.0 + - jupyter-resource-usage~=1.0.1 # 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 @@ -41,16 +41,16 @@ dependencies: - ipywidgets~=8.0.0 - jupyterlab-favorites==3.2.0 - - jupyterlab-geojson==3.4.0 + - jupyterlab-geojson~=3.4.0 - jupyter-collaboration~=2.0.1 - - jupyterlab-git==0.50.0 + - jupyterlab-git~=0.50.0 # - jupyter-ai==2.9.1 # Requires pandas>=2.0.1 - - jupyterlab-myst==2.1.0 + - jupyterlab-myst~=2.1.0 - jupyterlab-h5web~=11.1.0 - jupyter-book~=0.15.1 - jupytext~=1.16.1 - nbconvert==6.5.3 - - nbdime==4.0.1 + - nbdime~=4.0.1 # Core scientific python stack - cython==0.29.32 # optimization, C API access From 4c0e9709f3a087c7c069acf29f6c6d0490fb93d0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E2=80=9Ctsnow03=E2=80=9D?= Date: Thu, 25 Jan 2024 18:52:45 -0700 Subject: [PATCH 41/57] fix conflicts --- conda-linux-64.lock | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conda-linux-64.lock b/conda-linux-64.lock index 3d1f925..21baaf8 100644 --- a/conda-linux-64.lock +++ b/conda-linux-64.lock @@ -1,6 +1,6 @@ # Generated by conda-lock. # platform: linux-64 -# input_hash: b4ca4a9b51f7d1335bc925c6943786fde36051f5f5ed5a157efc1495f559775c +# input_hash: 48c4c420a07aac8bdf9d709383854c30ab3c896bf5e491e59ac7d7d611c2e329 @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2023.11.17-hbcca054_0.conda#01ffc8d36f9eba0ce0b3c1955fa780ee From da92fb9fe4939cf8dbd02eab1ec72c33572f41b8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E2=80=9Ctsnow03=E2=80=9D?= Date: Mon, 22 Jan 2024 10:15:06 -0700 Subject: [PATCH 42/57] scaling back env for testing --- environment.yml | 23 ++++++++++++----------- 1 file changed, 12 insertions(+), 11 deletions(-) diff --git a/environment.yml b/environment.yml index 5a12a62..e3954fe 100644 --- a/environment.yml +++ b/environment.yml @@ -5,16 +5,16 @@ channels: - nodefaults dependencies: - - python~=3.11.0 + - python~=3.10.10 # Required until https://github.com/jupyterhub/repo2docker/pull/1196 is merged - - jupyterhub-singleuser>=4.0 + - jupyterhub==4.0.2 # nbgitpuller is very helpful when distributing user content - - nbgitpuller==1.2.0 + - nbgitpuller==1.1.1 # Specify major version of jupyterlab to use. Manually bump it when you want to upgrade # jupyterlab version - jupyterlab>=4.0,<4.1 # This provides memory usage stats on JupyterLab and classic notebook - - jupyter-resource-usage~=1.0.1 + - jupyter-resource-usage~=0.7.1 # 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 @@ -32,21 +32,22 @@ dependencies: # - code-server==4.20.0 # Jupyter tools - - ipython~=8.17.0 + - ipython~=8.6.0 # Warning: There's a bug in ipykernel 6.18 that crashes hvplot. # See https://github.com/ipython/ipykernel/pull/1037. Restriction # can be relaxed once that's fixed. - ipykernel=6.16.0 - - ipywidgets~=8.0.0 - - jupyterlab-favorites==3.2.0 + - ipywidgets~=7.7.2 +# - jupyterlab-favorites~=3.2.0 + - jupyterlab-favorites==3.1.1 - jupyterlab-geojson~=3.4.0 - - jupyter-collaboration~=2.0.1 +# - jupyter-collaboration~=2.0.1 - jupyterlab-git~=0.50.0 # - jupyter-ai==2.9.1 # Requires pandas>=2.0.1 - jupyterlab-myst~=2.1.0 - - jupyterlab-h5web~=11.1.0 +# - jupyterlab-h5web~=11.1.0 - jupyter-book~=0.15.1 - jupytext~=1.16.1 - nbconvert==6.5.3 @@ -72,7 +73,7 @@ dependencies: - geoviews~=1.10.1 - hvplot~=0.8.4 - ipyleaflet~=0.17.3 - - ipympl~=0.9.3 # This enables matplotlib interaction with jupyter widgets + - ipympl==0.9.2 # This enables matplotlib interaction with jupyter widgets - matplotlib~=3.8.0 - plotly==5.18.0 - seaborn==0.12.1 # statistical plotting with matplotlib @@ -110,7 +111,7 @@ dependencies: # Distributed computing * - dask==2024.1.0 - - dask-labextension==7.0.0 + - dask-labextension==6.0.0 - dask-geopandas~=0.3.1 # Other useful generic python packages From 44757a41de685f92358321d734824c0d17fa0bbe Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E2=80=9Ctsnow03=E2=80=9D?= Date: Thu, 25 Jan 2024 18:54:06 -0700 Subject: [PATCH 43/57] fix conflicts --- environment.yml | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/environment.yml b/environment.yml index e3954fe..f486298 100644 --- a/environment.yml +++ b/environment.yml @@ -28,8 +28,7 @@ dependencies: # VS Code support - jupyter-vscode-proxy==0.5 -# - jupyter-vscode-server==0.0.10 -# - code-server==4.20.0 + - code-server~=4.16.1 # Jupyter tools - ipython~=8.6.0 @@ -41,17 +40,17 @@ dependencies: - ipywidgets~=7.7.2 # - jupyterlab-favorites~=3.2.0 - - jupyterlab-favorites==3.1.1 - - jupyterlab-geojson~=3.4.0 +# - jupyterlab-favorites==3.1.1 +# - jupyterlab-geojson~=3.4.0 # - jupyter-collaboration~=2.0.1 - - jupyterlab-git~=0.50.0 +# - jupyterlab-git~=0.50.0 # - jupyter-ai==2.9.1 # Requires pandas>=2.0.1 - jupyterlab-myst~=2.1.0 # - jupyterlab-h5web~=11.1.0 - jupyter-book~=0.15.1 - jupytext~=1.16.1 - nbconvert==6.5.3 - - nbdime~=4.0.1 +# - nbdime~=4.0.1 # Core scientific python stack - cython==0.29.32 # optimization, C API access From 4f7e6447ea518c93712c090b17a7e368be99c6ed Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E2=80=9Ctsnow03=E2=80=9D?= Date: Thu, 25 Jan 2024 18:36:43 -0700 Subject: [PATCH 44/57] fix conflicts --- environment.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/environment.yml b/environment.yml index f486298..ec866f1 100644 --- a/environment.yml +++ b/environment.yml @@ -48,8 +48,8 @@ dependencies: - jupyterlab-myst~=2.1.0 # - jupyterlab-h5web~=11.1.0 - jupyter-book~=0.15.1 - - jupytext~=1.16.1 - - nbconvert==6.5.3 + - jupytext==1.14.1 + - nbconvert==7.14.2 # - nbdime~=4.0.1 # Core scientific python stack From b25bb6a8a8814f6a7cc849e1391a2c6bf3c38aac Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E2=80=9Ctsnow03=E2=80=9D?= Date: Thu, 25 Jan 2024 18:54:42 -0700 Subject: [PATCH 45/57] fix conflicts --- environment.yml | 22 +++++++--------------- 1 file changed, 7 insertions(+), 15 deletions(-) diff --git a/environment.yml b/environment.yml index ec866f1..03f3e50 100644 --- a/environment.yml +++ b/environment.yml @@ -31,21 +31,13 @@ dependencies: - code-server~=4.16.1 # Jupyter tools - - ipython~=8.6.0 - - # Warning: There's a bug in ipykernel 6.18 that crashes hvplot. - # See https://github.com/ipython/ipykernel/pull/1037. Restriction - # can be relaxed once that's fixed. - - ipykernel=6.16.0 - - - ipywidgets~=7.7.2 -# - jupyterlab-favorites~=3.2.0 -# - jupyterlab-favorites==3.1.1 -# - jupyterlab-geojson~=3.4.0 -# - jupyter-collaboration~=2.0.1 -# - jupyterlab-git~=0.50.0 -# - jupyter-ai==2.9.1 # Requires pandas>=2.0.1 - - jupyterlab-myst~=2.1.0 + - ipython~=8.20.0 + - ipywidgets~=8.1.1 + - jupyterlab-favorites~=3.2.1 + - jupyterlab-geojson~=3.4.0 + - jupyter-collaboration~=2.0.1 + - jupyterlab-git~=0.50.0 + - jupyter-ai~=2.9.1 - jupyterlab-myst~=2.1.0 # - jupyterlab-h5web~=11.1.0 - jupyter-book~=0.15.1 - jupytext==1.14.1 From 63df944dc93cdc9e70626b1099007e01cb7d442f Mon Sep 17 00:00:00 2001 From: Tasha Snow Date: Tue, 23 Jan 2024 23:47:35 -0700 Subject: [PATCH 46/57] Update environment.yml Co-authored-by: Wei Ji <23487320+weiji14@users.noreply.github.com> --- environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/environment.yml b/environment.yml index 03f3e50..2394cf6 100644 --- a/environment.yml +++ b/environment.yml @@ -64,7 +64,7 @@ dependencies: - geoviews~=1.10.1 - hvplot~=0.8.4 - ipyleaflet~=0.17.3 - - ipympl==0.9.2 # 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 From c575637bc43ebbafcd0ca8275eb2b4aab61b045d Mon Sep 17 00:00:00 2001 From: Tasha Snow Date: Tue, 23 Jan 2024 23:47:57 -0700 Subject: [PATCH 47/57] Update environment.yml Co-authored-by: Wei Ji <23487320+weiji14@users.noreply.github.com> --- environment.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/environment.yml b/environment.yml index 2394cf6..3810b3c 100644 --- a/environment.yml +++ b/environment.yml @@ -104,7 +104,6 @@ dependencies: - dask==2024.1.0 - dask-labextension==6.0.0 - dask-geopandas~=0.3.1 - # Other useful generic python packages - pillow~=10.2.0 # Python imaging library, useful for many image-related tasks - pytest==7.2.0 From 9458ca3fb4dc428b9206b562b3340d42247ede09 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E2=80=9Ctsnow03=E2=80=9D?= Date: Thu, 25 Jan 2024 18:56:11 -0700 Subject: [PATCH 48/57] fix conflicts --- environment.yml | 24 +++++++++++++----------- 1 file changed, 13 insertions(+), 11 deletions(-) diff --git a/environment.yml b/environment.yml index 3810b3c..14f4cbd 100644 --- a/environment.yml +++ b/environment.yml @@ -9,7 +9,7 @@ dependencies: # Required until https://github.com/jupyterhub/repo2docker/pull/1196 is merged - jupyterhub==4.0.2 # nbgitpuller is very helpful when distributing user content - - nbgitpuller==1.1.1 + - nbgitpuller~=1.1.0 # Specify major version of jupyterlab to use. Manually bump it when you want to upgrade # jupyterlab version - jupyterlab>=4.0,<4.1 @@ -33,16 +33,18 @@ dependencies: # Jupyter tools - ipython~=8.20.0 - ipywidgets~=8.1.1 + - jupyter-ai~=2.9.1 + - jupyter-book~=0.15.1 + - jupyter-offlinenotebook~=0.2.2 + - jupyter-collaboration~=2.0.1 - jupyterlab-favorites~=3.2.1 - jupyterlab-geojson~=3.4.0 - - jupyter-collaboration~=2.0.1 - jupyterlab-git~=0.50.0 - - jupyter-ai~=2.9.1 - jupyterlab-myst~=2.1.0 -# - jupyterlab-h5web~=11.1.0 - - jupyter-book~=0.15.1 - - jupytext==1.14.1 - - nbconvert==7.14.2 -# - nbdime~=4.0.1 + - jupyterlab-h5web~=11.1.0 + - jupyterlab-myst~=2.1.0 + - jupytext~=1.16.1 + - nbconvert==6.5.3 + - nbdime~=4.0.1 # Core scientific python stack - cython==0.29.32 # optimization, C API access @@ -100,9 +102,9 @@ dependencies: - intake-xarray==0.6.1 - gcsfs>=2023.5.0 - # Distributed computing * - - dask==2024.1.0 - - dask-labextension==6.0.0 + # Distributed computing + - dask>=2023.12.1 + - dask-labextension~=7.0.0 - dask-geopandas~=0.3.1 # Other useful generic python packages - pillow~=10.2.0 # Python imaging library, useful for many image-related tasks From 56c6f5c07713b62a8bfa3393fdb8db195d467b78 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E2=80=9Ctsnow03=E2=80=9D?= Date: Thu, 25 Jan 2024 19:11:05 -0700 Subject: [PATCH 49/57] fix conflicts --- environment.yml | 45 ++++++++++++++++++++++++++------------------- 1 file changed, 26 insertions(+), 19 deletions(-) diff --git a/environment.yml b/environment.yml index 14f4cbd..c7bad14 100644 --- a/environment.yml +++ b/environment.yml @@ -5,16 +5,16 @@ channels: - nodefaults dependencies: - - python~=3.10.10 + - python~=3.11.0 # Required until https://github.com/jupyterhub/repo2docker/pull/1196 is merged - - jupyterhub==4.0.2 + - jupyterhub-singleuser>=4.0 # nbgitpuller is very helpful when distributing user content - - nbgitpuller~=1.1.0 + - 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 + - jupyterlab>=4.0 # This provides memory usage stats on JupyterLab and classic notebook - - jupyter-resource-usage~=0.7.1 + - jupyter-resource-usage~=1.0.0 # 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 @@ -28,23 +28,29 @@ dependencies: # VS Code support - jupyter-vscode-proxy==0.5 - - code-server~=4.16.1 +# - jupyter-vscode-server==0.0.10 +# - code-server==4.20.0 # Jupyter tools - - ipython~=8.20.0 - - ipywidgets~=8.1.1 - - jupyter-ai~=2.9.1 - - jupyter-book~=0.15.1 - - jupyter-offlinenotebook~=0.2.2 + - ipython~=8.17.0 + + # Warning: There's a bug in ipykernel 6.18 that crashes hvplot. + # See https://github.com/ipython/ipykernel/pull/1037. Restriction + # can be relaxed once that's fixed. + - ipykernel=6.16.0 + + - ipywidgets~=8.0.0 + - jupyterlab-favorites==3.2.0 + - jupyterlab-geojson==3.4.0 - jupyter-collaboration~=2.0.1 - - jupyterlab-favorites~=3.2.1 - - jupyterlab-geojson~=3.4.0 - - jupyterlab-git~=0.50.0 + - jupyterlab-git==0.50.0 +# - jupyter-ai==2.9.1 # Requires pandas>=2.0.1 + - jupyterlab-myst==2.1.0 - jupyterlab-h5web~=11.1.0 - - jupyterlab-myst~=2.1.0 + - jupyter-book~=0.15.1 - jupytext~=1.16.1 - nbconvert==6.5.3 - - nbdime~=4.0.1 + - nbdime==4.0.1 # Core scientific python stack - cython==0.29.32 # optimization, C API access @@ -102,10 +108,11 @@ dependencies: - intake-xarray==0.6.1 - gcsfs>=2023.5.0 - # Distributed computing - - dask>=2023.12.1 - - dask-labextension~=7.0.0 + # Distributed computing * + - dask==2024.1.0 + - dask-labextension==7.0.0 - dask-geopandas~=0.3.1 + # Other useful generic python packages - pillow~=10.2.0 # Python imaging library, useful for many image-related tasks - pytest==7.2.0 From bfe9caa21d8de41d537f9810a64a14a1fa8d0c58 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E2=80=9Ctsnow03=E2=80=9D?= Date: Thu, 25 Jan 2024 19:11:41 -0700 Subject: [PATCH 50/57] fix conflicts --- conda-linux-64.lock | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conda-linux-64.lock b/conda-linux-64.lock index 21baaf8..3d1f925 100644 --- a/conda-linux-64.lock +++ b/conda-linux-64.lock @@ -1,6 +1,6 @@ # Generated by conda-lock. # platform: linux-64 -# input_hash: 48c4c420a07aac8bdf9d709383854c30ab3c896bf5e491e59ac7d7d611c2e329 +# input_hash: b4ca4a9b51f7d1335bc925c6943786fde36051f5f5ed5a157efc1495f559775c @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2023.11.17-hbcca054_0.conda#01ffc8d36f9eba0ce0b3c1955fa780ee From 0c8313388c1f29f72b056b527bb51147330bc25f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E2=80=9Ctsnow03=E2=80=9D?= Date: Thu, 25 Jan 2024 19:12:27 -0700 Subject: [PATCH 51/57] fix conflicts --- environment.yml | 29 +++++++++++++++-------------- 1 file changed, 15 insertions(+), 14 deletions(-) diff --git a/environment.yml b/environment.yml index c7bad14..47a8b12 100644 --- a/environment.yml +++ b/environment.yml @@ -5,16 +5,16 @@ channels: - nodefaults dependencies: - - python~=3.11.0 + - python~=3.10.10 # Required until https://github.com/jupyterhub/repo2docker/pull/1196 is merged - - jupyterhub-singleuser>=4.0 + - jupyterhub==4.0.2 # nbgitpuller is very helpful when distributing user content - - nbgitpuller==1.2.0 + - nbgitpuller==1.1.1 # Specify major version of jupyterlab to use. Manually bump it when you want to upgrade # jupyterlab version - jupyterlab>=4.0 # This provides memory usage stats on JupyterLab and classic notebook - - jupyter-resource-usage~=1.0.0 + - jupyter-resource-usage~=0.7.1 # 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 @@ -32,21 +32,22 @@ dependencies: # - code-server==4.20.0 # Jupyter tools - - ipython~=8.17.0 + - ipython~=8.6.0 # Warning: There's a bug in ipykernel 6.18 that crashes hvplot. # See https://github.com/ipython/ipykernel/pull/1037. Restriction # can be relaxed once that's fixed. - ipykernel=6.16.0 - - ipywidgets~=8.0.0 - - jupyterlab-favorites==3.2.0 - - jupyterlab-geojson==3.4.0 - - jupyter-collaboration~=2.0.1 - - jupyterlab-git==0.50.0 + - ipywidgets~=7.7.2 +# - jupyterlab-favorites~=3.2.0 + - jupyterlab-favorites==3.1.1 + - jupyterlab-geojson~=3.4.0 +# - jupyter-collaboration~=2.0.1 + - jupyterlab-git~=0.50.0 # - jupyter-ai==2.9.1 # Requires pandas>=2.0.1 - - jupyterlab-myst==2.1.0 - - jupyterlab-h5web~=11.1.0 + - jupyterlab-myst~=2.1.0 +# - jupyterlab-h5web~=11.1.0 - jupyter-book~=0.15.1 - jupytext~=1.16.1 - nbconvert==6.5.3 @@ -72,7 +73,7 @@ dependencies: - geoviews~=1.10.1 - hvplot~=0.8.4 - ipyleaflet~=0.17.3 - - ipympl~=0.9.3 # This enables matplotlib interaction with jupyter widgets + - ipympl==0.9.2 # This enables matplotlib interaction with jupyter widgets - matplotlib~=3.8.0 - plotly==5.18.0 - seaborn==0.12.1 # statistical plotting with matplotlib @@ -110,7 +111,7 @@ dependencies: # Distributed computing * - dask==2024.1.0 - - dask-labextension==7.0.0 + - dask-labextension==6.0.0 - dask-geopandas~=0.3.1 # Other useful generic python packages From 581f22a7efb1be1fa2deda94fbd942dc2a82fa6c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E2=80=9Ctsnow03=E2=80=9D?= Date: Thu, 25 Jan 2024 19:12:54 -0700 Subject: [PATCH 52/57] fix conflicts --- environment.yml | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/environment.yml b/environment.yml index 47a8b12..949d92a 100644 --- a/environment.yml +++ b/environment.yml @@ -28,8 +28,7 @@ dependencies: # VS Code support - jupyter-vscode-proxy==0.5 -# - jupyter-vscode-server==0.0.10 -# - code-server==4.20.0 + - code-server~=4.16.1 # Jupyter tools - ipython~=8.6.0 @@ -41,17 +40,17 @@ dependencies: - ipywidgets~=7.7.2 # - jupyterlab-favorites~=3.2.0 - - jupyterlab-favorites==3.1.1 - - jupyterlab-geojson~=3.4.0 +# - jupyterlab-favorites==3.1.1 +# - jupyterlab-geojson~=3.4.0 # - jupyter-collaboration~=2.0.1 - - jupyterlab-git~=0.50.0 +# - jupyterlab-git~=0.50.0 # - jupyter-ai==2.9.1 # Requires pandas>=2.0.1 - jupyterlab-myst~=2.1.0 # - jupyterlab-h5web~=11.1.0 - jupyter-book~=0.15.1 - jupytext~=1.16.1 - nbconvert==6.5.3 - - nbdime==4.0.1 +# - nbdime~=4.0.1 # Core scientific python stack - cython==0.29.32 # optimization, C API access From fc431d7264a01dc8fc538fd5f56ffc0722038bf5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E2=80=9Ctsnow03=E2=80=9D?= Date: Thu, 25 Jan 2024 19:13:30 -0700 Subject: [PATCH 53/57] fix conflicts --- environment.yml | 21 +++++++-------------- 1 file changed, 7 insertions(+), 14 deletions(-) diff --git a/environment.yml b/environment.yml index 949d92a..3c1c0ad 100644 --- a/environment.yml +++ b/environment.yml @@ -31,20 +31,13 @@ dependencies: - code-server~=4.16.1 # Jupyter tools - - ipython~=8.6.0 - - # Warning: There's a bug in ipykernel 6.18 that crashes hvplot. - # See https://github.com/ipython/ipykernel/pull/1037. Restriction - # can be relaxed once that's fixed. - - ipykernel=6.16.0 - - - ipywidgets~=7.7.2 -# - jupyterlab-favorites~=3.2.0 -# - jupyterlab-favorites==3.1.1 -# - jupyterlab-geojson~=3.4.0 -# - jupyter-collaboration~=2.0.1 -# - jupyterlab-git~=0.50.0 -# - jupyter-ai==2.9.1 # Requires pandas>=2.0.1 + - ipython~=8.20.0 + - ipywidgets~=8.1.1 + - jupyterlab-favorites~=3.2.1 + - jupyterlab-geojson~=3.4.0 + - jupyter-collaboration~=2.0.1 + - jupyterlab-git~=0.50.0 + - jupyter-ai~=2.9.1 - jupyterlab-myst~=2.1.0 # - jupyterlab-h5web~=11.1.0 - jupyter-book~=0.15.1 From 548cc513730e39ed691cb2ae5390a0bcf7d5bd0c Mon Sep 17 00:00:00 2001 From: Tasha Snow Date: Tue, 23 Jan 2024 23:47:57 -0700 Subject: [PATCH 54/57] Update environment.yml Co-authored-by: Wei Ji <23487320+weiji14@users.noreply.github.com> --- environment.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/environment.yml b/environment.yml index 3c1c0ad..d508fae 100644 --- a/environment.yml +++ b/environment.yml @@ -105,7 +105,6 @@ dependencies: - dask==2024.1.0 - dask-labextension==6.0.0 - dask-geopandas~=0.3.1 - # Other useful generic python packages - pillow~=10.2.0 # Python imaging library, useful for many image-related tasks - pytest==7.2.0 From 43f05d425f3ff1cd2774f73c6ea96bb89f2476a2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E2=80=9Ctsnow03=E2=80=9D?= Date: Thu, 25 Jan 2024 19:14:06 -0700 Subject: [PATCH 55/57] fix conflicts --- environment.yml | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) diff --git a/environment.yml b/environment.yml index d508fae..a4febde 100644 --- a/environment.yml +++ b/environment.yml @@ -9,7 +9,7 @@ dependencies: # Required until https://github.com/jupyterhub/repo2docker/pull/1196 is merged - jupyterhub==4.0.2 # nbgitpuller is very helpful when distributing user content - - nbgitpuller==1.1.1 + - nbgitpuller~=1.1.0 # Specify major version of jupyterlab to use. Manually bump it when you want to upgrade # jupyterlab version - jupyterlab>=4.0 @@ -33,14 +33,15 @@ dependencies: # Jupyter tools - ipython~=8.20.0 - ipywidgets~=8.1.1 + - jupyter-ai~=2.9.1 + - jupyter-book~=0.15.1 + - jupyter-offlinenotebook~=0.2.2 + - jupyter-collaboration~=2.0.1 - jupyterlab-favorites~=3.2.1 - jupyterlab-geojson~=3.4.0 - - jupyter-collaboration~=2.0.1 - jupyterlab-git~=0.50.0 - - jupyter-ai~=2.9.1 + - jupyterlab-h5web~=11.1.0 - jupyterlab-myst~=2.1.0 -# - jupyterlab-h5web~=11.1.0 - - jupyter-book~=0.15.1 - jupytext~=1.16.1 - nbconvert==6.5.3 # - nbdime~=4.0.1 @@ -101,9 +102,9 @@ dependencies: - intake-xarray==0.6.1 - gcsfs>=2023.5.0 - # Distributed computing * - - dask==2024.1.0 - - dask-labextension==6.0.0 + # Distributed computing + - dask>=2023.12.1 + - dask-labextension~=7.0.0 - dask-geopandas~=0.3.1 # Other useful generic python packages - pillow~=10.2.0 # Python imaging library, useful for many image-related tasks From 0dbc9a0afde5f4a3ef5153a05f493a87d23a9b9e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E2=80=9Ctsnow03=E2=80=9D?= Date: Thu, 25 Jan 2024 19:15:22 -0700 Subject: [PATCH 56/57] fix conflicts --- environment.yml | 41 ++++++++++++++++++++++++----------------- 1 file changed, 24 insertions(+), 17 deletions(-) diff --git a/environment.yml b/environment.yml index a4febde..040e80f 100644 --- a/environment.yml +++ b/environment.yml @@ -7,14 +7,14 @@ channels: dependencies: - python~=3.10.10 # Required until https://github.com/jupyterhub/repo2docker/pull/1196 is merged - - jupyterhub==4.0.2 + - jupyterhub-singleuser>=4.0 # nbgitpuller is very helpful when distributing user content - - nbgitpuller~=1.1.0 + - nbgitpuller==1.2.0 # Specify major version of jupyterlab to use. Manually bump it when you want to upgrade # jupyterlab version - jupyterlab>=4.0 # This provides memory usage stats on JupyterLab and classic notebook - - jupyter-resource-usage~=0.7.1 + - jupyter-resource-usage~=1.0.0 # 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 @@ -28,23 +28,29 @@ dependencies: # VS Code support - jupyter-vscode-proxy==0.5 - - code-server~=4.16.1 +# - jupyter-vscode-server==0.0.10 +# - code-server==4.20.0 # Jupyter tools - - ipython~=8.20.0 - - ipywidgets~=8.1.1 - - jupyter-ai~=2.9.1 - - jupyter-book~=0.15.1 - - jupyter-offlinenotebook~=0.2.2 + - ipython~=8.17.0 + + # Warning: There's a bug in ipykernel 6.18 that crashes hvplot. + # See https://github.com/ipython/ipykernel/pull/1037. Restriction + # can be relaxed once that's fixed. + - ipykernel=6.16.0 + + - ipywidgets~=8.0.0 + - jupyterlab-favorites==3.2.0 + - jupyterlab-geojson==3.4.0 - jupyter-collaboration~=2.0.1 - - jupyterlab-favorites~=3.2.1 - - jupyterlab-geojson~=3.4.0 - - jupyterlab-git~=0.50.0 + - jupyterlab-git==0.50.0 +# - jupyter-ai==2.9.1 # Requires pandas>=2.0.1 + - jupyterlab-myst==2.1.0 - jupyterlab-h5web~=11.1.0 - - jupyterlab-myst~=2.1.0 + - jupyter-book~=0.15.1 - jupytext~=1.16.1 - nbconvert==6.5.3 -# - nbdime~=4.0.1 + - nbdime==4.0.1 # Core scientific python stack - cython==0.29.32 # optimization, C API access @@ -102,10 +108,11 @@ dependencies: - intake-xarray==0.6.1 - gcsfs>=2023.5.0 - # Distributed computing - - dask>=2023.12.1 - - dask-labextension~=7.0.0 + # Distributed computing * + - dask==2024.1.0 + - dask-labextension==7.0.0 - dask-geopandas~=0.3.1 + # Other useful generic python packages - pillow~=10.2.0 # Python imaging library, useful for many image-related tasks - pytest==7.2.0 From f57d1cedd43ca58bfaf59e7097731c4ab313ea69 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E2=80=9Ctsnow03=E2=80=9D?= Date: Thu, 25 Jan 2024 19:17:28 -0700 Subject: [PATCH 57/57] fix rebase --- environment.yml | 76 ++++++++++++++++++++++--------------------------- 1 file changed, 34 insertions(+), 42 deletions(-) diff --git a/environment.yml b/environment.yml index 040e80f..e27542b 100644 --- a/environment.yml +++ b/environment.yml @@ -1,20 +1,16 @@ name: cryocloud -channels: - - conda-forge - - nodefaults - dependencies: - - python~=3.10.10 + - python~=3.11.0 # Required until https://github.com/jupyterhub/repo2docker/pull/1196 is merged - - jupyterhub-singleuser>=4.0 + - jupyterhub-singleuser~=4.0.1 # nbgitpuller is very helpful when distributing user content - - nbgitpuller==1.2.0 + - nbgitpuller~=1.2.0 # Specify major version of jupyterlab to use. Manually bump it when you want to upgrade # jupyterlab version - - jupyterlab>=4.0 + - jupyterlab>=4.0,<4.1 # This provides memory usage stats on JupyterLab and classic notebook - - jupyter-resource-usage~=1.0.0 + - jupyter-resource-usage~=1.0.1 # 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 @@ -27,43 +23,39 @@ dependencies: - gh~=2.32.1 # VS Code support - - jupyter-vscode-proxy==0.5 -# - jupyter-vscode-server==0.0.10 -# - code-server==4.20.0 + - jupyter-vscode-proxy~=0.5 + - code-server~=4.16.1 # Jupyter tools - - ipython~=8.17.0 - - # Warning: There's a bug in ipykernel 6.18 that crashes hvplot. - # See https://github.com/ipython/ipykernel/pull/1037. Restriction - # can be relaxed once that's fixed. - - ipykernel=6.16.0 - - - ipywidgets~=8.0.0 - - jupyterlab-favorites==3.2.0 - - jupyterlab-geojson==3.4.0 - - jupyter-collaboration~=2.0.1 - - jupyterlab-git==0.50.0 -# - jupyter-ai==2.9.1 # Requires pandas>=2.0.1 - - jupyterlab-myst==2.1.0 - - jupyterlab-h5web~=11.1.0 + - ipython~=8.20.0 + - ipywidgets~=8.1.1 + - 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 +# - 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 + - nbdime~=4.0.1 # Core scientific python stack - cython==0.29.32 # optimization, C API access - hypothesis==6.58.0 # needed by numpy testing tools - networkx==2.8.8 - - numba==0.58.1 # high-performance numerics - - numpy~=1.26.0 - - pandas==1.5.1 - - scikit-image==0.22.0 - - scikit-learn==1.4.0 + - numba~=0.58.1 # high-performance numerics + - numpy==1.23.5 + - pandas>=2.0.1,<3.0 + - scikit-image==0.19.3 + - scikit-learn>=1.2.2,<2.0.0 - scipy==1.9.3 - statsmodels==0.13.5 - - sympy~=1.12.0 + - sympy~=1.12 - xarray>=2023.05.0 # Visualization packages @@ -72,9 +64,9 @@ dependencies: - geoviews~=1.10.1 - hvplot~=0.8.4 - ipyleaflet~=0.17.3 - - ipympl==0.9.2 # 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 + - plotly~=5.18.0 - seaborn==0.12.1 # statistical plotting with matplotlib - geemap~=0.30.0 @@ -108,9 +100,9 @@ dependencies: - intake-xarray==0.6.1 - gcsfs>=2023.5.0 - # Distributed computing * - - dask==2024.1.0 - - dask-labextension==7.0.0 + # Distributed computing + - dask>=2023.12.1 + - dask-labextension~=7.0.0 - dask-geopandas~=0.3.1 # Other useful generic python packages @@ -125,7 +117,7 @@ dependencies: - esmpy~=8.4.2 - xmip~=0.7.1 - # Packages specific to cryo work * + # Packages specific to cryo work - h5coro~=0.0.6 - icepyx~=0.8.1 - itslive~=0.3.2 @@ -137,7 +129,7 @@ dependencies: # 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 - # - ocl-icd-system + - ocl-icd-system # needed for Linux desktop to work - websockify>=0.10 # Includes new subcommands (`switch` & `restore`) and vulnerability fixes @@ -145,7 +137,7 @@ dependencies: - git>=2.39 # Not all packages will be available from conda-forge, we install from pip when we need to. - - pip==23.3.2 + - pip~=23.3.2 - pip: # Access linux desktop from inside JupyterHub - jupyter-desktop-server==0.1.3