From 5857db0ef4d4b1294a888ce11791ac17f1ebf4b7 Mon Sep 17 00:00:00 2001 From: Wei Ji <23487320+weiji14@users.noreply.github.com> Date: Tue, 29 Nov 2022 13:39:11 -0500 Subject: [PATCH 01/26] Rename environment.yml file to environment-cryocloud.yml So that repo2docker doesn't use it to build the docker image. --- .github/workflows/build.yaml | 2 +- .github/workflows/conda-lock-command.yml | 2 +- .github/workflows/test.yaml | 2 +- README.md | 2 +- environment.yml => environment-cryocloud.yml | 0 5 files changed, 4 insertions(+), 4 deletions(-) rename environment.yml => environment-cryocloud.yml (100%) diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml index 63db74f..f009ec1 100644 --- a/.github/workflows/build.yaml +++ b/.github/workflows/build.yaml @@ -7,7 +7,7 @@ on: paths: - 'apt.txt' - 'conda-linux-64.lock' - - 'environment.yml' + - 'environment-cryocloud.yml' jobs: build-and-push: diff --git a/.github/workflows/conda-lock-command.yml b/.github/workflows/conda-lock-command.yml index 4fa9b7f..f4d4e3e 100644 --- a/.github/workflows/conda-lock-command.yml +++ b/.github/workflows/conda-lock-command.yml @@ -47,7 +47,7 @@ jobs: # Run "conda-lock" for linux-64 only - name: Run conda-lock run: | - conda-lock lock --mamba --kind explicit --file environment.yml --platform linux-64 + conda-lock lock --mamba --kind explicit --file environment-cryocloud.yml --platform linux-64 # Commit the change to the PR branch if any changes - name: Commit condalock files to PR diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml index 8ab66ed..7225a8c 100644 --- a/.github/workflows/test.yaml +++ b/.github/workflows/test.yaml @@ -5,7 +5,7 @@ on: paths: - 'apt.txt' - 'conda-linux-64.lock' - - 'environment.yml' + - 'environment-cryocloud.yml' jobs: test-build: diff --git a/README.md b/README.md index cadc8ff..2b2f88d 100644 --- a/README.md +++ b/README.md @@ -9,7 +9,7 @@ hosted on https://quay.io/repository/cryointhecloud/cryo-hub-image ## Adding packages to this repository You can easily add more packages to the cryointhecloud hub by making pull requests to this -repository. Edit either the `environment.yml` file (for most packages) or `apt.txt` file +repository. Edit either the `environment-cryocloud.yml` file (for most packages) or `apt.txt` file (for packages that need to be used in the Linux Desktop environment in the cloud), and make a pull request - you can even do that just from the GitHub UI! A bot will comment with a link to [mybinder.org](https://mybinder.org) where you can test your pull request to make sure it works diff --git a/environment.yml b/environment-cryocloud.yml similarity index 100% rename from environment.yml rename to environment-cryocloud.yml From 90fe9f603fbb3df66a5cb1a9663e7e6807d451f0 Mon Sep 17 00:00:00 2001 From: Wei Ji <23487320+weiji14@users.noreply.github.com> Date: Tue, 29 Nov 2022 15:33:12 -0500 Subject: [PATCH 02/26] Bump to cartopy 0.21.0, rasterio 1.3.3, hdf5 1.12.2, qgis 3.22.11 Minor version updates to fix `mamba` solver. --- environment-cryocloud.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/environment-cryocloud.yml b/environment-cryocloud.yml index 198035f..10c6392 100644 --- a/environment-cryocloud.yml +++ b/environment-cryocloud.yml @@ -70,7 +70,7 @@ dependencies: - nbdime==3.1.1 # Visualization packages - - cartopy==0.20.2 # geospatial plotting with matplotlib + - cartopy==0.21.0 # geospatial plotting with matplotlib - seaborn==0.12.1 # statistical plotting with matplotlib - ipympl==0.9.2 # This enables matplotlib interaction with jupyter widgets - ipyleaflet==0.17.2 @@ -81,13 +81,13 @@ dependencies: # Geospatial data packages - geopandas==0.12.1 - - rasterio==1.2.10 + - rasterio==1.3.3 - rioxarray==0.13.1 - xarray-datatree==0.0.9 # File formats and file management, download, dataset caching - h5py==3.7.0 - - hdf5==1.12.1 + - hdf5==1.12.2 - h5netcdf==1.1.0 - pooch==1.6.0 @@ -108,7 +108,7 @@ dependencies: - icepyx==0.6.4 # Desktop tools whose versions are more recent on conda-forge than ubuntu - - qgis==3.18.3 + - qgis==3.22.11 # Not all packages will be available from conda-forge, we install from pip when we need to. - pip==22.3.1 From 1d23d26115e38ddad4a10732970c54ffe274385e Mon Sep 17 00:00:00 2001 From: Wei Ji <23487320+weiji14@users.noreply.github.com> Date: Tue, 29 Nov 2022 15:43:12 -0500 Subject: [PATCH 03/26] Replace explicit conda-linux-64.lock file with unified conda-lock.yml Handle both conda and pip dependencies by changing from the old explicit conda-lock (<1.0) format to the newer unified format. Deleting conda-linux-64.lock and replacing it with a placeholder conda-lock.yml for now. --- .github/workflows/conda-lock-command.yml | 2 +- conda-linux-64.lock | 518 ----------------------- conda-lock.yml | 1 + 3 files changed, 2 insertions(+), 519 deletions(-) delete mode 100644 conda-linux-64.lock create mode 100644 conda-lock.yml diff --git a/.github/workflows/conda-lock-command.yml b/.github/workflows/conda-lock-command.yml index f4d4e3e..f40ee24 100644 --- a/.github/workflows/conda-lock-command.yml +++ b/.github/workflows/conda-lock-command.yml @@ -47,7 +47,7 @@ jobs: # Run "conda-lock" for linux-64 only - name: Run conda-lock run: | - conda-lock lock --mamba --kind explicit --file environment-cryocloud.yml --platform linux-64 + conda-lock lock --mamba --file environment-cryocloud.yml --platform linux-64 # Commit the change to the PR branch if any changes - name: Commit condalock files to PR diff --git a/conda-linux-64.lock b/conda-linux-64.lock deleted file mode 100644 index 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https://files.pythonhosted.org/packages/4d/53/fc5f8fc3fa21aa463ec8002b25187e9e565753b6b0caf8bb3b020022497e/jupyter_syncthing_proxy-1.0.3-py3-none-any.whl#sha256=f4550a7a4d22b97128743205a6ea001487f9f07c561befedaadc265670cc77f2 diff --git a/conda-lock.yml b/conda-lock.yml new file mode 100644 index 0000000..e011283 --- /dev/null +++ b/conda-lock.yml @@ -0,0 +1 @@ +# This lock file was generated by conda-lock (https://github.com/conda-incubator/conda-lock). DO NOT EDIT! From 95d8ec804c339f7ba21e9f92930c951286885cca Mon Sep 17 00:00:00 2001 From: Wei Ji <23487320+weiji14@users.noreply.github.com> Date: Tue, 29 Nov 2022 15:44:48 -0500 Subject: [PATCH 04/26] Temporarily rename environment-cryocloud.yml back to environment.yml So that the /condalock slash command works. --- environment-cryocloud.yml => environment.yml | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename environment-cryocloud.yml => environment.yml (100%) diff --git a/environment-cryocloud.yml b/environment.yml similarity index 100% rename from environment-cryocloud.yml rename to environment.yml From 09ecd555b82c0eb8604182e998b8067f4027b461 Mon Sep 17 00:00:00 2001 From: Wei Ji <23487320+weiji14@users.noreply.github.com> Date: Tue, 29 Nov 2022 15:44:48 -0500 Subject: [PATCH 05/26] Revert "Temporarily rename environment-cryocloud.yml back to environment.yml" This reverts commit 95d8ec804c339f7ba21e9f92930c951286885cca. --- environment.yml => environment-cryocloud.yml | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename environment.yml => environment-cryocloud.yml (100%) diff --git a/environment.yml b/environment-cryocloud.yml similarity index 100% rename from environment.yml rename to environment-cryocloud.yml From 00cc29750c7815cd01dc3c5bd536c068968531dd Mon Sep 17 00:00:00 2001 From: Wei Ji <23487320+weiji14@users.noreply.github.com> Date: Tue, 29 Nov 2022 15:57:31 -0500 Subject: [PATCH 06/26] Add postBuild script to install dependencies from unified conda-lock.yml https://repo2docker.readthedocs.io/en/latest/config_files.html#postbuild-run-code-after-installing-the-environment --- .github/workflows/build.yaml | 2 ++ .github/workflows/test.yaml | 2 ++ postBuild | 4 ++++ 3 files changed, 8 insertions(+) create mode 100644 postBuild diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml index f009ec1..6d35084 100644 --- a/.github/workflows/build.yaml +++ b/.github/workflows/build.yaml @@ -8,6 +8,8 @@ on: - 'apt.txt' - 'conda-linux-64.lock' - 'environment-cryocloud.yml' + - 'postBuild' + - 'start' jobs: build-and-push: diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml index 7225a8c..38d02b7 100644 --- a/.github/workflows/test.yaml +++ b/.github/workflows/test.yaml @@ -6,6 +6,8 @@ on: - 'apt.txt' - 'conda-linux-64.lock' - 'environment-cryocloud.yml' + - 'postBuild' + - 'start' jobs: test-build: diff --git a/postBuild b/postBuild new file mode 100644 index 0000000..24c289a --- /dev/null +++ b/postBuild @@ -0,0 +1,4 @@ +#!/bin/bash +set -eux +pip install conda-lock==1.2.1 +conda-lock install --mamba --name cryocloud --file conda-lock.yml From d07eafb44117d47dc07b95aa516e6e024b047c49 Mon Sep 17 00:00:00 2001 From: Wei Ji <23487320+weiji14@users.noreply.github.com> Date: Tue, 29 Nov 2022 16:07:09 -0500 Subject: [PATCH 07/26] Minimal conda-lock.yml with only Python 3.10 Need a proper placeholder conda-lock.yml to prevent `AttributeError: 'NoneType' object has no attribute 'pop'` when running `conda-lock lock`. --- conda-lock.yml | 268 +++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 268 insertions(+) diff --git a/conda-lock.yml b/conda-lock.yml index e011283..1d539c2 100644 --- a/conda-lock.yml +++ b/conda-lock.yml @@ -1 +1,269 @@ # This lock file was generated by conda-lock (https://github.com/conda-incubator/conda-lock). DO NOT EDIT! +# +# A "lock file" contains a concrete list of package versions (with checksums) to be installed. Unlike +# e.g. `conda env create`, the resulting environment will not change as new package versions become +# available, unless you explicitly update the lock file. +# +# Install this environment as "YOURENV" with: +# conda-lock install -n YOURENV --file conda-lock.yml +# To update a single package to the latest version compatible with the version constraints in the source: +# conda-lock lock --lockfile conda-lock.yml --update PACKAGE +# To re-solve the entire environment, e.g. after changing a version constraint in the source file: +# conda-lock -f environment-cryocloud.yml --lockfile conda-lock.yml +metadata: + channels: + - url: conda-forge + used_env_vars: [] + - url: nodefaults + used_env_vars: [] + content_hash: + linux-64: 204146c4e8e9700bf19770089d10b073f3e20b78059e22fde23fbe9b39849f7c + platforms: + - linux-64 + sources: + - environment-cryocloud.yml +package: +- category: main + dependencies: {} + hash: + md5: d7c89558ba9fa0495403155b64376d81 + sha256: fe51de6107f9edc7aa4f786a70f4a883943bc9d39b3bb7307c04c41410990726 + manager: conda + name: _libgcc_mutex + optional: false + platform: linux-64 + url: https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2 + version: '0.1' +- category: main + dependencies: {} + hash: + md5: 41e4e87062433e283696cf384f952ef6 + sha256: 058355034667e77d15389700f6b2364cc74efce0af63a418eacc1ce252458942 + manager: conda + name: ca-certificates + optional: false + platform: linux-64 + url: https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2022.9.24-ha878542_0.tar.bz2 + version: 2022.9.24 +- category: main + dependencies: {} + hash: + md5: 737be0d34c22d24432049ab7a3214de4 + sha256: 3e7f203e33ea497b6e468279cc5fdef7d556473c25e7466b35fd672940392469 + manager: conda + name: ld_impl_linux-64 + optional: false + platform: linux-64 + url: https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.39-hcc3a1bd_1.conda + version: '2.39' +- category: main + dependencies: {} + hash: + md5: e366350e2343a798e29833286abe2560 + sha256: 419eaff0d20f418974ca27a40bc871bbe48217dba05936f147a574eb5f079005 + manager: conda + name: tzdata + optional: false + platform: linux-64 + url: https://conda.anaconda.org/conda-forge/noarch/tzdata-2022f-h191b570_0.tar.bz2 + version: 2022f +- category: main + dependencies: + _libgcc_mutex: 0.1 conda_forge + hash: + md5: cedcee7c064c01c403f962c9e8d3c373 + sha256: 81a76d20cfdee9fe0728b93ef057ba93494fd1450d42bc3717af4e468235661e + manager: conda + name: libgomp + optional: false + platform: linux-64 + url: https://conda.anaconda.org/conda-forge/linux-64/libgomp-12.2.0-h65d4601_19.tar.bz2 + version: 12.2.0 +- category: main + dependencies: + _libgcc_mutex: 0.1 conda_forge + libgomp: '>=7.5.0' + hash: + md5: 73aaf86a425cc6e73fcf236a5a46396d + sha256: fbe2c5e56a653bebb982eda4876a9178aedfc2b545f25d0ce9c4c0b508253d22 + manager: conda + name: _openmp_mutex + optional: false + platform: linux-64 + url: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2 + version: '4.5' +- category: main + dependencies: + _libgcc_mutex: 0.1 conda_forge + _openmp_mutex: '>=4.5' + hash: + md5: e4c94f80aef025c17ab0828cd85ef535 + sha256: f3899c26824cee023f1e360bd0859b0e149e2b3e8b1668bc6dd04bfc70dcd659 + manager: conda + name: libgcc-ng + optional: false + platform: linux-64 + url: https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-12.2.0-h65d4601_19.tar.bz2 + version: 12.2.0 +- category: main + dependencies: + libgcc-ng: '>=9.3.0' + hash: + md5: a1fd65c7ccbf10880423d82bca54eb54 + sha256: cb521319804640ff2ad6a9f118d972ed76d86bea44e5626c09a13d38f562e1fa + manager: conda + name: bzip2 + optional: false + platform: linux-64 + url: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h7f98852_4.tar.bz2 + version: 1.0.8 +- category: main + dependencies: + libgcc-ng: '>=9.4.0' + hash: + md5: d645c6d2ac96843a2bfaccd2d62b3ac3 + sha256: 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libgcc-ng: '>=12' + hash: + md5: f3f9de449d32ca9b9c66a22863c96f41 + sha256: 22f3663bcf294d349327e60e464a51cd59664a71b8ed70c28a9f512d10bc77dd + manager: conda + name: libzlib + optional: false + platform: linux-64 + url: https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-h166bdaf_4.tar.bz2 + version: 1.2.13 +- category: main + dependencies: + libgcc-ng: '>=10.3.0' + hash: + md5: 4acfc691e64342b9dae57cf2adc63238 + sha256: b801e8cf4b2c9a30bce5616746c6c2a4e36427f045b46d9fc08a4ed40a9f7065 + manager: conda + name: ncurses + optional: false + platform: linux-64 + url: https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.3-h27087fc_1.tar.bz2 + version: '6.3' +- category: main + dependencies: + ca-certificates: '' + libgcc-ng: '>=12' + hash: + md5: d1ad1824c71e67dea42f07e06cd177dc + sha256: 67fc8e91186ada002682bdd125e1ceece884ba309c68e9c5c981e8412196d226 + manager: conda + name: openssl + optional: false + platform: linux-64 + url: https://conda.anaconda.org/conda-forge/linux-64/openssl-3.0.7-h166bdaf_0.tar.bz2 + version: 3.0.7 +- category: main + dependencies: + libgcc-ng: '>=12' + hash: + md5: 2161070d867d1b1204ea749c8eec4ef0 + sha256: 03a6d28ded42af8a347345f82f3eebdd6807a08526d47899a42d62d319609162 + manager: conda + name: xz + optional: false + platform: linux-64 + url: https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2 + version: 5.2.6 +- category: main + dependencies: + libgcc-ng: '>=12' + libzlib: '>=1.2.13,<1.3.0a0' + hash: + md5: 2e5f9a37d487e1019fd4d8113adb2f9f + sha256: 6008a0b914bd1a3510a3dba38eada93aa0349ebca3a21e5fa276833c8205bf49 + manager: conda + name: libsqlite + optional: false + platform: linux-64 + url: https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.40.0-h753d276_0.tar.bz2 + version: 3.40.0 +- category: main + dependencies: + libgcc-ng: '>=12' + ncurses: '>=6.3,<7.0a0' + hash: + md5: db2ebbe2943aae81ed051a6a9af8e0fa + sha256: f5f383193bdbe01c41cb0d6f99fec68e820875e842e6e8b392dbe1a9b6c43ed8 + manager: conda + name: readline + optional: false + platform: linux-64 + url: https://conda.anaconda.org/conda-forge/linux-64/readline-8.1.2-h0f457ee_0.tar.bz2 + version: 8.1.2 +- category: main + dependencies: + libgcc-ng: '>=9.4.0' + libzlib: '>=1.2.11,<1.3.0a0' + hash: + md5: 5b8c42eb62e9fc961af70bdd6a26e168 + sha256: 032fd769aad9d4cad40ba261ab222675acb7ec951a8832455fce18ef33fa8df0 + manager: conda + name: tk + optional: false + platform: linux-64 + url: https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.12-h27826a3_0.tar.bz2 + version: 8.6.12 +- category: main + dependencies: + bzip2: '>=1.0.8,<2.0a0' + ld_impl_linux-64: '>=2.36.1' + libffi: '>=3.4,<4.0a0' + libgcc-ng: '>=12' + libnsl: '>=2.0.0,<2.1.0a0' + libsqlite: '>=3.40.0,<4.0a0' + libuuid: '>=2.32.1,<3.0a0' + libzlib: '>=1.2.13,<1.3.0a0' + ncurses: '>=6.3,<7.0a0' + openssl: '>=3.0.7,<4.0a0' + readline: '>=8.1.2,<9.0a0' + tk: '>=8.6.12,<8.7.0a0' + tzdata: '' + xz: '>=5.2.6,<6.0a0' + hash: + md5: be2a6d78752c2ab85f360ce37d2c64e2 + sha256: 79cc250d8f85da29c7a06116a51db4c9efbd46f62f21daef6cf10e8bccdc0523 + manager: conda + name: python + optional: false + platform: linux-64 + url: https://conda.anaconda.org/conda-forge/linux-64/python-3.10.8-h4a9ceb5_0_cpython.conda + version: 3.10.8 +version: 1 From ef9cc29d3d95a95f645d61c03a055b9ca464afa3 Mon Sep 17 00:00:00 2001 From: Wei Ji <23487320+weiji14@users.noreply.github.com> Date: Tue, 29 Nov 2022 16:09:38 -0500 Subject: [PATCH 08/26] Fix conda-lock install command in postBuild The `--file` option doesn't actually work, even though it's documented like so. --- postBuild | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/postBuild b/postBuild index 24c289a..eceafe0 100644 --- a/postBuild +++ b/postBuild @@ -1,4 +1,4 @@ #!/bin/bash set -eux pip install conda-lock==1.2.1 -conda-lock install --mamba --name cryocloud --file conda-lock.yml +conda-lock install --mamba --name cryocloud conda-lock.yml From e609d9cdd7c81941203a1eb24a07871aa115debb Mon Sep 17 00:00:00 2001 From: Wei Ji <23487320+weiji14@users.noreply.github.com> Date: Tue, 29 Nov 2022 16:24:06 -0500 Subject: [PATCH 09/26] Pin to conda-lock 1.0.5 to keep relative paths See https://github.com/CryoInTheCloud/hub-image/issues/15. --- .github/workflows/conda-lock-command.yml | 2 +- postBuild | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/conda-lock-command.yml b/.github/workflows/conda-lock-command.yml index f40ee24..2b79c23 100644 --- a/.github/workflows/conda-lock-command.yml +++ b/.github/workflows/conda-lock-command.yml @@ -42,7 +42,7 @@ jobs: # Install conda-lock library - name: Install conda-lock - run: pip install conda-lock + run: pip install conda-lock==1.0.5 # Run "conda-lock" for linux-64 only - name: Run conda-lock diff --git a/postBuild b/postBuild index eceafe0..c9eaf68 100644 --- a/postBuild +++ b/postBuild @@ -1,4 +1,4 @@ #!/bin/bash set -eux -pip install conda-lock==1.2.1 +pip install conda-lock==1.0.5 conda-lock install --mamba --name cryocloud conda-lock.yml From 4ea512b992760202e88ac6b40b08af01cecf248f Mon Sep 17 00:00:00 2001 From: Wei Ji <23487320+weiji14@users.noreply.github.com> Date: Tue, 29 Nov 2022 16:42:40 -0500 Subject: [PATCH 10/26] Document how to update conda-lock.yml file in the main README.md Update instructions on how to add or update dependencies in the cryocloud docker image. Specifically, the part where `conda-lock` is used for a fully reproducible conda environment. --- README.md | 26 +++++++++++++++++--------- 1 file changed, 17 insertions(+), 9 deletions(-) diff --git a/README.md b/README.md index 2b2f88d..3dfc36d 100644 --- a/README.md +++ b/README.md @@ -6,14 +6,22 @@ The JupyterHub docker image used for [hub.cryointhecloud.com](https://cryointhecloud.com), hosted on https://quay.io/repository/cryointhecloud/cryo-hub-image -## Adding packages to this repository +## Updating packages in this repository -You can easily add more packages to the cryointhecloud hub by making pull requests to this -repository. Edit either the `environment-cryocloud.yml` file (for most packages) or `apt.txt` file -(for packages that need to be used in the Linux Desktop environment in the cloud), and make -a pull request - you can even do that just from the GitHub UI! A bot will comment with a link to -[mybinder.org](https://mybinder.org) where you can test your pull request to make sure it works -as you would expect. +You can add or update packages on the cryointhecloud hub by making pull requests to this +repository. Follow these steps: -Once your PR gets merged, you can follow the [2i2c docs](https://docs.2i2c.org/en/latest/admin/howto/configurator.html) -to have the hub use them! +1. Edit either the `environment-cryocloud.yml` file (for most packages) or `apt.txt` file + (for packages that need to be used in the Linux Desktop environment in the cloud) +2. Start a [pull request](https://github.com/CryoInTheCloud/hub-image/pulls) - + you can even do that just from the GitHub UI! A bot will comment with a link to + [mybinder.org](https://mybinder.org) where you can test your pull request to make sure it works + as you would expect. +3. In the Pull Request, write a comment with the slash command `/condalock`. + This will refresh the [`conda-lock.yml`](https://conda-incubator.github.io/conda-lock/output/#unified-lockfile) + file that contains a snapshot of the exact library versions that will be + used in the conda environment. + +Once your Pull Request gets reviewed and merged, you can follow the +[2i2c docs](https://docs.2i2c.org/en/latest/admin/howto/configurator.html) +to have the JupyterHub use them! From abb8710cbba5f02521094e7c8a50c755d6ad27e7 Mon Sep 17 00:00:00 2001 From: Wei Ji <23487320+weiji14@users.noreply.github.com> Date: Tue, 29 Nov 2022 16:48:28 -0500 Subject: [PATCH 11/26] Install conda-lock with pip_support extras Needed to avoid `Warning: found pip deps, but conda-lock was installed without pypi support. pip dependencies will not be included in the lock file`. See https://conda-incubator.github.io/conda-lock/getting_started. --- .github/workflows/conda-lock-command.yml | 2 +- postBuild | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/conda-lock-command.yml b/.github/workflows/conda-lock-command.yml index 2b79c23..4194115 100644 --- a/.github/workflows/conda-lock-command.yml +++ b/.github/workflows/conda-lock-command.yml @@ -42,7 +42,7 @@ jobs: # Install conda-lock library - name: Install conda-lock - run: pip install conda-lock==1.0.5 + run: pip install conda-lock[pip_support]==1.0.5 # Run "conda-lock" for linux-64 only - name: Run conda-lock diff --git a/postBuild b/postBuild index c9eaf68..bdd51ef 100644 --- a/postBuild +++ b/postBuild @@ -1,4 +1,4 @@ #!/bin/bash set -eux -pip install conda-lock==1.0.5 +pip install conda-lock[pip_support]==1.0.5 conda-lock install --mamba --name cryocloud conda-lock.yml From 33436bc05463739e5763b6085ab22da84e455935 Mon Sep 17 00:00:00 2001 From: Wei Ji <23487320+weiji14@users.noreply.github.com> Date: Tue, 29 Nov 2022 16:55:04 -0500 Subject: [PATCH 12/26] Run docker build and test workflow when conda-linux.yml is modified No more explicit conda-linux-64.lock, just the unified conda-lock.yml. --- .github/workflows/build.yaml | 2 +- .github/workflows/test.yaml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml index 6d35084..8396e45 100644 --- a/.github/workflows/build.yaml +++ b/.github/workflows/build.yaml @@ -6,7 +6,7 @@ on: - main paths: - 'apt.txt' - - 'conda-linux-64.lock' + - 'conda-linux.yml' - 'environment-cryocloud.yml' - 'postBuild' - 'start' diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml index 38d02b7..d600514 100644 --- a/.github/workflows/test.yaml +++ b/.github/workflows/test.yaml @@ -4,7 +4,7 @@ on: pull_request: paths: - 'apt.txt' - - 'conda-linux-64.lock' + - 'conda-linux.yml' - 'environment-cryocloud.yml' - 'postBuild' - 'start' From 3e084687eabfbaa5869bfb1c3eef8e93f210d451 Mon Sep 17 00:00:00 2001 From: Wei Ji <23487320+weiji14@users.noreply.github.com> Date: Tue, 29 Nov 2022 17:00:30 -0500 Subject: [PATCH 13/26] Pin minimum jupyterlab to 3.5 --- environment-cryocloud.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/environment-cryocloud.yml b/environment-cryocloud.yml index 10c6392..29e8dd6 100644 --- a/environment-cryocloud.yml +++ b/environment-cryocloud.yml @@ -12,7 +12,7 @@ dependencies: - nbgitpuller==1.1.1 # Specify major version of jupyterlab to use. Manually bump it when you want to upgrade # jupyterlab version - - jupyterlab>=3.0,<4.0 + - jupyterlab>=3.5,<4.0 # This provides memory usage stats on JupyterLab and classic notebook - jupyter-resource-usage==0.6.4 # https://syncthing.net/ provides a dropbox-like interface for syncing directories across users, From 85b01cbcce12c0f60b60d31a51667a6cba916abd Mon Sep 17 00:00:00 2001 From: actions-bot <58130806+actions-bot@users.noreply.github.com> Date: Tue, 29 Nov 2022 22:06:52 +0000 Subject: [PATCH 14/26] [condalock-command] autogenerated conda-lock files --- conda-lock.yml | 7868 +++++++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 7793 insertions(+), 75 deletions(-) diff --git a/conda-lock.yml b/conda-lock.yml index 1d539c2..64c54b3 100644 --- a/conda-lock.yml +++ b/conda-lock.yml @@ -17,7 +17,7 @@ metadata: - url: nodefaults used_env_vars: [] content_hash: - linux-64: 204146c4e8e9700bf19770089d10b073f3e20b78059e22fde23fbe9b39849f7c + linux-64: 306f1d23978e521817e01748181d8db854404c253278e650b2cf62864bfb118d platforms: - linux-64 sources: @@ -45,6 +45,50 @@ package: platform: linux-64 url: https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2022.9.24-ha878542_0.tar.bz2 version: 2022.9.24 +- category: main + dependencies: {} + hash: + md5: 0c96522c6bdaed4b1566d11387caaf45 + sha256: 58d7f40d2940dd0a8aa28651239adbf5613254df0f75789919c4e6762054403b + manager: conda + name: font-ttf-dejavu-sans-mono + optional: false + platform: linux-64 + url: https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2 + version: '2.37' +- category: main + dependencies: {} + hash: + md5: 34893075a5c9e55cdafac56607368fc6 + sha256: c52a29fdac682c20d252facc50f01e7c2e7ceac52aa9817aaf0bb83f7559ec5c + manager: conda + name: font-ttf-inconsolata + optional: false + platform: linux-64 + url: https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2 + version: '3.000' +- category: main + dependencies: {} + hash: + md5: 4d59c254e01d9cde7957100457e2d5fb + sha256: 00925c8c055a2275614b4d983e1df637245e19058d79fc7dd1a93b8d9fb4b139 + manager: conda + name: font-ttf-source-code-pro + optional: false + platform: linux-64 + url: https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2 + version: '2.038' +- category: main + dependencies: {} + hash: + md5: 19410c3df09dfb12d1206132a1d357c5 + sha256: 470d5db54102bd51dbb0c5990324a2f4a0bc976faa493b22193338adb9882e2e + manager: conda + name: font-ttf-ubuntu + optional: false + platform: linux-64 + url: https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-hab24e00_0.tar.bz2 + version: '0.83' - category: main dependencies: {} hash: @@ -56,6 +100,61 @@ package: platform: linux-64 url: https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.39-hcc3a1bd_1.conda version: '2.39' +- category: main + dependencies: {} + hash: + md5: 164b4b1acaedc47ee7e658ae6b308ca3 + sha256: 03ea784edd12037dc3a7a0078ff3f9c3383feabb34d5ba910bb2fd7a21a2d961 + manager: conda + name: libgfortran5 + optional: false + platform: linux-64 + url: https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-12.2.0-h337968e_19.tar.bz2 + version: 12.2.0 +- category: main + dependencies: {} + hash: + md5: 1030b1f38c129f2634eae026f704fe60 + sha256: 0289e6a7b9a5249161a3967909e12dcfb4ab4475cdede984635d3fb65c606f08 + manager: conda + name: libstdcxx-ng + optional: false + platform: linux-64 + url: https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-12.2.0-h46fd767_19.tar.bz2 + version: 12.2.0 +- category: main + dependencies: {} + hash: + md5: abc27381c4f005da588cffa1f76403ee + sha256: ccd2857627c0f6e903a917b99e60860c0a2b7dc553a32cf7c1ab55f0af99ec11 + manager: conda + name: poppler-data + optional: false + platform: linux-64 + url: https://conda.anaconda.org/conda-forge/noarch/poppler-data-0.4.11-hd8ed1ab_0.tar.bz2 + version: 0.4.11 +- category: main + dependencies: {} + hash: + md5: 4eb33d14d794b0f4be116443ffed3853 + sha256: bcb15db27eb6fbc0fe15d23aa60dcfa58ef451d92771441068d4a911aea7bb9f + manager: conda + name: python_abi + optional: false + platform: linux-64 + url: https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.10-3_cp310.conda + version: '3.10' +- category: main + dependencies: {} + hash: + md5: 026b4546d0c4f64d2836ce7a72f0e1f2 + sha256: 39456be0440a006d17a4de7e8b191a46311687c97ff8db7e6167bf7cffd1f3dc + manager: conda + name: syncthing + optional: false + platform: linux-64 + url: https://conda.anaconda.org/conda-forge/linux-64/syncthing-1.22.1-ha8f183a_0.tar.bz2 + version: 1.22.1 - category: main dependencies: {} hash: @@ -67,6 +166,33 @@ package: platform: linux-64 url: https://conda.anaconda.org/conda-forge/noarch/tzdata-2022f-h191b570_0.tar.bz2 version: 2022f +- category: main + dependencies: + font-ttf-dejavu-sans-mono: '' + font-ttf-inconsolata: '' + font-ttf-source-code-pro: '' + font-ttf-ubuntu: '' + hash: + md5: f766549260d6815b0c52253f1fb1bb29 + sha256: 53f23a3319466053818540bcdf2091f253cbdbab1e0e9ae7b9e509dcaa2a5e38 + manager: conda + name: fonts-conda-forge + optional: false + platform: linux-64 + url: https://conda.anaconda.org/conda-forge/noarch/fonts-conda-forge-1-0.tar.bz2 + version: '1' +- category: main + dependencies: + libgfortran5: 12.2.0 h337968e_19 + hash: + md5: cd7a806282c16e1f2d39a7e80d3a3e0d + sha256: c7d061f323e80fbc09564179073d8af303bf69b953b0caddcf79b47e352c746f + manager: conda + name: libgfortran-ng + optional: false + platform: linux-64 + url: https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-12.2.0-h69a702a_19.tar.bz2 + version: 12.2.0 - category: main dependencies: _libgcc_mutex: 0.1 conda_forge @@ -92,6 +218,18 @@ package: platform: linux-64 url: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2 version: '4.5' +- category: main + dependencies: + fonts-conda-forge: '' + hash: + md5: fee5683a3f04bd15cbd8318b096a27ab + sha256: a997f2f1921bb9c9d76e6fa2f6b408b7fa549edd349a77639c9fe7a23ea93e61 + manager: conda + name: fonts-conda-ecosystem + optional: false + platform: linux-64 + url: https://conda.anaconda.org/conda-forge/noarch/fonts-conda-ecosystem-1-0.tar.bz2 + version: '1' - category: main dependencies: _libgcc_mutex: 0.1 conda_forge @@ -105,6 +243,43 @@ package: platform: linux-64 url: https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-12.2.0-h65d4601_19.tar.bz2 version: 12.2.0 +- category: main + dependencies: + libgcc-ng: '>=12' + hash: + md5: be733e69048951df1e4b4b7bb8c7666f + sha256: 2c0a618d0fa695e4e01a30e7ff31094be540c52e9085cbd724edb132c65cf9cd + manager: conda + name: alsa-lib + optional: false + platform: linux-64 + url: https://conda.anaconda.org/conda-forge/linux-64/alsa-lib-1.2.8-h166bdaf_0.tar.bz2 + version: 1.2.8 +- category: main + dependencies: + libgcc-ng: '>=12' + libstdcxx-ng: '>=12' + hash: + md5: a08150fd2298460cd1fcccf626305642 + sha256: ed05f72ffa891e3c6a507eac6f0221c85c1f0611491328cd098308060740891c + manager: conda + name: aom + optional: false + platform: linux-64 + url: https://conda.anaconda.org/conda-forge/linux-64/aom-3.5.0-h27087fc_0.tar.bz2 + version: 3.5.0 +- category: main + dependencies: + libgcc-ng: '>=12' + hash: + md5: d9c69a24ad678ffce24c6543a0176b00 + sha256: 82c13b1772c21fc4a17441734de471d3aabf82b61db9b11f4a1bd04a9c4ac324 + manager: conda + name: attr + optional: false + platform: linux-64 + url: https://conda.anaconda.org/conda-forge/linux-64/attr-2.5.1-h166bdaf_1.tar.bz2 + version: 2.5.1 - category: main dependencies: libgcc-ng: '>=9.3.0' @@ -121,149 +296,7692 @@ package: dependencies: libgcc-ng: '>=9.4.0' hash: - md5: d645c6d2ac96843a2bfaccd2d62b3ac3 - sha256: ab6e9856c21709b7b517e940ae7028ae0737546122f83c2aa5d692860c3b149e + md5: f26ef8098fab1f719c91eb760d63381a + sha256: ee735e60d2cf68e5635df17847e97b505a752985d10581d2438203e7c0f44c15 manager: conda - name: libffi + name: c-ares optional: false 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manager: pip + name: jupyter-desktop-server + optional: false + platform: linux-64 + source: null + url: https://files.pythonhosted.org/packages/15/df/6f249cd3c3db684c8f9e67bc5470c4b593f882fbb03b1649f72ae7a26566/jupyter-desktop-server-0.1.3.tar.gz + version: 0.1.3 +- category: main + dependencies: + jupyter-server-proxy: '*' + hash: + sha256: f4550a7a4d22b97128743205a6ea001487f9f07c561befedaadc265670cc77f2 + manager: pip + name: jupyter-syncthing-proxy + optional: false + platform: linux-64 + source: null + url: https://files.pythonhosted.org/packages/4d/53/fc5f8fc3fa21aa463ec8002b25187e9e565753b6b0caf8bb3b020022497e/jupyter_syncthing_proxy-1.0.3-py3-none-any.whl + version: 1.0.3 version: 1 From f82355e17566921953c3fb66c0103e75a435f041 Mon Sep 17 00:00:00 2001 From: Wei Ji <23487320+weiji14@users.noreply.github.com> Date: Tue, 29 Nov 2022 17:11:57 -0500 Subject: [PATCH 15/26] Set notebook as conda environment name in docker image Follow the default environment name on the JupyterHub rather than the conda environment's name. --- postBuild | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/postBuild b/postBuild index bdd51ef..fecbeb7 100644 --- a/postBuild +++ b/postBuild @@ -1,4 +1,4 @@ #!/bin/bash set -eux pip install conda-lock[pip_support]==1.0.5 -conda-lock install --mamba --name cryocloud conda-lock.yml +conda-lock install --mamba --name notebook conda-lock.yml From f0b86fe5c9f12d45ff2d49f875fc3a04f4e735d2 Mon Sep 17 00:00:00 2001 From: Wei Ji <23487320+weiji14@users.noreply.github.com> Date: Tue, 29 Nov 2022 17:37:29 -0500 Subject: [PATCH 16/26] Bump conda-lock from 1.0.5 to 1.2.1 Also drop the pip_support extras since poetry has been vendored in conda-lock 1.2.0. --- .github/workflows/conda-lock-command.yml | 2 +- postBuild | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/conda-lock-command.yml b/.github/workflows/conda-lock-command.yml index 4194115..56003cc 100644 --- a/.github/workflows/conda-lock-command.yml +++ b/.github/workflows/conda-lock-command.yml @@ -42,7 +42,7 @@ jobs: # Install conda-lock library - name: Install conda-lock - run: pip install conda-lock[pip_support]==1.0.5 + run: pip install conda-lock==1.2.1 # Run "conda-lock" for linux-64 only - name: Run conda-lock diff --git a/postBuild b/postBuild index fecbeb7..994b3d0 100644 --- a/postBuild +++ b/postBuild @@ -1,4 +1,4 @@ #!/bin/bash set -eux -pip install conda-lock[pip_support]==1.0.5 +pip install conda-lock==1.2.1 conda-lock install --mamba --name notebook conda-lock.yml From 20ec34b12a17b13c34131b45e0dcbbe6b8b2c478 Mon Sep 17 00:00:00 2001 From: Wei Ji <23487320+weiji14@users.noreply.github.com> Date: Tue, 29 Nov 2022 17:47:00 -0500 Subject: [PATCH 17/26] Update conda-lock's dependency file source Using GitHub Actions hosted runner filepath. --- conda-lock.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/conda-lock.yml b/conda-lock.yml index 64c54b3..4ac3c63 100644 --- a/conda-lock.yml +++ b/conda-lock.yml @@ -9,7 +9,7 @@ # To update a single package to the latest version compatible with the version constraints in the source: # conda-lock lock --lockfile conda-lock.yml --update PACKAGE # To re-solve the entire environment, e.g. after changing a version constraint in the source file: -# conda-lock -f environment-cryocloud.yml --lockfile conda-lock.yml +# conda-lock -f /home/runner/work/hub-image/hub-image/environment-cryocloud.yml --lockfile conda-lock.yml metadata: channels: - url: conda-forge @@ -21,7 +21,7 @@ metadata: platforms: - linux-64 sources: - - environment-cryocloud.yml + - /home/runner/work/hub-image/hub-image/environment-cryocloud.yml package: - category: main dependencies: {} From 3c6a82636cdb6f3434fc6c87cda116208ac9a8b3 Mon Sep 17 00:00:00 2001 From: actions-bot <58130806+actions-bot@users.noreply.github.com> Date: Tue, 29 Nov 2022 22:52:24 +0000 Subject: [PATCH 18/26] [condalock-command] autogenerated conda-lock files --- conda-lock.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conda-lock.yml b/conda-lock.yml index 4ac3c63..789cd4c 100644 --- a/conda-lock.yml +++ b/conda-lock.yml @@ -17,7 +17,7 @@ metadata: - url: nodefaults used_env_vars: [] content_hash: - linux-64: 306f1d23978e521817e01748181d8db854404c253278e650b2cf62864bfb118d + linux-64: 5a6ca91550e4347aabd8cfaa7b7b35d4e58e2e8437a5abe9c500dcc1af52092f platforms: - linux-64 sources: From 70fb920df8f2b8dbe6b373541ae185ba421decc5 Mon Sep 17 00:00:00 2001 From: Wei Ji <23487320+weiji14@users.noreply.github.com> Date: Tue, 29 Nov 2022 17:58:52 -0500 Subject: [PATCH 19/26] Improvements to postBuild script Co-Authored-By: Yuvi Panda --- postBuild | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/postBuild b/postBuild index 994b3d0..f7a88ac 100644 --- a/postBuild +++ b/postBuild @@ -1,4 +1,4 @@ #!/bin/bash -set -eux -pip install conda-lock==1.2.1 +set -euxo pipefail +pip install --no-cache conda-lock==1.2.1 conda-lock install --mamba --name notebook conda-lock.yml From 7f9db0cba3d8ed472d215a21e10fde397864545a Mon Sep 17 00:00:00 2001 From: Wei Ji <23487320+weiji14@users.noreply.github.com> Date: Sat, 3 Dec 2022 22:54:17 -0500 Subject: [PATCH 20/26] Fix incorrect merge conflict omission Add back in the 'start'` file to `.github/workflows/build.yaml`. --- .github/workflows/build.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml index 10f355a..93bf948 100644 --- a/.github/workflows/build.yaml +++ b/.github/workflows/build.yaml @@ -9,6 +9,7 @@ on: - 'conda-linux.yml' - 'environment-cryocloud.yml' - 'postBuild' + - 'start' # Trigger rebuilds if the build process changes - '.github/workflows/build.yaml' From 27f3a8bb0d6d5be06b172689fe7d57a3034c7d04 Mon Sep 17 00:00:00 2001 From: Wei Ji <23487320+weiji14@users.noreply.github.com> Date: Sat, 3 Dec 2022 22:59:16 -0500 Subject: [PATCH 21/26] Delete 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-https://conda.anaconda.org/conda-forge/noarch/intake-esm-2022.9.18-pyhd8ed1ab_0.tar.bz2#821a4e9dbb2c98ee0be773d542279ea3 -https://conda.anaconda.org/conda-forge/noarch/intake-xarray-0.6.1-pyhd8ed1ab_0.tar.bz2#6cc318952c249b55ae83f8a994342672 -https://conda.anaconda.org/conda-forge/noarch/jupyter-syncthing-proxy-1.0.3-pyhd8ed1ab_0.conda#85c9949446d54c1b80c83e0357703174 -https://conda.anaconda.org/conda-forge/noarch/nbclassic-0.4.8-pyhd8ed1ab_0.tar.bz2#f4f150f83ed90a1b833e6081bbf38257 -https://conda.anaconda.org/conda-forge/noarch/nbdime-3.1.1-pyhd8ed1ab_0.tar.bz2#38dc061ffabe665b79f4c7c52cefa809 -https://conda.anaconda.org/conda-forge/noarch/sphinx-book-theme-0.3.3-pyhd8ed1ab_0.tar.bz2#390f64013f742aaeaf00fcbec4e1c30a -https://conda.anaconda.org/conda-forge/noarch/geoviews-core-1.9.5-pyha770c72_0.tar.bz2#8bd65a48d838db0a95c3ca14728c3fb5 -https://conda.anaconda.org/conda-forge/noarch/hvplot-0.8.2-pyhd8ed1ab_0.conda#71d0b1e7bbe769e41b56daa3392cf2f6 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-https://conda.anaconda.org/conda-forge/noarch/dask-labextension-6.0.0-pyhd8ed1ab_0.tar.bz2#32a0ba2d4b9ed598d90463d0032aace3 -https://conda.anaconda.org/conda-forge/noarch/icepyx-0.6.4-pyhd8ed1ab_0.tar.bz2#0d986191ee449128e844d9ea14713f0f -https://conda.anaconda.org/conda-forge/noarch/ipywidgets-7.7.2-pyhd8ed1ab_0.tar.bz2#cf7965a899292d3f5e253603eb92fada -https://conda.anaconda.org/conda-forge/noarch/jupyterhub-singleuser-3.0.0-pyh2a2186d_1.tar.bz2#24d635991b94687abb2b6b2f9d43d5af -https://conda.anaconda.org/conda-forge/noarch/ipyleaflet-0.17.2-pyhd8ed1ab_0.tar.bz2#fd8408ecf1e341f6aaafb7d3b5471ccc -https://conda.anaconda.org/conda-forge/noarch/ipympl-0.9.2-pyhd8ed1ab_0.tar.bz2#2a6a7f37cc8dd03a8a7439c34f557e0e -https://conda.anaconda.org/conda-forge/noarch/jupyter-sphinx-0.3.2-pyhd8ed1ab_1.tar.bz2#a47ca0f91417e5d29d075ca416254466 -https://conda.anaconda.org/conda-forge/noarch/myst-nb-0.13.2-pyhd8ed1ab_0.tar.bz2#800e968e63eb593c651a14907fd82d26 -https://conda.anaconda.org/conda-forge/noarch/jupyter-book-0.13.1-pyhd8ed1ab_0.tar.bz2#e112217ae1fccaa26c5c256ac0994d07 -# pip fastjsonschema @ https://files.pythonhosted.org/packages/e4/be/cf1b876348070a23cb0c3ebfee7a452ad3a91b07b456dade3bd514656009/fastjsonschema-2.16.2-py3-none-any.whl#sha256=21f918e8d9a1a4ba9c22e09574ba72267a6762d47822db9add95f6454e51cc1c -# pip py @ https://files.pythonhosted.org/packages/f6/f0/10642828a8dfb741e5f3fbaac830550a518a775c7fff6f04a007259b0548/py-1.11.0-py2.py3-none-any.whl#sha256=607c53218732647dff4acdfcd50cb62615cedf612e72d1724fb1a0cc6405b378 -# pip pywinpty @ https://files.pythonhosted.org/packages/22/77/59645ee028f410ef1d582fc2923d2cb61016ed38e6ae5022f405227ca2ad/pywinpty-2.0.9.tar.gz#sha256=01b6400dd79212f50a2f01af1c65b781290ff39610853db99bf03962eb9a615f -# pip jupyter-desktop-server @ https://files.pythonhosted.org/packages/15/df/6f249cd3c3db684c8f9e67bc5470c4b593f882fbb03b1649f72ae7a26566/jupyter-desktop-server-0.1.3.tar.gz#sha256=5915a2dbbe250f59b3cc01859297b26b2e1836e03a5db4bfbfd438005649d7e4 From 18b1b258e2d563b26e4a2644f72d9f409c531bf3 Mon Sep 17 00:00:00 2001 From: Wei Ji <23487320+weiji14@users.noreply.github.com> Date: Mon, 29 May 2023 09:36:02 +1200 Subject: [PATCH 22/26] Bump conda-lock to 2.0.0 --- .github/workflows/conda-lock-command.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/conda-lock-command.yml b/.github/workflows/conda-lock-command.yml index 39409b5..167555f 100644 --- a/.github/workflows/conda-lock-command.yml +++ b/.github/workflows/conda-lock-command.yml @@ -44,7 +44,7 @@ jobs: # HACK: Temporarily pin urllib3<2 to resolve incompatibilities: # https://github.com/ionrock/cachecontrol/issues/292 - name: Install conda-lock - run: 'pip install conda-lock "urllib3<2"' + run: 'pip install "conda-lock>=2.0.0" "urllib3<2"' # Run "conda-lock" for linux-64 only - name: Run conda-lock From 8353e4d0c044fb55b20d4c9e1f27e6b4130841f8 Mon Sep 17 00:00:00 2001 From: Wei Ji <23487320+weiji14@users.noreply.github.com> Date: Mon, 29 May 2023 09:47:32 +1200 Subject: [PATCH 23/26] Use conda-lock 2.0.0 in postBuild --- postBuild | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/postBuild b/postBuild index e433b2b..0f3d3e3 100644 --- a/postBuild +++ b/postBuild @@ -8,5 +8,5 @@ set -euo pipefail cp custom_jupyter_server_config.json ${NB_PYTHON_PREFIX}/etc/jupyter/jupyter_server_config.d/ cp custom_jupyter_server_config.json ${NB_PYTHON_PREFIX}/etc/jupyter/jupyter_notebook_config.d/ -pip install --no-cache conda-lock==1.2.1 +pip install --no-cache conda-lock>=2.0.0 conda-lock install --mamba --name notebook conda-lock.yml From 4a21b81eb6ace79fae6f0a5c3ac5a122289bfd81 Mon Sep 17 00:00:00 2001 From: Wei Ji <23487320+weiji14@users.noreply.github.com> Date: Mon, 29 May 2023 10:32:03 +1200 Subject: [PATCH 24/26] Update conda-lock.yml to v1 schema --- conda-lock.yml | 8294 +++++++++++++++++++++++++----------------------- 1 file changed, 4341 insertions(+), 3953 deletions(-) diff --git a/conda-lock.yml b/conda-lock.yml index 789cd4c..2c4525a 100644 --- a/conda-lock.yml +++ b/conda-lock.yml @@ -1,4 +1,4 @@ -# This lock file was generated by conda-lock (https://github.com/conda-incubator/conda-lock). DO NOT EDIT! +# This lock file was generated by conda-lock (https://github.com/conda/conda-lock). DO NOT EDIT! # # A "lock file" contains a concrete list of package versions (with checksums) to be installed. Unlike # e.g. `conda env create`, the resulting environment will not change as new package versions become @@ -7,1630 +7,1678 @@ # Install this environment as "YOURENV" with: # conda-lock install -n YOURENV --file conda-lock.yml # To update a single package to the latest version compatible with the version constraints in the source: -# conda-lock lock --lockfile conda-lock.yml --update PACKAGE +# conda-lock lock --lockfile conda-lock.yml --update PACKAGE # To re-solve the entire environment, e.g. after changing a version constraint in the source file: -# conda-lock -f /home/runner/work/hub-image/hub-image/environment-cryocloud.yml --lockfile conda-lock.yml +# conda-lock -f environment-cryocloud.yml --lockfile conda-lock.yml +version: 1 metadata: + content_hash: + linux-64: b3df9de583480bede1c611ef25f522f416eb12a42bc6160babdd917680b99c12 channels: - url: conda-forge used_env_vars: [] - - url: nodefaults - used_env_vars: [] - content_hash: - linux-64: 5a6ca91550e4347aabd8cfaa7b7b35d4e58e2e8437a5abe9c500dcc1af52092f platforms: - linux-64 sources: - - /home/runner/work/hub-image/hub-image/environment-cryocloud.yml + - environment-cryocloud.yml package: -- category: main +- name: _libgcc_mutex + version: '0.1' + manager: conda + platform: linux-64 dependencies: {} + url: https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2 hash: md5: d7c89558ba9fa0495403155b64376d81 sha256: fe51de6107f9edc7aa4f786a70f4a883943bc9d39b3bb7307c04c41410990726 - manager: conda - name: _libgcc_mutex + category: main optional: false +- name: ca-certificates + version: 2023.5.7 + manager: conda platform: linux-64 - url: https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2 - version: '0.1' -- category: main dependencies: {} + url: https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2023.5.7-hbcca054_0.conda hash: - md5: 41e4e87062433e283696cf384f952ef6 - sha256: 058355034667e77d15389700f6b2364cc74efce0af63a418eacc1ce252458942 - manager: conda - name: ca-certificates + md5: f5c65075fc34438d5b456c7f3f5ab695 + sha256: 0cf1bb3d0bfc5519b60af2c360fa4888fb838e1476b1e0f65b9dbc48b45c7345 + category: main optional: false +- name: font-ttf-dejavu-sans-mono + version: '2.37' + manager: conda platform: linux-64 - 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version: 1.0.3 -version: 1 From 71a2f4e1b0baea70cef9b1ca140566e883445ed3 Mon Sep 17 00:00:00 2001 From: Wei Ji <23487320+weiji14@users.noreply.github.com> Date: Sat, 10 Jun 2023 14:01:59 +1200 Subject: [PATCH 25/26] Fix typo conda-linux.yml to conda-lock.yml Co-authored-by: Matt Fisher --- .github/workflows/build.yaml | 2 +- .github/workflows/test.yaml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml index d2e85a8..b2a3251 100644 --- a/.github/workflows/build.yaml +++ b/.github/workflows/build.yaml @@ -6,7 +6,7 @@ on: - main paths: - 'apt.txt' - - 'conda-linux.yml' + - 'conda-lock.yml' - 'environment-cryocloud.yml' - 'postBuild' - 'start' diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml index 3db981b..fe2ad4d 100644 --- a/.github/workflows/test.yaml +++ b/.github/workflows/test.yaml @@ -4,7 +4,7 @@ on: pull_request: paths: - 'apt.txt' - - 'conda-linux.yml' + - 'conda-lock.yml' - 'environment-cryocloud.yml' - 'postBuild' - 'start' From 9c8e894587bbc0635f41315288f0a69e13fcea74 Mon Sep 17 00:00:00 2001 From: Wei Ji <23487320+weiji14@users.noreply.github.com> Date: Sat, 17 Jun 2023 13:07:40 +1200 Subject: [PATCH 26/26] Bump conda-lock from 2.0.0 to 2.1.0 Bumps [conda-lock](https://github.com/conda/conda-lock) from 2.0.0 to 2.1.0. - [Release notes](https://github.com/conda/conda-lock/releases) - [Commits](https://github.com/conda/conda-lock/compare/v2.0.0...v2.1.0) --- .github/workflows/conda-lock-command.yml | 2 +- postBuild | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/conda-lock-command.yml b/.github/workflows/conda-lock-command.yml index 167555f..6808e90 100644 --- a/.github/workflows/conda-lock-command.yml +++ b/.github/workflows/conda-lock-command.yml @@ -44,7 +44,7 @@ jobs: # HACK: Temporarily pin urllib3<2 to resolve incompatibilities: # https://github.com/ionrock/cachecontrol/issues/292 - name: Install conda-lock - run: 'pip install "conda-lock>=2.0.0" "urllib3<2"' + run: 'pip install "conda-lock>=2.1.0" "urllib3<2"' # Run "conda-lock" for linux-64 only - name: Run conda-lock diff --git a/postBuild b/postBuild index 0f3d3e3..6df81fc 100644 --- a/postBuild +++ b/postBuild @@ -8,5 +8,5 @@ set -euo pipefail cp custom_jupyter_server_config.json ${NB_PYTHON_PREFIX}/etc/jupyter/jupyter_server_config.d/ cp custom_jupyter_server_config.json ${NB_PYTHON_PREFIX}/etc/jupyter/jupyter_notebook_config.d/ -pip install --no-cache conda-lock>=2.0.0 +pip install --no-cache conda-lock>=2.1.0 conda-lock install --mamba --name notebook conda-lock.yml