From 8c4c7c477620d2a3a579a8ad94f506fbdc4d69a7 Mon Sep 17 00:00:00 2001 From: Long Vu Date: Sat, 24 Jul 2021 10:33:58 -0400 Subject: [PATCH 01/14] docker: unpin jupyterlab to get v3, hopefully to fix jupyterlab-system-monitor jupyterlab-system-monitor has not been working with jupyterlab v2 --- docker/environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docker/environment.yml b/docker/environment.yml index 5612a01d..6e0f5044 100644 --- a/docker/environment.yml +++ b/docker/environment.yml @@ -91,7 +91,7 @@ dependencies: - jupyter # to be launched by image jupyterhub/jupyterhub - notebook - - jupyterlab==2.2.9 + - jupyterlab - jupyterhub # to diff .ipynb files - nbdime From b290b7919341df4205173c81fd37f516ba4cec8c Mon Sep 17 00:00:00 2001 From: Long Vu Date: Mon, 26 Jul 2021 13:07:23 -0400 Subject: [PATCH 02/14] docker: new jupyter-topbar install instructions for jupyterlab v3 --- docker/Dockerfile | 6 +----- docker/environment.yml | 2 ++ 2 files changed, 3 insertions(+), 5 deletions(-) diff --git a/docker/Dockerfile b/docker/Dockerfile index 152f3ab2..804f8624 100644 --- a/docker/Dockerfile +++ b/docker/Dockerfile @@ -44,11 +44,7 @@ RUN jupyter labextension install @jupyter-widgets/jupyterlab-manager \ && jupyter labextension install @pyviz/jupyterlab_pyviz \ && jupyter labextension install @jupyterlab/debugger \ && jupyter labextension install @jupyterlab/google-drive \ - && jupyter labextension install jupyterlab-topbar-extension \ - jupyterlab-system-monitor \ - jupyterlab-topbar-text \ - jupyterlab-logout \ - jupyterlab-theme-toggle \ + && jupyter labextension install jupyterlab-topbar-text \ jupyterlab_conda # && jupyter labextension install jupyterlab-clipboard diff --git a/docker/environment.yml b/docker/environment.yml index 6e0f5044..f8d0e211 100644 --- a/docker/environment.yml +++ b/docker/environment.yml @@ -104,6 +104,8 @@ dependencies: # Voila turns Jupyter notebooks into standalone web applications - voila - jupyter-archive + # https://github.com/jtpio/jupyterlab-topbar + - jupyterlab-topbar # xeus-python: back-end kernel implementing the Jupyter Debug Protocol - xeus-python - jupyter-dash From f9f1d73ccc1caf654326a654ef9a1558b8480597 Mon Sep 17 00:00:00 2001 From: Long Vu Date: Mon, 26 Jul 2021 13:16:46 -0400 Subject: [PATCH 03/14] docker: unpin pandas as xarray issue pydata/xarray/issues/5588 fixed --- docker/environment.yml | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/docker/environment.yml b/docker/environment.yml index f8d0e211..c6d4fa6a 100644 --- a/docker/environment.yml +++ b/docker/environment.yml @@ -23,9 +23,7 @@ dependencies: - rasterio - gdal # for osgeo - geopandas - # Pin pandas due to xarray - # https://github.com/pydata/xarray/issues/5588#issuecomment-885271773 - - pandas==1.2.5 + - pandas - rioxarray - scikit-image - ipyleaflet From e67dc471c1be0be933b9f7bf8feb30069a8fff37 Mon Sep 17 00:00:00 2001 From: Long Vu Date: Mon, 26 Jul 2021 15:39:56 -0400 Subject: [PATCH 04/14] docker: update jupyter_bokeh install step for jupyterlab v3 --- docker/Dockerfile | 1 - 1 file changed, 1 deletion(-) diff --git a/docker/Dockerfile b/docker/Dockerfile index 804f8624..c7e879d3 100644 --- a/docker/Dockerfile +++ b/docker/Dockerfile @@ -40,7 +40,6 @@ RUN jupyter lab build RUN jupyter labextension install @jupyter-widgets/jupyterlab-manager \ && jupyter serverextension enable voila --sys-prefix \ && jupyter labextension install @jupyter-widgets/jupyterlab-manager jupyter-leaflet \ - && jupyter labextension install @bokeh/jupyter_bokeh \ && jupyter labextension install @pyviz/jupyterlab_pyviz \ && jupyter labextension install @jupyterlab/debugger \ && jupyter labextension install @jupyterlab/google-drive \ From 21ae5729cb4aa611e977b8c58fad48c31f4555b3 Mon Sep 17 00:00:00 2001 From: Long Vu Date: Mon, 26 Jul 2021 16:02:40 -0400 Subject: [PATCH 05/14] docker: update jupyterlab_pyviz install instruction for jupyterlab v3 --- docker/Dockerfile | 1 - docker/environment.yml | 2 ++ 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/docker/Dockerfile b/docker/Dockerfile index c7e879d3..48205331 100644 --- a/docker/Dockerfile +++ b/docker/Dockerfile @@ -40,7 +40,6 @@ RUN jupyter lab build RUN jupyter labextension install @jupyter-widgets/jupyterlab-manager \ && jupyter serverextension enable voila --sys-prefix \ && jupyter labextension install @jupyter-widgets/jupyterlab-manager jupyter-leaflet \ - && jupyter labextension install @pyviz/jupyterlab_pyviz \ && jupyter labextension install @jupyterlab/debugger \ && jupyter labextension install @jupyterlab/google-drive \ && jupyter labextension install jupyterlab-topbar-text \ diff --git a/docker/environment.yml b/docker/environment.yml index c6d4fa6a..cb2c730e 100644 --- a/docker/environment.yml +++ b/docker/environment.yml @@ -35,6 +35,8 @@ dependencies: - pscript - h5netcdf - panel + # https://github.com/holoviz/panel + - pyviz_comms - holoviews - geoviews # this might still be relevant https://github.com/holoviz/hvplot/issues/498 From aeb37ec7d3a1e1827b2ee8cfa3a597d953762a59 Mon Sep 17 00:00:00 2001 From: Long Vu Date: Mon, 26 Jul 2021 16:40:45 -0400 Subject: [PATCH 06/14] docker: remove jupyterlab/google-drive since it still does not support jupyterlab v3 ``` Step 11/20 : RUN jupyter labextension install @jupyter-widgets/jupyterlab-manager && jupyter serverextension enable voila --sys-prefix && jupyter labextension install @jupyter-widgets/jupyterlab-manager jupyter-leaflet && jupyter labextension install @jupyterlab/debugger && jupyter labextension install @jupyterlab/google-drive && jupyter labextension install jupyterlab-topbar-text jupyterlab_conda ---> Running in 96e4392006b2 Building jupyterlab assets (production, minimized) Enabling: voila - Writing config: /opt/conda/envs/birdy/etc/jupyter - Validating... voila 0.2.10 OK Building jupyterlab assets (production, minimized) Building jupyterlab assets (production, minimized) \ An error occured. ValueError: The extension "@jupyterlab/google-drive" does not yet support the current version of JupyterLab. Conflicting Dependencies: JupyterLab Extension Package >=3.0.11 <3.1.0 >=2.0.0 <3.0.0 @jupyterlab/application >=3.0.9 <3.1.0 >=2.0.0 <3.0.0 @jupyterlab/apputils >=5.0.6 <5.1.0 >=4.0.0 <5.0.0 @jupyterlab/coreutils >=3.0.11 <3.1.0 >=2.0.0 <3.0.0 @jupyterlab/docmanager >=3.0.11 <3.1.0 >=2.0.0 <3.0.0 @jupyterlab/filebrowser >=3.0.9 <3.1.0 >=2.0.0 <3.0.0 @jupyterlab/mainmenu >=6.0.9 <6.1.0 >=5.0.0 <6.0.0 @jupyterlab/services >=3.0.6 <3.1.0 >=2.0.0 <3.0.0 @jupyterlab/settingregistry See the log file for details: /tmp/jupyterlab-debug-shgkoz6v.log The command '/bin/sh -c jupyter labextension install @jupyter-widgets/jupyterlab-manager && jupyter serverextension enable voila --sys-prefix && jupyter labextension install @jupyter-widgets/jupyterlab-manager jupyter-leaflet && jupyter labextension install @jupyterlab/debugger && jupyter labextension install @jupyterlab/google-drive && jupyter labextension install jupyterlab-topbar-text jupyterlab_conda' returned a non-zero code: 1 ``` --- docker/Dockerfile | 1 - 1 file changed, 1 deletion(-) diff --git a/docker/Dockerfile b/docker/Dockerfile index 48205331..f6ebef43 100644 --- a/docker/Dockerfile +++ b/docker/Dockerfile @@ -41,7 +41,6 @@ RUN jupyter labextension install @jupyter-widgets/jupyterlab-manager \ && jupyter serverextension enable voila --sys-prefix \ && jupyter labextension install @jupyter-widgets/jupyterlab-manager jupyter-leaflet \ && jupyter labextension install @jupyterlab/debugger \ - && jupyter labextension install @jupyterlab/google-drive \ && jupyter labextension install jupyterlab-topbar-text \ jupyterlab_conda # && jupyter labextension install jupyterlab-clipboard From 6d017ddabc41e1a2ebb5babb6ed7459d78803e13 Mon Sep 17 00:00:00 2001 From: Long Vu Date: Mon, 26 Jul 2021 16:55:39 -0400 Subject: [PATCH 07/14] docker: new install instruction for jupyterlab_conda for jupyterlab v3 --- docker/Dockerfile | 3 +-- docker/environment.yml | 2 ++ 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/docker/Dockerfile b/docker/Dockerfile index f6ebef43..8c3f6ab5 100644 --- a/docker/Dockerfile +++ b/docker/Dockerfile @@ -41,8 +41,7 @@ RUN jupyter labextension install @jupyter-widgets/jupyterlab-manager \ && jupyter serverextension enable voila --sys-prefix \ && jupyter labextension install @jupyter-widgets/jupyterlab-manager jupyter-leaflet \ && jupyter labextension install @jupyterlab/debugger \ - && jupyter labextension install jupyterlab-topbar-text \ - jupyterlab_conda + && jupyter labextension install jupyterlab-topbar-text # && jupyter labextension install jupyterlab-clipboard ADD https://raw.githubusercontent.com/jupyter/docker-stacks/master/base-notebook/start.sh /usr/local/bin/ diff --git a/docker/environment.yml b/docker/environment.yml index cb2c730e..808cb458 100644 --- a/docker/environment.yml +++ b/docker/environment.yml @@ -93,6 +93,8 @@ dependencies: - notebook - jupyterlab - jupyterhub + # https://github.com/mamba-org/gator (was jupyter_conda) + - mamba_gator # to diff .ipynb files - nbdime # extension to produce .py files from notebook .ipynb files From d370904d21a5e9623e155fb61a41c9b43896679b Mon Sep 17 00:00:00 2001 From: Long Vu Date: Tue, 27 Jul 2021 14:19:38 -0400 Subject: [PATCH 08/14] docker: jupyterlab/debugger enabled by default in jupyterlab v3 See https://blog.jupyter.org/jupyterlab-3-0-is-out-4f58385e25bb --- docker/Dockerfile | 1 - 1 file changed, 1 deletion(-) diff --git a/docker/Dockerfile b/docker/Dockerfile index 8c3f6ab5..cc34aa96 100644 --- a/docker/Dockerfile +++ b/docker/Dockerfile @@ -40,7 +40,6 @@ RUN jupyter lab build RUN jupyter labextension install @jupyter-widgets/jupyterlab-manager \ && jupyter serverextension enable voila --sys-prefix \ && jupyter labextension install @jupyter-widgets/jupyterlab-manager jupyter-leaflet \ - && jupyter labextension install @jupyterlab/debugger \ && jupyter labextension install jupyterlab-topbar-text # && jupyter labextension install jupyterlab-clipboard From 2941ed39401fc43967209fa0434dc825ef4783c9 Mon Sep 17 00:00:00 2001 From: Long Vu Date: Tue, 27 Jul 2021 14:36:12 -0400 Subject: [PATCH 09/14] docker: forgot to remove old jupyter_conda package, replaced by mamba_gator --- docker/environment.yml | 2 -- 1 file changed, 2 deletions(-) diff --git a/docker/environment.yml b/docker/environment.yml index 808cb458..4a27c7a7 100644 --- a/docker/environment.yml +++ b/docker/environment.yml @@ -101,8 +101,6 @@ dependencies: - jupytext # jupyterlab extension for git - jupyterlab-git - # jupyterlab extension for conda - - jupyter_conda # Voila turns Jupyter notebooks into standalone web applications - voila - jupyter-archive From 405b1896441db0a1e5a4790a54d1e408b991df96 Mon Sep 17 00:00:00 2001 From: Long Vu Date: Tue, 27 Jul 2021 14:41:41 -0400 Subject: [PATCH 10/14] docker: doc pyviz_comms is replacement for labextension pyviz/jupyterlab_pyviz in jupyterlab v2 --- docker/environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docker/environment.yml b/docker/environment.yml index 4a27c7a7..2196cb9e 100644 --- a/docker/environment.yml +++ b/docker/environment.yml @@ -36,7 +36,7 @@ dependencies: - h5netcdf - panel # https://github.com/holoviz/panel - - pyviz_comms + - pyviz_comms # (was labextension pyviz/jupyterlab_pyviz in jupyterlab v2) - holoviews - geoviews # this might still be relevant https://github.com/holoviz/hvplot/issues/498 From a133151e58711d330c8afb9ad933c139e17f235b Mon Sep 17 00:00:00 2001 From: Long Vu Date: Tue, 27 Jul 2021 14:53:31 -0400 Subject: [PATCH 11/14] docker: jupyterlab-system-monitor is now separated from jupyterlab-topbar --- docker/environment.yml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/docker/environment.yml b/docker/environment.yml index 2196cb9e..c0507a61 100644 --- a/docker/environment.yml +++ b/docker/environment.yml @@ -106,6 +106,10 @@ dependencies: - jupyter-archive # https://github.com/jtpio/jupyterlab-topbar - jupyterlab-topbar + # https://github.com/jtpio/jupyterlab-system-monitor (was from jupyterlab-topbar) + - jupyterlab-system-monitor + - jupyter-resource-usage # needed by jupyterlab-system-monitor + - nbresuse # needed by jupyterlab-system-monitor # xeus-python: back-end kernel implementing the Jupyter Debug Protocol - xeus-python - jupyter-dash @@ -128,8 +132,6 @@ dependencies: # https://github.com/ShopRunner/jupyter-notify # Jupyter Magic For Browser Notifications of Cell Completion. - jupyternotify - # Needed for https://github.com/jtpio/jupyterlab-topbar - - nbresuse # Needed to run notebook tests. Missing indirect recursive dependencies # somewhere, should not need to manually add it here. - pytest-tornasync From 7b1f54817b5cdf0d2b45b6cd870d7e0fbf83af18 Mon Sep 17 00:00:00 2001 From: Long Vu Date: Tue, 27 Jul 2021 14:59:40 -0400 Subject: [PATCH 12/14] docker: jupyterlab-logout is now separated from jupyterlab-topbar --- docker/environment.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/docker/environment.yml b/docker/environment.yml index c0507a61..ea589fb4 100644 --- a/docker/environment.yml +++ b/docker/environment.yml @@ -132,6 +132,8 @@ dependencies: # https://github.com/ShopRunner/jupyter-notify # Jupyter Magic For Browser Notifications of Cell Completion. - jupyternotify + # https://github.com/jupyterlab-contrib/jupyterlab-logout (was from jupyterlab-topbar) + - jupyterlab-logout # Needed to run notebook tests. Missing indirect recursive dependencies # somewhere, should not need to manually add it here. - pytest-tornasync From 08ff486cafc5e11626e1efbd8f1997f943ca1366 Mon Sep 17 00:00:00 2001 From: Long Vu Date: Tue, 27 Jul 2021 15:14:01 -0400 Subject: [PATCH 13/14] docker: jupyterlab-theme-toggle seems to still be part of jupyterlab-topbar --- docker/Dockerfile | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/docker/Dockerfile b/docker/Dockerfile index cc34aa96..00195c34 100644 --- a/docker/Dockerfile +++ b/docker/Dockerfile @@ -40,7 +40,8 @@ RUN jupyter lab build RUN jupyter labextension install @jupyter-widgets/jupyterlab-manager \ && jupyter serverextension enable voila --sys-prefix \ && jupyter labextension install @jupyter-widgets/jupyterlab-manager jupyter-leaflet \ - && jupyter labextension install jupyterlab-topbar-text + && jupyter labextension install jupyterlab-topbar-text \ + jupyterlab-theme-toggle # && jupyter labextension install jupyterlab-clipboard ADD https://raw.githubusercontent.com/jupyter/docker-stacks/master/base-notebook/start.sh /usr/local/bin/ From bcdb05cf402b83ee881fd6d785496ff89072846d Mon Sep 17 00:00:00 2001 From: Long Vu Date: Wed, 28 Jul 2021 13:55:34 -0400 Subject: [PATCH 14/14] release: update to use image pavics/workflow-tests:210728 --- Jenkinsfile | 2 +- binder/Dockerfile | 2 +- launchcontainer | 2 +- launchnotebook | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/Jenkinsfile b/Jenkinsfile index 8877b1ba..80d60b49 100644 --- a/Jenkinsfile +++ b/Jenkinsfile @@ -10,7 +10,7 @@ pipeline { // https://jenkins.io/doc/book/pipeline/syntax/ agent { docker { - image "pavics/workflow-tests:210723" + image "pavics/workflow-tests:210728" label 'linux && docker' } } diff --git a/binder/Dockerfile b/binder/Dockerfile index e702d7dd..55106612 100644 --- a/binder/Dockerfile +++ b/binder/Dockerfile @@ -1,4 +1,4 @@ -FROM pavics/workflow-tests:210723 +FROM pavics/workflow-tests:210728 USER root diff --git a/launchcontainer b/launchcontainer index 6f680d63..4fbf5ebd 100755 --- a/launchcontainer +++ b/launchcontainer @@ -1,7 +1,7 @@ #!/bin/sh -x if [ -z "$DOCKER_IMAGE" ]; then - DOCKER_IMAGE="pavics/workflow-tests:210723" + DOCKER_IMAGE="pavics/workflow-tests:210728" fi if [ -z "$CONTAINER_NAME" ]; then diff --git a/launchnotebook b/launchnotebook index be86e4a5..a974ce8e 100755 --- a/launchnotebook +++ b/launchnotebook @@ -7,7 +7,7 @@ if [ -z "$PORT" ]; then fi if [ -z "$DOCKER_IMAGE" ]; then - DOCKER_IMAGE="pavics/workflow-tests:210723" + DOCKER_IMAGE="pavics/workflow-tests:210728" fi if [ -z "$CONTAINER_NAME" ]; then