From 5adbb27389b166dcfea82735cd99d875cbcdf537 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Fr=C3=A9d=C3=A9ric=20Collonval?=
 <fcollonval@users.noreply.github.com>
Date: Mon, 12 Jun 2023 10:09:54 +0200
Subject: [PATCH] Switch to JupyterLab 4 (#115)

* Update for lab 4.0

Relax more versions to get a valid resolution

Fix typo

Further resolution fixes

More unpinning and bumping (need recent Python to install Lab 4)

Commend out offline notebook extension

Unpin invoke, comment out C kernel

Formatting for pip

Reinstate x stack

Try without leading slash

xleaflet 0.17 does not exist?

Though it is tagged: https://github.com/jupyter-xeus/xleaflet/releases/tag/0.17.0

Unpin x stack

Comment out all x stack except for xeus-cling

Co-authored-by: krassowski <5832902+krassowski@users.noreply.github.com>

* Try fixing setup-miniconda config
> The env file works locally...

* Give anothter try

* Add note about use-only-tar-bz2

* Test no r packages on binder

* Restore r installation

* Don't use nodefaults for r task

* Pre install r packages
This will optimize the cached layer and hopefully solve the postBuild bug

* Another try

* back to the working commit without r

* Restore nodefaults for r task as we skip it for now.

---------

Co-authored-by: krassowski <5832902+krassowski@users.noreply.github.com>
---
 .binder/environment.yml    | 45 +++++++++++++++++++-------------------
 .binder/postBuild          |  2 +-
 .github/workflows/main.yml | 10 +++++----
 tasks.py                   |  8 ++-----
 4 files changed, 32 insertions(+), 33 deletions(-)

diff --git a/.binder/environment.yml b/.binder/environment.yml
index 7618afa..25c86ad 100644
--- a/.binder/environment.yml
+++ b/.binder/environment.yml
@@ -3,35 +3,35 @@ channels:
 - nodefaults
 dependencies:
 # !! you can only use single `=` to set a version. Otherwise it will break the update job
-- invoke=1.7.3
+- invoke=2.1.2
 - packaging
 - pyyaml
 # applications
-- jupyterlab=3.5.0
-- retrolab=0.3.21
-- nbconvert=7.2.5
+- jupyterlab=4.0.1
+- jupyter-collaboration=1.0.0
+- nbconvert=7.4.0
+- pip:
+  - notebook==7.0.0b3
 # extensions
-- jupyter-offlinenotebook=0.2
-- jupyterlab-fasta=3.2.0
-- jupyterlab-geojson=3.3.1
-- jupyterlab-link-share=0.2
+- jupyter-offlinenotebook=0.2.2
+- jupyterlab-fasta=3.3
+- jupyterlab-geojson=3.4
 # Python Kernel
-- ipykernel=6.16.2
+- ipykernel=6.23.1
 - xeus-python=0.14.3
-- ipywidgets=8.0.2
-- widgetsnbextension=4.0.3
-- ipyleaflet=0.17.2
-- altair=4.2.0
-- bqplot=0.12.36
-- dask=2021.10.0
-- matplotlib-base=3.5.3
-- pandas=1
+- ipywidgets=8
+- ipyleaflet=0.17.3
+- altair=5.0.1
+- bqplot=0.12.39
+- dask=2023.5.1
+- matplotlib-base=3.7.1
+- pandas=2.0.2
 - python=3.9
-- scikit-image=0.19.2
-- scikit-learn=1.0.2
-- seaborn=0.12.1
-- tensorflow=2
-- sympy=1.10.1
+- scikit-image=0.20.0
+- scikit-learn=1.2.2
+- seaborn-base=0.12.2
+- tensorflow=2.11.0
+- sympy=1.12
 - traittypes=0.2.1
 # C++ Kernel
 - xeus-cling=0.13.0
@@ -40,4 +40,5 @@ dependencies:
 - xwidgets=0.26.1
 - xleaflet=0.16.0
 # CLI tools
+- pip
 - vim
diff --git a/.binder/postBuild b/.binder/postBuild
index 4ce345d..d88715f 100644
--- a/.binder/postBuild
+++ b/.binder/postBuild
@@ -1,6 +1,6 @@
 set -ex
 
-invoke r --env-name=notebook
+# invoke r --env-name=notebook
 invoke demofiles
 invoke talk -t demo
 rm -rf demofiles
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 810a146..f310cd6 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -26,12 +26,14 @@ jobs:
             ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('.binder/environment.yml') }}
       - uses: conda-incubator/setup-miniconda@v2
         with:
-          mamba-version: "*"
-          channels: conda-forge,defaults
-          channel-priority: true
+          mamba-version: ">=1.4.0"
+          # Defaults is added automatically
+          channels: conda-forge
+          channel-priority: "strict"
           activate-environment: jupyterlab-demo
           environment-file: .binder/environment.yml
-          use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
+          # The following option is blocking the environment resolution (newer versions are not found)
+          # use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
       - run: |
           conda info
           conda list
diff --git a/tasks.py b/tasks.py
index 35467be..6e5897d 100644
--- a/tasks.py
+++ b/tasks.py
@@ -61,10 +61,8 @@ def build(ctx, env_name=env_name, kernel=True):
     """
 
     if kernel:
-        path = os.environ.get("PATH")
         ctx.run(
-            f"{source!s} activate {env_name!s} && ipython kernel install --name {env_name!s} --display-name {env_name!s} --sys-prefix",
-            env={"PATH": f"{activate_path()}:{path}"},
+            f"conda run -n {env_name!s} ipython kernel install --name {env_name!s} --display-name {env_name!s} --sys-prefix"
         )
 
 
@@ -178,10 +176,8 @@ def r(ctx, env_name=env_name):
     """
     Installs the r kernel and associated libs.
     """
-    path = os.environ.get("PATH")
     ctx.run(
-        f"{source!s} activate {env_name!s} && mamba install -yc conda-forge -c nodefaults r-irkernel r-ggplot2",
-        env={"PATH": f"{activate_path()}:{path}"},
+        f"mamba install -yn {env_name!s} -c conda-forge -c nodefaults r-irkernel r-ggplot2",
     )