Merge branch 'main' into python3.13

Author: mathbunnyru

.pre-commit-config.yaml

@@ -47,7 +47,6 @@ repos:
             "requests",
             "urllib3",
             "types-beautifulsoup4",
-            "types-PyYAML",
             "types-requests",
             "types-tabulate",
             "types-urllib3",
@@ -124,21 +123,21 @@ repos:
 
   # Lint: Markdown
   - repo: https://github.com/igorshubovych/markdownlint-cli
-    rev: v0.42.0
+    rev: v0.43.0
     hooks:
       - id: markdownlint
         args: ["--fix"]
 
   # Strip output from Jupyter notebooks
   - repo: https://github.com/kynan/nbstripout
-    rev: 0.8.0
+    rev: 0.8.1
     hooks:
       - id: nbstripout
 
   # nbQA provides tools from the Python ecosystem like
   # pyupgrade, isort, black, and flake8, adjusted for notebooks.
   - repo: https://github.com/nbQA-dev/nbQA
-    rev: 1.8.7
+    rev: 1.9.1
     hooks:
       - id: nbqa-pyupgrade
         args: [--py39-plus]

CHANGELOG.md

@@ -9,6 +9,13 @@ Affected: all images.
 
 - **Breaking:** `docker-stacks-foundation`: switch to Python 3.13 ([#2163](https://github.com/jupyter/docker-stacks/pull/2163)).
 
+## 2024-12-03
+
+Affected: all images.
+
+- **Breaking:** Switch to `mamba` v2 ([#2147](https://github.com/jupyter/docker-stacks/pull/2147)).
+  More information about changes made: <https://mamba.readthedocs.io/en/latest/developer_zone/changes-2.0.html>.
+
 ## 2024-11-08
 
 Affected: all images except `docker-stacks-foundation`.

README.md

@@ -29,11 +29,11 @@ Older images are available on Docker Hub, but they will no longer be updated.
 
 ### Example 1
 
-This command pulls the `jupyter/scipy-notebook` image tagged `2024-10-07` from Quay.io if it is not already present on the local host.
+This command pulls the `jupyter/scipy-notebook` image tagged `2024-11-19` from Quay.io if it is not already present on the local host.
 It then starts a container running a Jupyter Server with the JupyterLab frontend and exposes the container's internal port `8888` to port `10000` of the host machine:
 
 ```bash
-docker run -p 10000:8888 quay.io/jupyter/scipy-notebook:2024-10-07
+docker run -p 10000:8888 quay.io/jupyter/scipy-notebook:2024-11-19
 ```
 
 You can modify the port on which the container's port is exposed by [changing the value of the `-p` option](https://docs.docker.com/engine/containers/run/#exposed-ports) to `-p 8888:8888`.
@@ -48,11 +48,11 @@ The container remains intact for restart after the Server exits.
 
 ### Example 2
 
-This command pulls the `jupyter/datascience-notebook` image tagged `2024-10-07` from Quay.io if it is not already present on the local host.
+This command pulls the `jupyter/datascience-notebook` image tagged `2024-11-19` from Quay.io if it is not already present on the local host.
 It then starts an _ephemeral_ container running a Jupyter Server with the JupyterLab frontend and exposes the server on host port 10000.
 
 ```bash
-docker run -it --rm -p 10000:8888 -v "${PWD}":/home/jovyan/work quay.io/jupyter/datascience-notebook:2024-10-07
+docker run -it --rm -p 10000:8888 -v "${PWD}":/home/jovyan/work quay.io/jupyter/datascience-notebook:2024-11-19
 ```
 
 The use of the `-v` flag in the command mounts the current working directory on the host (`${PWD}` in the example command) as `/home/jovyan/work` in the container.

binder/Dockerfile

@@ -4,7 +4,7 @@
 # https://quay.io/repository/jupyter/base-notebook?tab=tags
 ARG REGISTRY=quay.io
 ARG OWNER=jupyter
-ARG BASE_IMAGE=$REGISTRY/$OWNER/base-notebook:2024-10-07
+ARG BASE_IMAGE=$REGISTRY/$OWNER/base-notebook:2024-11-19
 FROM $BASE_IMAGE
 
 LABEL maintainer="Jupyter Project <[email protected]>"
@@ -13,7 +13,7 @@ LABEL maintainer="Jupyter Project <[email protected]>"
 # Fix: https://github.com/koalaman/shellcheck/wiki/SC3014
 SHELL ["/bin/bash", "-o", "pipefail", "-c"]
 
-ENV TAG="2024-10-07"
+ENV TAG="2024-11-19"
 
 COPY --chown=${NB_UID}:${NB_GID} binder/README.ipynb "${HOME}"/README.ipynb
 

docs/using/running.md

@@ -15,12 +15,12 @@ The following are some common patterns.
 
 ### Example 1
 
-This command pulls the `jupyter/scipy-notebook` image tagged `2024-10-07` from Quay.io if it is not already present on the local host.
+This command pulls the `jupyter/scipy-notebook` image tagged `2024-11-19` from Quay.io if it is not already present on the local host.
 It then starts a container running Jupyter Server with the JupyterLab frontend and exposes the server on host port 8888.
 The server logs appear in the terminal and include a URL to the server.
 
 ```bash
-docker run -it -p 8888:8888 quay.io/jupyter/scipy-notebook:2024-10-07
+docker run -it -p 8888:8888 quay.io/jupyter/scipy-notebook:2024-11-19
 
 # Entered start.sh with args: jupyter lab
 
@@ -39,7 +39,7 @@ Pressing `Ctrl-C` twice shuts down the Server but leaves the container intact on
 # list containers
 docker ps --all
 # CONTAINER ID   IMAGE                                       COMMAND                  CREATED              STATUS                     PORTS     NAMES
-# eca4aa01751c   quay.io/jupyter/scipy-notebook:2024-10-07   "tini -g -- start-no…"   About a minute ago   Exited (0) 5 seconds ago             silly_panini
+# eca4aa01751c   quay.io/jupyter/scipy-notebook:2024-11-19   "tini -g -- start-no…"   About a minute ago   Exited (0) 5 seconds ago             silly_panini
 
 # start the stopped container
 docker start --attach -i eca4aa01751c
@@ -53,12 +53,12 @@ docker rm eca4aa01751c
 
 ### Example 2
 
-This command pulls the `jupyter/r-notebook` image tagged `2024-10-07` from Quay.io if it is not already present on the local host.
+This command pulls the `jupyter/r-notebook` image tagged `2024-11-19` from Quay.io if it is not already present on the local host.
 It then starts a container running Server and exposes the server on host port 10000.
 The server logs appear in the terminal and include a URL to the Server but with the internal container port (8888) instead of the correct host port (10000).
 
 ```bash
-docker run -it --rm -p 10000:8888 -v "${PWD}":/home/jovyan/work quay.io/jupyter/r-notebook:2024-10-07
+docker run -it --rm -p 10000:8888 -v "${PWD}":/home/jovyan/work quay.io/jupyter/r-notebook:2024-11-19
 ```
 
 Pressing `Ctrl-C` twice shuts down the Server and immediately destroys the Docker container.
@@ -138,7 +138,7 @@ subuidSize=$(( $(podman info --format "{{ range .Host.IDMappings.UIDMap }}+{{.Si
 subgidSize=$(( $(podman info --format "{{ range .Host.IDMappings.GIDMap }}+{{.Size }}{{end }}" ) - 1 ))
 ```
 
-This command pulls the `quay.io/jupyter/r-notebook` image tagged `2024-10-07` from Quay.io if it is not already present on the local host.
+This command pulls the `quay.io/jupyter/r-notebook` image tagged `2024-11-19` from Quay.io if it is not already present on the local host.
 It then starts a container running a Jupyter Server with the JupyterLab frontend and exposes the server on host port 10000.
 The server logs appear in the terminal and include a URL to the server but with the internal container port (8888) instead of the correct host port (10000).
 
@@ -147,7 +147,7 @@ podman run -it --rm -p 10000:8888 \
     -v "${PWD}":/home/jovyan/work --user $uid:$gid \
     --uidmap $uid:0:1 --uidmap 0:1:$uid --uidmap $(($uid+1)):$(($uid+1)):$(($subuidSize-$uid)) \
     --gidmap $gid:0:1 --gidmap 0:1:$gid --gidmap $(($gid+1)):$(($gid+1)):$(($subgidSize-$gid)) \
-    quay.io/jupyter/r-notebook:2024-10-07
+    quay.io/jupyter/r-notebook:2024-11-19
 ```
 
 ```{warning}

images/docker-stacks-foundation/Dockerfile

@@ -124,9 +124,8 @@ RUN set -x && \
         --prefix="${CONDA_DIR}" \
         --yes \
         'jupyter_core' \
-        # excluding mamba 2.X due to several breaking changes
-        # https://github.com/jupyter/docker-stacks/pull/2147
-        'mamba<2.0.0' \
+        'conda' \
+        'mamba' \
         "${PYTHON_SPECIFIER}" && \
     rm -rf /tmp/bin/ && \
     # Pin major.minor version of python

requirements-dev.txt

@@ -6,6 +6,5 @@ pytest-retry
 # `pytest-xdist` is a plugin that provides the `--numprocesses` flag,
 # allowing us to run `pytest` tests in parallel
 pytest-xdist
-PyYAML
 requests
 tabulate

tests/docker-stacks-foundation/test_packages.py

@@ -70,16 +70,15 @@
 EXCLUDED_PACKAGES = [
     "bzip2",
     "ca-certificates",
-    "conda-forge::blas[build=openblas]",
+    "conda-forge::blas=*",
     "grpcio-status",
     "grpcio",
     "hdf5",
     "jupyterhub-singleuser",
     "jupyterlab-git",
-    "mamba[version='<2.0.0']",
-    "notebook[version='>",
+    "mamba",
+    "notebook>",
     "openssl",
-    "pandas[version='>",
     "protobuf",
     "python",
     "r-irkernel",

tests/package_helper.py

@@ -22,13 +22,13 @@
 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 # SOFTWARE.
 
+import json
 import logging
 import re
 from collections import defaultdict
 from itertools import chain
 from typing import Any, Optional
 
-import yaml
 from docker.models.containers import Container
 from tabulate import tabulate
 
@@ -61,7 +61,7 @@ def start_container(container: TrackedContainer) -> Container:
     @staticmethod
     def _conda_export_command(from_history: bool) -> list[str]:
         """Return the mamba export command with or without history"""
-        cmd = ["mamba", "env", "export", "--no-build"]
+        cmd = ["mamba", "env", "export", "--no-build", "--json"]
         if from_history:
             cmd.append("--from-history")
         return cmd
@@ -96,7 +96,7 @@ def _execute_command(self, command: list[str]) -> str:
     @staticmethod
     def _parse_package_versions(env_export: str) -> dict[str, set[str]]:
         """Extract packages and versions from the lines returned by the list of specifications"""
-        dependencies = yaml.safe_load(env_export).get("dependencies")
+        dependencies = json.loads(env_export).get("dependencies")
         # Filtering packages installed through pip
         # since we only manage packages installed through mamba here
         # They are represented by a dict with a key 'pip'