Simplify python environment setup (#310)

* add pyproject.toml

* simplify conda environment management

* flake8 fix, remove conda-lock references

* rebuild all pages without cache

* fix codespell

* fix for zarr v3

* use matrix for nocache workflow

* fix some broken links

Author: scottyhq

.binder/environment.yml

@@ -0,0 +1,42 @@
+name: default
+channels:
+  - conda-forge
+  - nodefaults
+dependencies:
+  - jupyter-book >=1.0.3,<2
+  - pre-commit >=4.1.0,<5
+  - dask-labextension >=7.0.0,<8
+  - jupyterlab >=4.3.5,<5
+  - jupyter_bokeh >=4.0.5,<5
+  - jupyterlab-myst >=2.4.2,<3
+  - jupyter-resource-usage >=1.1.1,<2
+  - cartopy >=0.24.0,<0.25
+  - cf_xarray >=0.10.0,<0.11
+  - dask >=2025.2.0,<2026
+  - datashader >=0.17.0,<0.18
+  - distributed >=2025.2.0,<2026
+  - gcsfs >=2025.2.0,<2026
+  - geoviews-core >=1.14.0,<2
+  - gsw >=3.6.19,<4
+  - hvplot >=0.11.2,<0.12
+  - h5netcdf >=1.5.0,<2
+  - ipykernel >=6.29.5,<7
+  - matplotlib-base >=3.10.0,<4
+  - netcdf4 >=1.7.2,<2
+  - numpy >=2.1.3,<3
+  - pint-xarray >=0.4,<0.5
+  - pydap >=3.5.3,<4
+  - python-graphviz >=0.20.3,<0.21
+  - pooch >=1.8.2,<2
+  - rioxarray >=0.18.2,<0.19
+  - scipy >=1.15.2,<2
+  - sphinx-codeautolink >=0.17.0,<0.18
+  - sphinxcontrib-mermaid >=1.0.0,<2
+  - sphinx-notfound-page >=1.0.4,<2
+  - sphinxext-rediraffe >=0.2.7,<0.3
+  - s3fs >=2025.2.0,<2026
+  - xarray >=2025.1.2,<2026
+  - zarr >=3.0.3,<4
+  - flox >=0.10.0,<0.11
+  - numbagg >=0.9.0,<0.10
+  - python >=3.10

.binder/environment.yml

@@ -1,8 +1,5 @@
 {
-  "build": {
-    "dockerfile": "./Dockerfile",
-    "context": "../conda"
-  },
+  "image": "quay.io/pangeo/pangeo-notebook:latest",
   "postCreateCommand": {
     "vscode": "mkdir ${containerWorkspaceFolder}/.vscode && cp ${containerWorkspaceFolder}/.devcontainer/tasks.json ${containerWorkspaceFolder}/.vscode/tasks.json"
   },

.devcontainer/Dockerfile

@@ -1,8 +1,5 @@
 {
-  "build": {
-    "dockerfile": "../Dockerfile",
-    "context": "../../conda"
-  },
+  "image": "quay.io/pangeo/pangeo-notebook:2023.07.05",
   "postCreateCommand": {
     "jupyterlab": "mkdir /home/jovyan/.jupyter && cp ${containerWorkspaceFolder}/.devcontainer/scipy2023/jupyter_lab_config.py /home/jovyan/.jupyter/jupyter_lab_config.py",
     "vscode": "mkdir ${containerWorkspaceFolder}/.vscode && cp ${containerWorkspaceFolder}/.devcontainer/scipy2023/tasks.json ${containerWorkspaceFolder}/.vscode/tasks.json"

.devcontainer/devcontainer.json

@@ -1,15 +1,3 @@
-# Configuration file for lab.
-
 c = get_config()  # noqa
-
-## The default URL to redirect to from `/`
-#  Default: '/lab'
 c.LabApp.default_url = '/lab/tree/workshops/scipy2023/index.ipynb'
-
-## Set the Access-Control-Allow-Origin header
-#
-#          Use '*' to allow any origin to access your server.
-#
-#          Takes precedence over allow_origin_pat.
-#  Default: ''
 c.ServerApp.allow_origin = '*'

.devcontainer/scipy2023/devcontainer.json

@@ -1,8 +1,5 @@
 {
-  "build": {
-    "dockerfile": "../Dockerfile",
-    "context": "../../conda"
-  },
+  "image": "quay.io/pangeo/pangeo-notebook:2024.07.08",
   "postCreateCommand": {
     "jupyterlab": "mkdir /home/jovyan/.jupyter && cp ${containerWorkspaceFolder}/.devcontainer/scipy2024/jupyter_lab_config.py /home/jovyan/.jupyter/jupyter_lab_config.py",
     "vscode": "mkdir ${containerWorkspaceFolder}/.vscode && cp ${containerWorkspaceFolder}/.devcontainer/scipy2024/tasks.json ${containerWorkspaceFolder}/.vscode/tasks.json"

.devcontainer/scipy2023/jupyter_lab_config.py

@@ -1,15 +1,3 @@
-# Configuration file for lab.
-
 c = get_config()  # noqa
-
-## The default URL to redirect to from `/`
-#  Default: '/lab'
 c.LabApp.default_url = '/lab/tree/workshops/scipy2024/index.ipynb'
-
-## Set the Access-Control-Allow-Origin header
-#
-#          Use '*' to allow any origin to access your server.
-#
-#          Takes precedence over allow_origin_pat.
-#  Default: ''
 c.ServerApp.allow_origin = '*'

.devcontainer/scipy2024/devcontainer.json

@@ -0,0 +1,2 @@
+# SCM syntax highlighting & preventing 3-way merges
+pixi.lock merge=binary linguist-language=YAML linguist-generated=true

.devcontainer/scipy2024/jupyter_lab_config.py

@@ -1,10 +1,6 @@
 # Regularly update Docker tags and Actions steps
 version: 2
 updates:
-  - package-ecosystem: "docker"
-    directory: "/.devcontainer"
-    schedule:
-      interval: "daily"
   - package-ecosystem: "github-actions"
     directory: "/.github"
     schedule: