simplify conda environment management

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

@@ -1,8 +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/devcontainer.json

@@ -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:

.devcontainer/scipy2024/devcontainer.json

@@ -32,16 +32,13 @@ jobs:
           # NOTE: change key to "jupyterbook-DATE" to force rebuilding cache
           key: jupyterbook-20240517
 
-      - name: Install Conda environment with Micromamba
-        uses: mamba-org/setup-micromamba@v1
+      - uses: prefix-dev/[email protected]
         with:
-          environment-file: conda/conda-lock.yml
-          environment-name: xarray-tutorial
-          cache-environment: true
+          manifest-path: pyproject.toml
+          cache: true
+          activate-environment: true
 
       - name: Build JupyterBook
-        # NOTE: login shell activates conda environment
-        shell: bash -el {0}
         run: |
           jupyter-book build ./ --warningiserror --keep-going
 

.github/dependabot.yml

@@ -13,9 +13,6 @@ concurrency:
 jobs:
   preview:
     runs-on: ubuntu-latest
-    defaults:
-      run:
-        shell: bash -el {0}
     steps:
       - name: Checkout repository
         if: github.event.action != 'closed'
@@ -29,13 +26,11 @@ jobs:
           # NOTE: change key to "jupyterbook-DATE" to force rebuilding cache
           key: jupyterbook-20240517
 
-      - name: Install Conda environment with Micromamba
-        if: github.event.action != 'closed'
-        uses: mamba-org/setup-micromamba@v1
+      - uses: prefix-dev/[email protected]
         with:
-          environment-file: conda/conda-lock.yml
-          environment-name: xarray-tutorial
-          cache-environment: true
+          manifest-path: pyproject.toml
+          cache: true
+          activate-environment: true
 
       - name: Build JupyterBook
         if: github.event.action != 'closed'

.github/workflows/main.yaml

@@ -14,19 +14,15 @@ concurrency:
 jobs:
   quality-control:
     runs-on: ubuntu-latest
-    defaults:
-      run:
-        shell: bash -el {0}
 
     steps:
       - uses: actions/checkout@v4
 
-      - name: Install Conda environment with Micromamba
-        uses: mamba-org/setup-micromamba@v1
+      - uses: prefix-dev/[email protected]
         with:
-          environment-file: conda/conda-lock.yml
-          environment-name: xarray-tutorial
-          cache-environment: true
+          manifest-path: pyproject.toml
+          cache: true
+          activate-environment: true
 
       # NOTE: this isn't a comprehensive spellcheck, just common typos
       - name: Spellcheck