Merge pull request #4 from scottyhq/use-pixi

gbrencher · web-flow · commit e9ee2c5301fe · 2026-05-13T13:29:54.000-07:00
Use pixi instead of conda for environment management
diff --git a/.gitattributes b/.gitattributes
@@ -0,0 +1,2 @@
+# SCM syntax highlighting & preventing 3-way merges
+pixi.lock merge=binary linguist-language=YAML linguist-generated=true -diff
diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -0,0 +1,11 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
+
+version: 2
+updates:
+  - package-ecosystem: "github-actions" # See documentation for possible values
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "weekly"
diff --git a/.github/workflows/batch_predict_sd.yml b/.github/workflows/batch_predict_sd.yml
@@ -2,9 +2,6 @@
 name: batch_predict_sd
 run-name: batch snow depth ${{ inputs.target_date }}
 
-env:
-  FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: "true"
-
 on:
   workflow_dispatch:
     inputs:
@@ -60,7 +57,7 @@ on:
             options:
             - 'False'
             - 'True'
-  
+
   workflow_call:
     inputs:
         target_date:
@@ -94,26 +91,20 @@ jobs:
     outputs:
       MATRIX: ${{ steps.prep_tiles.outputs.MATRIX_PARAMS_COMBINATIONS }}
       TILE_COUNT: ${{ steps.prep_tiles.outputs.TILE_COUNT }}
-    defaults:
-      run:
-        shell: bash -el {0}
+
     steps:
       - name: Checkout Repository
         uses: actions/checkout@v6
 
-      - name: Install Conda environment with Micromamba
-        uses: mamba-org/setup-micromamba@v3
+      - uses: prefix-dev/setup-pixi@v0.9.5
         with:
-          cache-environment: true
-          environment-file: environment.yml
-
-      - name: Install deep-snow
-        run: |
-          pip install .
+          cache: true
+          frozen: true
+          activate-environment: true
 
       - name: Prepare tiles over area of interest
         id: prep_tiles
-        run: | 
+        run: |
           python -u scripts/actions/prep_tiles.py ${{ inputs.target_date }} "${{ inputs.aoi }}"
 
       - name: Summarize Tile Preparation
@@ -141,7 +132,7 @@ jobs:
     uses: ./.github/workflows/predict_tile_sd.yml
     with:
       target_date: ${{ inputs.target_date }}
-      snow_off_date: ${{ inputs.snow_off_date }} 
+      snow_off_date: ${{ inputs.snow_off_date }}
       aoi: ${{ matrix.aoi }}
       clip_aoi: ${{ matrix.clip_aoi }}
       cloud_cover: ${{ inputs.cloud_cover }}
diff --git a/.github/workflows/batch_predict_ts.yml b/.github/workflows/batch_predict_ts.yml
@@ -2,9 +2,6 @@
 name: batch_sd_timeseries
 run-name: snow depth time series ${{ inputs.begin_date }}-${{ inputs.end_date }}
 
-env:
-  FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: "true"
-
 on:
   workflow_dispatch:
     inputs:
@@ -73,26 +70,20 @@ jobs:
     outputs:
       MATRIX: ${{ steps.prep_dates.outputs.MATRIX_PARAMS_COMBINATIONS }}
       DATE_COUNT: ${{ steps.prep_dates.outputs.DATE_COUNT }}
-    defaults:
-      run:
-        shell: bash -el {0}
+
     steps:
       - name: Checkout Repository
         uses: actions/checkout@v6
 
-      - name: Install Conda environment with Micromamba
-        uses: mamba-org/setup-micromamba@v3
+      - uses: prefix-dev/setup-pixi@v0.9.5
         with:
-          cache-environment: true
-          environment-file: environment.yml
-
-      - name: Install deep-snow
-        run: |
-          pip install .
+          cache: true
+          frozen: true
+          activate-environment: true
 
       - name: Select dates over time range
         id: prep_dates
-        run: | 
+        run: |
           python -u scripts/actions/prep_time_series.py ${{ inputs.begin_date }} ${{ inputs.end_date }}  ${{ inputs.snow_off_day }}
 
       - name: Summarize Time-Series Request
@@ -121,7 +112,7 @@ jobs:
     uses: ./.github/workflows/batch_predict_sd.yml
     with:
       target_date: ${{ matrix.target_date }}
-      snow_off_date: ${{ matrix.snow_off_date }} 
+      snow_off_date: ${{ matrix.snow_off_date }}
       aoi: ${{ inputs.aoi }}
       cloud_cover: ${{ inputs.cloud_cover }}
       selection_strategy: ${{ inputs.selection_strategy }}
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -5,56 +5,21 @@ on:
   push:
     branches:
       - main
-
-env:
-  FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: "true"
-  ACTIONLINT_VERSION: "1.7.12"
-
 jobs:
   test:
     name: test
     runs-on: ubuntu-latest
-    defaults:
-      run:
-        shell: bash -el {0}
 
     steps:
       - name: Checkout repository
         uses: actions/checkout@v6
 
-      - name: Install Conda environment with Micromamba
-        uses: mamba-org/setup-micromamba@v3
+      - uses: prefix-dev/setup-pixi@v0.9.5
         with:
-          cache-environment: true
-          cache-downloads: true
-          environment-file: environment.yml
-
-      - name: Install deep-snow
-        run: |
-          python -m pip install --upgrade pip
-          pip install -e .
+          cache: true
+          frozen: true
+          activate-environment: true
 
       - name: Run test suite
         run: |
           pytest -q tests
-
-  workflow_lint:
-    name: workflow lint
-    runs-on: ubuntu-latest
-    defaults:
-      run:
-        shell: bash
-
-    steps:
-      - name: Checkout repository
-        uses: actions/checkout@v6
-
-      - name: Install actionlint
-        run: |
-          curl -sSL "https://github.com/rhysd/actionlint/releases/download/v${ACTIONLINT_VERSION}/actionlint_${ACTIONLINT_VERSION}_linux_amd64.tar.gz" -o actionlint.tar.gz
-          tar -xzf actionlint.tar.gz actionlint
-          sudo mv actionlint /usr/local/bin/actionlint
-
-      - name: Lint GitHub Actions workflows
-        run: |
-          actionlint
diff --git a/.github/workflows/predict_tile_sd.yml b/.github/workflows/predict_tile_sd.yml
@@ -2,9 +2,6 @@
 name: predict_tile_sd
 run-name: tile snow depth ${{ inputs.target_date }}
 
-env:
-  FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: "true"
-
 on:
   workflow_dispatch:
     inputs:
@@ -69,7 +66,7 @@ on:
             required: false
             default: 'predict_tile_sd'
             type: string
-    
+
   workflow_call:
     inputs:
         target_date:
@@ -106,23 +103,16 @@ jobs:
     predict_tile_sd:
         name: ${{ inputs.workflow_name }}
         runs-on: ubuntu-latest
-        defaults:
-            run:
-                shell: bash -el {0}
 
         steps:
             - name: Checkout Repository
               uses: actions/checkout@v6
 
-            - name: Install Conda environment with Micromamba
-              uses: mamba-org/setup-micromamba@v3
+            - uses: prefix-dev/setup-pixi@v0.9.5
               with:
-                cache-environment: true
-                environment-file: environment.yml
-
-            - name: Install deep-snow
-              run: |
-                pip install .
+                cache: true
+                frozen: true
+                activate-environment: true
 
             - name: Download Data and Predict Snow Depth
               run: |
diff --git a/.gitignore b/.gitignore
@@ -1,3 +1,11 @@
+# deep-snow example outputs
+data/
+tmp-output/
+
+# pixi environments
+.pixi/*
+!.pixi/config.toml
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
diff --git a/README.md b/README.md
@@ -27,7 +27,17 @@ Fork the repo and run workflows from the Actions tab:
 
 See [docs/github-actions.md](docs/github-actions.md) for details.
 
-### Option 2: Local install
+### Option 2: Local install (we recommend pixi over conda)
+
+```
+git clone https://github.com/geo-smart/deep-snow.git
+cd deep-snow
+pixi shell  # 'exit'
+# test run
+pixi run predict-example
+```
+
+### Option 2: Local install (with conda)
 
 ```bash
 git clone https://github.com/geo-smart/deep-snow.git
@@ -82,13 +92,13 @@ The model uses the following input data sources:
 - Fractional forest cover
 - COP30 digital elevation model
 
-Sentinel-1 and Sentinel-2 inputs are selected close in time to the target date. Inputs are co-registered to a common grid and assembled into model-ready datasets. Airborne lidar snow depth maps are used for training and evaluation, but not for inference. 
+Sentinel-1 and Sentinel-2 inputs are selected close in time to the target date. Inputs are co-registered to a common grid and assembled into model-ready datasets. Airborne lidar snow depth maps are used for training and evaluation, but not for inference.
 
 <img src="imgs/inputs_v0.png" width="50%">
 
 ## Contributing
 
-Contributions are welcome! No matter what your level of experience, you CAN help make this package better. 
+Contributions are welcome! No matter what your level of experience, you CAN help make this package better.
 
 If you have a suggestion, please fork the repo and create a pull request. You can also simply open an issue.
 1. Fork the Project
diff --git a/pixi.lock b/pixi.lock
diff --git a/pixi.toml b/pixi.toml

Original file line number	Diff line number	Diff line change
`@@ -0,0 +1,2 @@`
	`1`	`+# SCM syntax highlighting & preventing 3-way merges`
	`2`	`+pixi.lock merge=binary linguist-language=YAML linguist-generated=true -diff`