Add CI

.github/workflows/calkit-run.yml

@@ -0,0 +1,55 @@
+name: Run Calkit pipeline
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+
+permissions:
+  contents: write
+
+# Make sure we only ever run one per branch so we don't have issues pushing
+# after running the pipeline
+concurrency:
+  group: calkit-run-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  main:
+    name: Run
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          # For PRs, checkout the head ref to avoid detached HEAD
+          ref: ${{ github.head_ref || github.ref_name }}
+          token: ${{ secrets.GITHUB_TOKEN }}
+          submodules: true
+      - name: Configure Git credentials
+        run: |
+          git config user.name github-actions[bot]
+          git config user.email 41898282+github-actions[bot]@users.noreply.github.com
+      - name: Setup uv
+        uses: astral-sh/setup-uv@v5
+      - name: Install Calkit
+        run: uv tool install calkit-python
+      - name: Setup matlab
+        uses: matlab-actions/setup-matlab@v2
+        with:
+          cache: true
+          release: R2024b
+          products: >
+            Parallel_Computing_Toolbox
+            Global_Optimization_Toolbox
+            Optimization_Toolbox
+            Statistics_and_Machine_Learning_Toolbox
+            MATLAB_Report_Generator
+            Simulink
+            Simscape
+            Simscape_Multibody
+      - name: Run Calkit
+        uses: calkit/run-action@378d217f814687b57b1b71fd710c43e8c75dfdef
+        with:
+          dvc_token: ${{ secrets.CALKIT_DVC_TOKEN }}
+          matlab: true

calkit.yaml

@@ -2,24 +2,24 @@ title: MATLAB example
 description: >
   This project shows how to incorporate MATLAB into a reproducible
   research project.
-environments:
-  matlab:
-    kind: matlab
-    version: R2024b
-    products:
-      - Statistics_and_Machine_Learning_Toolbox
-      - Parallel_Computing_Toolbox
+# environments:
+#   matlab:
+#     kind: matlab
+#     version: R2024b
+#     products:
+#       - Statistics_and_Machine_Learning_Toolbox
+#       - Parallel_Computing_Toolbox
 pipeline:
   stages:
     collect-data:
       kind: matlab-script
-      environment: matlab
+      environment: _system
       script_path: scripts/collect_data.m
       outputs:
         - data/raw/data.parquet
     plot-data:
       kind: matlab-script
-      environment: matlab
+      environment: _system
       script_path: scripts/plot_data.m
       outputs:
         - figures/plot.png

dvc.lock

@@ -13,50 +13,44 @@ stages:
       md5: 0b2be6aa89192942ea0e1263f9f7e55c
       size: 384
   plot-data:
-    cmd: calkit xenv -n matlab --no-check -- "run('scripts/plot_data.m');"
+    cmd: matlab -batch "run('scripts/plot_data.m');"
     deps:
-    - path: .calkit/env-locks/matlab.json
-      hash: md5
-      md5: 074a6771582255a621b5fda8cb2cc2d3
-      size: 5082
     - path: data/raw/data.parquet
       hash: md5
-      md5: 7d4fadae29fbf5fdf9eedc81a9f0cc9e
+      md5: e901c02a1a54165d5e6d5d5973d594e6
       size: 9853
     - path: scripts/plot_data.m
       hash: md5
-      md5: dd5ffb54107b06b64d0f3fb5be4429f9
-      size: 144
+      md5: ba7e2fcc376bc1f4b17fca546082cf7b
+      size: 148
     outs:
     - path: figures/plot.png
       hash: md5
-      md5: 0459648a57a7fd45c8264e4902a15494
-      size: 79715
+      md5: 8d280eaa88e1604646333ac52bbc2cc1
+      size: 39730
   collect-data:
-    cmd: calkit xenv -n matlab --no-check -- "run('scripts/collect_data.m');"
+    cmd: matlab -batch "run('scripts/collect_data.m');"
     deps:
-    - path: .calkit/env-locks/matlab.json
-      hash: md5
-      md5: 074a6771582255a621b5fda8cb2cc2d3
-      size: 5082
     - path: scripts/collect_data.m
       hash: md5
-      md5: e9f0c4b4277e253b9034dbc7e5495058
-      size: 142
+      md5: 990ebc3af464a6d91033e2450c9522e3
+      size: 174
     outs:
     - path: data/raw/data.parquet
       hash: md5
-      md5: 7d4fadae29fbf5fdf9eedc81a9f0cc9e
+      md5: e901c02a1a54165d5e6d5d5973d594e6
       size: 9853
   _check_env_matlab:
-    cmd: calkit check matlab-env --name matlab --output .calkit/env-locks/matlab.json
+    cmd: calkit check matlab-env --name matlab --output 
+      .calkit/env-locks/matlab.json
     outs:
     - path: .calkit/env-locks/matlab.json
       hash: md5
       md5: 71c8f7b71fac0c8a028a0b11a25cb685
       size: 806
   _check-env-matlab:
-    cmd: calkit check matlab-env --name matlab --output .calkit/env-locks/matlab.json
+    cmd: calkit check matlab-env --name matlab --output 
+      .calkit/env-locks/matlab.json
     outs:
     - path: .calkit/env-locks/matlab.json
       hash: md5

dvc.yaml

@@ -1,24 +1,18 @@
 stages:
-  _check-env-matlab:
-    cmd: calkit check matlab-env --name matlab --output .calkit/env-locks/matlab.json
-    deps: []
-    outs:
-      - .calkit/env-locks/matlab.json:
-          cache: false
-          persist: true
-    always_changed: true
   collect-data:
-    cmd: calkit xenv -n matlab --no-check -- "run('scripts/collect_data.m');"
+    cmd: matlab -batch "run('scripts/collect_data.m');"
     deps:
       - scripts/collect_data.m
-      - .calkit/env-locks/matlab.json
     outs:
       - data/raw/data.parquet
+    desc: Automatically generated from the 'collect-data' stage in 
+      calkit.yaml. Changes made here will be overwritten.
   plot-data:
-    cmd: calkit xenv -n matlab --no-check -- "run('scripts/plot_data.m');"
+    cmd: matlab -batch "run('scripts/plot_data.m');"
     deps:
       - scripts/plot_data.m
       - data/raw/data.parquet
-      - .calkit/env-locks/matlab.json
     outs:
       - figures/plot.png
+    desc: Automatically generated from the 'plot-data' stage in 
+      calkit.yaml. Changes made here will be overwritten.

scripts/collect_data.m

@@ -1,5 +1,11 @@
 disp("Processing data");
+
+% Set random seed
+rng(432);
+
 voltage = rand(1000, 1);
 data = table(voltage);
+
 mkdir("../data/raw");
-parquetwrite("../data/raw/data.parquet", data);
+
+parquetwrite("../data/raw/data.parquet", data);

scripts/plot_data.m

@@ -1,5 +1,8 @@
 disp("Plotting");
+
 data = parquetread("../data/raw/data.parquet");
+
 plot(data, "voltage");
+
 mkdir("../figures");
-saveas(gcf, "../figures/plot.png")
+saveas(gcf, "../figures/plot.png")