Migrate to GitHub Actions CI

.github/workflows/test-notebooks.yml

@@ -0,0 +1,45 @@
+name: Notebook Tests
+
+on:
+  # trigger on pull requests
+  pull_request:
+
+  # trigger on all commits to main
+  push:
+    branches:
+      - 'main'
+
+  # trigger on request
+  workflow_dispatch:
+concurrency:
+  group: "${{ github.workflow }}-${{ github.ref }}"
+  cancel-in-progress: true
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os:
+          - ubuntu-latest
+        config:
+          - python: '3.12'
+
+    steps:
+    - uses: actions/checkout@v3
+      with:
+        submodules: "recursive"
+    - name: Create Python Environment
+      uses: conda-incubator/[email protected]
+      with:
+        python-version: ${{ matrix.config.python }}
+        environment-file: environment.yml
+        activate-environment: test
+        channels: conda-forge
+        show-channel-urls: true
+        miniforge-version: latest
+        use-mamba: true
+    - name: Test notebooks
+      shell: bash -el {0}  # Required for conda activation
+      run: |
+        python -m pytest -v --nbval --nbval-lax notebooks/

.github/workflows/test-projects.yml

@@ -0,0 +1,46 @@
+name: Project Tests
+
+on:
+  # trigger on pull requests
+  pull_request:
+
+  # trigger on all commits to main
+  push:
+    branches:
+      - 'main'
+
+  # trigger on request
+  workflow_dispatch:
+concurrency:
+  group: "${{ github.workflow }}-${{ github.ref }}"
+  cancel-in-progress: true
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os:
+          - ubuntu-latest
+        config:
+          - python: '3.12'
+
+    steps:
+    - uses: actions/checkout@v3
+      with:
+        submodules: "recursive"
+    - name: Create Python Environment
+      uses: conda-incubator/[email protected]
+      with:
+        python-version: ${{ matrix.config.python }}
+        environment-file: environment.yml
+        activate-environment: test
+        channels: conda-forge
+        show-channel-urls: true
+        miniforge-version: latest
+        use-mamba: true
+    - name: Test projects
+      shell: bash -el {0}  # Required for conda activation
+      run: |
+        cd projects
+        . run-tests.sh --output

.render_all_notebooks.sh

@@ -3,7 +3,7 @@
 # Requires many dependencies specified in environment.yml
 
 # Remove existing signac workspaces used by notebooks
-rm -r notebooks/projects
+rm -rf notebooks/projects
 
 # Render all notebooks by executing them and overwriting contents
 jupyter nbconvert --execute --inplace notebooks/*.ipynb

environment.yml

@@ -3,18 +3,20 @@ channels:
 dependencies:
   - gsd
   - h5py
-  - hoomd>=3
+  - hoomd>=4
   - ipywidgets>=7
   - joblib
   - jupyter
   - jupyterlab>=3
   - matplotlib>=3
   - mistune<2  # Needed for .update_project_readme.py
   - nbconvert>=6
+  - nbval
   - notebook>=6
   - numpy>=1.21
   - pandas>=2.0
   - pre-commit
+  - pytest
   - python>=3.9
   - scikit-learn
   - signac-dashboard>=0.5

notebooks/index.ipynb

@@ -50,7 +50,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.2"
+   "version": "3.12.0"
   }
  },
  "nbformat": 4,

notebooks/signac_101_Getting_Started.ipynb

@@ -449,7 +449,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.2"
+   "version": "3.12.0"
   }
  },
  "nbformat": 4,

notebooks/signac_102_Exploring_Data.ipynb

@@ -155,7 +155,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "signac_job_document.json  signac_statepoint.json  V.txt\r\n",
+      "V.txt  signac_job_document.json  signac_statepoint.json\r\n",
       "1000.0\r\n"
      ]
     }
@@ -198,7 +198,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.2"
+   "version": "3.12.0"
   }
  },
  "nbformat": 4,

notebooks/signac_103_A_Basic_Workflow.ipynb

@@ -209,8 +209,8 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Computing volume of 973e29d6a4ed6cf7329c03c77df7f645\n",
       "Computing volume of 4cf2795722061df825ec9a4d5e31e494\n",
+      "Computing volume of 973e29d6a4ed6cf7329c03c77df7f645\n",
       "Computing volume of d03270cdbbae73c8bb1d9fa0ab370264\n"
      ]
     }
@@ -320,20 +320,20 @@
      "output_type": "stream",
      "text": [
       "Status: notebooks/projects/tutorial\n",
+      "22582e83c6b12336526ed304d4378ff8 1.2 init\n",
+      "4cf2795722061df825ec9a4d5e31e494 7.5 init, volume-computed\n",
       "b45a2485a44a46364cc60134360ea5af 4.5 init\n",
-      "8629822576debc2bfbeffa56787ca348 7.8 init\n",
-      "c0ab2e09a6f878019a6057175bf718e6 2.3 init\n",
-      "665547b1344fe40de5b2c7ace4204783 6.7 init\n",
+      "e8186b9b68e18a82f331d51a7b8c8c15 8.9 init\n",
       "5a6c687f7655319db24de59a2336eff8 0.1 init, volume-computed\n",
-      "5a456c131b0c5897804a4af8e77df5aa 10.0 init, volume-computed\n",
       "973e29d6a4ed6cf7329c03c77df7f645 5.0 init, volume-computed\n",
-      "9110d0837ad93ff6b4013bae30091edd 3.4 init\n",
-      "22582e83c6b12336526ed304d4378ff8 1.2 init\n",
-      "ee617ad585a90809947709a7a45dda9a 1.0 init, volume-computed\n",
-      "05061d2acea19d2d9a25ac3360f70e04 5.6 init\n",
-      "4cf2795722061df825ec9a4d5e31e494 7.5 init, volume-computed\n",
       "d03270cdbbae73c8bb1d9fa0ab370264 2.6 init, volume-computed\n",
-      "e8186b9b68e18a82f331d51a7b8c8c15 8.9 init\n"
+      "05061d2acea19d2d9a25ac3360f70e04 5.6 init\n",
+      "665547b1344fe40de5b2c7ace4204783 6.7 init\n",
+      "8629822576debc2bfbeffa56787ca348 7.8 init\n",
+      "5a456c131b0c5897804a4af8e77df5aa 10.0 init, volume-computed\n",
+      "c0ab2e09a6f878019a6057175bf718e6 2.3 init\n",
+      "9110d0837ad93ff6b4013bae30091edd 3.4 init\n",
+      "ee617ad585a90809947709a7a45dda9a 1.0 init, volume-computed\n"
      ]
     }
    ],
@@ -371,14 +371,14 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
+      "Computing volume of 22582e83c6b12336526ed304d4378ff8\n",
       "Computing volume of b45a2485a44a46364cc60134360ea5af\n",
+      "Computing volume of e8186b9b68e18a82f331d51a7b8c8c15\n",
+      "Computing volume of 05061d2acea19d2d9a25ac3360f70e04\n",
+      "Computing volume of 665547b1344fe40de5b2c7ace4204783\n",
       "Computing volume of 8629822576debc2bfbeffa56787ca348\n",
       "Computing volume of c0ab2e09a6f878019a6057175bf718e6\n",
-      "Computing volume of 665547b1344fe40de5b2c7ace4204783\n",
-      "Computing volume of 9110d0837ad93ff6b4013bae30091edd\n",
-      "Computing volume of 22582e83c6b12336526ed304d4378ff8\n",
-      "Computing volume of 05061d2acea19d2d9a25ac3360f70e04\n",
-      "Computing volume of e8186b9b68e18a82f331d51a7b8c8c15\n"
+      "Computing volume of 9110d0837ad93ff6b4013bae30091edd\n"
      ]
     }
    ],
@@ -410,20 +410,20 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
+      "Computing volume of 22582e83c6b12336526ed304d4378ff8\n",
+      "Computing volume of 4cf2795722061df825ec9a4d5e31e494\n",
       "Computing volume of b45a2485a44a46364cc60134360ea5af\n",
-      "Computing volume of 8629822576debc2bfbeffa56787ca348\n",
-      "Computing volume of c0ab2e09a6f878019a6057175bf718e6\n",
-      "Computing volume of 665547b1344fe40de5b2c7ace4204783\n",
+      "Computing volume of e8186b9b68e18a82f331d51a7b8c8c15\n",
       "Computing volume of 5a6c687f7655319db24de59a2336eff8\n",
-      "Computing volume of 5a456c131b0c5897804a4af8e77df5aa\n",
       "Computing volume of 973e29d6a4ed6cf7329c03c77df7f645\n",
+      "Computing volume of d03270cdbbae73c8bb1d9fa0ab370264\n",
+      "Computing volume of 05061d2acea19d2d9a25ac3360f70e04\n",
+      "Computing volume of 665547b1344fe40de5b2c7ace4204783\n",
+      "Computing volume of 8629822576debc2bfbeffa56787ca348\n",
+      "Computing volume of 5a456c131b0c5897804a4af8e77df5aa\n",
+      "Computing volume of c0ab2e09a6f878019a6057175bf718e6\n",
       "Computing volume of 9110d0837ad93ff6b4013bae30091edd\n",
-      "Computing volume of 22582e83c6b12336526ed304d4378ff8\n",
       "Computing volume of ee617ad585a90809947709a7a45dda9a\n",
-      "Computing volume of 05061d2acea19d2d9a25ac3360f70e04\n",
-      "Computing volume of 4cf2795722061df825ec9a4d5e31e494\n",
-      "Computing volume of d03270cdbbae73c8bb1d9fa0ab370264\n",
-      "Computing volume of e8186b9b68e18a82f331d51a7b8c8c15\n",
       "Done.\n"
      ]
     }
@@ -505,7 +505,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.2"
+   "version": "3.12.0"
   },
   "nbpresent": {
    "slides": {},

notebooks/signac_104_Modifying_the_Data_Space.ipynb

@@ -133,20 +133,20 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "{'p': 1.2000000000000002, 'kT': 1.0, 'N': 1000, 'a': 0, 'b': 0} {'V_liq': 0, 'V_gas': 833.3333333333333}\n",
+      "{'p': 3.4000000000000004, 'kT': 1.0, 'N': 1000, 'a': 0, 'b': 0} {'V_liq': 0, 'V_gas': 294.1176470588235}\n",
+      "{'p': 7.800000000000001, 'kT': 1.0, 'N': 1000, 'a': 0, 'b': 0} {'V_liq': 0, 'V_gas': 128.2051282051282}\n",
       "{'p': 1.0, 'kT': 1.0, 'N': 1000, 'a': 0, 'b': 0} {'V_liq': 0, 'V_gas': 1000.0}\n",
-      "{'p': 5.05, 'kT': 1.0, 'N': 1000, 'a': 0, 'b': 0} {'V_liq': 0, 'V_gas': 198.01980198019803}\n",
       "{'p': 2.3000000000000003, 'kT': 1.0, 'N': 1000, 'a': 0, 'b': 0} {'V_liq': 0, 'V_gas': 434.78260869565213}\n",
       "{'p': 8.9, 'kT': 1.0, 'N': 1000, 'a': 0, 'b': 0} {'V_liq': 0, 'V_gas': 112.35955056179775}\n",
-      "{'p': 6.7, 'kT': 1.0, 'N': 1000, 'a': 0, 'b': 0} {'V_liq': 0, 'V_gas': 149.2537313432836}\n",
-      "{'p': 5.6, 'kT': 1.0, 'N': 1000, 'a': 0, 'b': 0} {'V_liq': 0, 'V_gas': 178.57142857142858}\n",
-      "{'p': 10.0, 'kT': 1.0, 'N': 1000, 'a': 0, 'b': 0} {'V_liq': 0, 'V_gas': 100.0}\n",
+      "{'p': 5.05, 'kT': 1.0, 'N': 1000, 'a': 0, 'b': 0} {'V_liq': 0, 'V_gas': 198.01980198019803}\n",
+      "{'p': 2.575, 'kT': 1.0, 'N': 1000, 'a': 0, 'b': 0} {'V_liq': 0, 'V_gas': 388.34951456310677}\n",
+      "{'p': 4.5, 'kT': 1.0, 'N': 1000, 'a': 0, 'b': 0} {'V_liq': 0, 'V_gas': 222.22222222222223}\n",
       "{'p': 7.525, 'kT': 1.0, 'N': 1000, 'a': 0, 'b': 0} {'V_liq': 0, 'V_gas': 132.89036544850498}\n",
       "{'p': 0.1, 'kT': 1.0, 'N': 1000, 'a': 0, 'b': 0} {'V_liq': 0, 'V_gas': 10000.0}\n",
-      "{'p': 4.5, 'kT': 1.0, 'N': 1000, 'a': 0, 'b': 0} {'V_liq': 0, 'V_gas': 222.22222222222223}\n",
-      "{'p': 7.800000000000001, 'kT': 1.0, 'N': 1000, 'a': 0, 'b': 0} {'V_liq': 0, 'V_gas': 128.2051282051282}\n",
-      "{'p': 2.575, 'kT': 1.0, 'N': 1000, 'a': 0, 'b': 0} {'V_liq': 0, 'V_gas': 388.34951456310677}\n",
-      "{'p': 3.4000000000000004, 'kT': 1.0, 'N': 1000, 'a': 0, 'b': 0} {'V_liq': 0, 'V_gas': 294.1176470588235}\n"
+      "{'p': 5.6, 'kT': 1.0, 'N': 1000, 'a': 0, 'b': 0} {'V_liq': 0, 'V_gas': 178.57142857142858}\n",
+      "{'p': 10.0, 'kT': 1.0, 'N': 1000, 'a': 0, 'b': 0} {'V_liq': 0, 'V_gas': 100.0}\n",
+      "{'p': 1.2000000000000002, 'kT': 1.0, 'N': 1000, 'a': 0, 'b': 0} {'V_liq': 0, 'V_gas': 833.3333333333333}\n",
+      "{'p': 6.7, 'kT': 1.0, 'N': 1000, 'a': 0, 'b': 0} {'V_liq': 0, 'V_gas': 149.2537313432836}\n"
      ]
     }
    ],
@@ -292,7 +292,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.2"
+   "version": "3.12.0"
   }
  },
  "nbformat": 4,

notebooks/signac_107_Integration_with_Sacred.ipynb

@@ -75,7 +75,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.2"
+   "version": "3.12.0"
   }
  },
  "nbformat": 4,

projects/flow-test.py

@@ -77,7 +77,7 @@ def run_tests(path, output, timeout):
     except subprocess.TimeoutExpired:
         raise RuntimeWarning("Test failed due to timeout.")
     except FileNotFoundError:
-        logger.info("No test file!")
+        logger.info("No test.sh file, skipping tests.")
 
 
 def main(args):

projects/run-tests.sh

@@ -1,22 +1,25 @@
 #!/bin/bash
 
-set -e
+set -euo pipefail
 
-export USE_INDEX_CACHE=""
 for PROJECT in `ls -d */`; do
     if [ -e "${PROJECT}/.skipci" ]; then
-        echo "Skipping tests for project ${PROJECT}."
+        echo "Skipping ${PROJECT}"
         continue
     fi
+    if [[ "$CI" ]]; then
+        echo "::group::Executing ${PROJECT}"
+    else
+        echo "Executing ${PROJECT}"
+    fi
     REQUIREMENTS_FILE="${PROJECT}/requirements.txt"
-    echo "Run test for ${PROJECT}."
     if [ -e ${REQUIREMENTS_FILE} ]; then
         echo "Installing requirements:"
         cat ${REQUIREMENTS_FILE}
-
-        # Re-use the conda index cache after the first time.
-        conda install --yes ${USE_INDEX_CACHE} --file ${REQUIREMENTS_FILE}
-        export USE_INDEX_CACHE="--use-index-cache"
+        mamba install --yes --file ${REQUIREMENTS_FILE} --quiet
     fi
     python flow-test.py ${PROJECT} -vv --timeout=600 $@
+    if [[ "$CI" ]]; then
+        echo "::endgroup::"
+    fi
 done