Merge branch 'master' into issues/580/crow

Author: eduardojsbarroso

.github/workflows/ci.yml

@@ -35,7 +35,7 @@
 #
 # Performance Improvements:
 # - Quick feedback: 25-30 min → 2-3 min (90% faster)
-# - Coverage upload: 25-30 min → 8-12 min (60% faster) 
+# - Coverage upload: 25-30 min → 8-12 min (60% faster)
 # - Failed PRs: 25-30 min → 3-5 min (85% faster)
 # - Successful PRs: 25-30 min → 20-25 min (20% faster)
 #
@@ -50,18 +50,18 @@ name: firecrown-ci
 on:
   push:
     branches:
-      - 'master'
+      - "master"
     paths-ignore:
-      - 'docs/**/*.md'
-      - '*.md'
+      - "docs/**/*.md"
+      - "*.md"
   pull_request:
     branches:
-      - '*'
+      - "*"
     paths-ignore:
-      - 'docs/**/*.md'
-      - '*.md'
+      - "docs/**/*.md"
+      - "*.md"
   schedule:
-    - cron: '47 1 * * *'
+    - cron: "47 1 * * *"
 
 env:
   CONDA_ENV: firecrown_developer
@@ -72,12 +72,12 @@ jobs:
     name: Quick validation
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
       - name: Setting up Miniforge
         uses: conda-incubator/setup-miniconda@v3
         with:
           miniforge-version: latest
-          python-version: '3.12'
+          python-version: "3.12"
           show-channel-urls: true
           conda-remove-defaults: true
           environment-file: environment.yml
@@ -106,7 +106,7 @@ jobs:
             python-version: "3.12"
             coverage: true
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
       - name: Setting up Miniforge
         uses: conda-incubator/setup-miniconda@v3
         with:
@@ -117,12 +117,22 @@ jobs:
         id: get-date
         run: echo "today=$(/bin/date -u '+%Y%m%d')" >> $GITHUB_OUTPUT
         shell: bash
+      - name: Compute environment.yml hash
+        id: env-hash
+        run: |
+          if command -v sha256sum &>/dev/null 2>&1; then
+            h=$(sha256sum environment.yml | cut -d' ' -f1)
+          else
+            h=$(shasum -a 256 environment.yml | cut -d' ' -f1)
+          fi
+          echo "env_hash=${h}" >> $GITHUB_OUTPUT
+        shell: bash
       - name: Cache Conda env
         uses: actions/cache/restore@v4
         id: cache
         with:
           path: ${{ env.CONDA }}/envs
-          key: conda-${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-${{ steps.get-date.outputs.today }}-${{ hashFiles('environment.yml') }}-v${{ env.CACHE_VERSION }}
+          key: conda-${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-${{ steps.get-date.outputs.today }}-${{ steps.env-hash.outputs.env_hash }}-v${{ env.CACHE_VERSION }}
       - name: Update environment
         if: steps.cache.outputs.cache-hit != 'true'
         run: |
@@ -181,9 +191,9 @@ jobs:
             # All other jobs: full test suite including slow tests
             python -m pytest -vv --runslow -n auto
           fi
-      - name: Running integration tests
+      - name: Running example tests
         shell: bash -l {0}
-        run: python -m pytest -vv -s --integration tests/integration
+        run: python -m pytest -vv -s --example -m example tests/example
       - name: Upload coverage reports to Codecov
         if: ${{ matrix.coverage == true }}
         uses: codecov/codecov-action@v5
@@ -204,7 +214,7 @@ jobs:
     name: External dependencies and documentation
     runs-on: macos-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
       - name: Setting up Miniforge
         uses: conda-incubator/setup-miniconda@v3
         with:
@@ -215,12 +225,22 @@ jobs:
         id: get-date
         run: echo "today=$(/bin/date -u '+%Y%m%d')" >> $GITHUB_OUTPUT
         shell: bash
+      - name: Compute environment.yml hash
+        id: env-hash
+        run: |
+          if command -v sha256sum &>/dev/null 2>&1; then
+            h=$(sha256sum environment.yml | cut -d' ' -f1)
+          else
+            h=$(shasum -a 256 environment.yml | cut -d' ' -f1)
+          fi
+          echo "env_hash=${h}" >> $GITHUB_OUTPUT
+        shell: bash
       - name: Cache Conda env
         uses: actions/cache/restore@v4
         id: cache
         with:
           path: ${{ env.CONDA }}/envs
-          key: conda-${{ runner.os }}-${{ runner.arch }}-py3.13-${{ steps.get-date.outputs.today }}-${{ hashFiles('environment.yml') }}-v${{ env.CACHE_VERSION }}
+          key: conda-${{ runner.os }}-${{ runner.arch }}-py3.13-${{ steps.get-date.outputs.today }}-${{ steps.env-hash.outputs.env_hash }}-v${{ env.CACHE_VERSION }}
       - name: Update environment
         if: steps.cache.outputs.cache-hit != 'true'
         run: |
@@ -257,17 +277,17 @@ jobs:
           pip install --no-deps -e .
           conda list
       - name: Cloning Smokescreen
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
         with:
-          repository: 'lsstdesc/smokescreen'
-          path: 'smokescreen'
-          ref: 'v1.5.0'
+          repository: "marcpaterno/smokescreen"
+          path: "smokescreen"
+          ref: "adjust-to-firecrown-pr-586"
       - name: Cloning Augur
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
         with:
-          repository: 'lsstdesc/augur'
-          path: 'augur'
-          ref: '1.1.2'
+          repository: "lsstdesc/augur"
+          path: "augur"
+          ref: "b59cfaf3dec90aa606a4add453a5a77e0c8ea942"
       - name: Build tutorials and documentation and check links
         shell: bash -l {0}
         run: |

.gitignore

@@ -167,3 +167,5 @@ tutorial/theoretical_predictions_tutorial.html
 /.luarc.json
 *.Rproj
 coverage.json
+
+**/*.quarto_ipynb