Merge remote-tracking branch 'origin/main' into psteinb-explicit_noise_schedules-1437

Resolved the merge conflicts by aligning the score estimator with the vector-field API
changes from main and accepting the deletions of legacy score/NPSE paths.

Details:
- Cleaned and reconciled ConditionalScoreEstimator imports/init and typing in sbi/neural_nets/estimators/score_estimator.py, keeping beta_min/beta_max and device tracking consistent with the new base.
- Dropped deleted legacy files to match main: sbi/inference/trainers/npse/npse.py, sbi/neural_nets/net_builders/score_nets.py, and tests/score_estimator_test.py.

Author: janfb

.github/codecov.yml

@@ -22,6 +22,21 @@ coverage:
         threshold: 2% # allow the coverage to drop by X%, and posting a success status
         if_ci_failed: error # will set the status to success only if the CI is successful, alternative: success
 
+# Flag configuration for carryforward
+# - 'fast': coverage from fast tests (run on every PR)
+# - 'full': coverage from full test suite including slow tests (run on main)
+#   carryforward ensures slow test coverage from main is included in PR reports
+flag_management:
+  individual_flags:
+    - name: fast
+      paths:
+        - sbi/
+      carryforward: false
+    - name: full
+      paths:
+        - sbi/
+      carryforward: true
+
 comment:
   layout: "diff, flags, files"
   behavior: default # update if exists, otherwise post new

.github/workflows/build_docs.yml

@@ -36,6 +36,8 @@ jobs:
       run: |
         cd mkdocs
         uv run jupyter nbconvert --to markdown ../docs/tutorials/*.ipynb --output-dir docs/tutorials/
+        uv run jupyter nbconvert --to markdown ../docs/advanced_tutorials/*.ipynb --output-dir docs/tutorials/
+        uv run jupyter nbconvert --to markdown ../docs/how_to_guide/09_sampler_interface.ipynb --output-dir docs/tutorials/
 
     - name: Configure Git user for bot
       run: |

.github/workflows/cd.yml

@@ -29,24 +29,34 @@ jobs:
         fetch-depth: 0
         lfs: false
 
-    - name: Install uv and set the python version
-      uses: astral-sh/setup-uv@v5
+    - name: Set up Python
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
+
+    - name: Set up uv
+      uses: astral-sh/setup-uv@v5
+      with:
         enable-cache: true
         cache-dependency-glob: "pyproject.toml"
 
     - name: Install dependencies with uv
       run: uv sync --extra dev
 
     - name: Run the fast and the slow CPU tests with coverage
-      run: uv run pytest -v -x -n auto -m "not gpu" --cov=sbi --cov-report=xml tests/
+      run: uv run pytest -v -x -n auto -m "not gpu" --cov=sbi --cov-report=xml --junitxml=junit.xml -o junit_family=legacy tests/
 
     - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v4-beta
+      uses: codecov/codecov-action@v4
       with:
         env_vars: OS,PYTHON
         file: ./coverage.xml
-        flags: unittests
+        flags: full
         name: codecov-sbi-all-cpu
         token: ${{ secrets.CODECOV_TOKEN }}
+
+    - name: Upload test results to Codecov
+      if: ${{ !cancelled() }}
+      uses: codecov/test-results-action@v1
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/ci.yml

@@ -31,17 +31,19 @@ jobs:
         fetch-depth: 0
         lfs: false
 
-    - name: Install uv and set the python version
-      uses: astral-sh/setup-uv@v5
+    - name: Set up Python
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
+
+    - name: Set up uv
+      uses: astral-sh/setup-uv@v5
+      with:
         enable-cache: true
         cache-dependency-glob: "pyproject.toml"
 
     - name: Install dependencies with uv
-      run: |
-        uv pip install torch --extra-index-url https://download.pytorch.org/whl/cpu
-        uv pip install -e .[dev]
+      run: uv sync --extra dev
 
     - name: Cache uv dependencies
       uses: actions/cache@v4
@@ -51,26 +53,20 @@ jobs:
         restore-keys: |
           uv-${{ runner.os }}-${{ matrix.python-version }}-
 
-    # - name: Cache testmon data
-    #   uses: actions/cache@v4
-    #   with:
-    #     path: .testmondata
-    #     key: testmon-${{ runner.os }}-${{ matrix.python-version }}-${{ github.ref }}
-    #     restore-keys: |
-    #       testmon-${{ runner.os }}-${{ matrix.python-version }}-
-
-    # - name: Fix file permissions for testmondata
-    #   run: |
-    #     [ -f .testmondata ] && chmod u+w .testmondata || true
-
     - name: Run fast CPU tests with coverage
-      run: uv run pytest -v -n auto -m "not slow and not gpu" --cov=sbi --cov-report=xml --splitting-algorithm least_duration --splits ${{ matrix.split_size }} --group ${{ matrix.group_number }} tests/ #--testmon-forceselect
+      run: uv run pytest -v -n auto -m "not slow and not gpu" --cov=sbi --cov-report=xml --junitxml=junit.xml -o junit_family=legacy --splitting-algorithm least_duration --splits ${{ matrix.split_size }} --group ${{ matrix.group_number }} tests/
 
     - name: Upload coverage to Codecov
       uses: codecov/codecov-action@v4
       with:
         env_vars: OS,PYTHON
         file: ./coverage.xml
-        flags: unittests
+        flags: fast
         name: codecov-sbi-fast-cpu
         token: ${{ secrets.CODECOV_TOKEN }}
+
+    - name: Upload test results to Codecov
+      if: ${{ !cancelled() }}
+      uses: codecov/test-results-action@v1
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/license-check.yml

@@ -0,0 +1,64 @@
+name: License Header Check
+
+on: [pull_request, workflow_dispatch]
+
+defaults:
+  run:
+    shell: bash
+
+jobs:
+  check-license-headers:
+    name: Check License Headers
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+        lfs: false
+
+    - name: Check license headers
+      run: |
+          expected_header_1="# This file is part of sbi, a toolkit for simulation-based inference. sbi is licensed"
+          expected_header_2="# under the Apache License Version 2.0, see <https://www.apache.org/licenses/>"
+
+          invalid_files=()
+
+          while IFS= read -r file; do
+              file_header_1=$(head -n 1 "$file")
+              file_header_2=$(head -n 2 "$file" | tail -n 1)
+
+              invalid=false
+
+              # Check the first line
+              if [ "$file_header_1" != "$expected_header_1" ]; then
+                  invalid=true
+              fi
+
+              # Check the second line
+              if [ "$file_header_2" != "$expected_header_2" ]; then
+                  invalid=true
+              fi
+
+              # If either line is invalid, add to the list
+              if [ "$invalid" = true ]; then
+                  invalid_files+=("$file")
+              fi
+
+          done < <(find sbi tests -name "*.py" -type f)
+
+          # Report results
+          if [ ${#invalid_files[@]} -ne 0 ]; then
+              echo "❌ Missing or incorrect license headers in the following files:"
+              for file in "${invalid_files[@]}"; do
+                  echo "   $file"
+              done
+              echo "Make sure the following two lines are provided and correctly spelled at the very start of all above listed files"
+              echo "$expected_header_1"
+              echo "$expected_header_2"
+              exit 1
+          else
+              echo "✅ All files have the correct license headers."
+              exit 0
+          fi

.github/workflows/publish.yml

@@ -71,19 +71,18 @@ jobs:
         name: python-package-distributions
         path: dist/
     - name: Sign the dists with Sigstore
-      uses: sigstore/gh-action-sigstore-python@v2.1.1
+      uses: sigstore/gh-action-sigstore-python@v3.0.0
       with:
         inputs: >-
           ./dist/*.tar.gz
           ./dist/*.whl
-    - name: Create GitHub Release
+    - name: Ensure GitHub Release exists (no-op if already exists)
       env:
         GITHUB_TOKEN: ${{ github.token }}
-      run: >-
-        gh release create
-        '${{ github.ref_name }}'
-        --repo '${{ github.repository }}'
-        --notes ""
+      run: |
+        # If a release for this tag already exists (e.g., created via GH UI), skip creation.
+        gh release view '${{ github.ref_name }}' --repo '${{ github.repository }}' >/dev/null 2>&1 || \
+          gh release create '${{ github.ref_name }}' --repo '${{ github.repository }}' --notes ""
     - name: Upload artifact signatures to GitHub Release
       env:
         GITHUB_TOKEN: ${{ github.token }}

.gitignore

@@ -2,11 +2,13 @@
 .sbi_env/
 *sbi-logs/
 /docs/site/*
+/docs/reference/_autosummary/*
 
 # Development files and python cache
 /*.pyc
 /*.egg
 /*.egg-info
+.venv*
 
 # Notebook checkpoints
 .ipynb_checkpoints
@@ -100,3 +102,7 @@ target/
 # uv
 uv.lock
 .python-version
+
+# Serena cache
+.serena/
+.claude/