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‎.github/workflows/build_docs.yml‎

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

‎.github/workflows/cd.yml‎

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

‎.github/workflows/ci.yml‎

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fetch-depth: 0
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lfs: false
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- name: Install uv and set the python version
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uses: astral-sh/setup-uv@v5
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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- name: Set up uv
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uses: astral-sh/setup-uv@v5
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with:
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enable-cache: true
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cache-dependency-glob: "pyproject.toml"
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- name: Install dependencies with uv
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run: |
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uv pip install torch --extra-index-url https://download.pytorch.org/whl/cpu
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uv pip install -e .[dev]
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run: uv sync --extra dev
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- name: Cache uv dependencies
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uses: actions/cache@v4
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restore-keys: |
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uv-${{ runner.os }}-${{ matrix.python-version }}-
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# - name: Cache testmon data
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# uses: actions/cache@v4
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# with:
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# path: .testmondata
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# key: testmon-${{ runner.os }}-${{ matrix.python-version }}-${{ github.ref }}
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# restore-keys: |
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# testmon-${{ runner.os }}-${{ matrix.python-version }}-
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# - name: Fix file permissions for testmondata
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# run: |
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# [ -f .testmondata ] && chmod u+w .testmondata || true
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- name: Run fast CPU tests with coverage
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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
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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/
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- name: Upload coverage to Codecov
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uses: codecov/codecov-action@v4
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flags: unittests
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name: codecov-sbi-fast-cpu
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token: ${{ secrets.CODECOV_TOKEN }}
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- name: Upload test results to Codecov
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if: ${{ !cancelled() }}
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uses: codecov/test-results-action@v1
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with:
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token: ${{ secrets.CODECOV_TOKEN }}

‎.github/workflows/license-check.yml‎

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

‎.github/workflows/publish.yml‎

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name: python-package-distributions
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path: dist/
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- name: Sign the dists with Sigstore
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uses: sigstore/gh-action-sigstore-python@v2.1.1
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uses: sigstore/gh-action-sigstore-python@v3.0.0
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with:
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inputs: >-
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./dist/*.tar.gz

‎.gitignore‎

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.sbi_env/
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*sbi-logs/
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/docs/site/*
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/docs/reference/_autosummary/*
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# Development files and python cache
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/*.pyc
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/*.egg
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/*.egg-info
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.venv*
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# Notebook checkpoints
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.ipynb_checkpoints
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# uv
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uv.lock
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.python-version
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# Serena cache
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.serena/

‎CHANGELOG.md‎

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# Changelog
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## v0.25.0
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### ✨ Highlights
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#### 🚀 New Inference Methods
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* **MNPE class mixed parameter (similar to MNLE)** by @dgedon in https://github.com/sbi-dev/sbi/pull/1362
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* **Implementation of SNPE-B (#199)** by @etouron1 in https://github.com/sbi-dev/sbi/pull/1471
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#### 🧠 Neural Network Architectures & Embedding Networks
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* **Add transformer embedding net** by @NicolasRR in https://github.com/sbi-dev/sbi/pull/1494
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* **Add embedding net that uses 1D causal convolutions (#1459)** by @Aranka-S in https://github.com/sbi-dev/sbi/pull/1499
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* **Add LRU-backed embedding networks** by @famura in https://github.com/sbi-dev/sbi/pull/1512
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* **Add ResNet as embedding model** by @StefanWahl in https://github.com/sbi-dev/sbi/pull/1472
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* **Spectral convolution embedding net** by @L-in-da in https://github.com/sbi-dev/sbi/pull/1503
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#### ⭐ Major Features & Capabilities
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* **Unify flow matching and score-based models** by @StarostinV in https://github.com/sbi-dev/sbi/pull/1497
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* **Model misspecification detection based on MMD** by @coschroeder in https://github.com/sbi-dev/sbi/pull/1502
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* **Marginal estimator log-prob based test for misspecification** by @swag2198 in https://github.com/sbi-dev/sbi/pull/1522
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* **Adding interface for unconditional flow training** by @plcrodrigues in https://github.com/sbi-dev/sbi/pull/1470
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* **Support using trained estimators in Pyro models** by @sethaxen in https://github.com/sbi-dev/sbi/pull/1491
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* **Add util to generate mcmc samples from user defined potential (#1405)** by @hayden-johnson in https://github.com/sbi-dev/sbi/pull/1483
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* **Logit transform** by @anastasiakrouglova in https://github.com/sbi-dev/sbi/pull/1485
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#### 📚 Documentation & Tutorials
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* **Tutorial on new features for score-based methods #1392** by @touronc in https://github.com/sbi-dev/sbi/pull/1489
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* **Docs: Introduce Readthedocs website** by @michaeldeistler in https://github.com/sbi-dev/sbi/pull/1463
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### 🐛 Bug Fixes
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* z_score correct order in Zuko by @anastasiakrouglova in https://github.com/sbi-dev/sbi/pull/1492
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* Minor fix when moving thetas from GPU to CPU by @famura in https://github.com/sbi-dev/sbi/pull/1515
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* Minor fix while using unconditional density estimator and LRU embedding by @ARna06 in https://github.com/sbi-dev/sbi/pull/1556
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* fix: replace 'in' operator with '==' for proper classifier comparison by @abelaba in https://github.com/sbi-dev/sbi/pull/1550
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* flowmatching condition shape fix by @gmoss13 in https://github.com/sbi-dev/sbi/pull/1584
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* patch for torch bug in tarp, run torch.histogram with cpu-only tensor by @psteinb in https://github.com/sbi-dev/sbi/pull/1596
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* fix failing tarp test by @janfb in https://github.com/sbi-dev/sbi/pull/1628
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* fix: cap max_sampling_batch_size to prevent excessive memory by @janfb in https://github.com/sbi-dev/sbi/pull/1624
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* 1561 computation of denoising posterior precision matrix in jac method score fn iid by @manuelgloeckler in https://github.com/sbi-dev/sbi/pull/1636
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* fix xfail test, fix deprecation warnings by @janfb in https://github.com/sbi-dev/sbi/pull/1642
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* fix: iid-score device handling by @janfb in https://github.com/sbi-dev/sbi/pull/1650
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### 🛠️ Maintenance & Improvements
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#### 🔧 Code Quality & Refactoring
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* Refactoring flow and score matching classes and nets by @manuelgloeckler in https://github.com/sbi-dev/sbi/pull/1544
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* Rename inference trainer classes by @abelaba in https://github.com/sbi-dev/sbi/pull/1605
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* Rename VectorFieldInference to VectorFieldTrainer by @abelaba in https://github.com/sbi-dev/sbi/pull/1614
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* Refactor build_posterior to Eliminate Duplication Across Trainers by @abelaba in https://github.com/sbi-dev/sbi/pull/1610
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* Refactor build posterior method arguments to use Literals by @abelaba in https://github.com/sbi-dev/sbi/pull/1606
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* Refactor build_posterior Posterior Configuration Using Dataclasses by @abelaba in https://github.com/sbi-dev/sbi/pull/1619
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* Use TypeAlias and consistent naming for sbi types by @janfb in https://github.com/sbi-dev/sbi/pull/1637
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* Add protocol for estimator builder by @abelaba in https://github.com/sbi-dev/sbi/pull/1633
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* Improve abc implementation by @janfb in https://github.com/sbi-dev/sbi/pull/1615
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* Refactor RatioEstimator to subclass ConditionalEstimator @abelaba in https://github.com/sbi-dev/sbi/pull/1652
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#### 🏷️ Type Hints & API Improvements
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* fix: add enum for flow options to fix type hints. by @janfb in https://github.com/sbi-dev/sbi/pull/1562
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* fix LC2ST kwarg typing by @janfb in https://github.com/sbi-dev/sbi/pull/1565
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* fix: Update RatioEstimator classifier argument to use a Protocol by @abelaba in https://github.com/sbi-dev/sbi/pull/1582
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* Update append_simulations return type to Self by @abelaba in https://github.com/sbi-dev/sbi/pull/1622
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* Deprecation Warnings for build_posterior stringly typed parameters by @abelaba in https://github.com/sbi-dev/sbi/pull/1627
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#### 🧪 Testing & CI/CD
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* Testmon by @manuelgloeckler in https://github.com/sbi-dev/sbi/pull/1452
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* disable testmon for now by @manuelgloeckler in https://github.com/sbi-dev/sbi/pull/1467
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* chore: Use pytest-split plugin in ci workflow by @schroedk in https://github.com/sbi-dev/sbi/pull/1465
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* tests: refactor "not slow" tests to be not so slow by @janfb in https://github.com/sbi-dev/sbi/pull/1495
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* Test for known pytorch distribution transform issue by @dgedon in https://github.com/sbi-dev/sbi/pull/1504
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* xfail scan test on python 3.13 by @manuelgloeckler in https://github.com/sbi-dev/sbi/pull/1533
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* Gpu test for VectorFieldPosterior by @jorobledo in https://github.com/sbi-dev/sbi/pull/1542
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* set vector field iid-tests xfail by @janfb in https://github.com/sbi-dev/sbi/pull/1554
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* Changed the xfail condition for LRU tests with mode='scan' by @famura in https://github.com/sbi-dev/sbi/pull/1552
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* Fix/lru test by @Matthijspals in https://github.com/sbi-dev/sbi/pull/1568
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* refactor sbc funcs and tests by @janfb in https://github.com/sbi-dev/sbi/pull/1578
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* chore: remove testmon, add codecov test analytics by @janfb in https://github.com/sbi-dev/sbi/pull/1592
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* chore: reorder setup steps for Python and uv in CI/CD workflows by @janfb in https://github.com/sbi-dev/sbi/pull/1601
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* Fix/lc2st numpy type fixes by @janfb in https://github.com/sbi-dev/sbi/pull/1613
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* Fix failing CI on main. by @janfb in https://github.com/sbi-dev/sbi/pull/1618
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* Fix slow vector field tests by @janfb in https://github.com/sbi-dev/sbi/pull/1657
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#### 📖 Documentation & Website
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* Fix tests for new docs by @michaeldeistler in https://github.com/sbi-dev/sbi/pull/1475
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* Prevent notebook execution upon doc build by @michaeldeistler in https://github.com/sbi-dev/sbi/pull/1477
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* Fix broken links on website by @michaeldeistler in https://github.com/sbi-dev/sbi/pull/1480
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* fix: Update documentation folder path by @abelaba in https://github.com/sbi-dev/sbi/pull/1510
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* fix path to contribute.md by @psteinb in https://github.com/sbi-dev/sbi/pull/1507
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* Add utils to docs by @sethaxen in https://github.com/sbi-dev/sbi/pull/1520
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* Update new Readthedocs website by @michaeldeistler in https://github.com/sbi-dev/sbi/pull/1519
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* fix broken links on new website by @michaeldeistler in https://github.com/sbi-dev/sbi/pull/1538
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* Fixups for new website landing page by @michaeldeistler in https://github.com/sbi-dev/sbi/pull/1539
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* Fix: add tutorial page to mkdocs website by @michaeldeistler in https://github.com/sbi-dev/sbi/pull/1540
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* Fix broken links in some tutorials by @michaeldeistler in https://github.com/sbi-dev/sbi/pull/1541
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* Add examples to documentation by @jorobledo in https://github.com/sbi-dev/sbi/pull/1548
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* docs: Add importance_sampling_parameters to build_posterior docstring. by @abelaba in https://github.com/sbi-dev/sbi/pull/1558
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* Add missing arguments to LikelihoodEstimator and RatioEstimator docstrings. by @abelaba in https://github.com/sbi-dev/sbi/pull/1571
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* Fixups for new RTD website by @michaeldeistler in https://github.com/sbi-dev/sbi/pull/1573
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* Tutorial with a more representative training loop by @michaeldeistler in https://github.com/sbi-dev/sbi/pull/1574
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* Fixups for rendering of HH tutorial notebook by @michaeldeistler in https://github.com/sbi-dev/sbi/pull/1575
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* fix for colors in Hodgkin-Huxley notebook by @michaeldeistler in https://github.com/sbi-dev/sbi/pull/1576
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* Add citations to how-to guide by @michaeldeistler in https://github.com/sbi-dev/sbi/pull/1579
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* Clarify fullscreen view of applications-explorer by @michaeldeistler in https://github.com/sbi-dev/sbi/pull/1580
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* Fixups for the documentation by @michaeldeistler in https://github.com/sbi-dev/sbi/pull/1585
114+
* fixed misrendered bullet list, tested locally by @psteinb in https://github.com/sbi-dev/sbi/pull/1594
115+
* Improvements to L-C2ST tutorial by @michaeldeistler in https://github.com/sbi-dev/sbi/pull/1588
116+
* docs: Change colortheme in light mode by @michaeldeistler in https://github.com/sbi-dev/sbi/pull/1638
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* Posterior parameters doc by @abelaba in https://github.com/sbi-dev/sbi/pull/1644
118+
* fix contributing links by @janfb in https://github.com/sbi-dev/sbi/pull/1647
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* docs: add posterior parameters dataclass how to guide by @abelaba in https://github.com/sbi-dev/sbi/pull/1654
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#### 🏗️ Infrastructure & Dependencies
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* Add uv support by @abelaba in https://github.com/sbi-dev/sbi/pull/1518
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* switch to numfocus code of conduct by @janfb in https://github.com/sbi-dev/sbi/pull/1560
125+
* Update readme with new JOSS citation by @janfb in https://github.com/sbi-dev/sbi/pull/1564
126+
* update numfocus code of conduct by @janfb in https://github.com/sbi-dev/sbi/pull/1602
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* Added Apache License reference comments to source files + CI bash script check by @nMaax in https://github.com/sbi-dev/sbi/pull/1599
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#### 👥 User Experience & Warnings
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* Change xfail to skipif as outcome is not consistent by @gmoss13 in https://github.com/sbi-dev/sbi/pull/1487
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* Add warning when using append_simulations with exclude_invalid_x=True by @abelaba in https://github.com/sbi-dev/sbi/pull/1486
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* Batch sampling slow without warning by @dgedon in https://github.com/sbi-dev/sbi/pull/1490
134+
* Clarify pbar annotation in sample_batched for DirectPosterior by @StefanWahl in https://github.com/sbi-dev/sbi/pull/1493
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#### 🎮 GPU Support & Device Handling
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* Prior to(device) by @jorobledo in https://github.com/sbi-dev/sbi/pull/1505
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* posterior.to(device) by @jorobledo in https://github.com/sbi-dev/sbi/pull/1527
140+
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#### 🔧 Miscellaneous Improvements
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* ref: update tests, add types and docs to marginal trainer by @janfb in https://github.com/sbi-dev/sbi/pull/1516
144+
* integrate sbi application eplorer by @lappalainenj in https://github.com/sbi-dev/sbi/pull/1567
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* fix: update notebook references by @emmanuel-ferdman in https://github.com/sbi-dev/sbi/pull/1563
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* Update sbiutils.py to use one-dimensional batch by @vivienr in https://github.com/sbi-dev/sbi/pull/1577
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* fix: remove empty list default argument by @abelaba in https://github.com/sbi-dev/sbi/pull/1608
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* fix: throw exception on unsupported activation function by @emmanuel-ferdman in https://github.com/sbi-dev/sbi/pull/1609
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* fix: resolve logger warnings by @emmanuel-ferdman in https://github.com/sbi-dev/sbi/pull/1598
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* fix paths by @manuelgloeckler in https://github.com/sbi-dev/sbi/pull/1641
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### 🎉 New Contributors
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* @abelaba made their first contribution in https://github.com/sbi-dev/sbi/pull/1486
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* @dgedon made their first contribution in https://github.com/sbi-dev/sbi/pull/1490
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* @StefanWahl made their first contribution in https://github.com/sbi-dev/sbi/pull/1493
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* @touronc made their first contribution in https://github.com/sbi-dev/sbi/pull/1489
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* @jorobledo made their first contribution in https://github.com/sbi-dev/sbi/pull/1505
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* @hayden-johnson made their first contribution in https://github.com/sbi-dev/sbi/pull/1483
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* @sethaxen made their first contribution in https://github.com/sbi-dev/sbi/pull/1491
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* @etouron1 made their first contribution in https://github.com/sbi-dev/sbi/pull/1471
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* @Aranka-S made their first contribution in https://github.com/sbi-dev/sbi/pull/1499
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* @swag2198 made their first contribution in https://github.com/sbi-dev/sbi/pull/1522
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* @StarostinV made their first contribution in https://github.com/sbi-dev/sbi/pull/1497
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* @L-in-da made their first contribution in https://github.com/sbi-dev/sbi/pull/1503
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* @NicolasRR made their first contribution in https://github.com/sbi-dev/sbi/pull/1494
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* @vivienr made their first contribution in https://github.com/sbi-dev/sbi/pull/1577
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**Full Changelog**: https://github.com/sbi-dev/sbi/compare/v0.24.0...v0.25.0
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## v0.24.0
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### ✨ Highlights

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