Merge branch 'dev' of https://github.com/bayesflow-org/bayesflow into dev

Author: stefanradev93

.github/workflows/multiversion-docs.yaml

@@ -43,7 +43,7 @@ jobs:
         run: |
           cd ./repo/docsrc
           make clean
-          make docs-sequential
+          make production-docs-sequential
 
       - name: Checkout gh-pages-dev
         uses: actions/checkout@v3
@@ -55,7 +55,7 @@ jobs:
         run: |
           cd ./gh-pages-dev
           git rm --quiet -rf .
-          cp -R ../repo/docs/* ./
+          cp -r ../repo/docs/. ./
           git config --local user.email ""
           git config --local user.name "github-actions"
           git add -A

.github/workflows/style.yaml

@@ -0,0 +1,40 @@
+name: Check Code Style
+
+on:
+  workflow_dispatch:
+  pull_request:
+    branches:
+      - main
+      - dev
+      - update-workflows
+  push:
+    branches:
+      - main
+      - dev
+      - update-workflows
+
+jobs:
+  check-code-style:
+    name: Check Code Style
+
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+
+      - name: Install Ruff
+        run: |
+          pip install -U pip setuptools wheel
+          pip install ruff
+
+      - name: Run Linter
+        run: ruff check --config pyproject.toml --verbose
+
+      - name: Run Formatter
+        run: ruff format --config pyproject.toml --check --verbose

.github/workflows/test-docs.yaml

@@ -31,7 +31,7 @@ jobs:
         run: |
           cd ./docsrc
           make clean
-          make local
+          make local-docs
       - name: Clean up
         run: |
           cd ./docsrc

.github/workflows/tests.yaml

@@ -1,5 +1,5 @@
 
-name: Tests
+name: Multi-Backend Tests
 
 on:
   workflow_dispatch:
@@ -12,105 +12,82 @@ on:
       - main
       - dev
 
+defaults:
+  run:
+    shell: bash
 
-jobs:
-  lint:
-    runs-on: ubuntu-latest
-    defaults:
-      run:
-        shell: bash -el {0}
-
-    steps:
-      - name: Checkout code
-        uses: actions/checkout@v4
-
-      - name: Set up Conda
-        uses: conda-incubator/setup-miniconda@v3
-        with:
-          environment-file: environment.yaml
-          python-version: "3.10"
-
-      - name: Show Environment Info
-        run: |
-          conda info
-          conda list
-          conda config --show-sources
-          conda config --show
-          printenv | sort
-
-      - name: Run Linter
-        run: |
-          ruff check --config pyproject.toml --verbose
-
-      - name: Run Formatter
-        run: |
-          ruff format --check --config pyproject.toml --verbose
 
+jobs:
   test:
-    runs-on: ${{ matrix.os }}
+    name: Run Multi-Backend Tests
+
     strategy:
-      fail-fast: false
       matrix:
         os: [ubuntu-latest, windows-latest]
         python-version: ["3.10", "3.11"]
         backend: ["jax", "tensorflow", "torch"]
-    defaults:
-      run:
-        shell: bash -el {0}
+
+    runs-on: ${{ matrix.os }}
+
     env:
       KERAS_BACKEND: ${{ matrix.backend }}
 
     steps:
-      - name: Checkout code
+      - name: Checkout Repository
         uses: actions/checkout@v4
 
-      - name: Set up Conda
-        uses: conda-incubator/setup-miniconda@v3
+      - name: Set up Python
+        uses: actions/setup-python@v5
         with:
-          environment-file: environment.yaml
           python-version: ${{ matrix.python-version }}
 
+      - name: Install Dependencies
+        run: |
+          pip install -U pip setuptools wheel
+          pip install .[test]
+
       - name: Install JAX
         if: ${{ matrix.backend == 'jax' }}
         run: |
           pip install -U jax
-      - name: Install NumPy
-        if: ${{ matrix.backend == 'numpy' }}
-        run: |
-          conda install numpy
-      - name: Install Tensorflow
+
+      - name: Install TensorFlow
         if: ${{ matrix.backend == 'tensorflow' }}
         run: |
           pip install -U tensorflow
+
       - name: Install PyTorch
         if: ${{ matrix.backend == 'torch' }}
         run: |
-          pip install torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cpu
+          pip install -U torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cpu
 
       - name: Show Environment Info
         run: |
-          conda info
-          conda list
-          conda config --show-sources
-          conda config --show
+          python --version
+          pip --version
           printenv | sort
-          conda env export
           pip list
 
       - name: Run Tests
         run: |
-          pytest -x
+          pytest -x -m "not slow"
 
-      - name: Create Coverage Report
+      - name: Run Slow Tests
+        # run all slow tests only on manual trigger
+        if: github.event_name == 'workflow_dispatch'
         run: |
-          coverage xml
+          pytest -m "slow"
 
       - name: Upload test results to Codecov
         if: ${{ !cancelled() }}
-        uses: codecov/test-results-action@v1
+        uses: codecov/codecov-action@v4
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
 
+      - name: Create Coverage Report
+        run: |
+          coverage xml
+
       - name: Upload Coverage Reports to CodeCov
         uses: codecov/codecov-action@v4
         with:

CONTRIBUTING.md

@@ -171,17 +171,17 @@ You can re-build the for your local state with:
 
 ```bash
 cd docsrc
-make clean && make local
+make clean && make local-docs
 # in case of issues, try `make clean-all`
 ```
 
 Note that files ignored by git (i.e., listed in `.gitignore`) are not included in the documentation.
 
-We also provide a multi-version documentation. To generate it, run
+We also provide a multi-version documentation, which renders the branches `main` and `stable-legacy`. To generate it, run
 
 ```bash
 cd docsrc
-make clean && make docs
+make clean && make production-docs
 ```
 
 This will create and cache virtual environments for the build at `docsrc/.docs_venvs`.

README.md

@@ -20,7 +20,7 @@ fueled by continuous progress in generative AI and Bayesian inference.
 <picture>
   <source media="(prefers-color-scheme: dark)" srcset="./img/bayesflow_landing_dark.jpg">
   <source media="(prefers-color-scheme: light)" srcset="./img/bayesflow_landing_light.jpg">
-  <img alt="dsd" src="./img/bayesflow_landing_dark.jpg">
+  <img alt="Overview graphic on using BayesFlow. It is split in three columns: 1. Choose your backend: BayesFlow is based on Keras, so you can choose PyTorch, TensorFlow or JAX. 2. Define your simulator: You specify your simulator in Python, and use it to generate simulated data. 3. Choose your algorithm: You define a generative neural network that you can use for estimation after training." src="./img/bayesflow_landing_dark.jpg">
 </picture>
 </div>
 
@@ -37,14 +37,14 @@ Using the high-level interface is easy, as demonstrated by the minimal working e
 import bayesflow as bf
 
 workflow = bf.BasicWorkflow(
-    inference_network=bf.networks.FlowMatching(),
-    summary_network=bf.networks.TimeSeriesTransformer(),
+    inference_network=bf.networks.CouplingFlow(),
+    summary_network=bf.networks.TimeSeriesNetwork(),
     inference_variables=["parameters"],
     summary_variables=["observables"],
     simulator=bf.simulators.SIR()
 )
 
-history = workflow.fit_online(epochs=50, batch_size=32, num_batches_per_epoch=500)
+history = workflow.fit_online(epochs=15, batch_size=32, num_batches_per_epoch=200)
 
 diagnostics = workflow.plot_default_diagnostics(test_data=300)
 ```
@@ -54,7 +54,7 @@ For an in-depth exposition, check out our walkthrough notebooks below.
 1. [Linear regression starter example](examples/Linear_Regression_Starter.ipynb)
 2. [From ABC to BayesFlow](examples/From_ABC_to_BayesFlow.ipynb)
 3. [Two moons starter example](examples/Two_Moons_Starter.ipynb)
-4. [Rapid iteration with point estimators](examples/Lotka_Volterra_point_estimation_and_expert_stats.ipynb)
+4. [Rapid iteration with point estimators](examples/Lotka_Volterra_Point_Estimation_and_Expert_Stats.ipynb)
 5. [SIR model with custom summary network](examples/SIR_Posterior_Estimation.ipynb)
 6. [Bayesian experimental design](examples/Bayesian_Experimental_Design.ipynb)
 7. [Simple model comparison example](examples/One_Sample_TTest.ipynb)
@@ -63,12 +63,16 @@ More tutorials are always welcome! Please consider making a pull request if you
 
 ## Install
 
-BayesFlow is available to install via pip:
+BayesFlow v2 is not yet installable via PyPI, but you can use the following command to install the latest version of the `main` branch:
 
 ```bash
-pip install bayesflow
+pip install git+https://github.com/bayesflow-org/bayesflow.git
 ```
 
+If you encounter problems with this or require more control, please refer to the instructions to install from source below.
+
+Note: `pip install bayesflow` will install the v1 version of BayesFlow.
+
 ### Backend
 
 To use BayesFlow, you will also need to install one of the following machine learning backends.

bayesflow/__init__.py

@@ -40,9 +40,13 @@ def setup():
         torch.autograd.set_grad_enabled(False)
 
         logging.warning(
-            "Autograd is disabled by default to avoid excessive memory usage. "
-            "If you need gradients (e.g., custom training loops), use\n"
-            "with torch.enable_grad():"
+            "\n"
+            "When using torch backend, we need to disable autograd by default to avoid excessive memory usage. Use\n"
+            "\n"
+            "with torch.enable_grad():\n"
+            "    ...\n"
+            "\n"
+            "in contexts where you need gradients (e.g. custom training loops)."
         )
 
 

bayesflow/adapters/__init__.py

@@ -1,3 +1,8 @@
+"""
+A collection of :py:class:`~bayesflow.adapters.Adapter` transforms, which tell BayesFlow how to interpret your
+:py:class:`~bayesflow.simulators.Simulator` output and plug it into neural networks for training and inference.
+"""
+
 from . import transforms
 from .adapter import Adapter