Merge branch 'dev' into pr/202

.github/workflows/tests.yaml

@@ -37,15 +37,16 @@ jobs:
 
       - name: Run Linter
         run: |
-          ruff check --config pyproject.toml
+          ruff check --config pyproject.toml --verbose
 
       - name: Run Formatter
         run: |
-          ruff format --check --config pyproject.toml
+          ruff format --check --config pyproject.toml --verbose
 
   test:
     runs-on: ${{ matrix.os }}
     strategy:
+      fail-fast: false
       matrix:
         os: [ubuntu-latest, windows-latest]
         python-version: ["3.10", "3.11"]
@@ -69,7 +70,7 @@ jobs:
       - name: Install JAX
         if: ${{ matrix.backend == 'jax' }}
         run: |
-          pip install -U "jax[cpu]"
+          pip install -U jax
       - name: Install NumPy
         if: ${{ matrix.backend == 'numpy' }}
         run: |
@@ -90,6 +91,7 @@ jobs:
           conda config --show-sources
           conda config --show
           printenv | sort
+          conda env export
 
       - name: Run Tests
         run: |

CODE_OF_CONDUCT.md

@@ -0,0 +1,128 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, religion, or sexual identity
+and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the
+  overall community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or
+  advances of any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email
+  address, without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement, contact person is
+Stefan T. Radev (<[email protected]>).
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series
+of actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or
+permanent ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior,  harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within
+the community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.0, available at
+https://www.contributor-covenant.org/version/2/0/code_of_conduct.html.
+
+Community Impact Guidelines were inspired by [Mozilla's code of conduct
+enforcement ladder](https://github.com/mozilla/diversity).
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see the FAQ at
+https://www.contributor-covenant.org/faq. Translations are available at
+https://www.contributor-covenant.org/translations.

CONTRIBUTING.md

@@ -71,6 +71,16 @@ pre-commit install
 We recommend using the PyTorch backend for development.
 Be careful not to downgrade your keras version when installing the backend.
 
+You can also install a triple backend cuda environment using `cuda.yaml`:
+
+```bash
+conda env create --file cuda.yaml --name bf-cuda
+```
+
+Note that we cannot guarantee that this environment file will always work,
+as it is not tested frequently or across devices.
+It is provided merely as a convenience. For reliability, install only a single backend.
+
 ### 3. Implement your changes
 
 In general, we recommend a test-driven development approach:

README.md

@@ -1,6 +1,6 @@
 # BayesFlow <img src="img/bayesflow_hex.png" style="float: right; width: 20%; height: 20%;" align="right" alt="BayesFlow Logo" />
-![GitHub Actions Workflow Status](https://img.shields.io/github/actions/workflow/status/stefanradev93/bayesflow/tests.yaml?style=for-the-badge&label=Tests)
-![Codecov](https://img.shields.io/codecov/c/github/stefanradev93/bayesflow/streamlined-backend?style=for-the-badge)
+![GitHub Actions Workflow Status](https://img.shields.io/github/actions/workflow/status/bayesflow-org/bayesflow/tests.yaml?style=for-the-badge&label=Tests)
+![Codecov](https://img.shields.io/codecov/c/github/bayesflow-org/bayesflow/dev?style=for-the-badge)
 [![DOI](https://img.shields.io/badge/DOI-10.21105%2Fjoss.05702-blue?style=for-the-badge)](https://doi.org/10.21105/joss.05702)
 ![PyPI - License](https://img.shields.io/pypi/l/bayesflow?style=for-the-badge)
 
@@ -22,14 +22,14 @@ when working with intractable simulators whose behavior as a whole is too
 complex to be described analytically. The figure below presents a higher-level
 overview of neurally bootstrapped Bayesian inference.
 
-<img src="https://github.com/stefanradev93/BayesFlow/blob/master/img/high_level_framework.png?raw=true" width=80% height=80%>
+<img src="https://github.com/bayesflow-org/bayesflow/blob/master/img/high_level_framework.png?raw=true" width=80% height=80%>
 
 
 ## Disclaimer
 
 This is the current dev version of BayesFlow, which constitutes a complete refactor of the library built on Keras 3. This way, you can now use any of the major deep learning libraries as backend for BayesFlow. The refactor is still work in progress with some of the advanced features not yet implemented. We are actively working on them and promise to catch up soon.
 
-If you encounter any issues, please don't hesitate to open an issue here on [Github](https://github.com/stefanradev93/BayesFlow/issues) or ask questions on our [Discourse Forums](https://discuss.bayesflow.org/).
+If you encounter any issues, please don't hesitate to open an issue here on [Github](https://github.com/bayesflow-org/bayesflow/issues) or ask questions on our [Discourse Forums](https://discuss.bayesflow.org/).
 
 ## Install
 
@@ -41,20 +41,22 @@ First, install one machine learning backend of choice. Note that BayesFlow **wil
 - [Install PyTorch](https://pytorch.org/get-started/locally/)
 - [Install TensorFlow](https://www.tensorflow.org/install)
 
-If you are new to machine learning and don't know which one to use, we recommend PyTorch to get started.
+If you don't know which backend to use, we recommend JAX to get started.
+It is the fastest backend and already works pretty reliably with the current
+dev version of bayesflow.
 
 Once installed, [set the backend environment variable as required by keras](https://keras.io/getting_started/#configuring-your-backend). For example, inside your Python script write:
 
 ```python
 import os
-os.environ["KERAS_BACKEND"] = "torch"
+os.environ["KERAS_BACKEND"] = "jax"
 import bayesflow
 ```
 
 If you use conda, you can alternatively set this individually for each environment in your terminal. For example:
 
 ```bash
-conda env config vars set KERAS_BACKEND=torch
+conda env config vars set KERAS_BACKEND=jax
 ```
 
 This way, you also don't have to manually set the backend every time you are starting Python to use BayesFlow.
@@ -66,7 +68,7 @@ This way, you also don't have to manually set the backend every time you are sta
 You can install the dev version with pip:
 
 ```bash
-pip install git+https://github.com/stefanradev93/bayesflow@dev
+pip install git+https://github.com/bayesflow-org/bayesflow@dev
 ```
 
 ### Using Conda (coming soon)
@@ -78,7 +80,7 @@ The dev version is not conda-installable yet.
 If you want to contribute to BayesFlow, we recommend installing the dev branch from source:
 
 ```bash
-git clone -b dev [email protected]:stefanradev93/bayesflow.git
+git clone -b dev [email protected]:bayesflow-org/bayesflow.git
 cd <local-path-to-bayesflow-repository>
 conda env create --file environment.yaml --name bayesflow
 ```
@@ -87,11 +89,16 @@ conda env create --file environment.yaml --name bayesflow
 
 Check out some of our walk-through notebooks below. We are actively working on porting all notebooks to the new interface so more will be available soon!
 
-1. [Two moons toy example with flow matching](examples/TwoMoons_FlowMatching.ipynb)
+1. [Two moons starter toy example](examples/TwoMoons_StarterNotebook.ipynb)
+2. [Linear regression](examples/Linear_Regression.ipynb)
+3. [Bayesian experimental design](examples/Bayesian_Experimental_Design.ipynb)
+4. [SIR model with custom summary network](examples/SIR_PosteriorEstimation.ipynb)
+5. [Hyperparameter optimization](examples/Hyperparameter_Optimization.ipynb)
+6. Coming soon...
 
 ## Documentation \& Help
 
-Documentation is available at https://bayesflow.org. Please use the [BayesFlow Forums](https://discuss.bayesflow.org/) for any BayesFlow-related questions and discussions, and [GitHub Issues](https://github.com/stefanradev93/BayesFlow/issues) for bug reports and feature requests.
+Documentation is available at https://bayesflow.org. Please use the [BayesFlow Forums](https://discuss.bayesflow.org/) for any BayesFlow-related questions and discussions, and [GitHub Issues](https://github.com/bayesflow-org/bayesflow/issues) for bug reports and feature requests.
 
 ## Citing BayesFlow
 

bayesflow/__init__.py

@@ -1,7 +1,7 @@
 from . import (
     approximators,
     benchmarks,
-    data_adapters,
+    adapters,
     datasets,
     diagnostics,
     distributions,
@@ -11,8 +11,9 @@
 )
 
 from .approximators import ContinuousApproximator
+from .adapters import Adapter
 from .datasets import OfflineDataset, OnlineDataset, DiskDataset
-from .benchmarks import TwoMoons
+from .simulators import make_simulator
 
 
 def setup():

bayesflow/adapters/__init__.py

@@ -0,0 +1,2 @@
+from . import transforms
+from .adapter import Adapter