use ruff for linting and formatting, update CI

.github/workflows/tests.yml

@@ -1,40 +1,47 @@
-name: Tests
+name: Continuous Integration
 
 on:
   push:
     branches:
     - main
   pull_request:
-    branches:
-      - main
+  workflow_dispatch:
 
 jobs:
-  build:
+  pre-commit:
+    name: ruff and hooks.
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
+      with:
+        python-version: '3.8'
+    - uses: pre-commit/[email protected]
+      with:
+        extra_args: --all-files
+
+  test:
     name: Tests
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.8"]
+        torch-version: ["1.11", "2.2"]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         lfs: true
-
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       with:
-        python-version: '3.9.13'
-        architecture: 'x64'
+        python-version: ${{ matrix.python-version }}
 
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
+        pip install torch==${{ matrix.torch-version }} --extra-index-url https://download.pytorch.org/whl/cpu
         pip install -e .[dev]
-
-    - name: Check formatting with black
-      run: |
-        black --check sbi tests
-
-    - name: Check imports with isort
-      run: |
-        isort -c sbi tests
 
     - name: Check types with pyright
       run: |
@@ -45,7 +52,7 @@ jobs:
         pip install torchtestcase
         pip install pytest pytest-cov
         pytest -m "not slow and not gpu" tests/ --cov=sbi --cov-report=xml
-      
+
     - name: Upload coverage to Codecov
       uses: codecov/codecov-action@v3
       with:

.pre-commit-config.yaml

@@ -1,14 +1,18 @@
 repos:
-    -   repo: https://github.com/asottile/seed-isort-config
-        rev: v2.2.0
-        hooks:
-        - id: seed-isort-config
-    -   repo: https://github.com/PyCQA/isort
-        rev: 5.13.2
-        hooks:
-        - id: isort
-    -   repo: https://github.com/ambv/black
-        rev: 24.2.0
-        hooks:
-        - id: black
-          language_version: python3
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.2.2
+  hooks:
+    - id: ruff
+    - id: ruff-format
+      args: [--diff]
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.5.0
+  hooks:
+    - id: check-added-large-files
+    - id: check-merge-conflict
+    - id: check-toml
+    - id: check-yaml
+    - id: end-of-file-fixer
+    - id: mixed-line-ending
+      args: [--fix=lf]
+    - id: trailing-whitespace

MANIFEST.in

@@ -15,4 +15,4 @@ recursive-include docs *.py
 recursive-include examples *.py
 recursive-include sbi *.md
 recursive-include tests *.md
-recursive-include tests *.py
+recursive-include tests *.py

README.md

@@ -56,7 +56,7 @@ The following algorithms are currently available. You can find a tutorial on how
 ### Neural Posterior Estimation: amortized (NPE) and sequential (SNPE)
 
 * [`SNPE_A`](https://sbi-dev.github.io/sbi/reference/#sbi.inference.snpe.snpe_a.SNPE_A) (including amortized single-round `NPE`) from Papamakarios G and Murray I [_Fast ε-free Inference of Simulation Models with Bayesian Conditional Density Estimation_](https://proceedings.neurips.cc/paper/2016/hash/6aca97005c68f1206823815f66102863-Abstract.html) (NeurIPS 2016).
-  
+
 * [`SNPE_C`](https://sbi-dev.github.io/sbi/reference/#sbi.inference.snpe.snpe_c.SNPE_C) or `APT` from Greenberg D, Nonnenmacher M, and Macke J [_Automatic
   Posterior Transformation for likelihood-free
   inference_](https://arxiv.org/abs/1905.07488) (ICML 2019).
@@ -108,7 +108,7 @@ M. Durkan's `lfi`. `sbi` runs as a community project. See also [credits](https:/
 
 ## Citation
 
-If you use `sbi` consider citing the [sbi software paper](https://doi.org/10.21105/joss.02505), in addition to the original research articles describing the specific sbi-algorithm(s) you are using. 
+If you use `sbi` consider citing the [sbi software paper](https://doi.org/10.21105/joss.02505), in addition to the original research articles describing the specific sbi-algorithm(s) you are using.
 
 ```latex
 @article{tejero-cantero2020sbi,

docs/docs/citation.md

@@ -1,6 +1,6 @@
 # Citation
 
-If you use `sbi` consider citing the [sbi software paper](https://doi.org/10.21105/joss.02505), in addition to the original research articles describing the specific sbi-algorithm(s) you are using. 
+If you use `sbi` consider citing the [sbi software paper](https://doi.org/10.21105/joss.02505), in addition to the original research articles describing the specific sbi-algorithm(s) you are using.
 
 ```latex
 @article{tejero-cantero2020sbi,

docs/docs/faq/question_01_leakage.md

@@ -11,7 +11,7 @@ collect the remaining 10000 samples. Consider interrupting (Ctrl-C) and switchin
 
 The reason for this issue is described in more detail
 [here](https://arxiv.org/abs/2002.03712) and
-[here](https://arxiv.org/abs/1905.07488). The following fixes are possible:  
+[here](https://arxiv.org/abs/1905.07488). The following fixes are possible:
 
 - sample with MCMC: `samples = posterior((num_samples,), x=x_o, sample_with_mcmc=True)`.
 This approach will make sampling slower, but samples will not "leak".
@@ -26,4 +26,4 @@ interface](https://sbi-dev.github.io/sbi/tutorial/03_flexible_interface/), set
 statement "Using SNPE-C with non-atomic loss".
 
 - use a different algorithm, e.g., SNRE and SNLE. Note, however, that these algorithms
-can have different issues and potential pitfalls.  
+can have different issues and potential pitfalls.

docs/docs/faq/question_07_custom_prior.md

@@ -71,8 +71,8 @@ pass the bounds to the wrapper function such that `sbi` can pass them to torch
 from sbi.utils import process_prior
 
 custom_prior = CustomUniformPrior(torch.zeros(2), torch.ones(2))
-prior = process_prior(custom_prior, 
-                      custom_prior_wrapper_kwargs=dict(lower_bound=torch.zeros(2), 
+prior = process_prior(custom_prior,
+                      custom_prior_wrapper_kwargs=dict(lower_bound=torch.zeros(2),
                                                        upper_bound=torch.ones(2)))
 # use this wrapped prior in sbi...
 ```

docs/docs/reference.md

@@ -153,7 +153,7 @@
     selection:
       filters: [ "!^_", "^__", "!^__class__" ]
       inherited_members: true
-  
+
 ## Analysis
 
 ::: sbi.analysis.plot.pairplot

docs/docs/static/global.css

@@ -15,7 +15,7 @@ a[title="Edit this page"] {
 }
 
 .md-typeset .footnote-ref:before {
-  border-left: none !important; 
+  border-left: none !important;
   margin-left: -0.4em !important;
 }
 
@@ -62,4 +62,4 @@ td p {
 /* 100% width tables */
 .md-typeset__table {
   width: 100%;
-}
+}

docs/mkdocs.yml

@@ -21,14 +21,14 @@ nav:
       - Diagnostics:
         - Posterior predictive checks: tutorial/12_diagnostics_posterior_predictive_check.md
         - Simulation-based calibration: tutorial/13_diagnostics_simulation_based_calibration.md
-        - Density plots and MCMC diagnostics with ArviZ: tutorial/15_mcmc_diagnostics_with_arviz.md 
+        - Density plots and MCMC diagnostics with ArviZ: tutorial/15_mcmc_diagnostics_with_arviz.md
       - Analysis:
         - Conditional distributions: tutorial/07_conditional_distributions.md
         - Posterior sensitivity analysis: tutorial/09_sensitivity_analysis.md
       - Examples:
         - Hodgkin-Huxley example: examples/00_HH_simulator.md
         - Decision making model: examples/01_decision_making_model.md
-  - Contributing: 
+  - Contributing:
     - Guide: contribute.md
     - Code of Conduct: code_of_conduct.md
   - API Reference: reference.md
@@ -70,7 +70,7 @@ markdown_extensions:
   - pymdownx.critic
   - pymdownx.details
   - pymdownx.emoji:
-      emoji_generator: !!python/name:pymdownx.emoji.to_svg
+      emoji_generator: tag:yaml.org,2002:python/name:pymdownx.emoji.to_svg
   - pymdownx.inlinehilite
   - pymdownx.magiclink
   - pymdownx.mark
@@ -89,7 +89,7 @@ plugins:
           rendering:
             show_source: true
             heading_level: 3
-  
+
 watch:
   - ../sbi