Move to UV (#60)

This PR moves from using `hatch` to `uv` as a build system. While Hatch is great, e.g., due to its version management, there are some things that are not particularly practical:
- The envs are per default not installed locally but to some arcane location that can be hard to find for users.
- Having multiple separate envs is great for larger packages, but a bit too much for a package of this size.
- There is no way to automatically add packages as dependencies.

`uv` on the other hand
- makes it easy to replicate the exact versions that are used during development, 
- has only one base env containing all dependencies, 
- is very fast,
- and is imho easier to learn and use.

Author: dirmeier

.github/workflows/ci.yaml

@@ -8,75 +8,57 @@ on:
 
 jobs:
   precommit:
-    name: Pre-commit checks
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v3
       - uses: pre-commit/action@v3.0.0
 
-  build:
-    runs-on: ubuntu-latest
-    needs:
-      - precommit
-    strategy:
-      matrix:
-        python-version: [3.11]
-    steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v3
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
-      run: |
-        pip install hatch
-    - name: Build package
-      run: |
-        hatch build
-
   lints:
     runs-on: ubuntu-latest
     needs:
       - precommit
     strategy:
       matrix:
-        python-version: [3.11]
+        python-version: [ 3.12, 3.13 ]
     steps:
       - uses: actions/checkout@v3
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v3
         with:
           python-version: ${{ matrix.python-version }}
+      - uses: astral-sh/setup-uv@v5
+        with:
+          version: "latest"
       - name: Install dependencies
         run: |
-          pip install hatch
+          uv sync --all-groups
       - name: Run lints
         run: |
-          hatch run test:lint
+          make lints
 
   tests:
     runs-on: ubuntu-latest
     needs:
-      - precommit
+      - lints
     strategy:
       matrix:
-        python-version: [3.11]
+        python-version: [ 3.12, 3.13 ]
     steps:
       - uses: actions/checkout@v3
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v3
         with:
           python-version: ${{ matrix.python-version }}
+      - uses: astral-sh/setup-uv@v5
+        with:
+          version: "latest"
       - name: Install dependencies
         run: |
-          pip install hatch
-      - name: Build package
-        run: |
-          pip install jaxlib jax
+          uv sync
       - name: Run tests
         run: |
-          hatch run test:test
+          make tests
       - name: Upload coverage reports to Codecov
         uses: codecov/codecov-action@v3
         env:

.github/workflows/examples.yaml

@@ -19,31 +19,30 @@ jobs:
       - precommit
     strategy:
       matrix:
-        python-version: [3.11]
+        python-version: [ 3.12, 3.13 ]
     steps:
       - uses: actions/checkout@v3
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v3
         with:
           python-version: ${{ matrix.python-version }}
+      - uses: astral-sh/setup-uv@v5
+        with:
+          version: "latest"
       - name: Install dependencies
         run: |
-          pip install hatch matplotlib
-      - name: Build package
-        run: |
-          pip install jaxlib jax
-          pip install .
+          uv sync --all-groups
       - name: Run tests
         run: |
-            python examples/gaussian_linear-aio.py --n-iter 10
-            python examples/gaussian_linear-smcabc.py --n-rounds 1
-            python examples/mixture_model-cmpe.py --n-iter 10
-            python examples/mixture_model-nle.py --n-iter 10
-            python examples/mixture_model-nle.py --n-iter 10 --use-spf
-            python examples/mixture_model-npe.py --n-iter 10
-            python examples/mixture_model-nre.py --n-iter 10
-            python examples/mixture_model-npse.py --n-iter 10
-            python examples/slcp-fmpe.py --n-iter 10
-            python examples/slcp-nass_nle.py --n-iter 10 --n-rounds 1
-            python examples/slcp-nass_smcabc.py --n-iter 10 --n-rounds 1
-            python examples/slcp-snle.py --n-iter 10  --n-rounds 1
+            uv run python examples/gaussian_linear-aio.py --n-iter 10
+            uv run python examples/gaussian_linear-smcabc.py --n-rounds 1
+            uv run python examples/mixture_model-cmpe.py --n-iter 10
+            uv run python examples/mixture_model-nle.py --n-iter 10
+            uv run python examples/mixture_model-nle.py --n-iter 10 --use-spf
+            uv run python examples/mixture_model-npe.py --n-iter 10
+            uv run python examples/mixture_model-nre.py --n-iter 10
+            uv run python examples/mixture_model-npse.py --n-iter 10
+            uv run python examples/slcp-fmpe.py --n-iter 10
+            uv run python examples/slcp-nass_nle.py --n-iter 10 --n-rounds 1
+            uv run python examples/slcp-nass_smcabc.py --n-iter 10 --n-rounds 1
+            uv run python examples/slcp-snle.py --n-iter 10  --n-rounds 1

.python-version

@@ -0,0 +1 @@
+3.12.10

.readthedocs.yaml

@@ -3,7 +3,7 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.11"
+    python: "3.12"
 
 sphinx:
   builder: html

Makefile

@@ -1,20 +1,14 @@
-.PHONY: tag
-.PHONY: tests
-.PHONY: lints
-.PHONY: docs
-.PHONY: format
-
-PKG_VERSION=`hatch version`
-
-tag:
-	 git tag -a v${PKG_VERSION} -m v${PKG_VERSION}
-	 git push --tag
+.PHONY: tests, lints, docs, format
 
 tests:
-	hatch run test:test
+	uv run pytest
 
 lints:
-	hatch run test:lint
+	uv run ruff check sbijax examples
 
 format:
-	hatch run test:format
+	uv run ruff check --fix sbijax examples
+	uv run ruff format sbijax examples
+
+docs:
+	cd docs && make html

README.md

@@ -83,11 +83,18 @@ Contributions in the form of pull requests are more than welcome. A good way to
 
 In order to contribute:
 
-1) Clone `sbijax` and install `hatch` via `pip install hatch`,
-2) create a new branch locally `git checkout -b feature/my-new-feature` or `git checkout -b issue/fixes-bug`,
-3) implement your contribution and ideally a test case,
-4) test it by calling `make tests`, `make lints` and `make format` on the (Unix) command line,
-5) submit a PR 🙂
+1) Clone `sbijax` and install `uv` from [here](https://docs.astral.sh/uv/getting-started/installation/).
+2) Install all dependencies using `uv sync --all-groups`.
+3) Install `pre-commit` and `gitlint` via:
+
+   ```shell
+   pre-commit install
+   gitlint install-hook
+   ```
+4) Create a new branch locally `git checkout -b feature/my-new-feature` or `git checkout -b issue/fixes-bug`.
+5) Implement your contribution and ideally a test case.
+6) Test it by calling `make tests`, `make lints` and `make format` on the (Unix) command line.
+7) Submit a PR 🙂.
 
 ## Citing sbijax
 

docs/index.rst

@@ -79,11 +79,12 @@ Contributions in the form of pull requests are more than welcome. A good way to
 
 In order to contribute:
 
-1) Clone :code:`sbijax` and install :code:`hatch` via :code:`pip install hatch`,
-2) create a new branch locally :code:`git checkout -b feature/my-new-feature` or :code:`git checkout -b issue/fixes-bug`,
-3) implement your contribution and ideally a test case,
-4) test it by calling ``make tests``, ``make lints`` and ``make format`` on the (Unix) command line,
-5) submit a PR 🙂
+1) Clone :code:`sbijax` and install :code:`uv` from `here <https://docs.astral.sh/uv/getting-started/installation/>`_,
+2) install all dependencies using ```uv sync``,
+3) create a new branch locally :code:`git checkout -b feature/my-new-feature` or :code:`git checkout -b issue/fixes-bug`,
+4) implement your contribution and ideally a test case,
+5) test it by calling ``make tests``, ``make lints`` and ``make format`` on the (Unix) command line,
+6) submit a PR 🙂
 
 Acknowledgements
 ----------------
@@ -102,7 +103,6 @@ License
     :hidden:
 
     🏡 Home <self>
-    📰 News <news>
     📚 References <references>
 
 ..  toctree::

docs/news.rst

@@ -37,13 +37,13 @@ def distance_fn(y_simulated, y_observed):
 
 
 def run(n_rounds):
-    y_observed = jnp.array([-2.0, 1.0])
+    y_observed = jnp.array([-1.0, 1.0])
 
     fns = prior_fn, simulator_fn
 
     smc = SMCABC(fns, summary_fn, distance_fn)
     smc_samples, _ = smc.sample_posterior(
-        jr.PRNGKey(1), y_observed, n_rounds=n_rounds, n_particles=1000, ess_min=500
+        jr.PRNGKey(1), y_observed, n_rounds=1, n_particles=1000, ess_min=500, eps_step=0.9
     )
     plot_posterior(smc_samples)
     plt.show()

examples/gaussian_linear-smcabc.py

@@ -14,7 +14,7 @@
 
 def prior_fn():
     prior = tfd.JointDistributionNamed(dict(
-        theta=tfd.Normal(jnp.zeros(2), 1)
+        theta=tfd.Normal(jnp.zeros(2), jnp.array(1.0))
     ), batch_ndims=0)
     return prior