Merge pull request #159 from stefanradev93/streamlined-backend

Keras 3: Streamlined Backend

.github/workflows/docs.yml → .github/workflows/docs.yaml

@@ -1,3 +1,4 @@
+
 # From https://github.com/eeholmes/readthedoc-test/blob/main/.github/workflows/docs_pages.yml
 name: docs
 

.github/workflows/publish.yml → .github/workflows/publish.yaml

@@ -1,3 +1,4 @@
+
 name: Publish to PyPI.org
 on:
   release:

.github/workflows/tests.yaml

@@ -0,0 +1,106 @@
+
+name: Tests
+
+on:
+  pull_request:
+  push:
+    branches:
+      - master
+      - dev
+      - streamlined-backend
+
+
+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
+
+      - name: Run Formatter
+        run: |
+          ruff format --check --config pyproject.toml
+
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, windows-latest]
+        python-version: ["3.10", "3.11"]
+        backend: ["jax", "tensorflow", "torch"]
+    defaults:
+      run:
+        shell: bash -el {0}
+    env:
+      KERAS_BACKEND: ${{ matrix.backend }}
+
+    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: ${{ matrix.python-version }}
+
+      - name: Install JAX
+        if: ${{ matrix.backend == 'jax' }}
+        run: |
+          pip install -U "jax[cpu]"
+      - name: Install NumPy
+        if: ${{ matrix.backend == 'numpy' }}
+        run: |
+          conda install numpy
+      - name: Install Tensorflow
+        if: ${{ matrix.backend == 'tensorflow' }}
+        run: |
+          pip install -U tensorflow
+      - name: Install PyTorch
+        if: ${{ matrix.backend == 'torch' }}
+        run: |
+          conda install pytorch torchvision torchaudio cpuonly -c pytorch
+
+      - name: Show Environment Info
+        run: |
+          conda info
+          conda list
+          conda config --show-sources
+          conda config --show
+          printenv | sort
+
+      - name: Run Tests
+        run: |
+          pytest
+
+      - name: Create Coverage Report
+        run: |
+          coverage xml
+
+      - name: Upload Coverage Reports to CodeCov
+        uses: codecov/codecov-action@v4
+        with:
+          # do not use the files attribute here, otherwise the reports are not merged correctly
+          token: ${{ secrets.CODECOV_TOKEN }}

.gitignore

@@ -32,4 +32,4 @@ docs/
 .tox
 
 # MacOS
-.DS_Store
+.DS_Store

.pre-commit-config.yaml

@@ -12,32 +12,25 @@
 # Automatically run before every commit via once running `pre-commit install`
 
 repos:
-- repo: https://github.com/psf/black
-  rev: 23.1.0
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  # Ruff version.
+  rev: v0.4.9
   hooks:
-  - id: black
-    description: The uncompromising code formatter
-- repo: https://github.com/pycqa/isort
-  rev: 5.12.0
-  hooks:
-  - id: isort
-    name: isort (python)
-  - id: isort
-    name: isort (cython)
-    types: [cython]
-  - id: isort
-    name: isort (pyi)
-    types: [pyi]
-- repo: https://github.com/nbQA-dev/nbQA
-  rev: 1.6.3
-  hooks:
-    - id: nbqa-black
-    - id: nbqa-pyupgrade
-      args: [--py36-plus]
-    - id: nbqa-isort
+    # Run the linter.
+    - id: ruff
+      args: [ --fix ]
+    # Run the formatter.
+    - id: ruff-format
+#- repo: https://github.com/nbQA-dev/nbQA
+#  rev: 1.6.3
+#  hooks:
+#    # Run ruff for jupyter notebooks.
+#    - id: nbqa-ruff
+#      args: [--ignore=E402]  # E402: module level import not at top of file
 - repo: https://github.com/pre-commit/pre-commit-hooks
   rev: v4.4.0
   hooks:
+  # A bunch of other pre-defined hooks.
   - id: check-yaml
     description: Check yaml files for parseable syntax
   - id: check-added-large-files

CITATION.cff

@@ -69,4 +69,4 @@ preferred-citation:
   type: article
   url: "https://joss.theoj.org/papers/10.21105/joss.05702"
   volume: 8
-title: "BayesFlow: Amortized Bayesian Workflows With Neural Networks"
+title: "BayesFlow: Amortized Bayesian Workflows With Neural Networks"