Address issue 59 (refactor build system)

.github/workflows/ci-deploy.yml

@@ -0,0 +1,48 @@
+name: CI/Deploy
+
+on:
+  push:
+    tags: ["v*"]
+
+jobs:
+
+  unit:
+    uses: ./.github/workflows/unit.yml
+
+  notebooks:
+    uses: ./.github/workflows/notebook_smoke.yml
+
+  build_and_publish:
+    name: Upload release to PyPI
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/gpax
+    permissions:
+      id-token: write
+
+    needs:
+      - unit
+      - notebooks
+
+    steps:
+
+    - name: Checkout
+      uses: actions/checkout@v3
+      with:
+        fetch-depth: 0
+
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.9
+
+    - name: Build and apply version
+      run: bash scripts/build_project.sh
+
+    - name: Publish package distributions to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        # CURRENTLY USING TEST SERVER FOR NOW!!!!
+        repository-url: https://test.pypi.org/legacy/

.github/workflows/ci.yml

@@ -0,0 +1,17 @@
+name: CI
+
+on:
+
+  pull_request:
+    branches: ["master", "dev/*", mc/issue-59]
+
+  push:
+    branches: ["master", "dev/*", mc/issue-59]
+
+jobs: 
+
+  unit:
+    uses: ./.github/workflows/unit.yml
+
+  notebooks:
+    uses: ./.github/workflows/notebook_smoke.yml

.github/workflows/notebook_smoke.yml

@@ -4,14 +4,7 @@ env:
   CI_SMOKE: True
 
 on:
-  pull_request:
-    branches:
-      - '*'
-  push:
-    branches:
-      - '*'
-    tags:
-      - '*'
+  workflow_call:
 
 jobs:
   build-linux:
@@ -34,22 +27,9 @@ jobs:
 
     - name: Install dependencies
       run: |
-        sudo apt-get update -qq
-        python -m pip install --upgrade pip
-        python -m pip install flake8 pytest
-        python -m pip install jaxlib
-        python -m pip install jax
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-
-    - name: install package
-      run: |
-        pip install .
-        pip list
+        bash scripts/install.sh
 
     - name: Notebook smoke tests
       run: |
-        pip install ipython
-        pip install nbformat
-        pip install seaborn
         bash scripts/test_notebooks.sh
 

.github/workflows/unit.yml

@@ -0,0 +1,54 @@
+name: Unit
+
+env:
+  PYTHON_MAIN_VERSION: 3.9
+
+on:
+  workflow_call:
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        python-version: ["3.9", "3.10", "3.11"]
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          bash scripts/install.sh
+          bash scripts/install.sh test
+
+      - name: Lint with flake8
+        run: |
+          # stop the build if there are Python syntax errors or undefined names
+          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+          flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+
+      - name: Run tests
+        run: |
+          pytest -v --cov --cov-report xml tests
+
+      - name: Upload coverage to Codecov
+        if: ${{ matrix.python-version == env.PYTHON_MAIN_VERSION }}
+        uses: codecov/codecov-action@v1
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          files: ./coverage.xml
+          # directory: ./coverage/reports/
+          flags: unittests
+          env_vars: OS,PYTHON
+          name: codecov-umbrella
+          fail_ci_if_error: true
+          # path_to_write_report: ./coverage/codecov_report.txt
+          verbose: true

.gitignore

@@ -127,3 +127,6 @@ dmypy.json
 
 # Pyre type checker
 .pyre/
+
+# Pyright
+pyrightconfig.json

gpax/__init__.py

@@ -1,12 +1,46 @@
-from .__version__ import version as __version__
-from . import utils
-from . import kernels
-from . import acquisition
-from .hypo import sample_next
-from .models import (DKL, CoregGP, ExactGP, MultiTaskGP, iBNN, vExactGP,
-                     vi_iBNN, viDKL, viGP, sPM, viMTDKL, VarNoiseGP, UIGP,
-                     MeasuredNoiseGP, viSparseGP, BNN)
+from gpax import acquisition, kernels, utils
+from gpax._version import __version__
+from gpax.hypo import sample_next
+from gpax.models import (
+    BNN,
+    DKL,
+    UIGP,
+    CoregGP,
+    ExactGP,
+    MeasuredNoiseGP,
+    MultiTaskGP,
+    VarNoiseGP,
+    iBNN,
+    sPM,
+    vExactGP,
+    vi_iBNN,
+    viDKL,
+    viGP,
+    viMTDKL,
+    viSparseGP,
+)
 
-__all__ = ["utils", "kernels", "mtkernels", "acquisition", "ExactGP", "vExactGP", "DKL",
-           "viDKL", "iBNN", "vi_iBNN", "MultiTaskGP", "viMTDKL", "viGP", "sPM", "VarNoiseGP",
-           "UIGP", "MeasuredNoiseGP", "viSparseGP", "CoregGP", "BNN", "sample_next", "__version__"]
+__all__ = [
+    "utils",
+    "kernels",
+    "mtkernels",
+    "acquisition",
+    "ExactGP",
+    "vExactGP",
+    "DKL",
+    "viDKL",
+    "iBNN",
+    "vi_iBNN",
+    "MultiTaskGP",
+    "viMTDKL",
+    "viGP",
+    "sPM",
+    "VarNoiseGP",
+    "UIGP",
+    "MeasuredNoiseGP",
+    "viSparseGP",
+    "CoregGP",
+    "BNN",
+    "sample_next",
+    "__version__",
+]

gpax/_version.py

@@ -0,0 +1,10 @@
+"""Version file. This is overwritten during build and will contain a static
+__version__ variable."""
+
+try:
+    import dunamai as _dunamai
+
+    __version__ = _dunamai.Version.from_any_vcs().serialize()
+    del _dunamai
+except ImportError:
+    __version__ = "dev"