update CI to use poetry

.github/workflows/ci.yml

@@ -1,41 +1,93 @@
-name: pfb-imaging Workflow
+name: pfb-imaging CI Workflow
 
 on:
   push:
     tags:
       - 'v*'
   pull_request:
 
+env:
+  POETRY_VERSION: 1.5
+
 jobs:
   test:
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.os }}
+    continue-on-error: true
     if: "!contains(github.event.head_commit.message, '[skip ci]')"
+
+    env:
+      NUMBA_CACHE_DIR: /tmp/numba-cache
+
     strategy:
       matrix:
-        python-version: ["3.10", "3.11"]
+        os: [ubuntu-20.04, ubuntu-22.04]
+        python-version: ["3.9", "3.10", "3.11"]
 
     steps:
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version}}
 
+      - name: Install poetry
+        uses: abatilo/actions-poetry@v2
+        with:
+          poetry-version: ${{ env.POETRY_VERSION }}
+
+      - name: Check poetry install
+        run: poetry --version
+
       - name: Checkout source
         uses: actions/checkout@v3
         with:
-          fetch-depth: 1
+          fetch-depth: 0
+
+      - name: Restore repo times
+        uses: chetan/git-restore-mtime-action@v2
 
       - name: Upgrade pip and setuptools
         run: python -m pip install -U pip setuptools
 
-      # - name: Pin setuptools
-      #   run: python -m pip install setuptools==65.5
+      - name: Create Key and Numba Cache Directory
+        id: numba-key
+        run: |
+          mkdir -p ${{ env.NUMBA_CACHE_DIR }}
+          echo "timestamp=$(/bin/date -u '+%Y%m%d%H%M%S')" >> $GITHUB_OUTPUT
+
+      - name: Cache Numba Kernels
+        uses: actions/cache@v3
+        with:
+          key: numba-cache-${{ matrix.python-version }}-${{ steps.numba-key.outputs.timestamp }}
+          restore-keys: numba-cache-${{ matrix.python-version }}-
+          path: ${{ env.NUMBA_CACHE_DIR }}
+
+      - name: List the measures directory
+        run: curl ftp://ftp.astron.nl/outgoing/Measures/ > measures_dir.txt
+
+      - name: Load cached CASA Measures Data
+        id: load-cached-casa-measures
+        uses: actions/cache@v3
+        with:
+          key: casa-measures-${{ hashFiles('measures_dir.txt')}}
+          path: |
+            ~/measures
+            ~/.casarc
+
+      - name: Download and install CASA Measures Data
+        if: steps.load-cached-casa-measures.outputs.cache-hit != 'true'
+        run: |
+          mkdir -p ~/measures
+          curl ftp://ftp.astron.nl/outgoing/Measures/WSRT_Measures.ztar | tar xvzf - -C ~/measures
+          echo "measures.directory: ~/measures" > ~/.casarc
 
       - name: Install pfb-imaging
-        run: python -m pip install .[testing]
+        run: poetry install
+
+      - name: Run pfb-imaging
+        run: poetry run pfb --help
 
       - name: Run tests
-        run: pytest -s -vvv tests/
+        run: poetry rin pytest -v tests/
 
   deploy:
     needs: [test]
@@ -48,27 +100,32 @@ jobs:
         with:
           python-version: "3.10"
 
-      - name: Install latest setuptools, wheel, pip
-        run: python3 -m pip install -U pip setuptools wheel
+      - name: Install poetry
+        uses: abatilo/actions-poetry@v2
+        with:
+          poetry-version: ${{ env.POETRY_VERSION }}
+
+      - name: Check poetry install
+        run: poetry --version
 
       - name: Checkout source
         uses: actions/checkout@v4
         with:
           fetch-depth: 1
 
       - name: Build distributions
-        run: python setup.py sdist bdist_wheel
+        run: poetry build
 
       - name: Publish distribution to Test PyPI
-        uses: pypa/gh-action-pypi-publish@master
+        uses: pypa/gh-action-pypi-publish@1.8.6
         with:
           user: __token__
           password: ${{ secrets.PYPI_TEST_API_TOKEN }}
           repository_url: https://test.pypi.org/legacy/
         continue-on-error: false
 
       - name: Publish distribution 📦 to PyPI
-        uses: pypa/gh-action-pypi-publish@master
+        uses: pypa/gh-action-pypi-publish@1.8.6
         with:
           user: __token__
           password: ${{ secrets.PYPI_API_TOKEN }}

pyproject.toml

@@ -0,0 +1,49 @@
+[tool.poetry]
+name = "pfb-imaging"
+version = "0.0.4"
+description = "Radio interferometric imaging suite based on a preconditioned forward-backward approach"
+authors = ["Landman Bester <[email protected]>"]
+license = "MIT"
+readme = "README.rst"
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: POSIX :: Linux",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Topic :: Scientific/Engineering :: Astronomy"
+]
+packages = [{include = "pfb"}]
+
+[tool.poetry.dependencies]
+python = ">=3.10, <3.12"
+pytest = ">=8.0.0"
+scikit-image = ">=0.24.0"
+PyWavelets = ">=1.7.0"
+katbeam = ">=0.1"
+numexpr = ">=2.10.1"
+pyscilog = ">=0.1.2"
+Click = ">=8.1"
+ducc0 = ">=0.34.0"
+sympy = ">=1.13"
+stimela = { git = "https://github.com/caracal-pipeline/stimela.git", branch = "clickify_missing_as_none" }
+streamjoy = ">=0.0.8"
+codex-africanus = {extras = ["dask", "scipy", "astropy", "python-casacore"], version = ">=0.3.7, <=0.3.7"}
+dask-ms = {extras = ["s3", "xarray", "zarr"], version = ">=0.2.20, <=0.2.20"}
+tbb = ">=2021.13.1"
+jax = {extras = ["cpu"], version = ">=0.4.31"}
+lz4 = ">=4.3.3"
+bokeh = ">=3.1.0"
+regions = ">=0.9"
+psutil = ">=5.9.8"
+
+[tool.poetry.scripts]
+pfb = "pfb.workers.main:cli"
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"
+
+## add section for dev component which installs builder and Dockerfiles