deps: update code for x_orientation for new pyuvdata 3.2

.github/workflows/ci.yml → .github/workflows/tests.yml

@@ -16,7 +16,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest]
-        python-version: ["3.10", "3.11", "3.12"]
+        python-version: ["3.11", "3.12", "3.13"]
       fail-fast: false
 
     steps:
@@ -25,18 +25,22 @@ jobs:
         fetch-depth: 0
 
     - name: Setup Python
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
 
+    - name: Install uv
+      uses: astral-sh/setup-uv@v7
+      with:
+        enable-cache: true
+
     - name: Install
-      run: |
-        pip install .[dev]
+      run:  uv sync --all-extras --dev
 
     - name: Run Tests
       run: |
         export MPLBACKEND=agg
-        pytest --cov=hera_pspec --cov-config="./.coveragerc" \
+        uv run pytest --cov=hera_pspec --cov-config="./.coveragerc" \
                --cov-report xml:"./coverage.xml" --junitxml="./test-reports/xunit.xml"
 
     - name: Upload coverage to Codecov

.github/workflows/warnings-tests.yml

@@ -0,0 +1,41 @@
+name: Run Warnings Tests
+
+on:
+  pull_request:
+    branches: [ main ]
+  push:
+    branches: [ main ]
+
+jobs:
+  tests:
+    name: Tests
+    env:
+      OS: ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+      fail-fast: false
+
+    steps:
+    - uses: actions/checkout@main
+      with:
+        fetch-depth: 0
+
+    - name: Setup Python
+      uses: actions/setup-python@v6
+      with:
+        python-version-file: pyproject.toml
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v7
+      with:
+        enable-cache: true
+
+    - name: Install
+      run:  uv sync --all-extras --dev
+
+    - name: Run Tests
+      run: |
+        export MPLBACKEND=agg
+        uv run pytest -Werror

.readthedocs.yaml

@@ -11,30 +11,17 @@ build:
   os: ubuntu-22.04
   tools:
     python: "3.11"
+  jobs:
+      pre_create_environment:
+        - asdf plugin add uv
+        - asdf install uv latest
+        - asdf global uv latest
+      create_environment:
+        - uv venv "${READTHEDOCS_VIRTUALENV_PATH}"
+      install:
+        - UV_PROJECT_ENVIRONMENT="${READTHEDOCS_VIRTUALENV_PATH}" uv sync --frozen --group docs
 
-python:
-  install:
-    - method: pip
-      path: .
-      extra_requirements:
-        - docs
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
   configuration: docs/conf.py
-# You can configure Sphinx to use a different builder, for instance use the dirhtml builder for simpler URLs
-# builder: "dirhtml"
-# Fail on all warnings to avoid broken references
-# fail_on_warning: true
-
-# Optionally build your docs in additional formats such as PDF and ePub
-# formats:
-#    - pdf
-#    - epub
-
-# Optional but recommended, declare the Python requirements required
-# to build your documentation
-# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
-# python:
-#    install:
-#    - requirements: docs/requirements.txt

hera_pspec/pspecdata.py

@@ -2727,7 +2727,7 @@ def validate_pol(self, dsets, pol_pair):
         assert isinstance(pol_pair, tuple), err_msg
 
         # take x_orientation from first dset
-        x_orientation = self.dsets[0].telescope.x_orientation
+        x_orientation = self.dsets[0].telescope.get_x_orientation_from_feeds()
 
         # convert elements to integers if fed as strings
         if isinstance(pol_pair[0], str):
@@ -3114,14 +3114,15 @@ def pspec(self, bls1, bls2, dsets, pols, n_dlys=None,
         # convert all polarizations to integers if fed as strings
         _pols = []
         for p in pols:
+            x_orientation = self.dsets[0].telescope.get_x_orientation_from_feeds()
             if isinstance(p, str):
                 # Convert string to pol-integer pair
-                p = (uvutils.polstr2num(p, x_orientation=self.dsets[0].telescope.x_orientation),
-                     uvutils.polstr2num(p, x_orientation=self.dsets[0].telescope.x_orientation))
+                p = (uvutils.polstr2num(p, x_orientation=x_orientation),
+                     uvutils.polstr2num(p, x_orientation=x_orientation))
             if isinstance(p[0], str):
-                p = (uvutils.polstr2num(p[0], x_orientation=self.dsets[0].telescope.x_orientation), p[1])
+                p = (uvutils.polstr2num(p[0], x_orientation=x_orientation), p[1])
             if isinstance(p[1], str):
-                p = (p[0], uvutils.polstr2num(p[1], x_orientation=self.dsets[0].telescope.x_orientation))
+                p = (p[0], uvutils.polstr2num(p[1], x_orientation=x_orientation))
             _pols.append(p)
         pols = _pols
 
@@ -3592,7 +3593,7 @@ def pspec(self, bls1, bls2, dsets, pols, n_dlys=None,
             if exact_windows:
                 # compute and store exact window functions
                 uvp.get_exact_window_functions(ftbeam=ftbeam, verbose=verbose, 
-                                               x_orientation=self.dsets[0].telescope.x_orientation,
+                                               x_orientation=self.dsets[0].telescope.get_x_orientation_from_feeds(),
                                                inplace=True)
             else:
                 uvp.window_function_array = window_function_array
@@ -3694,7 +3695,7 @@ def rephase_to_dset(self, dset_index=0, inplace=True):
                 indices = dset.antpair2ind(k[:2], ordered=False)
 
                 # get index in polarization_array for this polarization
-                polind = pol_list.index(uvutils.polstr2num(k[-1], x_orientation=self.dsets[0].telescope.x_orientation))
+                polind = pol_list.index(uvutils.polstr2num(k[-1], x_orientation=self.dsets[0].telescope.get_x_orientation_from_feeds()))
 
                 # insert into dset
                 dset.data_array[indices, :, polind] = data[k]

hera_pspec/pstokes.py

@@ -356,7 +356,7 @@ def construct_pstokes(dset1, dset2, pstokes='pI', run_check=True, antenna_nums=N
 
     # convert pstokes to integer if fed as a string
     if isinstance(pstokes, str):
-        pstokes = pyuvdata.utils.polstr2num(pstokes, x_orientation=dset1.telescope.x_orientation)
+        pstokes = pyuvdata.utils.polstr2num(pstokes, x_orientation=dset1.telescope.get_x_orientation_from_feeds())
 
     # check if dset1 and dset2 habe the same spectral window
     spw1 = uvd1.spw_array
@@ -445,7 +445,7 @@ def filter_dset_on_stokes_pol(dsets, pstokes):
 
     # convert pstokes to integer if a string
     if isinstance(pstokes, str):
-        pstokes = pyuvdata.utils.polstr2num(pstokes, x_orientation=dsets[0].telescope.x_orientation)
+        pstokes = pyuvdata.utils.polstr2num(pstokes, x_orientation=dsets[0].telescope.get_x_orientation_from_feeds())
     assert pstokes in [1, 2, 3, 4], \
         "pstokes must be fed as a pseudo-Stokes parameter"
 

pyproject.toml

@@ -32,7 +32,7 @@ dependencies = [
     "numpy>=2.0",
     "scipy",
     "matplotlib>=3.0",
-    "pyuvdata>=3.2",
+    "pyuvdata>=3.2.5",
     "astropy>=6.0",
     "pyyaml",
     "h5py",
@@ -43,14 +43,15 @@ dependencies = [
     "typing-extensions>=4.5.0",
 ]
 dynamic = ['version']
+requires-python = ">=3.11"
 
 [project.urls]
 Documentation = "https://hera-pspec.readthedocs.io/en/latest/"
 Repository = "https://github.com/HERA-Team/hera_pspec"
 Changelog = "https://github.com/HERA-Team/hera_pspec/releases"
 Issues = "https://github.com/HERA-Team/hera_pspec/issues"
 
-[project.optional-dependencies]
+[dependency-groups]
 docs = [
     "sphinx>=5.3.0",
     "sphinx_rtd_theme>=1.1.1",
@@ -59,7 +60,6 @@ docs = [
     "ipython",
     "sphinx_autorun",
     "numpydoc>=0.8",
-    "nbsphinx",
     "mock==1.0.1",
 ]
 tests = [
@@ -69,8 +69,8 @@ tests = [
     "pytest-cases",
 ]
 dev = [
-    "hera_pspec[doc,tests]",
-    "hera_pspec[tests]",
+    {include-group = "docs"},
+    {include-group = "tests"},
 ]
 
 [project.scripts]

tests/test_uvpspec.py

@@ -1121,4 +1121,4 @@ def test_add_approximate_cov():
     uvp2 = uvp.add_approximate_covariance(inplace=False)
     assert hasattr(uvp, 'cov_array_real')
     assert np.allclose(np.diagonal(uvp.cov_array_real[0], axis1=1, axis2=2), 1.0)
-    assert np.allclose(np.diagonal(uvp2.cov_array_real[0], axis1=1, axis2=2), 4.0)
+    assert np.allclose(np.diagonal(uvp2.cov_array_real[0], axis1=1, axis2=2), 4.0)