Add initial CASA tests

.github/workflows/build.yml

@@ -3,20 +3,20 @@ name: Build
 on:
   push:
     branches:
+      - master
+    tags:
       - '*'
   pull_request:
-    branches:
-      - master
+  workflow_dispatch:
 
 jobs:
   job:
     name: Build
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        # Versions listed at https://raw.githubusercontent.com/actions/python-versions/main/versions-manifest.json
         python-version: [
-          "3.12",
+          '3.12',
         ]
     steps:
       - uses: actions/checkout@v6

.github/workflows/check-changelog.yml

@@ -2,7 +2,14 @@ name: Check Changelog
 
 on:
   pull_request:
-    types: [assigned, opened, synchronize, reopened, labeled, unlabeled]
+    types: [
+      assigned,
+      opened,
+      synchronize,
+      reopened,
+      labeled,
+      unlabeled,
+    ]
     branches:
       - master
 

.github/workflows/publish.yml

@@ -1,6 +1,10 @@
-name: Build and upload to PyPI
+name: Upload to PyPI
 
-on: [push, pull_request]
+on:
+  push:
+    tags:
+    - '*'
+  workflow_dispatch:
 
 jobs:
   build_sdist_and_wheel:
@@ -11,7 +15,7 @@ jobs:
       - uses: actions/setup-python@v6
         name: Install Python
         with:
-          python-version: "3.12"
+          python-version: '3.12'
       - name: Install build
         run: python -m pip install build
       - name: Build sdist

.github/workflows/tests.yml

@@ -0,0 +1,44 @@
+name: Run tests
+on:
+  push:
+    branches:
+      - master
+    tags:
+      - '*'
+  pull_request:
+  schedule:
+      # run every Tuesday at 5am UTC
+      - cron: '0 5 * * 2'
+  workflow_dispatch:
+
+jobs:
+  test:
+    strategy:
+      matrix:
+        os: [
+          ubuntu-latest,
+          macos-latest,
+        ]
+        python-version: [
+          '3.12',
+        ]
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v5
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+      - name: Install tox
+        run: |
+          uv tool install --python ${{ matrix.python-version }} tox --with tox-gh
+      - name: Run tests
+        run: tox
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v5
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+      - name: Upload test results to Codecov
+        if: ${{ !cancelled() }}
+        uses: codecov/codecov-action@v5
+        with:
+          report_type: "test_results"
+          token: ${{ secrets.CODECOV_TOKEN }}

CHANGES.rst

@@ -1,6 +1,7 @@
 4.0.0 (Unreleased)
 ==================
 
+- Added initial test suite, which checks the various CASA tasks and arguments used throughout the pipeline (#324)
 - Bump actions/upload-artifact from 6 to 7 (#313)
-- Update casaplotms requirement from >=2.7.4 to >=2.8.2 (#2.8.2)
+- Bump casaplotms requirement from >=2.7.4 to >=2.8.2 (#320)
 - Initial pip-installable version (#292)

phangsPipeline/__init__.py

@@ -12,7 +12,6 @@
     __version__ = "dev"
 
 from .handlerAlmaDownload import AlmaDownloadHandler
-from .handlerDerived import DerivedHandler
 from .handlerKeys import KeyHandler
 from .handlerRelease import ReleaseHandler
 from .phangsLogger import setup_logger
@@ -44,4 +43,7 @@
 
 # Modules that require spectral-cube to be installed
 if spectral_cube_enabled:
-    __all__.extend(["DerivedHandler"])
+    from .handlerDerived import DerivedHandler
+    __all__.extend([
+        "DerivedHandler",
+    ])

pyproject.toml

@@ -57,6 +57,17 @@ casa = [
     "pipeline@git+https://open-bitbucket.nrao.edu/scm/pipe/pipeline.git",
 ]
 
+# Optional packages for the test suite
+test = [
+    "pytest-cov >= 7.1.0",
+]
+test-casa = [
+    "zenodo-get >= 3.0.0",
+]
+test-ruff = [
+    "ruff >= 0.15.10",
+]
+
 [project.urls]
 "Homepage" = "https://github.com/phangsTeam/phangs_imaging_scripts"
 "Bug Reports" = "https://github.com/phangsTeam/phangs_imaging_scripts/issues"
@@ -68,6 +79,25 @@ exclude = [
     "scripts/*",
 ]
 
+# Omit in coverage. Notably here, we exclude
+# the CASA analysisutils
+[tool.coverage.run]
+omit = [
+    "docs/*",
+    "phangs-alma_keys/*",
+    "tests/*",
+    "*/analysis_scripts/*",
+]
+
+[tool.coverage.report]
+exclude_lines = [
+    'except ImportError',
+    'except ModuleNotFoundError',
+    'except \(ImportError, ModuleNotFoundError\)',
+    'raise AssertionError',
+    'raise NotImplementedError',
+]
+
 [build-system]
 requires = [
     "setuptools >= 80.9.0",

pytest.toml

@@ -0,0 +1,13 @@
+[pytest]
+minversion = "9.0"
+addopts = [
+    "-ra",
+    "-q",
+    "--strict-markers",
+]
+markers = [
+    "casa: marks tests as requiring CASA install (deselect with '-m \"not casa\"')",
+]
+testpaths = [
+    "tests",
+]

ruff.toml

@@ -0,0 +1,33 @@
+extend = "pyproject.toml"
+
+extend-exclude = [
+    ".github",
+    ".tmp",
+    "phangs-alma_keys",
+    "phangsPipelineTests",
+    "scripts",
+    "tests/casa_config_files/*",
+    "run_pipeline_phangs-alma.py",
+]
+
+line-length = 100
+
+target-version = "py312"
+
+[format]
+quote-style = "double"
+indent-style = "space"
+docstring-code-format = true
+
+[lint.pydocstyle]
+convention = "numpy"
+
+[lint.per-file-ignores]
+"phangsPipeline/__init__.py" = [
+    "E402", # module-level import not at top of file
+    "F401", # unused import
+]
+
+"tests/test_*_imports.py" = [
+    "F401", # unused import
+]

tests/__init__.py

@@ -0,0 +1,7 @@
+import os
+import sys
+
+# Add the analysisUtils directory to PATH
+envdir = os.environ.get("ENVDIR", os.getcwd())
+au_dir = os.path.join(envdir, "analysis_scripts")
+sys.path.append(au_dir)

tests/casa_config_files/config.py

@@ -0,0 +1,8 @@
+import os
+
+casadir = os.environ.get("CASADIR", os.getcwd())
+
+datapath = [os.path.join(casadir, "data")]
+measurespath = datapath[0]
+measures_auto_update = True
+data_auto_update = True

tests/casa_config_files/startup.py

@@ -0,0 +1,10 @@
+import os
+import sys
+
+envdir = os.environ.get("ENVDIR", os.getcwd())
+
+au_dir = os.path.join(envdir, "analysis_scripts")
+sys.path.append(au_dir)
+
+import analysisUtils as au
+aU = au