Merge branch 'main' into iterable_dataset

Author: mtauraso

.github/workflows/smoke-test.yml

@@ -39,4 +39,4 @@ jobs:
         pip list
     - name: Run unit tests with pytest
       run: |
-        python -m pytest
+        python -m pytest -m "not slow"

.github/workflows/testing-and-coverage.yml

@@ -31,7 +31,7 @@ jobs:
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
     - name: Run unit tests with pytest
       run: |
-        python -m pytest --cov=hyrax --cov-report=xml
+        python -m pytest --cov=hyrax --cov-report=xml -m "not slow"
     - name: Upload coverage report to codecov
       uses: codecov/codecov-action@v5
       with:

.pre-commit-config.yaml

@@ -50,7 +50,7 @@ repos:
       - id: xcxc-check
         name: Check for note-to-self comments (xcxc)
         description: Grep all source files for xcxc which signifies a comment that shouldn't be checked in.
-        entry: bash -c "[[ $(grep -riI xcxc --exclude .pre-commit-config.yaml --exclude-dir _readthedocs --exclude-dir htmlcov ./* >&2 ; echo $?) == 1 ]]"
+        entry: bash -c "[[ $(grep -rniI xcxc --exclude .pre-commit-config.yaml --exclude-dir _readthedocs --exclude-dir htmlcov ./* >&2 ; echo $?) == 1 ]]"
         language: system
         pass_filenames: false
         always_run: true
@@ -105,7 +105,7 @@ repos:
       - id: pytest-check
         name: Run unit tests
         description: Run unit tests with pytest.
-        entry: bash -c "if python -m pytest --co -qq; then python -m pytest --cov=./src --cov-report=html; fi"
+        entry: bash -c "if python -m pytest --co -qq -m 'not slow'; then python -m pytest --cov=./src --cov-report=html -m 'not slow'; fi"
         language: system
         pass_filenames: false
         always_run: true

pyproject.toml

@@ -65,6 +65,7 @@ dev = [
     "pre-commit", # Used to run checks before finalizing a git commit
     "pytest",
     "pytest-cov", # Used to report total code coverage
+    "pytest-env", # Used to set environment variables in testing
     "ruff", # Used for static linting of files
 ]
 
@@ -81,6 +82,15 @@ write_to = "src/hyrax/_version.py"
 [tool.pytest.ini_options]
 testpaths = [
     "tests",
+    "src",
+    "docs",
+]
+addopts = "--doctest-modules --doctest-glob=*.rst"
+env = [
+    "TQDM_DISABLE=1",
+]
+markers = [
+    "slow: marks tests as slow (deselect with '-m \"not slow\"')",
 ]
 
 [tool.black]

src/hyrax/data_sets/__init__.py

@@ -1,4 +1,5 @@
 from .data_set_registry import DATA_SET_REGISTRY, HyraxDataset
+from .fits_image_dataset import FitsImageDataSet
 from .hsc_data_set import HSCDataSet
 from .hyrax_cifar_data_set import HyraxCifarDataSet
 from .inference_dataset import InferenceDataSet
@@ -7,6 +8,7 @@
     "DATA_SET_REGISTRY",
     "HyraxCifarDataSet",
     "HyraxCifarIterableDataSet",
+    "FitsImageDataSet",
     "HSCDataSet",
     "InferenceDataSet",
     "Dataset",