Fix test pipeline (#680)

* Pinned upper version of dependencies ✨

* Using importlib is the prefered way to replace pkg_resources. 👒

* Notebook doesn't exist anymore. 🔐

Author: anawas

environment.yaml

@@ -55,7 +55,7 @@ dependencies:
   # casacore hast just no-mpi & open-mpi, but no mpich-wheel
   - conda-forge::fftw       =*=mpi_mpich*  # oskarpy(oskar(casacore)), tools21cm, bluebild(finufft) -> from conda-forge to ignore channel-prio & not take our legacy fftw-wheel
   # exclude buggy versions of other tools
-  - setuptools              !=71.0.0, !=71.0.1, !=71.0.2  # buggy with `importlib_metadata`
+  - setuptools              >=69.0.0,<70.0.0  # pkg_resources required by ska_sdp_datamodels and karabo code
   # for MWA measurement set, uvfits, hdf5, mir support (choc-234)
   # this [casa] syntax won't work with mamba!
   - pyuvdata[casa]          >=2.4,<3

karabo/simulation/signal/seg_u_net_segmentation.py

@@ -1,8 +1,8 @@
 """Segmentation with SegU-net."""
 
+from importlib.resources import files
 from typing import Literal
 
-import pkg_resources
 import tools21cm as t2c
 from typing_extensions import assert_never
 
@@ -78,15 +78,19 @@ def __init__(self, tta: _TtaType = 1, verbose: bool = False) -> None:
         self.NR_MANIP = len(self.MANIP)
 
         # load model
+        MODEL_NAME = "segunet_02-10T23-52-36_128slice_ep56.h5"
+        MODEL_FILENAME = str(files("tool21cm").joinpath(f"input_data/{MODEL_NAME}"))
+        """
         MODEL_NAME = pkg_resources.resource_filename(
             "tools21cm", "input_data/segunet_02-10T23-52-36_128slice_ep56.h5"
         )
+        """
         METRICS = {
             "balanced_cross_entropy": t2c.segmentation.balanced_cross_entropy,
             "iou": t2c.segmentation.iou,
             "dice_coef": t2c.segmentation.dice_coef,
         }
-        self.MODEL_LOADED = load_model(MODEL_NAME, custom_objects=METRICS)
+        self.MODEL_LOADED = load_model(MODEL_FILENAME, custom_objects=METRICS)
         print(f" Loaded model: {MODEL_NAME}")
         # pylint: enable=invalid-name
 

karabo/test/test_notebooks.py

@@ -59,14 +59,6 @@ def test_source_detection_assessment_notebook() -> None:
     _run_notebook(notebook="source_detection_assessment.ipynb")
 
 
-@pytest.mark.skipif(
-    IS_GITHUB_RUNNER or not RUN_NOTEBOOK_TESTS,
-    reason="'Error: The operation was canceled' when running this test on the package",
-)
-def test_LineEmission_notebook() -> None:
-    _run_notebook(notebook="LineEmissionBackendsComparison.ipynb")
-
-
 @pytest.mark.skipif(
     not RUN_NOTEBOOK_TESTS,
     reason="'Error: The operation was canceled' when running this test on the package",

pyproject.toml

@@ -58,5 +58,6 @@ testpaths = "karabo/test"
         'sphinx',
         'sphinx_rtd_theme',
         'types-requests',  # types for mypy
+        'types-setuptools==69.0.0.0',
         'versioneer',
     ]