Merge branch 'master' of github.com:cta-observatory/ctapipe into rect…

…_converter

.github/install.sh

@@ -8,10 +8,13 @@ if [[ "$INSTALL_METHOD" == "conda" ]]; then
   conda update -q conda  # get latest conda version
   # Useful for debugging any issues with conda
   conda info -a
+  conda install -c conda-forge mamba
 
   sed -i -e "s/- python=.*/- python=$PYTHON_VERSION/g" environment.yml
-  conda env create -n ci --file environment.yml
+  mamba env create -n ci --file environment.yml
   conda activate ci
+  echo 'source $CONDA/etc/profile.d/conda.sh' >> ~/.bash_profile
+  echo 'conda activate ci' >> ~/.bash_profile
 else
   echo "Using pip"
   pip install -U pip setuptools wheel

.github/workflows/ci.yml

@@ -32,19 +32,21 @@ jobs:
         run: |
           source .github/install.sh
           python --version
-          pip install codecov pytest-cov
+          pip install codecov pytest-cov pyflakes pytest-xdist
           pip install -e .[all]
           pip freeze
 
+      - name: Static codechecks
+        # need to use a login shell for the conda setup to work
+        shell: bash -leo pipefail {0}
+        run: |
+          pyflakes ctapipe
+
       - name: Tests
-        env:
-          INSTALL_METHOD: ${{ matrix.install-method }}
+        # need to use a login shell for the conda setup to work
+        shell: bash -leo pipefail {0}
         run: |
-          if [[ "$INSTALL_METHOD" == "conda" ]]; then
-            source $CONDA/etc/profile.d/conda.sh
-            conda activate ci;
-          fi
-          pytest --cov --cov-report=xml
+          pytest --cov --cov-report=xml -n auto --dist loadscope
           ctapipe-info --version
 
       - uses: codecov/codecov-action@v1

ctapipe/conftest.py

@@ -11,12 +11,27 @@
 from ctapipe.instrument import CameraGeometry
 
 
-@pytest.fixture(scope="session")
-def camera_geometries():
-    return [
-        CameraGeometry.from_name(name)
-        for name in ["LSTCam", "NectarCam", "CHEC", "FlashCam", "MAGICCam"]
-    ]
+# names of camera geometries available on the data server
+camera_names = [
+    "ASTRICam",
+    "CHEC",
+    "DigiCam",
+    "FACT",
+    "FlashCam",
+    "HESS-I",
+    "HESS-II",
+    "LSTCam",
+    "MAGICCam",
+    "NectarCam",
+    "SCTCam",
+    "VERITAS",
+    "Whipple490",
+]
+
+
+@pytest.fixture(scope="session", params=camera_names)
+def camera_geometry(request):
+    return CameraGeometry.from_name(request.param)
 
 
 @pytest.fixture(scope="session")

ctapipe/core/tests/test_component.py

@@ -290,7 +290,7 @@ def test_extra_config_missing():
     config["ExampleSubclass1"]["extra"] = 199.0
 
     with pytest.raises(TraitError):
-        comp = ExampleSubclass1(config=config)
+        ExampleSubclass1(config=config)
 
 
 def test_default():

ctapipe/core/tool.py

@@ -7,7 +7,7 @@
 import os
 import re
 
-from traitlets import default, TraitError
+from traitlets import default
 from traitlets.config import Application, Configurable
 
 from .. import __version__ as version
@@ -286,7 +286,7 @@ def run(self, argv=None):
 
             # check for any traitlets warnings using our custom handler
             if len(self.trait_warning_handler.errors) > 0:
-                raise ToolConfigurationError(f"Found config errors")
+                raise ToolConfigurationError("Found config errors")
 
             # remove handler to not impact performance with regex matching
             self.log.removeHandler(self.trait_warning_handler)

ctapipe/image/tests/test_cleaning.py

@@ -1,4 +1,3 @@
-import os
 import numpy as np
 from numpy.testing import assert_allclose
 from ctapipe.image import cleaning

ctapipe/image/tests/test_geometry_converter.py

@@ -12,14 +12,6 @@
 import astropy.units as u
 
 
-@pytest.fixture(params=["LSTCam", "CHEC", "FlashCam", "NectarCam", "MAGICCam", "FACT"])
-def camera_geometry(request):
-    """
-    Fixture to get one camera geometry at a time and perform tests with different geometries.
-    """
-    return CameraGeometry.from_name(request.param)
-
-
 def create_mock_image(geom):
     """
     creates a mock image, which parameters are adapted to the camera size
@@ -86,5 +78,3 @@ def test_convert_geometry_mock(camera_geometry, rot):
         # originally rectangular geometries don't need a buffer and therefore no mock
         # conversion
         return
-
-    assert_allclose(image, image1d)

ctapipe/instrument/camera/readout.py

@@ -7,7 +7,6 @@
 import numpy as np
 from astropy import units as u
 from astropy.table import Table
-from scipy.stats import norm
 from ctapipe.utils import get_table_dataset
 
 

ctapipe/instrument/camera/tests/test_description.py

@@ -1,14 +1,6 @@
 from ctapipe.instrument import CameraDescription
 
 
-def test_known_camera_names(camera_geometries):
+def test_known_camera_names(camera_geometry):
     """ Check that we can get a list of known camera names """
-    cams = CameraDescription.get_known_camera_names()
-    assert len(cams) > 4
-    assert "FlashCam" in cams
-    assert "NectarCam" in cams
-
-    # TODO: Requires camreadout files to be generated
-    # for cam in cams:
-    #     camera = CameraDescription.from_name(cam)
-    #     camera.info()
+    assert camera_geometry.camera_name in CameraDescription.get_known_camera_names()

ctapipe/instrument/camera/tests/test_geometry.py

@@ -1,11 +1,9 @@
 """ Tests for CameraGeometry """
 import numpy as np
 from astropy import units as u
-from ctapipe.instrument import CameraDescription, CameraGeometry, PixelShape
+from ctapipe.instrument import CameraGeometry, PixelShape
 import pytest
 
-camera_names = CameraDescription.get_known_camera_names()
-
 
 def test_construct():
     """ Check we can make a CameraGeometry from scratch """
@@ -93,15 +91,13 @@ def test_find_neighbor_pixels():
     assert set(neigh[11]) == {16, 6, 10, 12}
 
 
-@pytest.mark.parametrize("camera_name", camera_names)
-def test_neighbor_pixels(camera_name):
+def test_neighbor_pixels(camera_geometry):
     """
     test if each camera has a reasonable number of neighbor pixels (4 for
     rectangular, and 6 for hexagonal.  Other than edge pixels, the majority
     should have the same value
     """
-
-    geom = CameraGeometry.from_name(camera_name)
+    geom = camera_geometry
     n_pix = len(geom.pix_id)
     n_neighbors = [len(x) for x in geom.neighbors]
 
@@ -116,7 +112,7 @@ def test_neighbor_pixels(camera_name):
 
     # whipple has inhomogenious pixels that mess with pixel neighborhood
     # calculation
-    if camera_name != "Whipple490":
+    if not geom.camera_name.startswith("Whipple"):
         assert np.all(geom.neighbor_matrix == geom.neighbor_matrix.T)
         assert n_neighbors.count(1) == 0  # no pixel should have a single neighbor
 
@@ -229,15 +225,13 @@ def test_slicing():
     assert len(sliced2.pix_x) == 5
 
 
-@pytest.mark.parametrize("camera_name", camera_names)
-def test_slicing_rotation(camera_name):
+def test_slicing_rotation(camera_geometry):
     """ Check that we can rotate and slice """
-    cam = CameraGeometry.from_name(camera_name)
-    cam.rotate("25d")
+    camera_geometry.rotate("25d")
 
-    sliced1 = cam[5:10]
+    sliced1 = camera_geometry[5:10]
 
-    assert sliced1.pix_x[0] == cam.pix_x[5]
+    assert sliced1.pix_x[0] == camera_geometry.pix_x[5]
 
 
 def test_rectangle_patch_neighbors():
@@ -296,19 +290,17 @@ def test_hashing():
     assert len(set([cam1, cam2, cam3])) == 2
 
 
-@pytest.mark.parametrize("camera_name", camera_names)
-def test_camera_from_name(camera_name):
+def test_camera_from_name(camera_geometry):
     """ check we can construct all cameras from name"""
-    camera = CameraGeometry.from_name(camera_name)
-    assert str(camera) == camera_name
+    camera = CameraGeometry.from_name(camera_geometry.camera_name)
+    assert str(camera) == camera_geometry.camera_name
 
 
-@pytest.mark.parametrize("camera_name", camera_names)
-def test_camera_coordinate_transform(camera_name):
+def test_camera_coordinate_transform(camera_geometry):
     """test conversion of the coordinates stored in a camera frame"""
     from ctapipe.coordinates import EngineeringCameraFrame, CameraFrame, TelescopeFrame
 
-    geom = CameraGeometry.from_name(camera_name)
+    geom = camera_geometry
     trans_geom = geom.transform_to(EngineeringCameraFrame())
 
     unit = geom.pix_x.unit

ctapipe/instrument/camera/tests/test_readout.py

@@ -1,11 +1,9 @@
 """ Tests for CameraGeometry """
 import numpy as np
 from astropy import units as u
-from ctapipe.instrument import CameraDescription, CameraReadout
+from ctapipe.instrument import CameraReadout
 import pytest
 
-camera_names = CameraDescription.get_known_camera_names()
-
 
 def test_construct():
     """ Check we can make a CameraReadout from scratch """
@@ -142,14 +140,13 @@ def test_hashing():
     assert len({readout1, readout2, readout3}) == 2
 
 
-@pytest.mark.parametrize("camera_name", camera_names)
-def test_camera_from_name(camera_name):
+def test_camera_from_name(camera_geometry):
     """ check we can construct all cameras from name"""
 
     try:
-        camera = CameraReadout.from_name(camera_name)
-        assert str(camera) == camera_name
+        camera = CameraReadout.from_name(camera_geometry.camera_name)
+        assert str(camera) == camera_geometry.camera_name
     except FileNotFoundError:
-        # these two don't have readout definitions on the dataserver
-        if camera_name not in ["MAGICCam", "Whipple109"]:
+        # Most non-cta cameras don't have readout provided on the data server
+        if camera_geometry.camera_name in ["LSTCam", "NectarCam", "FlashCam", "CHEC"]:
             raise

ctapipe/instrument/subarray.py

@@ -1,7 +1,6 @@
 """
 Description of Arrays or Subarrays of telescopes
 """
-from collections import defaultdict
 from pathlib import Path
 
 import numpy as np

ctapipe/instrument/tests/test_telescope.py

@@ -29,17 +29,13 @@ def test_hash():
     assert len(set(telescopes)) == 3
 
 
-OPTICS_NAMES = OpticsDescription.get_known_optics_names()
-CAMERA_NAMES = CameraDescription.get_known_camera_names()
-
-
-@pytest.mark.parametrize("camera_name", CAMERA_NAMES)
-@pytest.mark.parametrize("optics_name", OPTICS_NAMES)
-def test_telescope_from_name(optics_name, camera_name):
+@pytest.mark.parametrize("optics_name", ["LST", "MST"])
+def test_telescope_from_name(optics_name, camera_geometry):
     """ Check we can construct all telescopes from their names """
+    camera_name = camera_geometry.camera_name
     tel = TelescopeDescription.from_name(optics_name, camera_name)
     assert optics_name in str(tel)
     assert camera_name in str(tel)
     assert tel.camera.geometry.pix_x.shape[0] > 0
     assert tel.optics.equivalent_focal_length.to("m") > 0
-    assert tel.type in ["MST", "SST", "LST", "UNKNOWN"]
+    assert tel.type in {"MST", "SST", "LST", "UNKNOWN"}

ctapipe/io/astropy_helpers.py

@@ -18,7 +18,7 @@
 
 from contextlib import ExitStack
 
-__all__ = ["h5_table_to_astropy"]
+__all__ = ["read_table"]
 
 
 def read_table(h5file, path, start=None, stop=None, step=None) -> Table: