Switch to src based repository structure

.gitignore

@@ -10,7 +10,7 @@ __pycache__
 
 # ignore version cache file (generated automatically when setup.py is run)
 ctapipe/_version_cache.py
-ctapipe/_version.py
+src/ctapipe/_version.py
 
 
 # Ignore .c files by default to avoid including generated code. If you want to

MANIFEST.in

@@ -8,6 +8,6 @@ recursive-include docs *
 prune build
 prune docs/_build
 prune docs/api
-prune ctapipe/_dev_version
+prune src/ctapipe/_dev_version
 
 global-exclude *.pyc *.o

pyproject.toml

@@ -3,7 +3,7 @@ requires = ["setuptools>=64", "setuptools_scm[toml]>=8"]
 build-backend = "setuptools.build_meta"
 
 [tool.setuptools_scm]
-write_to = "ctapipe/_version.py"
+write_to = "src/ctapipe/_version.py"
 
 [tool.black]
 line-length = 88

setup.cfg

@@ -20,7 +20,9 @@ classifiers =
 
 
 [options]
-packages = find:
+package_dir=
+    =src
+packages=find:
 python_requires = >=3.9
 zip_safe = False
 install_requires=
@@ -79,6 +81,7 @@ all =
     %(dev)s
 
 [options.packages.find]
+where=src
 exclude =
     ctapipe._dev_version
 

ctapipe/_dev_version/__init__.py → src/ctapipe/_dev_version/__init__.py

@@ -4,6 +4,6 @@
 try:
     from setuptools_scm import get_version
 
-    version = get_version(root="../..", relative_to=__file__)
+    version = get_version(root="../../..", relative_to=__file__)
 except Exception as e:
     raise ImportError(f"setuptools_scm broken or not installed: {e}")

ctapipe/calib/camera/gainselection.py → src/ctapipe/calib/camera/gainselection.py

@@ -3,7 +3,9 @@
 """
 from abc import abstractmethod
 from enum import IntEnum
+
 import numpy as np
+
 from ctapipe.core import Component, traits
 
 __all__ = [

ctapipe/calib/camera/tests/test_gainselection.py → src/ctapipe/calib/camera/tests/test_gainselection.py

@@ -1,9 +1,10 @@
 import numpy as np
+
 from ctapipe.calib.camera.gainselection import (
-    ManualGainSelector,
-    ThresholdGainSelector,
     GainChannel,
     GainSelector,
+    ManualGainSelector,
+    ThresholdGainSelector,
 )
 
 

ctapipe/coordinates/camera_frame.py → src/ctapipe/coordinates/camera_frame.py

@@ -1,23 +1,22 @@
-import numpy as np
 import astropy.units as u
+import numpy as np
 from astropy.coordinates import (
+    AffineTransform,
+    AltAz,
+    Attribute,
     BaseCoordinateFrame,
+    CartesianRepresentation,
     CoordinateAttribute,
-    QuantityAttribute,
-    Attribute,
-    TimeAttribute,
     EarthLocationAttribute,
     FunctionTransform,
-    frame_transform_graph,
-    CartesianRepresentation,
+    QuantityAttribute,
+    TimeAttribute,
     UnitSphericalRepresentation,
-    AltAz,
-    AffineTransform,
+    frame_transform_graph,
 )
 
-from .telescope_frame import TelescopeFrame
 from .representation import PlanarRepresentation
-
+from .telescope_frame import TelescopeFrame
 
 __all__ = ["CameraFrame"]
 

ctapipe/coordinates/representation.py → src/ctapipe/coordinates/representation.py

@@ -1,11 +1,11 @@
 """
 This module defines any reference systems which may be needed in addition
 """
-from astropy.coordinates import BaseRepresentation, CartesianRepresentation
-import astropy.units as u
 from collections import OrderedDict
-from numpy import broadcast_arrays
 
+import astropy.units as u
+from astropy.coordinates import BaseRepresentation, CartesianRepresentation
+from numpy import broadcast_arrays
 
 __all__ = ["PlanarRepresentation"]
 

ctapipe/coordinates/tests/test_engineering_frame.py → src/ctapipe/coordinates/tests/test_engineering_frame.py

@@ -1,8 +1,8 @@
 """
 Tests for the conversion between camera coordinate frames
 """
-from astropy.coordinates import SkyCoord
 import astropy.units as u
+from astropy.coordinates import SkyCoord
 
 
 def test_conversion():

ctapipe/coordinates/tests/test_nominal_frame.py → src/ctapipe/coordinates/tests/test_nominal_frame.py

@@ -1,5 +1,5 @@
-from astropy.coordinates import SkyCoord, AltAz
 import astropy.units as u
+from astropy.coordinates import AltAz, SkyCoord
 from pytest import approx
 
 

ctapipe/coordinates/tests/test_roundtrip.py → src/ctapipe/coordinates/tests/test_roundtrip.py

@@ -1,6 +1,6 @@
-from astropy.coordinates import SkyCoord, AltAz
-from pytest import approx
 import astropy.units as u
+from astropy.coordinates import AltAz, SkyCoord
+from pytest import approx
 
 
 def test_roundtrip_camera_horizon():

ctapipe/coordinates/tests/test_telescope_frame.py → src/ctapipe/coordinates/tests/test_telescope_frame.py

@@ -1,5 +1,5 @@
-from astropy.coordinates import SkyCoord, AltAz
 import astropy.units as u
+from astropy.coordinates import AltAz, SkyCoord
 from pytest import approx
 
 

ctapipe/core/logging.py → src/ctapipe/core/logging.py

@@ -3,7 +3,6 @@
 import logging
 from collections.abc import Mapping
 
-
 DEFAULT_LOGGING_FORMAT = (
     "%(asctime)s %(levelname)s [%(name)s] (%(module)s.%(funcName)s): %(message)s"
 )

ctapipe/core/support.py → src/ctapipe/core/support.py

@@ -1,5 +1,5 @@
 class Singleton(type):
-    """" metaclass for singleton pattern """
+    """ " metaclass for singleton pattern"""
 
     instance = None
 

ctapipe/fitting.py → src/ctapipe/fitting.py

@@ -1,6 +1,5 @@
-from numba import njit
 import numpy as np
-
+from numba import njit
 
 EPS = 2 * np.finfo(np.float64).eps
 

ctapipe/image/concentration.py → src/ctapipe/image/concentration.py

@@ -1,14 +1,14 @@
-import numpy as np
 import astropy.units as u
+import numpy as np
 
 from ..containers import (
+    CameraHillasParametersContainer,
     ConcentrationContainer,
     HillasParametersContainer,
-    CameraHillasParametersContainer,
 )
-from .hillas import camera_to_shower_coordinates
 from ..instrument import CameraGeometry
 from ..utils.quantities import all_to_value
+from .hillas import camera_to_shower_coordinates
 
 __all__ = ["concentration_parameters"]
 
@@ -53,15 +53,15 @@ def concentration_parameters(geom: CameraGeometry, image, hillas_parameters):
     delta_y = pix_y - y
 
     # take pixels within one pixel diameter from the cog
-    mask_cog = (delta_x ** 2 + delta_y ** 2) < pixel_width ** 2
+    mask_cog = (delta_x**2 + delta_y**2) < pixel_width**2
     conc_cog = np.sum(image[mask_cog]) / h.intensity
 
     if hillas_parameters.width.value != 0:
         # get all pixels inside the hillas ellipse
         longi, trans = camera_to_shower_coordinates(
             pix_x, pix_y, x, y, h.psi.to_value(u.rad)
         )
-        mask_core = (longi ** 2 / length ** 2) + (trans ** 2 / width ** 2) <= 1.0
+        mask_core = (longi**2 / length**2) + (trans**2 / width**2) <= 1.0
         conc_core = image[mask_core].sum() / h.intensity
     else:
         conc_core = 0.0

ctapipe/image/leakage.py → src/ctapipe/image/leakage.py

@@ -3,8 +3,8 @@
 """
 
 import numpy as np
-from ..containers import LeakageContainer
 
+from ..containers import LeakageContainer
 
 __all__ = ["leakage_parameters"]
 

ctapipe/image/muon/fitting.py → src/ctapipe/image/muon/fitting.py

@@ -1,6 +1,6 @@
 import numpy as np
-from iminuit import Minuit
 from astropy.units import Quantity
+from iminuit import Minuit
 
 from ctapipe.utils.quantities import all_to_value
 
@@ -35,8 +35,8 @@ def kundu_chaudhuri_circle_fit(x, y, weights):
     b1 = np.sum(weights * (x - mean_x) * y)
     b2 = np.sum(weights * (y - mean_y) * y)
 
-    c1 = 0.5 * np.sum(weights * (x - mean_x) * (x ** 2 + y ** 2))
-    c2 = 0.5 * np.sum(weights * (y - mean_y) * (x ** 2 + y ** 2))
+    c1 = 0.5 * np.sum(weights * (x - mean_x) * (x**2 + y**2))
+    c2 = 0.5 * np.sum(weights * (y - mean_y) * (x**2 + y**2))
 
     center_x = (b2 * c1 - b1 * c2) / (a1 * b2 - a2 * b1)
     center_y = (a2 * c1 - a1 * c2) / (a2 * b1 - a1 * b2)
@@ -109,7 +109,7 @@ def taubin_loss_function(xc, yc, r):
         """taubin fit formula
         reference : Barcelona_Muons_TPA_final.pdf (slide 6)
         """
-        upper_term = (((x - xc) ** 2 + (y - yc) ** 2 - r ** 2) ** 2).sum()
+        upper_term = (((x - xc) ** 2 + (y - yc) ** 2 - r**2) ** 2).sum()
 
         lower_term = (((x - xc) ** 2 + (y - yc) ** 2)).sum()
 

ctapipe/image/muon/tests/test_muon_features.py → src/ctapipe/image/muon/tests/test_muon_features.py

@@ -1,8 +1,9 @@
+import math
+
 import astropy.units as u
 import numpy as np
-import math
-from ctapipe.image.muon.features import ring_containment
-from ctapipe.image.muon.features import ring_completeness
+
+from ctapipe.image.muon.features import ring_completeness, ring_containment
 
 
 def test_ring_containment():

ctapipe/image/statistics.py → src/ctapipe/image/statistics.py

@@ -3,7 +3,6 @@
 
 from ..containers import StatisticsContainer
 
-
 __all__ = ["descriptive_statistics", "skewness", "kurtosis"]
 
 
@@ -82,7 +81,7 @@ def kurtosis(data, mean=None, std=None, fisher=True):
 def descriptive_statistics(
     values, container_class=StatisticsContainer
 ) -> StatisticsContainer:
-    """ compute intensity statistics of an image  """
+    """compute intensity statistics of an image"""
     mean = values.mean()
     std = values.std()
     return container_class(

ctapipe/image/timing.py → src/ctapipe/image/timing.py

@@ -2,20 +2,19 @@
 Image timing-based shower image parametrization.
 """
 
-import numpy as np
 import astropy.units as u
+import numpy as np
+from numba import njit
+
 from ..containers import (
-    CameraTimingParametersContainer,
-    TimingParametersContainer,
     CameraHillasParametersContainer,
+    CameraTimingParametersContainer,
     HillasParametersContainer,
+    TimingParametersContainer,
 )
-from .hillas import camera_to_shower_coordinates
-from ..utils.quantities import all_to_value
 from ..fitting import lts_linear_regression
-
-from numba import njit
-
+from ..utils.quantities import all_to_value
+from .hillas import camera_to_shower_coordinates
 
 __all__ = ["timing_parameters"]
 

ctapipe/instrument/camera/tests/test_image_conversion.py → src/ctapipe/instrument/camera/tests/test_image_conversion.py

@@ -1,16 +1,17 @@
+import astropy.units as u
 import numpy as np
+import pytest
 from numpy.testing import assert_allclose
-import astropy.units as u
+
 from ctapipe.image.toymodel import Gaussian
-import pytest
 
 
 def create_mock_image(geom, psi=25 * u.deg):
     """
     creates a mock image, which parameters are adapted to the camera size
     """
 
-    camera_r = np.max(np.sqrt(geom.pix_x ** 2 + geom.pix_y ** 2))
+    camera_r = np.max(np.sqrt(geom.pix_x**2 + geom.pix_y**2))
     model = Gaussian(
         x=0.3 * camera_r,
         y=0 * u.m,

ctapipe/io/tests/conftest.py → src/ctapipe/io/tests/conftest.py

@@ -1,5 +1,6 @@
 import pytest
-from ctapipe.io import EventSource, DataWriter
+
+from ctapipe.io import DataWriter, EventSource
 
 
 @pytest.fixture(scope="session")

ctapipe/io/tests/test_available_sources.py → src/ctapipe/io/tests/test_available_sources.py

@@ -1,6 +1,6 @@
 def test_available_sources():
-    from ctapipe.io.eventsource import EventSource
     from ctapipe.core import non_abstract_children
+    from ctapipe.io.eventsource import EventSource
 
     # make this before the explicit imports to make sure
     # all classes are avaialble even if not explicitly imported

ctapipe/io/tests/test_write_table.py → src/ctapipe/io/tests/test_write_table.py

@@ -1,14 +1,14 @@
 """Tests for the write_table function"""
-from astropy.time import Time
-from astropy.table import Table
 import astropy.units as u
 import numpy as np
 import pytest
+from astropy.table import Table
+from astropy.time import Time
 
 
 def test_write_table(tmp_path):
     """Test write_table"""
-    from ctapipe.io.astropy_helpers import write_table, read_table
+    from ctapipe.io.astropy_helpers import read_table, write_table
 
     table = Table(
         {