tidy up for release (#86)

.circleci/config.yml

@@ -32,7 +32,7 @@ jobs:
       jobname:
         type: string
     docker:
-      - image: circleci/python:3.8
+      - image: cimg/python:3.9
     environment:
       TOXENV=<< parameters.jobname >>
     steps:
@@ -55,7 +55,7 @@ jobs:
       jobname:
         type: string
     docker:
-      - image: circleci/python:3.8
+      - image: cimg/python:3.9
     environment:
       TOXENV: << parameters.jobname >>
       GIT_SSH_COMMAND: ssh -i ~/.ssh/id_rsa_6464b6a8248237ca368fd4690777d921

.pre-commit-config.yaml

@@ -1,33 +1,38 @@
-ci:
-  autofix_prs: false
 repos:
--   repo: https://github.com/psf/black
-    rev: 22.3.0
+  - repo: https://github.com/myint/docformatter
+    rev: v1.4
     hooks:
-    - id: black
--   repo: https://github.com/myint/autoflake
+      - id: docformatter
+        args: [--in-place, --pre-summary-newline, --make-summary-multi]
+  - repo: https://github.com/myint/autoflake
     rev: v1.4
     hooks:
       - id: autoflake
         args: ['--in-place', '--remove-all-unused-imports', '--remove-unused-variable']
         exclude: ".*(.fits|.fts|.fit|.txt|tca.*|extern.*|.rst|.md|__init__.py|docs/conf.py)$"
--   repo: https://github.com/PyCQA/isort
-    rev: 5.10.1
-    hooks:
+  -   repo: https://github.com/psf/black
+      rev: 22.3.0
+      hooks:
+      - id: black
+        exclude: ".*(.fits|.fts|.fit|.txt|.csv)$"
+  -   repo: https://github.com/PyCQA/isort
+      rev: 5.10.1
+      hooks:
       - id: isort
-        args: ['--sp','setup.cfg']
-        exclude: ".*(.fits|.fts|.fit|.txt|tca.*|extern.*|.rst|.md|docs/conf.py)$"
--   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.2.0
-    hooks:
+        exclude: ".*(.fits|.fts|.fit|.txt|.csv)$"
+  -   repo: https://github.com/pre-commit/pre-commit-hooks
+      rev: v4.2.0
+      hooks:
       - id: check-ast
       - id: check-case-conflict
       - id: trailing-whitespace
-        exclude: ".*(.fits|.fts|.fit|.txt)$"
+        exclude: ".*(.fits|.fts|.fit|.txt|.csv)$"
+      - id: mixed-line-ending
+        exclude: ".*(.fits|.fts|.fit|.txt|.csv)$"
+      - id: end-of-file-fixer
+        exclude: ".*(.fits|.fts|.fit|.txt|.csv)$"
       - id: check-yaml
       - id: debug-statements
-      - id: check-added-large-files
-      - id: end-of-file-fixer
-        exclude: ".*(.fits|.fts|.fit|.txt|tca.*)$"
-      - id: mixed-line-ending
-        exclude: ".*(.fits|.fts|.fit|.txt|tca.*)$"
+
+ci:
+  autofix_prs: false

CHANGELOG.rst

@@ -1,3 +1,11 @@
+0.4.2 (2022-05-24)
+==================
+
+Breaking Changes
+----------------
+
+- Minimum version of ``sunpy`` required is now 4.0.0
+
 0.4.1 (2022-04-05)
 ==================
 

azure-pipelines.yml

@@ -58,15 +58,13 @@ stages:
           apt:
             - graphviz
         envs:
-          - macos: py37
-          - windows: py38
+          - macos: py38
+          - windows: py39
           - linux: build_docs
             posargs: " "
             pytest: false
           - linux: py39-online
-          - linux: py37-oldestdeps
-          - linux: py39-conda
-            libraries: {}
+          - linux: py38-oldestdeps
 
   - ${{ if or(eq(variables['Build.Reason'], 'Schedule'), eq(variables['Build.Reason'], 'Manual')) }}:
     - stage: CronTests
@@ -81,6 +79,8 @@ stages:
           toxdeps: tox-pypi-filter
           envs:
             - linux: py310-devdeps
+            - linux: py39-conda
+              libraries: {}
 
   # On branches which aren't main, and not Pull Requests, build the wheels but only upload them on tags
   - ${{ if and(ne(variables['Build.Reason'], 'PullRequest'), or(ne(variables['Build.SourceBranchName'], 'main'), eq(variables['Build.Reason'], 'Schedule'), eq(variables['Build.Reason'], 'Manual'))) }}:

docs/conf.py

@@ -1,5 +1,6 @@
 """
 Configuration file for the Sphinx documentation builder.
+
 isort:skip_file
 """
 # flake8: NOQA: E402

examples/tracing_loops.py

@@ -45,9 +45,7 @@
 # The base flux and median flux ratio ``qthresh1`` is 0.0.
 # The noise threshold in the image with repect to median flux ``qthresh2`` is 3.0 .
 # For the meaning of these parameters please consult the OCCULT2 article.
-loops = trace.occult2(
-    trace_map.data, nsm1=3, rmin=30, lmin=25, nstruc=1000, ngap=0, qthresh1=0.0, qthresh2=3.0
-)
+loops = trace.occult2(trace_map.data, nsm1=3, rmin=30, lmin=25, nstruc=1000, ngap=0, qthresh1=0.0, qthresh2=3.0)
 
 ###############################################################################
 # `~sunkit_image.trace.occult2` returns a list, each element of which is a detected loop.

pyproject.toml

@@ -2,14 +2,14 @@
 requires = [
   "extension-helpers",
   "oldest-supported-numpy",
-  "setuptools_scm",
-  "setuptools",
+  "setuptools>=56,!=61.0.0",
+  "setuptools_scm[toml]>=6.2",
   "wheel",
 ]
 build-backend = 'setuptools.build_meta'
 
 [tool.black]
-line-length = 110
+line-length = 120
 include = '\.pyi?$'
 exclude = '''
 (

setup.cfg

@@ -19,20 +19,20 @@ classifiers =
   Operating System :: OS Independent
   Programming Language :: Python
   Programming Language :: Python :: 3
-  Programming Language :: Python :: 3.7
   Programming Language :: Python :: 3.8
   Programming Language :: Python :: 3.9
+  Programming Language :: Python :: 3.10
   Topic :: Scientific/Engineering :: Physics
 
 [options]
-python_requires = >=3.7
+python_requires = >=3.8
 packages = find:
 include_package_data = True
 setup_requires =
   setuptools_scm
 install_requires =
   scikit-image>=0.18.0
-  sunpy>=3.0.0
+  sunpy>=4.0.0
 
 [options.extras_require]
 tests =

sunkit_image/__init__.py

@@ -23,8 +23,6 @@ class UnsupportedPythonError(Exception):
 
 if sys.version_info < tuple(int(val) for val in __minimum_python_version__.split(".")):
     # This has to be .format to keep backwards compatibly.
-    raise UnsupportedPythonError(
-        "sunkit_image does not support Python < {}".format(__minimum_python_version__)
-    )
+    raise UnsupportedPythonError("sunkit_image does not support Python < {}".format(__minimum_python_version__))
 
 __all__ = []

sunkit_image/_dev/__init__.py

@@ -1,6 +1,7 @@
 """
-This package contains utilities that are only used when developing sunkit_image in a
-copy of the source repository.
+This package contains utilities that are only used when developing sunkit_image
+in a copy of the source repository.
+
 These files are not installed, and should not be assumed to exist at
 runtime.
 """

sunkit_image/asda.py

@@ -140,9 +140,7 @@ def gamma_values(self):
         vel = self.gen_vel(index[1], index[0])
         # Iterate over the array gamma
         for d, (i, j) in enumerate(
-            product(
-                np.arange(self.r, self.dshape[0] - self.r, 1), np.arange(self.r, self.dshape[1] - self.r, 1)
-            )
+            product(np.arange(self.r, self.dshape[0] - self.r, 1), np.arange(self.r, self.dshape[1] - self.r, 1))
         ):
             self.gamma[i, j, 0], self.gamma[i, j, 1] = calc_gamma(pm, vel[..., d], pnorm, N)
         # Transpose back vx & vy

sunkit_image/coalignment.py

@@ -1,7 +1,7 @@
 """
 This module provides routines for the co-alignment of images and
-`~sunpy.map.mapsequence.MapSequence` objects through both template
-matching and corrections due to solar rotation.
+`~sunpy.map.mapsequence.MapSequence` objects through both template matching and
+corrections due to solar rotation.
 """
 import warnings
 from copy import deepcopy
@@ -101,9 +101,7 @@ def clip_edges(data, yclips: u.pix, xclips: u.pix):
     nx = data.shape[1]
     # The purpose of the int below is to ensure integer type since by default
     # astropy quantities are converted to floats.
-    return data[
-        int(yclips[0].value) : ny - int(yclips[1].value), int(xclips[0].value) : nx - int(xclips[1].value)
-    ]
+    return data[int(yclips[0].value) : ny - int(yclips[1].value), int(xclips[0].value) : nx - int(xclips[1].value)]
 
 
 @u.quantity_input
@@ -291,7 +289,8 @@ def parabolic_turning_point(y):
 
 def check_for_nonfinite_entries(layer_image, template_image):
     """
-    Issue a warning if there is any nonfinite entry in the layer or template images.
+    Issue a warning if there is any nonfinite entry in the layer or template
+    images.
 
     Parameters
     ----------
@@ -579,8 +578,8 @@ def mapsequence_coalign_by_match_template(
 
 def calculate_solar_rotate_shift(mc, layer_index=0, **kwargs):
     """
-    Calculate the shift that must be applied to each map contained in a mapsequence
-    in order to compensate for solar rotation.
+    Calculate the shift that must be applied to each map contained in a
+    mapsequence in order to compensate for solar rotation.
 
     The center of the map is used to calculate the position of each mapsequence
     layer. Shifts are calculated relative to a specified layer in the mapsequence.
@@ -627,9 +626,7 @@ def calculate_solar_rotate_shift(mc, layer_index=0, **kwargs):
         # Calculate the rotation of the center of the map 'm' at its
         # observation time to the observation time of the reference layer
         # indicated by "layer_index".
-        new_coordinate = solar_rotate_coordinate(
-            m.center, observer=rotate_to_this_layer.observer_coordinate, **kwargs
-        )
+        new_coordinate = solar_rotate_coordinate(m.center, observer=rotate_to_this_layer.observer_coordinate, **kwargs)
 
         xshift_arcseconds[i] = new_coordinate.Tx - rotate_to_this_layer.center.Tx
         yshift_arcseconds[i] = new_coordinate.Ty - rotate_to_this_layer.center.Ty

sunkit_image/tests/figure_hashes_mpl_332_ft_261_sunkit_image_dev_sunpy_400.json

@@ -0,0 +1,6 @@
+{
+    "sunkit_image.tests.test_enhance.test_mgn": "ab39d3330a967a6f34fb53043aa820665e87c4a73002381883b9516d2983228d",
+    "sunkit_image.tests.test_radial.test_fig_nrgf": "a0efb4aa94724bf1b2ff97466decb6edcc1394c704315f5b16dbf458d9c1df84",
+    "sunkit_image.tests.test_radial.test_fig_fnrgf": "4a653738b96abebac537ebba5aadedce02f3c03dd13cf12de836600c800a650e",
+    "sunkit_image.tests.test_trace.test_occult2_fig": "c5ff1416cb51dc51ad1705174e5b13f8cb02486dc3c58fd79dc1b80534f6caf5"
+}

sunkit_image/tests/helpers.py

@@ -25,9 +25,9 @@ def get_hash_library_name():
 def figure_test(test_function):
     """
     A decorator which marks the test as comparing the hash of the returned
-    figure to the hash library in the repository.
-    A `matplotlib.figure.Figure` object should be returned or ``plt.gcf()``
-    will be called to get the figure object to compare to.
+    figure to the hash library in the repository. A `matplotlib.figure.Figure`
+    object should be returned or ``plt.gcf()`` will be called to get the figure
+    object to compare to.
 
     Examples
     --------

sunkit_image/tests/test_asda.py

@@ -23,16 +23,12 @@ def test_asda_artificial():
     with pytest.raises(ValueError, match="Keyword 'factor' must be an integer"):
         lo = asda.Lamb_Oseen(vmax=vmax, rmax=rmax, ratio_vradial=ratio, factor=1.2, r=1)
 
-    with pytest.warns(
-        UserWarning, match="One of the input parameters is missing," + "setting both to 'None'"
-    ):
+    with pytest.warns(UserWarning, match="One of the input parameters is missing," + "setting both to 'None'"):
         lo = asda.Lamb_Oseen(vmax=vmax, rmax=rmax, gamma=0.5, ratio_vradial=ratio, factor=1)
 
     lo = asda.Lamb_Oseen(vmax=vmax, rmax=rmax, ratio_vradial=ratio, factor=1)
     # Generate vx and vy
-    with pytest.warns(
-        UserWarning, match="One of the input parameters is missing, setting " + " both to 'None'"
-    ):
+    with pytest.warns(UserWarning, match="One of the input parameters is missing, setting " + " both to 'None'"):
         vx, vy = lo.get_vxvy(x_range=[-100, 100, 200], y_range=[-100, 100, 200], x=np.meshgrid)
 
     vx, vy = lo.get_vxvy(x_range=[-100, 100, 200], y_range=[-100, 100, 200])

sunkit_image/tests/test_coalignment.py

@@ -92,16 +92,12 @@ def test_check_for_nonfinite_entries():
             a[i] = non_number
             b = a.reshape(3, 3)
 
-            with pytest.warns(
-                SunpyUserWarning, match="The layer image has nonfinite entries."
-            ) as warning_list:
+            with pytest.warns(SunpyUserWarning, match="The layer image has nonfinite entries.") as warning_list:
                 check_for_nonfinite_entries(b, np.ones((3, 3)))
 
             assert len(warning_list) == 1
 
-            with pytest.warns(
-                SunpyUserWarning, match="The template image has nonfinite entries."
-            ) as warning_list:
+            with pytest.warns(SunpyUserWarning, match="The template image has nonfinite entries.") as warning_list:
                 check_for_nonfinite_entries(np.ones((3, 3)), b)
 
             assert len(warning_list) == 1
@@ -162,9 +158,7 @@ def test_find_best_match_location(aia171_test_map_layer, aia171_test_template, a
 
     result = match_template_to_layer(aia171_test_map_layer, aia171_test_template)
     match_location = u.Quantity(find_best_match_location(result))
-    assert_allclose(
-        match_location.value, np.array(result.shape) / 2.0 - 0.5 + aia171_test_shift, rtol=1e-3, atol=0
-    )
+    assert_allclose(match_location.value, np.array(result.shape) / 2.0 - 0.5 + aia171_test_shift, rtol=1e-3, atol=0)
 
 
 def test_lower_clip(aia171_test_clipping):
@@ -214,10 +208,8 @@ def aia171_test_mc_pixel_displacements():
 @pytest.fixture
 def aia171_mc_arcsec_displacements(aia171_test_mc_pixel_displacements, aia171_test_map):
     return {
-        "x": np.asarray([0.0, aia171_test_mc_pixel_displacements[1] * aia171_test_map.scale[0].value])
-        * u.arcsec,
-        "y": np.asarray([0.0, aia171_test_mc_pixel_displacements[0] * aia171_test_map.scale[1].value])
-        * u.arcsec,
+        "x": np.asarray([0.0, aia171_test_mc_pixel_displacements[1] * aia171_test_map.scale[0].value]) * u.arcsec,
+        "y": np.asarray([0.0, aia171_test_mc_pixel_displacements[0] * aia171_test_map.scale[1].value]) * u.arcsec,
     }
 
 
@@ -381,9 +373,7 @@ def test_apply_shifts(aia171_test_map):
 
     # Test that keywords are correctly passed
     # Test for an individual keyword
-    test_mc = apply_shifts(
-        mc, astropy_displacements["y"], astropy_displacements["x"], clip=False, cval=np.nan
-    )
+    test_mc = apply_shifts(mc, astropy_displacements["y"], astropy_displacements["x"], clip=False, cval=np.nan)
     assert np.all(np.logical_not(np.isfinite(test_mc[1].data[:, -1])))
 
     # Test for a combination of keywords, and that changing the interpolation
@@ -397,9 +387,7 @@ def test_apply_shifts(aia171_test_map):
 
 @pytest.fixture
 def aia171_test_submap(aia171_test_map):
-    return aia171_test_map.submap(
-        SkyCoord(((0, 0), (400, 500)) * u.arcsec, frame=aia171_test_map.coordinate_frame)
-    )
+    return aia171_test_map.submap(SkyCoord(((0, 0), (400, 500)) * u.arcsec, frame=aia171_test_map.coordinate_frame))
 
 
 @pytest.fixture
@@ -430,23 +418,15 @@ def test_calculate_solar_rotate_shift(
 ):
     # Test that the default works
     test_output = calculate_solar_rotate_shift(aia171_test_mapsequence)
-    assert_allclose(
-        test_output["x"].to("arcsec").value, known_displacements_layer_index0["x"], rtol=5e-2, atol=1e-5
-    )
-    assert_allclose(
-        test_output["y"].to("arcsec").value, known_displacements_layer_index0["y"], rtol=5e-2, atol=1e-5
-    )
+    assert_allclose(test_output["x"].to("arcsec").value, known_displacements_layer_index0["x"], rtol=5e-2, atol=1e-5)
+    assert_allclose(test_output["y"].to("arcsec").value, known_displacements_layer_index0["y"], rtol=5e-2, atol=1e-5)
 
     # Test that the rotation relative to a nonzero layer_index works
     test_output = calculate_solar_rotate_shift(aia171_test_mapsequence, layer_index=1)
     print(test_output["x"].to("arcsec").value)
     print(test_output["y"].to("arcsec").value)
-    assert_allclose(
-        test_output["x"].to("arcsec").value, known_displacements_layer_index1["x"], rtol=5e-2, atol=1e-5
-    )
-    assert_allclose(
-        test_output["y"].to("arcsec").value, known_displacements_layer_index1["y"], rtol=5e-2, atol=1e-5
-    )
+    assert_allclose(test_output["x"].to("arcsec").value, known_displacements_layer_index1["x"], rtol=5e-2, atol=1e-5)
+    assert_allclose(test_output["y"].to("arcsec").value, known_displacements_layer_index1["y"], rtol=5e-2, atol=1e-5)
 
 
 def test_mapsequence_solar_derotate(aia171_test_mapsequence, aia171_test_submap):