CI fix (#45)

sunpy · Feb 13, 2021 · e64cca3 · e64cca3
1 parent b815f60
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diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -1,3 +1,12 @@
+Sunkit_Instruments v0.2.0 (2021-02-13)
+======================================
+
+Features
+--------
+
+- Add :func:`sunkit_instruments.rhessi.imagecube2map` function to extract `sunpy.map.MapSequence` objects from a RHESSI 4D image cube. (`#35 <https://github.com/sunpy/sunkit-instruments/pull/35>`__)
+
+
 Sunkit_Instruments 0.1.0 (2020-09-30)
 =====================================
 

diff --git a/changelog/35.feature.rst b/changelog/35.feature.rst
diff --git a/docs/conf.py b/docs/conf.py
@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 #
 # Configuration file for the Sphinx documentation builder.
 #
@@ -10,31 +9,32 @@
 # -- Project information -----------------------------------------------------
 
 from sunkit_instruments import __version__
-project = 'sunkit_instruments'
-copyright = '2020, The SunPy Developers'
-author = 'The SunPy Developers'
+
+project = "sunkit_instruments"
+copyright = "2020, The SunPy Developers"
+author = "The SunPy Developers"
 
 # The full version, including alpha/beta/rc tags
 release = __version__
-is_development = '.dev' in __version__
+is_development = ".dev" in __version__
 
 # -- General configuration ---------------------------------------------------
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'sphinx.ext.autodoc',
-    'sphinx.ext.intersphinx',
-    'sphinx.ext.todo',
-    'sphinx.ext.coverage',
-    'sphinx.ext.inheritance_diagram',
-    'sphinx.ext.viewcode',
-    'sphinx.ext.napoleon',
-    'sphinx.ext.doctest',
-    'sphinx.ext.mathjax',
-    'sphinx_automodapi.automodapi',
-    'sphinx_automodapi.smart_resolver',
+    "sphinx.ext.autodoc",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.todo",
+    "sphinx.ext.coverage",
+    "sphinx.ext.inheritance_diagram",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.doctest",
+    "sphinx.ext.mathjax",
+    "sphinx_automodapi.automodapi",
+    "sphinx_automodapi.smart_resolver",
 ]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -43,33 +43,42 @@
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
-source_suffix = '.rst'
+source_suffix = ".rst"
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # The reST default role (used for this markup: `text`) to use for all
 # documents. Set to the "smart" one.
-default_role = 'obj'
+default_role = "obj"
 
 # -- Options for intersphinx extension ---------------------------------------
 
 # Example configuration for intersphinx: refer to the Python standard library.
 intersphinx_mapping = {
-    'python': ('https://docs.python.org/3/',
-               (None, 'http://data.astropy.org/intersphinx/python3.inv')),
-    'numpy': ('https://docs.scipy.org/doc/numpy/',
-              (None, 'http://data.astropy.org/intersphinx/numpy.inv')),
-    'scipy': ('https://docs.scipy.org/doc/scipy/reference/',
-              (None, 'http://data.astropy.org/intersphinx/scipy.inv')),
-    'matplotlib': ('https://matplotlib.org/',
-                   (None, 'http://data.astropy.org/intersphinx/matplotlib.inv')),
-    'astropy': ('http://docs.astropy.org/en/stable/', None),
-    'sunpy': ('https://docs.sunpy.org/en/stable/', None)}
+    "python": (
+        "https://docs.python.org/3/",
+        (None, "http://data.astropy.org/intersphinx/python3.inv"),
+    ),
+    "numpy": (
+        "https://docs.scipy.org/doc/numpy/",
+        (None, "http://data.astropy.org/intersphinx/numpy.inv"),
+    ),
+    "scipy": (
+        "https://docs.scipy.org/doc/scipy/reference/",
+        (None, "http://data.astropy.org/intersphinx/scipy.inv"),
+    ),
+    "matplotlib": (
+        "https://matplotlib.org/",
+        (None, "http://data.astropy.org/intersphinx/matplotlib.inv"),
+    ),
+    "astropy": ("http://docs.astropy.org/en/stable/", None),
+    "sunpy": ("https://docs.sunpy.org/en/stable/", None),
+}
 
 # -- Options for HTML output -------------------------------------------------
 
@@ -79,7 +88,7 @@
 try:
     from sunpy_sphinx_theme.conf import *
 except ImportError:
-    html_theme = 'default'
+    html_theme = "default"
 
 
 # Add any paths that contain custom static files (such as style sheets) here,
@@ -91,12 +100,12 @@
 graphviz_output_format = "svg"
 
 graphviz_dot_args = [
-    '-Nfontsize=10',
-    '-Nfontname=Helvetica Neue, Helvetica, Arial, sans-serif',
-    '-Efontsize=10',
-    '-Efontname=Helvetica Neue, Helvetica, Arial, sans-serif',
-    '-Gfontsize=10',
-    '-Gfontname=Helvetica Neue, Helvetica, Arial, sans-serif'
+    "-Nfontsize=10",
+    "-Nfontname=Helvetica Neue, Helvetica, Arial, sans-serif",
+    "-Efontsize=10",
+    "-Efontname=Helvetica Neue, Helvetica, Arial, sans-serif",
+    "-Gfontsize=10",
+    "-Gfontname=Helvetica Neue, Helvetica, Arial, sans-serif",
 ]
 
 
@@ -106,9 +115,10 @@
 target_file = os.path.abspath("./whatsnew/latest_changelog.txt")
 try:
     from sunpy.util.towncrier import generate_changelog_for_docs
+
     if is_development:
         generate_changelog_for_docs("../", target_file)
 except Exception as e:
     print(f"Failed to add changelog to docs with error {e}.")
 # Make sure the file exists or else sphinx will complain.
-open(target_file, 'a').close()
+open(target_file, "a").close()
diff --git a/setup.cfg b/setup.cfg
@@ -22,6 +22,7 @@ classifiers =
   Programming Language :: Python :: 3
   Programming Language :: Python :: 3.7
   Programming Language :: Python :: 3.8
+  Programming Language :: Python :: 3.9
   Topic :: Scientific/Engineering :: Physics
 
 [options]
@@ -36,7 +37,8 @@ install_requires =
   matplotlib
   numpy
   pandas
-  sunpy[net,timeseries] >= 2.0.0
+  scipy
+  sunpy[net,timeseries] >= 2.1.0rc3
 
 [options.extras_require]
 tests =
@@ -69,23 +71,60 @@ junit_family=xunit1
 filterwarnings =
     error
     error::sunpy.util.exceptions.SunpyDeprecationWarning
+    # Do not fail on pytest config issues (i.e. missing plugins) but do show them
+    always::pytest.PytestConfigWarning
     #
     # A list of warnings to ignore follows. If you add to this list, you MUST
     # add a comment or ideally a link to an issue that explains why the warning
     # is being ignored
     #
-    # These warnings are raised on our CI due to something odd about numpy installation,
-    # but don't impact the tests
-    ignore:numpy.ufunc size changed:RuntimeWarning
-    # See https://github.com/aio-libs/aiohttp/issues/4842
-    ignore:"@coroutine" decorator is deprecated
+    #
+    # See https://github.com/pandas-dev/pandas/issues/26367; this can be
+    # removed when our minimum pandas version is >=0.25
+    ignore:can't resolve package from __spec__ or __package__:ImportWarning
+    # See https://github.com/spacetelescope/asdf/issues/789
+    ignore:direct construction of AsdfSchemaFile has been deprecated
+    ignore:direct construction of AsdfSchemaItem has been deprecated
+    ignore:direct construction of AsdfSchemaExampleItem has been deprecated
     # See https://github.com/Cadair/parfive/issues/41
-    # Or other packages
     ignore:The loop argument is deprecated
+    # This is due to dependencies building with a numpy version different from
+    # the local installed numpy version, but should be fine
+    # See https://github.com/numpy/numpy/issues/15748#issuecomment-598584838
+    ignore:numpy.ufunc size changed:RuntimeWarning
+    ignore:numpy.ndarray size changed:RuntimeWarning
     # See https://github.com/mvantellingen/python-zeep/issues/956
-    ignore:defusedxml.lxml is no longer supported and will be removed in a future release.
-    # Sunpy Timeseries Warning.
-    ignore:Unknown units for.*
+    ignore:defusedxml.lxml is no longer supported:DeprecationWarning
+    # See https://github.com/aio-libs/aiohttp/issues/4842
+    ignore:"@coroutine" decorator is deprecated
+    # See https://github.com/spacetelescope/asdf/issues/789
+    ignore:direct construction of AsdfSchemaFile has been deprecated
+    ignore:direct construction of AsdfSchemaItem has been deprecated
+    ignore:direct construction of AsdfSchemaExampleItem has been deprecated
+    # See https://github.com/scikit-image/scikit-image/issues/4848
+    ignore:Converting `np.inexact` or `np.floating` to a dtype is deprecated
+    # See https://github.com/astropy/astropy/pull/10570
+    ignore:leap-second auto-update failed
+    # See https://github.com/astropy/extension-helpers/issues/23
+    ignore:Distutils was imported before Setuptools
+    # Figure tests use agg backend so show doesn't work but we use it in peek
+    ignore:Matplotlib is currently using agg, which is a non-GUI backend, so cannot show the figure.
+    # Ignore doctest issues: docs/guide/tour.rst
+    ignore:File may have been truncated*
+    # Some tests use data that have dates in the future and ERFA does not like.
+    ignore:ERFA function "d2dtf"*
+    ignore:ERFA function "dtf2d"*
+    # Currently helio makes unverified requests - this filter should be removed when
+    # https://github.com/sunpy/sunpy/issues/4401 is fixed
+    ignore:Unverified HTTPS request
+    # https://github.com/astropy/astropy/issues/11272
+    ignore:elementwise == comparison failed and returning scalar instead:FutureWarning:astropy.table
+    # This isn't really an issue it's an annoyance, it's triggered by printing
+    # an astropy table inside a test, which is generally only done when
+    # CHANNEL UNITS ISSUE.
+    ignore:Unknown units for CHANNEL.*:sunpy.util.exceptions.SunpyUserWarning:
+    # debugging.
+    ignore:the imp module is deprecated in favour of importlib:DeprecationWarning:ipykernel.iostream
 
 [pycodestyle]
 max_line_length = 100

diff --git a/setup.py b/setup.py
@@ -8,18 +8,18 @@
 ################################################################################
 # Programmatically generate some extras combos.
 ################################################################################
-extras = read_configuration("setup.cfg")['options']['extras_require']
+extras = read_configuration("setup.cfg")["options"]["extras_require"]
 
 # Dev is everything
-extras['dev'] = list(chain(*extras.values()))
+extras["dev"] = list(chain(*extras.values()))
 
 # All is everything but tests and docs
 exclude_keys = ("tests", "docs", "dev")
 ex_extras = dict(filter(lambda i: i[0] not in exclude_keys, extras.items()))
 # Concatenate all the values together for 'all'
-extras['all'] = list(chain.from_iterable(ex_extras.values()))
+extras["all"] = list(chain.from_iterable(ex_extras.values()))
 
 setup(
     extras_require=extras,
-    use_scm_version={'write_to': os.path.join('sunkit_instruments', '_version.py')}
+    use_scm_version={"write_to": os.path.join("sunkit_instruments", "_version.py")},
 )
diff --git a/sunkit_instruments/__init__.py b/sunkit_instruments/__init__.py
@@ -21,9 +21,12 @@ class UnsupportedPythonError(Exception):
     """
 
 
-if sys.version_info < tuple(int(val) for val in __minimum_python_version__.split('.')):
+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_instruments does not support Python < {}".format(__minimum_python_version__))
+        "sunkit_instruments does not support Python < {}".format(
+            __minimum_python_version__
+        )
+    )
 
 __all__ = []
diff --git a/sunkit_instruments/_dev/__init__.py b/sunkit_instruments/_dev/__init__.py
@@ -1,6 +1,7 @@
 """
 This package contains utilities that are only used when developing drms in a
 copy of the source repository.
+
 These files are not installed, and should not be assumed to exist at
 runtime.
 """
diff --git a/sunkit_instruments/_dev/scm_version.py b/sunkit_instruments/_dev/scm_version.py
@@ -5,8 +5,8 @@
 try:
     from setuptools_scm import get_version
 
-    version = get_version(root=os.path.join('..', '..'), relative_to=__file__)
+    version = get_version(root=os.path.join("..", ".."), relative_to=__file__)
 except ImportError:
-    raise ImportError('setuptools_scm not installed')
+    raise ImportError("setuptools_scm not installed")
 except Exception as e:
-    raise ValueError(f'setuptools_scm broken with {e}')
+    raise ValueError(f"setuptools_scm broken with {e}")
diff --git a/sunkit_instruments/conftest.py b/sunkit_instruments/conftest.py
@@ -1,4 +1,3 @@
-
 import pytest
 
 
@@ -14,22 +13,22 @@ def sunpy_cache(mocker, tmp_path):
     from sunpy.data.data_manager.cache import Cache
     from sunpy.data.data_manager.downloader import ParfiveDownloader
     from sunpy.data.data_manager.storage import InMemStorage
-    cache = Cache(
-        ParfiveDownloader(),
-        InMemStorage(),
-        tmp_path,
-        None
-    )
+
+    cache = Cache(ParfiveDownloader(), InMemStorage(), tmp_path, None)
 
     def add(self, url, path):
-        self._storage.store({
-            'url': url,
-            'file_path': path,
-            'file_hash': 'none',  # hash doesn't matter
-        })
+        self._storage.store(
+            {
+                "url": url,
+                "file_path": path,
+                "file_hash": "none",  # hash doesn't matter
+            }
+        )
+
     cache.add = MethodType(add, cache)
 
     def func(mocked):
         mocker.patch(mocked, cache)
         return cache
+
     yield func
diff --git a/sunkit_instruments/data/test/__init__.py b/sunkit_instruments/data/test/__init__.py
@@ -10,10 +10,10 @@
 
 import sunkit_instruments
 
-__all__ = ['rootdir', 'file_list', 'get_test_filepath', 'test_data_filenames']
+__all__ = ["rootdir", "file_list", "get_test_filepath", "test_data_filenames"]
 
 rootdir = os.path.join(os.path.dirname(sunkit_instruments.__file__), "data", "test")
-file_list = glob.glob(os.path.join(rootdir, '*.[!p]*'))
+file_list = glob.glob(os.path.join(rootdir, "*.[!p]*"))
 
 
 def get_test_filepath(filename, **kwargs):
@@ -35,7 +35,9 @@ def get_test_filepath(filename, **kwargs):
     This is a wrapper around `astropy.utils.data.get_pkg_data_filename` which
     sets the ``package`` kwarg to be 'sunkit_instruments.data.test`.
     """
-    return get_pkg_data_filename(filename, package="sunkit_instruments.data.test", **kwargs)
+    return get_pkg_data_filename(
+        filename, package="sunkit_instruments.data.test", **kwargs
+    )
 
 
 def test_data_filenames():
@@ -50,13 +52,13 @@ def test_data_filenames():
         The name of all test files in ``data/test`` directory.
     """
     test_data_filenames_list = []
-    excludes = ['*.pyc', '*'+os.path.sep+'__*__', '*.py']
-    excludes = r'|'.join([fnmatch.translate(x) for x in excludes]) or r'$.'
+    excludes = ["*.pyc", "*" + os.path.sep + "__*__", "*.py"]
+    excludes = r"|".join([fnmatch.translate(x) for x in excludes]) or r"$."
 
     for root, dirs, files in os.walk(rootdir):
         files = [os.path.join(root, f) for f in files]
         files = [f for f in files if not re.match(excludes, f)]
-        files = [file.replace(rootdir + os.path.sep, '') for file in files]
+        files = [file.replace(rootdir + os.path.sep, "") for file in files]
         test_data_filenames_list.extend(files)
 
     return test_data_filenames_list