WIP

.gitignore

@@ -264,3 +264,10 @@ package.json
 # repo specific
 examples/using_pfsspy/aia_map.fits
 docs/sg_execution_times.rst
+docs/manual/source/numerical-methods.aux
+docs/manual/source/numerical-methods.bbl
+docs/manual/source/numerical-methods.fdb_latexmk
+docs/manual/source/numerical-methods.fls
+docs/manual/source/numerical-methods.out
+docs/manual/source/numerical-methods.pdf
+docs/manual/source/numerical-methods.synctex.gz

.ruff.toml

@@ -12,7 +12,7 @@ exclude = [
 select = ["E", "F", "W", "UP", "PT"]
 extend-ignore = [
   # pycodestyle (E, W)
-  "E501", # LineTooLong                             # TODO! fix
+  "E501", # LineTooLong
   # pytest (PT)
   "PT001", # Always use pytest.fixture()
   "PT004", # Fixtures which don't return anything should have leading _

docs/conf.py

@@ -10,8 +10,8 @@
 
 # The full version, including alpha/beta/rc tags
 from sunkit_magex import __version__
-release = __version__
 
+release = __version__
 project = "sunkit-magex"
 copyright = "2024, The SunPy Community"
 author = "The SunPy Community"
@@ -73,27 +73,31 @@
 from sphinx_gallery.sorting import ExplicitOrder  # noqa
 
 sphinx_gallery_conf = {
+    "abort_on_example_error": False,
     "backreferences_dir": os.path.join("generated", "modules"),
-    "filename_pattern": "^((?!skip_).)*$",
-    "ignore_pattern": "helpers.py",
+    "default_thumb_file": PNG_ICON,
     "examples_dirs": os.path.join("..", "examples"),
-    "subsection_order": ExplicitOrder(["../examples/using_pfsspy",
-                                       "../examples/finding_data",
-                                       "../examples/utils",
-                                       "../examples/internals",
-                                       "../examples/testing"]),
+    "filename_pattern": '^((?!skip_).)*$',
     "gallery_dirs": os.path.join("generated", "gallery"),
+    "ignore_pattern": "helpers.py",
     "matplotlib_animations": True,
-    "default_thumb_file": PNG_ICON,
-    "abort_on_example_error": False,
+    "only_warn_on_example_error": True,
     "plot_gallery": "True",
     "remove_config_comments": True,
-    "only_warn_on_example_error": True,
+    "subsection_order": ExplicitOrder([
+        "../examples/using_pfsspy",
+        "../examples/finding_data",
+        "../examples/utils",
+        "../examples/internals",
+        "../examples/testing"
+    ]),
 }
 
 # -- Other options ----------------------------------------------------------
-# JSOC email os env
-# see https://github.com/sunpy/sunpy/wiki/Home:-JSOC
+
+# JSOC email OS ENV
+# See https://github.com/sunpy/sunpy/wiki/Home:-JSOC
 os.environ["JSOC_EMAIL"] = '[email protected]'
 
+default_role = 'py:obj'
 nitpicky = True

pyproject.toml

@@ -10,7 +10,7 @@ name = "sunkit_magex"
 description = "Solar Magnetic field Extrapollation"
 requires-python = ">=3.10"
 readme = { file = "README.rst", content-type = "text/x-rst" }
-license = { file = "licenses/LICENSE.rst", content-type = "text/plain" }
+license = { file = "licenses/LICENSE.rst"}
 authors = [
   { name = "The SunPy Community", email = "[email protected]" },
 ]
@@ -77,7 +77,24 @@ testpaths = [
 ]
 doctest_plus = "enabled"
 text_file_format = "rst"
-addopts = "--doctest-rst"
+addopts = "--doctest-rst -p no:unraisableexception -p no:threadexception"
+filterwarnings = [
+    "error",
+    # 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
+    # https://github.com/pytest-dev/pytest-cov/issues/557
+    # It was fixed and released but it does not seem to be fixed
+    "ignore:The --rsyncdir command line argument and rsyncdirs config variable are deprecated.:DeprecationWarning",
+    # https://github.com/pandas-dev/pandas/issues/54466
+    # Should stop when pandas 3.0.0 is released
+    "ignore:(?s).*Pyarrow will become a required dependency of pandas:DeprecationWarning",
+    # Can be removed when https://github.com/dateutil/dateutil/issues/1314 is resolved
+    # deprecated in Python 3.12, needs a release of dateutil 2.8.3 or higher
+    "ignore:datetime.datetime.utcfromtimestamp():DeprecationWarning",
+]
 
 [tool.coverage.run]
 omit = [

sunkit_magex/__init__.py

@@ -1,2 +1,3 @@
 from .version import version as __version__
+
 __all__ = []

tox.ini

@@ -11,22 +11,20 @@ envlist =
 
 [testenv]
 pypi_filter = https://raw.githubusercontent.com/sunpy/sunpy/main/.test_package_pins.txt
-# Run the tests in a temporary directory to make sure that we don't import
-# the package from the source tree
+# Run the tests in a temporary directory to make sure that we don't import the package from the source tree
+# This is only needed if you do not use a src directory like a sane person
 change_dir = .tmp/{envname}
 description =
     run tests
     oldestdeps: with the oldest supported version of key dependencies
     devdeps: with the latest developer version of key dependencies
-
 pass_env =
     # Custom compiler locations (such as ccache)
     CC
     # Location of locales (needed by sphinx on some systems)
     LOCALE_ARCHIVE
     # If the user has set a LC override we should follow it
     LC_ALL
-
 set_env =
     MPLBACKEND=agg
     devdeps: PIP_EXTRA_INDEX_URL = https://pypi.anaconda.org/astropy/simple https://pypi.anaconda.org/scientific-python-nightly-wheels/simple
@@ -40,22 +38,13 @@ deps =
     # devdeps: git+https://github.com/ndcube/ndcube
     oldestdeps: minimum_dependencies
     pytest-xdist
-
-# The following indicates which extras_require will be installed
 extras =
     tests
-
 commands_pre =
     oldestdeps: minimum_dependencies sunkit_magex --filename requirements-min.txt
     oldestdeps: pip install -r requirements-min.txt
     pip freeze --all --no-input
-
 commands =
-    # To run different commands for different factors exclude the factor from the default command like this
-    # !online: {env:PYTEST_COMMAND} {posargs}
-    # Then specify a specific one like this
-    # online: {env:PYTEST_COMMAND} --remote-data=any {posargs}
-    # If you have no factors which require different commands this is all you need:
     {env:PYTEST_COMMAND} {posargs}
 
 [testenv:codestyle]