retemplate dance

.pre-commit-config.yaml

@@ -0,0 +1,41 @@
+repos:
+  # The warnings/errors we check for here are:
+  # E101 - mix of tabs and spaces
+  # W191 - use of tabs
+  # W291 - trailing whitespace
+  # W292 - no newline at end of file
+  # W293 - trailing whitespace
+  # W391 - blank line at end of file
+  # E111 - 4 spaces per indentation level
+  # E112 - 4 spaces per indentation level
+  # E113 - 4 spaces per indentation level
+  # E303 - too many blank lines (3)
+  # E304 - blank lines found after function decorator
+  # E305 - expected 2 blank lines after class or function definition
+  # E306 - expected 1 blank line before a nested definition
+  # E502 - the backslash is redundant between brackets
+  # E722 - do not use bare except
+  # E901 - SyntaxError or IndentationError
+  # E902 - IOError
+  # F822: undefined name in __all__
+  # F823: local variable name referenced before assignment
+  - repo: https://gitlab.com/pycqa/flake8
+    rev: 3.7.9
+    hooks:
+      - id: flake8
+        args: ['--count', '--select', 'E101,W191,W291,W292,W293,W391,E111,E112,E113,E303,E304,E306,E502,E722,E901,E902,F822,F823']
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v2.4.0
+    hooks:
+      - id: check-ast
+      - id: check-case-conflict
+      - id: trailing-whitespace
+        exclude: ".*(.fits|.fts|.fit|.txt)$"
+      - id: check-yaml
+      - id: debug-statements
+      - id: check-added-large-files
+      - id: end-of-file-fixer
+        exclude: ".*(.fits|.fts|.fit|.txt|tca.*)$"
+      - id: mixed-line-ending
+        exclude: ".*(.fits|.fts|.fit|.txt|tca.*)$"

.readthedocs.yml

@@ -1,21 +1,18 @@
-# .readthedocs.yml
-# Read the Docs configuration file
-# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
-
-# Required
 version: 2
+build:
+  os: ubuntu-20.04
+  tools:
+    python: "3.9"
 
-# Build documentation in the docs/ directory with Sphinx
 sphinx:
+  builder: html
   configuration: docs/conf.py
+  fail_on_warning: false
 
-# Optionally build your docs in additional formats such as PDF and ePub
-formats: []
-
-# Optionally set the version of Python and requirements required to build your docs
 python:
-  version: 3.7
-  install:
-    - requirements: requirements/requirements-dev.txt
-    - method: setuptools
-      path: .
+   install:
+     - method: pip
+       extra_requirements:
+        - all
+        - docs
+       path: .

MANIFEST.in

@@ -1,3 +1,5 @@
 include README.md
 include LICENSE
-include pydrad/configure/templates/*
+include pyproject.toml
+include pydrad/configure/templates/*
+include pydrad/configure/data/*

pydrad/__init__.py

@@ -5,6 +5,8 @@
 import logging
 from astropy.logger import AstropyLogger
 
+from .version import version as __version__
+
 
 def _init_log():
     """
@@ -25,3 +27,5 @@ def _init_log():
 
 log = logging.getLogger()
 log = _init_log()
+
+__all__ = ['__version__', 'log']

pydrad/setup.cfg

@@ -0,0 +1,97 @@
+[metadata]
+name = pydrad
+author = Will Barnes
+author_email = [email protected]
+license = MIT
+license_file = LICENSE
+url = https://github.com/rice-solar-physics/pydrad
+description = Tools for configuring and parsing HYDRAD simulations.
+long_description = file: README.md
+long_description_content_type = text/markdown
+keywords = hydrodynamics, coronal loop, corona, solar physics, solar, science, sun
+classifiers =
+  Development Status :: 4 - Beta
+  Intended Audience :: Science/Research
+  License :: OSI Approved :: MIT License
+  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 :: Astronomy
+
+[options]
+zip_safe = False
+packages = find:
+python_requires = >=3.7
+setup_requires = setuptools_scm
+install_requires =
+    scipy
+    matplotlib
+    astropy
+    Jinja2
+    asdf
+    h5py
+    plasmapy[theory]
+
+[options.extras_require]
+test =
+    flake8
+    GitPython
+    pillow
+    pytest
+    pytest-cov
+    codecov
+docs =
+    sphinx
+    sphinx-automodapi
+    sphinx-changelog
+    sphinx-gallery
+    sphinx-rtd-theme
+
+[options.package_data]
+pydrad.configure = templates/*, data/*
+
+[tool:pytest]
+testpaths = "pydrad" "docs"
+doctest_plus = enabled
+text_file_format = rst
+addopts = --doctest-rst
+remote_data_strict = False
+filterwarnings =
+  error
+
+[coverage:run]
+omit =
+  pydrad/_sunpy_init*
+  pydrad/conftest.py
+  pydrad/*setup_package*
+  pydrad/tests/*
+  pydrad/*/tests/*
+  pydrad/extern/*
+  pydrad/version*
+  */pydrad/_sunpy_init*
+  */pydrad/conftest.py
+  */pydrad/*setup_package*
+  */pydrad/tests/*
+  */pydrad/*/tests/*
+  */pydrad/extern/*
+  */pydrad/version*
+
+[coverage:report]
+exclude_lines =
+  # Have to re-enable the standard pragma
+  pragma: no cover
+  # Don't complain about packages we have installed
+  except ImportError
+  # Don't complain if tests don't hit assertions
+  raise AssertionError
+  raise NotImplementedError
+  # Don't complain about script hooks
+  def main\(.*\):
+  # Ignore branches that don't pertain to this version of Python
+  pragma: py{ignore_python_version}
+  # Don't complain about IPython completion helper
+  def _ipython_key_completions_
+

pydrad/version.py

@@ -0,0 +1,17 @@
+# NOTE: First try _dev.scm_version if it exists and setuptools_scm is installed
+# This file is not included in wheels/tarballs, so otherwise it will
+# fall back on the generated _version module.
+try:
+    try:
+        from ._dev.scm_version import version
+    except ImportError:
+        from ._version import version
+except Exception:
+    import warnings
+
+    warnings.warn(
+        f'could not determine {__name__.split(".")[0]} package version; this indicates a broken installation'
+    )
+    del warnings
+
+    version = '0.0.0'

pyproject.toml

@@ -0,0 +1,7 @@
+[build-system]
+
+requires = ["setuptools",
+            "setuptools_scm",
+            "wheel"]
+
+build-backend = 'setuptools.build_meta'

setup.py

@@ -1,20 +1,30 @@
-from distutils.core import setup
+#!/usr/bin/env python
+import os
+from itertools import chain
 
+from setuptools import setup
+from setuptools.config import read_configuration
+
+################################################################################
+# Programmatically generate some extras combos.
+################################################################################
+extras = read_configuration("setup.cfg")['options']['extras_require']
+
+# Dev is everything
+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()))
+
+################################################################################
+# Version configuration and setup call
+################################################################################
 setup(
-    name='pydrad',
-    license='MIT',
-    version='0.1',
-    author='Will Barnes',
-    url='https://github.com/rice-solar-physics/pydrad',
-    package_data={'pydrad': ['configure/templates/*',
-                             'configure/data/defaults.asdf']},
-    packages=[
-        'pydrad',
-        'pydrad.configure',
-        'pydrad.configure.data',
-        'pydrad.parse',
-        'pydrad.visualize',
-    ],
-    author_email='[email protected]',
-    description='Tools for configuring and parsing HYDRAD simulations'
+    extras_require=extras,
+    use_scm_version={
+        'write_to': os.path.join('pydrad', '_version.py'),
+    },
 )

tox.ini

@@ -0,0 +1,60 @@
+[tox]
+envlist =
+    py{38,39,310}
+    build_docs
+    codestyle
+isolated_build = true
+requires =
+    setuptools >= 30.3.0
+    pip >= 19.3.1
+    tox-pypi-filter >= 0.10
+
+[testenv]
+
+# The following option combined with the use of the tox-pypi-filter above allows
+# project-wide pinning of dependencies, e.g. if new versions of pytest do not
+# work correctly with pytest-astropy plugins. Most of the time the pinnings file
+# should be empty.
+
+# Pass through the following environemnt variables which may be needed for the CI
+passenv = HOME WINDIR LC_ALL LC_CTYPE CC CI TRAVIS
+
+# Run the tests in a temporary directory to make sure that we don't import
+# the package from the source tree
+changedir = .tmp/{envname}
+
+# tox environments are constructued with so-called 'factors' (or terms)
+# separated by hyphens, e.g. test-devdeps-cov. Lines below starting with factor:
+# will only take effect if that factor is included in the environment name. To
+# see a list of example environments that can be run, along with a description,
+# run:
+#
+#     tox -l -v
+#
+description =
+    run tests
+
+deps =
+# The following indicates which extras_require from setup.cfg will be installed
+extras =
+    test
+commands =
+    pytest --pyargs pydrad {toxinidir}/docs --cov pydrad --cov-report=xml --cov-config={toxinidir}/setup.cfg {posargs}
+
+
+[testenv:build_docs]
+changedir = docs
+description = invoke sphinx-build to build the HTML docs
+extras = docs
+commands =
+    sphinx-build -b html . _build/html {posargs}
+
+
+[testenv:codestyle]
+skip_install = true
+description = Run all style and file checks with pre-commit
+deps =
+    pre-commit
+commands =
+    pre-commit install-hooks
+    pre-commit run --all-files