From 247f7661ec1b384051a55d7071f5cb85ee20829a Mon Sep 17 00:00:00 2001 From: Lee Date: Sat, 29 Aug 2020 09:02:54 +1000 Subject: [PATCH 01/26] manifest update --- MANIFEST.in | 29 ++--------------------------- 1 file changed, 2 insertions(+), 27 deletions(-) diff --git a/MANIFEST.in b/MANIFEST.in index d6891f4..387dc28 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -1,41 +1,16 @@ include README.rst include CHANGES.rst - -include ez_setup.py -include ah_bootstrap.py include setup.cfg -include gunagala/tests/coveragerc +include LICENSE.rst +include pyproject.toml recursive-include gunagala *.pyx *.c *.pxd recursive-include docs * recursive-include licenses * -recursive-include cextern * recursive-include scripts * prune build prune docs/_build prune docs/api - -# the next few stanzas are for astropy_helpers. It's derived from the -# astropy_helpers/MANIFEST.in, but requires additional includes for the actual -# package directory and egg-info. - -include astropy_helpers/README.rst -include astropy_helpers/CHANGES.rst -include astropy_helpers/LICENSE.rst -recursive-include astropy_helpers/licenses * - -include astropy_helpers/ez_setup.py -include astropy_helpers/ah_bootstrap.py - -recursive-include astropy_helpers/astropy_helpers *.py *.pyx *.c *.h *.rst -recursive-include astropy_helpers/astropy_helpers.egg-info * -# include the sphinx stuff with "*" because there are css/html/rst/etc. -recursive-include astropy_helpers/astropy_helpers/sphinx * - -prune astropy_helpers/build -prune astropy_helpers/astropy_helpers/tests - - global-exclude *.pyc *.o From 797d25f56a49c390d6730439c93f4aaf87cf26af Mon Sep 17 00:00:00 2001 From: Lee Date: Sat, 29 Aug 2020 09:03:10 +1000 Subject: [PATCH 02/26] new files --- pyproject.toml | 10 ++++++ tox.ini | 93 ++++++++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 103 insertions(+) create mode 100644 pyproject.toml create mode 100644 tox.ini diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..6c989ab --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,10 @@ +[build-system] + +requires = ["setuptools", + "setuptools_scm", + "wheel", + "extension-helpers", + "oldest-supported-numpy", + "cython==0.29.14"] + +build-backend = 'setuptools.build_meta' diff --git a/tox.ini b/tox.ini new file mode 100644 index 0000000..8bd5cc1 --- /dev/null +++ b/tox.ini @@ -0,0 +1,93 @@ +[tox] +envlist = + py{36,37,38}-test{,-alldeps,-devdeps}{,-cov} + py{36,37,38}-test-numpy{116,117,118} + py{36,37,38}-test-astropy{30,40,lts} + build_docs + linkcheck + codestyle +requires = + setuptools >= 30.3.0 + pip >= 19.3.1 +isolated_build = true +indexserver = + NIGHTLY = https://pypi.anaconda.org/scipy-wheels-nightly/simple + +[testenv] +# Suppress display of matplotlib plots generated during docs build +setenv = MPLBACKEND=agg + +# Pass through the following environment 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 +# this package from the source tree +changedir = .tmp/{envname} + +# tox environments are constructed 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 + alldeps: with all optional dependencies + devdeps: with the latest developer version of key dependencies + oldestdeps: with the oldest supported version of key dependencies + cov: and test coverage + numpy116: with numpy 1.16.* + numpy117: with numpy 1.17.* + numpy118: with numpy 1.18.* + astropy30: with astropy 3.0.* + astropy40: with astropy 4.0.* + astropylts: with the latest astropy LTS + +# The following provides some specific pinnings for key packages +deps = + + numpy116: numpy==1.16.* + numpy117: numpy==1.17.* + numpy118: numpy==1.18.* + + astropy30: astropy==3.0.* + astropy40: astropy==4.0.* + astropylts: astropy==4.0.* + + devdeps: :NIGHTLY:numpy + devdeps: git+https://github.com/astropy/astropy.git#egg=astropy + +# The following indicates which extras_require from setup.cfg will be installed +extras = + test + alldeps: all + +commands = + pip freeze + !cov: pytest --pyargs gunagala {toxinidir}/docs {posargs} + cov: pytest --pyargs gunagala {toxinidir}/docs --cov gunagala --cov-config={toxinidir}/setup.cfg {posargs} + +[testenv:build_docs] +changedir = docs +description = invoke sphinx-build to build the HTML docs +extras = docs +commands = + pip freeze + sphinx-build -W -b html . _build/html + +[testenv:linkcheck] +changedir = docs +description = check the links in the HTML docs +extras = docs +commands = + pip freeze + sphinx-build -W -b linkcheck . _build/html + +[testenv:codestyle] +skip_install = true +changedir = . +description = check code style, e.g. with flake8 +deps = flake8 +commands = flake8 gunagala --count --max-line-length=100 From 079ef979f8d397657d644b70a7459f2746c72f12 Mon Sep 17 00:00:00 2001 From: Lee Date: Sat, 29 Aug 2020 09:07:22 +1000 Subject: [PATCH 03/26] setup.py --- setup.py | 198 +++++++++++++++++++------------------------------------ 1 file changed, 67 insertions(+), 131 deletions(-) diff --git a/setup.py b/setup.py index b9cce97..c6a1239 100755 --- a/setup.py +++ b/setup.py @@ -1,142 +1,78 @@ #!/usr/bin/env python # Licensed under a 3-clause BSD style license - see LICENSE.rst -import glob +# NOTE: The configuration for the package, including the name, version, and +# other information are set in the setup.cfg file. + import os import sys -import ah_bootstrap from setuptools import setup -# A dirty hack to get around some early import/configurations ambiguities -if sys.version_info[0] >= 3: - import builtins -else: - import __builtin__ as builtins -builtins._ASTROPY_SETUP_ = True -from astropy_helpers.setup_helpers import (register_commands, get_debug_option, - get_package_info) -from astropy_helpers.git_helpers import get_git_devstr -from astropy_helpers.version_helpers import generate_version_py +# First provide helpful messages if contributors try and run legacy commands +# for tests or docs. + +TEST_HELP = """ +Note: running tests is no longer done using 'python setup.py test'. Instead +you will need to run: + + tox -e test + +If you don't already have tox installed, you can install it with: + + pip install tox + +If you only want to run part of the test suite, you can also use pytest +directly with:: + + pip install -e .[test] + pytest + +For more information, see: + + http://docs.astropy.org/en/latest/development/testguide.html#running-tests +""" + +if 'test' in sys.argv: + print(TEST_HELP) + sys.exit(1) + +DOCS_HELP = """ +Note: building the documentation is no longer done using +'python setup.py build_docs'. Instead you will need to run: + + tox -e build_docs + +If you don't already have tox installed, you can install it with: + + pip install tox + +You can also build the documentation with Sphinx directly using:: + + pip install -e .[docs] + cd docs + make html + +For more information, see: + + http://docs.astropy.org/en/latest/install.html#builddocs +""" + +if 'build_docs' in sys.argv or 'build_sphinx' in sys.argv: + print(DOCS_HELP) + sys.exit(1) -# Get some values from the setup.cfg +VERSION_TEMPLATE = """ +# Note that we need to fall back to the hard-coded version if either +# setuptools_scm can't be imported or setuptools_scm can't determine the +# version, so we catch the generic 'Exception'. try: - from ConfigParser import ConfigParser -except ImportError: - from configparser import ConfigParser - -conf = ConfigParser() -conf.read(['setup.cfg']) -metadata = dict(conf.items('metadata')) - -PACKAGENAME = metadata.get('package_name', 'packagename') -DESCRIPTION = metadata.get('description', 'packagename') -AUTHOR = metadata.get('author', 'Astropy Developers') -AUTHOR_EMAIL = metadata.get('author_email', '') -LICENSE = metadata.get('license', 'unknown') -URL = metadata.get('url', 'http://astropy.org') - -# order of priority for long_description: -# (1) set in setup.cfg, -# (2) load LONG_DESCRIPTION.rst, -# (3) load README.rst, -# (4) package docstring -readme_glob = 'README*' -_cfg_long_description = metadata.get('long_description', '') -if _cfg_long_description: - LONG_DESCRIPTION = _cfg_long_description - -elif os.path.exists('LONG_DESCRIPTION.rst'): - with open('LONG_DESCRIPTION.rst') as f: - LONG_DESCRIPTION = f.read() - -elif len(glob.glob(readme_glob)) > 0: - with open(glob.glob(readme_glob)[0]) as f: - LONG_DESCRIPTION = f.read() - -else: - # Get the long description from the package's docstring - __import__(PACKAGENAME) - package = sys.modules[PACKAGENAME] - LONG_DESCRIPTION = package.__doc__ - -# Store the package name in a built-in variable so it's easy -# to get from other parts of the setup infrastructure -builtins._ASTROPY_PACKAGE_NAME_ = PACKAGENAME - -# VERSION should be PEP440 compatible (http://www.python.org/dev/peps/pep-0440) -VERSION = metadata.get('version', '0.0.dev0') - -# Indicates if this version is a release version -RELEASE = 'dev' not in VERSION - -if not RELEASE: - VERSION += get_git_devstr(False) - -# Populate the dict of setup command overrides; this should be done before -# invoking any other functionality from distutils since it can potentially -# modify distutils' behavior. -cmdclassd = register_commands(PACKAGENAME, VERSION, RELEASE) - -# Freeze build information in version.py -generate_version_py(PACKAGENAME, VERSION, RELEASE, - get_debug_option(PACKAGENAME)) - -# Treat everything in scripts except README* as a script to be installed -scripts = [fname for fname in glob.glob(os.path.join('scripts', '*')) - if not os.path.basename(fname).startswith('README')] - - -# Get configuration information from all of the various subpackages. -# See the docstring for setup_helpers.update_package_files for more -# details. -package_info = get_package_info() - -# Add the project-global data -package_info['package_data'].setdefault(PACKAGENAME, []) -package_info['package_data'][PACKAGENAME].append('data/*.*') -package_info['package_data'][PACKAGENAME].append('data/performance_data/*') -package_info['package_data'][PACKAGENAME].append('data/sky_data/*') - -# Define entry points for command-line scripts -entry_points = {'console_scripts': []} - -if conf.has_section('entry_points'): - entry_point_list = conf.items('entry_points') - for entry_point in entry_point_list: - entry_points['console_scripts'].append('{0} = {1}'.format( - entry_point[0], entry_point[1])) - -# Include all .c files, recursively, including those generated by -# Cython, since we can not do this in MANIFEST.in with a "dynamic" -# directory name. -c_files = [] -for root, dirs, files in os.walk(PACKAGENAME): - for filename in files: - if filename.endswith('.c'): - c_files.append( - os.path.join( - os.path.relpath(root, PACKAGENAME), filename)) -package_info['package_data'][PACKAGENAME].extend(c_files) - -# Note that requires and provides should not be included in the call to -# ``setup``, since these are now deprecated. See this link for more details: -# https://groups.google.com/forum/#!topic/astropy-dev/urYO8ckB2uM - -setup(name=PACKAGENAME, - version=VERSION, - description=DESCRIPTION, - scripts=scripts, - install_requires=[s.strip() for s in metadata.get('install_requires', 'astropy').split(',')], - author=AUTHOR, - author_email=AUTHOR_EMAIL, - license=LICENSE, - url=URL, - long_description=LONG_DESCRIPTION, - cmdclass=cmdclassd, - zip_safe=False, - use_2to3=False, - entry_points=entry_points, - **package_info -) + from setuptools_scm import get_version + version = get_version(root='..', relative_to=__file__) +except Exception: + version = '{version}' +""".lstrip() + +setup(use_scm_version={'write_to': os.path.join('gunagala', 'version.py'), + 'write_to_template': VERSION_TEMPLATE}) From 559c478196a4ed70b96dad4aa9590d04d2dd25aa Mon Sep 17 00:00:00 2001 From: Lee Date: Sat, 29 Aug 2020 09:20:24 +1000 Subject: [PATCH 04/26] readme setup.cfg --- README.rst | 10 +++++ setup.cfg | 120 ++++++++++++++++++++++++++++++++++++----------------- 2 files changed, 93 insertions(+), 37 deletions(-) diff --git a/README.rst b/README.rst index 3930192..2a936c3 100644 --- a/README.rst +++ b/README.rst @@ -27,3 +27,13 @@ about Aboriginal astronomy please visit http://www.aboriginalastronomy.com.au/. .. image:: https://readthedocs.org/projects/gunagala/badge/?version=develop :target: http://gunagala.readthedocs.io/en/develop/?badge=develop :alt: Documentation Status + + +License +------- + +This project is Copyright (c) Anthony Horton and licensed under +the terms of the BSD 3-Clause license. This package is based upon +the `Astropy package template `_ +which is licensed under the BSD 3-clause license. See the licenses folder for +more information. \ No newline at end of file diff --git a/setup.cfg b/setup.cfg index ce2c837..eb10d7b 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,25 +1,91 @@ -[build_sphinx] -source-dir = docs -build-dir = docs/_build -all_files = 1 -[build_docs] -source-dir = docs -build-dir = docs/_build -all_files = 1 -[upload_docs] -upload-dir = docs/_build/html -show-response = 1 + + +[metadata] +package_name = gunagala +author = Anthony Horton +author_email = anthony.horton@mq.edu.au +license = BSD 3-Clause +license_file = licenses/LICENSE.rst +url = https://github.com/AstroHuntsman/gunagala.git +description = Performance modelling for astronomical instruments +long_description = file: README.rst +long_description_content_type = text/x-rst +edit_on_github = False +github_project = AstroHuntsman/gunagala + +[options] +zip_safe = False +packages = find: +python_requires = >=3.6 +setup_requires = setuptools_scm +install_requires = + astropy, pyYAML, numpy, scipy, matplotlib +# version should be PEP386 compatible (http://www.python.org/dev/peps/pep-0386) +version = 0.1.dev0 + + +[options.entry_points] +console_scripts = + astropy-package-template-example = packagename.example_mod:main + +[options.extras_require] +test = + pytest-astropy +docs = + sphinx-astropy + +[options.package_data] +gunagala = data/*.*, data/performance_data/*, data/sky_data/* + [tool:pytest] -minversion = 3.0 -norecursedirs = build docs/_build +testpaths = "gunagala" "docs" +astropy_header = true doctest_plus = enabled -addopts = -p no:warnings +text_file_format = rst +addopts = --doctest-rst, -p no:warnings + +[coverage:run] +omit = + gunagala/_astropy_init* + gunagala/conftest.py + gunagala/*setup_package* + gunagala/tests/* + gunagala/*/tests/* + gunagala/extern/* + gunagala/version* + */gunagala/_astropy_init* + */gunagala/conftest.py + */gunagala/*setup_package* + */gunagala/tests/* + */gunagala/*/tests/* + */gunagala/extern/* + */gunagala/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_ + + +[build_docs] +source-dir = docs +build-dir = docs/_build +all_files = 1 -[ah_bootstrap] -auto_use = True [pycodestyle] # E101 - mix of tabs and spaces @@ -34,24 +100,4 @@ auto_use = True # E901 - SyntaxError or IndentationError # E902 - IOError select = E101,W191,W291,W292,W293,W391,E111,E112,E113,E901,E902 -exclude = extern,sphinx,*parsetab.py - -[metadata] -package_name = gunagala -description = Performance modelling for astronomical instruments -long_description = This is a Python package for modelling the performance of astronomical instruments, including SNR/ETC/sensitivity limit calculations and generation of simulated data. -author = Anthony Horton -author_email = anthony.horton@aao.gov.au -license = BSD 3-Clause -url = https://github.com/AstroHuntsman/gunagala.git -edit_on_github = False -github_project = AstroHuntsman/gunagala -# install_requires should be formatted as a comma-separated list, e.g.: -# install_requires = astropy, scipy, matplotlib -install_requires = astropy, pyYAML, numpy, scipy, matplotlib -# version should be PEP386 compatible (http://www.python.org/dev/peps/pep-0386) -version = 0.1.dev0 - -[entry_points] - -#astropy-package-template-example = packagename.example_mod:main +exclude = extern,sphinx,*parsetab.py \ No newline at end of file From cf3abb2d1b1f485af2ba6ebcd4570ff011940b94 Mon Sep 17 00:00:00 2001 From: Lee Date: Sat, 29 Aug 2020 09:27:18 +1000 Subject: [PATCH 05/26] travis --- .travis.yml | 223 ++++++++++++++++++++++++++++------------------------ 1 file changed, 121 insertions(+), 102 deletions(-) diff --git a/.travis.yml b/.travis.yml index 253138b..1e26719 100644 --- a/.travis.yml +++ b/.travis.yml @@ -1,14 +1,12 @@ -# We set the language to c because python isn't supported on the MacOS X nodes -# on Travis. However, the language ends up being irrelevant anyway, since we -# install Python ourselves using conda. -language: c +language: python + +# We need a full clone to make sure setuptools_scm works properly +git: + depth: false os: - linux -# Setting sudo to false opts in to Travis-CI container-based builds. -sudo: false - # The apt packages below are needed for sphinx builds. A full list of packages # that can be included can be found here: # @@ -21,134 +19,155 @@ addons: - texlive-latex-extra - dvipng + + +stages: + # Do the style check and a single test job, don't proceed if it fails + - name: Initial tests + # Test docs, astropy dev, and without optional dependencies + - name: Comprehensive tests + # These will only run when cron is opted in + - name: Cron tests + if: type = cron + + + env: global: # The following versions are the 'default' for tests, unless # overridden underneath. They are defined here in order to save having # to repeat them for all configurations. - - PYTHON_VERSION=3.6 - - NUMPY_VERSION=stable - - ASTROPY_VERSION=stable - - MAIN_CMD='python setup.py' - - SETUP_CMD='test' - - PIP_DEPENDENCIES='scipy matplotlib PyYAML' - - EVENT_TYPE='pull_request push' - - - # For this package-template, we include examples of Cython modules, - # so Cython is required for testing. If your package does not include - # Cython code, you can set CONDA_DEPENDENCIES='' - - CONDA_DEPENDENCIES='' - - # List other runtime dependencies for the package that are available as - # pip packages here. - # - PIP_DEPENDENCIES='' - - # Conda packages for affiliated packages are hosted in channel - # "astropy" while builds for astropy LTS with recent numpy versions - # are in astropy-ci-extras. If your package uses either of these, - # add the channels to CONDA_CHANNELS along with any other channels - # you want to use. - - CONDA_CHANNELS='astropy-ci-extras astropy' - - # If there are matplotlib or other GUI tests, uncomment the following - # line to use the X virtual framebuffer. - # - SETUP_XVFB=True - - matrix: - # Make sure that egg_info works without dependencies - #- PYTHON_VERSION=2.7 SETUP_CMD='egg_info' - - PYTHON_VERSION=3.4 SETUP_CMD='egg_info' - - PYTHON_VERSION=3.5 SETUP_CMD='egg_info' - - PYTHON_VERSION=3.6 SETUP_CMD='egg_info' + + # The following three variables are for tox. TOXENV is a standard + # variable that tox uses to determine the environment to run, + # TOXARGS are arguments passed to tox, and TOXPOSARGS are arguments + # that tox passes through to the {posargs} indicator in tox.ini. + # The latter can be used for example to pass arguments to pytest. + - TOXENV='test' + - TOXARGS='-v' + - TOXPOSARGS='' + + # The following is needed to avoid issues if e.g. Matplotlib tries + # to open a GUI window. + - SETUP_XVFB=True matrix: # Don't wait for allowed failures fast_finish: true - include: - # Try MacOS X + # Try MacOS X, usually enough only to run from cron as hardly there are + # issues that are not picked up by a linux worker. We set language to + # 'c' since 'python' doesn't work on non-Linux platforms. - os: osx - env: SETUP_CMD='test' + language: c + name: Python 3.7 with required dependencies + stage: Cron tests + env: PYTHON_VERSION=3.7 TOXENV=py37-test - # Do a coverage test. + # Do a regular build on Linux with Python 3.8, with cov + # For Linux we use language: python to avoid using conda. - os: linux - env: SETUP_CMD='test --coverage' + python: 3.8 + name: Python 3.8 with required dependencies and measure coverage + stage: Initial tests + env: TOXENV=py38-test-cov - # Check for sphinx doc build warnings - we do this first because it - # may run for a long time + # Check for sphinx doc build warnings - os: linux - env: SETUP_CMD='build_docs -w' + python: 3.8 + name: Documentation build + stage: Comprehensive tests + env: TOXENV=build_docs - # Now try Astropy dev with the latest Python and LTS with Python 2.7 and 3.x. + # Now try Astropy dev with the latest Python - os: linux - env: ASTROPY_VERSION=development - EVENT_TYPE='pull_request push cron' - #- os: linux - # env: PYTHON_VERSION=2.7 ASTROPY_VERSION=lts - # - os: linux - # env: ASTROPY_VERSION=lts + python: 3.8 + name: Python 3.8 with developer version of astropy + stage: Comprehensive tests + env: TOXENV=py38-test-devdeps - # Try all python versions and Numpy versions. Since we can assume that + # And with an older Python, Astropy LTS, and the oldest supported Numpy + - os: linux + python: 3.6 + name: Python 3.6 astropy LTS and Numpy 1.16 + stage: Comprehensive tests + env: TOXENV=py36-test-astropylts-numpy116 + + # Add a job that runs from cron only and tests against astropy dev and + # numpy dev to give a change for early discovery of issues and feedback + # for both developer teams. + - os: linux + python: 3.8 + name: Python 3.8 latest developer version of key dependencies + stage: Cron tests + env: TOXENV=py38-test-devdeps + + # Try on Windows. + - os: windows + language: c + name: Python 3.8 with required dependencies + stage: Comprehensive tests + env: PYTHON_VERSION=3.8 TOXENV=py38-test + + # Try other python versions and Numpy versions. Since we can assume that # the Numpy developers have taken care of testing Numpy with different # versions of Python, we can vary Python and Numpy versions at the same # time. - #- os: linux - # env: PYTHON_VERSION=2.7 NUMPY_VERSION=1.9 - - os: linux - env: PYTHON_VERSION=3.4 NUMPY_VERSION=1.11 - os: linux - env: PYTHON_VERSION=3.5 NUMPY_VERSION=1.12 - - os: linux - env: NUMPY_VERSION=1.13 + python: 3.7 + name: Python 3.7 with astropy 3.0 and Numpy 1.17 + stage: Comprehensive tests + env: TOXENV=py37-test-astropy30-numpy117 - # Try numpy pre-release + # Do a code style check - os: linux - env: NUMPY_VERSION=prerelease - EVENT_TYPE='pull_request push cron' - - # Do a PEP8 test with pycodestyle - - os: linux - env: MAIN_CMD='pycodestyle gunagala --count' SETUP_CMD='' + python: 3.8 + name: Code style checks + stage: Initial tests + env: TOXENV=codestyle allow_failures: - # Do a PEP8 test with pycodestyle - # (allow to fail unless your code completely compliant) - #- os: linux - # env: MAIN_CMD='pycodestyle gunagala --count' SETUP_CMD='' + # Do a PEP8 test with flake8 + # (do allow to fail unless your code completely compliant) + # - os: linux + # python: 3.8 + # name: Code style checks + # stage: Initial tests + # env: TOXENV=codestyle + +before_install: + # Create a coverage.xml for use by coveralls or codecov + - if [[ $TOXENV == *-cov ]]; then + export TOXPOSARGS=$TOXPOSARGS" --cov-report=xml:"$TRAVIS_BUILD_DIR"/coverage.xml"; + fi install: - # We now use the ci-helpers package to set up our testing environment. - # This is done by using Miniconda and then using conda and pip to install - # dependencies. Which dependencies are installed using conda and pip is - # determined by the CONDA_DEPENDENCIES and PIP_DEPENDENCIES variables, - # which should be space-delimited lists of package names. See the README - # in https://github.com/astropy/ci-helpers for information about the full - # list of environment variables that can be used to customize your - # environment. In some cases, ci-helpers may not offer enough flexibility - # in how to install a package, in which case you can have additional - # commands in the install: section below. - - - git clone --depth 1 git://github.com/astropy/ci-helpers.git - - source ci-helpers/travis/setup_conda.sh - - # As described above, using ci-helpers, you should be able to set up an - # environment with dependencies installed using conda and pip, but in some - # cases this may not provide enough flexibility in how to install a - # specific dependency (and it will not be able to install non-Python - # dependencies). Therefore, you can also include commands below (as - # well as at the start of the install section or in the before_install - # section if they are needed before setting up conda) to install any - # other dependencies. + # We now use the ci-helpers package to set up our Python environment + # on Windows and MacOS X but we don't set up any other dependencies, + # instead using tox to do this. See https://github.com/astropy/ci-helpers + # for more information about ci-helpers. + + - if [[ $TRAVIS_OS_NAME != linux ]]; then + git clone --depth 1 git://github.com/astropy/ci-helpers.git; + source ci-helpers/travis/setup_conda.sh; + fi script: - - $MAIN_CMD $SETUP_CMD + - pip install tox + - tox $TOXARGS -- $TOXPOSARGS after_success: - # If coveralls.io is set up for this package, uncomment the line below. - # The coveragerc file may be customized as needed for your package. - - if [[ $SETUP_CMD == *coverage* ]]; then coveralls --rcfile='gunagala/tests/coveragerc'; fi + # if either coveralls or codecov is used, uncomment the if and fi statements + # and the appropriate two lines inside the if statement + # - if [[ $TOXENV == *-cov ]]; then + # # If coveralls.io is set up for this package, uncomment the two lines below. + # pip install coveralls; + # coveralls; + # # If codecov is set up for this package, uncomment the two lines below + # pip install codecov; + # codecov; + # fi From 8a6801e29e99d8eec388753891e30fc6c295babd Mon Sep 17 00:00:00 2001 From: Lee Date: Sat, 29 Aug 2020 09:29:04 +1000 Subject: [PATCH 06/26] rtd file --- .readthedocs.yml | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 .readthedocs.yml diff --git a/.readthedocs.yml b/.readthedocs.yml new file mode 100644 index 0000000..1425481 --- /dev/null +++ b/.readthedocs.yml @@ -0,0 +1,18 @@ +version: 2 + +conda: + file: .rtd-environment.yml + +build: + image: latest + +python: + version: 3.7 + install: + - method: pip + path: . + extra_requirements: + - docs + - all + +formats: [] \ No newline at end of file From 0312f1f7cf25a2775d09ef0dabfaf1a4ad1a512f Mon Sep 17 00:00:00 2001 From: Lee Date: Sun, 30 Aug 2020 08:21:09 +1000 Subject: [PATCH 07/26] gitignore --- .gitignore | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/.gitignore b/.gitignore index 4520101..145cfb5 100644 --- a/.gitignore +++ b/.gitignore @@ -1,9 +1,6 @@ # Large data files HFI_CompMap_ThermalDustModel_2048_R1.20.fits -# Oddly this isn't in the template. -.eggs - # Compiled files *.py[cod] *.a @@ -39,12 +36,16 @@ docs/_build .floo .flooignore +# Visual Studio Code project files +.vscode + # Packages/installer info *.egg *.egg-info dist build eggs +.eggs parts bin var @@ -61,6 +62,7 @@ distribute-*.tar.gz .project .pydevproject .settings +pip-wheel-metadata/ # Mac OSX .DS_Store From 495ad0a8b3ee02b4b2ee4f91e7f32136cf026322 Mon Sep 17 00:00:00 2001 From: Lee Date: Sun, 30 Aug 2020 08:25:03 +1000 Subject: [PATCH 08/26] yaml syntax issue --- setup.cfg | 37 ++++++++++++++++++++++++++++--------- 1 file changed, 28 insertions(+), 9 deletions(-) diff --git a/setup.cfg b/setup.cfg index eb10d7b..851cc2b 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,7 +1,3 @@ - - - - [metadata] package_name = gunagala author = Anthony Horton @@ -21,7 +17,11 @@ packages = find: python_requires = >=3.6 setup_requires = setuptools_scm install_requires = - astropy, pyYAML, numpy, scipy, matplotlib + astropy + pyYAML + numpy + scipy + matplotlib # version should be PEP386 compatible (http://www.python.org/dev/peps/pep-0386) version = 0.1.dev0 @@ -37,7 +37,10 @@ docs = sphinx-astropy [options.package_data] -gunagala = data/*.*, data/performance_data/*, data/sky_data/* +gunagala = + data/*.* + data/performance_data/* + data/sky_data/* [tool:pytest] @@ -45,7 +48,9 @@ testpaths = "gunagala" "docs" astropy_header = true doctest_plus = enabled text_file_format = rst -addopts = --doctest-rst, -p no:warnings +addopts = + --doctest-rst + -p no:warnings [coverage:run] omit = @@ -99,5 +104,19 @@ all_files = 1 # E113 - 4 spaces per indentation level # E901 - SyntaxError or IndentationError # E902 - IOError -select = E101,W191,W291,W292,W293,W391,E111,E112,E113,E901,E902 -exclude = extern,sphinx,*parsetab.py \ No newline at end of file +select = + E101 + W191 + W291 + W292 + W293 + W391 + E111 + E112 + E113 + E901 + E902 +exclude = + extern + sphinx + *parsetab.py \ No newline at end of file From ff718a2dee4f9d6519ef396c2b011aa6885fdd7b Mon Sep 17 00:00:00 2001 From: Lee Date: Sun, 30 Aug 2020 08:38:08 +1000 Subject: [PATCH 09/26] update conftest see https://github.com/astropy/pytest-astropy-header#migrating-from-the-astropy-header-plugin-to-pytest-astropy --- gunagala/conftest.py | 60 +++++++++----------------------------------- 1 file changed, 12 insertions(+), 48 deletions(-) diff --git a/gunagala/conftest.py b/gunagala/conftest.py index ebab8a1..bac300b 100644 --- a/gunagala/conftest.py +++ b/gunagala/conftest.py @@ -1,57 +1,21 @@ -# This file is used to configure the behavior of pytest when using the Astropy -# test infrastructure. +import os from astropy.version import version as astropy_version if astropy_version < '3.0': - # With older versions of Astropy, we actually need to import the pytest - # plugins themselves in order to make them discoverable by pytest. from astropy.tests.pytest_plugins import * + del pytest_report_header else: - # As of Astropy 3.0, the pytest plugins provided by Astropy are - # automatically made available when Astropy is installed. This means it's - # not necessary to import them here, but we still need to import global - # variables that are used for configuration. - from astropy.tests.plugins.display import PYTEST_HEADER_MODULES, TESTED_VERSIONS + from pytest_astropy_header.display import PYTEST_HEADER_MODULES, TESTED_VERSIONS -from astropy.tests.helper import enable_deprecations_as_exceptions -## Uncomment the following line to treat all DeprecationWarnings as -## exceptions. For Astropy v2.0 or later, there are 2 additional keywords, -## as follow (although default should work for most cases). -## To ignore some packages that produce deprecation warnings on import -## (in addition to 'compiler', 'scipy', 'pygments', 'ipykernel', and -## 'setuptools'), add: -## modules_to_ignore_on_import=['module_1', 'module_2'] -## To ignore some specific deprecation warning messages for Python version -## MAJOR.MINOR or later, add: -## warnings_to_ignore_by_pyver={(MAJOR, MINOR): ['Message to ignore']} -# enable_deprecations_as_exceptions() +def pytest_configure(config): -## Uncomment and customize the following lines to add/remove entries from -## the list of packages for which version numbers are displayed when running -## the tests. Making it pass for KeyError is essential in some cases when -## the package uses other astropy affiliated packages. -# try: -# PYTEST_HEADER_MODULES['Astropy'] = 'astropy' -# PYTEST_HEADER_MODULES['scikit-image'] = 'skimage' -# del PYTEST_HEADER_MODULES['h5py'] -# except (NameError, KeyError): # NameError is needed to support Astropy < 1.0 -# pass + config.option.astropy_header = True -## Uncomment the following lines to display the version number of the -## package rather than the version number of Astropy in the top line when -## running the tests. -# import os -# -## This is to figure out the package version, rather than -## using Astropy's -# try: -# from .version import version -# except ImportError: -# version = 'dev' -# -# try: -# packagename = os.path.basename(os.path.dirname(__file__)) -# TESTED_VERSIONS[packagename] = version -# except NameError: # Needed to support Astropy <= 1.0.0 -# pass + PYTEST_HEADER_MODULES.pop('Pandas', None) + PYTEST_HEADER_MODULES['scikit-image'] = 'skimage' + + from .version import version, astropy_helpers_version + packagename = os.path.basename(os.path.dirname(__file__)) + TESTED_VERSIONS[packagename] = version + TESTED_VERSIONS['astropy_helpers'] = astropy_helpers_version From f9b94aca17e7bcc7c9e86734b95573bd355fa93b Mon Sep 17 00:00:00 2001 From: Lee Date: Sun, 30 Aug 2020 16:09:25 +1000 Subject: [PATCH 10/26] doc changes --- docs/conf.py | 67 +++++++++------ docs/gunagala/index.rst | 174 +++++++++++++++++++++++++++++++++++++++ docs/index.rst | 178 ++-------------------------------------- docs/make.bat | 2 + 4 files changed, 225 insertions(+), 196 deletions(-) create mode 100644 docs/gunagala/index.rst diff --git a/docs/conf.py b/docs/conf.py index 62b81cb..f45b8d7 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -25,28 +25,19 @@ # Thus, any C-extensions that are needed to build the documentation will *not* # be accessible, and the documentation will not build correctly. -import datetime import os import sys +import datetime +from importlib import import_module try: - import astropy_helpers + from sphinx_astropy.conf.v1 import * # noqa except ImportError: - # Building from inside the docs/ directory? - if os.path.basename(os.getcwd()) == 'docs': - a_h_path = os.path.abspath(os.path.join('..', 'astropy_helpers')) - if os.path.isdir(a_h_path): - sys.path.insert(1, a_h_path) - -# Load all of the global Astropy configuration -#from astropy_helpers.sphinx.conf import * -from sphinx_astropy.conf import * + print('ERROR: the documentation requires the sphinx-astropy package to be installed') + sys.exit(1) # Get configuration information from setup.cfg -try: - from ConfigParser import ConfigParser -except ImportError: - from configparser import ConfigParser +from configparser import ConfigParser conf = ConfigParser() conf.read([os.path.join(os.path.dirname(__file__), '..', 'setup.cfg')]) @@ -76,7 +67,7 @@ # -- Project information ------------------------------------------------------ # This does not *have* to match the package name, but typically does -project = setup_cfg['package_name'] +project = setup_cfg['name'] author = setup_cfg['author'] copyright = '{0}, {1}'.format( datetime.datetime.now().year, setup_cfg['author']) @@ -85,8 +76,8 @@ # |version| and |release|, also used in various other places throughout the # built documents. -__import__(setup_cfg['package_name']) -package = sys.modules[setup_cfg['package_name']] +import_module(setup_cfg['name']) +package = sys.modules[setup_cfg['name']] # The short X.Y version. version = package.__version__.split('-', 1)[0] @@ -113,7 +104,7 @@ # name of a builtin theme or the name of a custom theme in html_theme_path. #html_theme = None -# Please update these texts to match the name of your package. + html_theme_options = { 'logotext1': 'guna', # white, semi-bold 'logotext2': 'gala', # orange, light @@ -121,7 +112,6 @@ } - # Custom sidebar templates, maps document names to template names. #html_sidebars = {} @@ -164,18 +154,41 @@ # -- Options for the edit_on_github extension --------------------------------- -if eval(setup_cfg.get('edit_on_github')): - extensions += ['astropy_helpers.sphinx.ext.edit_on_github'] +if setup_cfg.get('edit_on_github').lower() == 'true': + + extensions += ['sphinx_astropy.ext.edit_on_github'] - versionmod = __import__(setup_cfg['package_name'] + '.version') edit_on_github_project = setup_cfg['github_project'] - if versionmod.version.release: - edit_on_github_branch = "v" + versionmod.version.version - else: - edit_on_github_branch = "master" + edit_on_github_branch = "master" edit_on_github_source_root = "" edit_on_github_doc_root = "docs" # -- Resolving issue number to links in changelog ----------------------------- github_issues_url = 'https://github.com/{0}/issues/'.format(setup_cfg['github_project']) + +# -- Turn on nitpicky mode for sphinx (to warn about references not found) ---- +# +# nitpicky = True +# nitpick_ignore = [] +# +# Some warnings are impossible to suppress, and you can list specific references +# that should be ignored in a nitpick-exceptions file which should be inside +# the docs/ directory. The format of the file should be: +# +# +# +# for example: +# +# py:class astropy.io.votable.tree.Element +# py:class astropy.io.votable.tree.SimpleElement +# py:class astropy.io.votable.tree.SimpleElementWithContent +# +# Uncomment the following lines to enable the exceptions: +# +# for line in open('nitpick-exceptions'): +# if line.strip() == "" or line.startswith("#"): +# continue +# dtype, target = line.split(None, 1) +# target = target.strip() +# nitpick_ignore.append((dtype, six.u(target))) diff --git a/docs/gunagala/index.rst b/docs/gunagala/index.rst new file mode 100644 index 0000000..ce76b44 --- /dev/null +++ b/docs/gunagala/index.rst @@ -0,0 +1,174 @@ +**************** +Gunagala +**************** + +Introduction +============ + +Gungala is a Python package for modelling the performance of astronomical instruments, including +SNR/ETC/sensitivity limit calculations and generation of simulated data. + +This package is not intended for rigorous, end-to-end simulations of telescope and instrument +systems. Instead gunagala implements parameterised models of instrument components in order to +enable rapid, efficient evaluation of instrument performance. Anticipated uses include exposure time +calculators, selection of commercial off the shelf components and exploration of the design +parameter space for custom components. + +Gunagala includes a library of performance parameters for a number of existing commercial off the +shelf instrument components (e.g. CCD cameras, optical filters, telescopes and camera lenses) and +the user can easily add new/custom components either through YAML based config files or +programmatically in Python. + +Gunagala is named as a gesture of respect to the traditional custodians of the land on which Siding +Spring Observatory sits, the Kamilaroi people of northern New South Wales. Gunagala is 'sky' in +the Kamilaroi/Gamilaraay language +(ref: `www.dnathan.com `_). Aboriginal +Australians have studied the night skies above Australia for at least 50000 years. To learn more +about Aboriginal astronomy please visit http://www.aboriginalastronomy.com.au/. + + +Installation +============ + +Installing with pip +------------------- +.. highlight:: console + +To install using the Python package manager `pip` use the following command:: + + $ pip install git+https://github.com/AstroHuntsman/gunagala.git + +Alternatively to install in 'editable mode' use:: + + $ pip install -e git+https://github.com/AstroHuntsman/gunagala.git + +Depending on the configuration of your system you may want to use `pip`'s ``--user`` or ``--root`` +options to change the install location. See the pip documentation for details. + +`Pip` will automatically install the Python packages required by Gunagala (`numpy`, `scipy`, +`astropy`, `PyYAML`, `matplotlib` and their dependencies) if they are not already installed. If you +want to install specific versions of the required packages from other sources do this before +installing Gunagala. + +Installing from source +---------------------- + +The project source is in a GitHub repository at https://github.com/AstroHuntsman/gunagala. To +install using git on the command line:: + + $ cd ~/Build + $ git clone https://github.com/AstroHuntsman/gunagala.git + $ cd gunagala + $ python setup.py install + +Alternatively if you expect to make changes to the Gunagala code install with the ``develop`` +command instead:: + + $ python setup.py develop + +Setuptools will automatically install the Python packages required by Gunagala (`numpy`, `scipy`, +`astropy`, `PyYAML`, `matplotlib` and their dependencies) if they are not already installed. If you +want to install specific versions of the required packages from other sources do this before +installing Gunagala. + +Running the test suite +---------------------- + +After installing Gunagala it is recommended that you run the suite of units tests. This can be done +at the command line using:: + + $ python setup.py test + +.. highlight:: python3 + +or from within a Python interpreter with:: + + >> import gunagala + >> gunagala.test() + +Examples +======== + +The Gunagala package includes several examples in the form of `Jupyter `_ +notebooks. These can be found in the `gungala/examples` directory after installing Gunagala, or they +can be viewed directly in the GitHub repository by going to +https://github.com/AstroHuntsman/gunagala/tree/master/examples and clicking on the ``.ipynb`` files. + +Contributing +============ + +Please submit bug reports or feature requests in the form of GitHub Issues at +https://github.com/AstroHuntsman/gunagala/issues. For code contributions please fork and clone the +repository, create a feature branch and submit a Pull Request. We recommend the +`astropy Developer Documentation `_ +for a description of suitable workflows. + +Changelog +========= + +.. include:: ../CHANGES.rst + +Reference/API +============= + +.. automodapi:: gunagala + :no-main-docstr: + +.. automodapi:: gunagala.imager + :skip: ensure_unit + :skip: load_config + :skip: Filter + :skip: Optic + :skip: Camera + :skip: PSF + :skip: Sky + :skip: Simple + :skip: MoffatPSF + :skip: ZodiacalLight + :skip: WCS + :skip: SkyCoord + :skip: CCDData + :skip: interp1d + :skip: InvalidTransformError + :no-inheritance-diagram: + +.. automodapi:: gunagala.optic + :skip: Table + :skip: ensure_unit + :skip: get_table_data + :skip: array_sequence_equal + :no-inheritance-diagram: + +.. automodapi:: gunagala.optical_filter + :skip: Table + :skip: interp1d + :skip: brentq + :skip: ensure_unit + :skip: get_table_data + :skip: minimize_scalar + :skip: eval_chebyt + :no-inheritance-diagram: + +.. automodapi:: gunagala.camera + :skip: Table + :skip: ensure_unit + :no-inheritance-diagram: + +.. automodapi:: gunagala.psf + :skip: discretize_model + :skip: Fittable2DModel + :skip: Moffat2D + +.. automodapi:: gunagala.sky + :skip: interp1d + :skip: RectSphereBivariateSpline + :skip: SmoothBivariateSpline + :skip: SkyCoord + :skip: GeocentricTrueEcliptic + :skip: get_sun + :skip: Angle + :skip: Time + :skip: ensure_unit + +.. automodapi:: gunagala.utils + :skip: get_pkg_data_filename diff --git a/docs/index.rst b/docs/index.rst index ce76b44..cd4866c 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -1,174 +1,14 @@ -**************** -Gunagala -**************** - -Introduction -============ - -Gungala is a Python package for modelling the performance of astronomical instruments, including -SNR/ETC/sensitivity limit calculations and generation of simulated data. - -This package is not intended for rigorous, end-to-end simulations of telescope and instrument -systems. Instead gunagala implements parameterised models of instrument components in order to -enable rapid, efficient evaluation of instrument performance. Anticipated uses include exposure time -calculators, selection of commercial off the shelf components and exploration of the design -parameter space for custom components. - -Gunagala includes a library of performance parameters for a number of existing commercial off the -shelf instrument components (e.g. CCD cameras, optical filters, telescopes and camera lenses) and -the user can easily add new/custom components either through YAML based config files or -programmatically in Python. - -Gunagala is named as a gesture of respect to the traditional custodians of the land on which Siding -Spring Observatory sits, the Kamilaroi people of northern New South Wales. Gunagala is 'sky' in -the Kamilaroi/Gamilaraay language -(ref: `www.dnathan.com `_). Aboriginal -Australians have studied the night skies above Australia for at least 50000 years. To learn more -about Aboriginal astronomy please visit http://www.aboriginalastronomy.com.au/. - - -Installation -============ - -Installing with pip -------------------- -.. highlight:: console - -To install using the Python package manager `pip` use the following command:: - - $ pip install git+https://github.com/AstroHuntsman/gunagala.git - -Alternatively to install in 'editable mode' use:: - - $ pip install -e git+https://github.com/AstroHuntsman/gunagala.git - -Depending on the configuration of your system you may want to use `pip`'s ``--user`` or ``--root`` -options to change the install location. See the pip documentation for details. - -`Pip` will automatically install the Python packages required by Gunagala (`numpy`, `scipy`, -`astropy`, `PyYAML`, `matplotlib` and their dependencies) if they are not already installed. If you -want to install specific versions of the required packages from other sources do this before -installing Gunagala. - -Installing from source ----------------------- - -The project source is in a GitHub repository at https://github.com/AstroHuntsman/gunagala. To -install using git on the command line:: - - $ cd ~/Build - $ git clone https://github.com/AstroHuntsman/gunagala.git - $ cd gunagala - $ python setup.py install - -Alternatively if you expect to make changes to the Gunagala code install with the ``develop`` -command instead:: - - $ python setup.py develop - -Setuptools will automatically install the Python packages required by Gunagala (`numpy`, `scipy`, -`astropy`, `PyYAML`, `matplotlib` and their dependencies) if they are not already installed. If you -want to install specific versions of the required packages from other sources do this before -installing Gunagala. - -Running the test suite ----------------------- - -After installing Gunagala it is recommended that you run the suite of units tests. This can be done -at the command line using:: - - $ python setup.py test - -.. highlight:: python3 - -or from within a Python interpreter with:: - - >> import gunagala - >> gunagala.test() - -Examples -======== - -The Gunagala package includes several examples in the form of `Jupyter `_ -notebooks. These can be found in the `gungala/examples` directory after installing Gunagala, or they -can be viewed directly in the GitHub repository by going to -https://github.com/AstroHuntsman/gunagala/tree/master/examples and clicking on the ``.ipynb`` files. - -Contributing -============ - -Please submit bug reports or feature requests in the form of GitHub Issues at -https://github.com/AstroHuntsman/gunagala/issues. For code contributions please fork and clone the -repository, create a feature branch and submit a Pull Request. We recommend the -`astropy Developer Documentation `_ -for a description of suitable workflows. - -Changelog -========= - -.. include:: ../CHANGES.rst - -Reference/API +Documentation ============= -.. automodapi:: gunagala - :no-main-docstr: - -.. automodapi:: gunagala.imager - :skip: ensure_unit - :skip: load_config - :skip: Filter - :skip: Optic - :skip: Camera - :skip: PSF - :skip: Sky - :skip: Simple - :skip: MoffatPSF - :skip: ZodiacalLight - :skip: WCS - :skip: SkyCoord - :skip: CCDData - :skip: interp1d - :skip: InvalidTransformError - :no-inheritance-diagram: - -.. automodapi:: gunagala.optic - :skip: Table - :skip: ensure_unit - :skip: get_table_data - :skip: array_sequence_equal - :no-inheritance-diagram: - -.. automodapi:: gunagala.optical_filter - :skip: Table - :skip: interp1d - :skip: brentq - :skip: ensure_unit - :skip: get_table_data - :skip: minimize_scalar - :skip: eval_chebyt - :no-inheritance-diagram: - -.. automodapi:: gunagala.camera - :skip: Table - :skip: ensure_unit - :no-inheritance-diagram: +This is the documentation for gunagala. -.. automodapi:: gunagala.psf - :skip: discretize_model - :skip: Fittable2DModel - :skip: Moffat2D +.. toctree:: + :maxdepth: 2 -.. automodapi:: gunagala.sky - :skip: interp1d - :skip: RectSphereBivariateSpline - :skip: SmoothBivariateSpline - :skip: SkyCoord - :skip: GeocentricTrueEcliptic - :skip: get_sun - :skip: Angle - :skip: Time - :skip: ensure_unit + gunagala/index.rst -.. automodapi:: gunagala.utils - :skip: get_pkg_data_filename +.. note:: The layout of this directory is simply a suggestion. To follow + traditional practice, do *not* edit this page, but instead place + all documentation for the package inside ``gunagala/``. + You can follow this practice or choose your own layout. diff --git a/docs/make.bat b/docs/make.bat index 93dfe92..aa93013 100644 --- a/docs/make.bat +++ b/docs/make.bat @@ -37,6 +37,8 @@ if "%1" == "help" ( if "%1" == "clean" ( for /d %%i in (%BUILDDIR%\*) do rmdir /q /s %%i del /q /s %BUILDDIR%\* + del /q /s api + del /q /s generated goto end ) From e3ebe2781c22475fbeff95bc07e56ca1d037aaa5 Mon Sep 17 00:00:00 2001 From: Lee Date: Sun, 30 Aug 2020 16:17:43 +1000 Subject: [PATCH 11/26] functools not needed --- gunagala/utils/__init__.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gunagala/utils/__init__.py b/gunagala/utils/__init__.py index e4d98a8..8de6cca 100644 --- a/gunagala/utils/__init__.py +++ b/gunagala/utils/__init__.py @@ -1,9 +1,9 @@ # Licensed under a 3-clause BSD style license - see LICENSE.rst # This sub-module is destined for common non-package specific utility -# functions that will ultimately be merged into `astropy.utils` +# functions. + import os -import functools import numpy as np import astropy.units as u from astropy.table import Table From 5a7f6df99a61fd1ab9f8a1256215c47edee34968 Mon Sep 17 00:00:00 2001 From: Lee Date: Sun, 30 Aug 2020 16:18:53 +1000 Subject: [PATCH 12/26] fix gunagala dir --- gunagala/__init__.py | 20 +++---- gunagala/_astropy_init.py | 107 +++----------------------------------- gunagala/conftest.py | 47 +++++++++++++---- 3 files changed, 53 insertions(+), 121 deletions(-) diff --git a/gunagala/__init__.py b/gunagala/__init__.py index 196dc84..8c9ddef 100644 --- a/gunagala/__init__.py +++ b/gunagala/__init__.py @@ -1,20 +1,14 @@ # Licensed under a 3-clause BSD style license - see LICENSE.rst -""" -Performance modelling for astronomical instruments - -This is a Python package for modelling the performance of astronomical instruments, including -SNR/ETC/sensitivity limit calculations and generation of simulated data. -""" - # Packages may add whatever they like to this file, but # should keep this content at the top. # ---------------------------------------------------------------------------- -from ._astropy_init import * +from ._astropy_init import * # noqa # ---------------------------------------------------------------------------- -if not _ASTROPY_SETUP_: - # For egg_info test builds to pass, put package imports here. - - #from .example_mod import * - pass +__all__ = [] +# from .example_mod import * # noqa +# Then you can be explicit to control what ends up in the namespace, +# __all__ += ['do_primes'] # noqa +# or you can keep everything from the subpackage with the following instead +# __all__ += example_mod.__all__ diff --git a/gunagala/_astropy_init.py b/gunagala/_astropy_init.py index 73a52fb..2dffe8f 100644 --- a/gunagala/_astropy_init.py +++ b/gunagala/_astropy_init.py @@ -1,116 +1,19 @@ # Licensed under a 3-clause BSD style license - see LICENSE.rst -__all__ = ['__version__', '__githash__', 'test'] +__all__ = ['__version__'] # this indicates whether or not we are in the package's setup.py try: _ASTROPY_SETUP_ except NameError: - from sys import version_info - if version_info[0] >= 3: - import builtins - else: - import __builtin__ as builtins + import builtins builtins._ASTROPY_SETUP_ = False try: from .version import version as __version__ except ImportError: __version__ = '' -try: - from .version import githash as __githash__ -except ImportError: - __githash__ = '' - - -# set up the test command -def _get_test_runner(): - import os - from astropy.tests.helper import TestRunner - return TestRunner(os.path.dirname(__file__)) - - -def test(package=None, test_path=None, args=None, plugins=None, - verbose=False, pastebin=None, remote_data=False, pep8=False, - pdb=False, coverage=False, open_files=False, **kwargs): - """ - Run the tests using `py.test `__. A proper set - of arguments is constructed and passed to `pytest.main`_. - - .. _py.test: http://pytest.org/latest/ - .. _pytest.main: http://pytest.org/latest/builtin.html#pytest.main - - Parameters - ---------- - package : str, optional - The name of a specific package to test, e.g. 'io.fits' or 'utils'. - If nothing is specified all default tests are run. - - test_path : str, optional - Specify location to test by path. May be a single file or - directory. Must be specified absolutely or relative to the - calling directory. - - args : str, optional - Additional arguments to be passed to pytest.main_ in the ``args`` - keyword argument. - plugins : list, optional - Plugins to be passed to pytest.main_ in the ``plugins`` keyword - argument. - - verbose : bool, optional - Convenience option to turn on verbose output from py.test_. Passing - True is the same as specifying ``'-v'`` in ``args``. - - pastebin : {'failed','all',None}, optional - Convenience option for turning on py.test_ pastebin output. Set to - ``'failed'`` to upload info for failed tests, or ``'all'`` to upload - info for all tests. - - remote_data : bool, optional - Controls whether to run tests marked with @remote_data. These - tests use online data and are not run by default. Set to True to - run these tests. - - pep8 : bool, optional - Turn on PEP8 checking via the `pytest-pep8 plugin - `_ and disable normal - tests. Same as specifying ``'--pep8 -k pep8'`` in ``args``. - - pdb : bool, optional - Turn on PDB post-mortem analysis for failing tests. Same as - specifying ``'--pdb'`` in ``args``. - - coverage : bool, optional - Generate a test coverage report. The result will be placed in - the directory htmlcov. - - open_files : bool, optional - Fail when any tests leave files open. Off by default, because - this adds extra run time to the test suite. Requires the - `psutil `_ package. - - parallel : int, optional - When provided, run the tests in parallel on the specified - number of CPUs. If parallel is negative, it will use the all - the cores on the machine. Requires the - `pytest-xdist `_ plugin - installed. Only available when using Astropy 0.3 or later. - - kwargs - Any additional keywords passed into this function will be passed - on to the astropy test runner. This allows use of test-related - functionality implemented in later versions of astropy without - explicitly updating the package template. - - """ - test_runner = _get_test_runner() - return test_runner.run_tests( - package=package, test_path=test_path, args=args, - plugins=plugins, verbose=verbose, pastebin=pastebin, - remote_data=remote_data, pep8=pep8, pdb=pdb, - coverage=coverage, open_files=open_files, **kwargs) if not _ASTROPY_SETUP_: # noqa import os @@ -120,6 +23,12 @@ def test(package=None, test_path=None, args=None, plugins=None, ConfigurationDefaultMissingError, ConfigurationDefaultMissingWarning) + # Create the test function for self test + from astropy.tests.runner import TestRunner + test = TestRunner.make_test_runner_in(os.path.dirname(__file__)) + test.__test__ = False + __all__ += ['test'] + # add these here so we only need to cleanup the namespace at the end config_dir = None diff --git a/gunagala/conftest.py b/gunagala/conftest.py index bac300b..7d6dea3 100644 --- a/gunagala/conftest.py +++ b/gunagala/conftest.py @@ -1,21 +1,50 @@ +# This file is used to configure the behavior of pytest when using the Astropy +# test infrastructure. It needs to live inside the package in order for it to +# get picked up when running the tests inside an interpreter using +# packagename.test + import os from astropy.version import version as astropy_version + +# For Astropy 3.0 and later, we can use the standalone pytest plugin if astropy_version < '3.0': - from astropy.tests.pytest_plugins import * + from astropy.tests.pytest_plugins import * # noqa del pytest_report_header + ASTROPY_HEADER = True else: - from pytest_astropy_header.display import PYTEST_HEADER_MODULES, TESTED_VERSIONS + try: + from pytest_astropy_header.display import PYTEST_HEADER_MODULES, TESTED_VERSIONS + ASTROPY_HEADER = True + except ImportError: + ASTROPY_HEADER = False def pytest_configure(config): - config.option.astropy_header = True + if ASTROPY_HEADER: + + config.option.astropy_header = True + + # Customize the following lines to add/remove entries from the list of + # packages for which version numbers are displayed when running the tests. + PYTEST_HEADER_MODULES.pop('Pandas', None) + PYTEST_HEADER_MODULES['scikit-image'] = 'skimage' + + from . import __version__ + packagename = os.path.basename(os.path.dirname(__file__)) + TESTED_VERSIONS[packagename] = __version__ - PYTEST_HEADER_MODULES.pop('Pandas', None) - PYTEST_HEADER_MODULES['scikit-image'] = 'skimage' - from .version import version, astropy_helpers_version - packagename = os.path.basename(os.path.dirname(__file__)) - TESTED_VERSIONS[packagename] = version - TESTED_VERSIONS['astropy_helpers'] = astropy_helpers_version +# Uncomment the last two lines in this block to treat all DeprecationWarnings as +# exceptions. For Astropy v2.0 or later, there are 2 additional keywords, +# as follow (although default should work for most cases). +# To ignore some packages that produce deprecation warnings on import +# (in addition to 'compiler', 'scipy', 'pygments', 'ipykernel', and +# 'setuptools'), add: +# modules_to_ignore_on_import=['module_1', 'module_2'] +# To ignore some specific deprecation warning messages for Python version +# MAJOR.MINOR or later, add: +# warnings_to_ignore_by_pyver={(MAJOR, MINOR): ['Message to ignore']} +from astropy.tests.helper import enable_deprecations_as_exceptions # noqa +enable_deprecations_as_exceptions() From 0379b39e6fc8630b69ea0f8060c796c5962967a4 Mon Sep 17 00:00:00 2001 From: Lee Date: Sun, 30 Aug 2020 16:29:53 +1000 Subject: [PATCH 13/26] linspace now requires int ranges --- gunagala/psf.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gunagala/psf.py b/gunagala/psf.py index acbe974..01e57f2 100644 --- a/gunagala/psf.py +++ b/gunagala/psf.py @@ -191,15 +191,15 @@ def pixellated(self, size=(21, 21), offsets=(0.0, 0.0)): PSF wings by the edge of the image. """ size = tuple(int(s) for s in size) - if size[0] <= 0 or size[1] <=0: + if size[0] <= 0 or size[1] <= 0: raise ValueError("`size` must be > 0, got {}!".format(size)) # Update PSF centre coordinates self.x_0 = offsets[1] self.y_0 = offsets[0] - xrange = (-(size[1] - 1) / 2, (size[1] + 1) / 2) - yrange = (-(size[0] - 1) / 2, (size[0] + 1) / 2) + xrange = (int(-(size[1] - 1) / 2), int((size[1] + 1) / 2)) + yrange = (int(-(size[0] - 1) / 2), int((size[0] + 1) / 2)) return discretize_model(self, xrange, yrange, mode='oversample', factor=10) From d0dbe39c802186200dcaf27db666ec5110202d35 Mon Sep 17 00:00:00 2001 From: Lee Date: Sun, 30 Aug 2020 16:38:15 +1000 Subject: [PATCH 14/26] setup cfg --- setup.cfg | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/setup.cfg b/setup.cfg index 851cc2b..e2eb8f9 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,5 +1,5 @@ [metadata] -package_name = gunagala +name = gunagala author = Anthony Horton author_email = anthony.horton@mq.edu.au license = BSD 3-Clause @@ -50,7 +50,7 @@ doctest_plus = enabled text_file_format = rst addopts = --doctest-rst - -p no:warnings +# -p no:warnings [coverage:run] omit = From 79ded978350369c40c7bba3d6a884fc5f97e2346 Mon Sep 17 00:00:00 2001 From: Lee Date: Sun, 30 Aug 2020 16:38:49 +1000 Subject: [PATCH 15/26] removed conftest thing not needed --- gunagala/conftest.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gunagala/conftest.py b/gunagala/conftest.py index 7d6dea3..4cc5279 100644 --- a/gunagala/conftest.py +++ b/gunagala/conftest.py @@ -46,5 +46,5 @@ def pytest_configure(config): # To ignore some specific deprecation warning messages for Python version # MAJOR.MINOR or later, add: # warnings_to_ignore_by_pyver={(MAJOR, MINOR): ['Message to ignore']} -from astropy.tests.helper import enable_deprecations_as_exceptions # noqa -enable_deprecations_as_exceptions() +# from astropy.tests.helper import enable_deprecations_as_exceptions # noqa +# enable_deprecations_as_exceptions() From bb8868de5572053ff6305f0761a0b3854b3a8be5 Mon Sep 17 00:00:00 2001 From: Lee Date: Sun, 30 Aug 2020 16:39:01 +1000 Subject: [PATCH 16/26] deleted things not needed --- .gitmodules | 3 - ah_bootstrap.py | 958 ------------------------------------------------ astropy_helpers | 1 - ez_setup.py | 414 --------------------- readthedocs.yml | 9 - 5 files changed, 1385 deletions(-) delete mode 100644 .gitmodules delete mode 100644 ah_bootstrap.py delete mode 160000 astropy_helpers delete mode 100644 ez_setup.py delete mode 100644 readthedocs.yml diff --git a/.gitmodules b/.gitmodules deleted file mode 100644 index 6a20fa6..0000000 --- a/.gitmodules +++ /dev/null @@ -1,3 +0,0 @@ -[submodule "astropy_helpers"] - path = astropy_helpers - url = https://github.com/astropy/astropy-helpers.git diff --git a/ah_bootstrap.py b/ah_bootstrap.py deleted file mode 100644 index 786b8b1..0000000 --- a/ah_bootstrap.py +++ /dev/null @@ -1,958 +0,0 @@ -""" -This bootstrap module contains code for ensuring that the astropy_helpers -package will be importable by the time the setup.py script runs. It also -includes some workarounds to ensure that a recent-enough version of setuptools -is being used for the installation. - -This module should be the first thing imported in the setup.py of distributions -that make use of the utilities in astropy_helpers. If the distribution ships -with its own copy of astropy_helpers, this module will first attempt to import -from the shipped copy. However, it will also check PyPI to see if there are -any bug-fix releases on top of the current version that may be useful to get -past platform-specific bugs that have been fixed. When running setup.py, use -the ``--offline`` command-line option to disable the auto-upgrade checks. - -When this module is imported or otherwise executed it automatically calls a -main function that attempts to read the project's setup.cfg file, which it -checks for a configuration section called ``[ah_bootstrap]`` the presences of -that section, and options therein, determine the next step taken: If it -contains an option called ``auto_use`` with a value of ``True``, it will -automatically call the main function of this module called -`use_astropy_helpers` (see that function's docstring for full details). -Otherwise no further action is taken (however, -``ah_bootstrap.use_astropy_helpers`` may be called manually from within the -setup.py script). - -Additional options in the ``[ah_boostrap]`` section of setup.cfg have the same -names as the arguments to `use_astropy_helpers`, and can be used to configure -the bootstrap script when ``auto_use = True``. - -See https://github.com/astropy/astropy-helpers for more details, and for the -latest version of this module. -""" - -import contextlib -import errno -import imp -import io -import locale -import os -import re -import subprocess as sp -import sys - -try: - from ConfigParser import ConfigParser, RawConfigParser -except ImportError: - from configparser import ConfigParser, RawConfigParser - - -if sys.version_info[0] < 3: - _str_types = (str, unicode) - _text_type = unicode - PY3 = False -else: - _str_types = (str, bytes) - _text_type = str - PY3 = True - - -# What follows are several import statements meant to deal with install-time -# issues with either missing or misbehaving pacakges (including making sure -# setuptools itself is installed): - - -# Some pre-setuptools checks to ensure that either distribute or setuptools >= -# 0.7 is used (over pre-distribute setuptools) if it is available on the path; -# otherwise the latest setuptools will be downloaded and bootstrapped with -# ``ez_setup.py``. This used to be included in a separate file called -# setuptools_bootstrap.py; but it was combined into ah_bootstrap.py -try: - import pkg_resources - _setuptools_req = pkg_resources.Requirement.parse('setuptools>=0.7') - # This may raise a DistributionNotFound in which case no version of - # setuptools or distribute is properly installed - _setuptools = pkg_resources.get_distribution('setuptools') - if _setuptools not in _setuptools_req: - # Older version of setuptools; check if we have distribute; again if - # this results in DistributionNotFound we want to give up - _distribute = pkg_resources.get_distribution('distribute') - if _setuptools != _distribute: - # It's possible on some pathological systems to have an old version - # of setuptools and distribute on sys.path simultaneously; make - # sure distribute is the one that's used - sys.path.insert(1, _distribute.location) - _distribute.activate() - imp.reload(pkg_resources) -except: - # There are several types of exceptions that can occur here; if all else - # fails bootstrap and use the bootstrapped version - from ez_setup import use_setuptools - use_setuptools() - - -# typing as a dependency for 1.6.1+ Sphinx causes issues when imported after -# initializing submodule with ah_boostrap.py -# See discussion and references in -# https://github.com/astropy/astropy-helpers/issues/302 - -try: - import typing # noqa -except ImportError: - pass - - -# Note: The following import is required as a workaround to -# https://github.com/astropy/astropy-helpers/issues/89; if we don't import this -# module now, it will get cleaned up after `run_setup` is called, but that will -# later cause the TemporaryDirectory class defined in it to stop working when -# used later on by setuptools -try: - import setuptools.py31compat # noqa -except ImportError: - pass - - -# matplotlib can cause problems if it is imported from within a call of -# run_setup(), because in some circumstances it will try to write to the user's -# home directory, resulting in a SandboxViolation. See -# https://github.com/matplotlib/matplotlib/pull/4165 -# Making sure matplotlib, if it is available, is imported early in the setup -# process can mitigate this (note importing matplotlib.pyplot has the same -# issue) -try: - import matplotlib - matplotlib.use('Agg') - import matplotlib.pyplot -except: - # Ignore if this fails for *any* reason* - pass - - -# End compatibility imports... - - -# In case it didn't successfully import before the ez_setup checks -import pkg_resources - -from setuptools import Distribution -from setuptools.package_index import PackageIndex -from setuptools.sandbox import run_setup - -from distutils import log -from distutils.debug import DEBUG - - -# TODO: Maybe enable checking for a specific version of astropy_helpers? -DIST_NAME = 'astropy-helpers' -PACKAGE_NAME = 'astropy_helpers' - -# Defaults for other options -DOWNLOAD_IF_NEEDED = True -INDEX_URL = 'https://pypi.python.org/simple' -USE_GIT = True -OFFLINE = False -AUTO_UPGRADE = True - -# A list of all the configuration options and their required types -CFG_OPTIONS = [ - ('auto_use', bool), ('path', str), ('download_if_needed', bool), - ('index_url', str), ('use_git', bool), ('offline', bool), - ('auto_upgrade', bool) -] - - -class _Bootstrapper(object): - """ - Bootstrapper implementation. See ``use_astropy_helpers`` for parameter - documentation. - """ - - def __init__(self, path=None, index_url=None, use_git=None, offline=None, - download_if_needed=None, auto_upgrade=None): - - if path is None: - path = PACKAGE_NAME - - if not (isinstance(path, _str_types) or path is False): - raise TypeError('path must be a string or False') - - if PY3 and not isinstance(path, _text_type): - fs_encoding = sys.getfilesystemencoding() - path = path.decode(fs_encoding) # path to unicode - - self.path = path - - # Set other option attributes, using defaults where necessary - self.index_url = index_url if index_url is not None else INDEX_URL - self.offline = offline if offline is not None else OFFLINE - - # If offline=True, override download and auto-upgrade - if self.offline: - download_if_needed = False - auto_upgrade = False - - self.download = (download_if_needed - if download_if_needed is not None - else DOWNLOAD_IF_NEEDED) - self.auto_upgrade = (auto_upgrade - if auto_upgrade is not None else AUTO_UPGRADE) - - # If this is a release then the .git directory will not exist so we - # should not use git. - git_dir_exists = os.path.exists(os.path.join(os.path.dirname(__file__), '.git')) - if use_git is None and not git_dir_exists: - use_git = False - - self.use_git = use_git if use_git is not None else USE_GIT - # Declared as False by default--later we check if astropy-helpers can be - # upgraded from PyPI, but only if not using a source distribution (as in - # the case of import from a git submodule) - self.is_submodule = False - - @classmethod - def main(cls, argv=None): - if argv is None: - argv = sys.argv - - config = cls.parse_config() - config.update(cls.parse_command_line(argv)) - - auto_use = config.pop('auto_use', False) - bootstrapper = cls(**config) - - if auto_use: - # Run the bootstrapper, otherwise the setup.py is using the old - # use_astropy_helpers() interface, in which case it will run the - # bootstrapper manually after reconfiguring it. - bootstrapper.run() - - return bootstrapper - - @classmethod - def parse_config(cls): - if not os.path.exists('setup.cfg'): - return {} - - cfg = ConfigParser() - - try: - cfg.read('setup.cfg') - except Exception as e: - if DEBUG: - raise - - log.error( - "Error reading setup.cfg: {0!r}\n{1} will not be " - "automatically bootstrapped and package installation may fail." - "\n{2}".format(e, PACKAGE_NAME, _err_help_msg)) - return {} - - if not cfg.has_section('ah_bootstrap'): - return {} - - config = {} - - for option, type_ in CFG_OPTIONS: - if not cfg.has_option('ah_bootstrap', option): - continue - - if type_ is bool: - value = cfg.getboolean('ah_bootstrap', option) - else: - value = cfg.get('ah_bootstrap', option) - - config[option] = value - - return config - - @classmethod - def parse_command_line(cls, argv=None): - if argv is None: - argv = sys.argv - - config = {} - - # For now we just pop recognized ah_bootstrap options out of the - # arg list. This is imperfect; in the unlikely case that a setup.py - # custom command or even custom Distribution class defines an argument - # of the same name then we will break that. However there's a catch22 - # here that we can't just do full argument parsing right here, because - # we don't yet know *how* to parse all possible command-line arguments. - if '--no-git' in argv: - config['use_git'] = False - argv.remove('--no-git') - - if '--offline' in argv: - config['offline'] = True - argv.remove('--offline') - - return config - - def run(self): - strategies = ['local_directory', 'local_file', 'index'] - dist = None - - # First, remove any previously imported versions of astropy_helpers; - # this is necessary for nested installs where one package's installer - # is installing another package via setuptools.sandbox.run_setup, as in - # the case of setup_requires - for key in list(sys.modules): - try: - if key == PACKAGE_NAME or key.startswith(PACKAGE_NAME + '.'): - del sys.modules[key] - except AttributeError: - # Sometimes mysterious non-string things can turn up in - # sys.modules - continue - - # Check to see if the path is a submodule - self.is_submodule = self._check_submodule() - - for strategy in strategies: - method = getattr(self, 'get_{0}_dist'.format(strategy)) - dist = method() - if dist is not None: - break - else: - raise _AHBootstrapSystemExit( - "No source found for the {0!r} package; {0} must be " - "available and importable as a prerequisite to building " - "or installing this package.".format(PACKAGE_NAME)) - - # This is a bit hacky, but if astropy_helpers was loaded from a - # directory/submodule its Distribution object gets a "precedence" of - # "DEVELOP_DIST". However, in other cases it gets a precedence of - # "EGG_DIST". However, when activing the distribution it will only be - # placed early on sys.path if it is treated as an EGG_DIST, so always - # do that - dist = dist.clone(precedence=pkg_resources.EGG_DIST) - - # Otherwise we found a version of astropy-helpers, so we're done - # Just active the found distribution on sys.path--if we did a - # download this usually happens automatically but it doesn't hurt to - # do it again - # Note: Adding the dist to the global working set also activates it - # (makes it importable on sys.path) by default. - - try: - pkg_resources.working_set.add(dist, replace=True) - except TypeError: - # Some (much) older versions of setuptools do not have the - # replace=True option here. These versions are old enough that all - # bets may be off anyways, but it's easy enough to work around just - # in case... - if dist.key in pkg_resources.working_set.by_key: - del pkg_resources.working_set.by_key[dist.key] - pkg_resources.working_set.add(dist) - - @property - def config(self): - """ - A `dict` containing the options this `_Bootstrapper` was configured - with. - """ - - return dict((optname, getattr(self, optname)) - for optname, _ in CFG_OPTIONS if hasattr(self, optname)) - - def get_local_directory_dist(self): - """ - Handle importing a vendored package from a subdirectory of the source - distribution. - """ - - if not os.path.isdir(self.path): - return - - log.info('Attempting to import astropy_helpers from {0} {1!r}'.format( - 'submodule' if self.is_submodule else 'directory', - self.path)) - - dist = self._directory_import() - - if dist is None: - log.warn( - 'The requested path {0!r} for importing {1} does not ' - 'exist, or does not contain a copy of the {1} ' - 'package.'.format(self.path, PACKAGE_NAME)) - elif self.auto_upgrade and not self.is_submodule: - # A version of astropy-helpers was found on the available path, but - # check to see if a bugfix release is available on PyPI - upgrade = self._do_upgrade(dist) - if upgrade is not None: - dist = upgrade - - return dist - - def get_local_file_dist(self): - """ - Handle importing from a source archive; this also uses setup_requires - but points easy_install directly to the source archive. - """ - - if not os.path.isfile(self.path): - return - - log.info('Attempting to unpack and import astropy_helpers from ' - '{0!r}'.format(self.path)) - - try: - dist = self._do_download(find_links=[self.path]) - except Exception as e: - if DEBUG: - raise - - log.warn( - 'Failed to import {0} from the specified archive {1!r}: ' - '{2}'.format(PACKAGE_NAME, self.path, str(e))) - dist = None - - if dist is not None and self.auto_upgrade: - # A version of astropy-helpers was found on the available path, but - # check to see if a bugfix release is available on PyPI - upgrade = self._do_upgrade(dist) - if upgrade is not None: - dist = upgrade - - return dist - - def get_index_dist(self): - if not self.download: - log.warn('Downloading {0!r} disabled.'.format(DIST_NAME)) - return None - - log.warn( - "Downloading {0!r}; run setup.py with the --offline option to " - "force offline installation.".format(DIST_NAME)) - - try: - dist = self._do_download() - except Exception as e: - if DEBUG: - raise - log.warn( - 'Failed to download and/or install {0!r} from {1!r}:\n' - '{2}'.format(DIST_NAME, self.index_url, str(e))) - dist = None - - # No need to run auto-upgrade here since we've already presumably - # gotten the most up-to-date version from the package index - return dist - - def _directory_import(self): - """ - Import astropy_helpers from the given path, which will be added to - sys.path. - - Must return True if the import succeeded, and False otherwise. - """ - - # Return True on success, False on failure but download is allowed, and - # otherwise raise SystemExit - path = os.path.abspath(self.path) - - # Use an empty WorkingSet rather than the man - # pkg_resources.working_set, since on older versions of setuptools this - # will invoke a VersionConflict when trying to install an upgrade - ws = pkg_resources.WorkingSet([]) - ws.add_entry(path) - dist = ws.by_key.get(DIST_NAME) - - if dist is None: - # We didn't find an egg-info/dist-info in the given path, but if a - # setup.py exists we can generate it - setup_py = os.path.join(path, 'setup.py') - if os.path.isfile(setup_py): - with _silence(): - run_setup(os.path.join(path, 'setup.py'), - ['egg_info']) - - for dist in pkg_resources.find_distributions(path, True): - # There should be only one... - return dist - - return dist - - def _do_download(self, version='', find_links=None): - if find_links: - allow_hosts = '' - index_url = None - else: - allow_hosts = None - index_url = self.index_url - - # Annoyingly, setuptools will not handle other arguments to - # Distribution (such as options) before handling setup_requires, so it - # is not straightforward to programmatically augment the arguments which - # are passed to easy_install - class _Distribution(Distribution): - def get_option_dict(self, command_name): - opts = Distribution.get_option_dict(self, command_name) - if command_name == 'easy_install': - if find_links is not None: - opts['find_links'] = ('setup script', find_links) - if index_url is not None: - opts['index_url'] = ('setup script', index_url) - if allow_hosts is not None: - opts['allow_hosts'] = ('setup script', allow_hosts) - return opts - - if version: - req = '{0}=={1}'.format(DIST_NAME, version) - else: - req = DIST_NAME - - attrs = {'setup_requires': [req]} - - try: - if DEBUG: - _Distribution(attrs=attrs) - else: - with _silence(): - _Distribution(attrs=attrs) - - # If the setup_requires succeeded it will have added the new dist to - # the main working_set - return pkg_resources.working_set.by_key.get(DIST_NAME) - except Exception as e: - if DEBUG: - raise - - msg = 'Error retrieving {0} from {1}:\n{2}' - if find_links: - source = find_links[0] - elif index_url != INDEX_URL: - source = index_url - else: - source = 'PyPI' - - raise Exception(msg.format(DIST_NAME, source, repr(e))) - - def _do_upgrade(self, dist): - # Build up a requirement for a higher bugfix release but a lower minor - # release (so API compatibility is guaranteed) - next_version = _next_version(dist.parsed_version) - - req = pkg_resources.Requirement.parse( - '{0}>{1},<{2}'.format(DIST_NAME, dist.version, next_version)) - - package_index = PackageIndex(index_url=self.index_url) - - upgrade = package_index.obtain(req) - - if upgrade is not None: - return self._do_download(version=upgrade.version) - - def _check_submodule(self): - """ - Check if the given path is a git submodule. - - See the docstrings for ``_check_submodule_using_git`` and - ``_check_submodule_no_git`` for further details. - """ - - if (self.path is None or - (os.path.exists(self.path) and not os.path.isdir(self.path))): - return False - - if self.use_git: - return self._check_submodule_using_git() - else: - return self._check_submodule_no_git() - - def _check_submodule_using_git(self): - """ - Check if the given path is a git submodule. If so, attempt to initialize - and/or update the submodule if needed. - - This function makes calls to the ``git`` command in subprocesses. The - ``_check_submodule_no_git`` option uses pure Python to check if the given - path looks like a git submodule, but it cannot perform updates. - """ - - cmd = ['git', 'submodule', 'status', '--', self.path] - - try: - log.info('Running `{0}`; use the --no-git option to disable git ' - 'commands'.format(' '.join(cmd))) - returncode, stdout, stderr = run_cmd(cmd) - except _CommandNotFound: - # The git command simply wasn't found; this is most likely the - # case on user systems that don't have git and are simply - # trying to install the package from PyPI or a source - # distribution. Silently ignore this case and simply don't try - # to use submodules - return False - - stderr = stderr.strip() - - if returncode != 0 and stderr: - # Unfortunately the return code alone cannot be relied on, as - # earlier versions of git returned 0 even if the requested submodule - # does not exist - - # This is a warning that occurs in perl (from running git submodule) - # which only occurs with a malformatted locale setting which can - # happen sometimes on OSX. See again - # https://github.com/astropy/astropy/issues/2749 - perl_warning = ('perl: warning: Falling back to the standard locale ' - '("C").') - if not stderr.strip().endswith(perl_warning): - # Some other unknown error condition occurred - log.warn('git submodule command failed ' - 'unexpectedly:\n{0}'.format(stderr)) - return False - - # Output of `git submodule status` is as follows: - # - # 1: Status indicator: '-' for submodule is uninitialized, '+' if - # submodule is initialized but is not at the commit currently indicated - # in .gitmodules (and thus needs to be updated), or 'U' if the - # submodule is in an unstable state (i.e. has merge conflicts) - # - # 2. SHA-1 hash of the current commit of the submodule (we don't really - # need this information but it's useful for checking that the output is - # correct) - # - # 3. The output of `git describe` for the submodule's current commit - # hash (this includes for example what branches the commit is on) but - # only if the submodule is initialized. We ignore this information for - # now - _git_submodule_status_re = re.compile( - '^(?P[+-U ])(?P[0-9a-f]{40}) ' - '(?P\S+)( .*)?$') - - # The stdout should only contain one line--the status of the - # requested submodule - m = _git_submodule_status_re.match(stdout) - if m: - # Yes, the path *is* a git submodule - self._update_submodule(m.group('submodule'), m.group('status')) - return True - else: - log.warn( - 'Unexpected output from `git submodule status`:\n{0}\n' - 'Will attempt import from {1!r} regardless.'.format( - stdout, self.path)) - return False - - def _check_submodule_no_git(self): - """ - Like ``_check_submodule_using_git``, but simply parses the .gitmodules file - to determine if the supplied path is a git submodule, and does not exec any - subprocesses. - - This can only determine if a path is a submodule--it does not perform - updates, etc. This function may need to be updated if the format of the - .gitmodules file is changed between git versions. - """ - - gitmodules_path = os.path.abspath('.gitmodules') - - if not os.path.isfile(gitmodules_path): - return False - - # This is a minimal reader for gitconfig-style files. It handles a few of - # the quirks that make gitconfig files incompatible with ConfigParser-style - # files, but does not support the full gitconfig syntax (just enough - # needed to read a .gitmodules file). - gitmodules_fileobj = io.StringIO() - - # Must use io.open for cross-Python-compatible behavior wrt unicode - with io.open(gitmodules_path) as f: - for line in f: - # gitconfig files are more flexible with leading whitespace; just - # go ahead and remove it - line = line.lstrip() - - # comments can start with either # or ; - if line and line[0] in (':', ';'): - continue - - gitmodules_fileobj.write(line) - - gitmodules_fileobj.seek(0) - - cfg = RawConfigParser() - - try: - cfg.readfp(gitmodules_fileobj) - except Exception as exc: - log.warn('Malformatted .gitmodules file: {0}\n' - '{1} cannot be assumed to be a git submodule.'.format( - exc, self.path)) - return False - - for section in cfg.sections(): - if not cfg.has_option(section, 'path'): - continue - - submodule_path = cfg.get(section, 'path').rstrip(os.sep) - - if submodule_path == self.path.rstrip(os.sep): - return True - - return False - - def _update_submodule(self, submodule, status): - if status == ' ': - # The submodule is up to date; no action necessary - return - elif status == '-': - if self.offline: - raise _AHBootstrapSystemExit( - "Cannot initialize the {0} submodule in --offline mode; " - "this requires being able to clone the submodule from an " - "online repository.".format(submodule)) - cmd = ['update', '--init'] - action = 'Initializing' - elif status == '+': - cmd = ['update'] - action = 'Updating' - if self.offline: - cmd.append('--no-fetch') - elif status == 'U': - raise _AHBootstrapSystemExit( - 'Error: Submodule {0} contains unresolved merge conflicts. ' - 'Please complete or abandon any changes in the submodule so that ' - 'it is in a usable state, then try again.'.format(submodule)) - else: - log.warn('Unknown status {0!r} for git submodule {1!r}. Will ' - 'attempt to use the submodule as-is, but try to ensure ' - 'that the submodule is in a clean state and contains no ' - 'conflicts or errors.\n{2}'.format(status, submodule, - _err_help_msg)) - return - - err_msg = None - cmd = ['git', 'submodule'] + cmd + ['--', submodule] - log.warn('{0} {1} submodule with: `{2}`'.format( - action, submodule, ' '.join(cmd))) - - try: - log.info('Running `{0}`; use the --no-git option to disable git ' - 'commands'.format(' '.join(cmd))) - returncode, stdout, stderr = run_cmd(cmd) - except OSError as e: - err_msg = str(e) - else: - if returncode != 0: - err_msg = stderr - - if err_msg is not None: - log.warn('An unexpected error occurred updating the git submodule ' - '{0!r}:\n{1}\n{2}'.format(submodule, err_msg, - _err_help_msg)) - -class _CommandNotFound(OSError): - """ - An exception raised when a command run with run_cmd is not found on the - system. - """ - - -def run_cmd(cmd): - """ - Run a command in a subprocess, given as a list of command-line - arguments. - - Returns a ``(returncode, stdout, stderr)`` tuple. - """ - - try: - p = sp.Popen(cmd, stdout=sp.PIPE, stderr=sp.PIPE) - # XXX: May block if either stdout or stderr fill their buffers; - # however for the commands this is currently used for that is - # unlikely (they should have very brief output) - stdout, stderr = p.communicate() - except OSError as e: - if DEBUG: - raise - - if e.errno == errno.ENOENT: - msg = 'Command not found: `{0}`'.format(' '.join(cmd)) - raise _CommandNotFound(msg, cmd) - else: - raise _AHBootstrapSystemExit( - 'An unexpected error occurred when running the ' - '`{0}` command:\n{1}'.format(' '.join(cmd), str(e))) - - - # Can fail of the default locale is not configured properly. See - # https://github.com/astropy/astropy/issues/2749. For the purposes under - # consideration 'latin1' is an acceptable fallback. - try: - stdio_encoding = locale.getdefaultlocale()[1] or 'latin1' - except ValueError: - # Due to an OSX oddity locale.getdefaultlocale() can also crash - # depending on the user's locale/language settings. See: - # http://bugs.python.org/issue18378 - stdio_encoding = 'latin1' - - # Unlikely to fail at this point but even then let's be flexible - if not isinstance(stdout, _text_type): - stdout = stdout.decode(stdio_encoding, 'replace') - if not isinstance(stderr, _text_type): - stderr = stderr.decode(stdio_encoding, 'replace') - - return (p.returncode, stdout, stderr) - - -def _next_version(version): - """ - Given a parsed version from pkg_resources.parse_version, returns a new - version string with the next minor version. - - Examples - ======== - >>> _next_version(pkg_resources.parse_version('1.2.3')) - '1.3.0' - """ - - if hasattr(version, 'base_version'): - # New version parsing from setuptools >= 8.0 - if version.base_version: - parts = version.base_version.split('.') - else: - parts = [] - else: - parts = [] - for part in version: - if part.startswith('*'): - break - parts.append(part) - - parts = [int(p) for p in parts] - - if len(parts) < 3: - parts += [0] * (3 - len(parts)) - - major, minor, micro = parts[:3] - - return '{0}.{1}.{2}'.format(major, minor + 1, 0) - - -class _DummyFile(object): - """A noop writeable object.""" - - errors = '' # Required for Python 3.x - encoding = 'utf-8' - - def write(self, s): - pass - - def flush(self): - pass - - -@contextlib.contextmanager -def _silence(): - """A context manager that silences sys.stdout and sys.stderr.""" - - old_stdout = sys.stdout - old_stderr = sys.stderr - sys.stdout = _DummyFile() - sys.stderr = _DummyFile() - exception_occurred = False - try: - yield - except: - exception_occurred = True - # Go ahead and clean up so that exception handling can work normally - sys.stdout = old_stdout - sys.stderr = old_stderr - raise - - if not exception_occurred: - sys.stdout = old_stdout - sys.stderr = old_stderr - - -_err_help_msg = """ -If the problem persists consider installing astropy_helpers manually using pip -(`pip install astropy_helpers`) or by manually downloading the source archive, -extracting it, and installing by running `python setup.py install` from the -root of the extracted source code. -""" - - -class _AHBootstrapSystemExit(SystemExit): - def __init__(self, *args): - if not args: - msg = 'An unknown problem occurred bootstrapping astropy_helpers.' - else: - msg = args[0] - - msg += '\n' + _err_help_msg - - super(_AHBootstrapSystemExit, self).__init__(msg, *args[1:]) - - -BOOTSTRAPPER = _Bootstrapper.main() - - -def use_astropy_helpers(**kwargs): - """ - Ensure that the `astropy_helpers` module is available and is importable. - This supports automatic submodule initialization if astropy_helpers is - included in a project as a git submodule, or will download it from PyPI if - necessary. - - Parameters - ---------- - - path : str or None, optional - A filesystem path relative to the root of the project's source code - that should be added to `sys.path` so that `astropy_helpers` can be - imported from that path. - - If the path is a git submodule it will automatically be initialized - and/or updated. - - The path may also be to a ``.tar.gz`` archive of the astropy_helpers - source distribution. In this case the archive is automatically - unpacked and made temporarily available on `sys.path` as a ``.egg`` - archive. - - If `None` skip straight to downloading. - - download_if_needed : bool, optional - If the provided filesystem path is not found an attempt will be made to - download astropy_helpers from PyPI. It will then be made temporarily - available on `sys.path` as a ``.egg`` archive (using the - ``setup_requires`` feature of setuptools. If the ``--offline`` option - is given at the command line the value of this argument is overridden - to `False`. - - index_url : str, optional - If provided, use a different URL for the Python package index than the - main PyPI server. - - use_git : bool, optional - If `False` no git commands will be used--this effectively disables - support for git submodules. If the ``--no-git`` option is given at the - command line the value of this argument is overridden to `False`. - - auto_upgrade : bool, optional - By default, when installing a package from a non-development source - distribution ah_boostrap will try to automatically check for patch - releases to astropy-helpers on PyPI and use the patched version over - any bundled versions. Setting this to `False` will disable that - functionality. If the ``--offline`` option is given at the command line - the value of this argument is overridden to `False`. - - offline : bool, optional - If `False` disable all actions that require an internet connection, - including downloading packages from the package index and fetching - updates to any git submodule. Defaults to `True`. - """ - - global BOOTSTRAPPER - - config = BOOTSTRAPPER.config - config.update(**kwargs) - - # Create a new bootstrapper with the updated configuration and run it - BOOTSTRAPPER = _Bootstrapper(**config) - BOOTSTRAPPER.run() diff --git a/astropy_helpers b/astropy_helpers deleted file mode 160000 index 6a6d403..0000000 --- a/astropy_helpers +++ /dev/null @@ -1 +0,0 @@ -Subproject commit 6a6d40322d30739581503d5c4ab7b5264d110f81 diff --git a/ez_setup.py b/ez_setup.py deleted file mode 100644 index 800c31e..0000000 --- a/ez_setup.py +++ /dev/null @@ -1,414 +0,0 @@ -#!/usr/bin/env python - -""" -Setuptools bootstrapping installer. - -Maintained at https://github.com/pypa/setuptools/tree/bootstrap. - -Run this script to install or upgrade setuptools. - -This method is DEPRECATED. Check https://github.com/pypa/setuptools/issues/581 for more details. -""" - -import os -import shutil -import sys -import tempfile -import zipfile -import optparse -import subprocess -import platform -import textwrap -import contextlib - -from distutils import log - -try: - from urllib.request import urlopen -except ImportError: - from urllib2 import urlopen - -try: - from site import USER_SITE -except ImportError: - USER_SITE = None - -# 33.1.1 is the last version that supports setuptools self upgrade/installation. -DEFAULT_VERSION = "33.1.1" -DEFAULT_URL = "https://pypi.io/packages/source/s/setuptools/" -DEFAULT_SAVE_DIR = os.curdir -DEFAULT_DEPRECATION_MESSAGE = "ez_setup.py is deprecated and when using it setuptools will be pinned to {0} since it's the last version that supports setuptools self upgrade/installation, check https://github.com/pypa/setuptools/issues/581 for more info; use pip to install setuptools" - -MEANINGFUL_INVALID_ZIP_ERR_MSG = 'Maybe {0} is corrupted, delete it and try again.' - -log.warn(DEFAULT_DEPRECATION_MESSAGE.format(DEFAULT_VERSION)) - - -def _python_cmd(*args): - """ - Execute a command. - - Return True if the command succeeded. - """ - args = (sys.executable,) + args - return subprocess.call(args) == 0 - - -def _install(archive_filename, install_args=()): - """Install Setuptools.""" - with archive_context(archive_filename): - # installing - log.warn('Installing Setuptools') - if not _python_cmd('setup.py', 'install', *install_args): - log.warn('Something went wrong during the installation.') - log.warn('See the error message above.') - # exitcode will be 2 - return 2 - - -def _build_egg(egg, archive_filename, to_dir): - """Build Setuptools egg.""" - with archive_context(archive_filename): - # building an egg - log.warn('Building a Setuptools egg in %s', to_dir) - _python_cmd('setup.py', '-q', 'bdist_egg', '--dist-dir', to_dir) - # returning the result - log.warn(egg) - if not os.path.exists(egg): - raise IOError('Could not build the egg.') - - -class ContextualZipFile(zipfile.ZipFile): - - """Supplement ZipFile class to support context manager for Python 2.6.""" - - def __enter__(self): - return self - - def __exit__(self, type, value, traceback): - self.close() - - def __new__(cls, *args, **kwargs): - """Construct a ZipFile or ContextualZipFile as appropriate.""" - if hasattr(zipfile.ZipFile, '__exit__'): - return zipfile.ZipFile(*args, **kwargs) - return super(ContextualZipFile, cls).__new__(cls) - - -@contextlib.contextmanager -def archive_context(filename): - """ - Unzip filename to a temporary directory, set to the cwd. - - The unzipped target is cleaned up after. - """ - tmpdir = tempfile.mkdtemp() - log.warn('Extracting in %s', tmpdir) - old_wd = os.getcwd() - try: - os.chdir(tmpdir) - try: - with ContextualZipFile(filename) as archive: - archive.extractall() - except zipfile.BadZipfile as err: - if not err.args: - err.args = ('', ) - err.args = err.args + ( - MEANINGFUL_INVALID_ZIP_ERR_MSG.format(filename), - ) - raise - - # going in the directory - subdir = os.path.join(tmpdir, os.listdir(tmpdir)[0]) - os.chdir(subdir) - log.warn('Now working in %s', subdir) - yield - - finally: - os.chdir(old_wd) - shutil.rmtree(tmpdir) - - -def _do_download(version, download_base, to_dir, download_delay): - """Download Setuptools.""" - py_desig = 'py{sys.version_info[0]}.{sys.version_info[1]}'.format(sys=sys) - tp = 'setuptools-{version}-{py_desig}.egg' - egg = os.path.join(to_dir, tp.format(**locals())) - if not os.path.exists(egg): - archive = download_setuptools(version, download_base, - to_dir, download_delay) - _build_egg(egg, archive, to_dir) - sys.path.insert(0, egg) - - # Remove previously-imported pkg_resources if present (see - # https://bitbucket.org/pypa/setuptools/pull-request/7/ for details). - if 'pkg_resources' in sys.modules: - _unload_pkg_resources() - - import setuptools - setuptools.bootstrap_install_from = egg - - -def use_setuptools( - version=DEFAULT_VERSION, download_base=DEFAULT_URL, - to_dir=DEFAULT_SAVE_DIR, download_delay=15): - """ - Ensure that a setuptools version is installed. - - Return None. Raise SystemExit if the requested version - or later cannot be installed. - """ - to_dir = os.path.abspath(to_dir) - - # prior to importing, capture the module state for - # representative modules. - rep_modules = 'pkg_resources', 'setuptools' - imported = set(sys.modules).intersection(rep_modules) - - try: - import pkg_resources - pkg_resources.require("setuptools>=" + version) - # a suitable version is already installed - return - except ImportError: - # pkg_resources not available; setuptools is not installed; download - pass - except pkg_resources.DistributionNotFound: - # no version of setuptools was found; allow download - pass - except pkg_resources.VersionConflict as VC_err: - if imported: - _conflict_bail(VC_err, version) - - # otherwise, unload pkg_resources to allow the downloaded version to - # take precedence. - del pkg_resources - _unload_pkg_resources() - - return _do_download(version, download_base, to_dir, download_delay) - - -def _conflict_bail(VC_err, version): - """ - Setuptools was imported prior to invocation, so it is - unsafe to unload it. Bail out. - """ - conflict_tmpl = textwrap.dedent(""" - The required version of setuptools (>={version}) is not available, - and can't be installed while this script is running. Please - install a more recent version first, using - 'easy_install -U setuptools'. - - (Currently using {VC_err.args[0]!r}) - """) - msg = conflict_tmpl.format(**locals()) - sys.stderr.write(msg) - sys.exit(2) - - -def _unload_pkg_resources(): - sys.meta_path = [ - importer - for importer in sys.meta_path - if importer.__class__.__module__ != 'pkg_resources.extern' - ] - del_modules = [ - name for name in sys.modules - if name.startswith('pkg_resources') - ] - for mod_name in del_modules: - del sys.modules[mod_name] - - -def _clean_check(cmd, target): - """ - Run the command to download target. - - If the command fails, clean up before re-raising the error. - """ - try: - subprocess.check_call(cmd) - except subprocess.CalledProcessError: - if os.access(target, os.F_OK): - os.unlink(target) - raise - - -def download_file_powershell(url, target): - """ - Download the file at url to target using Powershell. - - Powershell will validate trust. - Raise an exception if the command cannot complete. - """ - target = os.path.abspath(target) - ps_cmd = ( - "[System.Net.WebRequest]::DefaultWebProxy.Credentials = " - "[System.Net.CredentialCache]::DefaultCredentials; " - '(new-object System.Net.WebClient).DownloadFile("%(url)s", "%(target)s")' - % locals() - ) - cmd = [ - 'powershell', - '-Command', - ps_cmd, - ] - _clean_check(cmd, target) - - -def has_powershell(): - """Determine if Powershell is available.""" - if platform.system() != 'Windows': - return False - cmd = ['powershell', '-Command', 'echo test'] - with open(os.path.devnull, 'wb') as devnull: - try: - subprocess.check_call(cmd, stdout=devnull, stderr=devnull) - except Exception: - return False - return True -download_file_powershell.viable = has_powershell - - -def download_file_curl(url, target): - cmd = ['curl', url, '--location', '--silent', '--output', target] - _clean_check(cmd, target) - - -def has_curl(): - cmd = ['curl', '--version'] - with open(os.path.devnull, 'wb') as devnull: - try: - subprocess.check_call(cmd, stdout=devnull, stderr=devnull) - except Exception: - return False - return True -download_file_curl.viable = has_curl - - -def download_file_wget(url, target): - cmd = ['wget', url, '--quiet', '--output-document', target] - _clean_check(cmd, target) - - -def has_wget(): - cmd = ['wget', '--version'] - with open(os.path.devnull, 'wb') as devnull: - try: - subprocess.check_call(cmd, stdout=devnull, stderr=devnull) - except Exception: - return False - return True -download_file_wget.viable = has_wget - - -def download_file_insecure(url, target): - """Use Python to download the file, without connection authentication.""" - src = urlopen(url) - try: - # Read all the data in one block. - data = src.read() - finally: - src.close() - - # Write all the data in one block to avoid creating a partial file. - with open(target, "wb") as dst: - dst.write(data) -download_file_insecure.viable = lambda: True - - -def get_best_downloader(): - downloaders = ( - download_file_powershell, - download_file_curl, - download_file_wget, - download_file_insecure, - ) - viable_downloaders = (dl for dl in downloaders if dl.viable()) - return next(viable_downloaders, None) - - -def download_setuptools( - version=DEFAULT_VERSION, download_base=DEFAULT_URL, - to_dir=DEFAULT_SAVE_DIR, delay=15, - downloader_factory=get_best_downloader): - """ - Download setuptools from a specified location and return its filename. - - `version` should be a valid setuptools version number that is available - as an sdist for download under the `download_base` URL (which should end - with a '/'). `to_dir` is the directory where the egg will be downloaded. - `delay` is the number of seconds to pause before an actual download - attempt. - - ``downloader_factory`` should be a function taking no arguments and - returning a function for downloading a URL to a target. - """ - # making sure we use the absolute path - to_dir = os.path.abspath(to_dir) - zip_name = "setuptools-%s.zip" % version - url = download_base + zip_name - saveto = os.path.join(to_dir, zip_name) - if not os.path.exists(saveto): # Avoid repeated downloads - log.warn("Downloading %s", url) - downloader = downloader_factory() - downloader(url, saveto) - return os.path.realpath(saveto) - - -def _build_install_args(options): - """ - Build the arguments to 'python setup.py install' on the setuptools package. - - Returns list of command line arguments. - """ - return ['--user'] if options.user_install else [] - - -def _parse_args(): - """Parse the command line for options.""" - parser = optparse.OptionParser() - parser.add_option( - '--user', dest='user_install', action='store_true', default=False, - help='install in user site package') - parser.add_option( - '--download-base', dest='download_base', metavar="URL", - default=DEFAULT_URL, - help='alternative URL from where to download the setuptools package') - parser.add_option( - '--insecure', dest='downloader_factory', action='store_const', - const=lambda: download_file_insecure, default=get_best_downloader, - help='Use internal, non-validating downloader' - ) - parser.add_option( - '--version', help="Specify which version to download", - default=DEFAULT_VERSION, - ) - parser.add_option( - '--to-dir', - help="Directory to save (and re-use) package", - default=DEFAULT_SAVE_DIR, - ) - options, args = parser.parse_args() - # positional arguments are ignored - return options - - -def _download_args(options): - """Return args for download_setuptools function from cmdline args.""" - return dict( - version=options.version, - download_base=options.download_base, - downloader_factory=options.downloader_factory, - to_dir=options.to_dir, - ) - - -def main(): - """Install or upgrade setuptools and EasyInstall.""" - options = _parse_args() - archive = download_setuptools(**_download_args(options)) - return _install(archive, _build_install_args(options)) - -if __name__ == '__main__': - sys.exit(main()) diff --git a/readthedocs.yml b/readthedocs.yml deleted file mode 100644 index a518486..0000000 --- a/readthedocs.yml +++ /dev/null @@ -1,9 +0,0 @@ -conda: - file: .rtd-environment.yml - -build: - image: latest - -python: - version: 3.6 - setup_py_install: true From f256e740dcea17df44d02bea33c15b645d3063b5 Mon Sep 17 00:00:00 2001 From: Lee Spitler Date: Sun, 30 Aug 2020 17:14:24 +1000 Subject: [PATCH 17/26] i see why no:warnings is needed! --- setup.cfg | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/setup.cfg b/setup.cfg index e2eb8f9..c921ed2 100644 --- a/setup.cfg +++ b/setup.cfg @@ -37,7 +37,7 @@ docs = sphinx-astropy [options.package_data] -gunagala = +gunagala = data/*.* data/performance_data/* data/sky_data/* @@ -50,7 +50,7 @@ doctest_plus = enabled text_file_format = rst addopts = --doctest-rst -# -p no:warnings + -p no:warnings [coverage:run] omit = @@ -116,7 +116,7 @@ select = E113 E901 E902 -exclude = +exclude = extern sphinx - *parsetab.py \ No newline at end of file + *parsetab.py From 2d5118934e66dc0c20343811ce11e70610b2d236 Mon Sep 17 00:00:00 2001 From: Lee Spitler Date: Sun, 30 Aug 2020 17:19:30 +1000 Subject: [PATCH 18/26] skip tests so others can help debug --- gunagala/tests/test_imager.py | 2 +- gunagala/tests/test_psf.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/gunagala/tests/test_imager.py b/gunagala/tests/test_imager.py index f5ba6d9..3655cfd 100644 --- a/gunagala/tests/test_imager.py +++ b/gunagala/tests/test_imager.py @@ -611,7 +611,7 @@ def test_point_sat_exp(imager, filter_name): assert imager.point_source_saturation_mag(sub_exp_time=sat_exp, filter_name=filter_name) == b - +@pytest.mark.xfail def test_sequence(imager, filter_name): brightest = 10 * u.ABmag ratio = 2.0 diff --git a/gunagala/tests/test_psf.py b/gunagala/tests/test_psf.py index e8085a9..4e64a2a 100644 --- a/gunagala/tests/test_psf.py +++ b/gunagala/tests/test_psf.py @@ -97,7 +97,7 @@ def test_pixel_scale(psf, t_pixel_scale, pixel_scale): assert psf.pixel_scale == t_pixel_scale * u.arcsecond / u.pixel psf.pixel_scale = pixel_scale * u.arcsecond / u.pixel - +@pytest.mark.xfail @pytest.mark.parametrize("psf, expected_n_pix, pixel_scale", [ (make_moffat(), 4.25754067000986, 2.85), (make_pixellated(), 21.06994544, (2 / 3))], From ba3d081c911b99b6c8cd7c008f5865a25cbb69cd Mon Sep 17 00:00:00 2001 From: Lee Spitler Date: Sun, 30 Aug 2020 17:32:44 +1000 Subject: [PATCH 19/26] revert small doc change after build --- docs/gunagala/index.rst | 174 --------------------------------------- docs/index.rst | 178 ++++++++++++++++++++++++++++++++++++++-- 2 files changed, 169 insertions(+), 183 deletions(-) delete mode 100644 docs/gunagala/index.rst diff --git a/docs/gunagala/index.rst b/docs/gunagala/index.rst deleted file mode 100644 index ce76b44..0000000 --- a/docs/gunagala/index.rst +++ /dev/null @@ -1,174 +0,0 @@ -**************** -Gunagala -**************** - -Introduction -============ - -Gungala is a Python package for modelling the performance of astronomical instruments, including -SNR/ETC/sensitivity limit calculations and generation of simulated data. - -This package is not intended for rigorous, end-to-end simulations of telescope and instrument -systems. Instead gunagala implements parameterised models of instrument components in order to -enable rapid, efficient evaluation of instrument performance. Anticipated uses include exposure time -calculators, selection of commercial off the shelf components and exploration of the design -parameter space for custom components. - -Gunagala includes a library of performance parameters for a number of existing commercial off the -shelf instrument components (e.g. CCD cameras, optical filters, telescopes and camera lenses) and -the user can easily add new/custom components either through YAML based config files or -programmatically in Python. - -Gunagala is named as a gesture of respect to the traditional custodians of the land on which Siding -Spring Observatory sits, the Kamilaroi people of northern New South Wales. Gunagala is 'sky' in -the Kamilaroi/Gamilaraay language -(ref: `www.dnathan.com `_). Aboriginal -Australians have studied the night skies above Australia for at least 50000 years. To learn more -about Aboriginal astronomy please visit http://www.aboriginalastronomy.com.au/. - - -Installation -============ - -Installing with pip -------------------- -.. highlight:: console - -To install using the Python package manager `pip` use the following command:: - - $ pip install git+https://github.com/AstroHuntsman/gunagala.git - -Alternatively to install in 'editable mode' use:: - - $ pip install -e git+https://github.com/AstroHuntsman/gunagala.git - -Depending on the configuration of your system you may want to use `pip`'s ``--user`` or ``--root`` -options to change the install location. See the pip documentation for details. - -`Pip` will automatically install the Python packages required by Gunagala (`numpy`, `scipy`, -`astropy`, `PyYAML`, `matplotlib` and their dependencies) if they are not already installed. If you -want to install specific versions of the required packages from other sources do this before -installing Gunagala. - -Installing from source ----------------------- - -The project source is in a GitHub repository at https://github.com/AstroHuntsman/gunagala. To -install using git on the command line:: - - $ cd ~/Build - $ git clone https://github.com/AstroHuntsman/gunagala.git - $ cd gunagala - $ python setup.py install - -Alternatively if you expect to make changes to the Gunagala code install with the ``develop`` -command instead:: - - $ python setup.py develop - -Setuptools will automatically install the Python packages required by Gunagala (`numpy`, `scipy`, -`astropy`, `PyYAML`, `matplotlib` and their dependencies) if they are not already installed. If you -want to install specific versions of the required packages from other sources do this before -installing Gunagala. - -Running the test suite ----------------------- - -After installing Gunagala it is recommended that you run the suite of units tests. This can be done -at the command line using:: - - $ python setup.py test - -.. highlight:: python3 - -or from within a Python interpreter with:: - - >> import gunagala - >> gunagala.test() - -Examples -======== - -The Gunagala package includes several examples in the form of `Jupyter `_ -notebooks. These can be found in the `gungala/examples` directory after installing Gunagala, or they -can be viewed directly in the GitHub repository by going to -https://github.com/AstroHuntsman/gunagala/tree/master/examples and clicking on the ``.ipynb`` files. - -Contributing -============ - -Please submit bug reports or feature requests in the form of GitHub Issues at -https://github.com/AstroHuntsman/gunagala/issues. For code contributions please fork and clone the -repository, create a feature branch and submit a Pull Request. We recommend the -`astropy Developer Documentation `_ -for a description of suitable workflows. - -Changelog -========= - -.. include:: ../CHANGES.rst - -Reference/API -============= - -.. automodapi:: gunagala - :no-main-docstr: - -.. automodapi:: gunagala.imager - :skip: ensure_unit - :skip: load_config - :skip: Filter - :skip: Optic - :skip: Camera - :skip: PSF - :skip: Sky - :skip: Simple - :skip: MoffatPSF - :skip: ZodiacalLight - :skip: WCS - :skip: SkyCoord - :skip: CCDData - :skip: interp1d - :skip: InvalidTransformError - :no-inheritance-diagram: - -.. automodapi:: gunagala.optic - :skip: Table - :skip: ensure_unit - :skip: get_table_data - :skip: array_sequence_equal - :no-inheritance-diagram: - -.. automodapi:: gunagala.optical_filter - :skip: Table - :skip: interp1d - :skip: brentq - :skip: ensure_unit - :skip: get_table_data - :skip: minimize_scalar - :skip: eval_chebyt - :no-inheritance-diagram: - -.. automodapi:: gunagala.camera - :skip: Table - :skip: ensure_unit - :no-inheritance-diagram: - -.. automodapi:: gunagala.psf - :skip: discretize_model - :skip: Fittable2DModel - :skip: Moffat2D - -.. automodapi:: gunagala.sky - :skip: interp1d - :skip: RectSphereBivariateSpline - :skip: SmoothBivariateSpline - :skip: SkyCoord - :skip: GeocentricTrueEcliptic - :skip: get_sun - :skip: Angle - :skip: Time - :skip: ensure_unit - -.. automodapi:: gunagala.utils - :skip: get_pkg_data_filename diff --git a/docs/index.rst b/docs/index.rst index cd4866c..5185657 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -1,14 +1,174 @@ -Documentation +**************** +Gunagala +**************** + +Introduction +============ + +Gungala is a Python package for modelling the performance of astronomical instruments, including +SNR/ETC/sensitivity limit calculations and generation of simulated data. + +This package is not intended for rigorous, end-to-end simulations of telescope and instrument +systems. Instead gunagala implements parameterised models of instrument components in order toa +enable rapid, efficient evaluation of instrument performance. Anticipated uses include exposure time +calculators, selection of commercial off the shelf components and exploration of the design +parameter space for custom components. + +Gunagala includes a library of performance parameters for a number of existing commercial off the +shelf instrument components (e.g. CCD cameras, optical filters, telescopes and camera lenses) and +the user can easily add new/custom components either through YAML based config files or +programmatically in Python. + +Gunagala is named as a gesture of respect to the traditional custodians of the land on which Siding +Spring Observatory sits, the Kamilaroi people of northern New South Wales. Gunagala is 'sky' in +the Kamilaroi/Gamilaraay language +(ref: `www.dnathan.com `_). Aboriginal +Australians have studied the night skies above Australia for at least 50000 years. To learn more +about Aboriginal astronomy please visit http://www.aboriginalastronomy.com.au/. + + +Installation +============ + +Installing with pip +------------------- +.. highlight:: console + +To install using the Python package manager `pip` use the following command:: + + $ pip install git+https://github.com/AstroHuntsman/gunagala.git + +Alternatively to install in 'editable mode' use:: + + $ pip install -e git+https://github.com/AstroHuntsman/gunagala.git + +Depending on the configuration of your system you may want to use `pip`'s ``--user`` or ``--root`` +options to change the install location. See the pip documentation for details. + +`Pip` will automatically install the Python packages required by Gunagala (`numpy`, `scipy`, +`astropy`, `PyYAML`, `matplotlib` and their dependencies) if they are not already installed. If you +want to install specific versions of the required packages from other sources do this before +installing Gunagala. + +Installing from source +---------------------- + +The project source is in a GitHub repository at https://github.com/AstroHuntsman/gunagala. To +install using git on the command line:: + + $ cd ~/Build + $ git clone https://github.com/AstroHuntsman/gunagala.git + $ cd gunagala + $ python setup.py install + +Alternatively if you expect to make changes to the Gunagala code install with the ``develop`` +command instead:: + + $ python setup.py develop + +Setuptools will automatically install the Python packages required by Gunagala (`numpy`, `scipy`, +`astropy`, `PyYAML`, `matplotlib` and their dependencies) if they are not already installed. If you +want to install specific versions of the required packages from other sources do this before +installing Gunagala. + +Running the test suite +---------------------- + +After installing Gunagala it is recommended that you run the suite of units tests. This can be done +at the command line using:: + + $ python setup.py test + +.. highlight:: python3 + +or from within a Python interpreter with:: + + >> import gunagala + >> gunagala.test() + +Examples +======== + +The Gunagala package includes several examples in the form of `Jupyter `_ +notebooks. These can be found in the `gungala/examples` directory after installing Gunagala, or they +can be viewed directly in the GitHub repository by going to +https://github.com/AstroHuntsman/gunagala/tree/master/examples and clicking on the ``.ipynb`` files. + +Contributing +============ + +Please submit bug reports or feature requests in the form of GitHub Issues at +https://github.com/AstroHuntsman/gunagala/issues. For code contributions please fork and clone the +repository, create a feature branch and submit a Pull Request. We recommend the +`astropy Developer Documentation `_ +for a description of suitable workflows. + +Changelog +========= + +.. include:: ../CHANGES.rst + +Reference/API ============= -This is the documentation for gunagala. +.. automodapi:: gunagala + :no-main-docstr: + +.. automodapi:: gunagala.imager + :skip: ensure_unit + :skip: load_config + :skip: Filter + :skip: Optic + :skip: Camera + :skip: PSF + :skip: Sky + :skip: Simple + :skip: MoffatPSF + :skip: ZodiacalLight + :skip: WCS + :skip: SkyCoord + :skip: CCDData + :skip: interp1d + :skip: InvalidTransformError + :no-inheritance-diagram: + +.. automodapi:: gunagala.optic + :skip: Table + :skip: ensure_unit + :skip: get_table_data + :skip: array_sequence_equal + :no-inheritance-diagram: + +.. automodapi:: gunagala.optical_filter + :skip: Table + :skip: interp1d + :skip: brentq + :skip: ensure_unit + :skip: get_table_data + :skip: minimize_scalar + :skip: eval_chebyt + :no-inheritance-diagram: + +.. automodapi:: gunagala.camera + :skip: Table + :skip: ensure_unit + :no-inheritance-diagram: -.. toctree:: - :maxdepth: 2 +.. automodapi:: gunagala.psf + :skip: discretize_model + :skip: Fittable2DModel + :skip: Moffat2D - gunagala/index.rst +.. automodapi:: gunagala.sky + :skip: interp1d + :skip: RectSphereBivariateSpline + :skip: SmoothBivariateSpline + :skip: SkyCoord + :skip: GeocentricTrueEcliptic + :skip: get_sun + :skip: Angle + :skip: Time + :skip: ensure_unit -.. note:: The layout of this directory is simply a suggestion. To follow - traditional practice, do *not* edit this page, but instead place - all documentation for the package inside ``gunagala/``. - You can follow this practice or choose your own layout. +.. automodapi:: gunagala.utils + :skip: get_pkg_data_filename From d7a7ad7b309650b4e1de9644ae01755c2e0ef38d Mon Sep 17 00:00:00 2001 From: Lee Spitler Date: Sun, 30 Aug 2020 17:41:12 +1000 Subject: [PATCH 20/26] update test command --- docs/index.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/index.rst b/docs/index.rst index 5185657..1de84cb 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -75,9 +75,9 @@ Running the test suite ---------------------- After installing Gunagala it is recommended that you run the suite of units tests. This can be done -at the command line using:: +at the command line using the `tox` automation command (install via `pip install tox`):: - $ python setup.py test + $ tox -e test .. highlight:: python3 From 3300edf15eb49229f0b88ace7c5423e0803aeca2 Mon Sep 17 00:00:00 2001 From: Lee Spitler Date: Sun, 30 Aug 2020 17:42:14 +1000 Subject: [PATCH 21/26] small doc fix --- docs/index.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/index.rst b/docs/index.rst index 1de84cb..8eb94b2 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -75,7 +75,7 @@ Running the test suite ---------------------- After installing Gunagala it is recommended that you run the suite of units tests. This can be done -at the command line using the `tox` automation command (install via `pip install tox`):: +at the command line using the `tox` automation command (install via ``pip install tox``):: $ tox -e test From c36bc12dd8c4bc8a033691d5096310d5ca48f59c Mon Sep 17 00:00:00 2001 From: Lee Spitler Date: Tue, 1 Sep 2020 22:09:07 +1000 Subject: [PATCH 22/26] docstring edit to trigger travis? --- docs/index.rst | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/docs/index.rst b/docs/index.rst index 8eb94b2..5b8e962 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -101,7 +101,8 @@ Please submit bug reports or feature requests in the form of GitHub Issues at https://github.com/AstroHuntsman/gunagala/issues. For code contributions please fork and clone the repository, create a feature branch and submit a Pull Request. We recommend the `astropy Developer Documentation `_ -for a description of suitable workflows. +for a description of suitable workflows. Be sure to follow coding styles outlined there, which can +be checked during development with ``tox -e codestyle``. Changelog ========= From 8195c49f04f6ca59264ca380c5236f36e6d51168 Mon Sep 17 00:00:00 2001 From: Lee Spitler Date: Fri, 4 Sep 2020 08:35:36 +1000 Subject: [PATCH 23/26] require astropy >= 4.02 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index c921ed2..6c3ec11 100644 --- a/setup.cfg +++ b/setup.cfg @@ -17,7 +17,7 @@ packages = find: python_requires = >=3.6 setup_requires = setuptools_scm install_requires = - astropy + astropy>=4.02 pyYAML numpy scipy From 365dd12092dbf81c44c0934ad050bc70ce1d6a18 Mon Sep 17 00:00:00 2001 From: Lee Spitler Date: Tue, 27 Oct 2020 10:38:16 +1100 Subject: [PATCH 24/26] fix astropy version typo --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 6c3ec11..8ab53f2 100644 --- a/setup.cfg +++ b/setup.cfg @@ -17,7 +17,7 @@ packages = find: python_requires = >=3.6 setup_requires = setuptools_scm install_requires = - astropy>=4.02 + astropy>=4.0.2 pyYAML numpy scipy From acc5f73d84b32b8339b8f4d44751c1a9653beeee Mon Sep 17 00:00:00 2001 From: Lee Date: Sun, 30 Aug 2020 16:29:53 +1000 Subject: [PATCH 25/26] Revert "linspace now requires int ranges" This reverts commit 0379b39e6fc8630b69ea0f8060c796c5962967a4. --- gunagala/psf.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gunagala/psf.py b/gunagala/psf.py index 01e57f2..acbe974 100644 --- a/gunagala/psf.py +++ b/gunagala/psf.py @@ -191,15 +191,15 @@ def pixellated(self, size=(21, 21), offsets=(0.0, 0.0)): PSF wings by the edge of the image. """ size = tuple(int(s) for s in size) - if size[0] <= 0 or size[1] <= 0: + if size[0] <= 0 or size[1] <=0: raise ValueError("`size` must be > 0, got {}!".format(size)) # Update PSF centre coordinates self.x_0 = offsets[1] self.y_0 = offsets[0] - xrange = (int(-(size[1] - 1) / 2), int((size[1] + 1) / 2)) - yrange = (int(-(size[0] - 1) / 2), int((size[0] + 1) / 2)) + xrange = (-(size[1] - 1) / 2, (size[1] + 1) / 2) + yrange = (-(size[0] - 1) / 2, (size[0] + 1) / 2) return discretize_model(self, xrange, yrange, mode='oversample', factor=10) From 45ddcdaf4e0440677516f1a6867a6de730ef6519 Mon Sep 17 00:00:00 2001 From: Lee Spitler Date: Sun, 30 Aug 2020 17:19:30 +1000 Subject: [PATCH 26/26] Revert "skip tests so others can help debug" This reverts commit 2d5118934e66dc0c20343811ce11e70610b2d236. --- gunagala/tests/test_imager.py | 2 +- gunagala/tests/test_psf.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/gunagala/tests/test_imager.py b/gunagala/tests/test_imager.py index 3655cfd..f5ba6d9 100644 --- a/gunagala/tests/test_imager.py +++ b/gunagala/tests/test_imager.py @@ -611,7 +611,7 @@ def test_point_sat_exp(imager, filter_name): assert imager.point_source_saturation_mag(sub_exp_time=sat_exp, filter_name=filter_name) == b -@pytest.mark.xfail + def test_sequence(imager, filter_name): brightest = 10 * u.ABmag ratio = 2.0 diff --git a/gunagala/tests/test_psf.py b/gunagala/tests/test_psf.py index 4e64a2a..e8085a9 100644 --- a/gunagala/tests/test_psf.py +++ b/gunagala/tests/test_psf.py @@ -97,7 +97,7 @@ def test_pixel_scale(psf, t_pixel_scale, pixel_scale): assert psf.pixel_scale == t_pixel_scale * u.arcsecond / u.pixel psf.pixel_scale = pixel_scale * u.arcsecond / u.pixel -@pytest.mark.xfail + @pytest.mark.parametrize("psf, expected_n_pix, pixel_scale", [ (make_moffat(), 4.25754067000986, 2.85), (make_pixellated(), 21.06994544, (2 / 3))],