From c483abd44f8e6be59aa7b593ca26515159d2f957 Mon Sep 17 00:00:00 2001 From: Shannon Osborne Date: Fri, 12 Jul 2019 17:21:12 -0500 Subject: [PATCH 1/3] remove astropy-helpers --- .eggs/README.txt | 6 + .gitignore | 1 + .gitmodules | 4 - MANIFEST.in | 22 - ah_bootstrap.py | 975 ---------------------------- astropy_helpers | 1 - docs/conf.py | 8 +- fgscountrate/__init__.py | 17 +- fgscountrate/_astropy_init.py | 89 +-- fgscountrate/tests/setup_package.py | 11 - pyproject.toml | 2 + setup.cfg | 48 +- setup.py | 172 +---- 13 files changed, 110 insertions(+), 1246 deletions(-) create mode 100644 .eggs/README.txt delete mode 100644 ah_bootstrap.py delete mode 160000 astropy_helpers delete mode 100644 fgscountrate/tests/setup_package.py create mode 100644 pyproject.toml diff --git a/.eggs/README.txt b/.eggs/README.txt new file mode 100644 index 0000000..5d01668 --- /dev/null +++ b/.eggs/README.txt @@ -0,0 +1,6 @@ +This directory contains eggs that were downloaded by setuptools to build, test, and run plug-ins. + +This directory caches those eggs to prevent repeated downloads. + +However, it is safe to delete this directory. + diff --git a/.gitignore b/.gitignore index 55e2af0..a93055a 100644 --- a/.gitignore +++ b/.gitignore @@ -46,6 +46,7 @@ sdist develop-eggs .installed.cfg distribute-*.tar.gz +pip-wheel-metadata # Other .cache diff --git a/.gitmodules b/.gitmodules index 78f45da..e69de29 100644 --- a/.gitmodules +++ b/.gitmodules @@ -1,4 +0,0 @@ -[submodule "astropy_helpers"] - url = https://github.com/astropy/astropy-helpers.git - path = astropy_helpers - branch = refs/heads/v3.0.2 diff --git a/MANIFEST.in b/MANIFEST.in index ebe0a71..0f7968d 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -1,7 +1,6 @@ include README.rst include CHANGES.rst -include ah_bootstrap.py include setup.cfg include fgscountrate/tests/coveragerc @@ -15,25 +14,4 @@ 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/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 diff --git a/ah_bootstrap.py b/ah_bootstrap.py deleted file mode 100644 index ece5aa9..0000000 --- a/ah_bootstrap.py +++ /dev/null @@ -1,975 +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 and by default the system-installed version -of astropy-helpers will be used (however, ``ah_bootstrap.use_astropy_helpers`` -may be called manually from within the setup.py script). - -This behavior can also be controlled using the ``--auto-use`` and -``--no-auto-use`` command-line flags. For clarity, an alias for -``--no-auto-use`` is ``--use-system-astropy-helpers``, and we recommend using -the latter if needed. - -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 io -import locale -import os -import re -import subprocess as sp -import sys - -__minimum_python_version__ = (3, 5) - -if sys.version_info < __minimum_python_version__: - print("ERROR: Python {} or later is required by astropy-helpers".format( - __minimum_python_version__)) - sys.exit(1) - -try: - from ConfigParser import ConfigParser, RawConfigParser -except ImportError: - from configparser import ConfigParser, RawConfigParser - - -_str_types = (str, bytes) - - -# 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): - -# Check that setuptools 1.0 or later is present -from distutils.version import LooseVersion - -try: - import setuptools - assert LooseVersion(setuptools.__version__) >= LooseVersion('1.0') -except (ImportError, AssertionError): - print("ERROR: setuptools 1.0 or later is required by astropy-helpers") - sys.exit(1) - -# 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 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' -UPPER_VERSION_EXCLUSIVE = None - -# 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 not isinstance(path, str): - 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') - - if '--auto-use' in argv: - config['auto_use'] = True - argv.remove('--auto-use') - - if '--no-auto-use' in argv: - config['auto_use'] = False - argv.remove('--no-auto-use') - - if '--use-system-astropy-helpers' in argv: - config['auto_use'] = False - argv.remove('--use-system-astropy-helpers') - - 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): - # We use subprocess instead of run_setup from setuptools to - # avoid segmentation faults - see the following for more details: - # https://github.com/cython/cython/issues/2104 - sp.check_output([sys.executable, 'setup.py', 'egg_info'], cwd=path) - - 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: - if UPPER_VERSION_EXCLUSIVE is None: - req = DIST_NAME - else: - req = '{0}<{1}'.format(DIST_NAME, UPPER_VERSION_EXCLUSIVE) - - attrs = {'setup_requires': [req]} - - # NOTE: we need to parse the config file (e.g. setup.cfg) to make sure - # it honours the options set in the [easy_install] section, and we need - # to explicitly fetch the requirement eggs as setup_requires does not - # get honored in recent versions of setuptools: - # https://github.com/pypa/setuptools/issues/1273 - - try: - - context = _verbose if DEBUG else _silence - with context(): - dist = _Distribution(attrs=attrs) - try: - dist.parse_config_files(ignore_option_errors=True) - dist.fetch_build_eggs(req) - except TypeError: - # On older versions of setuptools, ignore_option_errors - # doesn't exist, and the above two lines are not needed - # so we can just continue - pass - - # 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, str): - stdout = stdout.decode(stdio_encoding, 'replace') - if not isinstance(stderr, str): - 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 _verbose(): - yield - -@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 ca63040..0000000 --- a/astropy_helpers +++ /dev/null @@ -1 +0,0 @@ -Subproject commit ca630405b54d40695b7bbd2824cb0f142b5811b6 diff --git a/docs/conf.py b/docs/conf.py index fe5822f..4259a53 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -125,11 +125,9 @@ def check_sphinx_version(expected_version): # |version| and |release|, also used in various other places throughout the # build documents. # -# The short X.Y version. -package = importlib.import_module(setup_cfg['package_name']) -version = package.__version__.split('-', 1)[0] -# The full version, including alpha/beta/rc tags. -release = package.__version__ +from pkg_resources import get_distribution +release = get_distribution(project).version +version = '.'.join(release.split('.')[:2]) # for example take major/minor # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. diff --git a/fgscountrate/__init__.py b/fgscountrate/__init__.py index 3196f1b..8c09087 100644 --- a/fgscountrate/__init__.py +++ b/fgscountrate/__init__.py @@ -6,9 +6,14 @@ from ._astropy_init import * # ---------------------------------------------------------------------------- -# Enforce Python version check during package import. -# This is the same check as the one at the top of setup.py import sys +from pkg_resources import get_distribution, DistributionNotFound + +try: + __version__ = get_distribution(__name__).version +except DistributionNotFound: + # package is not installed + __version__ = "unknown" __minimum_python_version__ = "3.5" @@ -18,8 +23,6 @@ class UnsupportedPythonError(Exception): if sys.version_info < tuple((int(val) for val in __minimum_python_version__.split('.'))): raise UnsupportedPythonError("fgscountrate does not support Python < {}".format(__minimum_python_version__)) -if not _ASTROPY_SETUP_: - # For egg_info test builds to pass, put package imports here. - from .fgs_countrate_core import * - from .conversions import * - from .utils import * +from .fgs_countrate_core import * +from .utils import * +from .conversions import * \ No newline at end of file diff --git a/fgscountrate/_astropy_init.py b/fgscountrate/_astropy_init.py index 5371878..cca859a 100644 --- a/fgscountrate/_astropy_init.py +++ b/fgscountrate/_astropy_init.py @@ -1,59 +1,36 @@ # Licensed under a 3-clause BSD style license - see LICENSE.rst -__all__ = ['__version__', '__githash__'] - -# 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 - builtins._ASTROPY_SETUP_ = False - -try: - from .version import version as __version__ -except ImportError: - __version__ = '' -try: - from .version import githash as __githash__ -except ImportError: - __githash__ = '' - - -if not _ASTROPY_SETUP_: # noqa - import os - from warnings import warn - from astropy.config.configuration import ( - update_default_config, - 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__)) - __all__ += ['test'] - - # add these here so we only need to cleanup the namespace at the end - config_dir = None - - if not os.environ.get('ASTROPY_SKIP_CONFIG_UPDATE', False): - config_dir = os.path.dirname(__file__) - config_template = os.path.join(config_dir, __package__ + ".cfg") - if os.path.isfile(config_template): +import os +from warnings import warn +from astropy.config.configuration import ( + update_default_config, + 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 + +if not os.environ.get('ASTROPY_SKIP_CONFIG_UPDATE', False): + config_dir = os.path.dirname(__file__) + config_template = os.path.join(config_dir, __package__ + ".cfg") + if os.path.isfile(config_template): + try: + update_default_config( + __package__, config_dir, version=__version__) + except TypeError as orig_error: try: - update_default_config( - __package__, config_dir, version=__version__) - except TypeError as orig_error: - try: - update_default_config(__package__, config_dir) - except ConfigurationDefaultMissingError as e: - wmsg = (e.args[0] + - " Cannot install default profile. If you are " - "importing from source, this is expected.") - warn(ConfigurationDefaultMissingWarning(wmsg)) - del e - except Exception: - raise orig_error + update_default_config(__package__, config_dir) + except ConfigurationDefaultMissingError as e: + wmsg = (e.args[0] + + " Cannot install default profile. If you are " + "importing from source, this is expected.") + warn(ConfigurationDefaultMissingWarning(wmsg)) + del e + except Exception: + raise orig_error diff --git a/fgscountrate/tests/setup_package.py b/fgscountrate/tests/setup_package.py deleted file mode 100644 index 118325c..0000000 --- a/fgscountrate/tests/setup_package.py +++ /dev/null @@ -1,11 +0,0 @@ -# import os - -# If this package has tests data in the tests/data directory, add them to -# the paths here, see commented example -paths = ['coveragerc', -# os.path.join('data', '*fits') - ] - -def get_package_data(): - return { - _ASTROPY_PACKAGE_NAME_ + '.tests': paths} diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..c953815 --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,2 @@ +[build-system] +requires = ["setuptools", "wheel"] \ No newline at end of file diff --git a/setup.cfg b/setup.cfg index 1775223..0483e65 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,3 +1,26 @@ +[metadata] +name = fgscountrate +package_name = fgscountrate +description = JWST FGS countrate estimation +long_description = JWST FGS countrate estimation and related functionality. +author = Space Telescope Science Institute +author_email = help@stsci.edu +license = Aura +url = http://stsci.edu +edit_on_github = False +github_project = spacetelescope/jwst-fgs-countrate +minimum_python_version = 3.5 + +[options] +packages = find: +zip_safe = False +python_requires = >=3.5 +include_package_data = True +install_requires = + pandas + numpy + requests + [build_sphinx] source-dir = docs build-dir = docs/_build @@ -18,33 +41,8 @@ norecursedirs = build docs/_build doctest_plus = enabled addopts = -p no:warnings -[ah_bootstrap] -auto_use = True - [flake8] exclude = extern,sphinx,*parsetab.py [pycodestyle] exclude = extern,sphinx,*parsetab.py - -[metadata] -package_name = fgscountrate -description = JWST FGS countrate estimation -long_description = JWST FGS countrate estimation and related functionality. -author = Space Telescope Science Institute -author_email = help@stsci.edu -license = Aura -url = http://stsci.edu -edit_on_github = False -github_project = spacetelescope/jwst-fgs-countrate -# install_requires should be formatted as a comma-separated list, e.g.: -# install_requires = astropy, scipy, matplotlib -# version should be PEP440 compatible (https://www.python.org/dev/peps/pep-0440/) -version = 0.0.dev -# Note: you will also need to change this in your package's __init__.py -minimum_python_version = 3.6 - -[entry_points] - -astropy-package-template-example = packagename.example_mod:main - diff --git a/setup.py b/setup.py index 1076d30..e9e4437 100755 --- a/setup.py +++ b/setup.py @@ -1,144 +1,36 @@ #!/usr/bin/env python # Licensed under a 3-clause BSD style license - see LICENSE.rst -import glob -import os -import sys -from configparser import ConfigParser - -# Get some values from the setup.cfg -conf = ConfigParser() -conf.read(['setup.cfg']) -metadata = dict(conf.items('metadata')) - -PACKAGENAME = metadata.get('package_name', 'fgscountrate') -DESCRIPTION = metadata.get('description', 'JWST FGS countrate estimation') -AUTHOR = metadata.get('author', 'Space Telescope Science Institute') -AUTHOR_EMAIL = metadata.get('author_email', '') -LICENSE = metadata.get('license', 'unknown') -URL = metadata.get('url', 'http://stsci.edu') -__minimum_python_version__ = metadata.get("minimum_python_version", "3.6") - -# Enforce Python version check - this is the same check as in __init__.py but -# this one has to happen before importing ah_bootstrap. -if sys.version_info < tuple((int(val) for val in __minimum_python_version__.split('.'))): - sys.stderr.write("ERROR: fgscountrate requires Python {} or later\n".format(__minimum_python_version__)) - sys.exit(1) - -# Import ah_bootstrap after the python version validation - -import ah_bootstrap -from setuptools import setup - -import 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 - - -# 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.dev') - -# 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/*') - -# 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=['pandas', 'numpy', 'astropy', 'requests'], - 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, - python_requires='>={}'.format(__minimum_python_version__), - **package_info -) +from __future__ import (absolute_import, division, + print_function, unicode_literals) + +from setuptools import setup, find_packages + +INSTALL_REQUIRES = [ + 'numpy', + 'pytest', + 'requests', + 'pandas' +] + +setup(name='fgscountrate', + version='0.0', + description='JWST FGS countrate estimation', + long_description='JWST FGS countrate and magnitude estimation and related functionality.', + classifiers=[ + # 'Development Status :: 3 - Alpha', + # 'License :: OSI Approved :: MIT License', + 'Intended Audience :: Science/Research', + 'Programming Language :: Python :: 3', + 'Programming Language :: Python :: 3.5', + 'Topic :: Software Development :: Libraries :: Python Modules', + 'Topic :: Scientific/Engineering :: Astronomy' + ], + keywords='jwst fgs', + url='https://github.com/spacetelescope/jwst-fgs-countrate', + author='Shannon Osborne', + packages=find_packages(), + install_requires=INSTALL_REQUIRES, + include_package_data=True, + zip_safe=False) From 014d01bb77bc45d390f90e43f89c27779d7afb2a Mon Sep 17 00:00:00 2001 From: Shannon Osborne Date: Fri, 12 Jul 2019 17:29:57 -0500 Subject: [PATCH 2/3] fixing merge conflict --- setup.cfg | 25 ------------------------- 1 file changed, 25 deletions(-) diff --git a/setup.cfg b/setup.cfg index e0b817c..0483e65 100644 --- a/setup.cfg +++ b/setup.cfg @@ -46,28 +46,3 @@ exclude = extern,sphinx,*parsetab.py [pycodestyle] exclude = extern,sphinx,*parsetab.py -<<<<<<< HEAD -======= - -[metadata] -package_name = fgscountrate -description = JWST FGS countrate estimation -long_description = JWST FGS countrate estimation and related functionality. -author = Space Telescope Science Institute -author_email = help@stsci.edu -license = Aura -url = http://stsci.edu -edit_on_github = False -github_project = spacetelescope/jwst-fgs-countrate -# install_requires should be formatted as a comma-separated list, e.g.: -# install_requires = astropy, scipy, matplotlib -# version should be PEP440 compatible (https://www.python.org/dev/peps/pep-0440/) -version = 0.0.dev -# Note: you will also need to change this in your package's __init__.py -minimum_python_version = 3.5 - -[entry_points] - -astropy-package-template-example = packagename.example_mod:main - ->>>>>>> b25f23607681f7d935bfc06918d04f63d46cf343 From 2a78ce29fadb0bd1f176d7b1d9fa562f40e23ede Mon Sep 17 00:00:00 2001 From: Shannon Osborne Date: Fri, 12 Jul 2019 18:05:14 -0500 Subject: [PATCH 3/3] missing astropy import --- setup.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/setup.py b/setup.py index e9e4437..9281c8b 100755 --- a/setup.py +++ b/setup.py @@ -11,7 +11,8 @@ 'numpy', 'pytest', 'requests', - 'pandas' + 'pandas', + 'astropy' ] setup(name='fgscountrate',