MNT: Infrastructure update

.bandit.yaml

@@ -0,0 +1,2 @@
+exclude_dirs:
+  - acstools/tests

.gitignore

@@ -35,6 +35,8 @@ sdist
 develop-eggs
 .installed.cfg
 distribute-*.tar.gz
+pip-wheel-metadata/
+acstools/version.py
 
 # Other
 .cache

.readthedocs.yml

@@ -12,9 +12,10 @@ python:
   version: 3.7
   system_packages: true
   install:
-    - requirements: doc/rtd-pip-requirements
-    - method: setuptools
+    - method: pip
       path: .
+      extra_requirements:
+        - docs
 
 # Don't build any extra formats
 formats: []

CHANGES.rst

@@ -0,0 +1 @@
+See https://github.com/spacetelescope/acstools/releases

Jenkinsfile

@@ -8,25 +8,18 @@ bc1.name = "release"
 // Would be nice if Jenkins can access /grp/hst/cdbs/xxxx directly.
 bc1.env_vars = ['TEST_BIGDATA=https://bytesalad.stsci.edu/artifactory']
 bc1.conda_channels = ['http://ssb.stsci.edu/astroconda']
-bc1.conda_packages = ['python=3.6',
-                      'requests',
-                      'numpy',
-                      'matplotlib',
-                      'scipy',
-                      'stsci.tools']
-bc1.build_cmds = ["pip install scikit-image ci-watson",
-                  "python setup.py install"]
+bc1.conda_packages = ['python=3.6']
+bc1.build_cmds = ["pip install -e .[test,all]"]
 bc1.test_cmds = ["pytest --basetemp=tests_output --junitxml results.xml --bigdata -v"]
 bc1.failedUnstableThresh = 1
 bc1.failedFailureThresh = 6
 
-// Run with astropy dev and Python 3.7
+// Run with astropy dev and Python 3.8
 bc2 = utils.copy(bc1)
 bc2.name = "dev"
-bc2.conda_packages[0] = "python=3.7"
-bc2.build_cmds = ["pip install scikit-image ci-watson",
-                  "pip install git+https://github.com/astropy/astropy.git#egg=astropy --upgrade --no-deps",
-                  "python setup.py install"]
+bc2.conda_packages[0] = "python=3.8"
+bc2.build_cmds = ["pip install git+https://github.com/astropy/astropy.git#egg=astropy --upgrade --no-deps",
+                  "pip install -e [test,all]"]
 
 // Iterate over configurations that define the (distibuted) build matrix.
 // Spawn a host of the given nodetype for each combination and run in parallel.

JenkinsfileRT

@@ -14,25 +14,18 @@ bc.name = "release"
 bc.env_vars = ['TEST_BIGDATA=https://bytesalad.stsci.edu/artifactory',
                'jref=/grp/hst/cdbs/jref/']
 bc.conda_channels = ['http://ssb.stsci.edu/astroconda']
-bc.conda_packages = ['python=3.6',
-                     'requests',
-                     'numpy',
-                     'matplotlib',
-                     'scipy',
-                     'stsci.tools']
-bc.build_cmds = ["pip install scikit-image ci-watson",
-                 "python setup.py install"]
+bc.conda_packages = ['python=3.6']
+bc.build_cmds = ["pip install -e .[test,all]"]
 bc.test_cmds = ["pytest --basetemp=tests_output --junitxml results.xml --bigdata --slow -v"]
 bc.failedUnstableThresh = 1
 bc.failedFailureThresh = 6
 
-// Astropy dev and Python 3.7
+// Astropy dev and Python 3.8
 bc1 = utils.copy(bc)
 bc1.name = "dev"
-bc1.conda_packages[0] = "python=3.7"
-bc1.build_cmds = ["pip install scikit-image",
-                  "pip install git+https://github.com/astropy/astropy.git#egg=astropy --upgrade --no-deps",
-                  "python setup.py install"]
+bc1.conda_packages[0] = "python=3.8"
+bc1.build_cmds = ["pip install git+https://github.com/astropy/astropy.git#egg=astropy --upgrade --no-deps",
+                  "pip install -e [test,all]"]
 
 // Iterate over configurations that define the (distributed) build matrix.
 // Spawn a host (or workdir) for each combination and run in parallel.

LICENSE.md

@@ -1,6 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2018, Space Telescope Science Institute, AURA
+Copyright (c) 2020, Space Telescope Science Institute, AURA
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

MANIFEST.in

@@ -1,6 +1,8 @@
 include README.rst
 include LICENSE.txt
+include CHANGES.rst
 include setup.cfg
+include pyproject.toml
 recursive-include doc *
 
 prune build

acstools/__init__.py

@@ -1,31 +1,21 @@
-"""The acstools package holds Python tasks useful for analyzing ACS data.
-
-These tasks include:
-
-Utility and library functions used by these tasks are also included in this
-module.
-
-"""
-from pkg_resources import get_distribution, DistributionNotFound
-
-
+"""The acstools package holds Python tasks useful for analyzing ACS data."""
 try:
-    __version__ = get_distribution(__name__).version
-except DistributionNotFound:
+    from .version import version as __version__
+except ImportError:
     # package is not installed
-    __version__ = 'unknown'
+    __version__ = ''
 
 
-from . import acs_destripe
-from . import acs_destripe_plus
-from . import calacs
-from . import acsccd
-from . import acscte
-from . import acscteforwardmodel
-from . import acs2d
-from . import acsrej
-from . import acssum
-from . import acszpt
-from . import acsphotcte
-from . import satdet
-from . import utils_calib
+from . import acs_destripe  # noqa
+from . import acs_destripe_plus  # noqa
+from . import calacs  # noqa
+from . import acsccd  # noqa
+from . import acscte  # noqa
+from . import acscteforwardmodel  # noqa
+from . import acs2d  # noqa
+from . import acsrej  # noqa
+from . import acssum  # noqa
+from . import acszpt  # noqa
+from . import acsphotcte  # noqa
+from . import satdet  # noqa
+from . import utils_calib  # noqa

azure-pipelines.yml

@@ -5,18 +5,19 @@ trigger:
 - master
 
 jobs:
-- job: 'EggInfo'
+- job: 'PEP517'
   pool:
     vmImage: 'Ubuntu-16.04'
 
   steps:
   - task: UsePythonVersion@0
 
-  # Make sure that egg_info works without dependencies
+  # Make sure that packaging will work
   - script: |
-      python -m pip install --upgrade pip setuptools
-      python setup.py egg_info
-    displayName: 'egg_info'
+      python -m pip install --upgrade pip setuptools pep517 twine
+      python -m pep517.build --source .
+      twine check dist/*
+    displayName: 'pep517 build'
 
 - job: 'PEP8'
   pool:
@@ -32,3 +33,36 @@ jobs:
       pip install flake8
       flake8 acstools --count
     displayName: 'PEP 8 check'
+
+- job: 'Audit'
+  pool:
+    vmImage: 'Ubuntu-16.04'
+
+  steps:
+  - task: UsePythonVersion@0
+    inputs:
+      versionSpec: '3.x'
+
+  - script: |
+      python -m pip install --upgrade pip setuptools
+      pip install bandit
+      bandit -r . -c .bandit.yaml
+    displayName: 'Security audit'
+
+- job: 'LinkCheck'
+  pool:
+    vmImage: 'Ubuntu-16.04'
+  strategy:
+    maxParallel: 4
+
+  steps:
+  - task: UsePythonVersion@0
+
+  - script: |
+      python -m pip install --upgrade pip setuptools
+      pip install -e .[docs]
+
+  - bash: |
+      cd doc
+      make linkcheck
+    displayName: 'Run docs link check'

conftest.py

@@ -1,34 +1,31 @@
 """Custom ``pytest`` configurations."""
+try:
+    from pytest_astropy_header.display import (PYTEST_HEADER_MODULES,
+                                               TESTED_VERSIONS)
+except ImportError:
+    PYTEST_HEADER_MODULES = {}
+    TESTED_VERSIONS = {}
 
-from astropy.tests.helper import enable_deprecations_as_exceptions
+try:
+    from acstools.version import version
+except ImportError:
+    version = 'unknown'
 
-# Turn deprecation warnings into exceptions.
+# Uncomment the following line to treat all DeprecationWarnings as
+# exceptions
 # NOTE: socks warning fixed by https://github.com/Anorov/PySocks/pull/106
 #       but not released yet.
+from astropy.tests.helper import enable_deprecations_as_exceptions
 enable_deprecations_as_exceptions(warnings_to_ignore_entire_module=['socks'])
 
+# 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.
+PYTEST_HEADER_MODULES['Astropy'] = 'astropy'
+PYTEST_HEADER_MODULES['beautifulsoup4'] = 'bs4'
+PYTEST_HEADER_MODULES['requests'] = 'requests'
+PYTEST_HEADER_MODULES['stsci.tools'] = 'stsci.tools'
+PYTEST_HEADER_MODULES.pop('Pandas')
+PYTEST_HEADER_MODULES.pop('h5py')
 
-# For easy inspection on what dependencies were used in test.
-def pytest_report_header(config):
-    import sys
-    import warnings
-    from astropy.utils.introspection import resolve_name
-
-    s = "\nFull Python Version: \n{0}\n\n".format(sys.version)
-
-    for module_name in ('numpy', 'astropy', 'scipy', 'matplotlib',
-                        'stsci.tools'):
-        try:
-            with warnings.catch_warnings():
-                warnings.simplefilter("ignore", DeprecationWarning)
-                module = resolve_name(module_name)
-        except ImportError:
-            s += "{0}: not available\n".format(module_name)
-        else:
-            try:
-                version = module.__version__
-            except AttributeError:
-                version = 'unknown (no __version__ attribute)'
-            s += "{0}: {1}\n".format(module_name, version)
-
-    return s
+TESTED_VERSIONS['acstools'] = version

doc/source/conf.py

@@ -205,10 +205,10 @@
 
 # Example configuration for intersphinx: refer to the Python standard library.
 intersphinx_mapping = {
-    'python': ('http://docs.python.org/', None),
-    'numpy': ('http://docs.scipy.org/doc/numpy/', None),
-    'scipy': ('http://docs.scipy.org/doc/scipy/reference/', None),
-    'skimage': ('http://scikit-image.org/docs/0.11.x/', None),
-    'matplotlib': ('http://matplotlib.org/', None),
-    'astropy': ('http://docs.astropy.org/en/stable/', None)
+    'python': ('https://docs.python.org/', None),
+    'numpy': ('https://docs.scipy.org/doc/numpy/', None),
+    'scipy': ('https://docs.scipy.org/doc/scipy/reference/', None),
+    'skimage': ('https://scikit-image.org/docs/0.11.x/', None),
+    'matplotlib': ('https://matplotlib.org/', None),
+    'astropy': ('https://docs.astropy.org/en/stable/', None)
 }

pyproject.toml

@@ -0,0 +1,5 @@
+[build-system]
+requires = ["setuptools>=30.3.0",
+            "setuptools_scm",
+            "wheel"]
+build-backend = "setuptools.build_meta"

setup.cfg

@@ -1,26 +1,62 @@
 [metadata]
-package_name = acstools
-description = Python Tools for ACS (Advanced Camera for Surveys) Data
+name = acstools
+description = Python Tools for HST ACS
+long_description = Python Tools for HST ACS (Advanced Camera for Surveys) Data
+long_description_content_type = text/plain
+keywords = astronomy, astrophysics, calibration
 author = Matt Davis, Warren Hack, Norman Grogin, Pey Lian Lim, Sara Ogaz, Leornado Ubeda, Mihai Cara, David Borncamp, Nathan Miles
 author_email = [email protected]
 license = BSD
+license_file = LICENSE.md
 url = https://github.com/spacetelescope/acstools
+edit_on_github = False
+github_project = spacetelescope/acstools
 classifier =
     Intended Audience :: Science/Research
     License :: OSI Approved :: BSD License
     Operating System :: OS Independent
     Programming Language :: Python :: 3
+    Programming Language :: Python :: Implementation :: CPython
     Topic :: Scientific/Engineering :: Astronomy
     Topic :: Scientific/Engineering :: Physics
     Topic :: Software Development :: Libraries :: Python Modules
 
+[options]
+packages = find:
+zip_safe = False
+setup_requires=
+    setuptools_scm
+install_requires =
+    numpy
+    astropy>=2
+    beautifulsoup4
+    requests
+python_requires = >=3.5
+
+[options.extras_require]
+all =
+    matplotlib
+    scipy
+    scikit-image
+    stsci.tools
+    stsci.imagestats
+test =
+    pytest
+    pytest-astropy-header
+    ci-watson
+docs =
+    sphinx-automodapi
+
 [entry_points]
 acs_destripe = acstools.acs_destripe:main
 acs_destripe_plus = acstools.acs_destripe_plus:main
 
 [tool:pytest]
-minversion = 3.0
+minversion = 4.0
+testpaths = "acstools" "doc"
 norecursedirs = build doc/build
+astropy_header = true
+xfail_strict = true
 junit_family=xunit2
 
 [flake8]
@@ -33,4 +69,3 @@ junit_family=xunit2
 # E704: multiple statements on one line (def)
 # W504: line break after binary operator
 ignore = E221,E226,E262,E265,E501,E704,W504
-exclude = __init__.py