updated versioning system and moved configuration to pyproject.toml

.gitignore

@@ -5,3 +5,7 @@ build/*
 *__pycache__*
 *.egg-info/*
 .tox/*
+/coverage.xml
+/.tox/
+/.coverage*
+/goodman_focus/version.py

environment.yml

@@ -1,6 +1,6 @@
 name: goodman_focus
 dependencies:
-  - python=3.8
+  - python=3.12
   - astropy
   - matplotlib
   - numpy

pyproject.toml

@@ -1,7 +1,72 @@
 [build-system]
+requires = ["setuptools>=64", "setuptools_scm>=8"]
+build-backend = "setuptools.build_meta"
 
-requires = ["setuptools",
-            "setuptools_scm",
-            "wheel"]
+[project]
+name = "goodman_focus"
+dynamic = ["version"]
+description = "Finds best focus for Goodman HTS based on a series of images obtained with different focus values"
+readme = "README.md"
+requires-python = ">=3.8"
+license = {file = "LICENSE"}
+keywords = [
+    "soar",
+    "pipelines",
+    "astronomy",
+    "images",
+    "spectroscopy",
+    "focus"
+]
 
-build-backend = 'setuptools.build_meta'
+authors = [
+  {name = "Simón Torres", email = "[email protected]"}
+]
+maintainers = [
+  {name = "Simón Torres", email = "[email protected]"}
+]
+
+classifiers = [
+  'Development Status :: 5 - Production/Stable',
+  'Environment :: Console',
+  'Intended Audience :: Developers',
+  'Intended Audience :: Education',
+  'Intended Audience :: Science/Research',
+  'License :: OSI Approved :: BSD License',
+  'Programming Language :: Python :: 3.8',
+  'Programming Language :: Python :: 3.9',
+  'Programming Language :: Python :: 3.10',
+  'Programming Language :: Python :: 3.11',
+  'Programming Language :: Python :: 3.12',
+  'Natural Language :: English',
+  'Operating System :: POSIX :: Linux',
+  'Operating System :: POSIX :: Other',
+  'Operating System :: MacOS :: MacOS X',
+  'Topic :: Scientific/Engineering :: Astronomy',
+  'Topic :: Scientific/Engineering :: Information Analysis',
+  'Topic :: Software Development :: Libraries :: Python Modules',
+]
+
+dependencies = [
+  "astropy",
+  "ccdproc",
+  "matplotlib",
+  "numpy",
+  "packaging",
+  "pandas",
+  "scipy",
+]
+
+[project.urls]
+"Homepage" = "https://soardocs.readthedocs.io/projects/goodmanfocus/en/latest/"
+"Bug Reports" = "https://github.com/soar-telescope/goodman_focus/issues"
+"Source" = "https://github.com/soar-telescope/goodman_focus"
+
+[project.scripts]
+goodman-focus = "goodman_focus:run_goodman_focus"
+
+[tool.setuptools]
+[tool.setuptools.packages.find]
+where = ["goodman_focus"]
+
+[tool.setuptools_scm]
+version_file = "goodman_focus/version.py"

setup.cfg

@@ -11,25 +11,3 @@ build_dir = docs/_build
 [upload_docs]
 upload_dir = docs/_build/html
 show_response = 1
-
-[metadata]
-package_name = goodman_focus
-description = Finds best focus for Goodman HTS based on a series of images obtained with different focus values
-long_description = Standalone app to get the best focus.
-author = Simon Torres
-author_email = [email protected]
-license = BSD-3-Clause
-# url =
-edit_on_github = False
-github_project = soar-telescope/goodman_focus
-install_requires =
-    astropy
-    matplotlib
-    numpy
-    pandas
-    scipy
-    ccdproc
-    sphinx
-
-# version should be PEP440 compatible (http://www.python.org/dev/peps/pep-0440)
-version = 2.0.3

setup.py

@@ -1,93 +1,3 @@
-import os
-
-from codecs import open
 from setuptools import setup
 
-try:
-    from ConfigParser import ConfigParser
-except ImportError:
-    from configparser import ConfigParser
-
-CONF = ConfigParser()
-
-HERE = os.path.abspath(os.path.dirname(__file__))
-
-
-def create_version_py(packagename, version, source_dir='.'):
-    package_dir = os.path.join(source_dir, packagename)
-    version_py = os.path.join(package_dir, 'version.py')
-
-    version_str = "# This is an automatic generated file please do not edit\n" \
-                  "__version__ = '{:s}'".format(version)
-
-    with open(version_py, 'w') as f:
-        f.write(version_str)
-
-
-# read content from README.md
-with open(os.path.join(HERE, 'README.md')) as f:
-    long_description = f.read()
-
-CONF.read([os.path.join(os.path.dirname(__file__), 'setup.cfg')])
-
-metadata = dict(CONF.items('metadata'))
-
-PACKAGENAME = metadata['package_name']
-
-VERSION = metadata['version']
-
-LICENSE = metadata['license']
-
-DESCRIPTION = metadata['description']
-
-LONG_DESCRIPTION = long_description
-
-LONG_DESCRIPTION_CONTENT_TYPE = 'text/markdown'
-
-AUTHOR = metadata['author']
-
-AUTHOR_EMAIL = metadata['author_email']
-
-INSTALL_REQUIRES = metadata['install_requires'].split()
-
-# freezes version information in version.py
-create_version_py(PACKAGENAME, VERSION)
-
-
-setup(
-    name=metadata['package_name'],
-
-    version=VERSION,
-
-    description=DESCRIPTION,
-
-    long_description=LONG_DESCRIPTION,
-
-    long_description_content_type=LONG_DESCRIPTION_CONTENT_TYPE,
-
-    # The project's main homepage.
-    url='https://github.com/soar-telescope/goodman_focus',
-
-    # Author details
-    author=u'Simon Torres R., ',
-
-    author_email='[email protected]',
-
-    # Choose your license
-    license=LICENSE,
-
-    packages=['goodman_focus'],
-
-    package_dir={'goodman_focus': 'goodman_focus'},
-
-    python_requires=">=3.6",
-
-    install_requires=INSTALL_REQUIRES,
-
-    entry_points={
-        'console_scripts': [
-            'goodman-focus=goodman_focus:run_goodman_focus',
-        ]
-    }
-
-)
+setup()

tox.ini

@@ -1,103 +1,19 @@
 [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}
-    py{36,37,38}-test-external
-    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
+env_list =
+    py{38, 39, 310, 311, 312}-test{,-cov}
+minversion = 4.4.12
 
 [testenv]
-# Suppress display of matplotlib plots generated during docs build
-setenv =
-    MPLBACKEND=agg
-    # Disable the accelerate linear algebra library when running on macos as
-    # latest numpy versions do not work with it
-    NPY_BLAS_ORDER=
-    NPY_LAPACK_ORDER=
+description = run the tests with pytest
+package = wheel
+wheel_build_env = .pkg
 
-# 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
-    external: with outside packages as dependencies
-
-# The following provides some specific pinnings for key packages
 deps =
+    pytest>=6
+    cov: pytest-cov
 
-    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
-
-    external: asdf
-    external: git+https://github.com/spacetelescope/jwst@stable
-
-# The following indicates which extras_require from setup.cfg will be installed
-extras =
-    test
-    alldeps: all
-
-commands =
-    pip freeze
-    !cov: pytest --pyargs specutils {toxinidir}/docs {posargs}
-    cov: pytest --pyargs specutils {toxinidir}/docs --cov specutils --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 specutils --count --max-line-length=100 --select=E101,W191,W291,W292,W293,W391,E111,E112,E113,E502,E722,E901,E902
+    pytest {tty:--color=yes} {posargs}
+    cov: pytest {tty:--color=yes} --cov goodman_focus {posargs}
+    cov: coverage xml -o '{toxinidir}/coverage.xml'
+    html: coverage html -d .coverage_html