Github action for coveralls, readme badges, metadata refactor

.github/workflows/coveralls.yaml

@@ -0,0 +1,41 @@
+name: coveralls
+
+on:
+  push:
+    branches: [ $default-branch ]
+  pull_request:
+
+jobs:
+  coveralls_test:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python 3.8
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.8
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip setuptools wheel
+        pip install --only-binary=numpy,scipy -r requirements-dev.txt
+    - name: Install package
+      run: |
+        pip install -e .
+    - name: Test with pytest
+      run: |
+        pytest
+    - name: Coveralls
+      uses: AndreMiras/coveralls-python-action@develop
+      with:
+        parallel: true
+        flag-name: Unit Test
+
+  coveralls_finish:
+    needs: coveralls_test
+    runs-on: ubuntu-latest
+    steps:
+    - name: Coveralls Finished
+      uses: AndreMiras/coveralls-python-action@develop
+      with:
+        parallel-finished: true
+        debug: true

.github/workflows/pip_build_test.yaml → .github/workflows/tests.yaml

@@ -1,9 +1,9 @@
 # This workflow will install dependencies, install becquerel and run tests.
-# It runs on multiple python3 versions on macOS and Ubuntu.
+# It runs on multiple python3 versions on macOS, Ubuntu and Windows.
 # It runs when a commit (merge) is push to the main (default) branch or for updates to a PR targeting main.
 # Based on: https://github.com/actions/starter-workflows/blob/main/ci/python-package.yml
 
-name: Python package
+name: tests
 
 on:
 
@@ -38,7 +38,7 @@ jobs:
           pip install -r requirements-dev.txt
       - name: Install package
         run: |
-          pip install -e .
+          pip install .
       - name: Test with pytest
         run: |
           python -c 'import becquerel;'

.gitignore

@@ -176,4 +176,3 @@ $RECYCLE.BIN/
 
 # Becquerel settings
 __df_cache_*.csv
-__metadata__.py

README.md

@@ -1,5 +1,8 @@
 # becquerel
 
+[![tests](https://github.com/lbl-anp/becquerel/actions/workflows/tests.yaml/badge.svg)](https://github.com/lbl-anp/becquerel/actions/workflows/tests.yaml)
+[![Coverage Status](https://coveralls.io/repos/github/lbl-anp/becquerel/badge.svg?branch=main)](https://coveralls.io/github/lbl-anp/becquerel?branch=main)
+
 Becquerel is a Python package for analyzing nuclear spectroscopic
 measurements. The core functionalities are reading and writing different
 spectrum file types, fitting spectral features, performing detector

becquerel/__init__.py

@@ -1,68 +1,78 @@
 """Becquerel: Tools for radiation spectral analysis."""
 
-from . import core
-from . import parsers
-from . import tools
-from .__metadata__ import __description__, __url__
-from .__metadata__ import __version__, __license__, __copyright__
+from .__metadata__ import (
+    __description__,
+    __url__,
+    __version__,
+    __license__,
+    __copyright__,
+)
 
-from .core.rebin import rebin, RebinError, RebinWarning
-from .core.spectrum import Spectrum, SpectrumError, UncalibratedError
-from .core.spectrum import SpectrumWarning
+from . import core
+from .core import utils, fitting
+from .core.autocal import AutoCalibrator, AutoCalibratorError
 from .core.energycal import LinearEnergyCal, EnergyCalError, BadInput
-from .core.utils import UncertaintiesError
-from .core.plotting import SpectrumPlotter, PlottingError
+from .core.fitting import Fitter
 from .core.peakfinder import (
     PeakFilter,
     PeakFilterError,
     GaussianPeakFilter,
     PeakFinder,
     PeakFinderError,
 )
-from .core.autocal import AutoCalibrator, AutoCalibratorError
+from .core.plotting import SpectrumPlotter, PlottingError
+from .core.rebin import rebin, RebinError, RebinWarning
+from .core.spectrum import Spectrum, SpectrumError, UncalibratedError, SpectrumWarning
+from .core.utils import UncertaintiesError
 
-from .core import utils
-from .core import fitting
-from .core.fitting import Fitter
+from . import parsers
 
-from .tools import nndc
+from . import tools
+from .tools import nndc, xcom, materials
 from .tools.element import Element
 from .tools.isotope import Isotope
 from .tools.isotope_qty import IsotopeQuantity
-from .tools import xcom
-from .tools import materials
 
 import warnings
 
 warnings.simplefilter("default", DeprecationWarning)
 
 __all__ = [
+    "__description__",
+    "__url__",
+    "__version__",
+    "__license__",
+    "__copyright__",
     "core",
-    "parsers",
-    "tools",
-    "rebin",
-    "RebinError",
-    "RebinWarning",
-    "Spectrum",
-    "SpectrumError",
-    "SpectrumWarning",
-    "SpectrumPlotter",
-    "PlottingError",
-    "UncalibratedError",
+    "utils",
+    "fitting",
+    "AutoCalibrator",
+    "AutoCalibratorError",
     "LinearEnergyCal",
     "EnergyCalError",
     "BadInput",
-    "UncertaintiesError",
+    "Fitter",
     "PeakFilter",
     "PeakFilterError",
     "GaussianPeakFilter",
     "PeakFinder",
     "PeakFinderError",
-    "AutoCalibrator",
-    "AutoCalibratorError",
-    "__description__",
-    "__url__",
-    "__version__",
-    "__license__",
-    "__copyright__",
+    "SpectrumPlotter",
+    "PlottingError",
+    "rebin",
+    "RebinError",
+    "RebinWarning",
+    "Spectrum",
+    "SpectrumError",
+    "UncalibratedError",
+    "SpectrumWarning",
+    "UncertaintiesError",
+    "parsers",
+    "tools",
+    "nndc",
+    "xcom",
+    "materials",
+    "Element",
+    "Isotope",
+    "IsotopeQuantity",
 ]

becquerel/__metadata__.py

@@ -0,0 +1,40 @@
+"""becquerel package metadata."""
+
+__name__ = "becquerel"
+__author__ = "The Becquerel Development Team"
+__maintainer__ = __author__
+__email__ = "becquerel-dev@lbl.gov"
+__description__ = "Tools for radiation spectral analysis."
+__url__ = "https://github.com/lbl-anp/becquerel"
+__version__ = "0.3.0"
+# classifiers from list at https://pypi.org/classifiers/
+__classifiers__ = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Science/Research",
+    "License :: Other/Proprietary License",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3 :: Only",
+    "Programming Language :: Python :: 3.6",
+    "Programming Language :: Python :: 3.7",
+    "Programming Language :: Python :: 3.8",
+    "Topic :: Scientific/Engineering",
+    "Topic :: Scientific/Engineering :: Physics",
+]
+__license__ = "Other/Proprietary License (see LICENSE.txt)"
+__copyright__ = """\
+Becquerel v. 0.3.0, Copyright (c) 2017, The Regents of the University of
+California (UC), through Lawrence Berkeley National Laboratory, and the UC
+Berkeley campus (subject to receipt of any required approvals from the U.S.
+Dept. of Energy). All rights reserved. If you have questions about your rights
+to use or distribute this software, please contact Berkeley Lab's Innovation &
+Partnerships Office at  IPO@lbl.gov.
+
+NOTICE.  This Software was developed under funding from the U.S. Department of
+Energy and the U.S. Government consequently retains certain rights.  As such,
+the U.S. Government has been granted for itself and others acting on its
+behalf a paid-up, nonexclusive, irrevocable, worldwide license in the Software
+to reproduce, distribute copies to the public, prepare derivative works, and
+perform publicly and display publicly, and to permit other to do so.
+"""

requirements-dev.txt

@@ -1,4 +1,5 @@
 -r requirements.txt
+coverage
 flake8
 black>=20.8b1
 pydocstyle

setup.cfg

@@ -1,5 +1,5 @@
 [aliases]
-test=pytest
+test = pytest
 
 [tool:pytest]
 addopts = --black --cov=becquerel --cov-report term --cov-report html:htmlcov -m "not plottest"
@@ -10,3 +10,6 @@ filterwarnings =
     always
     ; Not fixing the problem: https://github.com/pytest-dev/pytest/pull/3613
     ignore:.*t resolve package from __spec__ or __package__.*:ImportWarning
+
+[coverage:run]
+relative_files = True

setup.py

@@ -4,85 +4,54 @@
 import sys
 import site
 from setuptools import setup, find_packages
+import importlib.util
 
 # Enables --editable install with --user
 # https://github.com/pypa/pip/issues/7953
 site.ENABLE_USER_SITE = "--user" in sys.argv[1:]
 
-NAME = "becquerel"
-
-MAJOR = 0
-MINOR = 3
-MICRO = 0
-VERSION = f"{MAJOR}.{MINOR}.{MICRO}"
-
-DESCRIPTION = __doc__.split("\n")[0].split(": ")[-1]
-URL = "https://github.com/lbl-anp/becquerel"
-MAINTAINER = "The Becquerel Development Team"
-EMAIL = "becquerel-dev@lbl.gov"
+_spec = importlib.util.spec_from_file_location(
+    "__metadata__", "./becquerel/__metadata__.py"
+)
+METADATA = importlib.util.module_from_spec(_spec)
+_spec.loader.exec_module(METADATA)
 
-# classifiers from list at https://pypi.org/classifiers/
-CLASSIFIERS = """\
-Development Status :: 3 - Alpha
-Intended Audience :: Science/Research
-License :: Other/Proprietary License
-Operating System :: OS Independent
-Programming Language :: Python
-Programming Language :: Python :: 3
-Programming Language :: Python :: 3 :: Only
-Programming Language :: Python :: 3.6
-Programming Language :: Python :: 3.7
-Programming Language :: Python :: 3.8
-Topic :: Scientific/Engineering
-Topic :: Scientific/Engineering :: Physics
-"""
+# Enables --editable install with --user
+# https://github.com/pypa/pip/issues/7953
+site.ENABLE_USER_SITE = "--user" in sys.argv[1:]
 
-with open("README.md", "r") as fh:
-    README = fh.read()
 # remove package title from description
-README = "\n".join(README.split("\n")[2:])
+with open("README.md", "r") as fh:
+    README = "\n".join(fh.readlines()[2:])
 
 with open("CONTRIBUTING.md", "r") as fh:
     CONTRIBUTING = fh.read()
 
-with open("LICENSE.txt", "r") as fh:
-    LICENSE = fh.read()
-
 with open("requirements.txt", "r") as fh:
-    REQUIREMENTS = fh.read()
+    REQUIREMENTS = [_line for _line in fh.readlines() if _line]
 
 # make long description from README and CONTRIBUTING
 # but move copyright notice to the end
-LONG_DESCRIPTION, COPYRIGHT = README.split("## Copyright Notice")
-LONG_DESCRIPTION += "\n" + CONTRIBUTING
-LONG_DESCRIPTION += "\n" + "## Copyright Notice" + COPYRIGHT
-
-# write metadata to a file that will be imported by becquerel
-with open("becquerel/__metadata__.py", "w") as f:
-    print('"""Becquerel package metadata."""', file=f)
-    print("", file=f)
-    print(f'__description__ = "{DESCRIPTION}"', file=f)
-    print(f'__url__ = "{URL}"', file=f)
-    print(f'__version__ = "{VERSION}"', file=f)
-    print(f'__license__ = """{LICENSE}"""', file=f)
-    print(f'__copyright__ = """{COPYRIGHT}"""', file=f)
+LONG_DESCRIPTION = "{0}\n{2}\n## Copyright Notice\n{1}".format(
+    *README.split("## Copyright Notice"), CONTRIBUTING
+)
 
 setup(
-    name=NAME,
-    version=VERSION,
-    description=DESCRIPTION,
+    name=METADATA.__name__,
+    version=METADATA.__version__,
+    description=METADATA.__description__,
     long_description=LONG_DESCRIPTION,
     long_description_content_type="text/markdown",
-    url=URL,
-    download_url=URL + "/releases",
-    maintainer=MAINTAINER,
-    maintainer_email=EMAIL,
-    classifiers=[_f for _f in CLASSIFIERS.split("\n") if _f],
+    url=METADATA.__url__,
+    download_url=f"{METADATA.__url__}/releases",
+    maintainer=METADATA.__maintainer__,
+    maintainer_email=METADATA.__email__,
+    classifiers=METADATA.__classifiers__,
     platforms="any",
     packages=find_packages(),
     python_requires=">=3.6",
-    install_requires=[_f for _f in REQUIREMENTS.split("\n") if _f],
+    install_requires=REQUIREMENTS,
     setup_requires=["pytest-runner"],
     tests_require=["pytest", "pytest-cov"],
-    license="Other/Proprietary License (see LICENSE.txt)",
+    license=METADATA.__license__,
 )

tests/autocal_test.py

@@ -8,14 +8,11 @@
 
 
 # read in spectra
-filename1 = os.path.join(os.path.dirname(bq.__file__), "../tests/samples/sim_spec.csv")
-filename2 = os.path.join(
-    os.path.dirname(bq.__file__), "../tests/samples/Mendocino_07-10-13_Acq-10-10-13.Spe"
-)
-filename3 = os.path.join(
-    os.path.dirname(bq.__file__), "../tests/samples/nai_detector.csv"
-)
-filename4 = os.path.join(os.path.dirname(bq.__file__), "../tests/samples/SGM102432.csv")
+SAMPLES_PATH = os.path.join(os.path.dirname(__file__), "samples")
+filename1 = os.path.join(SAMPLES_PATH, "sim_spec.csv")
+filename2 = os.path.join(SAMPLES_PATH, "Mendocino_07-10-13_Acq-10-10-13.Spe")
+filename3 = os.path.join(SAMPLES_PATH, "nai_detector.csv")
+filename4 = os.path.join(SAMPLES_PATH, "SGM102432.csv")
 
 counts = []
 with open(filename1, "r") as f: