Merge pull request #246 from lbl-anp/gh-actions-coveralls

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

COPYRIGHT.txt

@@ -0,0 +1,13 @@
+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.

LICENSE.txt

@@ -1,13 +1,20 @@
-*** License Agreement ***
-
 *** Copyright Notice ***
 
-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.
+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.
+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.
 
-**************************************************************************
+*** License Agreement ***
 
  Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
 
@@ -20,5 +27,3 @@ NOTICE.  This Software was developed under funding from the U.S. Department of E
 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
 You are under no obligation whatsoever to provide any bug fixes, patches, or upgrades to the features, functionality or performance of the source code ("Enhancements") to anyone; however, if you choose to make your Enhancements available either publicly, or directly to Lawrence Berkeley National Laboratory, without imposing a separate written license agreement for such Enhancements, then you hereby grant the following license to Lawrence Berkeley National Laboratory, University if California, Berkeley, and the U.S. Dept. of Energy: a  non-exclusive, royalty-free perpetual license to install, use, modify, prepare derivative works, incorporate into other computer software, distribute, and sublicense such enhancements or derivative works thereof, in binary and source code form.
-
-***************************************************************************

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
@@ -60,8 +63,8 @@ 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,
+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

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 +1,6 @@
 -r requirements.txt
+coverage
+flake8
 black>=20.8b1
 pytest>=3.0.0
 pytest-cov

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