Merge pull request #81 from aburrell/rc_v2.6.3

Release Candidate version 2.6.3

.github/pull_request_template.md

@@ -26,9 +26,9 @@ your test configuration
 - [ ] Test B
 
 **Test Configuration**:
-* Operating system
-* Version number
-* Any details about your local setup that are relevant
+* Operating system: Hal
+* Version number: Python 3.0
+* Any details about your local setup that are relevant: 
 
 # Checklist:
 
@@ -42,4 +42,4 @@ your test configuration
 - [ ] New and existing unit tests pass locally with my changes
 - [ ] Any dependent changes have been merged and published in downstream modules
 - [ ] Add a note to ``Changelog.rst``, summarising the changes
-- [ ] Add yourself to ``AUTHORS.rst``
+- [ ] Add yourself to ``AUTHORS.rst`` and ``.zenodo.json``

.github/workflows/docs.yml

@@ -0,0 +1,43 @@
+# This workflow will install Python dependencies, run tests and lint with a
+# variety of Python versions. For more information see:
+# https://help.github.com/actions/language-and-framework-guides/
+# using-python-with-github-actions
+
+name: Documentation test
+
+on: [push, pull_request]
+
+jobs:
+  build:
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest]
+        python-version: ["3.9"]
+
+    env:
+       FC: gfortran
+
+    name: Docs ${{ matrix.python-version }} on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install standard and test dependencies, then apexpy
+      run: |
+        pip install build
+        python -m build .
+        pip install -r docs/requirements.txt
+
+    - name: Check documentation build
+      run: sphinx-build -E -b html docs dist/docs
+
+    - name: Check documentation links
+      run: sphinx-build -b linkcheck docs dist/docs
+
+    - name: Load .zenodo.json to check for errors
+      run: python -c "import json; json.loads(open('.zenodo.json').read())"

.github/workflows/main.yml

@@ -0,0 +1,65 @@
+# This workflow will install Python dependencies, run tests and lint with a
+# variety of Python versions. For more information see:
+# https://help.github.com/actions/language-and-framework-guides/
+# using-python-with-github-actions
+
+name: pytest with flake8
+
+on: [push, pull_request]
+
+jobs:
+  build:
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ["3.7", "3.8", "3.9", "3.10"]
+
+    name: Python ${{ matrix.python-version }} on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+        architecture: 'x64'
+
+    - name: Install standard and test dependencies
+      run: pip install build coverage coveralls flake8 numpy pytest
+
+    - name: Install on Linux/Windows
+      if: ${{ matrix.os != 'macos-latest' }}
+      run: |
+          python -m build .
+          pip install -e .
+
+    - name: Install on MacOS
+      if: ${{ matrix.os == 'macos-latest' }}
+      run: |
+          brew reinstall gcc
+          python -m build .
+          pip install -e .
+
+    - name: Test PEP8 compliance
+      run: flake8 . --count --select=D,E,F,H,W --show-source --statistics
+
+    - name: Evaluate complexity
+      run: flake8 . --count --exit-zero --max-complexity=10 --statistics
+
+    - name: Run unit and integration tests
+      run: coverage run --rcfile=setup.cfg -m pytest
+
+    - name: Publish results to coveralls upon success
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      run: |
+           coverage combine
+           coverage report -m
+           coveralls --rcfile=setup.cfg --service=github
+
+    - name: Upload wheels
+      uses: actions/upload-artifact@v3
+      with:
+         path: dist/*.whl
+         if-no-files-found: warn

AUTHORS.rst

@@ -3,11 +3,13 @@ Authors
 =======
 
 * Angeline G. Burrell - https://github.com/aburrell
-* Christer van der Meeren
-* Karl M. Laundal
+* Christer van der Meeren - https://github.com/cmeeren
+* Karl M. Laundal - https://github.com/klaundal
 * Hugo van Kemenade - https://github.com/hugovk
 
 Thanks
 ======
+
 * Marina Shmidt - Testing and code review
 * Bill Rideout - Testing
+* dinsmoro - Testing - https://github.com/dinsmoro

CHANGELOG.rst

@@ -2,6 +2,18 @@
 Changelog
 =========
 
+2.6.3 (2023-02-08)
+------------------
+
+* Moved CI support to GitHub actions
+* Added a pyproject.toml for PyPi support
+* Updated unit tests to current pytest standards
+* Updated links in the documentation
+* Improved the documentation style and added docstring tests
+* Fixed memory leak in the array C wrappers
+* Fixed longitude output format for `convert_mlt`
+* Added more examples to the documentation
+
 2.6.2 (2020-01-13)
 ------------------
 

CONTRIBUTING.rst

@@ -14,7 +14,8 @@ time you have given to improve this project.
 Short version
 =============
 
-* Submit bug reports and feature requests at `GitHub <https://github.com/aburrell/aacgmv2/issues>`_
+* Submit bug reports and feature requests at
+  `GitHub <https://github.com/aburrell/aacgmv2/issues>`_
 * Make pull requests to the ``develop`` branch
 
 Bug reports
@@ -50,7 +51,11 @@ To set up `aacgmv2` for local development:
 
     git clone git@github.com:your_name_here/aacgmv2.git
 
-3. Create a branch for local development::
+3. Build the local code to allow for local Python development::
+
+    pip install -e .
+
+4. Create a branch for local development::
 
     git checkout -b name-of-your-bugfix-or-feature
 
@@ -62,18 +67,17 @@ To set up `aacgmv2` for local development:
    written as normal functions (starting with ``test_``) containing a standard
    ``assert`` statement for testing output, or use the numpy testing suite.
 
-4. When you're done making changes, run all the checks, doc builder and spell
-   checker with `tox <https://tox.readthedocs.io/en/latest/install.html>`_ [1]_::
+5. When you're done making changes, run the local unit tests using pytest::
 
-    tox
+    python -m pytest
 
-5. Commit your changes and push your branch to GitHub::
+6. Commit your changes and push your branch to GitHub::
 
     git add .
     git commit -m "Brief description of your changes"
     git push origin name-of-your-bugfix-or-feature
 
-6. Submit a pull request through the GitHub website. Pull requests should be
+7. Submit a pull request through the GitHub website. Pull requests should be
    made to the ``develop`` branch.
 
 Pull Request Guidelines
@@ -91,16 +95,5 @@ For merging, you should:
 
 .. [1] If you don't have all the necessary Python versions available locally or
        have trouble building all the testing environments, you can rely on
-       Travis and AppVeyor - they will run the tests for each change you add in
+       GitHub Actions - it will run the tests for each change you add in
        the pull request.
-
-Tips
-----
-
-To run a subset of tests::
-
-    tox -e envname -- pytest -k test_myfeature
-
-To run all the test environments in parallel (you need to ``pip install detox``)::
-
-    detox

MANIFEST.in

@@ -1,5 +1,4 @@
 graft docs
-graft ci
 graft aacgmv2/tests
 graft c_aacgmv2
 
@@ -17,7 +16,6 @@ include LICENSE-AstAlg.txt
 include README.rst
 include CODE_OF_CONDUCT.md
 
-include tox.ini
 include *.yml
 include .*.yml
 include .zenodo.json

README.rst

@@ -64,31 +64,27 @@ Badges
     :stub-columns: 1
 
     * - docs
-      - |docs|
+      - |docs| |links|
     * - tests
-      - | |travis| |appveyor| |requires|
-        | |codeclimate| |scrutinizer| |codacy| |coveralls|
+      - | |ga| |coveralls|
+        | |codeclimate| |scrutinizer| |codacy|
     * - package
       - | |version| |supported-versions|
         | |wheel| |supported-implementations|
 
 .. |docs| image:: https://readthedocs.org/projects/aacgmv2/badge/?version=latest
     :target: https://aacgmv2.readthedocs.io/en/latest/?badge=latest
-    :alt: Documentation Status
+    :alt: RTD Documentation Status
 
-.. |travis| image:: https://api.travis-ci.org/aburrell/aacgmv2.svg?branch=main
-    :alt: Travis-CI Build Status
-    :target: https://travis-ci.org/github/aburrell/aacgmv2
+.. |links| image:: https://github.com/aburrell/aacgmv2/actions/workflows/docs.yml/badge.svg
+    :target: https://github.com/aburrell/aacgmv2/actions/workflows/docs.yml
+    :alt: GitHub Actions Documentation Status
 
-.. |appveyor| image:: https://ci.appveyor.com/api/projects/status/qo01t2obf7bscveu?svg=true
-    :alt: AppVeyor Build Status
-    :target: https://ci.appveyor.com/project/aburrell/aacgmv2
+.. |ga| image:: https://github.com/aburrell/aacgmv2/actions/workflows/main.yml/badge.svg
+    :alt: GitHub Actions-CI Build Status
+    :target: https://github.com/aburrell/aacgmv2/actions/workflows/main.yml
 
-.. |requires| image:: https://requires.io/github/aburrell/aacgmv2/requirements.svg?branch=main
-    :alt: Requirements Status
-    :target: https://requires.io/github/aburrell/aacgmv2/requirements/?branch=main
-
-.. |coveralls| image:: https://coveralls.io/repos/github/aburrell/aacgmv2/badge.svg
+.. |coveralls| image:: https://s3.amazonaws.com/assets.coveralls.io/badges/coveralls_97.svg
     :alt: Coverage Status (Coveralls)
     :target: https://coveralls.io/github/aburrell/aacgmv2
 

aacgmv2/__init__.py

@@ -4,11 +4,10 @@
 # the root in the LICENSE file
 #
 # -*- coding: utf-8 -*-
-""" Functions to convert between geographic/geodetic and AACGM-V2 magnetic
-coordinates
+"""Conversion functions between geo-graphic/detic and AACGM-V2 magnetic coords.
 
 Attributes
----------------------------------------------------------------------------
+----------
 logger : (logger)
     Logger handle
 high_alt_coeff : (float)
@@ -26,15 +25,19 @@
 import os as _os
 from sys import stderr
 
-from aacgmv2.wrapper import (convert_latlon, convert_mlt, get_aacgm_coord)
-from aacgmv2.wrapper import (convert_latlon_arr, get_aacgm_coord_arr)
-from aacgmv2.wrapper import (convert_bool_to_bit, convert_str_to_bit)
-from aacgmv2 import (utils)
-from aacgmv2 import (deprecated)
-from aacgmv2 import (_aacgmv2)
+from aacgmv2.wrapper import convert_bool_to_bit  # noqa F401
+from aacgmv2.wrapper import convert_latlon  # noqa F401
+from aacgmv2.wrapper import convert_latlon_arr  # noqa F401
+from aacgmv2.wrapper import convert_mlt  # noqa F401
+from aacgmv2.wrapper import convert_str_to_bit  # noqa F401
+from aacgmv2.wrapper import get_aacgm_coord  # noqa F401
+from aacgmv2.wrapper import get_aacgm_coord_arr  # noqa F401
+from aacgmv2 import _aacgmv2  # noqa F401
+from aacgmv2 import deprecated  # noqa F401
+from aacgmv2 import utils  # noqa F401
 
 # Define global variables
-__version__ = "2.6.2"
+__version__ = "2.6.3"
 
 # Define a logger object to allow easier log handling
 logger = logging.getLogger('aacgmv2_logger')
@@ -43,7 +46,7 @@
 high_alt_coeff = 2000.0  # Tested and published in Shepherd (2014)
 high_alt_trace = 6378.0  # 1 RE, these are ionospheric coordinates
 
-# path and filename prefix for the IGRF coefficients
+# Path and filename prefix for the IGRF coefficients
 AACGM_v2_DAT_PREFIX = _os.path.join(_os.path.realpath(
     _os.path.dirname(__file__)), 'aacgm_coeffs', 'aacgm_coeffs-13-')
 IGRF_COEFFS = _os.path.join(_os.path.realpath(_os.path.dirname(__file__)),