Merge pull request #37 from pysat/develop

Version 0.5 Release

Author: rstoneback

.coveragerc

@@ -0,0 +1,3 @@
+[report]
+omit =
+  */tests/*

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,29 @@
+---
+name: Bug report
+about: Create a report to help us improve
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Desktop (please complete the following information):**
+ - OS: [e.g. iOS]
+ - Version [e.g. 22]
+ - Other details about your setup that could be relevant
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,17 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/pull_request_template.md

@@ -0,0 +1,44 @@
+# Description
+
+Addresses #(issue)
+
+Please include a summary of the change and which issue is fixed. Please also
+include relevant motivation and context. List any dependencies that are required
+for this change.  Please see ``CONTRIBUTING.md`` for more guidelines.
+
+## Type of change
+
+Please delete options that are not relevant.
+
+- Bug fix (non-breaking change which fixes an issue)
+- New feature (non-breaking change which adds functionality)
+- Breaking change (fix or feature that would cause existing functionality
+      to not work as expected)
+- This change requires a documentation update
+
+# How Has This Been Tested?
+
+Please describe the tests that you ran to verify your changes. Provide
+instructions so we can reproduce. Please also list any relevant details for
+your test configuration
+
+- Test A
+- Test B
+
+**Test Configuration**:
+* Operating system
+* Version number
+* Any details about your local setup that are relevant
+
+# Checklist:
+
+- [ ] Make sure you are merging into the ``develop`` (not ``master``) branch
+- [ ] My code follows the style guidelines of this project
+- [ ] I have performed a self-review of my own code
+- [ ] I have commented my code, particularly in hard-to-understand areas
+- [ ] I have made corresponding changes to the documentation
+- [ ] My changes generate no new warnings
+- [ ] I have added tests that prove my fix is effective or that my feature works
+- [ ] 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.md``, summarizing the changes

.travis.yml

@@ -1,44 +1,45 @@
-language: python
-python:
-  - "2.7"
-  - "3.6"
-sudo: false
-
-addons:
-  apt:
-    packages:
-    - gfortran
-    - libncurses5-dev
-
-# Setup anaconda
-before_install:
-  #- apt-get update
-  - if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then
-      wget https://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh;
-    else
-      wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
-    fi
-  - bash miniconda.sh -b -p $HOME/miniconda
-  - export PATH="$HOME/miniconda/bin:$PATH"
-  - hash -r
-  - conda config --set always_yes yes --set changeps1 no
-  - conda update -q --yes conda
-  # Useful for debugging any issues with conda
-  - conda info -a
-
-  # Replace dep1 dep2 ... with your dependencies
-  - conda create -q -n test-environment python=$TRAVIS_PYTHON_VERSION atlas numpy scipy matplotlib nose pandas statsmodels coverage netCDF4 xarray
-
-# command to install dependencies
-install:
-  - source activate test-environment
-  - pip install coveralls
-  - pip install pysatCDF >/dev/null
-  - pip install pysat
-  - "python setup.py develop"
-# command to run tests
-script: 
-  - nosetests  -vs --with-coverage --cover-package=pysatMagVect
-  #coverage run --source=pysat setup.py test
-after_success:
-  coveralls
+language: python
+dist: xenial
+matrix:
+  include:
+    - python: 2.7
+    - python: 3.6
+    - python: 3.7
+    - python: 3.8
+
+addons:
+  apt:
+    packages:
+    - gfortran
+
+before_install:
+  - pip install pytest-cov
+  - pip install coveralls
+  - pip install future
+  # Install version specific packages for 2.7 and 3.5
+  - pip install 'pandas<0.25'
+  - pip install xarray
+  - pip install matplotlib
+  - pip install apexpy
+  - pip install numpy
+  - pip install pysatCDF >/dev/null
+  - cd ..
+  - git clone https://github.com/pysat/pysat.git >/dev/null
+  - cd ./pysat
+  - python setup.py install >/dev/null
+  - cd ..
+  # set up data directory
+  - mkdir /home/travis/build/pysatData
+  - python -c 'import pysat; pysat.utils.set_data_dir("/home/travis/build/pysatData")'
+
+install:
+  # install pysatMagVect
+  - cd ./pysatMagVect
+  - python setup.py develop
+
+# command to run tests
+script:
+  - nosetests  -vs --with-coverage --cover-package=pysatMagVect
+
+after_success:
+  - coveralls

CHANGELOG.md

@@ -0,0 +1,39 @@
+# Change Log
+All notable changes to this project will be documented in this file.
+This project adheres to [Semantic Versioning](http://semver.org/).
+
+## [0.5.0] - 2020-02-01
+- Added community documents
+- Implemented new algorithm for basis vectors. First system valid for multipole fields.
+- Implemented new E and D scaling vectors similar to Richmond (apexpy)
+- Implemented high accuracy numerical path that minimizes geodetic transformations
+- Reviewed and updated default parameters based upon observed peformance
+- Validated meridional vector along maximum apex height gradient
+- Retained previous basis methods, identified by heritage or integrated
+- Improved accuracy and robustness of heritage techniques though new methods recommended
+- Validated accuracy of scaling methods
+- Incorporated IGRF13
+- Expanded and organized unit tests
+- Removed pysat as a dependency
+- Docstring improvements
+
+## [0.4.0] - 2018-11-26
+- Testing routines have been expanded significantly.
+- Default parameters have been updated based upon this testing.
+- Numerous corrections have been implemented.
+
+## [0.3.1] - 2018-08-06
+- Improved use of ECEF and ENU vectors.
+
+## [0.3.0] - 2018-07-24
+- Improved robustness of setup.py
+- Corrected Earth Centered Earth Fixed (ECEF) and East, North, Up (ENU) conversion routines.
+
+## [0.2.0] - 2018-07-05
+- Improved documentation and metadata.
+
+## [0.1.6] - 2018-06-29
+- Improved installation process
+
+## [0.1.0] - 2018-06-27
+- Initial release

CODE_OF_CONDUCT.md

@@ -0,0 +1,76 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers pledge to making participation in our project and
+our community a harassment-free experience for everyone, regardless of age, body
+size, disability, ethnicity, sex characteristics, gender identity and expression,
+level of experience, education, socio-economic status, nationality, personal
+appearance, race, religion, or sexual identity and orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment
+include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or
+ advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic
+ address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+ professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or
+reject comments, commits, code, wiki edits, issues, and other contributions
+that are not aligned to this Code of Conduct, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community. Examples of
+representing a project or community include using an official project e-mail
+address, posting via an official social media account, or acting as an appointed
+representative at an online or offline event. Representation of a project may be
+further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting the project team at pysat.developers@gmail.com. All
+complaints will be reviewed and investigated and will result in a response that
+is deemed necessary and appropriate to the circumstances. The project team is
+obligated to maintain confidentiality with regard to the reporter of an incident.
+Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
+available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see
+https://www.contributor-covenant.org/faq

CONTRIBUTING.md

@@ -8,13 +8,13 @@ contributions.
 Short version
 =============
 
-* Submit bug reports and feature requests at `GitHub <https://github.com/rstoneback/pysatMagVect/issues>`_
+* Submit bug reports and feature requests at `GitHub <https://github.com/pysat/pysatMagVect/issues>`_
 * Make pull requests to the ``develop`` branch
 
 Bug reports
 ===========
 
-When `reporting a bug <https://github.com/rstoneback/pysatMagVect/issues>`_ please
+When `reporting a bug <https://github.com/pysat/pysatMagVect/issues>`_ please
 include:
 
 * Your operating system name and version
@@ -25,7 +25,7 @@ Feature requests and feedback
 =============================
 
 The best way to send feedback is to file an issue at
-`GitHub <https://github.com/rstoneback/pysatMagVect/issues>`_.
+`GitHub <https://github.com/pysat/pysatMagVect/issues>`_.
 
 If you are proposing a feature:
 
@@ -39,7 +39,7 @@ Development
 
 To set up `pysat` for local development:
 
-1. `Fork pysat on GitHub <https://github.com/rstoneback/pysatMagVect/fork>`_.
+1. `Fork pysat on GitHub <https://github.com/pysat/pysatMagVect/fork>`_.
 2. Clone your fork locally::
 
     git clone git@github.com:your_name_here/pysatMagVect.git

MANIFEST.in

@@ -1,3 +1,4 @@
 include pysatMagVect/version.txt
 include LICENSE
-include CONTRIBUTING.md
+include CONTRIBUTING.md
+prune pysatMagVect/tests

README.md

@@ -1,33 +1,33 @@
 # pysatMagVect
-[![Build Status](https://travis-ci.org/rstoneback/pysatMagVect.svg?branch=master)](https://travis-ci.org/rstoneback/pysatMagVect)
-[![Coverage Status](https://coveralls.io/repos/github/rstoneback/pysatMagVect/badge.svg?branch=master)](https://coveralls.io/github/rstoneback/pysatMagVect?branch=master)
+[![Build Status](https://travis-ci.org/pysat/pysatMagVect.svg?branch=master)](https://travis-ci.org/pysat/pysatMagVect)
+[![Coverage Status](https://coveralls.io/repos/github/pysat/pysatMagVect/badge.svg?branch=master)](https://coveralls.io/github/pysat/pysatMagVect?branch=master)
 [![Documentation Status](https://readthedocs.org/projects/pysatmagvect/badge/?version=latest)](https://pysatmagvect.readthedocs.io/en/latest/?badge=latest)
 [![DOI](https://zenodo.org/badge/138220240.svg)](https://zenodo.org/badge/latestdoi/138220240)
 
-The motion of plasma in the ionosphere is the result of forcing from netural winds, electric fields, neutral collisions, as well as the orientation of the background magnetic field. Plasma moves easily along the magnetic field line and less so across it. PysatMagVect calculates directions (unit vectors) based upon the geomagnetic field that are most relevant for understanding the movement of plasma. In addition, pysatMagVect includes methods for scaling ion drifts at one location to either the magnetic footpoint or to the magnetic equator. Scaling to the footpoint is critical for understanding how neutral atmosphere winds at low altitudes (footpoint heights) will be expressed either at the satellite location or at the magnetic equator. Scaling to the magnetic equator can be particularly effective when creating a common basis for integrating measurements from multiple platforms.
+The motion of plasma in the ionosphere is the result of forcing from neutral winds, electric fields, neutral collisions, as well as the orientation of the background magnetic field. Plasma moves easily along the magnetic field line and less so across it. PysatMagVect calculates directions (unit vectors) based upon the geomagnetic field that are most relevant for understanding the movement of plasma. In addition, pysatMagVect includes methods for scaling ion drifts at one location to either the magnetic footpoint or to the magnetic equator. Scaling to the footpoint is critical for understanding how neutral atmosphere winds at low altitudes (footpoint heights) will be expressed either at the satellite location or at the magnetic equator. Scaling to the magnetic equator can be particularly effective when creating a common basis for integrating measurements from multiple platforms.
 
 PysatMagVect is used by the upcoming NASA Ionospheric Connections (ICON) Explorer Mission to understand how remote measurements of neutral motions at 120 km impacts the motion of plasma measured in situ (at the satellite location). This package is also being used by the upcoming NOAA/NSPO COSMIC-2 constellation to express plasma measurements made at the satellite locations in a more geophysically useful basis. PysatMagVect is currently being incorporated into analysis routines suitable for integrating physics-based models (TIEGCM) and measurements from the Communications/Navigation Outage Forecasting System (C/NOFS) satellite.
 
 The development of this software has been supported, in part, by multiple agencies under the following grants: National Aeronautics and Space Agency (NASA NNG12FA45C), National Oceanic and Atmospheric Administration(NOAA NSF AGS-1033112), and the National Science Foundation (NSF 1651393).
 
 # Field-Line Tracing
 The International Geomagnetic Reference Field (IGRF) is coupled into SciPy's odeint to produce an accurate field
-line tracing algorithm that terminates at a supplied reference height, or after a fixed number of steps. The SciPy integrator is an adaptive method that internally determines an appropriate step size thus the performance of the technique is both robust and accurate. The sensitivity of the field line tracing and other quantities in this package have been established via direct comparison (when possible) as well as sensitvity and consistency tests.
+line tracing algorithm that terminates at a supplied reference height, or after a fixed number of steps. The SciPy integrator is an adaptive method that internally determines an appropriate step size thus the performance of the technique is both robust and accurate. The sensitivity of the field line tracing and other quantities in this package have been established via direct comparison (when possible) as well as sensitivity and consistency tests.
 
 # Geomagnetic Unit Vectors
 Plasma in the ionosphere is constrained by the geomagnetic field. Motion along magnetic field lines is easy while motion across field lines is comparatively hard. To understand the motion of ions it is generally best to do so along these directions.
 
  - Field Aligned: Along the geomagnetic field, pointing generally from south to north at the equator.
 
- - Zonal: Prependicular to the field aligned vector and the meridional plane of the field line (plane formed by the large scale distribution of the field line)
+ - Zonal: Perpendicular to the field aligned vector and the meridional plane of the field line (plane formed by the large scale distribution of the field line)
 
  - Meridional: Perpendicular to the zonal and field aligned directions. This vector is positive upward and is vertical at the geomagnetic equator. To remain perpendicular to the field, the meridional vector has a poleward component when away from the magnetic equator. Note that meridional may sometimes be used in other contexts to be north/south. Here, the vector is generally up/down.
- 
+
  # Ion Drift Mapping
  Calculates scalars for mapping ion motions expressed in geomagnetic unit vectors to either the magnetic footpoint or to the magnetic equator. These scalars are determined assuming that magnetic field lines are equipotential, thus the electric field associated with ion motion will vary as the distance between two geomagnetic field lines changes. The ExB/B^2 motion accounted for here also varies with magnetic field strength. Either the mappings for just the electric field, or the ion drift, are available. Scaling from the equator or footpoint to a different location is achieved by taking the inverse of the supplied parameters.
 
  # Coordinate Transformations
- Supports the conversion of geographic and geodetic (WGS84) into eachother and into Earth Centered Earth Fixed (ECEF). ECEF coordinates are fixed with respect to the Earth, x points from the center towards 0 degrees longitude at the geographic equator, y similarly points to 90 degrees east, while z points along the Earth's rotation axis.
- 
+ Supports the conversion of geographic and geodetic (WGS84) into each other and into Earth Centered Earth Fixed (ECEF). ECEF coordinates are fixed with respect to the Earth, x points from the center towards 0 degrees longitude at the geographic equator, y similarly points to 90 degrees east, while z points along the Earth's rotation axis.
+
  # Vector Transformations
  Supports expressing a vector known in one basis into the same vector expressed in another basis. This supports translating measurements made in a spacecraft frame into frames more relevant for scientific analysis.