Merge pull request #58 from jklenzing/develop

Merge from develop - 0.1.0-alpha

.github/pull_request_template.md

@@ -0,0 +1,43 @@
+# Description
+
+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.
+
+Fixes # (issue)
+
+## 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

.travis.yml

@@ -1,21 +1,28 @@
 language: python
-python:
-  - "2.7"
-  - "3.4"
-  - "3.5"
-  - "3.6"
-sudo: false
+dist: xenial
+matrix:
+  include:
+    - python: 2.7
+    - python: 3.4
+    - python: 3.5
+    - python: 3.6
+    - python: 3.7
 
 addons:
   apt:
     packages:
     - gfortran
 
 before_install:
+  - pip install coveralls
+  - pip install future
   - pip install matplotlib
 install:
   - source activate test-environment
   - python setup.py install
   - make -C sami2py/fortran compile
 script:
   - nosetests -vs --with-coverage --cover-package=sami2py
+
+after_success:
+  - coveralls

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 sami2py.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

@@ -6,13 +6,13 @@ appreciated!  Sami2py is a community-driven project and welcomes both feedback a
 contributions.
 
 Short version
-=============
+-------------
 
 * Submit bug reports and feature requests through [GitHub](https://github.com/jklenzing/sami2py/issues)
 * Make pull requests to the ``develop`` branch
 
 Bug reports
-===========
+-----------
 
 When [reporting a bug](https://github.com/jklenzing/sami2py/issues>) please
 include:
@@ -22,7 +22,7 @@ include:
 * Detailed steps to reproduce the bug
 
 Feature requests and feedback
-=============================
+-----------------------------
 
 The best way to send feedback is to file an issue at
 `GitHub <https://github.com/jklenzing/sami2py/issues>`_.
@@ -35,7 +35,7 @@ If you are proposing a feature:
   are welcome :)
 
 Development
-===========
+-----------
 
 To set up `sami2py` for local development:
 
@@ -54,15 +54,15 @@ To set up `sami2py` for local development:
 
    Now you can make your changes locally. Tests for new instruments are
    performed automatically.  Tests for custom functions should be added to the
-   appropriately named file in ``sami2py/tests``.   If no test file exists, then 
-   you should create one.  This testing uses nose, which will run tests on any 
+   appropriately named file in ``sami2py/tests``.   If no test file exists, then
+   you should create one.  This testing uses nose, which will run tests on any
    python file in the test directory that starts with ``test_``.
-    
+
 4. When you're done making changes, run all the checks to ensure that nothing
    is broken on your local system
-   
+
 ::
-   
+
     nosetests -vs sami2py
 
 5. Update/add documentation (in ``docs``), if relevant

README.md

@@ -1,15 +1,16 @@
 # sami2py: sami2py is another model of the ionosphere python style
-
-[![Build Status](https://travis-ci.com/jklenzing/sami2py.svg?branch=master)](https://travis-ci.org/jklenzing/sami2py)
+[![Build Status](https://travis-ci.com/jklenzing/sami2py.svg?branch=master)](https://travis-ci.com/jklenzing/sami2py)
+[![Coverage Status](https://coveralls.io/repos/github/jklenzing/sami2py/badge.svg?branch=master)](https://coveralls.io/github/jklenzing/sami2py?branch=master)
+[![Documentation Status](https://readthedocs.org/projects/sami2py/badge/?version=latest)](http://sami2py.readthedocs.io/en/latest/?badge=latest)
 
 # Overview
 
 Sami2py is a python module that runs the SAMI2 model, as well as archives, loads and plots the resulting modeled values. SAMI2 is a model developed by the Naval Research Laboratory to simulate the motions of plasma in a 2D ionospheric environment along a dipole magnetic field [Huba et al, 2000].  SAMI2 solves for the chemical and dynamical evolution of seven ion species in this environment (H<sup>+</sup>, He<sup>+</sup>, N<sup>+</sup>, O<sup>+</sup>, N<sub>2</sub><sup>+</sup>, NO<sup>+</sup>, and O<sub>2</sub><sup>+</sup>).
 
-The implementation used here includes several added options to the original release of SAMI2.  A full list is included in ***add link to changes page***, but several of these include:
+The implementation used here includes several added options to the original release of SAMI2.  A full list is included in https://sami2py.readthedocs.io/en/latest/modifications.html, but several of these include:
  - The ability to scale the neutral atmosphere in which the ions form through direct modification of the exospheric neutral temperature for extreme solar minimum conditions, as discussed by Emmert et al [2010].  
- - The ability to switch between HWM93, HWM07, and HWM14 as a user option.
- This implementation is based on the version used in Klenzing et al [2013].
+ - The ability to switch input custom ExB drifts as a Fourier series.
+ This implementation is based on the matlab version used in Klenzing et al [2013].
 
 # Installation
 
@@ -48,18 +49,18 @@ Note that the sami2 model runs for 24 hours to clear transients, then begins to
 Now load the resultant data:
 
 ```
-  ModelRun = sami2py.model(tag='test', lon=0, year=2012, day=210)
+  ModelRun = sami2py.Model(tag='test', lon=0, year=2012, day=210)
 ```
 
 Plotting features coming soon...
 
 # How to Cite
-When referring to this software package, please cite the original paper by Huba et al [2000] https://doi.org/10.1029/2000JA000035 as well as the package by Klenzing et al [2018]. ***add doi here***.
+When referring to this software package, please cite the original paper by Huba et al [2000] https://doi.org/10.1029/2000JA000035 as well as the package by Klenzing et al [2019]. ***add doi here***.
 
 Additionally, please include the following text in the acknowledgements: "This
 work uses the SAMI2 ionosphere model written and developed by the Naval Research Laboratory."
 
 # References
 - Huba, J.D., G. Joyce, and J.A. Fedder, Sami2 is Another Model of the Ionosphere (SAMI2): A new low‐latitude ionosphere model, *J. Geophys. Res.*, 105, Pages 23035-23053, https://doi.org/10.1029/2000JA000035, 2000.
 - Emmert, J.T., J.L. Lean, and J.M. Picone, Record‐low thermospheric density during the 2008 solar minimum, *Geophys. Res. Lett.*, 37, https://doi.org/10.1029/2010GL043671, 2010.
-- Klenzing, J., Burrell, A. G., Heelis, R. A., Huba, J. D., Pfaff, R., and Simões, F.: Exploring the role of ionospheric drivers during the extreme solar minimum of 2008, *Ann. Geophys.*, 31, 2147-2156, https://doi.org/10.5194/angeo-31-2147-2013, 2013.
+- Klenzing, J., A. G. Burrell, R. A. Heelis, J. D. Huba, R. Pfaff, and F. Simões, Exploring the role of ionospheric drivers during the extreme solar minimum of 2008, *Ann. Geophys.*, 31, 2147-2156, https://doi.org/10.5194/angeo-31-2147-2013, 2013.