Merge pull request #75 from pysat/rc_0_3_0

Release Candidate 0.3.0

.codeclimate.yml

@@ -2,16 +2,13 @@
 plugins:
   radon:
     enabled: true
-  pep8:
-    enabled: true
   sonar-python:
     enabled: true
 ratings:
   paths:
   - "**.py"
 exclude_paths:
   - ".github/**/*"
-  - "pysatMissions/tests/**/*"
   - "docs/**/*"
   - "setup.py"
   - ".*"

.github/workflows/main.yml

@@ -11,32 +11,35 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.7, 3.8, 3.9]
+        python-version: ["3.8", "3.9", "3.10"]
         os: [ubuntu-latest]
+        numpy_ver: ["latest"]
 
-    name: Python ${{ matrix.python-version }} on ${{ matrix.os }}
+    name: Python ${{ matrix.python-version }} on ${{ matrix.os }} with numpy ${{ matrix.numpy_ver }}
     runs-on: ${{ matrix.os }}
     steps:
     - uses: actions/checkout@v2
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v2
       with:
         python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
+
+    - name: Install requirements for testing setup
       run: |
         python -m pip install --upgrade pip
         pip install -r test_requirements.txt
+
+    - name: Install dependencies
+      run: |
         pip install -r requirements.txt
-        # Manual install of OMMBV
-        pip install --no-binary :OMMBV: OMMBV
 
     - name: Set up pysat
       run: |
         mkdir pysatData
         python -c "import pysat; pysat.params['data_dirs'] = 'pysatData'"
 
     - name: Test PEP8 compliance
-      run: flake8 . --count --select=E,F,W --show-source --statistics
+      run: flake8 . --count --select=D,E,F,H,W --show-source --statistics
 
     - name: Evaluate complexity
       run: flake8 . --count --exit-zero --max-complexity=10 --statistics

.zenodo.json

@@ -6,7 +6,7 @@
         "orcid": "0000-0001-8321-6074"
       },
       {
-        "affiliation": "The University of Texas at Dallas",
+        "affiliation": "Stoneris",
         "name": "Stoneback, Russell",
         "orcid": "0000-0001-7216-4336"
       },

CHANGELOG.md

@@ -2,6 +2,22 @@
 All notable changes to this project will be documented in this file.
 This project adheres to [Semantic Versioning](https://semver.org/).
 
+## [0.3.0] - 2022-05-13
+* Add Keplerian orbital inputs into missions_sgp4
+* Update sgp4 interface to use new syntax for initialization from TLEs
+* Include conversions to geodetic latitude / longitude / altitude for sgp4
+* Improve metadata generation in missions_sgp4
+* Update syntax to be compliant with OMMBV 1.0
+* Documentation
+  * Improve docstrings throughout
+  * Added bypass for apexpy for readthedocs build
+* Deprecations
+  * Deprecated missions_ephem, as pyephem will no longer be updated
+* Testing
+  * Add style check for docstrings
+  * Added checks for deprecation warnings
+  * Improve checks in codeclimate
+
 ## [0.2.2] - 2021-06-18
 * Migrate pyglow interface to pysatIncubator
 * Style updates for consistency with pysat 3.0

CONTRIBUTING.md

@@ -4,16 +4,21 @@ Contributing
 Bug reports, feature suggestions and other contributions are greatly
 appreciated!  pysatMissions is a community-driven project and welcomes both feedback and contributions.
 
+Come join us on Slack! An invitation to the pysat workspace is available
+in the 'About' section of the
+[pysat GitHub Repository.](https://github.com/pysat/pysat) Development meetings
+are generally held fortnightly.
+
 Short version
 -------------
 
-* Submit bug reports and feature requests at `GitHub <https://github.com/pysat/pysatMissions/issues>`_
+* Submit bug reports and feature requests at [GitHub](https://github.com/pysat/pysatMissions/issues)
 * Make pull requests to the ``develop`` branch
 
 Bug reports
 -----------
 
-When `reporting a bug <https://github.com/pysat/pysatMissions/issues>`_ please
+When [reporting a bug](https://github.com/pysat/pysatMissions/issues) please
 include:
 
 * Your operating system name and version
@@ -24,7 +29,7 @@ Feature requests and feedback
 -----------------------------
 
 The best way to send feedback is to file an issue at
-`GitHub <https://github.com/pysat/pysatMissions/issues>`_.
+[GitHub](https://github.com/pysat/pysatMissions/issues).
 
 If you are proposing a feature:
 
@@ -38,14 +43,17 @@ Development
 
 To set up `pysatMissions` for local development:
 
-1. `Fork pysat on GitHub <https://github.com/pysat/pysatMissions/fork>`_.
-2. Clone your fork locally::
-
-    git clone git@github.com:your_name_here/pysatMissions.git
+1. [Fork pysat on GitHub](https://github.com/pysat/pysatMissions/fork).
 
-3. Create a branch for local development::
+3. Clone your fork locally:
+   ```
+   git clone git@github.com:your_name_here/pysatMissions.git
+   ```
 
-    git checkout -b name-of-your-bugfix-or-feature
+3. Create a branch for local development:
+   ```
+   git checkout -b name-of-your-bugfix-or-feature
+   ```
 
    Now you can make your changes locally. Tests for new instruments are
    performed automatically.  Tests for custom functions should be added to
@@ -55,19 +63,31 @@ To set up `pysatMissions` for local development:
    ``test_``.
 
 4. When you're done making changes, run all the checks to ensure that nothing
-   is broken on your local system::
-
-    pytest -vs
+   is broken on your local system:
+   ```
+   pytest -vs
+   ```
 
 5. Update/add documentation (in ``docs``), if relevant
 
-5. Commit your changes and push your branch to GitHub::
+6. Add your name to the .zenodo.json file as an author
+
+7. Commit your changes:
+   ```
+   git add .
+   git commit -m "AAA: Brief description of your changes"
+   ```
+   Where AAA is a standard shorthand for the type of change (eg, BUG or DOC).
+   `pysat` follows the [numpy development workflow](https://numpy.org/doc/stable/dev/development_workflow.html),
+   see the discussion there for a full list of this shorthand notation.  
 
-    git add .
-    git commit -m "Brief description of your changes"
-    git push origin name-of-your-bugfix-or-feature
+8. Once you are happy with the local changes, push to Github:
+   ```
+   git push origin name-of-your-bugfix-or-feature
+   ```
+   Note that each push will trigger the Continuous Integration workflow.
 
-6. Submit a pull request through the GitHub website. Pull requests should be
+9. Submit a pull request through the GitHub website. Pull requests should be
    made to the ``develop`` branch.
 
 Pull Request Guidelines
@@ -81,45 +101,45 @@ For merging, you should:
 1. Include an example for use
 2. Add a note to ``CHANGELOG.md`` about the changes
 3. Ensure that all checks passed (current checks include GitHub Actions
-   and Coveralls) [1]_
-
-.. [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
-       GitHub Actions to run the tests for each change you add in the pull
-       request. Because testing here will delay tests by other developers,
-       please ensure that the code passes all tests on your local system first.
-
- Project Style Guidelines
- ^^^^^^^^^^^^^^^^^^^^^^^^
-
- In general, pysat follows PEP8 and numpydoc guidelines.  Pytest runs the unit
- and integration tests, flake8 checks for style, and sphinx-build performs
- documentation tests.  However, there are certain additional style elements that
- have been settled on to ensure the project maintains a consistent coding style.
- These include:
-
- * Line breaks should occur before a binary operator (ignoring flake8 W503)
- * Combine long strings using `join`
- * Preferably break long lines on open parentheses rather than using `\`
- * Use no more than 80 characters per line
- * Avoid using Instrument class key attribute names as unrelated variable names:
-   `platform`, `name`, `tag`, and `inst_id`
- * The pysat logger is imported into each sub-module and provides status updates
-   at the info and warning levels (as appropriate)
- * Several dependent packages have common nicknames, including:
-   * `import datetime as dt`
-   * `import numpy as np`
-   * `import pandas as pds`
-   * `import xarray as xr`
- * All classes should have `__repr__` and `__str__` functions
- * Docstrings use `Note` instead of `Notes`
- * Try to avoid creating a try/except statement where except passes
- * Use setup and teardown in test classes
- * Use pytest parametrize in test classes when appropriate
- * Provide testing class methods with informative failure statements and
-   descriptive, one-line docstrings
- * Block and inline comments should use proper English grammar and punctuation
-   with the exception of single sentences in a block, which may then omit the
-   final period
- * When casting is necessary, use `np.int64` and `np.float64` to ensure operating
-   system agnosticism
+   and Coveralls)
+
+If you don't have all the necessary Python versions available locally or
+have trouble building all the testing environments, you can rely on
+the project's Continuous Integration (CI) service to run the tests for each change you add in the pull
+request. Because testing here will delay tests by other developers,
+please ensure that the code passes all tests on your local system first.
+
+Project Style Guidelines
+^^^^^^^^^^^^^^^^^^^^^^^^
+
+In general, pysat follows PEP8 and numpydoc guidelines.  Pytest runs the unit
+and integration tests, flake8 checks for style, and sphinx-build performs
+documentation tests.  However, there are certain additional style elements that
+have been settled on to ensure the project maintains a consistent coding style.
+These include:
+
+* Line breaks should occur before a binary operator (ignoring flake8 W503)
+* Combine long strings using `join`
+* Preferably break long lines on open parentheses rather than using `\`
+* Use no more than 80 characters per line
+* Avoid using Instrument class key attribute names as unrelated variable names:
+  `platform`, `name`, `tag`, and `inst_id`
+* The pysat logger is imported into each sub-module and provides status updates
+  at the info and warning levels (as appropriate)
+* Several dependent packages have common nicknames, including:
+  * `import datetime as dt`
+  * `import numpy as np`
+  * `import pandas as pds`
+  * `import xarray as xr`
+* All classes should have `__repr__` and `__str__` functions
+* Docstrings use `Note` instead of `Notes`
+* Try to avoid creating a try/except statement where except passes
+* Use setup and teardown in test classes
+* Use pytest parametrize in test classes when appropriate
+* Provide testing class methods with informative failure statements and
+  descriptive, one-line docstrings
+* Block and inline comments should use proper English grammar and punctuation
+  with the exception of single sentences in a block, which may then omit the
+  final period
+* When casting is necessary, use `np.int64` and `np.float64` to ensure operating
+  system agnosticism

README.md

@@ -16,7 +16,6 @@ pysatMissions allows users to run build simulated satellites for Two-Line Elemen
 Main Features
 -------------
 - Simulate satellite orbits from TLEs and add data from empirical models
-- Import ionosphere and thermosphere model values through pyglow
 - Import magnetic coordinates through apexpy and aacgmv2
 - Import geomagnetic basis vectors through OMMBV
 
@@ -31,14 +30,14 @@ Documentation
 
 pysatMissions uses common Python modules, as well as modules developed by
 and for the Space Physics community.  This module officially supports
-Python 3.7+.  
+Python 3.8+.  
 
 | Common modules | Community modules |
 | -------------- | ----------------- |
 | numpy          | aacgmv2           |
 | pandas         | apexpy            |
-| pyEphem        | OMMBV             |
-| sgp4           | pysat>=3.0        |
+| pyEphem        | OMMBV>=1.0        |
+| sgp4>=2.7      | pysat>=3.0        |
 
 
 One way to install is through pip.  Just type

docs/conf.py

@@ -1,10 +1,13 @@
 # -*- coding: utf-8 -*-
-#
-# Configuration file for the Sphinx documentation builder.
-#
-# This file does only contain a selection of the most common options. For a
-# full list see the documentation:
-# https://www.sphinx-doc.org/en/master/config
+
+"""Configuration file for the Sphinx documentation builder.
+
+Note
+----
+For a full list see the documentation:
+https://www.sphinx-doc.org/en/master/config
+
+"""
 
 # -- Path setup --------------------------------------------------------------
 
@@ -22,8 +25,8 @@
 project = 'pysatMissions'
 title = '{:s} Documentation'.format(project)
 zenodo = json.loads(open('../.zenodo.json').read())
-author = ', '.join([x['name'] for x in zenodo['creators']])
-copyright = ', '.join(['2021', author])
+author = ', '.join([creator['name'] for creator in zenodo['creators']])
+copyright = ', '.join(['2022', author])
 description = 'Tools for generating simulated instruments in pysat.'
 
 # The short X.Y version
@@ -52,11 +55,14 @@
               'sphinx.ext.imgmath',
               'sphinx.ext.autosummary',
               'sphinx.ext.napoleon',
+              'sphinx.ext.githubpages',
+              'sphinx.ext.autosectionlabel',
               'numpydoc',
               'IPython.sphinxext.ipython_console_highlighting',
               'm2r2']
 
-numpydoc_show_class_members = False
+autosectionlabel_prefix_document = True
+autosectionlabel_maxdepth = 3
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']

docs/index.rst

@@ -14,6 +14,7 @@ as well as apply geomagnetic field models to existing pysat instruments.
    installation.rst
    citing.rst
    supported_instruments.rst
+   methods.rst
    tutorial.rst
    references.rst
    develop_guide.rst

docs/installation.rst

@@ -22,8 +22,8 @@ Python 3.7+ and pysat 3.0.0+.
  ================ ==================
   numpy            aacgmv2
   pandas           apexpy
-  pyEphem          OMMBV
-  sgp4             pysat>=3.0
+  pyEphem          OMMBV>=1.0
+  sgp4>=2.7        pysat>=3.0
  ================ ==================
 
 
@@ -55,3 +55,28 @@ Python 3.7+ and pysat 3.0.0+.
 
 
          python setup.py develop --user
+
+
+.. _post-install:
+
+Post Installation
+-----------------
+
+After installation, you may register the :py:mod:`pysatMissions`
+:py:class:`Instrument` sub-modules with pysat.  If this is your first time using
+pysat, check out the `quickstart guide
+<https://pysat.readthedocs.io/en/latest/quickstart.html>`_ for pysat. Once pysat
+is set up, you may choose to register the the :py:mod:`pysatMissions`
+:py:class:`Instruments` sub-modules by:
+
+.. code:: python
+
+
+   import pysat
+   import pysatMissions
+
+   pysat.utils.registry.register_by_module(pysatMissions.instruments)
+
+You may then use the pysat :py:attr:`platform` and :py:attr:`name` keywords to
+initialize the model :py:class:`Instrument` instead of the
+:py:attr:`inst_module` keyword argument.