Merge pull request #117 from pysat/rc_0_0_3

Release Candidate v0.0.3

.github/workflows/docs.yml

@@ -31,7 +31,7 @@ jobs:
     - name: Set up pysat
       run: |
         mkdir pysatData
-        python -c "import pysat; pysat.params['data_dirs'] = './pysatData'"
+        python -c "import pysat; pysat.params['data_dirs'] = 'pysatData'"
 
     - name: Check documentation build
       run: sphinx-build -E -b html docs dist/docs

.github/workflows/main.yml

@@ -10,12 +10,12 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest]
-        python-version: ["3.8", "3.9"]
+        os: [ubuntu-latest, windows-latest]
+        python-version: ["3.9", "3.10"]
         numpy_ver: [latest]
         include:
-          - python-version: "3.7"
-            numpy_ver: "1.17"
+          - python-version: "3.8"
+            numpy_ver: "1.19"
             os: ubuntu-latest
 
     name: Python ${{ matrix.python-version }} on ${{ matrix.os }} with numpy ${{ matrix.numpy_ver }}
@@ -29,7 +29,6 @@ jobs:
 
     - name: Install standard dependencies
       run: |
-        python -m pip install --upgrade pip
         pip install -r requirements.txt
         pip install -r test_requirements.txt
 
@@ -41,10 +40,10 @@ jobs:
     - name: Set up pysat
       run: |
         mkdir pysatData
-        python -c "import pysat; pysat.params['data_dirs'] = './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

CHANGELOG.md

@@ -2,6 +2,21 @@
 All notable changes to this project will be documented in this file.
 This project adheres to [Semantic Versioning](https://semver.org/).
 
+## [0.0.3] - 2022-05-16
+* Include flake8 linting of docstrings and style in Github Actions
+* Include Windows tests in Github Actions
+* Bug Fixes
+  * Expanded cleaning of ICON IVM ion drifts to more variables
+  * Fixed a bug in loading ICON IVM data (added multi_file_day = True)
+  * Fixed a bug where OMNI meta data float values are loaded as arrays
+* Maintenance
+  * Removed dummy vars after importing instruments and constellations
+  * Updated NEP29 compliance in Github Actions
+  * Limit versions of hacking for improved pip compliance
+  * Update instrument template standards
+  * Updated documentation style
+  * Removed cap on cdflib
+
 ## [0.0.2] - 2021-06-07
 * Updated Instruments and routines to conform with changes made for pysat 3.0
 * Added documentation

CONTRIBUTING.md

@@ -1,36 +1,46 @@
 Contributing
 ============
 
-Bug reports, feature suggestions and other contributions are greatly
+Bug reports, feature suggestions, and other contributions are greatly
 appreciated!  pysat 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/pysatNASA/issues>`_
+* Submit bug reports and feature requests at [GitHub](https://github.com/pysat/pysatNASA/issues)
+
 * Make pull requests to the ``develop`` branch
 
 Bug reports
 -----------
 
-When `reporting a bug <https://github.com/pysat/pysatNASA/issues>`_ please
+When [reporting a bug](https://github.com/pysat/pysatNASA/issues) please
 include:
 
 * Your operating system name and version
+
 * Any details about your local setup that might be helpful in troubleshooting
+
 * 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/pysat/pysatNASA/issues>`_.
+[GitHub](https://github.com/pysat/pysatNASA/issues).
 
 If you are proposing a feature:
 
 * Explain in detail how it would work.
+
 * Keep the scope as narrow as possible, to make it easier to implement.
+
 * Remember that this is a volunteer-driven project, and that code contributions
   are welcome :)
 
@@ -39,19 +49,24 @@ Development
 
 To set up `pysatNASA` for local development:
 
-1. `Fork pysatNASA on GitHub <https://github.com/pysat/pysatNASA/fork>`_.
-2. Clone your fork locally::
+1. [Fork pysatNASA on GitHub](https://github.com/pysat/pysatNASA/fork).
+
+2. Clone your fork locally:
 
+  ```
     git clone [email protected]:your_name_here/pysatNASA.git
+  ```
 
-3. Create a branch for local development::
+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.  See discussion
-   `here <https://pysat.readthedocs.io/en/main/new_instrument.html#testing-support>`_
+   [here](https://pysat.readthedocs.io/en/main/new_instrument.html#testing-support)
    for more information on triggering these standard tests.
 
    Tests for custom functions should be added to the appropriately named file
@@ -63,21 +78,32 @@ To set up `pysatNASA` for local development:
 
 
 4. When you're done making changes, run all the checks to ensure that nothing
-   is broken on your local system, as well as check for flake8 compliance::
+   is broken on your local system, as well as check for flake8 compliance:
 
+   ```
     pytest -vs --flake8 pysatNASA
+   ```
 
 5. Update/add documentation (in ``docs``), if relevant
 
 6. Add your name to the .zenodo.json file as an author
 
-7. 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
-
-8. Submit a pull request through the GitHub website. Pull requests should be
+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.  
+
+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.
+
+9. Submit a pull request through the GitHub website. Pull requests should be
    made to the ``develop`` branch.
 
 Pull Request Guidelines
@@ -91,44 +117,46 @@ For merging, you should:
 1. Include an example for use
 2. Add a note to ``CHANGELOG.md`` about the changes
 3. Update the author list in ``zenodo.json`` if applicable
-4. Ensure that all checks passed (current checks include Travis-CI (pytest and
-   flake8) 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
-      Travis 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 adopted 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
+4. Ensure that all checks passed (current checks include Github Actions 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
+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 adopted 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`
+* When incrementing a timestamp, use `dt.timedelta` instead of `pds.DateOffset`
+  when possible to reduce program runtime
+* 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

README.md

@@ -67,6 +67,6 @@ Another way to use the instruments in an external repository is to register the
 ```
 import pysat
 
-pysat.utils.registry.register('pysatNASA.instruments.icon_ivm')
+pysat.utils.registry.register(['pysatNASA.instruments.icon_ivm'])
 ivm = pysat.Instrument('icon', 'ivm', inst_id='a')
 ```

docs/conf.py

@@ -1,21 +1,13 @@
 # -*- coding: utf-8 -*-
-#
-# pysatNASA documentation build configuration file, created by
-# sphinx-quickstart on Wed Jul  5 16:25:26 2017.
-#
-# This file is execfile()d with the current directory set to its
-# containing dir.
-#
-# Note that not all possible configuration values are present in this
-# autogenerated file.
-#
-# All configuration values have a default; values that are commented out
-# serve to show the default.
+"""Configuration file for the Sphinx documentation builder.
+
+Note
+----
+For a full list see the documentation:
+https://www.sphinx-doc.org/en/master/config
+
+"""
 
-# If extensions (or modules to document with autodoc) are in another directory,
-# add these directories to sys.path here. If the directory is relative to the
-# documentation root, use os.path.abspath to make it absolute, like shown here.
-#
 import json
 import os
 import sys

docs/examples/ex_init.rst

@@ -13,7 +13,8 @@ Meter on board the Ionospheric CONnection Explorer `(ICON) <https://www.nasa.gov
    import datetime as dt
    import pysat
    import pysatNASA as py_nasa
-pysat.utils.registry.register_by_module(py_nasa.instruments)
+
+   pysat.utils.registry.register_by_module(py_nasa.instruments)
 
    old_time = dt.datetime(2020, 1, 1)
    ivm = pysat.Instrument(platform='icon', name='ivm',

docs/installation.rst

@@ -19,8 +19,8 @@ Python 3.7+ and pysat 3.0.0+.
  ================ =================
  Common modules   Community modules
  ================ =================
-  beautifulsoup4   cdflib
-  lxml             pysat
+  beautifulsoup4   cdflib>=0.4.4
+  lxml             pysat>=3.0.0
   netCDF4
   numpy
   pandas
@@ -55,3 +55,27 @@ Installation Options
 
 
         python setup.py develop --user
+
+.. _post-install:
+
+Post Installation
+-----------------
+
+After installation, you may register the :py:mod:`pysatNASA`
+: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:`pysatNASA`
+:py:class:`Instruments` sub-modules by:
+
+.. code:: python
+
+
+   import pysat
+   import pysatNASA
+
+   pysat.utils.registry.register_by_module(pysatNASA.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.

pysatNASA/__init__.py

@@ -1,3 +1,11 @@
+"""Core library for pysatNASA.
+
+This is a library of `pysat` instrument modules and methods designed to support
+NASA instruments and missions archived at the Community Data Analysis Web
+portal.
+
+"""
+
 import os
 from pysatNASA import constellations  # noqa F401
 from pysatNASA import instruments  # noqa F401

pysatNASA/constellations/__init__.py

@@ -1,4 +1,14 @@
+"""Interface for pysatNASA to manage and analyze multiple pysat instruments.
+
+Each instrument is contained within a subpackage of the pysatNASA.instruments
+package.
+"""
+
+
 __all__ = ['de2', 'icon']
 
 for const in __all__:
     exec("from pysatNASA.constellations import {:}".format(const))
+
+# Remove dummy variable
+del const