Merge pull request #78 from pysat/rc0.0.5

RC v0.0.5

.github/workflows/main.yml

@@ -11,12 +11,12 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest]
-        python-version: ["3.8", "3.9"]
+        os: [ubuntu-latest, macos-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 }}
@@ -42,10 +42,10 @@ 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

.zenodo.json

@@ -1,4 +1,17 @@
 {
+    "keywords": [
+	"pysat",
+	"ionosphere",
+	"atmosphere",
+	"thermosphere",
+	"magnetosphere",
+	"heliosphere",
+	"observations",
+	"space-weather",
+	"solar-index",
+	"geomagnetic-index",
+	"forecasts"
+    ],
     "creators": [
       {
         "affiliation": "U.S. Naval Research Laboratory", 
@@ -11,17 +24,22 @@
         "orcid": "0000-0001-8321-6074"
       }, 
       {
-        "affiliation": "The University of Texas at Dallas", 
+        "affiliation": "Stoneris LLC", 
         "name": "Stoneback, Russell",
         "orcid": "0000-0001-7216-4336"  
-      }, 
+      },
       {
         "affiliation": "Predictive Science", 
         "name": "Pembroke, Asher"
       }, 
       {
         "name": "Spence, Carey",
         "orcid": "0000-0001-8340-5625"
+      },
+      {
+        "affiliation": "Goddard Space Flight Center", 
+        "name": "Smith, Jonathon M.",
+        "orcid": "0000-0002-8191-4765"  
       }
     ]
 }

CHANGELOG.md

@@ -3,8 +3,24 @@ Change Log
 All notable changes to this project will be documented in this file.
 This project adheres to [Semantic Versioning](https://semver.org/).
 
+[0.0.5] - 2022-06-10
+--------------------
+* Updated the docstrings to conform to pysat standards
+* Added docstring tests to Flake8 portion of CI testing
+* Fixed bug in `combine_kp` that occurs if no times are provided
+* Improved unit test style and expanded unit test coverage
+* Updated package organization documentation
+* Added a function to normalize ACE SWEPAM variables as described in the OMNI
+  processing guide
+* Deprecated `load_csv_data` method, which was moved to pysat
+* Added the LASP predicted Dst to the Dst Instrument
+* Updated pandas usage to remove existing deprecation warnings
+* Updated `pysat.Instrument.load` calls to remove `use_header` deprecation
+  warning
+
 [0.0.4] - 2021-05-19
 --------------------
+* New Logo
 * Implements GitHub Actions for primary CI testing
 * Updated tested python versions
 * Removed non-document testing from Travis-CI and updated installation method

CONTRIBUTING.md

@@ -5,6 +5,11 @@ Bug reports, feature suggestions and other contributions are greatly
 appreciated!  pysat and pysatSpaceWeather are community-driven projects 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
 -------------
 
@@ -40,17 +45,26 @@ Development
 
 To set up `pysatSpaceWeather` for local development:
 
-1. `Fork pysatSpaceWeather on GitHub <https://github.com/pysat/pysatSpaceWeather/fork>`_.
-2. Clone your fork locally::
+1. [Fork pysatSpaceWeather on GitHub](https://github.com/pysat/pysatSpaceWeather/fork>).
+
+2. Clone your fork locally:
 
+  ```
     git clone [email protected]:your_name_here/pysatSpaceWeather.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.  Tests for custom functions should be added to the
+   performed automatically.  See discussion
+   [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 in ``pysatSpaceWeather/tests``.  For example,
    space weather methods should be named
    ``pysatSpaceWeather/tests/test_methods_sw.py``.  If no test file exists,
@@ -59,20 +73,28 @@ To set up `pysatSpaceWeather` for local development:
    must begin with ``Test``, and test methods must also begin with ``test``.
 
 4. When you're done making changes, run all the checks to ensure that nothing
-   is broken on your local system::
+   is broken on your local system:
 
+   ```
     pytest -vs pysatSpaceWeather
+   ```
 
 5. Update/add documentation (in ``docs``).  Even if you don't think it's
    relevant, check to see if any existing examples have changed.
 
 6. Add your name to the .zenodo.json file as an author
 
-7. Commit your changes and push your branch to GitHub::
+7. Commit your changes and push your branch to GitHub:
 
+   ```
     git add .
-    git commit -m "Brief description of your changes"
+    git commit -m "CODE: Brief description of your changes"
     git push origin name-of-your-bugfix-or-feature
+   ```
+
+   Where CODE 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. Submit a pull request through the GitHub website. Pull requests should be
    made to the ``develop`` branch.
@@ -87,8 +109,8 @@ 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 Travis-CI
-   and Coveralls) [1]_
+3. Ensure that all checks passed (current checks include GitHub Actions,
+   Coveralls, and ReadTheDocs) [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
@@ -118,6 +140,8 @@ These include:
   * `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

docs/conf.py

@@ -16,6 +16,8 @@
 # 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.
 #
+"""Configuration script for Sphinx documentation."""
+
 import json
 import os
 import sys

docs/supported_instruments.rst

@@ -75,7 +75,10 @@ The Disturbance Storm Time (Dst) Index is a measure of magnetic activity
 associated with the ring current.  The National Geophysical Data Center (NGDC)
 maintains the
 `current database <https://www.ngdc.noaa.gov/stp/geomag/dst.html>`_ from which
-the Dst is downloaded.  You can learn more about the Dst Index at the
+the historic Dst is downloaded.
+`LASP <https://lasp.colorado.edu/space_weather/dsttemerin/dsttemerin.html>`_
+performs the calculates and provides the predicted Dst for the last 96 hours.
+You can learn more about the Dst Index at the
 `WDC Kyoto Observatory page <http://wdc.kugi.kyoto-u.ac.jp/dstdir/index.html>`_.
 
 

pysatSpaceWeather/__init__.py

@@ -1,3 +1,5 @@
+"""Initialization file for pysatSpaceWeather module."""
+
 import os
 
 from pysatSpaceWeather import instruments  # noqa F401

pysatSpaceWeather/instruments/ace_epam.py

@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-"""Supports ACE Electron, Proton, and Alpha Monitor data
+"""Supports ACE Electron, Proton, and Alpha Monitor data.
 
 Properties
 ----------
@@ -17,6 +17,8 @@
 ----
 This is not the ACE scientific data set, which will be available at pysatNASA
 
+Examples
+--------
 The real-time data is stored by generation date, where each file contains the
 data for the current day.  If you leave download dates empty, though, it will
 grab today's file three times and assign dates from yesterday, today, and
@@ -42,6 +44,7 @@
 import functools
 import numpy as np
 
+from pysat.instruments.methods.general import load_csv_data
 from pysat import logger
 
 from pysatSpaceWeather.instruments.methods import ace as mm_ace
@@ -74,11 +77,7 @@
 
 
 def init(self):
-    """Initializes the Instrument object with instrument specific values.
-
-    Runs once upon instantiation.
-
-    """
+    """Initialize the Instrument object with instrument specific values."""
 
     # Set the appropriate acknowledgements and references
     self.acknowledgements = mm_ace.acknowledgements()
@@ -90,7 +89,7 @@ def init(self):
 
 
 def clean(self):
-    """Routine to clean real-time ACE data using the status flag
+    """Clean the real-time ACE data using the status flag.
 
     Note
     ----
@@ -132,17 +131,17 @@ def clean(self):
 list_files = functools.partial(mm_ace.list_files, name=name)
 
 
-def load(fnames, tag=None, inst_id=None):
-    """Load the ACE space weather prediction data
+def load(fnames, tag='', inst_id=''):
+    """Load the ACE space weather prediction data.
 
     Parameters
     ----------
     fnames : array-like
-        Series, list, or array of filenames
-    tag : str or NoneType
-        tag or None (default=None)
-    inst_id : str or NoneType
-        ACE instrument or None (default=None)
+        Series, list, or array of filenames.
+    tag : str
+        Instrument tag (default='').
+    inst_id : str
+        ACE instrument ID (default='').
 
     Returns
     -------
@@ -151,10 +150,9 @@ def load(fnames, tag=None, inst_id=None):
     meta : pysat.Meta
         Object containing metadata such as column names and units
 
-    Raises
-    ------
-    ValueError
-        When unknown inst_id is supplied.
+    See Also
+    --------
+    pysat.instruments.methods.general.load_csv_data
 
     Note
     ----
@@ -163,8 +161,8 @@ def load(fnames, tag=None, inst_id=None):
     """
 
     # Save each file to the output DataFrame
-    data = mm_ace.load_csv_data(fnames, read_csv_kwargs={'index_col': 0,
-                                                         'parse_dates': True})
+    data = load_csv_data(fnames, read_csv_kwargs={'index_col': 0,
+                                                  'parse_dates': True})
 
     # Assign the meta data
     meta, status_desc = mm_ace.common_metadata()