Merge pull request #130 from pysat/rc_0_0_4

Release Candidate 0.0.4
pysat · Nov 7, 2022 · 7d2b86c · 7d2b86c
2 parents 9b9b4fd + 3ff8001
commit 7d2b86c
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diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -16,9 +16,9 @@ jobs:
 
     name: Documentation tests
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
 

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -10,32 +10,39 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, windows-latest]
+        os: [ubuntu-latest, macos-latest, windows-latest]
         python-version: ["3.9", "3.10"]
         numpy_ver: [latest]
         include:
           - python-version: "3.8"
-            numpy_ver: "1.19"
+            numpy_ver: "1.20"
             os: ubuntu-latest
 
     name: Python ${{ matrix.python-version }} on ${{ matrix.os }} with numpy ${{ matrix.numpy_ver }}
     runs-on: ${{ matrix.os }}
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
 
-    - name: Install standard dependencies
-      run: |
-        pip install -r requirements.txt
-        pip install -r test_requirements.txt
+    - name: Reinstall fortran on MacOS
+      if: ${{ matrix.os == 'macos-latest' }}
+      run: brew reinstall gcc
 
     - name: Install NEP29 dependencies
       if: ${{ matrix.numpy_ver != 'latest'}}
       run: |
         pip install --no-binary :numpy: numpy==${{ matrix.numpy_ver }}
+        # Need to force a version of pandas compliant with NEP29
+        pip install "pandas<1.5"
+
+    - name: Install standard dependencies
+      run: |
+        pip install -r requirements.txt
+        pip install pysatCDF --no-binary=pysatCDF
+        pip install -r test_requirements.txt
 
     - name: Set up pysat
       run: |
@@ -50,7 +57,7 @@ jobs:
 
     - name: Test with pytest
       run: |
-        pytest --cov=pysatNASA/
+        pytest -vs --cov=pysatNASA/
 
     - name: Publish results to coveralls
       env:

diff --git a/.github/workflows/pysat_rc.yml b/.github/workflows/pysat_rc.yml
@@ -0,0 +1,49 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Test with latest pysat RC
+
+on: [workflow_dispatch]
+
+jobs:
+  build:
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ["3.10"]
+
+    name: Python ${{ matrix.python-version }} on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Reinstall fortran on MacOS
+      if: ${{ matrix.os == 'macos-latest' }}
+      run: brew reinstall gcc
+
+    - name: Install pysat RC
+      run: pip install --no-deps -i https://test.pypi.org/simple/ pysat
+
+    - name: Install standard dependencies
+      run: |
+        pip install -r requirements.txt
+        pip install pysatCDF --no-binary=pysatCDF
+        pip install -r test_requirements.txt
+
+    - name: Set up pysat
+      run: |
+        mkdir pysatData
+        python -c "import pysat; pysat.params['data_dirs'] = 'pysatData'"
+
+    - name: Test with pytest
+      run: pytest -vs --cov=pysatNASA/
+
+    - name: Publish results to coveralls
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      run: coveralls --rcfile=setup.cfg --service=github
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,13 +2,41 @@
 All notable changes to this project will be documented in this file.
 This project adheres to [Semantic Versioning](https://semver.org/).
 
+## [0.0.4] - 2022-11-11
+* Update instrument tests with new test class
+* Support xarray datasets through cdflib
+* Preferentially loads data into pandas using pysatCDF if installed
+* Adds pysatCDF to optional requirements invoked via '[all]' option at installation
+* New Instruments
+  * JPL GPS ROTI
+* Bug Fixes
+  * Fixed a bug in metadata when loading GOLD Nmax data.
+  * Fixed a bug in user feedback for `methods.cdaweb.download`
+  * Fixed a bug in loading ICON IVM data (added multi_file_day = True)
+  * Allow for array-like OMNI HRO meta data
+  * Fixed date handling for OMNI HRO downloads
+  * Updated filenames for TIMED SABER
+* Maintenance
+  * Reduce duplication of code in instrument modules
+  * Include flake8 linting of docstrings and style in Github Actions
+  * Move OMNI HRO custom functions to a methods module
+  * Deprecate OMNI HRO custom functions in instrument module
+  * Update GitHub actions to the latest versions
+  * Added downstream test to test code with pysat RC
+  * Remove deprecated `convert_timestamp_to_datetime` calls
+  * Remove deprecated pandas syntax
+  * Added version cap for xarray 2022.11
+* Documentation
+  * New logo added
+
 ## [0.0.3] - 2022-05-18
 * 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
+  * Fixed metadata type issues when loading ICON instrument data.
 * Maintenance
   * Removed dummy vars after importing instruments and constellations
   * Updated NEP29 compliance in Github Actions

diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md
@@ -42,5 +42,5 @@ Project maintainers who do not follow or enforce the Code of Conduct in good fai
 
 This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4, available at [https://contributor-covenant.org/version/1/4][version]
 
-[homepage]: https://contributor-covenant.org
-[version]: https://contributor-covenant.org/version/1/4/
+[homepage]: https://www.contributor-covenant.org
+[version]: https://www.contributor-covenant.org/version/1/4/
diff --git a/README.md b/README.md
@@ -1,6 +1,6 @@
 <div align="left">
         <img height="0" width="0px">
-        <img width="20%" src="https://raw.githubusercontent.com/pysat/pysatNASA/main/docs/figures/pysatnasa_logo.jpg" alt="pysatNASA" title="pysatNASA" </img>
+        <img width="20%" src="https://raw.githubusercontent.com/pysat/pysatNASA/main/docs/figures/logo.png" alt="pysatNASA" title="pysatNASA" </img>
 </div>
 
 # pysatNASA: pysat support for NASA Space Science instruments
@@ -20,17 +20,17 @@ some examples on how to use the routines
 
 pysatNASA uses common Python modules, as well as modules developed by
 and for the Space Physics community.  This module officially supports
-Python 3.7+.
-
-| Common modules | Community modules |
-| -------------- | ----------------- |
-| beautifulsoup4 | cdflib            |
-| lxml           | pysat             |
-| netCDF4        |                   |
-| numpy          |                   |
-| pandas         |                   |
-| requests       |                   |
-| xarray         |                   |
+Python 3.8+.
+
+| Common modules   | Community modules |
+| ---------------- | ----------------- |
+| beautifulsoup4   | cdflib            |
+| lxml             | pysat>=3.0.4      |
+| netCDF4          |                   |
+| numpy            |                   |
+| pandas           |                   |
+| requests         |                   |
+| xarray<2022.11   |                   |
 
 ## GitHub Installation
 
@@ -50,7 +50,7 @@ python setup.py install
 
 Note: pre-1.0.0 version
 -----------------------
-pysatNASA is currently in an initial development phase and requires pysat 3.0.0.  
+pysatNASA is currently in an initial development phase and requires pysat 3.0.4.  
 
 # Using with pysat
 

diff --git a/docs/conf.py b/docs/conf.py
@@ -19,10 +19,14 @@
 #
 # needs_sphinx = '1.0'
 
+package_root = "."
+
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = ['sphinx.ext.autodoc',
+extensions = ['sphinxcontrib.extras_require',
+              'sphinx-prompt',
+              'sphinx.ext.autodoc',
               'sphinx.ext.intersphinx',
               'sphinx.ext.todo',
               'sphinx.ext.coverage',
@@ -68,7 +72,7 @@
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = 'en'
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -92,7 +96,7 @@
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
 # documentation.
-html_logo = os.path.join(os.path.abspath('.'), 'figures', 'pysatnasa_logo.jpg')
+html_logo = os.path.join(os.path.abspath('.'), 'figures', 'logo.png')
 html_theme_options = {'logo_only': True}
 
 # Add any paths that contain custom static files (such as style sheets) here,

diff --git a/docs/figures/logo.png b/docs/figures/logo.png
diff --git a/docs/figures/pysatnasa_logo.jpg b/docs/figures/pysatnasa_logo.jpg
diff --git a/docs/installation.rst b/docs/installation.rst
@@ -14,19 +14,19 @@ Prerequisites
 
 pysatNASA uses common Python modules, as well as modules developed by
 and for the Space Physics community.  This module officially supports
-Python 3.7+ and pysat 3.0.0+.
+Python 3.8+ and pysat 3.0.4+.
 
- ================ =================
- Common modules   Community modules
- ================ =================
-  beautifulsoup4   cdflib>=0.4.4
-  lxml             pysat>=3.0.0
+ ================== =================
+ Common modules     Community modules
+ ================== =================
+  beautifulsoup4     cdflib>=0.4.4
+  lxml               pysat>=3.0.4
   netCDF4
   numpy
   pandas
   requests
-  xarray
- ================ =================
+  xarray<2022.11
+ ================== =================
 
 
 Installation Options
@@ -56,6 +56,9 @@ Installation Options
 
         python setup.py develop --user
 
+.. extras-require:: all
+    :setup.cfg:
+
 .. _post-install:
 
 Post Installation

diff --git a/docs/overview.rst b/docs/overview.rst
@@ -5,7 +5,7 @@ This is a library of ``pysat`` instrument modules and methods designed to suppor
 NASA instruments and missions archived at the Community Data Analysis Web
 portal.
 
-.. image:: figures/pysatnasa_logo.jpg
+.. image:: figures/logo.png
     :width: 400px
     :align: center
     :alt: pysatNASA Logo, a blue planet with red orbiting python and the module name superimposed
diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -1,3 +1,4 @@
+extras_require
 m2r2
 numpydoc
 pysat

diff --git a/docs/supported_instruments.rst b/docs/supported_instruments.rst
@@ -106,6 +106,14 @@ ISS FPMU
 .. automodule:: pysatNASA.instruments.iss_fpmu
    :members:
 
+.. _jpl_gps:
+
+JPL GPS
+-------
+
+.. automodule:: pysatNASA.instruments.jpl_gps
+   :members:
+
 .. _omni_hro:
 
 OMNI HRO

diff --git a/pysatNASA/constellations/__init__.py b/pysatNASA/constellations/__init__.py
@@ -4,11 +4,23 @@
 package.
 """
 
+import logging
+
+import pysat
 
 __all__ = ['de2', 'icon']
 
+# TODO(#89): reevaluate logger suppression if fixes implemented in pysat
+# Save current level and turn off before constellation import
+user_level = pysat.logger.level
+pysat.logger.setLevel(logging.WARNING)
+
+# Import constellation objects
 for const in __all__:
     exec("from pysatNASA.constellations import {:}".format(const))
 
+# Restore user level
+pysat.logger.setLevel(user_level)
+
 # Remove dummy variable
-del const
+del const, user_level
diff --git a/pysatNASA/instruments/__init__.py b/pysatNASA/instruments/__init__.py
@@ -9,7 +9,7 @@
            'de2_lang', 'de2_nacs', 'de2_rpa', 'de2_wats',
            'formosat1_ivm',
            'icon_euv', 'icon_fuv', 'icon_ivm', 'icon_mighti',
-           'iss_fpmu', 'omni_hro', 'ses14_gold',
+           'iss_fpmu', 'jpl_gps', 'omni_hro', 'ses14_gold',
            'timed_saber', 'timed_see']
 
 for inst in __all__:

diff --git a/pysatNASA/instruments/cnofs_ivm.py b/pysatNASA/instruments/cnofs_ivm.py
@@ -60,10 +60,10 @@
 import numpy as np
 
 from pysat.instruments.methods import general as mm_gen
-from pysat import logger
 
 from pysatNASA.instruments.methods import cdaweb as cdw
 from pysatNASA.instruments.methods import cnofs as mm_cnofs
+from pysatNASA.instruments.methods import general as mm_nasa
 
 # ----------------------------------------------------------------------------
 # Instrument attributes
@@ -82,18 +82,8 @@
 # Instrument methods
 
 
-def init(self):
-    """Initialize the Instrument object with instrument specific values.
-
-    Runs once upon instantiation.
-
-    """
-    logger.info(mm_cnofs.ackn_str)
-    self.acknowledgements = mm_cnofs.ackn_str
-    self.references = '\n'.join((mm_cnofs.refs['mission'],
-                                 mm_cnofs.refs['ivm']))
-
-    return
+# Use standard init routine
+init = functools.partial(mm_nasa.init, module=mm_cnofs, name=name)
 
 
 def preprocess(self):