Merge branch 'develop-3' into new_version_test

.github/ISSUE_TEMPLATE/bug_report.md

@@ -1,32 +1,29 @@
 ---
 name: Bug report
 about: Create a report to help us improve
-title: ''
-labels: ''
-assignees: ''
+labels: bug
+title: "BUG: "
 
 ---
 
-**Describe the bug**
-A clear and concise description of what the bug is.
+# Description
+A clear and concise description of what the bug is, including a description
+of what you expected the outcome to be.
 
-**To Reproduce**
+# To Reproduce this bug:
 Steps to reproduce the behavior:
 1. Go to '...'
 2. Click on '....'
 3. Scroll down to '....'
 4. See error
 
-**Expected behavior**
-A clear and concise description of what you expected to happen.
+Consider including images or test files to help others reproduce the bug and
+solve the problem.
 
-**Screenshots**
-If applicable, add screenshots to help explain your problem.
-
-**Desktop (please complete the following information):**
- - OS: [e.g. iOS]
- - Version [e.g. 22]
+## Test configuration
+ - OS: [e.g. Hal]
+ - Version [e.g. Python 3.47]
  - Other details about your setup that could be relevant
 
-**Additional context**
+# Additional context
 Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -1,20 +1,27 @@
 ---
 name: Feature request
 about: Suggest an idea for this project
-title: ''
-labels: ''
-assignees: ''
+title: "ENH: "
+labels: enhancement
 
 ---
 
-**Is your feature request related to a problem? Please describe.**
-A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+# Description
+A clear and concise description of the new feature or behaviour you would like.
 
-**Describe the solution you'd like**
+## Potential impact
+
+- Is the feature related to an existing problem?
+- How critical is this feature to your workflow?
+- How wide of an impact to you anticipate this enhancement having?
+- Would this break any existing functionality?
+
+## Potential solution(s)
 A clear and concise description of what you want to happen.
 
-**Describe alternatives you've considered**
-A clear and concise description of any alternative solutions or features you've considered.
+# Alternatives
+A clear description of any alternative solutions or features you've considered.
 
-**Additional context**
-Add any other context or screenshots about the feature request here.
+# Additional context
+Add any other context or screenshots about the feature request here, potentially
+including your operational configuration.

.github/workflows/docs.yml

@@ -12,19 +12,18 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.7]
+        python-version: ["3.9"]
 
     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 }}
 
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip
         pip install -r test_requirements.txt
         pip install -r requirements.txt
 

.github/workflows/main.yml

@@ -15,28 +15,29 @@ jobs:
         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 dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install -r test_requirements.txt
-        pip install -r requirements.txt
-
     - 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 dependencies
+      run: |
+        pip install -r test_requirements.txt
+        pip install -r requirements.txt
 
     - name: Test PEP8 compliance
       run: flake8 . --count --select=E,F,W --show-source --statistics

.github/workflows/pysat_rc.yml

@@ -0,0 +1,51 @@
+# 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]
+        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 -r test_requirements.txt
+
+    - name: Set up pysat
+      run: |
+        mkdir pysatData
+        python -c "import pysat; pysat.params['data_dirs'] = 'pysatData'"
+
+    - name: Install
+      run: python setup.py develop
+
+    - name: Test with pytest
+      run: pytest -vs --cov=pysatCDF/
+
+    - name: Publish results to coveralls
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      run: coveralls --rcfile=setup.cfg --service=github

.zenodo.json

@@ -20,6 +20,16 @@
       {
         "affiliation": "Predictive Science",
         "name": "Pembroke, Asher"
+      },
+      {
+        "affiliation": "The Johns Hopkins Applied Physics Laboratory",
+        "name": "Starr, Greg",
+        "orcid": "0000-0002-3487-3630"
+      },
+      {
+        "affiliation": "SRI International",
+        "name": "Reimer, Ashton",
+        "orcid": "0000-0002-4621-3453"
       }
     ]
 }

CHANGELOG.md

@@ -3,14 +3,37 @@ Change Log
 All notable changes to this project will be documented in this file.
 This project adheres to [Semantic Versioning](https://semver.org/).
 
-[0.4.0] - 2022-XX-XX
+[0.3.2] - 2022-05-13
 --------------------
 * New Features
   * Compatible with pysat v3.0+
 * Deprecations
 * Documentation
+  * Added pull request templates and other GitHub project documentation.
+  * Switched Windows installation instructions to favor installing WSL.
 * Bug Fix
   * Improved builds for newer compilers.
+  * Replaces uninterpretable characters with '*' so data loading may continue.
 * Maintenance
   * Adopted latest pysat development standards.
+  * Shifted from TravisCI to GitHub Actions for online testing.
+  * Adopted setup.cfg
+  * Improved PEP8 compliance
+  * Adopt pytest syntax
 
+[0.3.2] - 2022-05-13
+--------------------
+* New Features
+  * Compatible with pysat v3.0+
+* Deprecations
+* Documentation
+  * Added pull request templates and other GitHub project documentation.
+  * Switched Windows installation instructions to favor installing WSL.
+* Bug Fix
+  * Improved builds for newer compilers.
+  * Replaces uninterpretable characters with '*' so data loading may continue.
+* Maintenance
+  * Adopted latest pysat development standards.
+  * Shifted from TravisCI to GitHub Actions for online testing.
+  * Adopted setup.cfg
+  * Improved PEP8 compliance

CONTRIBUTING.md

@@ -0,0 +1,146 @@
+Contributing
+============
+
+Bug reports, feature suggestions and other contributions are greatly
+appreciated!  pysatCDF 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/pysatCDF/issues)
+* Make pull requests to the ``develop`` branch
+
+Bug reports
+-----------
+
+When [reporting a bug](https://github.com/pysat/pysatCDF/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/pysatCDF/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 :)
+
+Development
+-----------
+
+To set up `pysatCDF` for local development:
+
+1. [Fork pysat on GitHub](https://github.com/pysat/pysatCDF/fork).
+
+2. Clone your fork locally:
+   ```
+   git clone [email protected]:your_name_here/pysatCDF.git
+   ```
+
+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 appropriately named file in ``pysatCDF/tests``.  If no test
+   file exists, then you should create one.  This testing uses pytest, 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:
+   ```
+   pytest -vs
+   ```
+
+5. Update/add documentation (in ``docs``), if relevant
+
+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.  
+
+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
+-----------------------
+
+If you need some code review or feedback while you're developing the code, just
+make a pull request. Pull requests should be made to the ``develop`` branch.
+
+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)
+
+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