Merge pull request #98 from pysat/rc_version_0.2.0

RC version 0.2.0

.github/ISSUE_TEMPLATE/bug_report.md

@@ -26,4 +26,4 @@ solve the problem.
  - Other details about your setup that could be relevant
 
 # Additional context
-Add any other context about the problem here.
+Add any other context about the problem here, including expected behaviour.

.github/ISSUE_TEMPLATE/question.md

@@ -15,5 +15,5 @@ the full context of your question.
 
 ## Configuration
  - OS: [e.g. Hal]
- - Version [e.g. Python 3.47]
+ - Version: [e.g. Python 3.47]
  - Other details about your setup that could be relevant

.github/pull_request_template.md

@@ -1,6 +1,6 @@
 # Description
 
-Addresses # (issue)
+Addresses #(issue)
 
 Please include a summary of the change and which issue is fixed. Please also
 include relevant motivation and context. List any dependencies that are required
@@ -47,6 +47,7 @@ Test B
 - [ ] New and existing unit tests pass locally with my changes
 - [ ] Any dependent changes have been merged and published in downstream modules
 - [ ] Add a note to ``CHANGELOG.md``, summarizing the changes
+- [ ] Update zenodo.json file for new code contributors
 
 If this is a release PR, replace the first item of the above checklist with the
 release checklist on the pysat wiki:

.github/workflows/docs.yml

@@ -1,5 +1,6 @@
-# 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
+# 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: Documentation Check
 
@@ -8,24 +9,21 @@ on: [push, pull_request]
 jobs:
   build:
 
-    runs-on: ubuntu-latest
+    runs-on: ["ubuntu-latest"]
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.9]
+        python-version: ["3.11"]
 
     name: Documentation tests
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       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 with dependencies
+      run: pip install .[doc]
 
     - name: Set up pysat
       run: |

.github/workflows/main.yml

@@ -12,35 +12,47 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, macos-latest]  # TODO(76): add windows-latest
-        python-version: ["3.9", "3.10"]
-        numpy_ver: ["latest"]
+        os: ["ubuntu-latest", "macos-latest", "windows-latest"]
+        python-version: ["3.10", "3.11"]
+        test_config: ["latest"]
         include:
-          - python-version: "3.8"
-            numpy_ver: "1.21"
+          # NEP29 compliance settings
+          - python-version: "3.9"
+            numpy_ver: "1.23"
             os: ubuntu-latest
+            test_config: "NEP29"
+          # Operational compliance settings
           - python-version: "3.6.8"
             numpy_ver: "1.19.5"
             os: "ubuntu-20.04"
+            test_config: "Ops"
 
-    name: Python ${{ matrix.python-version }} on ${{ matrix.os }} with numpy ${{ matrix.numpy_ver }}
+    name: ${{ matrix.test_config }} Python ${{ matrix.python-version }} on ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
-    - name: Install standard dependencies
+    - name: Install Operational dependencies
+      if: ${{ matrix.test_config == 'Ops'}}
       run: |
+        pip install numpy==${{ matrix.numpy_ver }}
+        pip install -r requirements.txt
         pip install -r test_requirements.txt
-        pip install -r requirements.txt;
+        pip install .
 
     - name: Install NEP29 dependencies
-      if: ${{ matrix.numpy_ver != 'latest'}}
+      if: ${{ matrix.test_config == 'NEP29'}}
       run: |
         pip install numpy==${{ matrix.numpy_ver }}
+        pip install --upgrade-strategy only-if-needed .[test]
+
+    - name: Install standard dependencies
+      if: ${{ matrix.test_config == 'latest'}}
+      run: pip install .[test]
 
     - name: Set up pysat
       run: |
@@ -54,9 +66,22 @@ jobs:
       run: flake8 . --count --exit-zero --max-complexity=10 --statistics
 
     - name: Test with pytest
-      run: pytest -x --cov=pysatMadrigal/
+      run: pytest
 
     - name: Publish results to coveralls
       env:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      run: coveralls --rcfile=setup.cfg --service=github
+        COVERALLS_PARALLEL: true
+      run: coveralls --rcfile=pyproject.toml --service=github
+
+  finish:
+    name: Finish Coverage Analysis
+    needs: build
+    runs-on: ubuntu-latest
+    steps:
+    - name: Coveralls Finished
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      run: |
+        pip install --upgrade coveralls
+        coveralls --service=github --finish

.github/workflows/pip_rc_install.yml

@@ -0,0 +1,41 @@
+# This workflow will install Python dependencies and the latest RC of
+# pysatMadrigal from test pypi. This test should be manually run before an RC is
+# officially approved and versioned. For more information see:
+# https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Test install of latest RC from pip
+
+on: [workflow_dispatch]
+
+jobs:
+  build:
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ["ubuntu-latest", "macos-latest", "windows-latest"]
+        python-version: ["3.12"]  # Keep this version at the highest supported Python version
+
+    name: Python ${{ matrix.python-version }} on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install standard dependencies
+      run: pip install -r requirements.txt
+
+    - name: Install pysatMadrigal RC
+      run: pip install --no-deps --pre -i https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple/ pysatMadrigal
+
+    - name: Set up pysat
+      run: |
+        mkdir pysatData
+        python -c "import pysat; pysat.params['data_dirs'] = 'pysatData'"
+
+    - name: Check that install imports correctly
+      run: |
+        cd ..
+        python -c "import pysatMadrigal; print(pysatMadrigal.__version__)"

.github/workflows/pysat_rc.yml

@@ -1,5 +1,6 @@
-# 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
+# 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
 
@@ -10,36 +11,46 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-# TODO(#76): add windows tests when bugs are sorted
-        os: [ubuntu-latest, macos-latest]
-        python-version: ["3.10"]
+        os: ["ubuntu-latest", "macos-latest", "windows-latest"]
+        python-version: ["3.11"]
 
     name: Python ${{ matrix.python-version }} on ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
     - name: Install pysat RC
-      run: pip install --no-deps -i https://test.pypi.org/simple/ pysat
+      run: pip install --pre -i https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple/ pysat
 
-    - name: Install standard dependencies
-      run: |
-        pip install -r requirements.txt
-        pip install -r test_requirements.txt
+    - name: Install standard dependencies and package
+      run: pip install .[test]
 
     - name: Set up pysat
       run: |
         mkdir pysatData
         python -c "import pysat; pysat.params['data_dirs'] = 'pysatData'"
 
     - name: Test with pytest
-      run: pytest -vs -x --cov=pysatMadrigal/
+      run: pytest
 
     - name: Publish results to coveralls
       env:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      run: coveralls --rcfile=setup.cfg --service=github
+        COVERALLS_PARALLEL: true
+      run: coveralls --rcfile=pyproject.toml --service=github
+
+  finish:
+    name: Finish Coverage Analysis
+    needs: build
+    runs-on: ubuntu-latest
+    steps:
+    - name: Coveralls Finished
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      run: |
+        pip install --upgrade coveralls
+        coveralls --service=github --finish

.readthedocs.yml

@@ -0,0 +1,25 @@
+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required version of readthedocs
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+   configuration: docs/conf.py
+
+
+# Declare the Python requirements required to build your docs
+python:
+   install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - doc

ACKNOWLEDGEMENTS.md

@@ -0,0 +1,31 @@
+Funding
+=======
+The following institutions, missions, and programs have provided funding
+for pysatMadrigal development.
+
+Institutions
+------------
+ - The Catholic University of America (CUA)
+ - Cosmic Studio
+ - Defense Advanced Research Projects Agency (DARPA) Defense Sciences Office
+ - National Aeronautics and Space Administration (NASA)
+ - National Science Foundation (NSF)
+ - Office of Naval Research (ONR)
+
+Programs
+--------
+ - NSF 125908, AGS-1651393
+ - Naval Research Laboratory N00173191G016 and N0017322P0744
+
+Disclaimers
+===========
+Any opinions or actions taken by the listed funding institutions are those of 
+the institutions and do not necessarily reflect the views of the pysat development
+team or individual authors. Any opinions, findings, and conclusions or recommendations 
+expressed in this material are those of the author(s) and do not necessarily reflect the views
+of the funding agencies.
+
+Support and Thanks
+==================
+Thanks to Bill Rideout, who provided help when learning how to use the
+madrigalWeb package.

CHANGELOG.md

@@ -3,6 +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/).
 
+[0.2.0] - 2024-03-15
+--------------------
+* Enhancements
+  * Moved the OMNI-2 IMF, Dst, and Geomagnetic index Instruments from the
+    general Madrigal Pandas instrument into new ones
+  * Moved the NGDC AE index Instrument from the general Madrigal Pandas
+    instrument to a new one, fixing the Windows memory issue and a problem
+    with duplicated times
+  * Added slant TEC (tag of 'los') to the gnss_tec Instrument
+  * Refactored general load function to extract useful parts of the code that
+    were used for specific load functions
+* Maintenance
+  * Add manual GitHub Actions tests for pysatMadrigal RC
+  * Update GitHub Actions workflows for newer versions of pip, updated actions
+  * Added clean warning test attributes to all Instruments
+  * Updated documentation to comply with current Ecosystem guidelines
+  * Replaced setup.py with pyproject.toml
+
 [0.1.0] - 2023-04-11
 --------------------
 * Enhancements
@@ -16,6 +34,7 @@ This project adheres to [Semantic Versioning](https://semver.org/).
      between '.' delimiters, required for some Madrigal file formats
    * Standardized the Instrument method kwarg defaults
    * Added 'site' tag to the GNSS TEC Instrument
+   * Added a 'dmsp_ssj' instrument for Auroral Boundary Index data
    * Added support for varied use of `two_digit_year_break` to
      `methods.general.list_remote_files`
    * Implemented `two_digit_year_break` support for `vtec` GNSS TEC Instrument
@@ -29,11 +48,13 @@ This project adheres to [Semantic Versioning](https://semver.org/).
    * Added quick-fail for main pytest command
 * Bug
    * Fixed bugs in the coordinate conversion functions
+   * Fixed bug in the general download function that sets the stop date
 * Maintenance
    * Updated GitHub action and NEP29 versions
    * Updated the minimum Madrigal version to allow HDF4 downloads
    * Update pysat instrument testing suite, pytest syntax
    * Add manual GitHub Actions tests for pysat RC
+   * Removed code needed to work around pysat bugs
 
 [0.0.4] - 2021-06-11
 --------------------

CODE_OF_CONDUCT.md

@@ -56,9 +56,9 @@ project may be further defined and clarified by project maintainers.
 
 Instances of abusive, harassing, or otherwise unacceptable behavior may be
 reported by contacting the project team at [email protected]. The
-project team will review and investigate all complaints, and will respond in a
-way that it deems appropriate to the circumstances. The project team is
-obligated to maintain confidentiality with regard to the reporter of an
+pysatMadrigal project team will review and investigate all complaints, and will
+respond in a way that it deems appropriate to the circumstances. The project
+team is obligated to maintain confidentiality with regard to the reporter of an
 incident. Further details of specific enforcement policies may be posted
 separately.
 
@@ -69,7 +69,14 @@ members of the project's leadership.
 ## Attribution
 
 This Code of Conduct is adapted from the [Contributor Covenant][homepage],
-version 1.4, available at [https://contributor-covenant.org/version/1/4][version]
+version 1.4, available at
+[https://contributor-covenant.org/version/1/4][version]
+
+## FAQ
+
+For answers to common questions about this code of conduct, see
+[https://www.contributor-covenant.org/faq][faq]
 
 [homepage]: https://contributor-covenant.org
 [version]: https://contributor-covenant.org/version/1/4/
+[faq]: https://www.contributor-covenant.org/faq