Merge pull request #131 from aburrell/bug_and_updates

MAINT: Bugs and updates
aburrell · Apr 5, 2024 · 24f1bd9 · 24f1bd9
2 parents 1046849 + 294ddd6
commit 24f1bd9
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diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -11,28 +11,27 @@ 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: Set CDF Lib environment variable
       run: echo "CDF_LIB=$HOME/lib" >> $GITHUB_ENV
 
-    - name: Install standard and test dependencies, then ocbpy
+    - name: Install dependencies
       run: |
-        pip install -r docs/requirements.txt sphinx sphinx_rtd_theme numpydoc
+        pip install .[doc]
         bash requirements.extra 2
-        python setup.py install
 
     - name: Check documentation build
       run: sphinx-build -E -b html docs dist/docs

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -12,19 +12,19 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ["3.7", "3.8", "3.9", "3.10"]
-        install-extras: [0, 1, 2]
+        os: ["ubuntu-latest", "macos-latest", "windows-latest"]
+        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
+        install-extras: [0, 1, 2]  # TODO(#129): update to replace extra flag
         exclude:
-          - os: windows-latest
+          - os: "windows-latest"
             install-extras: 2
 
     name: Python ${{ matrix.python-version }} on ${{ matrix.os }} with extras ${{ matrix.install-extras }}
     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 }}
 
@@ -37,16 +37,14 @@ jobs:
       env:
         CDF_LIB: $HOME/lib
       run: |
-        pip install -r requirements.txt
+        pip install .[test]
         bash requirements.extra ${{ matrix.install-extras }}
-        python setup.py install
 
     - name: Install standard and test dependencies, then ocbpy without SSJ
       if: ${{ matrix.install-extras != 2 }}
       run: |
-        pip install -r requirements.txt
+        pip install .[test]
         bash requirements.extra ${{ matrix.install-extras }}
-        python setup.py install
 
     - name: Test PEP8 compliance
       run: flake8 . --count --show-source --statistics
@@ -55,30 +53,48 @@ jobs:
       run: flake8 . --count --exit-zero --max-complexity=10 --statistics
 
     - name: Run unit and integration tests
-      run: coverage run --rcfile=setup.cfg -m unittest discover
+      run: |
+        coverage run --rcfile=pyproject.toml -m unittest discover
+        coverage report
+        coverage xml --rcfile=pyproject.toml
+
+    - name: Install and run Coveralls Reporter(Linux)
+      if: startsWith(matrix.os, 'ubuntu')
+      env:
+        COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }}
+        COVERALLS_PARALLEL: true
+      run: |
+        curl -sL https://coveralls.io/coveralls-linux.tar.gz | tar -xz
+        ./coveralls report -f coverage.xml --parallel --repo-token=${{ secrets.COVERALLS_REPO_TOKEN }} --build-number ${{ github.run_number }}
+
+    - name: Install and run Coveralls Reporter (Windows)
+      if: startsWith(matrix.os, 'windows')
+      env:
+        COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }}
+        COVERALLS_PARALLEL: true
+      run: |
+        curl -L https://github.com/coverallsapp/coverage-reporter/releases/latest/download/coveralls-windows.exe -o coveralls.exe
+        ./coveralls.exe report -f coverage.xml --parallel --repo-token=${{ secrets.COVERALLS_REPO_TOKEN }} --build-number ${{ github.run_number }}
 
-    - name: Publish results to coveralls upon success
+    - name: Report  and run Coveralls (macOS)
+      if: startsWith(matrix.os, 'macos')
       env:
-        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }}
         COVERALLS_PARALLEL: true
-        COVERALLS_FLAG_NAME: run-${{ matrix.python-version }}-${{ matrix.os }}-${{ matrix.install-extras }}
-      run: coveralls --rcfile=setup.cfg --service=github || true
+      run: |
+        brew tap coverallsapp/coveralls --quiet
+        brew install coveralls --quiet
+        coveralls report -f coverage.xml --parallel --repo-token=${{ secrets.COVERALLS_REPO_TOKEN }} --build-number ${{ github.run_number }}
 
   finish:
+    name: Finish Coverage Analysis
     needs: build
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: ["3.10"]
+    runs-on: "ubuntu-latest"
     steps:
-      - uses: actions/checkout@v3
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
-        with:
-          python-version: ${{ matrix.python-version }}
       - name: Coveralls Finished
         env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }}
+          COVERALLS_PARALLEL: true
         run: |
-          pip install --upgrade coveralls
-          coveralls --service=github --finish || true
+          curl -sL https://coveralls.io/coveralls-linux.tar.gz | tar -xz
+          ./coveralls done --build-number ${{ github.run_number }}
diff --git a/.github/workflows/pip_rc_install.yml b/.github/workflows/pip_rc_install.yml
@@ -0,0 +1,36 @@
+# This workflow will install Python dependencies and the latest RC of ocbpy from
+# Test PyPi. This test should be manually run before a Release Candidate 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: ["3.11"]  # 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 pysat RC
+      run: pip install --no-deps --pre -i https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple/ ocbpy
+
+    - name: Check that installation imports correctly
+      run: |
+        cd ..
+        python -c "import ocbpy; print(ocbpy.__version__)"
diff --git a/.gitignore b/.gitignore
@@ -1,13 +1,15 @@
 # Autosaves
 *~
+.DS_Store
 
 # Compiled python modules.
 *.py[cod]
 
-# Test directories
+# Test directories and files
 /build/
 .tox
 .coverage
+coverage.xml
 
 # Setuptools distribution folder.
 /dist/

diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -0,0 +1,24 @@
+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+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
+# This method includes a local build of the package
+python:
+   install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - doc
diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md
@@ -2,11 +2,17 @@
 
 ## Our Pledge
 
-In the interest of fostering an open and welcoming environment, we as contributors and maintainers pledge to making participation in our project and our community a harassment-free experience for everyone, regardless of age, body size, disability, ethnicity, gender identity and expression, level of experience, nationality, personal appearance, race, religion, or sexual identity and orientation.
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers pledge to making participation in our project and
+our community a harassment-free experience for everyone, regardless of age, body
+size, disability, ethnicity, gender identity and expression, level of
+experience, nationality, personal appearance, race, religion, or sexual
+identity and orientation.
 
 ## Our Standards
 
-Examples of behavior that contributes to creating a positive environment include:
+Examples of behavior that contributes to creating a positive environment
+include:
 
 * Using welcoming and inclusive language
 * Being respectful of differing viewpoints and experiences
@@ -16,31 +22,55 @@ Examples of behavior that contributes to creating a positive environment include
 
 Examples of unacceptable behavior by participants include:
 
-* The use of sexualized language or imagery and unwelcome sexual attention or advances
+* The use of sexualized language or imagery and unwelcome sexual attention or
+  advances
 * Trolling, insulting/derogatory comments, and personal or political attacks
 * Public or private harassment
-* Publishing others' private information, such as a physical or electronic address, without explicit permission
-* Other conduct which could reasonably be considered inappropriate in a professional setting
+* Publishing others' private information, such as a physical or electronic
+  address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
 
 ## Our Responsibilities
 
-Project maintainers are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behavior.
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
 
-Project maintainers have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful.
+Project maintainers have the right and responsibility to remove, edit, or
+reject comments, commits, code, wiki edits, issues, and other contributions that
+are not aligned to this Code of Conduct, or to ban temporarily or permanently
+any contributor for other behaviors that they deem inappropriate, threatening,
+offensive, or harmful.
 
 ## Scope
 
-This Code of Conduct applies both within project spaces and in public spaces when an individual is representing the project or its community. Examples of representing a project or community include using an official project e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event. Representation of a project may be further defined and clarified by project maintainers.
+This Code of Conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community. Examples of
+representing a project or community include using an official project e-mail
+address, posting via an official social media account, or acting as an appointed
+representative at an online or offline event. Representation of a project may
+be further defined and clarified by project maintainers.
 
 ## Enforcement
 
-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 incident. Further details of specific enforcement policies may be posted separately.
+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
+incident. Further details of specific enforcement policies may be posted
+separately.
 
-Project maintainers who do not follow or enforce the Code of Conduct in good faith may face temporary or permanent repercussions as determined by other members of the project's leadership.
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
 
 ## Attribution
 
-This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4, available at [http://contributor-covenant.org/version/1/4][version]
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 1.4, available at
+[https://www.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/CODE_OF_CONDUCT.rst b/CODE_OF_CONDUCT.rst
@@ -61,9 +61,9 @@ Enforcement
 -----------
 
 Instances of abusive, harassing, or otherwise unacceptable behavior may be
-reported by contacting the project team at angeline.burrell@nrl.navy.mil. 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
+reported by contacting the project team at angeline.g.burrell.civ@us.navy.mil.
+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
 incident. Further details of specific enforcement policies may be posted
 separately.
@@ -78,5 +78,5 @@ Attribution
 This Code of Conduct is adapted from the Contributor Covenant [homepage]_,
 version [1.4]_.
 
-.. [homepage] https://contributor-covenant.org
-.. [1.4] https://contributor-covenant.org/version/1/4/
+.. [homepage] https://www.contributor-covenant.org/
+.. [1.4] https://www.contributor-covenant.org/version/1/4/
diff --git a/Changelog.rst b/Changelog.rst
@@ -3,13 +3,24 @@ Changelog
 
 Summary of all changes made since the first stable release
 
-0.X.X (XX-XX-2023)
+0.4.0 (XX-XX-2024)
 ------------------
 * DEP: Deprecated functions that depend on ssj_auroral_boundary_package
 * DEP: Removed classes and kwargs deprecated in v0.3.0
-* MAINT: Added a pyproject.toml file
+* MAINT: Added a pyproject.toml file and removed setup.py
+* MAINT: Updated numpy logic to address DeprecationWarnings
+* MAINT: Updated GitHub Action yamls to use pyproject.toml and cycle versions
+* MAINT: Updated GitHub Action yamls to use coveralls-reporter
 * ENH: Added AMPERE OCBs up to 2022, using updated AMPERE data
 * ENH: Added AMPERE EABs, using the Heppner-Maynard boundary as a valid EAB
+* ENH: Changed default directory ID to use `pathlib`
+* ENH: Allow data padding in `pysat_instrument` functions
+* BUG: Fixed a typo in the documentation's pysat example
+* BUG: Added an error catch for badly formatted SuperMAG file reading
+* TST: Added a new CI test for the Test PyPi Release Candidate
+* TST: Reduced duplication by creating a common test class and test variable
+* TST: Added a ReadTheDocs yaml
+* DOC: Improved docstring style compliance and correctness
 
 0.3.0 (10-21-2022)
 ------------------

diff --git a/docs/examples/ex_pysat_eab.rst b/docs/examples/ex_pysat_eab.rst
@@ -74,8 +74,8 @@ using the following commands.
 
    # Replace `user` with a string holding your name and `password` with your
    # email.  Madrigal uses these to demonstrate their utility to funders.
-   tec = pysat.Instrumet(inst_module=py_mad.instruments.gnss_tec, tag='vtec',
-                         user=user, password=password)
+   tec = pysat.Instrument(inst_module=py_mad.instruments.gnss_tec, tag='vtec',
+                          user=user, password=password)
    tec.download(start=eab.dtime[eab.rec_ind])
    print(tec.files.files)
 

diff --git a/docs/index.rst b/docs/index.rst
@@ -10,7 +10,7 @@ This documentation describes the Open Closed field line Boundary (OCB) gridding
 process and provides examples for usage.
 
 .. toctree::
-   :maxdepth: -1
+   :maxdepth: 2
 
    overview.rst
    citing.rst