Merge pull request pysat#1162 from pysat/rc_3_2_0

Release Candidate 3.2.0

.github/ISSUE_TEMPLATE/bug_report.md

@@ -1,29 +1,29 @@
 ---
 name: Bug report
 about: Create a report to help us improve
+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**
-Add any other context about the problem here.
+# Additional context
+Add any other context about the problem here, including expected behaviour.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -1,17 +1,27 @@
 ---
 name: Feature request
 about: Suggest an idea for this project
+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/ISSUE_TEMPLATE/question.md

@@ -0,0 +1,19 @@
+---
+name: Question
+about: A question about this project
+title: "QUEST: "
+labels: question
+
+---
+
+# Description
+A clear and concise summary of your query
+
+## Example code (optional)
+If relevant, include sample code, images, or files so that others can understand
+the full context of your question.
+
+## Configuration
+ - OS: [e.g., Hal]
+ - 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
@@ -23,7 +23,10 @@ instructions so we can reproduce. Please also list any relevant details for
 your test configuration
 
 - Test A
-- Test B
+
+```
+Test B
+```
 
 **Test Configuration**:
 * Operating system: Hal
@@ -35,13 +38,16 @@ your test configuration
 - [ ] Make sure you are merging into the ``develop`` (not ``main``) branch
 - [ ] My code follows the style guidelines of this project
 - [ ] I have performed a self-review of my own code
+- [ ] I have linted the files updated in this pull request
 - [ ] I have commented my code, particularly in hard-to-understand areas
 - [ ] I have made corresponding changes to the documentation
 - [ ] My changes generate no new warnings
 - [ ] I have added tests that prove my fix is effective or that my feature works
 - [ ] 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 wiki: https://github.com/pysat/pysat/wiki/Checklist-for-Release
+If this is a release PR, replace the first item of the above checklist with the
+release checklist on the wiki:
+https://github.com/pysat/pysat/wiki/Checklist-for-Release

.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
 
@@ -8,25 +9,22 @@ 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: ["3.10"]
 
     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
+      run: pip install .[doc]
 
     - name: Set up pysat
       run: |

.github/workflows/main.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: Pytest with Flake8
 
@@ -10,39 +11,48 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, windows-latest]
-        python-version: ["3.9", "3.10"]
+        os: ["ubuntu-latest", "windows-latest", "macos-latest"]
+        python-version: ["3.10", "3.11", "3.12"]
         numpy_ver: ["latest"]
+        test_config: ["latest"]
         include:
-          - python-version: "3.8"
-            numpy_ver: "1.20"
+          # 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 }}
     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 NEP29/Operational dependencies
-      if: ${{ matrix.numpy_ver != 'latest'}}
+    - name: Install Operational dependencies
+      if: ${{ matrix.test_config == 'Ops'}}
       run: |
-        pip install --no-binary :numpy: numpy==${{ matrix.numpy_ver }}
+        pip install numpy==${{ matrix.numpy_ver }}
+        pip install -r requirements.txt
+        pip install -r test_requirements.txt
+        pip install .
 
-    - name: Install standard dependencies and pysat
+    - name: Install NEP29 dependencies
+      if: ${{ matrix.test_config == 'NEP29'}}
       run: |
-        python -m pip install --upgrade pip
-        pip install -r requirements.txt
-        python setup.py install
+        pip install numpy==${{ matrix.numpy_ver }}
+        pip install --upgrade-strategy only-if-needed .[test]
 
-    - name: Install requirements for testing setup
-      run: pip install -r test_requirements.txt
+    - name: Install standard dependencies
+      if: ${{ matrix.test_config == 'latest'}}
+      run: pip install .[test]
 
     - name: Set up pysat
       run: |
@@ -56,9 +66,22 @@ jobs:
       run: flake8 . --count --exit-zero --max-complexity=10 --statistics
 
     - name: Test with pytest
-      run: pytest --cov=pysat/
+      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 pysat from
+# test pypi. This test should be manually run before a pysat 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: ["3.11"]  # 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/ pysat
+
+    - 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 pysat; print(pysat.__version__)"

.github/workflows/stats.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: Statistics of supported instruments
 
@@ -9,26 +10,23 @@ on:
 jobs:
   build:
 
-    runs-on: ubuntu-latest
+    runs-on: ["ubuntu-latest"]
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9"]
+        python-version: ["3.11"]
 
     name: Summary of instrument libraries
     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: |
-        pip install -r requirements.txt
-        # Need to install pysat before ecosystem
-        python setup.py install
-        pip install -r test_requirements.txt
+        pip install .[test]
         pip install `awk '{print $1}' ecosystem.txt`
 
     - name: Set up pysat

.readthedocs.yml

@@ -5,22 +5,20 @@
 # Required
 version: 2
 
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.10"
+
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
-  configuration: docs/conf.py
-
-# Build documentation with MkDocs
-#mkdocs:
-#  configuration: mkdocs.yml
+   configuration: docs/conf.py
 
-# Optionally build your docs in additional formats such as PDF
-formats:
-  - pdf
-
-# Optionally set the version of Python and requirements
-# required to build your docs
+# Declare the Python requirements required to build your docs
+# This method includes a local build of the package
 python:
-  version: 3.7
-  install:
-    - requirements: docs/requirements.txt
-
+   install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - doc