Merge pull request #46 from pysat/rc0_2_1

RC 0.2.1

.github/ISSUE_TEMPLATE/bug_report.md

@@ -1,32 +1,29 @@
 ---
 name: Bug report
-about: Create a report to help us improve
-title: ''
-labels: ''
-assignees: ''
+about: Create a report to report a problem that needs to be fixed
+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

@@ -1,20 +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/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/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
 
@@ -8,30 +9,35 @@ on: [push, pull_request]
 jobs:
   build:
 
-    runs-on: ubuntu-latest
+    runs-on: ["ubuntu-latest"]
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.7]
+        python-version: ["3.11"]
 
     name: Documentation tests
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      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
+        pip install .[doc]
 
     - name: Set up pysat
       run: |
         mkdir pysatData
         python -c "import pysat; pysat.params['data_dirs'] = './pysatData'"
 
+    - name: Check documentation build
+      run: sphinx-build -E -b html docs dist/docs
+
+    - name: Check documentation links
+      run: sphinx-build -b linkcheck docs dist/docs
+
     - name: Load .zenodo.json to check for errors
       run: python -c "import json; json.loads(open('.zenodo.json').read())"

.github/workflows/main.yml

@@ -10,35 +10,35 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10"]
-        os: [ubuntu-latest, macos-latest, windows-latest]
-        numpy_ver: [latest]
+        os: ["ubuntu-latest", "macos-latest", "windows-latest"]
+        python-version: ["3.11", "3.12"]
+        numpy_ver: ["latest"]
+        test_config: ["latest"]
         include:
-           - python-version: "3.8"
-             numpy_ver: "1.21"
+           # NEP29 compliance settings
+           - python-version: "3.10"
+             numpy_ver: "1.24"
              os: "ubuntu-latest"
+             test_config: "NEP29"
 
     name: Python ${{ matrix.python-version }} on ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
-    - name: Install requirements for testing setup
-      run: |
-        pip install -r test_requirements.txt
-
-    - name: Install dependencies
-      run: |
-        pip install -r requirements.txt
-
     - name: Install NEP29 dependencies
-      if: ${{ matrix.numpy_ver != 'latest'}}
+      if: ${{ matrix.test_config == 'NEP29'}}
       run: |
-        pip install --no-binary :numpy: numpy==${{ matrix.numpy_ver }}
+        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: |
@@ -52,9 +52,22 @@ jobs:
       run: flake8 . --count --exit-zero --max-complexity=10 --statistics
 
     - name: Test with pytest
-      run: pytest --cov=pysatSeasons/
+      run: pytest
+
+    - name: Coveralls Parallel
+      uses: coverallsapp/github-action@v2
+      with:
+        flag-name: run-${{ join(matrix.*, '-') }}
+        parallel: true
+
+  finish:
+    name: Finish Coverage Analysis
+    needs: build
+    if: ${{ always() }}
+    runs-on: ubuntu-latest
+    steps:
+    - name: Coveralls Finished
+      uses: coverallsapp/github-action@v2
+      with:
+        parallel-finished: true
 
-    - name: Publish results to coveralls
-      env:
-        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      run: coveralls --rcfile=setup.cfg --service=github

.github/workflows/pip_rc_install.yml

@@ -0,0 +1,40 @@
+# This workflow will install Python dependencies and the latest RC of pysatNASA from test pypi.
+# This test should be manually run before a pysatSeasons 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 pysatSeasons RC
+      run: pip install --no-deps --pre -i https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple/ pysatSeasons
+
+    - 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 pysatSeasons; print(pysatSeasons.__version__)"

.github/workflows/pysat_rc.yml

@@ -0,0 +1,55 @@
+# 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: ["3.12"]
+
+    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: ${{ matrix.python-version }}
+
+    - name: Install pysat RC
+      run: pip install --no-deps --pre -i https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple/ pysat
+
+    - name: Install with standard dependencies
+      run:  pip install .[test]
+
+    - name: Set up pysat
+      run: |
+        mkdir pysatData
+        python -c "import pysat; pysat.params['data_dirs'] = 'pysatData'"
+
+    - name: Test with pytest
+      run: pytest
+
+    - name: Coveralls Parallel
+      uses: coverallsapp/github-action@v2
+      with:
+        flag-name: run-${{ join(matrix.*, '-') }}
+        parallel: true
+
+  finish:
+    name: Finish Coverage Analysis
+    needs: build
+    if: ${{ always() }}
+    runs-on: ubuntu-latest
+    steps:
+    - name: Coveralls Finished
+      uses: coverallsapp/github-action@v2
+      with:
+        parallel-finished: true
+

.gitignore

@@ -11,6 +11,7 @@ __pycache__/
 
 # Distribution / packaging
 .Python
+.python-version
 env/
 build/
 develop-eggs/

.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: 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
+
+
+# Optionally declare the Python requirements required to build your docs
+python:
+   install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - doc