Merge pull request #192 from pysat/rc_0_0_5

Author: jklenzing

.github/ISSUE_TEMPLATE/bug_report.md

@@ -1,35 +1,29 @@
 ---
 name: Bug report
-about: Create a report to help us improve
+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
 
-or
+Consider including images or test files to help others reproduce the bug and
+solve the problem.
 
-```
-# test code here
-```
-
-**Expected behavior**
-A clear and concise description of what you expected to happen.
-
-**Screenshots**
-If applicable, add screenshots to help explain your problem.
-
-**Desktop (please complete the following information):**
- - OS: [e.g. iOS]
- - Version [e.g. Python 3.7]
+## 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

@@ -1,12 +1,12 @@
 # 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
 for this change.  Please see ``CONTRIBUTING.md`` for more guidelines.
 
-## Type of change
+# Type of change
 
 Please delete options that are not relevant.
 
@@ -25,9 +25,9 @@ your test configuration
 - Test A
 - Test B
 
-## Test Configuration
-* Operating system: [Os Type]
-* Version number: [Python 2.9]
+**Test Configuration**:
+* Operating system: Hal
+* Version number: Python 3.X
 * Any details about your local setup that are relevant
 
 # Checklist:
@@ -43,3 +43,6 @@ your test configuration
 - [ ] 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

.github/workflows/docs.yml

@@ -1,4 +1,4 @@
-# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# This workflow will install Python dependencies and check the sphinx build, links in the docs, and the readability of the zenodo file
 # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
 
 name: Documentation Check
@@ -8,11 +8,11 @@ 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"]  # Keep this version at the highest supported Python version
 
     name: Documentation tests
     steps:
@@ -25,8 +25,7 @@ jobs:
     - 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: |

.github/workflows/main.yml

@@ -10,13 +10,19 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ["3.9", "3.10"]
-        numpy_ver: [latest]
+        os: ["ubuntu-latest", "macos-latest", "windows-latest"]
+        python-version: ["3.10", "3.11"]
+        numpy_ver: ["latest"]
+        test_config: ["latest"]
         include:
-          - python-version: "3.8"
-            numpy_ver: "1.20"
+          - python-version: "3.9"
+            numpy_ver: "1.21"
             os: ubuntu-latest
+            test_config: "NEP29"
+          - 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 }}
@@ -31,18 +37,25 @@ jobs:
       if: ${{ matrix.os == 'macos-latest' }}
       run: brew reinstall gcc
 
+    - name: Install Operational dependencies
+      if: ${{ matrix.test_config == 'Ops'}}
+      run: |
+        pip install --no-cache-dir numpy==${{ matrix.numpy_ver }}
+        pip install "cdflib<1.0"
+        pip install -r requirements.txt
+        pip install -r test_requirements.txt
+        pip install .
+
     - name: Install NEP29 dependencies
-      if: ${{ matrix.numpy_ver != 'latest'}}
+      if: ${{ matrix.test_config == 'NEP29'}}
       run: |
-        pip install --no-binary :numpy: numpy==${{ matrix.numpy_ver }}
-        # Need to force a version of pandas compliant with NEP29
-        pip install "pandas<1.5"
+        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 -r requirements.txt
-        pip install pysatCDF --no-binary=pysatCDF
-        pip install -r test_requirements.txt
+        pip install .[test]
 
     - name: Set up pysat
       run: |
@@ -56,10 +69,9 @@ jobs:
       run: flake8 . --count --exit-zero --max-complexity=10 --statistics
 
     - name: Test with pytest
-      run: |
-        pytest -vs --cov=pysatNASA/
+      run: pytest
 
     - name: Publish results to coveralls
       env:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      run: coveralls --rcfile=setup.cfg --service=github
+      run: coveralls --rcfile=pyproject.toml --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 pysatNASA 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@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install standard dependencies
+      run: pip install -r requirements.txt
+
+    - name: Install pysatNASA RC
+      run: pip install --no-deps --pre -i https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple/ pysatNASA
+
+    - 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 pysatNASA; print(pysatNASA.__version__)"

.github/workflows/pysat_rc.yml

@@ -1,4 +1,6 @@
-# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# This workflow will install Python dependencies and the latest RC of pysat from test pypi.
+# All unit tests for pysatNASA will be run using the pysat RC.
+# 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 with latest pysat RC
@@ -10,8 +12,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ["3.10"]
+        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 }}
@@ -27,14 +29,12 @@ jobs:
       run: brew reinstall gcc
 
     - name: Install pysat RC
-      run: |
-        pip install -r test_requirements.txt
-        pip install --no-deps -i https://test.pypi.org/simple/ pysat
+      run: pip install --no-deps --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 pysatCDF --no-binary=pysatCDF
+        pip install -r test_requirements.txt
 
     - name: Set up pysat
       run: |

.gitignore

@@ -70,3 +70,6 @@ custom_lint.sh
 
 # IDEs
 .idea/
+
+# vscode
+.vscode

.readthedocs.yml

@@ -0,0 +1,22 @@
+# .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: "3.10"
+
+# 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:
+   - requirements: docs/requirements.txt

.zenodo.json

@@ -20,6 +20,11 @@
         "name": "Smith, Jonathon",
         "orcid": "0000-0002-8191-4765"
       },
+      {
+        "affilitation":"University of Colorado at Boulder",
+        "name": "Navarro, Luis",
+        "orcid": "0000-0002-6362-6575"
+      },
       {
         "affiliation": "Predictive Science",
         "name": "Pembroke, Asher"