Updates to Master Conflicts rosscastle

.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: Bug report
+about: Use this template for submitting bug reports.
+title: "[ISSUE TITLE]"
+labels: bug
+assignees:
+---
+
+<!--
+Thank you for taking the time to create an issue for your topic/question.
+This issue provides a permanent record for others with similar questions
+to gain insight at a later date - your contributions here are significant
+to the community and much appreciated!
+
+Please always remember to be courteous to others posting on this forum as
+we are all here voluntarily to help others use Isca.
+
+NOTE:
+Isca team members are all full-time research scientists, so while we are very happy to provide
+some support, response times may vary. If you need in-depth support, then we may suggest that one
+ of us becomes a co-author on your next paper by providing long-term support on the issue.
+-->
+
+<!--
+Please be sure to add an informative title to this issue
+-->
+
+## Description
+<!--
+Fill out a concise description of your topic/question in this section.
+Feel free to post your code here using Markdown formatting
+-->
+
+-----
+**Screenshots**
+<!--
+If applicable, add screenshots to help explain your problem.
+-->
+
+-----
+**Isca version**
+<!--
+Please provide here your recent commit ID and tell us if you are working off your own fork or just
+using the main Execlim verion.
+-->
+
+-----
+**System Information:**
+To help us track down bugs faster, please provide the details about the machine where you run Isca.
+
+To do this, run the following code in Python:
+```py
+import platform
+print(platform.uname())
+```
+and paste the output below.
+```txt
+# Paste system info here
+
+```
+-----
+## Minimal reproducible example
+<!--
+It greatly helps us address your question if you have example data or script for us to work with.
+-->

.github/ISSUE_TEMPLATE/docs_issue.md

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+---
+name: Documentation issue
+about: Use this template for submitting documentation-related issues.
+title: "[ISSUE TITLE]"
+labels: docs
+assignees:
+---
+
+<!--
+Thank you for taking the time to create an issue for your topic/question.
+This issue provides a permanent record for others with similar questions
+to gain insight at a later date - your contributions here are significant
+to the community and much appreciated!
+
+Please always remember to be courteous to others posting on this forum as
+we are all here voluntarily to help others use Isca.
+
+NOTE:
+Isca team members are all full-time research scientists, so while we are very happy to provide
+some support, response times may vary. If you need in-depth support, then we may suggest that one
+ of us becomes a co-author on your next paper by providing long-term support on the issue.
+-->
+
+<!--
+Please be sure to add an informative title to this issue
+-->
+
+## Description
+<!--
+Fill out a concise description of your topic/question in this section.
+Feel free to post your code here using Markdown formatting
+-->
+

.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: Feature Request
+about: Suggest an idea for something new to add
+labels: 
+---
+<!--
+Thank you for taking the time to create an issue for your topic/question.
+This issue provides a permanent record for others with similar questions
+to gain insight at a later date - your contributions here are significant
+to the community and much appreciated!
+
+Please always remember to be courteous to others posting on this forum as
+we are all here voluntarily to help others use Isca.
+
+NOTE:
+Isca team members are all full-time research scientists, so while we are very happy to provide
+some support, response times may vary. If you need in-depth support, then we may suggest that one
+ of us becomes a co-author on your next paper by providing long-term support on the issue.
+-->
+## Description
+<!--
+Include a clear description and an example or even a scholarly source of information about the feature.
+-->

.github/ISSUE_TEMPLATE/installation_issue.md

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+---
+name: Installation issue
+about: Use this template if you have an issue related to installing Isca.
+title: "[YOUR QUESTION]"
+labels: infrastructure
+assignees:
+---
+
+<!--
+Thank you for taking the time to create an issue for your topic/question.
+This issue provides a permanent record for others with similar questions
+to gain insight at a later date - your contributions here are significant
+to the community and much appreciated!
+
+Please always remember to be courteous to others posting on this forum as
+we are all here voluntarily to help others use Isca.
+
+NOTE:
+Isca team members are all full-time research scientists, so while we are very happy to provide
+some support, response times may vary. If you need in-depth support, then we may suggest that one
+ of us becomes a co-author on your next paper by providing long-term support on the issue.
+-->
+
+<!--
+Please be sure to add an informative title to this issue
+-->
+
+## Description
+<!--
+Fill out a concise description of your topic/question in this section.
+Feel free to post your code here using Markdown formatting
+-->
+
+-----
+**Screenshots**
+<!--
+If applicable, add screenshots to help explain your problem.
+-->
+
+-----
+**Isca version**
+<!--
+Please provide here your recent commit ID and tell us if you are working off your own fork or just
+using the main Execlim verion.
+-->
+
+-----
+**System Information:**
+To help us help you, provide the details about the machine where you are trying to install Isca.
+
+To do this, please run the following code in Python:
+```py
+import platform
+print(platform.uname())
+```
+and paste the output below.
+```txt
+# Paste system info here
+
+```

.github/ISSUE_TEMPLATE/science_issue.md

@@ -0,0 +1,42 @@
+---
+name: Science issue
+about: Use this template for submitting science-related issues.
+title: "[YOUR QUESTION]"
+labels:
+assignees:
+---
+
+<!--
+Thank you for taking the time to create an issue for your topic/question.
+This issue provides a permanent record for others with similar questions
+to gain insight at a later date - your contributions here are significant
+to the community and much appreciated!
+
+Please always remember to be courteous to others posting on this forum as
+we are all here voluntarily to help others use Isca.
+
+NOTE:
+Isca team members are all full-time research scientists, so while we are very happy to provide
+some support, response times may vary. If you need in-depth support, then we may suggest that one
+ of us becomes a co-author on your next paper by providing long-term support on the issue.
+-->
+
+<!--
+Please be sure to add an informative title to this issue
+-->
+
+## Description
+<!--
+Fill out a concise description of your topic/question in this section.
+Feel free to post your code here using Markdown formatting
+-->
+
+### Screenshots
+<!--
+If applicable, add screenshots to help explain your problem.
+-->
+
+## Minimal reproducible example
+<!--
+It greatly helps us address your question if you have example data or script for us to work with.
+-->

.github/workflows/docs.yml

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+name: docs
+
+on:
+  push:
+    branches: [ master ]
+    paths:
+      - '.github/workflows/docs.yml'
+      - 'docs/**'
+      - 'src/**'
+
+env:
+  GFDL_BASE: ${{ github.workspace }}
+  GFDL_ENV: "ubuntu_conda"
+  GFDL_WORK: "$HOME/gfdl_work"
+  GFDL_DATA: "$HOME/gfdl_data"
+  GFDL_PYDIR: "${{ github.workspace }}/src/extra/python"
+
+jobs:
+  docs:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        python-version: ['3.9']
+
+    steps:
+      - name: Checkout source
+        uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+
+      # - name: Check environment variables
+      #   run: |
+      #     echo "Testing"
+      #     echo $PWD
+      #     echo $GFDL_BASE
+      #     echo $GFDL_PYDIR
+      #     echo $GITHUB_WORKSPACE
+      #     echo $GITHUB_SERVER_URL/$GITHUB_REPOSITORY/actions/runs/$GITHUB_RUN_ID
+
+      - name: Setup Conda Environment
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+          environment-file: docs/environment.yml
+          miniforge-variant: Mambaforge
+          miniforge-version: "latest"
+          use-mamba: true
+          activate-environment: isca_docs
+          auto-activate-base: false
+
+      - name: List installed packages
+        shell: bash -l {0}
+        run: conda list
+
+      - name: Install
+        shell: bash -l {0}
+        run: |
+          cd $GFDL_PYDIR
+          python -m pip install -e .
+          cd $GFDL_BASE
+
+      - name: Build docs
+        shell: bash -l {0}
+        run: |
+          cd docs/
+          make html -e
+
+      - name: Commit documentation changes
+        run: |
+          git clone https://github.com/$GITHUB_REPOSITORY.git --branch gh-pages --single-branch gh-pages
+          cp -r docs/_build/html/* gh-pages/
+          cd gh-pages
+          git config --local user.email "action@github.com"
+          git config --local user.name "GitHub Action"
+          git add .
+          git commit -m "Update documentation" -a || true
+          # The above command will fail if no changes were present, so we ignore that.
+
+      - name: Push changes
+        uses: ad-m/github-push-action@master
+        with:
+          branch: gh-pages
+          directory: gh-pages
+          github_token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/tests.yml

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+name: tests
+
+on:
+  push:
+    branches: [ master ]
+    paths:
+      - '.github/workflows/tests.yml'
+      - 'bin/**'
+      - 'bin/**'
+      - 'ci/**'
+      - 'exp/**'
+      - 'input/**'
+      - 'src/**'
+      - 'test/**'
+  pull_request:
+    branches: [ master ]
+    paths:
+      - '.github/workflows/tests.yml'
+      - 'bin/**'
+      - 'ci/**'
+      - 'exp/**'
+      - 'input/**'
+      - 'src/**'
+      - 'test/**'
+
+env:
+  GFDL_BASE: ${{ github.workspace }}
+  GFDL_ENV: "ubuntu_conda"
+  GFDL_WORK: "${{ github.workspace }}/../gfdl_work"
+  GFDL_DATA: "${{ github.workspace }}/../gfdl_data"
+  GFDL_PYDIR: "${{ github.workspace }}/src/extra/python"
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest]  # ,  macos-latest]
+        python-version: ['3.12']
+
+    steps:
+      - name: Checkout source
+        uses: actions/checkout@v2
+
+      - name: Setup Conda for OS ${{ matrix.os }} and Python ${{ matrix.python-version }}
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+          environment-file: ci/environment-py${{ matrix.python-version }}_frozen.yml
+          miniforge-variant: Mambaforge
+          miniforge-version: "latest"
+          use-mamba: true
+          activate-environment: isca_env
+          auto-activate-base: false
+
+      - name: Install
+        shell: bash -l {0}
+        run: |
+          cd $GFDL_PYDIR
+          python -m pip install -e .
+          cd $GFDL_BASE
+
+      - name: List installed packages
+        shell: bash -l {0}
+        run: conda list
+
+      - name: Run tests
+        shell: bash -l {0}
+        run: |
+          python -m pytest