merge in latest changes from RC_v1.5.x and solve merge conflicts in doc/

.github/ISSUE_TEMPLATE/bug-report.md

@@ -0,0 +1,13 @@
+---
+name: Bug Report
+about: Report a bug in the tobac library
+title: ''
+labels: bug
+assignees: ''
+
+---
+
+* [ ] Have you searched the issue tracker for the same problem?
+* [ ] Have you checked if you're using the latest version? If not, which version are you using?
+* [ ] Have you mentioned the steps to reproduce the issue?
+* [ ] Have you, if applicable, included error messages?

.github/ISSUE_TEMPLATE/question.md

@@ -0,0 +1,12 @@
+---
+name: Question
+about: 'Ask a general question about tobac '
+title: ''
+labels: question
+assignees: ''
+
+---
+
+* [ ] Have you searched the issue tracker for similar questions?
+* [ ] Have you read the documentation to ensure your question isn't already answered?
+* [ ] Have you searched Stack Overflow or other relevant forums to see if your question has been answered elsewhere?

.github/ISSUE_TEMPLATE/release.md

@@ -0,0 +1,20 @@
+---
+name: Release
+about: Prepare a new release for tobac
+title: Release v.X.Y.Z
+labels: release
+assignees: ''
+
+---
+
+Checklist for releasing vX.Y.Z:
+
+* [ ]  Re-run notebooks and commit updates to repository
+* [ ]  Bump version in `__init__.py` in `RC_vX.Y.Z`
+* [ ]  Add changelog in `RC_vX.Y.Z`
+* [ ]  Add new contributors to vX.Y.Z
+* [ ]  Merge `RC_vX.Y.Z` into `main`
+* [ ]  Delete `RC_vX.Y.Z` branch
+* [ ]  Create release
+* [ ]  Push release to conda-forge
+* [ ]  E-mail tobac mailing list

.github/workflows/check_formatting.yml

@@ -5,10 +5,19 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
+      - name: Set up conda
+        uses: conda-incubator/setup-miniconda@v2
         with:
-          python-version: '3.8'
-      - run: pip install .
-      - run: pip install black==22.6.0 
-      - run: black tobac --check
-
+          miniforge-version: latest
+          miniforge-variant: mambaforge
+          channel-priority: strict
+          channels: conda-forge
+          show-channel-urls: true
+          use-only-tar-bz2: true
+
+      - name: Install dependencies and check formatting
+        shell: bash -l {0}
+        run:
+          mamba install --quiet --yes --file requirements.txt black &&
+          black --version &&
+          black tobac --check --diff 

.github/workflows/check_json.yml

@@ -0,0 +1,23 @@
+name: Check Zenodo JSON Formatting
+on: [push, pull_request]
+jobs:
+  check-json-formatting:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -el {0}
+    steps:
+      - name: check out repository code
+        uses: actions/checkout@v3
+      - name: set up conda environment
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          auto-activate-base: false
+          activate-environment: checkjson-env
+      - name: Install check-jsonschema
+        run: |
+          pip install check-jsonschema
+      - name: Check zenodo JSON formatting
+        run: |
+          check-jsonschema --schemafile https://zenodraft.github.io/metadata-schema-zenodo/latest/schema.json .zenodo.json

.github/workflows/check_notebooks.yml

@@ -0,0 +1,40 @@
+name: Jupyter Notebooks CI
+on: [push, pull_request]
+jobs:
+  Check-Notebooks:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -el {0}
+    steps:
+      - name: check out repository code
+        uses: actions/checkout@v3
+      - name: set up conda environment
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          miniforge-version: latest
+          miniforge-variant: mambaforge
+          channel-priority: strict
+          channels: conda-forge
+          show-channel-urls: true
+          use-only-tar-bz2: true
+          auto-update-conda: true
+          auto-activate-base: false
+          activate-environment: notebook-env
+      - name: Install tobac dependencies
+        run: |
+          mamba install -c conda-forge --yes ffmpeg gcc jupyter pytables
+          mamba install -c conda-forge --yes --file example_requirements.txt
+      - name: Install tobac
+        run: |
+          pip install .
+      - name: Find all notebook files
+        run: |
+          find . -type f -name '*.ipynb' > nbfiles.txt
+          cat nbfiles.txt
+      - name: Execute all notebook files
+        run: |
+          while IFS= read -r nbpath; do
+            jupyter nbconvert --inplace --ClearMetadataPreprocessor.enabled=True --clear-output $nbpath
+            jupyter nbconvert --to notebook --inplace --execute $nbpath
+          done < nbfiles.txt

.github/workflows/codecov-CI.yml

@@ -29,5 +29,6 @@ jobs:
       - name: Upload Coverage to Codecov
         uses: codecov/codecov-action@v3
         with:
+          token: ${{ secrets.CODECOV_TOKEN }}
           fail_ci_if_error: true
           flags: unittests

.github/workflows/matrix_ci.yml

@@ -0,0 +1,53 @@
+name: Matrix Testing CI
+# this is similar to the pyart CI action
+on: [push, pull_request]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+# This job installs dependencies and runs tests across a matrix of python and OS versions.
+#Add if: github.repository == 'tobac-project/tobac' to limit runs to tobac repo
+
+jobs:
+  build:
+    name: ${{ matrix.os }}-${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}-latest
+    if: github.repository == 'tobac-project/tobac'
+    defaults:
+      run:
+        shell: bash -l {0}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        os: [macos, ubuntu, windows]
+
+    steps:
+      - uses: actions/checkout@v2
+
+      # Install micromamba and dependencies
+      - name: Setup Conda Environment
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-file: environment-ci.yml
+          activate-environment: pyart-dev
+          cache-downloads: true
+          channels: conda-forge
+          channel-priority: strict
+          python-version: ${{ matrix.python-version }}
+
+      - name: Fetch all history for all tags and branches
+        run: |
+           git fetch --prune --unshallow
+
+      - name: Install tobac
+        shell: bash -l {0}
+        run: |
+          python -m pip install -e . --no-deps --force-reinstall
+
+      - name: Run Tests
+        id: run_tests
+        shell: bash -l {0}
+        run: |
+          python -m pytest -v 

.github/workflows/pylint.yml

@@ -0,0 +1,86 @@
+name: Linting
+on:
+  pull_request_target:
+    branches:
+      - '*'
+permissions:
+  pull-requests: write
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+      - name: Check out Git repository
+        uses: actions/checkout@v3
+
+      - name: Set up conda
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          miniforge-version: latest
+          miniforge-variant: mambaforge
+          channel-priority: strict
+          channels: conda-forge
+          show-channel-urls: true
+          use-only-tar-bz2: true
+
+      - name: Install tobac and pylint
+        run: |
+          mamba install --yes pylint
+          pip install .
+
+      - name: Store the PR branch
+        run: |
+          echo "SHA=$(git rev-parse "$GITHUB_SHA")" >> $GITHUB_OUTPUT
+        id: git
+
+      - name: Checkout RC branch
+        uses: actions/checkout@v3
+        with:
+          ref: ${{ github.base_ref }}
+
+      - name: Get pylint score of RC branch
+        run: |
+          pylint tobac --disable=C --exit-zero
+        id: main_score
+
+      - name: Checkout PR branch
+        uses: actions/checkout@v3
+        with:
+          ref: "${{ steps.git.outputs.SHA }}"  
+
+      - name: Get pylint score of PR branch
+        run: |
+          # use shell script to save only tail of output  
+          OUTPUT_PART=$(pylint tobac --disable=C --exit-zero | tail -n 2)
+          # but post entire output in the action details 
+          pylint tobac --disable=C --exit-zero
+          # define random delimiter for multiline string
+          EOF=$(dd if=/dev/urandom bs=15 count=1 status=none | base64)
+          echo "MESSAGE<<$EOF" >> "$GITHUB_OUTPUT"
+          echo "$OUTPUT_PART" >> "$GITHUB_OUTPUT"
+          echo "$EOF" >> "$GITHUB_OUTPUT"
+        id: pr_score
+
+      - name: Find Comment
+        uses: peter-evans/find-comment@v2
+        id: comment
+        with:
+          issue-number: ${{ github.event.pull_request.number }}
+          comment-author: 'github-actions[bot]'
+          body-includes: Linting results by Pylint
+
+      - name: Post result to PR
+        uses: peter-evans/create-or-update-comment@v3
+        with:
+          issue-number: ${{ github.event.pull_request.number }}
+          comment-id: ${{ steps.comment.outputs.comment-id }}
+          edit-mode: replace
+          body: |
+            Linting results by Pylint:
+            --------------------------
+            ${{ steps.pr_score.outputs.MESSAGE }}
+            <sub>The linting score is an indicator that reflects how well your code version follows Pylint’s coding standards and quality metrics with respect to the ${{ github.base_ref }} branch.
+            A decrease usually indicates your new code does not fully meet style guidelines or has potential errors.<sup>

.gitignore

@@ -4,4 +4,11 @@ __pycache__
 htmlcov
 .coverage
 build
-.idea
+.idea
+examples/*/Save
+examples/*/Plot
+examples/climate-processes-tobac_example_data-b3e69ee
+.ipynb_checkpoints
+.DS_Store
+*.egg-info
+

.readthedocs.yml

@@ -1,7 +1,9 @@
 version: 2
 formats: all
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.9"
 python:
-  version: 3
   install:
     - requirements: doc/requirements.txt
-  system_packages: true