GCPy 1.4.0 release

This is the official release commit of GCPy 1.4.0, which includes:

- Improvements and updates for benchmark plotting/tabling routines
- Reorganized directory structure
- Refactoring of plotting code into shorter routines
- Improved example scripts

For complete details, please see CHANGELOG.md.

Signed-off-by: Bob Yantosca <[email protected]>

.github/ISSUE_TEMPLATE/config.yml

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+blank_issues_enabled: false
+contact_links:
+  - name: GCPy user manual
+    url: https://gcpy.readthedocs.io/en/stable
+    about: Click this link to read the GCPy user manual.

.github/ISSUE_TEMPLATE/new-feature-or-discussion.md

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+---
+name: Request a new GCPy feature or start a discussion
+about: Use this form to request a new GCPy feature or start a discussion
+---
+
+### Name and Institution (Required)
+
+Name:
+Institution:
+
+### Confirm you have reviewed the following documentation
+
+- [ ] [Contributing guidelines](https://gcpy.readthedocs.io/en/stable/reference/CONTRIBUTING.html)
+
+### New GCPy feature or discussion
+
+Please provide a clear and concise overview of the discussion topic or new feature requested.

.github/ISSUE_TEMPLATE/question-issue.md

@@ -0,0 +1,20 @@
+---
+name: Ask a question about or report an issue with GCPy
+about: Use this form to ask a question about GCPy or to report an issue
+---
+
+### Name and Institution (Required)
+
+Name:
+Institution:
+
+### Confirm you have reviewed the following documentation
+
+- [ ] [Support guidelines](https://gcpy.readthedocs.io/en/stable/reference/SUPPORT.html)
+- [ ] [User manual](https://gcpy.readthedocs.io/en/stable)
+- [ ] [Current and past Github issues](https://github.com/geoschem/gcpy/issues)
+
+### Description of your issue or question
+
+Please provide as much detail as possible. Always include the GCPy version number and any relevant configuration and log files.
+

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,24 @@
+### Name and Institution (Required)
+
+Name:
+Institution:
+
+### Confirm you have reviewed the following documentation
+
+- [ ] [Contributing guidelines](https://gcpy.readthedocs.io/en/stable/reference/CONTRIBUTING.html)
+
+### Describe the update
+
+Please provide a clear and concise overview of the update.
+
+### Expected changes
+
+Please provide details on how this update will impact GCPy output and include plots or tables as needed.
+
+### Reference(s)
+
+If this is a science update, please provide a literature citation.
+
+### Related Github Issue(s)
+
+Please link to the corresponding Github issue here. If fixing a bug, there should be an issue describing it with steps to reproduce.

.github/workflows/codeql.yml

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+# For most projects, this workflow file will not need changing; you simply need
+# to commit it to your repository.
+#
+# You may wish to alter this file to override the set of languages analyzed,
+# or to provide custom queries or build logic.
+#
+# ******** NOTE ********
+# We have attempted to detect the languages in your repository. Please check
+# the `language` matrix defined below to confirm you have the correct set of
+# supported CodeQL languages.
+#
+name: "CodeQL"
+
+on:
+  push:
+    branches: [ "main", "dev" ]
+  pull_request:
+    # The branches below must be a subset of the branches above
+    branches: [ "main", "dev" ]
+  schedule:
+    - cron: '21 14 * * 2'
+
+jobs:
+  analyze:
+    name: Analyze
+    # Runner size impacts CodeQL analysis time. To learn more, please see:
+    #   - https://gh.io/recommended-hardware-resources-for-running-codeql
+    #   - https://gh.io/supported-runners-and-hardware-resources
+    #   - https://gh.io/using-larger-runners
+    # Consider using larger runners for possible analysis time improvements.
+    runs-on: ${{ (matrix.language == 'swift' && 'macos-latest') || 'ubuntu-latest' }}
+    timeout-minutes: ${{ (matrix.language == 'swift' && 120) || 360 }}
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ 'python' ]
+        # CodeQL supports [ 'c-cpp', 'csharp', 'go', 'java-kotlin', 'javascript-typescript', 'python', 'ruby', 'swift' ]
+        # Use only 'java-kotlin' to analyze code written in Java, Kotlin or both
+        # Use only 'javascript-typescript' to analyze code written in JavaScript, TypeScript or both
+        # Learn more about CodeQL language support at https://aka.ms/codeql-docs/language-support
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v3
+
+    # Initializes the CodeQL tools for scanning.
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v2
+      with:
+        languages: ${{ matrix.language }}
+        # If you wish to specify custom queries, you can do so here or in a config file.
+        # By default, queries listed here will override any specified in a config file.
+        # Prefix the list here with "+" to use these queries and those in the config file.
+
+        # For more details on CodeQL's query packs, refer to: https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs
+        # queries: security-extended,security-and-quality
+
+
+    # Autobuild attempts to build any compiled languages (C/C++, C#, Go, Java, or Swift).
+    # If this step fails, then you should remove it and run the build manually (see below)
+    - name: Autobuild
+      uses: github/codeql-action/autobuild@v2
+
+    # ℹ️ Command-line programs to run using the OS shell.
+    # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
+
+    #   If the Autobuild fails above, remove it and uncomment the following three lines.
+    #   modify them (or add more) to build your code if your project, please refer to the EXAMPLE below for guidance.
+
+    # - run: |
+    #     echo "Run, Build Application using script"
+    #     ./location_of_script_within_repo/buildscript.sh
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v2
+      with:
+        category: "/language:${{matrix.language}}"

.github/workflows/pylint.yml

@@ -0,0 +1,23 @@
+name: Pylint
+
+on: [push]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10", "3.11"]
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install pylint
+    - name: Analysing the code with pylint
+      run: |
+        pylint $(git ls-files '*.py')

.github/workflows/stale.yml

@@ -0,0 +1,27 @@
+# This workflow warns and then closes issues and PRs that have had no activity for a specified amount of time.
+#
+# You can adjust the behavior by modifying this file.
+# For more information, see:
+# https://github.com/actions/stale
+name: Mark stale issues and pull requests
+
+on:
+  schedule:
+  - cron: '32 22 * * *'
+
+jobs:
+  stale:
+
+    runs-on: ubuntu-latest
+    permissions:
+      issues: write
+      pull-requests: write
+
+    steps:
+    - uses: actions/stale@v5
+      with:
+        repo-token: ${{ secrets.GITHUB_TOKEN }}
+        stale-issue-message: 'Stale issue message'
+        stale-pr-message: 'Stale pull request message'
+        stale-issue-label: 'no-issue-activity'
+        stale-pr-label: 'no-pr-activity'

.readthedocs.yaml

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+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+#
+# NOTE: This is now needed in order to prevent builds from failing due
+# to Python package issues at the ReadTheDocs site. For more info, see:
+# https://github.com/readthedocs/readthedocs.org/issues/10290
+#   -- Bob Yantosca (10 May 2023)
+
+# Required
+version: 2
+
+## Set the version of Python and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.7"
+    nodejs: "14"
+    rust:   "1.55"
+    golang: "1.17"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  builder: html
+  configuration: docs/source/conf.py
+
+# If using Sphinx, optionally build your docs in additional formats such as PDF
+formats: all
+
+# Optionally declare the Python requirements required to build your docs
+python:
+  install:
+  - requirements: docs/requirements.txt
+
+# Tell RTD to clone all submodules
+submodules:
+  include: all
+  recursive: true