Release Cantera 3.1.0

.github/SUPPORT.md

@@ -17,16 +17,14 @@ be able to help you out.
 
 ## Documentation
 
-The [documentation](https://cantera.org/documentation)
+The [Cantera Website](https://cantera.org)
 offers a number of starting points:
 
-- [Python tutorial](https://cantera.org/tutorials/python-tutorial.html)
-- [Application Examples in Python (Jupyter)](https://github.com/Cantera/cantera-jupyter#cantera-jupyter)
-- [A guide to Cantera's input file format](https://cantera.org/tutorials/input-files.html)
+- [Python tutorial](https://cantera.org/stable/userguide/python-tutorial.html)
+- [Gallery of Python Examples](https://cantera.org/stable/examples/python/index.html)
+- [A guide to Cantera's input file format](https://cantera.org/stable/userguide/input-tutorial.html)
 - [Information about the Cantera community](https://cantera.org/community.html)
-
-Documentation for the [development version of
-Cantera](https://cantera.org/documentation/dev-docs.html) is also available.
+- [Developers: Compile and Modify Cantera](https://cantera.org/stable/develop/index.html)
 
 ## Contributions
 

.github/workflows/main.yml

@@ -5,14 +5,16 @@ on:
     # Build on tags that look like releases
     tags:
       - v*
-    # Build when main or testing is pushed to
+    # Build when main, testing, or the maintenance branch is pushed to
     branches:
       - main
       - testing
+      - "3.1"
   pull_request:
-    # Build when a pull request targets main
+    # Build when a pull request targets main or the maintenance branch
     branches:
       - main
+      - "3.1"
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
@@ -329,8 +331,6 @@ jobs:
     defaults:
       run:
         shell: bash -l {0}
-    env:
-      DEPLOY: ${{ github.event_name == 'push' && github.repository_owner == 'Cantera' && endsWith(github.ref, 'main') }}
     steps:
       - uses: actions/checkout@v4
         name: Checkout the repository
@@ -379,28 +379,72 @@ jobs:
           cd build/doc
           tar --exclude="*.map" --exclude="*.md5" -czf docs.tar.gz html
         if: failure() || success()
-      - name: Store archive of docs output
+      - name: Store a copy of docs output
         uses: actions/upload-artifact@v4
         with:
           path: build/doc/docs.tar.gz
           name: docs
           retention-days: 14
         if: failure() || success()
+      - name: Determine whether to deploy
+        id: deploy-conf
+        if: ${{ github.event_name == 'push' && github.repository_owner == 'Cantera' }}
+        run: |
+          if [[ ${{ github.ref }} =~ ^refs\/heads\/([0-9]+\.[0-9]+)$ ]]; then
+              echo "match=true" >> $GITHUB_OUTPUT
+              echo "rsync_dest=cantera/${BASH_REMATCH[1]}" >> $GITHUB_OUTPUT
+              echo "commit=true" >> $GITHUB_OUTPUT
+              echo "git_dest=${BASH_REMATCH[1]}" >> $GITHUB_OUTPUT
+              echo "git_branch=staging" >> $GITHUB_OUTPUT
+          elif [[ ${{ github.ref }} == "refs/heads/main" ]]; then
+              echo "match=true" >> $GITHUB_OUTPUT
+              echo "rsync_dest=cantera/dev" >> $GITHUB_OUTPUT
+          elif [[ ${{ github.ref }} == "refs/heads/testing" ]]; then
+              echo "match=true" >> $GITHUB_OUTPUT
+              echo "rsync_dest=testing.cantera.org/dev" >> $GITHUB_OUTPUT
+              echo "commit=true" >> $GITHUB_OUTPUT
+              echo "git_dest=testing" >> $GITHUB_OUTPUT
+              echo "git_branch=testing" >> $GITHUB_OUTPUT
+          fi
       # The known_hosts key is generated with `ssh-keygen -F cantera.org` from a
       # machine that has previously logged in to cantera.org and trusts
       # that it logged in to the right machine
       - name: Set up SSH key and host for deploy
-        if: env.DEPLOY == 'true'
+        if: steps.deploy-conf.outputs.match == 'true'
         uses: shimataro/ssh-key-action@v2
         with:
           key: ${{ secrets.CTDEPLOY_KEY }}
           known_hosts: ${{ secrets.CTDEPLOY_HOST }}
-      - name: Upload the docs
-        if: env.DEPLOY == 'true'
+      - name: Commit docs to api-docs repo
+        if: steps.deploy-conf.outputs.commit == 'true'
+        env:
+          CANTERABOT_DOCS_TOKEN: ${{ secrets.CANTERABOT_DOCS_TOKEN }}
+          # Directory in api-docs repo: either the version (X.Y) or "testing"
+          GIT_DEST: ${{ steps.deploy-conf.outputs.git_dest }}
+          # Branch in api-docs to commit to: either 'staging' or 'testing'
+          BRANCH: ${{ steps.deploy-conf.outputs.git_branch }}
+        run: |
+          set -ex
+          REPO_SHA=`git rev-parse --short=8 HEAD`
+          git clone https://canterabot:${CANTERABOT_DOCS_TOKEN}@github.com/Cantera/api-docs
+
+          cd api-docs
+          git config user.name "CanteraBot"
+          git config user.email "96191898+CanteraBot@users.noreply.github.com"
+
+          git checkout --track origin/${BRANCH}
+          mkdir -p ${GIT_DEST}
+          tar -zxf ../build/doc/docs.tar.gz -C ${GIT_DEST}
+          git add .
+          git commit -m "Update for Cantera ${GIT_DEST} - Cantera/cantera@${REPO_SHA}"
+          git show --stat HEAD
+          git push origin
+      - name: Upload the docs to cantera.org
+        if: steps.deploy-conf.outputs.match == 'true'
         env:
           RSYNC_USER: "ctdeploy"
           RSYNC_SERVER: "cantera.org"
-          RSYNC_DEST: "cantera/dev"
+          RSYNC_DEST: ${{ steps.deploy-conf.outputs.rsync_dest }}
           DOCS_OUTPUT_DIR: "./build/doc/html/"
         run: |
           rsync -avzP --checksum --exclude='*.map' --exclude='*.md5' \

AUTHORS

@@ -10,6 +10,7 @@ Halla Ali (@hallaali)
 Emil Atz (@EmilAtz)
 Jongyoon Bae (@jongyoonbae), Brown University
 Philip Berndt
+Guus Bertens (@guusbertens), Eindhoven University of Technology
 Wolfgang Bessler (@wbessler), Offenburg University of Applied Science
 Paul Blum (@paulblum)
 Tilman Bremer
@@ -20,6 +21,8 @@ Ryan Crisanti
 Nicholas Curtis (@arghdos)
 Steven DeCaluwe (@decaluwe), Colorado School of Mines
 Vishesh Devgan (@vdevgan)
+Matthias Diener (@matthiasdiener), University of Illinois at Urbana-Champaign
+Martey Dodoo (@martey)
 Thomas Fiala (@thomasfiala), Technische Universität München
 David Fronczek
 Mark E. Fuller (@mefuller), Technion
@@ -30,6 +33,8 @@ Dave Goodwin, California Institute of Technology
 China Hagström (@chinahg), Massachusetts Institute of Technology
 John Hewson (@jchewson), Sandia National Laboratory
 Trevor Hickey (@luxe)
+David Holland (@dholland88)
+Zbigniew Jędrzejewski-Szmek (@keszybz), Red Hat
 Yuanjie Jiang
 Benjamin Kee (@lionkey)
 Cory Kinney (@corykinney)
@@ -51,6 +56,7 @@ Harry Moffat (@hkmoffat), Sandia National Laboratory
 Christopher Neal (@wandadars)
 Kyle Niemeyer (@kyleniemeyer), Oregon State University
 Paul Northrop (@pwcnorthrop)
+Chris Pilko (@cpilko)
 Sebastian Pinnau (@spinnau)
 Corey R. Randall (@c-randall), Colorado School of Mines
 Andreas Rücker (@cannondale1492)
@@ -59,11 +65,13 @@ Satyam Saxena (@CyberDrudge)
 Ingmar Schoegl (@ischoegl), Louisiana State University
 Santosh Shanbhogue (@santoshshanbhogue), Massachusetts Institute of Technology
 Travis Sikes (@tsikes)
+Patrick Singal (@pjsingal) Columbia University
 Harsh Sinha (@sin-ha)
 Sai Krishna Sirumalla (@skrsna), Northeastern University
 David Sondak
 Raymond Speth (@speth), Massachusetts Institute of Technology
 Su Sun (@ssun30), Northeastern University
+Daniel Thomas (@d-e-t), University of Minnesota
 Sergey Torokhov (@band-a-prend)
 Laurien Vandewalle (@lavdwall)
 Guillaume Vignat (@gvignat), Stanford University

CITATION.cff

@@ -16,6 +16,6 @@ authors:
   given-names: Bryan W.
   orcid: https://orcid.org/0000-0003-0815-9270
 title: "Cantera: An Object-oriented Software Toolkit for Chemical Kinetics, Thermodynamics, and Transport Processes"
-version: "3.0.0"
-doi: 10.5281/zenodo.8137090
-date-released: 2023-08-22
+version: "3.1.0"
+doi: 10.5281/zenodo.14455267
+date-released: 2024-12-14

INSTALL.md

@@ -15,4 +15,7 @@ shown by running `scons help`.
 
 ## Detailed Instructions
 
-See the instructions available [online](https://cantera.org/install/compiling-install.html).
+See the instructions available for installing packages providing the
+[current stable version](https://cantera.org/stable/install/index.html) or compilation
+instructions for building the
+[latest development version](https://cantera.org/dev/develop/index.html).

README.rst

@@ -33,10 +33,10 @@ using the following MyBinder link:
 Installation
 ============
 
-|pip| |anaconda| |conda-forge|
+|pip| |conda-forge|
 
 `Installation instructions for the current release of Cantera
-<https://cantera.org/install/index.html>`_ are available from the main `Cantera
+<https://cantera.org/stable/install/index.html>`_ are available from the main `Cantera
 documentation site <https://cantera.org>`_.
 
 - The Python module can also be installed using pip on Windows, macOS, and Linux.
@@ -48,28 +48,26 @@ documentation site <https://cantera.org>`_.
   RHEL, Gentoo, and FreeBSD.
 
 - For other platforms, or for users wishing to install a development version of
-  Cantera, `compilation instructions <https://cantera.org/install/compiling-install.html#sec-compiling>`_
+  Cantera, `compilation instructions <https://cantera.org/stable/develop/index.html>`_
   are also available.
 
 Documentation
 =============
 
-The `documentation <https://cantera.org/documentation>`_
-offers a number of starting points:
+The `documentation <https://cantera.org>`_ offers a number of starting points:
 
 - `Python tutorial
-  <https://cantera.org/tutorials/python-tutorial.html>`_
+  <https://cantera.org/stable/userguide/python-tutorial.html>`_
 - `Application Examples in Python
-  <https://cantera.org/examples/jupyter/index.html>`_
+  <https://cantera.org/stable/examples/python/index.html>`_
 - `A guide to Cantera's input file format
-  <https://cantera.org/tutorials/input-files.html>`_
+  <https://cantera.org/stable/userguide/input-tutorial.html>`_
+- `User Guide: Tutorials, FAQ, and Task Guides
+  <https://cantera.org/stable/userguide/index.html>`
 - `Information about the Cantera community
   <https://cantera.org/community.html>`_
 - `Affiliated packages
-  <https://cantera.org/affiliated-packages.html>`_
-
-`Documentation for the development version of Cantera
-<https://cantera.org/documentation/dev-docs.html>`_ is also available.
+  <https://cantera.org/affiliated.html>`_
 
 Code of Conduct
 ===============
@@ -94,8 +92,8 @@ possible.
 Development Site
 ================
 
-The current development version is 3.1.0b1. The current stable version is
-3.0.0. The `latest Cantera source code <https://github.com/Cantera/cantera>`_,
+The current development version is 3.1.0. The current stable version is
+3.1.0. The `latest Cantera source code <https://github.com/Cantera/cantera>`_,
 the `issue tracker <https://github.com/Cantera/cantera/issues>`_ for bugs and
 enhancement requests, `downloads of Cantera releases and binary installers
 <https://github.com/Cantera/cantera/releases>`_ , and the `Cantera wiki
@@ -125,7 +123,7 @@ development of Cantera through NumFOCUS.
     :target: https://numfocus.org/donate-to-cantera
     :alt: Powered by NumFOCUS
 
-.. |cantera| image:: https://cantera.org/assets/img/cantera-logo.png
+.. |cantera| image:: https://cantera.org/_static/cantera-logo.png
     :target: https://cantera.org
     :alt: cantera logo
     :width: 675px
@@ -134,8 +132,8 @@ development of Cantera through NumFOCUS.
 .. |ci| image:: https://github.com/Cantera/cantera/workflows/CI/badge.svg
     :target: https://github.com/Cantera/cantera/actions?query=workflow%3ACI+event%3Apush
 
-.. |doi| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.8137090.svg
-   :target: https://doi.org/10.5281/zenodo.8137090
+.. |doi| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.14455267.svg
+   :target: https://doi.org/10.5281/zenodo.14455267
 
 .. |codecov| image:: https://img.shields.io/codecov/c/github/Cantera/cantera/main.svg
    :target: https://codecov.io/gh/Cantera/cantera?branch=main
@@ -147,8 +145,5 @@ development of Cantera through NumFOCUS.
 .. |pip| image:: https://img.shields.io/pypi/v/cantera
    :target: https://pypi.org/project/Cantera/
 
-.. |anaconda| image:: https://img.shields.io/conda/v/cantera/cantera
-   :target: https://anaconda.org/Cantera/cantera
-
 .. |conda-forge| image:: https://img.shields.io/conda/v/conda-forge/cantera
    :target: https://anaconda.org/conda-forge/cantera

SConstruct

@@ -163,7 +163,7 @@ logger.info(
     f"SCons {SCons.__version__} is using the following Python interpreter:\n"
     f"    {sys.executable} (Python {python_version})", print_level=False)
 
-cantera_version = "3.1.0b1"
+cantera_version = "3.1.0"
 # For use where pre-release tags are not permitted (MSI, sonames)
 cantera_pure_version = re.match(r'(\d+\.\d+\.\d+)', cantera_version).group(0)
 cantera_short_version = re.match(r'(\d+\.\d+)', cantera_version).group(0)

doc/doxygen/Doxyfile

@@ -48,7 +48,7 @@ PROJECT_NAME           = Cantera
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = 3.1.0b1
+PROJECT_NUMBER         = 3.1.0
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a

doc/doxygen/versions.md

@@ -2,16 +2,16 @@
 
 > **Note:** For release notes and previous versions of the Python/MATLAB
 > interface documentation, refer to
-> [cantera.org](https://cantera.org/documentation/index.html#need-something-else).
+> [cantera.org](https://cantera.org/stable/reference/index.html).
 
-**%Cantera Developer API** versions:
+**%Cantera C++ API** versions:
 
-* [dev/latest](https://cantera.org/documentation/dev/doxygen/html/index.html) (unstable)
-* [v3.0.0](https://cantera.org/documentation/docs-3.0/doxygen/html/index.html)
-* [v2.6.0](https://cantera.org/documentation/docs-2.6/doxygen/html/modules.html)
-* [v2.5.1](https://cantera.org/documentation/docs-2.5/doxygen/html/modules.html)
-* [v2.4.0](https://cantera.org/documentation/docs-2.4/doxygen/html/modules.html)
-* [v2.3.0](https://cantera.org/documentation/docs-2.3/doxygen/html/modules.html)
-* [v2.2.1](https://cantera.org/documentation/docs-2.2/doxygen/html/modules.html)
-* [v2.1.2](https://cantera.org/documentation/docs-2.1/doxygen/html/modules.html)
-* [v2.0.2](https://cantera.org/documentation/docs-2.0/doxygen/html/modules.html)
+* [dev/latest](https://cantera.org/dev/cxx/index.html) (unstable)
+* [v3.0.0](https://cantera.org/3.0/doxygen/html/index.html)
+* [v2.6.0](https://cantera.org/2.6/doxygen/html/modules.html)
+* [v2.5.1](https://cantera.org/2.5/doxygen/html/modules.html)
+* [v2.4.0](https://cantera.org/2.4/doxygen/html/modules.html)
+* [v2.3.0](https://cantera.org/2.3/doxygen/html/modules.html)
+* [v2.2.1](https://cantera.org/2.2/doxygen/html/modules.html)
+* [v2.1.2](https://cantera.org/2.1/doxygen/html/modules.html)
+* [v2.0.2](https://cantera.org/2.0/doxygen/html/modules.html)

doc/sphinx/_static/doc-versions.json

@@ -1,40 +1,45 @@
 [
     {
-        "name": "3.1 (dev)",
-        "version": "3.1",
+        "name": "3.2 (dev)",
+        "version": "3.2",
         "url": "/dev/"
     },
     {
-        "name": "3.0.0 (stable)",
+        "name": "3.1.0 (stable)",
+        "version": "3.1",
+        "url": "/3.1/"
+    },
+    {
+        "name": "3.0.0",
         "version": "3.0.0",
-        "url": "/documentation/docs-3.0/sphinx/html/"
+        "url": "/3.0/sphinx/html/"
     },
     {
         "version": "2.6.0",
-        "url": "/documentation/docs-2.6/sphinx/html/"
+        "url": "/2.6/sphinx/html/"
     },
     {
         "version": "2.5.1",
-        "url": "/documentation/docs-2.5/sphinx/html/"
+        "url": "/2.5/sphinx/html/"
     },
     {
         "version": "2.4.0",
-        "url": "/documentation/docs-2.4/sphinx/html/"
+        "url": "/2.4/sphinx/html/"
     },
     {
         "version": "2.3.0",
-        "url": "/documentation/docs-2.3/sphinx/html/"
+        "url": "/2.3/sphinx/html/"
     },
     {
         "version": "2.2.1",
-        "url": "/documentation/docs-2.2/sphinx/html/"
+        "url": "/2.2/sphinx/html/"
     },
     {
         "version": "2.1.2",
-        "url": "/documentation/docs-2.1/sphinx/html/"
+        "url": "/2.1/sphinx/html/"
     },
     {
         "version": "2.0.2",
-        "url": "/documentation/docs-2.0/sphinx/html/"
+        "url": "/2.0/sphinx/html/"
     }
 ]