Merge branch 'Cantera:main' into nonIdealFlame

.github/workflows/main.yml

@@ -45,8 +45,8 @@ jobs:
     - name: Upgrade pip
       run: python3 -m pip install -U pip setuptools wheel
     - name: Install Python dependencies
-      run: python3 -m pip install ruamel.yaml scons numpy cython h5py pandas pytest
-        pytest-github-actions-annotate-failures
+      run: python3 -m pip install ruamel.yaml scons==3.1.2 numpy cython h5py pandas
+        pytest pytest-github-actions-annotate-failures
     - name: Build Cantera
       run: python3 `which scons` build env_vars=all -j2 debug=n --debug=time
     - name: Test Cantera
@@ -178,6 +178,20 @@ jobs:
         files: ./coverage.xml
         fail_ci_if_error: true
 
+  example-keywords:
+    name: Check example keywords
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+    steps:
+      - uses: actions/checkout@v2
+        name: Checkout the repository
+      - name: Setup Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: '3.10'
+      - name: Check keywords
+        run: python3 doc/example-keywords.py compare
+
   docs:
     name: Build docs
     runs-on: ubuntu-latest
@@ -345,41 +359,12 @@ jobs:
       - name: Test Essentials
         # ensure that Python package loads and converter scripts work
         run: |
-          python -c 'import cantera as ct; import sys; sys.exit(0) if ct.__version__.startswith("2.6.0") else sys.exit(1)'
+          python -c 'import cantera as ct; import sys; sys.exit(0) if ct.__version__.startswith("3.0.0") else sys.exit(1)'
           ck2yaml --input=test/data/h2o2.inp --output=h2o2-test.yaml
           test -f h2o2-test.yaml
           cti2yaml test/data/air-no-reactions.cti air-no-reaction-test.yaml
           test -f air-no-reaction-test.yaml
 
-  cython-latest:
-    name: Test pre-release version of Cython
-    runs-on: ubuntu-latest
-    timeout-minutes: 60
-    steps:
-    - uses: actions/checkout@v2
-      name: Checkout the repository
-      with:
-        submodules: recursive
-    - name: Setup python
-      uses: actions/setup-python@v2
-      with:
-        python-version: '3.8'
-        architecture: x64
-    - name: Install Apt dependencies
-      run: |
-        sudo apt update
-        sudo apt install libboost-dev liblapack-dev libblas-dev
-    - name: Upgrade pip
-      run: python3 -m pip install -U pip setuptools wheel
-    - name: Install Python dependencies
-      run: |
-        python3 -m pip install ruamel.yaml scons numpy h5py pandas pytest pytest-github-actions-annotate-failures
-        python3 -m pip install https://github.com/cython/cython/archive/master.zip --install-option='--no-cython-compile';
-    - name: Build Cantera
-      run: python3 `which scons` build blas_lapack_libs=lapack,blas python_package='full' -j2 debug=n
-    - name: Test Cantera
-      run: python3 `which scons` test show_long_tests=yes verbose_tests=yes
-
   check-deprecations:
     name: Run test suite without legacy typedefs
     runs-on: ubuntu-latest
@@ -462,7 +447,7 @@ jobs:
     - name: Test Essentials
       # ensure that Python package loads and converter scripts work
       run: |
-        python -c 'import cantera as ct; import sys; sys.exit(0) if ct.__version__.startswith("2.6.0") else sys.exit(1)'
+        python -c 'import cantera as ct; import sys; sys.exit(0) if ct.__version__.startswith("3.0.0") else sys.exit(1)'
         ck2yaml --input=test/data/h2o2.inp --output=h2o2-test.yaml
         test -f h2o2-test.yaml
         cti2yaml test/data/air-no-reactions.cti air-no-reaction-test.yaml
@@ -507,8 +492,8 @@ jobs:
           BOOST_ROOT=$(echo $BOOST_ROOT | sed 's/\\/\//g')
           mkdir -p $BOOST_ROOT
           curl --progress-bar --location --output $BOOST_ROOT/download.7z $BOOST_URL
-          7z -o$BOOST_ROOT x $BOOST_ROOT/download.7z -y -bd boost_1_75_0/boost
-          mv $BOOST_ROOT/boost_1_75_0/boost $BOOST_ROOT/boost
+          7z -o$BOOST_ROOT x $BOOST_ROOT/download.7z -y -bd boost_1_78_0/boost
+          mv $BOOST_ROOT/boost_1_78_0/boost $BOOST_ROOT/boost
           rm $BOOST_ROOT/download.7z
         shell: bash
       - name: Build Cantera
@@ -647,8 +632,8 @@ jobs:
         BOOST_ROOT=$(echo $BOOST_ROOT | sed 's/\\/\//g')
         mkdir -p $BOOST_ROOT
         curl --progress-bar --location --output $BOOST_ROOT/download.7z $BOOST_URL
-        7z -o$BOOST_ROOT x $BOOST_ROOT/download.7z -y -bd boost_1_75_0/boost
-        mv $BOOST_ROOT/boost_1_75_0/boost $BOOST_ROOT/boost
+        7z -o$BOOST_ROOT x $BOOST_ROOT/download.7z -y -bd boost_1_78_0/boost
+        mv $BOOST_ROOT/boost_1_78_0/boost $BOOST_ROOT/boost
         rm $BOOST_ROOT/download.7z
       shell: bash
     - name: Build Cantera

.gitignore

@@ -27,6 +27,7 @@ interfaces/matlab/Contents.m
 stage/
 .sconsign.dblite
 .sconf_temp
+.vscode
 cantera.conf*
 config.log
 *.lib

CONTRIBUTING.md

@@ -21,9 +21,9 @@
     followed by a blank line and a more detailed summary, if any)
   * Make related changes in a single commit, and unrelated changes in separate
     commits
-  * Make sure that your commits do not include any undesired files, e.g., files
+  * Make sure that your commits do not include any undesired files, such as files
     produced as part of the build process or other temporary files.
-  * Use Git's history-rewriting features (i.e., `git rebase -i`; see
+  * Use Git's history-rewriting features (such as `git rebase -i`; see
     https://help.github.com/articles/about-git-rebase/) to organize your commits
     and squash "fixup" commits and reversions.
   * Do not merge your branch with `main`. If needed, you should rebase your branch
@@ -60,11 +60,13 @@
   (`&&`/`||`/...), and comparisons (`<`/`>`/`==`/...); before and after equality
   signs `=` unless used for the assignment of a default parameter)
 * Do not go out of your way to change formatting in otherwise unmodified code
+* Write 'for example', 'such as', or 'that is' instead of using the Latin
+  abbreviations 'i.e.' and 'e.g.'.
 
 ## C++
 
 * All classes, member variables, and methods should have Doxygen-style comments
-  (e.g., comment lines starting with `//!` or comment blocks starting with `/*!`)
+  (for example, comment lines starting with `//!` or comment blocks starting with `/*!`)
 * Avoid defining non-trivial functions in header files
 * Header files should include an 'include guard'
 * Protected and private member variable names are generally prefixed with
@@ -74,7 +76,7 @@
 * Do not indent the contents of namespaces
 * Code should follow the C++11 standard, with minimum required compiler versions
   GCC 4.8, Clang 3.4, MSVC 14.0 (2015) and Intel 15.0.
-* Avoid manual memory management (i.e. `new` and `delete`), preferring to use
+* Avoid manual memory management (that is, `new` and `delete`), preferring to use
   standard library containers, as well as `std::unique_ptr` and
   `std::shared_ptr` when dynamic allocation is required.
 * Portions of Boost which are "header only" may be used. If possible, include

INSTALL.md

@@ -0,0 +1,18 @@
+# Installing Cantera
+
+## Basic Instructions
+
+To compile using the default options, run `scons build` followed by
+`scons install`.
+
+Configuration options are specified with `name=value` on the command line, for example:
+`scons build optimize=n prefix=/home/$USER/cantera`
+
+The full list of configuration options and their default values can be shown by running
+`scons help --options`. The list of available `scons` commands (such as `build`) can be
+shown by running `scons help`.
+
+
+## Detailed Instructions
+
+See the instructions available [online](https://cantera.org/install/compiling-install.html).

README.rst

@@ -33,18 +33,23 @@ using the following MyBinder link:
 Installation
 ============
 
+|pip| |anaconda| |conda-forge|
+
 `Installation instructions for the current release of Cantera
 <https://cantera.org/install/index.html>`_ are available from the main `Cantera
-documentation site <https://cantera.org>`_. Installers are provided for Windows (MSI
-packages), macOS, and Ubuntu. Anaconda packages containing the Cantera Python and Matlab
-modules are also available for Windows, macOS, and Linux.
+documentation site <https://cantera.org>`_.
+
+- The Python module can also be installed using pip on Windows, macOS, and Linux.
 
-.. image:: https://anaconda.org/cantera/cantera/badges/installer/conda.svg
-    :target: https://anaconda.org/Cantera/cantera
+- Conda packages containing the Cantera Python and Matlab modules are also available
+  for Windows, macOS, and Linux.
 
-For other platforms, or for users wishing to install a development version of
-Cantera, `compilation instructions <https://cantera.org/install/index.html>`_
-are also available.
+- Additional installation packages are provided for Windows, macOS, Ubuntu, Fedora,
+  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>`_
+  are also available.
 
 Documentation
 =============
@@ -55,7 +60,7 @@ offers a number of starting points:
 - `Python tutorial
   <https://cantera.org/tutorials/python-tutorial.html>`_
 - `Application Examples in Python
-  <https://github.com/Cantera/cantera-jupyter#cantera-jupyter>`_
+  <https://cantera.org/examples/jupyter/index.html>`_
 - `A guide to Cantera's input file format
   <https://cantera.org/tutorials/input-files.html>`_
 - `Information about the Cantera community
@@ -69,9 +74,9 @@ offers a number of starting points:
 Code of Conduct
 ===============
 
-.. image:: https://img.shields.io/badge/code%20of%20conduct-contributor%20covenant-green.svg?style=flat-square
+.. image:: https://img.shields.io/badge/Contributor%20Covenant-2.0-4baaaa.svg
     :alt: conduct
-    :target: https://www.contributor-covenant.org/version/1/4/code-of-conduct.html
+    :target: https://www.contributor-covenant.org/version/2/0/code-of-conduct.html
 
 In order to have a more open and welcoming community, Cantera adheres to a
 `code of conduct <CODE_OF_CONDUCT.md>`_ adapted from the `Contributor Covenant
@@ -89,8 +94,8 @@ possible.
 Development Site
 ================
 
-The current development version is 2.6.0b1. The current stable version is
-2.5.1. The `latest Cantera source code <https://github.com/Cantera/cantera>`_,
+The current development version is 3.0.0a1. The current stable version is
+2.6.0. 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
@@ -107,7 +112,6 @@ Continuous Integration Status
 
 |ci|
 
-
 NumFOCUS
 ========
 
@@ -130,12 +134,21 @@ 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.170284.svg
-   :target: https://doi.org/10.5281/zenodo.1174508
+.. |doi| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.6387882.svg
+   :target: https://doi.org/10.5281/zenodo.6387882
 
 .. |codecov| image:: https://img.shields.io/codecov/c/github/Cantera/cantera/main.svg
    :target: https://codecov.io/gh/Cantera/cantera?branch=main
 
 .. |release| image:: https://img.shields.io/github/release/cantera/cantera.svg
    :target: https://github.com/Cantera/cantera/releases
    :alt: GitHub release
+
+.. |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