From 57de3cece6158e9fe0a1a27ad69fa53c05826ec2 Mon Sep 17 00:00:00 2001
From: Jared O'Neal <joneal@anl.gov>
Date: Mon, 15 Dec 2025 14:27:34 -0600
Subject: [PATCH 01/11] (Issue #19) Automatically & temporarily install ninja
 for building pkg.

Without this change, Meson failed in a macOS system with no ninja installation.
With the change, it installed and the package tests ran through successfully.
---
 README.md                         | 10 +++-------
 openbtmixing_pypkg/pyproject.toml |  1 +
 2 files changed, 4 insertions(+), 7 deletions(-)

diff --git a/README.md b/README.md
index b4a77ef..5752add 100644
--- a/README.md
+++ b/README.md
@@ -35,8 +35,8 @@ the above
 * the [Meson build system](https://mesonbuild.com) and its prerequistes such as
   Python 3 and [ninja](https://ninja-build.org).
 
-While Meson is used internally to build the Python package, it is installed
-automatically just for building the package.
+While both Meson and ninja are used internally to build the Python package, they
+are installed automatically just for building the package.
 
 The Meson build system is setup to automatically detect the compiler suite and
 MPI installation to use.  If Eigen already exists in the system and Meson can
@@ -104,12 +104,8 @@ $ python
 The package can also be built and installed from a clone of this repository with
 ```
 $ cd /path/to/OpenBT/openbtmixing_pypkg
-$ python -m build --sdist
-$ python -m pip install -v dist/openbtmixing-<version>.tar.gz
+$ python -m pip install .
 ```
-where we assume that the [build](https://build.pypa.io/en/stable/index.html)
-package has already been installed.
-
 Developers can setup a virtual environment with a developer/editable mode
 installation of the package with
 ```
diff --git a/openbtmixing_pypkg/pyproject.toml b/openbtmixing_pypkg/pyproject.toml
index 29848b6..975c9fa 100644
--- a/openbtmixing_pypkg/pyproject.toml
+++ b/openbtmixing_pypkg/pyproject.toml
@@ -1,6 +1,7 @@
 [build-system]
 requires = [
     "setuptools",
+    "ninja",
     "meson>=1.6.0"
 ]
 build-backend = "setuptools.build_meta"

From fb889d65428fde7527a55746a4630a1b72d043dc Mon Sep 17 00:00:00 2001
From: Jared O'Neal <joneal@anl.gov>
Date: Mon, 15 Dec 2025 15:07:15 -0600
Subject: [PATCH 02/11] macos-13 action runner is deprecated.

This was the only Intel-based macOS runner that we were running on.  So include
the macOS-15-intel runner now as well.
---
 .github/workflows/test_CLTs.yml     | 2 +-
 .github/workflows/test_anaconda.yml | 8 +++-----
 .github/workflows/test_py_sdist.yml | 2 +-
 3 files changed, 5 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/test_CLTs.yml b/.github/workflows/test_CLTs.yml
index 503d8b4..3be91ea 100644
--- a/.github/workflows/test_CLTs.yml
+++ b/.github/workflows/test_CLTs.yml
@@ -21,7 +21,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [macos-13, macos-14, macos-15,
+        os: [macos-14, macos-15, macos-15-intel,
              ubuntu-22.04, ubuntu-24.04]
         mpi_impl: ["openmpi", "mpich"]
         python-version: ["3.13"]
diff --git a/.github/workflows/test_anaconda.yml b/.github/workflows/test_anaconda.yml
index 4643af1..3f5275c 100644
--- a/.github/workflows/test_anaconda.yml
+++ b/.github/workflows/test_anaconda.yml
@@ -23,14 +23,14 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [macos-13, macos-14, macos-15,
+        os: [macos-14, macos-15, macos-15-intel,
              ubuntu-22.04, ubuntu-24.04]
         mpi_impl: ["openmpi"]
         python-version: ["3.12"]
         miniconda-version: [py312_24.11.1-0]
         exclude:
           # Prebuilt Intel MPI package not available for macOS
-          - os: [macos-13, macos-14, macos-15]
+          - os: [macos-14, macos-15, macos-15-intel]
             mpi_impl: "impi_rt"
 
     steps:
@@ -48,7 +48,6 @@ jobs:
         which python
         which pip
         python --version
-        python -m pip install build
         conda info
         conda list
         python -m pip list
@@ -68,7 +67,6 @@ jobs:
       run: |
         which python
         pushd $PKG_ROOT
-        python -m build --sdist
-        python -m pip install -v dist/openbtmixing-*.tar.gz
+        python -m pip install .
         popd
         $CLONE_PATH/tools/test_python_installation.py
diff --git a/.github/workflows/test_py_sdist.yml b/.github/workflows/test_py_sdist.yml
index dfe969e..3981dc7 100644
--- a/.github/workflows/test_py_sdist.yml
+++ b/.github/workflows/test_py_sdist.yml
@@ -20,7 +20,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [macos-13, macos-14, macos-15,
+        os: [macos-14, macos-15, macos-15-intel,
              ubuntu-22.04, ubuntu-24.04]
         mpi_impl: ["openmpi", "mpich"]
         python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]

From a53310eaedf7bf6230016159d561ddf7925bb9a1 Mon Sep 17 00:00:00 2001
From: Jared O'Neal <joneal@anl.gov>
Date: Mon, 15 Dec 2025 16:18:19 -0600
Subject: [PATCH 03/11] Try Python 3.14.

---
 .github/workflows/measure_coverage.yml | 4 ++--
 .github/workflows/test_CLTs.yml        | 2 +-
 .github/workflows/test_py_devmode.yml  | 4 ++--
 .github/workflows/test_py_sdist.yml    | 2 +-
 4 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/measure_coverage.yml b/.github/workflows/measure_coverage.yml
index f10e691..4f63f91 100644
--- a/.github/workflows/measure_coverage.yml
+++ b/.github/workflows/measure_coverage.yml
@@ -17,10 +17,10 @@ jobs:
   #####----- FULL TESTING WITH COVERAGE
   # This also confirms that tox with coverage & report works.
   coverage:
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
     strategy:
       matrix:
-        python-version: ["3.13"]
+        python-version: ["3.14"]
 
     steps:
     ##-- Setup Testing Environment
diff --git a/.github/workflows/test_CLTs.yml b/.github/workflows/test_CLTs.yml
index 3be91ea..e70246c 100644
--- a/.github/workflows/test_CLTs.yml
+++ b/.github/workflows/test_CLTs.yml
@@ -24,7 +24,7 @@ jobs:
         os: [macos-14, macos-15, macos-15-intel,
              ubuntu-22.04, ubuntu-24.04]
         mpi_impl: ["openmpi", "mpich"]
-        python-version: ["3.13"]
+        python-version: ["3.14"]
 
     steps:
     ##-- Setup Testing Environment
diff --git a/.github/workflows/test_py_devmode.yml b/.github/workflows/test_py_devmode.yml
index 0576b9b..1c83e90 100644
--- a/.github/workflows/test_py_devmode.yml
+++ b/.github/workflows/test_py_devmode.yml
@@ -18,8 +18,8 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [macos-14, ubuntu-22.04]
-        python-version: ["3.13"]
+        os: [macos-15, ubuntu-24.04]
+        python-version: ["3.14"]
 
     steps:
     ##-- Setup Testing Environment
diff --git a/.github/workflows/test_py_sdist.yml b/.github/workflows/test_py_sdist.yml
index 3981dc7..4300d06 100644
--- a/.github/workflows/test_py_sdist.yml
+++ b/.github/workflows/test_py_sdist.yml
@@ -23,7 +23,7 @@ jobs:
         os: [macos-14, macos-15, macos-15-intel,
              ubuntu-22.04, ubuntu-24.04]
         mpi_impl: ["openmpi", "mpich"]
-        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13", "3.14"]
         exclude:
           # MPICH+Ubuntu24.04 tests presently fail because they detect only one
           # MPI process instead of two.  I suspect that this is related to using

From 24b8f71c9fd4dc9ec2b3efe7c827fb31fbe32b82 Mon Sep 17 00:00:00 2001
From: Jared O'Neal <joneal@anl.gov>
Date: Mon, 15 Dec 2025 17:09:52 -0600
Subject: [PATCH 04/11] 3.14 worked in general.  See if this fixes extra
 actions.

---
 .github/workflows/measure_coverage.yml | 2 +-
 .github/workflows/test_py_devmode.yml  | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/measure_coverage.yml b/.github/workflows/measure_coverage.yml
index 4f63f91..d88ce30 100644
--- a/.github/workflows/measure_coverage.yml
+++ b/.github/workflows/measure_coverage.yml
@@ -29,7 +29,7 @@ jobs:
     - name: Install mpich
       run: |
         sudo apt-get update
-        sudo apt-get -y install mpich
+        sudo apt-get -y install mpich libmpich-dev
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v5
       with:
diff --git a/.github/workflows/test_py_devmode.yml b/.github/workflows/test_py_devmode.yml
index 1c83e90..18382f1 100644
--- a/.github/workflows/test_py_devmode.yml
+++ b/.github/workflows/test_py_devmode.yml
@@ -29,7 +29,7 @@ jobs:
       run: |
         if   [ "${{ runner.os }}" = "Linux" ]; then
            sudo apt-get update
-           sudo apt-get -y install mpich
+           sudo apt-get -y install mpich libmpich-dev
         elif [ "${{ runner.os }}" = "macOS" ]; then
            brew install mpich
         fi

From 83e1e779b11f922c5aee751f8e46ecdd4ffea83f Mon Sep 17 00:00:00 2001
From: Jared O'Neal <joneal@anl.gov>
Date: Mon, 15 Dec 2025 17:20:04 -0600
Subject: [PATCH 05/11] Go back to Ubuntu 22.

According to exclude comments in test_py_sdist, MPICH and Ubuntu 24 don't work
correctly.
---
 .github/workflows/measure_coverage.yml | 4 ++--
 .github/workflows/test_py_devmode.yml  | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/measure_coverage.yml b/.github/workflows/measure_coverage.yml
index d88ce30..1a8c675 100644
--- a/.github/workflows/measure_coverage.yml
+++ b/.github/workflows/measure_coverage.yml
@@ -17,7 +17,7 @@ jobs:
   #####----- FULL TESTING WITH COVERAGE
   # This also confirms that tox with coverage & report works.
   coverage:
-    runs-on: ubuntu-24.04
+    runs-on: ubuntu-22.04
     strategy:
       matrix:
         python-version: ["3.14"]
@@ -29,7 +29,7 @@ jobs:
     - name: Install mpich
       run: |
         sudo apt-get update
-        sudo apt-get -y install mpich libmpich-dev
+        sudo apt-get -y install mpich
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v5
       with:
diff --git a/.github/workflows/test_py_devmode.yml b/.github/workflows/test_py_devmode.yml
index 18382f1..3602b5f 100644
--- a/.github/workflows/test_py_devmode.yml
+++ b/.github/workflows/test_py_devmode.yml
@@ -18,7 +18,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [macos-15, ubuntu-24.04]
+        os: [macos-15, ubuntu-22.04]
         python-version: ["3.14"]
 
     steps:
@@ -29,7 +29,7 @@ jobs:
       run: |
         if   [ "${{ runner.os }}" = "Linux" ]; then
            sudo apt-get update
-           sudo apt-get -y install mpich libmpich-dev
+           sudo apt-get -y install mpich
         elif [ "${{ runner.os }}" = "macOS" ]; then
            brew install mpich
         fi

From 0d70925e6aafbac2ecc458ab63e4a2bb77e382b8 Mon Sep 17 00:00:00 2001
From: Jared O'Neal <joneal@anl.gov>
Date: Mon, 15 Dec 2025 17:39:08 -0600
Subject: [PATCH 06/11] Try using latest and greatest Eigen version.

Build fails if you try to build with C++-11 standard with error message that
states that 14 is needed.
---
 README.md              |  2 +-
 meson.build            |  4 ++--
 subprojects/eigen.wrap | 20 ++++++++++----------
 3 files changed, 13 insertions(+), 13 deletions(-)

diff --git a/README.md b/README.md
index 5752add..a75d028 100644
--- a/README.md
+++ b/README.md
@@ -25,7 +25,7 @@ implementation provided by the user.
 ## Requirements
 Before building and installing the Python package, users
 must provide
-* a compiler suite that includes a C++ compiler that supports the C++11
+* a compiler suite that includes a C++ compiler that supports the C++14
   standard,
 * an MPI installation that is compatible with the compiler suite, and
 * optionally the [Eigen software package](https://gitlab.com/libeigen/eigen).
diff --git a/meson.build b/meson.build
index bddeae6..1ff649e 100644
--- a/meson.build
+++ b/meson.build
@@ -1,5 +1,5 @@
 # ----- SPECIFY PROJECT
-# eigen dependency requires at least C++11
+# eigen dependency requires at least C++14
 #
 # The version provided here is the version of the C++ library and command line
 # tools.  The Python package maintains a separate version.  If the C++ code is
@@ -14,7 +14,7 @@ project('openbtmixing', 'cpp',
         license: 'MIT',
         license_files: 'LICENSE',
         default_options: [
-          'cpp_std=c++11',
+          'cpp_std=c++14',
           'buildtype=debug',
           'default_library=shared',
           'b_ndebug=if-release',
diff --git a/subprojects/eigen.wrap b/subprojects/eigen.wrap
index becc476..79465dd 100644
--- a/subprojects/eigen.wrap
+++ b/subprojects/eigen.wrap
@@ -1,13 +1,13 @@
 [wrap-file]
-directory = eigen-3.4.0
-source_url = https://gitlab.com/libeigen/eigen/-/archive/3.4.0/eigen-3.4.0.tar.bz2
-source_filename = eigen-3.4.0.tar.bz2
-source_hash = b4c198460eba6f28d34894e3a5710998818515104d6e74e5cc331ce31e46e626
-patch_filename = eigen_3.4.0-2_patch.zip
-patch_url = https://wrapdb.mesonbuild.com/v2/eigen_3.4.0-2/get_patch
-patch_hash = cb764fd9fec02d94aaa2ec673d473793c0d05da4f4154c142f76ef923ea68178
-source_fallback_url = https://github.com/mesonbuild/wrapdb/releases/download/eigen_3.4.0-2/eigen-3.4.0.tar.bz2
-wrapdb_version = 3.4.0-2
+directory = eigen-5.0.1
+source_url = https://gitlab.com/libeigen/eigen/-/archive/5.0.1/eigen-5.0.1.tar.bz2
+source_filename = eigen-5.0.1.tar.bz2
+source_hash = e4de6b08f33fd8b8985d2f204381408c660bffa6170ac65b68ae1bd3cd575c0a
+patch_filename = eigen_5.0.1-1_patch.zip
+patch_url = https://wrapdb.mesonbuild.com/v2/eigen_5.0.1-1/get_patch
+patch_hash = 23407632af9388f4585547028c4ed363ff54875872cbf3e89c2085a14397f555
+source_fallback_url = https://github.com/mesonbuild/wrapdb/releases/download/eigen_5.0.1-1/eigen-5.0.1.tar.bz2
+wrapdb_version = 5.0.1-1
 
 [provide]
-eigen3 = eigen_dep
+dependency_names = eigen3

From 81106bcdb558e03580575ba6a4680cda05cbe343 Mon Sep 17 00:00:00 2001
From: Jared O'Neal <joneal@anl.gov>
Date: Mon, 15 Dec 2025 18:31:36 -0600
Subject: [PATCH 07/11] Get rid of variable warning.

---
 meson.build           | 2 +-
 subprojects/README.md | 5 +++++
 2 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/meson.build b/meson.build
index 1ff649e..f861425 100644
--- a/meson.build
+++ b/meson.build
@@ -29,7 +29,7 @@ project('openbtmixing', 'cpp',
 # If users have a local install of eigen that can be discovered with pkg-config
 # or other Meson tricks, then that installation will be used.  Otherwise, meson
 # will download the specific tarball as defined in eigen.wrap and use that.
-eigen_dep = dependency('eigen3', fallback: ['eigen', 'eigen_dep'])
+eigen_dep = dependency('eigen3', fallback: 'eigen')
 deps_all = [eigen_dep]
 
 # ----- USER ARGUMENTS
diff --git a/subprojects/README.md b/subprojects/README.md
index df2aeed..397cd1c 100644
--- a/subprojects/README.md
+++ b/subprojects/README.md
@@ -5,3 +5,8 @@ History
 ----------
 * Pulled down `eigen.wrap` from meson's wrapDB as part of switching
   from autotools to meson.
+
+2025-12-15
+----------
+* Pulled down `eigen.wrap` from meson's wrapDB so that OpenBT can use the eigen
+  implementations for the newest major version (v5).

From 049ebbe1760406ec30275de8ac524e376394374c Mon Sep 17 00:00:00 2001
From: Jared O'Neal <joneal@anl.gov>
Date: Wed, 17 Dec 2025 14:45:03 -0600
Subject: [PATCH 08/11] (Issue #19) This would be a patch update.

---
 openbtmixing_pypkg/VERSION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/openbtmixing_pypkg/VERSION b/openbtmixing_pypkg/VERSION
index 45a1b3f..781dcb0 100644
--- a/openbtmixing_pypkg/VERSION
+++ b/openbtmixing_pypkg/VERSION
@@ -1 +1 @@
-1.1.2
+1.1.3

From 1c64164edc4646b9721c989b793378e427856caa Mon Sep 17 00:00:00 2001
From: Jared O'Neal <joneal@anl.gov>
Date: Fri, 13 Feb 2026 10:39:58 -0600
Subject: [PATCH 09/11] (Issue #19) Add MPI installation troubleshooting hints.

These lines were originally in the Taweret installations docs.  However, they
are most useful here.  They are being simultaneously removed from the Taweret
docs.  This (hopefully) finalizes the decoupling of these two packages.
---
 README.md | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/README.md b/README.md
index a75d028..1c622b9 100644
--- a/README.md
+++ b/README.md
@@ -30,6 +30,11 @@ must provide
 * an MPI installation that is compatible with the compiler suite, and
 * optionally the [Eigen software package](https://gitlab.com/libeigen/eigen).
 
+Note that if installing MPI using a package manager, related developer library
+packages such as ``libopenmpi-dev`` or ``libmpich-dev`` might need to be
+installed in addition to the base MPI packages such as ``openmpi-bin`` or
+``mpich``.
+
 To build and install just the bare C++ tools, users must provide in addition to
 the above
 * the [Meson build system](https://mesonbuild.com) and its prerequistes such as

From ade1ee843d9afc5fcbf7a5b49db035c4fbe7ef21 Mon Sep 17 00:00:00 2001
From: Jared O'Neal <joneal@anl.gov>
Date: Fri, 13 Feb 2026 14:23:00 -0600
Subject: [PATCH 10/11] (Issue #19) Clean as part of PR review.

Installation logs generated when installing the package indicate that the codecs
package is now deprecated.   We followed suggestions in the log to just use
open.  This issue was already found and handled identically with surmise.  IIRC,
the use of codecs was actually causing issues with surmise at some point.

I did one successful build with these changes in place.
---
 .github/workflows/test_py_devmode.yml | 2 +-
 openbtmixing_pypkg/setup.py           | 3 +--
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/test_py_devmode.yml b/.github/workflows/test_py_devmode.yml
index 3602b5f..1c83e90 100644
--- a/.github/workflows/test_py_devmode.yml
+++ b/.github/workflows/test_py_devmode.yml
@@ -18,7 +18,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [macos-15, ubuntu-22.04]
+        os: [macos-15, ubuntu-24.04]
         python-version: ["3.14"]
 
     steps:
diff --git a/openbtmixing_pypkg/setup.py b/openbtmixing_pypkg/setup.py
index 5273765..8d1181f 100644
--- a/openbtmixing_pypkg/setup.py
+++ b/openbtmixing_pypkg/setup.py
@@ -1,7 +1,6 @@
 import os
 import sys
 import shutil
-import codecs
 
 import subprocess as sbp
 
@@ -104,7 +103,7 @@ def run(self, *args, **kwargs):
 # ----- SPECIFY THE PACKAGE
 def readme_md():
     fname = PKG_ROOT.joinpath("README.md")
-    with codecs.open(fname, "r", encoding="utf8") as fptr:
+    with open(fname, "r", encoding="utf8") as fptr:
         return fptr.read()
 
 

From 5e99c8d91ab4b137841be5296daae55d117b64f7 Mon Sep 17 00:00:00 2001
From: Jared O'Neal <joneal@anl.gov>
Date: Fri, 13 Feb 2026 14:33:32 -0600
Subject: [PATCH 11/11] (Issue #19) Try Open-MPI for sake of Ubuntu 24.04.

See notes in test_py_sdist.yml
---
 .github/workflows/test_py_devmode.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/test_py_devmode.yml b/.github/workflows/test_py_devmode.yml
index 1c83e90..5bac601 100644
--- a/.github/workflows/test_py_devmode.yml
+++ b/.github/workflows/test_py_devmode.yml
@@ -25,13 +25,13 @@ jobs:
     ##-- Setup Testing Environment
     - name: Checkout OpenBTMixing
       uses: actions/checkout@v4
-    - name: Install MPICH
+    - name: Install Open-MPI
       run: |
         if   [ "${{ runner.os }}" = "Linux" ]; then
            sudo apt-get update
-           sudo apt-get -y install mpich
+           sudo apt-get -y install openmpi-bin libopenmpi-dev
         elif [ "${{ runner.os }}" = "macOS" ]; then
-           brew install mpich
+           brew install open-mpi
         fi
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v5