From 08170faee8d95faf0a854d3fb3859135cbcdcf03 Mon Sep 17 00:00:00 2001
From: Mark Piper <mark.piper@colorado.edu>
Date: Tue, 5 Mar 2024 12:46:27 -0700
Subject: [PATCH 01/36] Move zest.releaser config to pyproject.toml

---
 babelizer/data/{{cookiecutter.package_name}}/pyproject.toml | 4 ++++
 babelizer/data/{{cookiecutter.package_name}}/setup.cfg      | 3 ---
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/babelizer/data/{{cookiecutter.package_name}}/pyproject.toml b/babelizer/data/{{cookiecutter.package_name}}/pyproject.toml
index b0077dce..deade262 100644
--- a/babelizer/data/{{cookiecutter.package_name}}/pyproject.toml
+++ b/babelizer/data/{{cookiecutter.package_name}}/pyproject.toml
@@ -107,3 +107,7 @@ underlines = "-^\""
 issue_format = "`#{issue} <https://github.com/{{ cookiecutter.info.github_username }}/{{ cookiecutter.package_name }}/issues/{issue}>`_"
 title_format = "{version} ({project_date})"
 wrap = true
+
+[tool.zest-releaser]
+tag-format = "v{version}"
+python-file-with-version = "{{ cookiecutter.package_name }}/_version.py"
diff --git a/babelizer/data/{{cookiecutter.package_name}}/setup.cfg b/babelizer/data/{{cookiecutter.package_name}}/setup.cfg
index 45fca16c..f3d7d5c3 100644
--- a/babelizer/data/{{cookiecutter.package_name}}/setup.cfg
+++ b/babelizer/data/{{cookiecutter.package_name}}/setup.cfg
@@ -5,6 +5,3 @@ ignore =
 	E501
 	W503
 max-line-length = 88
-
-[zest.releaser]
-tag-format = v{version}

From 78aaec340d78ab5b539c2252c94701cbab752f81 Mon Sep 17 00:00:00 2001
From: Mark Piper <mark.piper@colorado.edu>
Date: Tue, 5 Mar 2024 16:16:19 -0700
Subject: [PATCH 02/36] Set up Meson build for a single Fortran component

This is WIP, but the project files are in the right place.
---
 .../{{cookiecutter.package_name}}/meson.build | 70 +++++++++++++++++++
 .../pyproject.toml                            |  6 +-
 2 files changed, 75 insertions(+), 1 deletion(-)
 create mode 100644 babelizer/data/{{cookiecutter.package_name}}/meson.build

diff --git a/babelizer/data/{{cookiecutter.package_name}}/meson.build b/babelizer/data/{{cookiecutter.package_name}}/meson.build
new file mode 100644
index 00000000..d3ae3d4f
--- /dev/null
+++ b/babelizer/data/{{cookiecutter.package_name}}/meson.build
@@ -0,0 +1,70 @@
+project('{{ cookiecutter.package_name }}', '{{ cookiecutter.language }}', 'cython', version: '{{ cookiecutter.package_version }}')
+
+py = import('python').find_installation(pure: false)
+fc = meson.get_compiler('fortran')
+
+python_inc = py.get_path('data') / 'include'
+numpy_inc = run_command(
+    py,
+    [
+        '-c',
+        'import numpy; print(numpy.get_include())'
+    ],
+    check: true
+).stdout().strip()
+incs = include_directories(
+    [
+        '{{ cookiecutter.package_name }}/lib',
+        python_inc,
+        numpy_inc,
+    ]
+)
+
+deps = [
+    fc.find_library('bmif'),
+    fc.find_library('heatf'),
+    fc.find_library('bmiheatf'),
+]
+
+{# This is temporary until I figure out how to do multiple components. #}
+{%- set babelized_class = 'HeatModelF' -%}
+
+srcs = [
+    '{{ cookiecutter.package_name }}/lib/bmi_interoperability.f90',
+    '{{ cookiecutter.package_name }}/lib/{{ babelized_class|lower }}.pyx',
+]
+
+# Files get copied to <python directory>/site-packages/<subdir>
+install_pkg_srcs = [
+    '{{ cookiecutter.package_name }}/__init__.py',
+    '{{ cookiecutter.package_name }}/_bmi.py',
+]
+py.install_sources(
+    install_pkg_srcs,
+    subdir: '{{ cookiecutter.package_name }}',
+)
+install_lib_srcs = [
+    '{{ cookiecutter.package_name }}/lib/__init__.py',
+    '{{ cookiecutter.package_name }}/lib/{{ babelized_class|lower }}.pyx',
+]
+py.install_sources(
+    install_lib_srcs,
+    subdir: '{{ cookiecutter.package_name }}/lib',
+)
+
+install_subdir(
+    'meta/{{ babelized_class }}',
+    install_dir: py.get_install_dir() / '{{ cookiecutter.package_name }}/data',
+)
+
+py.extension_module(
+    '{{ babelized_class|lower }}',
+    srcs,
+    dependencies: deps,
+    include_directories: incs,
+    install: true,
+    subdir: '{{ cookiecutter.package_name }}/lib',
+)
+
+# This is a temporary fix for editable installs.
+run_command('cp', '-r', '{{ cookiecutter.package_name }}/data', 'build')
diff --git a/babelizer/data/{{cookiecutter.package_name}}/pyproject.toml b/babelizer/data/{{cookiecutter.package_name}}/pyproject.toml
index deade262..c0db505a 100644
--- a/babelizer/data/{{cookiecutter.package_name}}/pyproject.toml
+++ b/babelizer/data/{{cookiecutter.package_name}}/pyproject.toml
@@ -1,5 +1,6 @@
 [build-system]
-requires = ["cython", "numpy", "setuptools", "wheel"]
+build-backend = "mesonpy"
+requires = ["cython", "numpy", "meson-python", "wheel"]
 
 [project]
 name = "{{cookiecutter.package_name}}"
@@ -39,6 +40,9 @@ homepage = "https://github.com/{{ cookiecutter.info.github_username }}/{{ cookie
 
 [project.optional-dependencies]
 dev = [
+  "meson",
+  "meson-python",
+  "ninja",
   "nox",
 ]
 docs = [

From 109a9a0cd5e3707223828571e173a60b8ba0bc4f Mon Sep 17 00:00:00 2001
From: Mark Piper <mark.piper@colorado.edu>
Date: Tue, 5 Mar 2024 21:29:06 -0700
Subject: [PATCH 03/36] Remove setuptools config from pyproject.toml

---
 .../{{cookiecutter.package_name}}/pyproject.toml    | 13 -------------
 1 file changed, 13 deletions(-)

diff --git a/babelizer/data/{{cookiecutter.package_name}}/pyproject.toml b/babelizer/data/{{cookiecutter.package_name}}/pyproject.toml
index c0db505a..b56ade47 100644
--- a/babelizer/data/{{cookiecutter.package_name}}/pyproject.toml
+++ b/babelizer/data/{{cookiecutter.package_name}}/pyproject.toml
@@ -58,19 +58,6 @@ testing = [
   "bmi-tester>=0.5.4",
 ]
 
-[tool.setuptools.dynamic]
-readme = {file = ["README.rst", "CREDITS.rst", "CHANGES.rst", "LICENSE.rst"]}
-version = {attr = "{{ cookiecutter.package_name }}._version.__version__"}
-
-[tool.setuptools]
-include-package-data = true
-packages = ["{{ cookiecutter.package_name }}"]
-
-[tool.setuptools.package-data]
-{{ cookiecutter.package_name }} = [
-  "data/*",
-]
-
 [tool.pytest.ini_options]
 minversion = "5.0"
 testpaths = ["{{ cookiecutter.package_name }}", "tests"]

From 4fe09ad781656913a75d8ecaa144e0a5114f6369 Mon Sep 17 00:00:00 2001
From: Mark Piper <mark.piper@colorado.edu>
Date: Tue, 5 Mar 2024 21:47:28 -0700
Subject: [PATCH 04/36] Set version, but not readme, in dynamic metadata

It looks like meson doesn't allow readme in dynamic metadata.

Be sure to install _version.py.
---
 babelizer/data/{{cookiecutter.package_name}}/meson.build    | 1 +
 babelizer/data/{{cookiecutter.package_name}}/pyproject.toml | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/babelizer/data/{{cookiecutter.package_name}}/meson.build b/babelizer/data/{{cookiecutter.package_name}}/meson.build
index d3ae3d4f..cd75be5f 100644
--- a/babelizer/data/{{cookiecutter.package_name}}/meson.build
+++ b/babelizer/data/{{cookiecutter.package_name}}/meson.build
@@ -38,6 +38,7 @@ srcs = [
 install_pkg_srcs = [
     '{{ cookiecutter.package_name }}/__init__.py',
     '{{ cookiecutter.package_name }}/_bmi.py',
+    '{{ cookiecutter.package_name }}/_version.py',
 ]
 py.install_sources(
     install_pkg_srcs,
diff --git a/babelizer/data/{{cookiecutter.package_name}}/pyproject.toml b/babelizer/data/{{cookiecutter.package_name}}/pyproject.toml
index b56ade47..91694789 100644
--- a/babelizer/data/{{cookiecutter.package_name}}/pyproject.toml
+++ b/babelizer/data/{{cookiecutter.package_name}}/pyproject.toml
@@ -25,7 +25,7 @@ classifiers=[
 ]
 requires-python = ">=3.10"
 keywords=["bmi", "pymt"]
-dynamic = ["readme", "version"]
+dynamic = ["version"]
 dependencies = [
   "numpy",
 ]

From 731111aa9a4692e13fd0bd4074d1084364a81485 Mon Sep 17 00:00:00 2001
From: Mark Piper <mark.piper@colorado.edu>
Date: Wed, 6 Mar 2024 12:10:37 -0700
Subject: [PATCH 05/36] Read package dependencies from babel.toml file

I got help on this from https://stackoverflow.com/a/30517735.
---
 babelizer/data/{{cookiecutter.package_name}}/meson.build | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/babelizer/data/{{cookiecutter.package_name}}/meson.build b/babelizer/data/{{cookiecutter.package_name}}/meson.build
index cd75be5f..840d5fd1 100644
--- a/babelizer/data/{{cookiecutter.package_name}}/meson.build
+++ b/babelizer/data/{{cookiecutter.package_name}}/meson.build
@@ -20,10 +20,11 @@ incs = include_directories(
     ]
 )
 
+{% set dependency_list = cookiecutter.package_requirements.split(',') -%}
 deps = [
-    fc.find_library('bmif'),
-    fc.find_library('heatf'),
-    fc.find_library('bmiheatf'),
+{%- for dependency in dependency_list %}
+    fc.find_library('{{ dependency }}'),
+{%- endfor %}
 ]
 
 {# This is temporary until I figure out how to do multiple components. #}

From 1e5a1a1c575b57f8fa2102f49063f9f64871d82c Mon Sep 17 00:00:00 2001
From: Mark Piper <mark.piper@colorado.edu>
Date: Wed, 6 Mar 2024 21:23:05 -0700
Subject: [PATCH 06/36] Filter dependencies on default empty string

---
 babelizer/data/{{cookiecutter.package_name}}/meson.build | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/babelizer/data/{{cookiecutter.package_name}}/meson.build b/babelizer/data/{{cookiecutter.package_name}}/meson.build
index 840d5fd1..0f45a5e2 100644
--- a/babelizer/data/{{cookiecutter.package_name}}/meson.build
+++ b/babelizer/data/{{cookiecutter.package_name}}/meson.build
@@ -22,7 +22,7 @@ incs = include_directories(
 
 {% set dependency_list = cookiecutter.package_requirements.split(',') -%}
 deps = [
-{%- for dependency in dependency_list %}
+{%- for dependency in dependency_list if dependency != '' %}
     fc.find_library('{{ dependency }}'),
 {%- endfor %}
 ]

From af3f7e562e1bfdbd5946fd3ba9318240ddf3606b Mon Sep 17 00:00:00 2001
From: Mark Piper <mark.piper@colorado.edu>
Date: Wed, 6 Mar 2024 21:23:45 -0700
Subject: [PATCH 07/36] Update bmi-example-fortran

---
 external/bmi-example-fortran | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/external/bmi-example-fortran b/external/bmi-example-fortran
index 819757c7..6909f22b 160000
--- a/external/bmi-example-fortran
+++ b/external/bmi-example-fortran
@@ -1 +1 @@
-Subproject commit 819757c77a779d13f8c67431cc3d13f6f36b0dcc
+Subproject commit 6909f22b61b0b3fec0d3b0d0bdec7ee58e4ad8a0

From 1632c4856420ce37318ddf8bd625984171c9851a Mon Sep 17 00:00:00 2001
From: Mark Piper <mark.piper@colorado.edu>
Date: Wed, 6 Mar 2024 21:25:19 -0700
Subject: [PATCH 08/36] Get the name of the first component to babelize

This is a temporary fix until I can handle multiple components
in the `meson.build` file.
---
 babelizer/data/{{cookiecutter.package_name}}/meson.build | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/babelizer/data/{{cookiecutter.package_name}}/meson.build b/babelizer/data/{{cookiecutter.package_name}}/meson.build
index 0f45a5e2..80a093e7 100644
--- a/babelizer/data/{{cookiecutter.package_name}}/meson.build
+++ b/babelizer/data/{{cookiecutter.package_name}}/meson.build
@@ -20,6 +20,9 @@ incs = include_directories(
     ]
 )
 
+{% set babelized_class = cookiecutter.components|list|first -%}
+# babelized_class = {{ babelized_class }}
+
 {% set dependency_list = cookiecutter.package_requirements.split(',') -%}
 deps = [
 {%- for dependency in dependency_list if dependency != '' %}
@@ -27,9 +30,6 @@ deps = [
 {%- endfor %}
 ]
 
-{# This is temporary until I figure out how to do multiple components. #}
-{%- set babelized_class = 'HeatModelF' -%}
-
 srcs = [
     '{{ cookiecutter.package_name }}/lib/bmi_interoperability.f90',
     '{{ cookiecutter.package_name }}/lib/{{ babelized_class|lower }}.pyx',

From e421ff08e4b7f460db2bb572642759d27d89ce92 Mon Sep 17 00:00:00 2001
From: Mark Piper <mark.piper@colorado.edu>
Date: Wed, 6 Mar 2024 21:30:48 -0700
Subject: [PATCH 09/36] Set --no-build-isolation for editable installs

This is a *meson-python* behavior. See https://meson-python.readthedocs.io/en/stable/how-to-guides/editable-installs.html
---
 babelizer/data/{{cookiecutter.package_name}}/Makefile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/babelizer/data/{{cookiecutter.package_name}}/Makefile b/babelizer/data/{{cookiecutter.package_name}}/Makefile
index 03d43225..3b25c3d6 100644
--- a/babelizer/data/{{cookiecutter.package_name}}/Makefile
+++ b/babelizer/data/{{cookiecutter.package_name}}/Makefile
@@ -91,4 +91,4 @@ dist: clean ## builds source and wheel package
 	ls -l dist
 
 install: clean ## install the package to the active Python's site-packages
-	pip install -e .
+	pip install --no-build-isolation --editable .

From 3fb374b49cca215569afa19f6ad6741ac310d830 Mon Sep 17 00:00:00 2001
From: Mark Piper <mark.piper@colorado.edu>
Date: Fri, 8 Mar 2024 13:14:56 -0700
Subject: [PATCH 10/36] Include package requirements for example

---
 external/tests/test_fortran/babel.toml | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/external/tests/test_fortran/babel.toml b/external/tests/test_fortran/babel.toml
index 60c816b9..9f1f0398 100644
--- a/external/tests/test_fortran/babel.toml
+++ b/external/tests/test_fortran/babel.toml
@@ -15,7 +15,11 @@ extra_compile_args = []
 
 [package]
 name = "pymt_heatf"
-requirements = [""]
+requirements = [
+    "bmif",
+    "heatf",
+    "bmiheatf",
+]
 
 [info]
 github_username = "pymt-lab"

From f76483780b901f42deed30af2d8d0feec91174a3 Mon Sep 17 00:00:00 2001
From: mcflugen <mcflugen@gmail.com>
Date: Fri, 8 Mar 2024 22:17:20 -0700
Subject: [PATCH 11/36] use conda; install bmiheatf in _inst; create
 bmiheatf.pc

---
 noxfile.py | 49 +++++++++++++++++++++++++++++++++++++------------
 1 file changed, 37 insertions(+), 12 deletions(-)

diff --git a/noxfile.py b/noxfile.py
index 662698e6..e19ea57d 100644
--- a/noxfile.py
+++ b/noxfile.py
@@ -23,11 +23,7 @@ def test(session: nox.Session) -> None:
     session.run("pytest", *args)
 
 
-@nox.session(
-    name="test-langs",
-    python=PYTHON_VERSIONS,
-    venv_backend="mamba",
-)
+@nox.session(name="test-langs", python=PYTHON_VERSIONS, venv_backend="conda")
 @nox.parametrize("lang", ["c", "cxx", "fortran", "python"])
 def test_langs(session: nox.session, lang) -> None:
     datadir = ROOT / "external" / "tests" / f"test_{lang}"
@@ -40,11 +36,30 @@ def test_langs(session: nox.session, lang) -> None:
     session.debug(library)
     session.debug(config_file)
 
-    build_examples(session, lang)
+    instdir = build_examples(session, lang)
+
+    session.install("bmi-tester>=0.5.4", "ninja")
+    session.conda_install("pip", "cmake", "make", "pkg-config")
 
-    session.conda_install("pip", "bmi-tester>=0.5.4", "cmake")
     session.install(".[testing]")
 
+    bmiheatf_pc = f"""\
+prefix={instdir!s}
+exec_prefix=${{prefix}}
+libdir=${{exec_prefix}}/lib
+includedir=${{prefix}}/include
+
+Name: bmiheatf
+Description: BMI Heat Fortran
+Version: 1.0.0
+Libs: -L${{libdir}} -lheatf -lbmiheatf
+Cflags: -I${{includedir}}
+"""
+
+    os.makedirs(instdir / "lib" / "pkgconfig", exist_ok=True)
+    with open(instdir / "lib" / "pkgconfig" / "bmiheatf.pc", "w") as fp:
+        print(bmiheatf_pc, file=fp)
+
     with session.chdir(tmpdir):
         session.run(
             "babelize",
@@ -56,7 +71,14 @@ def test_langs(session: nox.session, lang) -> None:
             session.debug(f"{k}: {v!r}")
 
         with session.chdir(package):
-            session.run("python", "-m", "pip", "install", "-e", ".")
+            session.run(
+                "python",
+                "-m",
+                "pip",
+                "install",
+                ".[dev]",
+                env={"PKG_CONFIG_PATH": os.path.join(instdir, "lib", "pkgconfig")},
+            )
 
     with session.chdir(testdir):
         shutil.copy(datadir / config_file, ".")
@@ -85,17 +107,19 @@ def _get_package_metadata(datadir):
     return package, library, config_files[0]
 
 
-@nox.session(name="build-examples", venv_backend="mamba")
+@nox.session(name="build-examples", venv_backend="conda")
 @nox.parametrize("lang", ["c", "cxx", "fortran", "python"])
 def build_examples(session: nox.Session, lang):
     """Build the language examples."""
     srcdir = ROOT / "external" / f"bmi-example-{lang}"
-    builddir = pathlib.Path(session.create_tmp()) / "_build"
+    tmpdir = ROOT / pathlib.Path(session.create_tmp())
+    builddir = tmpdir / "_build"
+    instdir = tmpdir / "_inst"
 
     if lang == "python":
         session.conda_install("bmipy", "make")
     else:
-        session.conda_install(f"bmi-{lang}", "cmake", "make", "pkg-config")
+        session.conda_install(f"bmi-{lang}", "make", "pkg-config")
 
     for k, v in sorted(session.env.items()):
         session.debug(f"{k}: {v!r}")
@@ -111,9 +135,10 @@ def build_examples(session: nox.Session, lang):
                 str(srcdir),
                 "-B",
                 ".",
-                f"-DCMAKE_INSTALL_PREFIX={session.env['CONDA_PREFIX']}",
+                f"-DCMAKE_INSTALL_PREFIX={instdir}",
             )
             session.run("make", "install")
+    return instdir
 
 
 @nox.session(name="test-cli")

From 87c465033408aac6b80f66a677fcce52f7241adf Mon Sep 17 00:00:00 2001
From: mcflugen <mcflugen@gmail.com>
Date: Fri, 8 Mar 2024 22:18:11 -0700
Subject: [PATCH 12/36] add bmiheatf as a dependency

---
 babelizer/data/{{cookiecutter.package_name}}/meson.build | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/babelizer/data/{{cookiecutter.package_name}}/meson.build b/babelizer/data/{{cookiecutter.package_name}}/meson.build
index 80a093e7..591de519 100644
--- a/babelizer/data/{{cookiecutter.package_name}}/meson.build
+++ b/babelizer/data/{{cookiecutter.package_name}}/meson.build
@@ -3,6 +3,8 @@ project('{{ cookiecutter.package_name }}', '{{ cookiecutter.language }}', 'cytho
 py = import('python').find_installation(pure: false)
 fc = meson.get_compiler('fortran')
 
+bmiheatf = dependency('bmiheatf', method : 'pkg-config')
+
 python_inc = py.get_path('data') / 'include'
 numpy_inc = run_command(
     py,
@@ -25,6 +27,7 @@ incs = include_directories(
 
 {% set dependency_list = cookiecutter.package_requirements.split(',') -%}
 deps = [
+    bmiheatf,
 {%- for dependency in dependency_list if dependency != '' %}
     fc.find_library('{{ dependency }}'),
 {%- endfor %}

From 5ae3a8f00b58f2a6498b1d6d75fa734dcf34f275 Mon Sep 17 00:00:00 2001
From: mcflugen <mcflugen@gmail.com>
Date: Fri, 8 Mar 2024 22:20:25 -0700
Subject: [PATCH 13/36] remove requirements from babel.toml

---
 external/tests/test_fortran/babel.toml | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/external/tests/test_fortran/babel.toml b/external/tests/test_fortran/babel.toml
index 9f1f0398..0aaf3760 100644
--- a/external/tests/test_fortran/babel.toml
+++ b/external/tests/test_fortran/babel.toml
@@ -15,11 +15,7 @@ extra_compile_args = []
 
 [package]
 name = "pymt_heatf"
-requirements = [
-    "bmif",
-    "heatf",
-    "bmiheatf",
-]
+requirements = []
 
 [info]
 github_username = "pymt-lab"

From a88ff05294a05e6ac8ff37f5d0138731735ef792 Mon Sep 17 00:00:00 2001
From: mcflugen <mcflugen@gmail.com>
Date: Sat, 9 Mar 2024 18:43:19 -0700
Subject: [PATCH 14/36] install build tools on a per language basis

---
 .github/workflows/test-langs.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/test-langs.yml b/.github/workflows/test-langs.yml
index 2b32dd0e..be4af0bc 100644
--- a/.github/workflows/test-langs.yml
+++ b/.github/workflows/test-langs.yml
@@ -41,7 +41,8 @@ jobs:
         run: python -m pip install nox tomli
 
       - name: Install compilers
-        run: mamba install c-compiler cxx-compiler fortran-compiler
+        if: matrix.language != 'python'
+        run: mamba install ${{ matrix.language }}-compiler bmi-${{ matrix.language }} cmake make pkg-config
 
       - name: Run the language tests
         run: nox -s "test-langs-${{ matrix.python-version }}(lang='${{ matrix.language }}')" --python ${{ matrix.python-version }} --verbose

From 6feaaa97aa67b966456aaec63353de0a5fa7248d Mon Sep 17 00:00:00 2001
From: mcflugen <mcflugen@gmail.com>
Date: Sun, 10 Mar 2024 23:00:31 -0600
Subject: [PATCH 15/36] add bmi-tester as a testing dependency

---
 pyproject.toml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pyproject.toml b/pyproject.toml
index f5b36f1b..04357a5a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -78,6 +78,7 @@ docs = [
     "sphinxcontrib.towncrier",
 ]
 testing = [
+    "bmi-tester>=0.5.9",
     "coverage[toml]",
     "coveralls",
     "pytest",

From 5ce7b93ed9e7bceb3c816463986cf162a81de956 Mon Sep 17 00:00:00 2001
From: mcflugen <mcflugen@gmail.com>
Date: Sun, 10 Mar 2024 23:01:18 -0600
Subject: [PATCH 16/36] install language-specific build tools

---
 .github/workflows/test-langs.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test-langs.yml b/.github/workflows/test-langs.yml
index be4af0bc..47d45759 100644
--- a/.github/workflows/test-langs.yml
+++ b/.github/workflows/test-langs.yml
@@ -42,7 +42,7 @@ jobs:
 
       - name: Install compilers
         if: matrix.language != 'python'
-        run: mamba install ${{ matrix.language }}-compiler bmi-${{ matrix.language }} cmake make pkg-config
+        run: mamba install ${{ matrix.language }}-compiler cmake make pkg-config
 
       - name: Run the language tests
         run: nox -s "test-langs-${{ matrix.python-version }}(lang='${{ matrix.language }}')" --python ${{ matrix.python-version }} --verbose

From 170623c439903f8b7d9826a32e5cda9c936eea8d Mon Sep 17 00:00:00 2001
From: mcflugen <mcflugen@gmail.com>
Date: Sun, 10 Mar 2024 23:01:47 -0600
Subject: [PATCH 17/36] create a pkg-config file for heatf; back to using conda

---
 noxfile.py | 31 +++++++++++++++++++++++--------
 1 file changed, 23 insertions(+), 8 deletions(-)

diff --git a/noxfile.py b/noxfile.py
index e19ea57d..38ad6e35 100644
--- a/noxfile.py
+++ b/noxfile.py
@@ -38,9 +38,6 @@ def test_langs(session: nox.session, lang) -> None:
 
     instdir = build_examples(session, lang)
 
-    session.install("bmi-tester>=0.5.4", "ninja")
-    session.conda_install("pip", "cmake", "make", "pkg-config")
-
     session.install(".[testing]")
 
     bmiheatf_pc = f"""\
@@ -52,7 +49,8 @@ def test_langs(session: nox.session, lang) -> None:
 Name: bmiheatf
 Description: BMI Heat Fortran
 Version: 1.0.0
-Libs: -L${{libdir}} -lheatf -lbmiheatf
+Requires: heatf
+Libs: -L${{libdir}} -lbmiheatf
 Cflags: -I${{includedir}}
 """
 
@@ -60,6 +58,23 @@ def test_langs(session: nox.session, lang) -> None:
     with open(instdir / "lib" / "pkgconfig" / "bmiheatf.pc", "w") as fp:
         print(bmiheatf_pc, file=fp)
 
+    heatf_pc = f"""\
+_prefix={os.environ.get('CMAKE_PREFIX_PATH', instdir)}
+exec_prefix=${{_prefix}}
+libdir=${{exec_prefix}}/lib
+includedir=${{_prefix}}/include
+
+Name: heatf
+Description: Heat Fortran
+Version: 1.0.0
+Libs: -L${{libdir}} -lheatf
+Cflags: -I${{includedir}}
+"""
+
+    os.makedirs(instdir / "lib" / "pkgconfig", exist_ok=True)
+    with open(instdir / "lib" / "pkgconfig" / "heatf.pc", "w") as fp:
+        print(heatf_pc, file=fp)
+
     with session.chdir(tmpdir):
         session.run(
             "babelize",
@@ -107,19 +122,19 @@ def _get_package_metadata(datadir):
     return package, library, config_files[0]
 
 
-@nox.session(name="build-examples", venv_backend="conda")
+@nox.session(name="build-examples", python=PYTHON_VERSIONS, venv_backend="conda")
 @nox.parametrize("lang", ["c", "cxx", "fortran", "python"])
 def build_examples(session: nox.Session, lang):
     """Build the language examples."""
     srcdir = ROOT / "external" / f"bmi-example-{lang}"
     tmpdir = ROOT / pathlib.Path(session.create_tmp())
     builddir = tmpdir / "_build"
-    instdir = tmpdir / "_inst"
+    instdir = pathlib.Path(session.virtualenv.location)
 
     if lang == "python":
-        session.conda_install("bmipy", "make")
+        session.install("bmipy")
     else:
-        session.conda_install(f"bmi-{lang}", "make", "pkg-config")
+        session.conda_install(f"bmi-{lang}")
 
     for k, v in sorted(session.env.items()):
         session.debug(f"{k}: {v!r}")

From 9bd813949258cbed72e113ed379a6ef2890835a9 Mon Sep 17 00:00:00 2001
From: mcflugen <mcflugen@gmail.com>
Date: Sun, 10 Mar 2024 23:02:24 -0600
Subject: [PATCH 18/36] add c and cpp to builds

---
 .../{{cookiecutter.package_name}}/meson.build | 42 +++++++++++++++----
 1 file changed, 35 insertions(+), 7 deletions(-)

diff --git a/babelizer/data/{{cookiecutter.package_name}}/meson.build b/babelizer/data/{{cookiecutter.package_name}}/meson.build
index 591de519..5126f54d 100644
--- a/babelizer/data/{{cookiecutter.package_name}}/meson.build
+++ b/babelizer/data/{{cookiecutter.package_name}}/meson.build
@@ -1,11 +1,32 @@
-project('{{ cookiecutter.package_name }}', '{{ cookiecutter.language }}', 'cython', version: '{{ cookiecutter.package_version }}')
+project(
+    '{{ cookiecutter.package_name }}',
+{%- if cookiecutter.language == 'c' %}
+    'c',
+{%- elif cookiecutter.language == 'c++' %}
+    'cpp',
+{%- elif cookiecutter.language == 'fortran' %}
+    'fortran',
+{%- endif %}
+    'cython',
+    version: '{{ cookiecutter.package_version }}',
+)
+
+{%- if cookiecutter.language == 'c' %}
+lang = 'c'
+bmilib = 'bmiheatc'
+{%- elif cookiecutter.language == 'c++' %}
+lang = 'cpp'
+bmilib = 'bmiheatcxx'
+{%- elif cookiecutter.language == 'fortran' %}
+lang = 'fortran'
+bmilib = 'bmiheatf'
+{%- endif %}
 
 py = import('python').find_installation(pure: false)
-fc = meson.get_compiler('fortran')
 
-bmiheatf = dependency('bmiheatf', method : 'pkg-config')
+compiler = meson.get_compiler(lang)
 
-python_inc = py.get_path('data') / 'include'
+# python_inc = py.get_path('data') / 'include'
 numpy_inc = run_command(
     py,
     [
@@ -17,7 +38,7 @@ numpy_inc = run_command(
 incs = include_directories(
     [
         '{{ cookiecutter.package_name }}/lib',
-        python_inc,
+        # python_inc,
         numpy_inc,
     ]
 )
@@ -27,14 +48,18 @@ incs = include_directories(
 
 {% set dependency_list = cookiecutter.package_requirements.split(',') -%}
 deps = [
-    bmiheatf,
+{%- if cookiecutter.language in ['c', 'c++', 'fortran'] %}
+    dependency(bmilib, method : 'pkg-config'),
+{% endif %}
 {%- for dependency in dependency_list if dependency != '' %}
-    fc.find_library('{{ dependency }}'),
+    compiler.find_library('{{ dependency }}'),
 {%- endfor %}
 ]
 
 srcs = [
+{%- if cookiecutter.language == 'fortran' %}
     '{{ cookiecutter.package_name }}/lib/bmi_interoperability.f90',
+{%- endif %}
     '{{ cookiecutter.package_name }}/lib/{{ babelized_class|lower }}.pyx',
 ]
 
@@ -69,6 +94,9 @@ py.extension_module(
     include_directories: incs,
     install: true,
     subdir: '{{ cookiecutter.package_name }}/lib',
+{%- if cookiecutter.language == 'c++' %}
+    override_options : ['cython_language=cpp'],
+{%- endif %}
 )
 
 # This is a temporary fix for editable installs.

From 91a37041c3666c07ce349a385fc144c94fc740e3 Mon Sep 17 00:00:00 2001
From: mcflugen <mcflugen@gmail.com>
Date: Mon, 11 Mar 2024 09:22:39 -0600
Subject: [PATCH 19/36] update setup-miniconda

---
 .github/workflows/test-langs.yml | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/test-langs.yml b/.github/workflows/test-langs.yml
index 47d45759..2acae11e 100644
--- a/.github/workflows/test-langs.yml
+++ b/.github/workflows/test-langs.yml
@@ -29,11 +29,10 @@ jobs:
         with:
           submodules: true
 
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: conda-incubator/setup-miniconda@v3
         with:
           auto-update-conda: true
           python-version: ${{ matrix.python-version }}
-          mamba-version: "*"
           channels: conda-forge
           channel-priority: true
 
@@ -42,7 +41,7 @@ jobs:
 
       - name: Install compilers
         if: matrix.language != 'python'
-        run: mamba install ${{ matrix.language }}-compiler cmake make pkg-config
+        run: conda install ${{ matrix.language }}-compiler cmake make
 
       - name: Run the language tests
         run: nox -s "test-langs-${{ matrix.python-version }}(lang='${{ matrix.language }}')" --python ${{ matrix.python-version }} --verbose

From c795a9de3fa6560e4d288a0e3ea5e730ae43177e Mon Sep 17 00:00:00 2001
From: mcflugen <mcflugen@gmail.com>
Date: Mon, 11 Mar 2024 09:23:49 -0600
Subject: [PATCH 20/36] install pkg-config in test environment

---
 noxfile.py | 11 ++---------
 1 file changed, 2 insertions(+), 9 deletions(-)

diff --git a/noxfile.py b/noxfile.py
index 38ad6e35..1dba261e 100644
--- a/noxfile.py
+++ b/noxfile.py
@@ -86,14 +86,7 @@ def test_langs(session: nox.session, lang) -> None:
             session.debug(f"{k}: {v!r}")
 
         with session.chdir(package):
-            session.run(
-                "python",
-                "-m",
-                "pip",
-                "install",
-                ".[dev]",
-                env={"PKG_CONFIG_PATH": os.path.join(instdir, "lib", "pkgconfig")},
-            )
+            session.run("python", "-m", "pip", "install", ".[dev]")
 
     with session.chdir(testdir):
         shutil.copy(datadir / config_file, ".")
@@ -134,7 +127,7 @@ def build_examples(session: nox.Session, lang):
     if lang == "python":
         session.install("bmipy")
     else:
-        session.conda_install(f"bmi-{lang}")
+        session.conda_install(f"bmi-{lang}", "pkg-config")
 
     for k, v in sorted(session.env.items()):
         session.debug(f"{k}: {v!r}")

From a16ef56302e4816b9b324e2e189f92f2272da436 Mon Sep 17 00:00:00 2001
From: mcflugen <mcflugen@gmail.com>
Date: Mon, 11 Mar 2024 10:10:44 -0600
Subject: [PATCH 21/36] fix heatf pkg-config file and bmic, bmicxx pkg-config
 names

---
 babelizer/data/{{cookiecutter.package_name}}/meson.build | 4 ++--
 noxfile.py                                               | 7 ++++---
 2 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/babelizer/data/{{cookiecutter.package_name}}/meson.build b/babelizer/data/{{cookiecutter.package_name}}/meson.build
index 5126f54d..13368271 100644
--- a/babelizer/data/{{cookiecutter.package_name}}/meson.build
+++ b/babelizer/data/{{cookiecutter.package_name}}/meson.build
@@ -13,10 +13,10 @@ project(
 
 {%- if cookiecutter.language == 'c' %}
 lang = 'c'
-bmilib = 'bmiheatc'
+bmilib = 'BmiHeatC'
 {%- elif cookiecutter.language == 'c++' %}
 lang = 'cpp'
-bmilib = 'bmiheatcxx'
+bmilib = 'BmiHeatCXX'
 {%- elif cookiecutter.language == 'fortran' %}
 lang = 'fortran'
 bmilib = 'bmiheatf'
diff --git a/noxfile.py b/noxfile.py
index 1dba261e..636d52f4 100644
--- a/noxfile.py
+++ b/noxfile.py
@@ -59,10 +59,10 @@ def test_langs(session: nox.session, lang) -> None:
         print(bmiheatf_pc, file=fp)
 
     heatf_pc = f"""\
-_prefix={os.environ.get('CMAKE_PREFIX_PATH', instdir)}
-exec_prefix=${{_prefix}}
+prefix={instdir!s}
+exec_prefix=${{prefix}}
 libdir=${{exec_prefix}}/lib
-includedir=${{_prefix}}/include
+includedir=${{prefix}}/include
 
 Name: heatf
 Description: Heat Fortran
@@ -86,6 +86,7 @@ def test_langs(session: nox.session, lang) -> None:
             session.debug(f"{k}: {v!r}")
 
         with session.chdir(package):
+            session.run("pkg-config", "--list-all")
             session.run("python", "-m", "pip", "install", ".[dev]")
 
     with session.chdir(testdir):

From 74852c2e7e486dd7e40b4ee207bbf379d920168c Mon Sep 17 00:00:00 2001
From: mcflugen <mcflugen@gmail.com>
Date: Mon, 11 Mar 2024 10:28:42 -0600
Subject: [PATCH 22/36] update c, cxx submodules

---
 external/bmi-example-c   | 2 +-
 external/bmi-example-cxx | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/external/bmi-example-c b/external/bmi-example-c
index 5d39005f..f47d0a65 160000
--- a/external/bmi-example-c
+++ b/external/bmi-example-c
@@ -1 +1 @@
-Subproject commit 5d39005f1aad3c2bb38c2661d68c8e453269cefe
+Subproject commit f47d0a65edf848ccd9d57d375e9fdd90354c1f4f
diff --git a/external/bmi-example-cxx b/external/bmi-example-cxx
index 1c2d0902..07c3dd51 160000
--- a/external/bmi-example-cxx
+++ b/external/bmi-example-cxx
@@ -1 +1 @@
-Subproject commit 1c2d0902963894a96d80d852777769a8d14f0779
+Subproject commit 07c3dd518ddcd7db50e22be0db6ff3fc067053fb

From b3210a9b9f2df86ef1e9578ae69115572f532796 Mon Sep 17 00:00:00 2001
From: mcflugen <mcflugen@gmail.com>
Date: Mon, 11 Mar 2024 10:33:15 -0600
Subject: [PATCH 23/36] back to lowercase for pkg-config names

---
 babelizer/data/{{cookiecutter.package_name}}/meson.build | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/babelizer/data/{{cookiecutter.package_name}}/meson.build b/babelizer/data/{{cookiecutter.package_name}}/meson.build
index 13368271..5126f54d 100644
--- a/babelizer/data/{{cookiecutter.package_name}}/meson.build
+++ b/babelizer/data/{{cookiecutter.package_name}}/meson.build
@@ -13,10 +13,10 @@ project(
 
 {%- if cookiecutter.language == 'c' %}
 lang = 'c'
-bmilib = 'BmiHeatC'
+bmilib = 'bmiheatc'
 {%- elif cookiecutter.language == 'c++' %}
 lang = 'cpp'
-bmilib = 'BmiHeatCXX'
+bmilib = 'bmiheatcxx'
 {%- elif cookiecutter.language == 'fortran' %}
 lang = 'fortran'
 bmilib = 'bmiheatf'

From b7f33b64585cd6df7d75498c49f06b7165398a3a Mon Sep 17 00:00:00 2001
From: mcflugen <mcflugen@gmail.com>
Date: Mon, 11 Mar 2024 10:58:16 -0600
Subject: [PATCH 24/36] use setuptools for pure-python projects

---
 .../{{cookiecutter.package_name}}/pyproject.toml    | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/babelizer/data/{{cookiecutter.package_name}}/pyproject.toml b/babelizer/data/{{cookiecutter.package_name}}/pyproject.toml
index 91694789..7df13701 100644
--- a/babelizer/data/{{cookiecutter.package_name}}/pyproject.toml
+++ b/babelizer/data/{{cookiecutter.package_name}}/pyproject.toml
@@ -1,6 +1,13 @@
 [build-system]
+{%- if cookiecutter.language == 'python' %}
+build-backend = "setuptools.build_meta"
+requires = [
+    "setuptools >=61",
+]
+{% else %}
 build-backend = "mesonpy"
 requires = ["cython", "numpy", "meson-python", "wheel"]
+{% endif %}
 
 [project]
 name = "{{cookiecutter.package_name}}"
@@ -58,6 +65,12 @@ testing = [
   "bmi-tester>=0.5.4",
 ]
 
+{%- if cookiecutter.language == 'python' %}
+[tool.setuptools.packages.find]
+where = ["."]
+include = ["{{cookiecutter.package_name}}*"]
+{% endif %}
+
 [tool.pytest.ini_options]
 minversion = "5.0"
 testpaths = ["{{ cookiecutter.package_name }}", "tests"]

From ec29a4b7ea636e7f587c07b095cf40ccb2b22f00 Mon Sep 17 00:00:00 2001
From: mcflugen <mcflugen@gmail.com>
Date: Mon, 11 Mar 2024 12:35:14 -0600
Subject: [PATCH 25/36] build multiple extension; remove bmiheat dependency

---
 .../{{cookiecutter.package_name}}/meson.build | 54 +++++++++----------
 1 file changed, 25 insertions(+), 29 deletions(-)

diff --git a/babelizer/data/{{cookiecutter.package_name}}/meson.build b/babelizer/data/{{cookiecutter.package_name}}/meson.build
index 5126f54d..6edc29d5 100644
--- a/babelizer/data/{{cookiecutter.package_name}}/meson.build
+++ b/babelizer/data/{{cookiecutter.package_name}}/meson.build
@@ -11,21 +11,16 @@ project(
     version: '{{ cookiecutter.package_version }}',
 )
 
+py = import('python').find_installation(pure: false)
+
 {%- if cookiecutter.language == 'c' %}
-lang = 'c'
-bmilib = 'bmiheatc'
+compiler = meson.get_compiler('c')
 {%- elif cookiecutter.language == 'c++' %}
-lang = 'cpp'
-bmilib = 'bmiheatcxx'
+compiler = meson.get_compiler('cpp')
 {%- elif cookiecutter.language == 'fortran' %}
-lang = 'fortran'
-bmilib = 'bmiheatf'
+compiler = meson.get_compiler('fortran')
 {%- endif %}
 
-py = import('python').find_installation(pure: false)
-
-compiler = meson.get_compiler(lang)
-
 # python_inc = py.get_path('data') / 'include'
 numpy_inc = run_command(
     py,
@@ -43,26 +38,13 @@ incs = include_directories(
     ]
 )
 
-{% set babelized_class = cookiecutter.components|list|first -%}
-# babelized_class = {{ babelized_class }}
-
 {% set dependency_list = cookiecutter.package_requirements.split(',') -%}
 deps = [
-{%- if cookiecutter.language in ['c', 'c++', 'fortran'] %}
-    dependency(bmilib, method : 'pkg-config'),
-{% endif %}
 {%- for dependency in dependency_list if dependency != '' %}
     compiler.find_library('{{ dependency }}'),
 {%- endfor %}
 ]
 
-srcs = [
-{%- if cookiecutter.language == 'fortran' %}
-    '{{ cookiecutter.package_name }}/lib/bmi_interoperability.f90',
-{%- endif %}
-    '{{ cookiecutter.package_name }}/lib/{{ babelized_class|lower }}.pyx',
-]
-
 # Files get copied to <python directory>/site-packages/<subdir>
 install_pkg_srcs = [
     '{{ cookiecutter.package_name }}/__init__.py',
@@ -73,24 +55,31 @@ py.install_sources(
     install_pkg_srcs,
     subdir: '{{ cookiecutter.package_name }}',
 )
+
 install_lib_srcs = [
     '{{ cookiecutter.package_name }}/lib/__init__.py',
+{%- for babelized_class in cookiecutter.components|list|sort %}
     '{{ cookiecutter.package_name }}/lib/{{ babelized_class|lower }}.pyx',
+{%- endfor %}
 ]
 py.install_sources(
     install_lib_srcs,
     subdir: '{{ cookiecutter.package_name }}/lib',
 )
 
-install_subdir(
-    'meta/{{ babelized_class }}',
-    install_dir: py.get_install_dir() / '{{ cookiecutter.package_name }}/data',
-)
 
+{%- for babelized_class, component in cookiecutter.components|dictsort %}
 py.extension_module(
     '{{ babelized_class|lower }}',
-    srcs,
-    dependencies: deps,
+    [
+{%- if cookiecutter.language == 'fortran' %}
+        '{{ cookiecutter.package_name }}/lib/bmi_interoperability.f90',
+{%- endif %}
+        '{{ cookiecutter.package_name }}/lib/{{ babelized_class|lower }}.pyx',
+    ],
+    dependencies: [
+        dependency('{{ component.library }}', method : 'pkg-config'),
+    ],
     include_directories: incs,
     install: true,
     subdir: '{{ cookiecutter.package_name }}/lib',
@@ -99,5 +88,12 @@ py.extension_module(
 {%- endif %}
 )
 
+install_subdir(
+    'meta/{{ babelized_class }}',
+    install_dir: py.get_install_dir() / '{{ cookiecutter.package_name }}/data',
+)
+
+{%- endfor %}
+
 # This is a temporary fix for editable installs.
 run_command('cp', '-r', '{{ cookiecutter.package_name }}/data', 'build')

From 3c3a1aa067e44dafb3551a4d6f1a9f6ed32bff12 Mon Sep 17 00:00:00 2001
From: mcflugen <mcflugen@gmail.com>
Date: Mon, 11 Mar 2024 18:33:04 -0600
Subject: [PATCH 26/36] remove setup.py, setup_utils.py

---
 .../{{cookiecutter.package_name}}/setup.py    |  14 --
 .../setup_utils.py                            | 123 ------------------
 2 files changed, 137 deletions(-)
 delete mode 100644 babelizer/data/{{cookiecutter.package_name}}/setup.py
 delete mode 100644 babelizer/data/{{cookiecutter.package_name}}/setup_utils.py

diff --git a/babelizer/data/{{cookiecutter.package_name}}/setup.py b/babelizer/data/{{cookiecutter.package_name}}/setup.py
deleted file mode 100644
index 76102434..00000000
--- a/babelizer/data/{{cookiecutter.package_name}}/setup.py
+++ /dev/null
@@ -1,14 +0,0 @@
-from setuptools import setup
-
-{%- if cookiecutter.language in ['c', 'c++', 'fortran'] %}
-from setup_utils import build_ext, get_extension_modules
-{% endif %}
-
-setup(
-{%- if cookiecutter.language in ['c', 'c++', 'fortran'] %}
-    ext_modules=get_extension_modules(),
-{%- endif %}
-{%- if cookiecutter.language == 'fortran' %}
-    cmdclass={"build_ext": build_ext},
-{%- endif %}
-)
diff --git a/babelizer/data/{{cookiecutter.package_name}}/setup_utils.py b/babelizer/data/{{cookiecutter.package_name}}/setup_utils.py
deleted file mode 100644
index b2bbca13..00000000
--- a/babelizer/data/{{cookiecutter.package_name}}/setup_utils.py
+++ /dev/null
@@ -1,123 +0,0 @@
-import contextlib
-import os
-import subprocess
-import sys
-
-import numpy as np
-from numpy.distutils.fcompiler import new_fcompiler
-from setuptools import Extension
-from setuptools.command.build_ext import build_ext as _build_ext
-
-
-def get_compiler_flags():
-    flags = {
-        "include_dirs": [
-            np.get_include(),
-            os.path.join(sys.prefix, "include"),
-            {%- for dir in cookiecutter.build.include_dirs %}
-                "{{ dir|trim }}",
-            {% endfor %}
-        ],
-        "library_dirs": [
-            {%- for libdir in cookiecutter.build.library_dirs %}
-                "{{ libdir|trim }}",
-            {% endfor %}
-        ],
-        "define_macros": [
-            {%- if cookiecutter.build.define_macros -%}
-            {%- for item in cookiecutter.build.define_macros %}
-            {%- set key_value = item.split('=') %}
-                ("{{ key_value[0]|trim }}", "{{ key_value[1]|trim }}"),{% endfor %}
-            {%- endif %}
-        ],
-        "undef_macros": [
-            {%- if cookiecutter.build.undef_macros -%}
-            {%- for macro in cookiecutter.build.undef_macros %}
-                "{{ macro|trim }}",{% endfor %}
-            {%- endif %}
-        ],
-        "extra_compile_args": [
-            {%- if cookiecutter.build.extra_compile_args -%}
-            {%- for arg in cookiecutter.build.extra_compile_args %}
-                "{{ arg|trim }}",{% endfor %}
-            {%- endif %}
-        ],
-    {%- if cookiecutter.language == 'fortran' %}
-        "language": "c",
-    {% else %}
-        "language": "{{ cookiecutter.language }}",
-    {% endif -%}
-    }
-
-    # Locate directories under Windows %LIBRARY_PREFIX%.
-    if sys.platform.startswith("win"):
-        flags["include_dirs"].append(os.path.join(sys.prefix, "Library", "include"))
-        flags["library_dirs"].append(os.path.join(sys.prefix, "Library", "lib"))
-
-    return flags
-
-
-def get_extension_modules():
-    flags = get_compiler_flags()
-
-    libraries = [
-    {%- if cookiecutter.build.libraries -%}
-    {%- for lib in cookiecutter.build.libraries %}
-        "{{ lib|trim }}",{% endfor %}
-    {%- endif %}
-    ]
-
-    ext_modules = [
-    {%- for babelized_class, component in cookiecutter.components|dictsort %}
-        Extension(
-            "{{cookiecutter.package_name}}.lib.{{ babelized_class|lower }}",
-            ["{{cookiecutter.package_name}}/lib/{{ babelized_class|lower }}.pyx"],
-            libraries=libraries + ["{{ component.library }}"],
-            {% if cookiecutter.language == 'fortran' -%}
-            extra_objects=["{{cookiecutter.package_name}}/lib/bmi_interoperability.o"],
-            {% endif -%}
-            **flags,
-        ),
-    {%- endfor %}
-    ]
-
-    return ext_modules
-
-
-@contextlib.contextmanager
-def as_cwd(path):
-    prev_cwd = os.getcwd()
-    os.chdir(path)
-    yield
-    os.chdir(prev_cwd)
-
-
-def build_interoperability():
-    compiler = new_fcompiler()
-    compiler.customize()
-
-    flags = get_compiler_flags()
-
-    cmd = []
-    cmd.append(compiler.compiler_f90[0])
-    cmd.append(compiler.compile_switch)
-    if sys.platform.startswith("win") is False:
-        cmd.append("-fPIC")
-    for include_dir in flags["include_dirs"]:
-        if os.path.isabs(include_dir) is False:
-            include_dir = os.path.join(sys.prefix, "include", include_dir)
-        cmd.append(f"-I{include_dir}")
-    cmd.append("bmi_interoperability.f90")
-
-    try:
-        subprocess.check_call(cmd)
-    except subprocess.CalledProcessError:
-        raise
-
-
-class build_ext(_build_ext):
-
-    def run(self):
-        with as_cwd("{{cookiecutter.package_name}}/lib"):
-            build_interoperability()
-        _build_ext.run(self)

From 227bbf9f68d012fa432bde1549ad20d2b916eb35 Mon Sep 17 00:00:00 2001
From: mcflugen <mcflugen@gmail.com>
Date: Mon, 11 Mar 2024 18:39:03 -0600
Subject: [PATCH 27/36] bump versions of setup-miniconda, checkout

---
 .../.github/workflows/test.yml                        | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/babelizer/data/{{cookiecutter.package_name}}/.github/workflows/test.yml b/babelizer/data/{{cookiecutter.package_name}}/.github/workflows/test.yml
index f69190dd..35416232 100644
--- a/babelizer/data/{{cookiecutter.package_name}}/.github/workflows/test.yml
+++ b/babelizer/data/{{cookiecutter.package_name}}/.github/workflows/test.yml
@@ -23,9 +23,9 @@ jobs:
         python-version: [{{ cookiecutter.ci.python_version | join(", ") }}]
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: conda-incubator/setup-miniconda@v3
         with:
           auto-update-conda: true
           python-version: ${{ '{{' }} matrix.python-version {{ '}}' }}
@@ -39,16 +39,15 @@ jobs:
 
       - name: Install requirements
         run: |
-          conda install mamba
-          mamba install --file=requirements-build.txt --file=requirements-library.txt
-          mamba list
+          conda install --file=requirements-build.txt --file=requirements-library.txt
+          conda list
 
       - name: Build and install package
         run: |
           pip install -e .
 
       - name: Install testing dependencies
-        run: mamba install --file=requirements-testing.txt
+        run: conda install --file=requirements-testing.txt
 
       - name: Test
         run: |

From 4b66408fcddc7b0a6ead84368312fb5c8e9c48bb Mon Sep 17 00:00:00 2001
From: mcflugen <mcflugen@gmail.com>
Date: Tue, 12 Mar 2024 09:49:35 -0600
Subject: [PATCH 28/36] remove meson.build for python projects

---
 babelizer/data/hooks/post_gen_project.py | 4 ++++
 noxfile.py                               | 1 -
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/babelizer/data/hooks/post_gen_project.py b/babelizer/data/hooks/post_gen_project.py
index e6218f5a..27f2fbe6 100644
--- a/babelizer/data/hooks/post_gen_project.py
+++ b/babelizer/data/hooks/post_gen_project.py
@@ -114,6 +114,10 @@ def write_api_yaml(folderpath, **kwds):
     if "Not open source" == "{{ cookiecutter.open_source_license }}":
         remove_file("LICENSE")
 
+    {%- if cookiecutter.language == 'python' %}
+    remove_file("meson.build")
+    {%- endif %}
+
     datadir = Path("meta")
     package_datadir = Path("{{ cookiecutter.package_name }}") / "data"
     if not package_datadir.exists():
diff --git a/noxfile.py b/noxfile.py
index 636d52f4..279b842a 100644
--- a/noxfile.py
+++ b/noxfile.py
@@ -86,7 +86,6 @@ def test_langs(session: nox.session, lang) -> None:
             session.debug(f"{k}: {v!r}")
 
         with session.chdir(package):
-            session.run("pkg-config", "--list-all")
             session.run("python", "-m", "pip", "install", ".[dev]")
 
     with session.chdir(testdir):

From 016c13efac61a1dd790e8a869952d8db72fa407f Mon Sep 17 00:00:00 2001
From: mcflugen <mcflugen@gmail.com>
Date: Tue, 12 Mar 2024 11:54:27 -0600
Subject: [PATCH 29/36] remove setup.py setup_utils.py from prettification

---
 babelizer/render.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/babelizer/render.py b/babelizer/render.py
index e7d4d1df..5edb0d46 100644
--- a/babelizer/render.py
+++ b/babelizer/render.py
@@ -168,8 +168,6 @@ def prettify_python(path_to_repo):
     module_name = meta["package"]["name"]
 
     files_to_fix = [
-        path_to_repo / "setup.py",
-        path_to_repo / "setup_utils.py",
         path_to_repo / module_name / "_bmi.py",
         path_to_repo / module_name / "__init__.py",
         path_to_repo / "docs" / "conf.py",

From a32086a63a05708175dd8df7f3adb3f2a48cf889 Mon Sep 17 00:00:00 2001
From: Mark Piper <mark.piper@colorado.edu>
Date: Wed, 13 Mar 2024 14:10:30 -0600
Subject: [PATCH 30/36] Update bmi-example-fortran to tip of
 mdpiper/use-pkgconfig branch

---
 external/bmi-example-fortran | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/external/bmi-example-fortran b/external/bmi-example-fortran
index 6909f22b..613740d1 160000
--- a/external/bmi-example-fortran
+++ b/external/bmi-example-fortran
@@ -1 +1 @@
-Subproject commit 6909f22b61b0b3fec0d3b0d0bdec7ee58e4ad8a0
+Subproject commit 613740d1fc16a62a380930948f0e5f284a8dca25

From 06d2544fbe6d7368847b26ae1639dcc93e5fb981 Mon Sep 17 00:00:00 2001
From: Mark Piper <mark.piper@colorado.edu>
Date: Wed, 13 Mar 2024 14:12:18 -0600
Subject: [PATCH 31/36] Remove hardcoded pkg-config files

---
 noxfile.py | 35 -----------------------------------
 1 file changed, 35 deletions(-)

diff --git a/noxfile.py b/noxfile.py
index ec044379..2d006c0b 100644
--- a/noxfile.py
+++ b/noxfile.py
@@ -40,41 +40,6 @@ def test_langs(session: nox.session, lang) -> None:
 
     session.install(".[testing]")
 
-    bmiheatf_pc = f"""\
-prefix={instdir!s}
-exec_prefix=${{prefix}}
-libdir=${{exec_prefix}}/lib
-includedir=${{prefix}}/include
-
-Name: bmiheatf
-Description: BMI Heat Fortran
-Version: 1.0.0
-Requires: heatf
-Libs: -L${{libdir}} -lbmiheatf
-Cflags: -I${{includedir}}
-"""
-
-    os.makedirs(instdir / "lib" / "pkgconfig", exist_ok=True)
-    with open(instdir / "lib" / "pkgconfig" / "bmiheatf.pc", "w") as fp:
-        print(bmiheatf_pc, file=fp)
-
-    heatf_pc = f"""\
-prefix={instdir!s}
-exec_prefix=${{prefix}}
-libdir=${{exec_prefix}}/lib
-includedir=${{prefix}}/include
-
-Name: heatf
-Description: Heat Fortran
-Version: 1.0.0
-Libs: -L${{libdir}} -lheatf
-Cflags: -I${{includedir}}
-"""
-
-    os.makedirs(instdir / "lib" / "pkgconfig", exist_ok=True)
-    with open(instdir / "lib" / "pkgconfig" / "heatf.pc", "w") as fp:
-        print(heatf_pc, file=fp)
-
     with session.chdir(tmpdir):
         session.run(
             "babelize",

From 9839e43c37e297d7790cf61b88ead71ebc1303f7 Mon Sep 17 00:00:00 2001
From: Mark Piper <mark.piper@colorado.edu>
Date: Wed, 13 Mar 2024 14:26:47 -0600
Subject: [PATCH 32/36] Clean lint

---
 noxfile.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/noxfile.py b/noxfile.py
index 2d006c0b..e5fc20b9 100644
--- a/noxfile.py
+++ b/noxfile.py
@@ -36,7 +36,7 @@ def test_langs(session: nox.session, lang) -> None:
     session.debug(library)
     session.debug(config_file)
 
-    instdir = build_examples(session, lang)
+    build_examples(session, lang)
 
     session.install(".[testing]")
 

From ef40631d3bdba9045a67d046ad72b8f2ef0d9b60 Mon Sep 17 00:00:00 2001
From: Mark Piper <mark.piper@colorado.edu>
Date: Wed, 13 Mar 2024 14:52:49 -0600
Subject: [PATCH 33/36] Add a news fragment

---
 news/90.feature | 3 +++
 1 file changed, 3 insertions(+)
 create mode 100644 news/90.feature

diff --git a/news/90.feature b/news/90.feature
new file mode 100644
index 00000000..3798cf28
--- /dev/null
+++ b/news/90.feature
@@ -0,0 +1,3 @@
+
+Use *meson* to build babelized projects with Fortran, C, and C++ sources.
+Projects with Python sources are still built with *setuptools*.

From e7175350a5fc7f32cecbd7cff1e2abb75a1e75a1 Mon Sep 17 00:00:00 2001
From: Mark Piper <mark.piper@colorado.edu>
Date: Wed, 13 Mar 2024 19:22:06 -0600
Subject: [PATCH 34/36] Update bmi-example-fortran to v2.1.3

---
 external/bmi-example-fortran | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/external/bmi-example-fortran b/external/bmi-example-fortran
index 613740d1..98b4e339 160000
--- a/external/bmi-example-fortran
+++ b/external/bmi-example-fortran
@@ -1 +1 @@
-Subproject commit 613740d1fc16a62a380930948f0e5f284a8dca25
+Subproject commit 98b4e3394db6f2b032d8945c125e77435c6d5d03

From 1848402db85f6d96cd733956f04236332f2290bf Mon Sep 17 00:00:00 2001
From: Mark Piper <mark.piper@colorado.edu>
Date: Thu, 14 Mar 2024 10:49:07 -0600
Subject: [PATCH 35/36] Remove Makefile; trim .gitignore

---
 .../{{cookiecutter.package_name}}/.gitignore  | 105 ++----------------
 .../{{cookiecutter.package_name}}/Makefile    |  94 ----------------
 2 files changed, 8 insertions(+), 191 deletions(-)
 delete mode 100644 babelizer/data/{{cookiecutter.package_name}}/Makefile

diff --git a/babelizer/data/{{cookiecutter.package_name}}/.gitignore b/babelizer/data/{{cookiecutter.package_name}}/.gitignore
index 3b80cb7c..35c0374f 100644
--- a/babelizer/data/{{cookiecutter.package_name}}/.gitignore
+++ b/babelizer/data/{{cookiecutter.package_name}}/.gitignore
@@ -1,114 +1,25 @@
-# Byte-compiled / optimized / DLL files
+.DS_Store
 __pycache__/
 *.py[cod]
-*$py.class
-
-# C extensions
-*.so
-
-# Distribution / packaging
-.Python
-env/
+.ipynb_checkpoints
 build/
-develop-eggs/
 dist/
-downloads/
-eggs/
-.eggs/
-# lib/
-lib64/
-parts/
 sdist/
-var/
-wheels/
 *.egg-info/
-.installed.cfg
-*.egg
-
-# PyInstaller
-#  Usually these files are written by a python script from a template
-#  before PyInstaller builds the exe, so as to inject date/other infos into it.
-*.manifest
-*.spec
-
-# Installer logs
-pip-log.txt
-pip-delete-this-directory.txt
-
-# Unit test / coverage reports
 htmlcov/
-.tox/
 .coverage
-.coverage.*
-.cache
-nosetests.xml
 coverage.xml
-*.cover
-.hypothesis/
-
-# Translations
-*.mo
-*.pot
-
-# Django stuff:
-*.log
-local_settings.py
-
-# Flask stuff:
-instance/
-.webassets-cache
-
-# Scrapy stuff:
-.scrapy
-
-# Sphinx documentation
 docs/_build/
-
-# PyBuilder
-target/
-
-# Jupyter Notebook
-.ipynb_checkpoints
-
-# pyenv
-.python-version
-
-# celery beat schedule file
-celerybeat-schedule
-
-# SageMath parsed files
-*.sage.py
-
-# dotenv
-.env
-
-# virtualenv
+docs/_generated/
 .venv
-venv/
-ENV/
-
-# Spyder project settings
-.spyderproject
-.spyproject
-
-# Rope project settings
-.ropeproject
-
-# mkdocs documentation
-/site
-
-# mypy
-.mypy_cache/
-
-# nox virtual envs
 .nox/
+*.so
+*.o
+*.mod
+*.smod
 
-{% if cookiecutter.language == 'fortran' -%}
+{%- if cookiecutter.language != 'python' -%}
 {%- for babelized_class in cookiecutter.components %}
-# Fortran files generated by the babelizer
-{{cookiecutter.package_name}}/lib/bmi_interoperability.mod
-{{cookiecutter.package_name}}/lib/bmi_interoperability.smod
-{{cookiecutter.package_name}}/lib/bmi_interoperability.o
 {{cookiecutter.package_name}}/lib/{{ babelized_class|lower }}.c
 {%- endfor %}
 {%- endif %}
diff --git a/babelizer/data/{{cookiecutter.package_name}}/Makefile b/babelizer/data/{{cookiecutter.package_name}}/Makefile
deleted file mode 100644
index 3b25c3d6..00000000
--- a/babelizer/data/{{cookiecutter.package_name}}/Makefile
+++ /dev/null
@@ -1,94 +0,0 @@
-.PHONY: clean clean-test clean-pyc clean-build docs help
-.DEFAULT_GOAL := help
-
-define BROWSER_PYSCRIPT
-import os, webbrowser, sys
-
-try:
-	from urllib import pathname2url
-except:
-	from urllib.request import pathname2url
-
-webbrowser.open("file://" + pathname2url(os.path.abspath(sys.argv[1])))
-endef
-export BROWSER_PYSCRIPT
-
-define PRINT_HELP_PYSCRIPT
-import re, sys
-
-for line in sys.stdin:
-	match = re.match(r'^([a-zA-Z_-]+):.*?## (.*)$$', line)
-	if match:
-		target, help = match.groups()
-		print("%-20s %s" % (target, help))
-endef
-export PRINT_HELP_PYSCRIPT
-
-BROWSER := python -c "$$BROWSER_PYSCRIPT"
-
-help:
-	@python -c "$$PRINT_HELP_PYSCRIPT" < $(MAKEFILE_LIST)
-
-clean: clean-build clean-pyc clean-test ## remove all build, test, coverage and Python artifacts
-
-clean-build: ## remove build artifacts
-	rm -fr build/
-	rm -fr dist/
-	rm -fr .eggs/
-	find . -name '*.egg-info' -exec rm -fr {} +
-	find . -name '*.egg' -exec rm -f {} +
-
-clean-pyc: ## remove Python file artifacts
-	find . -name '*.pyc' -exec rm -f {} +
-	find . -name '*.pyo' -exec rm -f {} +
-	find . -name '*~' -exec rm -f {} +
-	find . -name '__pycache__' -exec rm -fr {} +
-
-clean-test: ## remove test and coverage artifacts
-	rm -fr .tox/
-	rm -f .coverage
-	rm -fr htmlcov/
-	rm -fr .pytest_cache
-
-lint: ## check style with flake8
-	flake8 {{ cookiecutter.package_name }}
-
-pretty:
-	find {{ cookiecutter.package_name }} -name '*.py' | xargs isort
-	black setup.py {{ cookiecutter.package_name }}
-
-test: ## run tests quickly with the default Python
-{%- for babelized_class, component in cookiecutter.components|dictsort %}
-	bmi-test {{ cookiecutter.package_name }}.bmi:{{ babelized_class }} -vvv
-{%- endfor %}
-
-test-all: ## run tests on every Python version with tox
-	tox
-
-coverage: ## check code coverage quickly with the default Python
-	coverage run --source {{ cookiecutter.package_name }} -m pytest
-	coverage report -m
-	coverage html
-	$(BROWSER) htmlcov/index.html
-
-docs: ## generate Sphinx HTML documentation, including API docs
-	rm -f docs/{{ cookiecutter.package_name }}.rst
-	rm -f docs/modules.rst
-	sphinx-apidoc -o docs/ {{ cookiecutter.package_name }}
-	$(MAKE) -C docs clean
-	$(MAKE) -C docs html
-	$(BROWSER) docs/_build/html/index.html
-
-servedocs: docs ## compile the docs watching for changes
-	watchmedo shell-command -p '*.rst' -c '$(MAKE) -C docs html' -R -D .
-
-release: dist ## package and upload a release
-	twine upload dist/*
-
-dist: clean ## builds source and wheel package
-	python setup.py sdist
-	python setup.py bdist_wheel
-	ls -l dist
-
-install: clean ## install the package to the active Python's site-packages
-	pip install --no-build-isolation --editable .

From 4d7dbb243f139e6742b978cb2d7e3b5eec08ed5d Mon Sep 17 00:00:00 2001
From: Mark Piper <mark.piper@colorado.edu>
Date: Thu, 14 Mar 2024 13:39:57 -0600
Subject: [PATCH 36/36] Include brief instructions for installing from source

---
 .../{{cookiecutter.package_name}}/README.rst  | 44 ++++++++++++++-----
 1 file changed, 34 insertions(+), 10 deletions(-)

diff --git a/babelizer/data/{{cookiecutter.package_name}}/README.rst b/babelizer/data/{{cookiecutter.package_name}}/README.rst
index 39a573a8..05ccf4f9 100644
--- a/babelizer/data/{{cookiecutter.package_name}}/README.rst
+++ b/babelizer/data/{{cookiecutter.package_name}}/README.rst
@@ -65,20 +65,44 @@ Quickstart
 
 .. start-quickstart
 
-To get started you will need to install the *{{ cookiecutter.package_name }}* package, which is currently distributed
-on *conda-forge*. The easiest way to install *{{ cookiecutter.package_name }}* into your current environment using either *mamba* or *conda*.
+To get started you will need to install the *{{ cookiecutter.package_name }}* package.
+Here are two ways to do so.
 
-.. tab:: mamba
+Install from conda-forge
+------------------------
 
-  .. code:: bash
+If the *{{ cookiecutter.package_name }}* package is distributed on *conda-forge*, install it into your current environment with *conda*.
 
-    mamba install {{ cookiecutter.package_name }}
+.. code:: bash
 
-.. tab:: conda
+  conda install -c conda-forge {{ cookiecutter.package_name }}
 
-  .. code:: bash
+Install from source
+-------------------
+
+You can build and install the *{{ cookiecutter.package_name }}* package from source using *conda* and *pip*.
+
+First, from the source directory, install package dependencies into your current environment with *conda*.
+
+.. code:: bash
+
+  conda install -c conda-forge --file requirements.txt --file requirements-build.txt --file requirements-library.txt
+
+Then install the package itself with *pip*.
+{%- if cookiecutter.language == 'python' %}
 
-    conda install {{ cookiecutter.package_name }}
+.. code:: bash
+
+  pip install -e .
+
+{%- else %}
+
+.. code:: bash
+
+  pip install --no-build-isolation --editable .
+
+Note that for an editable install, the ``--no-build-isolation`` flag must be set.
+{%- endif %}
 
 .. end-quickstart
 
@@ -87,8 +111,8 @@ Usage
 
 .. start-usage
 
-There are two ways to use the data components provided by this package: directly through it's Basic
-Model Interface, or as a PyMT plugin.
+There are two ways to use the components provided by this package: directly through its Basic
+Model Interface (BMI), or as a PyMT plugin.
 
 A BMI is provided by each component in this package:
 {%- for babelized_class, component in cookiecutter.components|dictsort -%}