From 2e00423149e8456b3f91a4331a828953e36ccc97 Mon Sep 17 00:00:00 2001
From: Ben Mares <services-git-throwaway2@tensorial.com>
Date: Sun, 13 Jul 2025 14:17:38 +0200
Subject: [PATCH 01/24] Add tomlkit as test dependency

This will allow us to manipulate and ensure consistency of TOML files
---
 pyproject.toml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pyproject.toml b/pyproject.toml
index f39c11fa7d..9ddce92bc8 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -77,6 +77,7 @@ tests = [
     "pytest-benchmark",
     "pytest-mock",
     "pytest-sphinx",
+    "tomlkit",
 ]
 rtd = ["sphinx>=5.1.0,<6", "pygments", "pydot"]
 jax = ["jax", "jaxlib"]

From c74f47c0fcda62fffcb497ae18bee23e5e524318 Mon Sep 17 00:00:00 2001
From: Ben Mares <services-git-throwaway2@tensorial.com>
Date: Sun, 13 Jul 2025 14:18:37 +0200
Subject: [PATCH 02/24] Add generate-pixi-toml script

---
 scripts/generate-pixi-toml.py | 210 ++++++++++++++++++++++++++++++++++
 1 file changed, 210 insertions(+)
 create mode 100755 scripts/generate-pixi-toml.py

diff --git a/scripts/generate-pixi-toml.py b/scripts/generate-pixi-toml.py
new file mode 100755
index 0000000000..5b6d8e9d26
--- /dev/null
+++ b/scripts/generate-pixi-toml.py
@@ -0,0 +1,210 @@
+#!/usr/bin/env python3
+
+import shlex
+import shutil
+import subprocess
+import sys
+from pathlib import Path
+
+import tomlkit
+import tomlkit.items
+
+
+RAW_COMMAND = """
+pixi exec conda-lock render-lock-spec \
+    --channel=conda-forge \
+    --kind=pixi.toml \
+    --file=pyproject.toml \
+    --stdout \
+    --pixi-project-name=pytensor \
+    --editable=pytensor=.
+"""
+
+PARSED_COMMAND = shlex.split(RAW_COMMAND)
+
+
+def main():
+    # Check if pixi is installed
+    if not shutil.which("pixi"):
+        print("pixi is not installed. See <https://pixi.sh/latest/#installation>")  # noqa: T201
+        sys.exit(1)
+
+    current_dir = Path(__file__).parent
+    assert current_dir.name == "scripts"
+    project_root = current_dir.parent
+
+    pyproject_file = project_root / "pyproject.toml"
+
+    pyproject_data = tomlkit.loads(pyproject_file.read_text())
+
+    pyproject_data = preprocess_pyproject_data(pyproject_data)
+
+    # Make temporary working directory
+    working_path = project_root / "pixi-working"
+    working_path.mkdir(parents=True, exist_ok=True)
+    gitignore_file = working_path / ".gitignore"
+    gitignore_file.write_text("*")
+
+    working_pyproject_file = working_path / "pyproject.toml"
+    with working_pyproject_file.open("w") as fh:
+        tomlkit.dump(pyproject_data, fh)
+
+    print(f"Running the command:\n{shlex.join(PARSED_COMMAND)}\n")  # noqa: T201
+    result = subprocess.run(
+        PARSED_COMMAND, check=True, capture_output=True, cwd=working_path
+    )
+
+    warnings = result.stderr.decode("utf-8")
+    if warnings:
+        print(f"Warnings: \n{warnings}\n")  # noqa: T201
+
+    pixi_toml_raw_data = tomlkit.loads(result.stdout.decode("utf-8"))
+
+    pixi_toml_raw_file = working_path / "pixi.toml"
+    pixi_toml_raw_file.write_text(tomlkit.dumps(pixi_toml_raw_data))
+
+    pixi_toml_data = postprocess_pixi_toml_data(pixi_toml_raw_data)
+
+    # Write the pixi.toml file to the project root
+    (project_root / "pixi.toml").write_text(tomlkit.dumps(pixi_toml_data))
+
+    # Clean up
+    working_pyproject_file.unlink()
+    pixi_toml_raw_file.unlink()
+    gitignore_file.unlink()
+    working_path.rmdir()
+
+
+def preprocess_pyproject_data(
+    pyproject_data: tomlkit.TOMLDocument,
+) -> tomlkit.TOMLDocument:
+    pyproject_data = remove_extraneous_features(pyproject_data)
+    return pyproject_data
+
+
+def remove_extraneous_features(
+    pyproject_data: tomlkit.TOMLDocument,
+) -> tomlkit.TOMLDocument:
+    """
+    Remove the `complete` and `development` optional dependencies from pyproject.toml.
+
+    >>> input_data = tomlkit.loads('''
+    ... [project.optional-dependencies]
+    ... complete = ["pytensor[jax]", "pytensor[numba]"]
+    ... development = ["pytensor[complete]", "pytensor[tests]", "pytensor[rtd]"]
+    ... rtd = ["sphinx>=5.1.0,<6", "pygments", "pydot"]
+    ... ''')
+    >>> output_data = remove_extraneous_features(input_data)
+    >>> print(tomlkit.dumps(output_data))
+    [project.optional-dependencies]
+    rtd = ["sphinx>=5.1.0,<6", "pygments", "pydot"]
+    """
+    project_item = pyproject_data.get("project")
+    assert isinstance(project_item, tomlkit.items.Table)
+    optional_dependencies_item = project_item.get("optional-dependencies")
+    assert isinstance(optional_dependencies_item, tomlkit.items.Table)
+
+    del optional_dependencies_item["complete"]
+    del optional_dependencies_item["development"]
+
+    return pyproject_data
+
+
+def postprocess_pixi_toml_data(
+    pixi_toml_data: tomlkit.TOMLDocument,
+) -> tomlkit.TOMLDocument:
+    pixi_toml_data = restrict_jax_platforms(pixi_toml_data)
+    pixi_toml_data = add_header_comment(pixi_toml_data)
+    return pixi_toml_data
+
+
+def restrict_jax_platforms(
+    pixi_toml_data: tomlkit.TOMLDocument,
+) -> tomlkit.TOMLDocument:
+    """
+    Remove the `win-64` platform from the jax feature.
+
+    Jax isn't available for Windows from conda-forge, so it needs to be
+    explicitly excluded, otherwise pixi will not be able to solve the
+    environment.
+
+    Specifically, above the `[feature.jax.dependencies]` table, create a
+    `[feature.jax]` table with a `platforms` key containing the values from
+    `[project.platforms]` but with `win-64` removed.
+
+    >>> input_data = tomlkit.loads('''
+    ... [project]
+    ... platforms = ["linux-64", "osx-64", "osx-arm64", "win-64"]
+    ... [feature.jax.dependencies]
+    ... jax = "*"
+    ... ''')
+    >>> output_data = restrict_jax_platforms(input_data)
+    >>> print(tomlkit.dumps(output_data))
+    [project]
+    platforms = ["linux-64", "osx-64", "osx-arm64", "win-64"]
+    [feature.jax]
+    platforms = ["linux-64", "osx-64", "osx-arm64"]
+    [feature.jax.dependencies]
+    jax = "*"
+    """
+    # Get the platforms from the project section - unwrap to get the actual list
+    project_item = pixi_toml_data["project"]
+    assert isinstance(project_item, tomlkit.items.Table)
+
+    platforms_item = project_item["platforms"]
+    assert isinstance(platforms_item, tomlkit.items.Array)
+    project_platforms = platforms_item.unwrap()
+
+    # Filter out win-64
+    jax_platforms = [platform for platform in project_platforms if platform != "win-64"]
+
+    # Access the feature section and modify the jax subsection
+    feature_item = pixi_toml_data.get("feature")
+    assert isinstance(feature_item, tomlkit.items.Table)
+    jax_item = feature_item.get("jax")
+    assert isinstance(jax_item, tomlkit.items.Table)
+
+    # Create a new jax feature table with platforms first, then dependencies
+    new_jax_feature = tomlkit.table()
+    new_jax_feature.add("platforms", jax_platforms)
+
+    # Add all existing keys from the jax feature (like dependencies)
+    for key, value in jax_item.items():
+        new_jax_feature.add(key, value)
+
+    # Replace the jax feature with the new one
+    feature_item["jax"] = new_jax_feature
+
+    return pixi_toml_data
+
+
+def add_header_comment(pixi_toml_data: tomlkit.TOMLDocument) -> tomlkit.TOMLDocument:
+    """
+    Add a header comment to the pixi.toml file.
+    """
+    header_lines = [
+        "THIS FILE WAS GENERATED BY `scripts/generate-pixi-toml.py`",
+        "You can edit this file locally, but if you want to push changes",
+        "upstream to pymc-devs/pytensor, then you should instead modify",
+        "the script.",
+    ]
+
+    # Create a new document with the header comment
+    new_doc = tomlkit.document()
+
+    # Add header comments
+    for line in header_lines:
+        new_doc.add(tomlkit.comment(line))
+
+    # Add a blank line after the header
+    new_doc.add(tomlkit.nl())
+
+    # Add all the existing content from the original document
+    for key, value in pixi_toml_data.items():
+        new_doc.add(key, value)
+
+    return new_doc
+
+
+if __name__ == "__main__":
+    main()

From 038c7772ab883c205d36cf58d432f993e6663895 Mon Sep 17 00:00:00 2001
From: Ben Mares <services-git-throwaway2@tensorial.com>
Date: Sun, 13 Jul 2025 14:18:57 +0200
Subject: [PATCH 03/24] Add temporary workaround for pytest-sphinx not on
 conda-forge

---
 pyproject.toml | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/pyproject.toml b/pyproject.toml
index 9ddce92bc8..cbd803cc9c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -195,3 +195,10 @@ test-skip = ["cp37*", "*musllinux*", "*win32*", "*i686*"]
 # Testing seems to be running into issues locating libs where expected
 # test-requires = ["pytest", "numba", "jax", "jaxlib"]
 # test-command = "pytest {package}/tests"
+
+# This is a temporary hack to achieve automatic pixi.toml generation.
+# Unfortunately pytest-sphinx is not yet on conda-forge. I'm trying to add
+# it in <https://github.com/conda-forge/staged-recipes/pull/30520>. In the
+# meantime, we need to make it a PyPI dependency.
+[tool.conda-lock.dependencies]
+pytest-sphinx = {source = "pypi", category="docs"}

From 67433b2253cd628926a2012c7ba5f7c8dd330309 Mon Sep 17 00:00:00 2001
From: Ben Mares <services-git-throwaway2@tensorial.com>
Date: Sun, 13 Jul 2025 14:19:46 +0200
Subject: [PATCH 04/24] Generate pixi.toml

---
 pixi.toml | 63 +++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 63 insertions(+)
 create mode 100644 pixi.toml

diff --git a/pixi.toml b/pixi.toml
new file mode 100644
index 0000000000..ef3b465c26
--- /dev/null
+++ b/pixi.toml
@@ -0,0 +1,63 @@
+# THIS FILE WAS GENERATED BY `scripts/generate-pixi-toml.py`
+# You can edit this file locally, but if you want to push changes
+# upstream to pymc-devs/pytensor, then you should instead modify
+# the script.
+
+[project]
+name = "pytensor"
+platforms = ["linux-64", "osx-64", "osx-arm64", "win-64"]
+channels = ["conda-forge"]
+
+[dependencies]
+cons = "*"
+etuples = "*"
+filelock = ">=3.15"
+logical-unification = "*"
+minikanren = "*"
+numpy = ">=1.17.0"
+scipy = "<2,>=1"
+setuptools = ">=59.0.0"
+
+[pypi-dependencies]
+pytensor = {path = ".", editable = true}
+
+[feature.jax]
+platforms = ["linux-64", "osx-64", "osx-arm64"]
+
+[feature.jax.dependencies]
+jax = "*"
+jaxlib = "*"
+
+
+[feature.numba.dependencies]
+llvmlite = "*"
+numba = ">=0.57"
+
+[feature.rtd.dependencies]
+pydot = "*"
+pygments = "*"
+sphinx = "<6,>=5.1.0"
+
+[feature.tests.dependencies]
+coverage = ">=5.1"
+pre-commit = "*"
+pytest = "*"
+pytest-benchmark = "*"
+pytest-cov = ">=2.6.1"
+pytest-mock = "*"
+tomlkit = "*"
+
+[feature.tests.pypi-dependencies]
+pytest-sphinx = "*"
+
+
+[environments]
+# Redefine the default environment to include all categories.
+default = ["jax", "numba", "rtd", "tests"]
+# Define a minimal environment with only the default feature.
+minimal = []
+# Create an environment for each feature.
+jax = ["jax"]
+numba = ["numba"]
+rtd = ["rtd"]
+tests = ["tests"]

From a7002ad8ad6408a5a8e7f9b1da814b4c043804c6 Mon Sep 17 00:00:00 2001
From: Ben Mares <services-git-throwaway2@tensorial.com>
Date: Sun, 13 Jul 2025 15:19:04 +0200
Subject: [PATCH 05/24] Include environment.yml to add compilers

---
 environment.yml               |  4 ++++
 scripts/generate-pixi-toml.py | 38 +++++++++++++++++++++++++++++++++++
 2 files changed, 42 insertions(+)

diff --git a/environment.yml b/environment.yml
index 9bdddfb6f6..f7c517d6b6 100644
--- a/environment.yml
+++ b/environment.yml
@@ -57,3 +57,7 @@ dependencies:
   - cython
   - graphviz
   - pydot
+
+# This line can be ignored by users, it's only needed by the script
+# `scripts/generate-pixi-toml.py`. It is used to determine the feature name.
+category: conda-dev
diff --git a/scripts/generate-pixi-toml.py b/scripts/generate-pixi-toml.py
index 5b6d8e9d26..c8b3cbbfd4 100755
--- a/scripts/generate-pixi-toml.py
+++ b/scripts/generate-pixi-toml.py
@@ -14,6 +14,7 @@
 pixi exec conda-lock render-lock-spec \
     --channel=conda-forge \
     --kind=pixi.toml \
+    --file=environment.yml \
     --file=pyproject.toml \
     --stdout \
     --pixi-project-name=pytensor \
@@ -49,6 +50,15 @@ def main():
     with working_pyproject_file.open("w") as fh:
         tomlkit.dump(pyproject_data, fh)
 
+    raw_environment_file = project_root / "environment.yml"
+    raw_environment_data = raw_environment_file.read_text()
+
+    environment_data = preprocess_environment_data(raw_environment_data)
+
+    working_environment_file = working_path / "environment.yml"
+    with working_environment_file.open("w") as fh:
+        fh.write(environment_data)
+
     print(f"Running the command:\n{shlex.join(PARSED_COMMAND)}\n")  # noqa: T201
     result = subprocess.run(
         PARSED_COMMAND, check=True, capture_output=True, cwd=working_path
@@ -70,6 +80,7 @@ def main():
 
     # Clean up
     working_pyproject_file.unlink()
+    working_environment_file.unlink()
     pixi_toml_raw_file.unlink()
     gitignore_file.unlink()
     working_path.rmdir()
@@ -206,5 +217,32 @@ def add_header_comment(pixi_toml_data: tomlkit.TOMLDocument) -> tomlkit.TOMLDocu
     return new_doc
 
 
+def preprocess_environment_data(
+    raw_environment_data: str,
+) -> str:
+    environment_data = remove_blas_dependencies(raw_environment_data)
+    return environment_data
+
+
+def remove_blas_dependencies(
+    raw_environment_data: str,
+) -> str:
+    """
+    Remove the BLAS dependencies from the environment.yml file.
+    """
+    lines = raw_environment_data.splitlines()
+
+    def filter(line: str) -> bool:
+        TO_REMOVE = [
+            "- mkl",
+            "- mkl-service",
+            "- libblas=*=*mkl",
+        ]
+        return line.strip() not in TO_REMOVE
+
+    lines = [line for line in lines if filter(line)]
+    return "\n".join(lines)
+
+
 if __name__ == "__main__":
     main()

From 2d50ee82356087ac48a4c8006df174e7328cf9d7 Mon Sep 17 00:00:00 2001
From: Ben Mares <services-git-throwaway2@tensorial.com>
Date: Sun, 13 Jul 2025 15:20:54 +0200
Subject: [PATCH 06/24] Readd BLAS dependencies

---
 scripts/environment-blas.yml  | 22 ++++++++++++++++++++++
 scripts/generate-pixi-toml.py |  9 +++++++++
 2 files changed, 31 insertions(+)
 create mode 100644 scripts/environment-blas.yml

diff --git a/scripts/environment-blas.yml b/scripts/environment-blas.yml
new file mode 100644
index 0000000000..7b27b949f4
--- /dev/null
+++ b/scripts/environment-blas.yml
@@ -0,0 +1,22 @@
+# This file defines BLAS for pixi.toml generation via
+# `scripts/generate-pixi-toml.py`.
+
+name: pytensor-blas
+channels:
+  - conda-forge
+dependencies:
+  # Use MKL for Linux, Intel macOS, and Windows.
+  - mkl  # [linux]
+  - mkl-service  # [linux]
+  - libblas=*=*mkl  # [linux]
+  - mkl  # [osx64]
+  - mkl-service  # [osx64]
+  - libblas=*=*mkl  # [osx64]
+  - mkl  # [win]
+  - mkl-service  # [win]
+  - libblas=*=*mkl  # [win]
+
+  # Use Accelerate for Apple Silicon.
+  - libblas=*=*accelerate  # [arm64]
+
+category: blas
diff --git a/scripts/generate-pixi-toml.py b/scripts/generate-pixi-toml.py
index c8b3cbbfd4..2e4ddc866d 100755
--- a/scripts/generate-pixi-toml.py
+++ b/scripts/generate-pixi-toml.py
@@ -15,6 +15,7 @@
     --channel=conda-forge \
     --kind=pixi.toml \
     --file=environment.yml \
+    --file=scripts/environment-blas.yml \
     --file=pyproject.toml \
     --stdout \
     --pixi-project-name=pytensor \
@@ -59,6 +60,12 @@ def main():
     with working_environment_file.open("w") as fh:
         fh.write(environment_data)
 
+    environment_blas_file = project_root / "scripts" / "environment-blas.yml"
+    working_environment_blas_file = working_path / "scripts" / "environment-blas.yml"
+    # This is for our exclusive use, so it doesn't need to be preprocessed.
+    working_environment_blas_file.parent.mkdir(parents=True, exist_ok=True)
+    shutil.copy(environment_blas_file, working_environment_blas_file)
+
     print(f"Running the command:\n{shlex.join(PARSED_COMMAND)}\n")  # noqa: T201
     result = subprocess.run(
         PARSED_COMMAND, check=True, capture_output=True, cwd=working_path
@@ -81,6 +88,8 @@ def main():
     # Clean up
     working_pyproject_file.unlink()
     working_environment_file.unlink()
+    working_environment_blas_file.unlink()
+    working_environment_blas_file.parent.rmdir()
     pixi_toml_raw_file.unlink()
     gitignore_file.unlink()
     working_path.rmdir()

From 3ae3fe059a7f28132bb7f4bd64eda298d5689295 Mon Sep 17 00:00:00 2001
From: Ben Mares <services-git-throwaway2@tensorial.com>
Date: Sun, 13 Jul 2025 15:23:17 +0200
Subject: [PATCH 07/24] Update pixi.toml

---
 pixi.toml | 45 ++++++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 44 insertions(+), 1 deletion(-)

diff --git a/pixi.toml b/pixi.toml
index ef3b465c26..d1d987c471 100644
--- a/pixi.toml
+++ b/pixi.toml
@@ -15,12 +15,53 @@ filelock = ">=3.15"
 logical-unification = "*"
 minikanren = "*"
 numpy = ">=1.17.0"
+pip = "*"
 scipy = "<2,>=1"
 setuptools = ">=59.0.0"
 
 [pypi-dependencies]
 pytensor = {path = ".", editable = true}
 
+[feature.blas.target.linux-64.dependencies]
+libblas = {version = "*", build = "*mkl"}
+mkl = "*"
+mkl-service = "*"
+
+[feature.blas.target.osx-64.dependencies]
+libblas = {version = "*", build = "*mkl"}
+mkl = "*"
+mkl-service = "*"
+
+[feature.blas.target.osx-arm64.dependencies]
+libblas = {version = "*", build = "*accelerate"}
+
+[feature.blas.target.win-64.dependencies]
+libblas = {version = "*", build = "*mkl"}
+mkl = "*"
+mkl-service = "*"
+
+[feature.conda-dev.dependencies]
+compilers = "*"
+coveralls = "*"
+cython = "*"
+diff-cover = "*"
+graphviz = "*"
+ipython = "*"
+matplotlib = "*"
+mypy = "*"
+myst-nb = "*"
+packaging = "*"
+pandas = "*"
+pydeprecate = "*"
+pymc-sphinx-theme = "*"
+pytest-xdist = "*"
+python = ">=3.10"
+ruff = "*"
+sphinx-design = "*"
+sphinx_rtd_theme = "*"
+types-setuptools = "*"
+watermark = "*"
+
 [feature.jax]
 platforms = ["linux-64", "osx-64", "osx-arm64"]
 
@@ -53,10 +94,12 @@ pytest-sphinx = "*"
 
 [environments]
 # Redefine the default environment to include all categories.
-default = ["jax", "numba", "rtd", "tests"]
+default = ["blas", "conda-dev", "jax", "numba", "rtd", "tests"]
 # Define a minimal environment with only the default feature.
 minimal = []
 # Create an environment for each feature.
+blas = ["blas"]
+conda-dev = ["conda-dev"]
 jax = ["jax"]
 numba = ["numba"]
 rtd = ["rtd"]

From b6df9894d870b8215e901da3c85421ab8fc457c6 Mon Sep 17 00:00:00 2001
From: Ben Mares <services-git-throwaway2@tensorial.com>
Date: Sun, 13 Jul 2025 20:45:20 +0200
Subject: [PATCH 08/24] Improve comment

---
 pyproject.toml | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index cbd803cc9c..a468d00227 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -196,9 +196,13 @@ test-skip = ["cp37*", "*musllinux*", "*win32*", "*i686*"]
 # test-requires = ["pytest", "numba", "jax", "jaxlib"]
 # test-command = "pytest {package}/tests"
 
+
+# Conda-lock is used to generate pixi.toml via scripts/generate-pixi-toml.py
+[tool.conda-lock.dependencies]
+
 # This is a temporary hack to achieve automatic pixi.toml generation.
 # Unfortunately pytest-sphinx is not yet on conda-forge. I'm trying to add
 # it in <https://github.com/conda-forge/staged-recipes/pull/30520>. In the
-# meantime, we need to make it a PyPI dependency.
-[tool.conda-lock.dependencies]
+# meantime before this is merged, we need to make it a PyPI dependency.
+# After it's merged, we should delete this line.
 pytest-sphinx = {source = "pypi", category="docs"}

From 0a9d152b6237df535a9e97be296f6daa3593feb8 Mon Sep 17 00:00:00 2001
From: Ben Mares <services-git-throwaway2@tensorial.com>
Date: Sun, 13 Jul 2025 20:50:53 +0200
Subject: [PATCH 09/24] Add more postprocessing of pixi.toml

---
 scripts/generate-pixi-toml.py | 124 ++++++++++++++++++++++++++++++++++
 1 file changed, 124 insertions(+)

diff --git a/scripts/generate-pixi-toml.py b/scripts/generate-pixi-toml.py
index 2e4ddc866d..47670fe70f 100755
--- a/scripts/generate-pixi-toml.py
+++ b/scripts/generate-pixi-toml.py
@@ -135,6 +135,8 @@ def postprocess_pixi_toml_data(
 ) -> tomlkit.TOMLDocument:
     pixi_toml_data = restrict_jax_platforms(pixi_toml_data)
     pixi_toml_data = add_header_comment(pixi_toml_data)
+    pixi_toml_data = use_only_default_solve_group(pixi_toml_data)
+    pixi_toml_data = comment_out_environments_that_wont_solve(pixi_toml_data)
     return pixi_toml_data
 
 
@@ -226,6 +228,128 @@ def add_header_comment(pixi_toml_data: tomlkit.TOMLDocument) -> tomlkit.TOMLDocu
     return new_doc
 
 
+def comment_out_environments_that_wont_solve(
+    pixi_toml_data: tomlkit.TOMLDocument,
+) -> tomlkit.TOMLDocument:
+    """
+    Comment out the lines defining environments that won't solve.
+
+    TODO: Understand why these environments won't solve.
+    This happens when I set everything to use the default solve group.
+    Ordinarily the dependencies in each environment would just be subsets
+    of the dependencies in the full default environment. Perhaps there's
+    some non-monotonic constraint like a run-constrained dependency. But
+    this needs to be investigated.
+
+    >>> input_data = tomlkit.loads('''
+    ... [environments]
+    ... tests = {features = ["tests"]}
+    ... dev = {features = ["dev"]}
+    ... ''')
+    >>> output_data = comment_out_environments_that_wont_solve(input_data)
+    >>> print(tomlkit.dumps(output_data))
+    [environments]
+    dev = {features = ["dev"]}
+    # tests = {features = ["tests"]}
+    """
+    TO_COMMENT_OUT = ["conda-dev", "numba", "rtd", "tests"]
+    environments_item = pixi_toml_data.get("environments")
+    assert isinstance(environments_item, tomlkit.items.Table)
+
+    # Modify the table in-place to preserve comments and formatting
+    for key, value in list(environments_item.items()):
+        if key in TO_COMMENT_OUT:
+            # Create a comment with the key-value pair
+            comment_text = f"{key} = {value.as_string()}"
+
+            # If the original value had a comment, append it to the comment text
+            if hasattr(value, "trivia") and value.trivia.comment:
+                comment_text += f"  {value.trivia.comment}"
+
+            # Remove the original key-value pair and add a comment
+            del environments_item[key]
+            environments_item.add(tomlkit.comment(comment_text))
+
+    return pixi_toml_data
+
+
+def use_only_default_solve_group(
+    pixi_toml_data: tomlkit.TOMLDocument,
+) -> tomlkit.TOMLDocument:
+    """
+    Use only the default solve group.
+
+    TODO: upstream this to conda-lock.
+    """
+    pixi_toml_data = _convert_environment_items_to_dict_form(pixi_toml_data)
+    pixi_toml_data = _add_default_solve_group(pixi_toml_data)
+    return pixi_toml_data
+
+
+def _convert_environment_items_to_dict_form(
+    pixi_toml_data: tomlkit.TOMLDocument,
+) -> tomlkit.TOMLDocument:
+    """
+    Convert the environment items to dict form.
+
+    >>> input_data = tomlkit.loads('''
+    ... [environments]
+    ... tests = ["tests"]
+    ... dev = {features = ["dev"]}
+    ... ''')
+    >>> output_data = _convert_environment_items_to_dict_form(input_data)
+    >>> print(tomlkit.dumps(output_data))
+    [environments]
+    tests = {features = ["tests"]}
+    dev = {features = ["dev"]}
+    """
+    environments_item = pixi_toml_data.get("environments")
+    assert isinstance(environments_item, tomlkit.items.Table)
+
+    # Modify the table in-place to preserve comments and formatting
+    for key, value in list(environments_item.items()):
+        if isinstance(value, tomlkit.items.Array):
+            # Create an inline table and try to preserve comments
+            inline_table = tomlkit.inline_table()
+            inline_table["features"] = value.unwrap()
+
+            # Try to preserve any comment from the original array
+            if hasattr(value, "trivia") and value.trivia.comment:
+                inline_table.comment(value.trivia.comment)
+
+            environments_item[key] = inline_table
+
+    return pixi_toml_data
+
+
+def _add_default_solve_group(
+    pixi_toml_data: tomlkit.TOMLDocument,
+) -> tomlkit.TOMLDocument:
+    """
+    Add the default solve group to each environment entry.
+
+    >>> input_data = tomlkit.loads('''
+    ... [environments]
+    ... tests = {features = ["tests"]}
+    ... dev = {features = ["dev"]}
+    ... ''')
+    >>> output_data = _add_default_solve_group(input_data)
+    >>> print(tomlkit.dumps(output_data))
+    [environments]
+    tests = {features = ["tests"], solve-group = "default"}
+    dev = {features = ["dev"], solve-group = "default"}
+    """
+    environments_item = pixi_toml_data.get("environments")
+    assert isinstance(environments_item, tomlkit.items.Table)
+
+    for value in environments_item.values():
+        if isinstance(value, tomlkit.items.InlineTable):
+            if "solve-group" not in value:
+                value["solve-group"] = "default"
+
+    return pixi_toml_data
+
+
 def preprocess_environment_data(
     raw_environment_data: str,
 ) -> str:

From 570154088897f97e8419635a1dae3c2d838713bb Mon Sep 17 00:00:00 2001
From: Ben Mares <services-git-throwaway2@tensorial.com>
Date: Sun, 13 Jul 2025 20:51:04 +0200
Subject: [PATCH 10/24] Update pixi.toml

---
 pixi.toml | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/pixi.toml b/pixi.toml
index d1d987c471..9d8c37aa9d 100644
--- a/pixi.toml
+++ b/pixi.toml
@@ -94,13 +94,13 @@ pytest-sphinx = "*"
 
 [environments]
 # Redefine the default environment to include all categories.
-default = ["blas", "conda-dev", "jax", "numba", "rtd", "tests"]
+default = {features = ["blas", "conda-dev", "jax", "numba", "rtd", "tests"], solve-group = "default"}
 # Define a minimal environment with only the default feature.
-minimal = []
+minimal = {features = [], solve-group = "default"}
 # Create an environment for each feature.
-blas = ["blas"]
-conda-dev = ["conda-dev"]
-jax = ["jax"]
-numba = ["numba"]
-rtd = ["rtd"]
-tests = ["tests"]
+blas = {features = ["blas"], solve-group = "default"}
+jax = {features = ["jax"], solve-group = "default"}
+# conda-dev = {features = ["conda-dev"], solve-group = "default"}
+# numba = {features = ["numba"], solve-group = "default"}
+# rtd = {features = ["rtd"], solve-group = "default"}
+# tests = {features = ["tests"], solve-group = "default"}

From 55267861e6d8ce73a865739fcd6021e8eb335d5f Mon Sep 17 00:00:00 2001
From: Ben Mares <services-git-throwaway2@tensorial.com>
Date: Mon, 14 Jul 2025 17:15:27 +0200
Subject: [PATCH 11/24] Comment out non-default environments

---
 scripts/generate-pixi-toml.py | 38 +++++++++++++++++++----------------
 1 file changed, 21 insertions(+), 17 deletions(-)

diff --git a/scripts/generate-pixi-toml.py b/scripts/generate-pixi-toml.py
index 47670fe70f..ef1584ddb1 100755
--- a/scripts/generate-pixi-toml.py
+++ b/scripts/generate-pixi-toml.py
@@ -234,12 +234,7 @@ def comment_out_environments_that_wont_solve(
     """
     Comment out the lines defining environments that won't solve.
 
-    TODO: Understand why these environments won't solve.
-    This happens when I set everything to use the default solve group.
-    Ordinarily the dependencies in each environment would just be subsets
-    of the dependencies in the full default environment. Perhaps there's
-    some non-monotonic constraint like a run-constrained dependency. But
-    this needs to be investigated.
+    Reference: <https://github.com/prefix-dev/pixi/issues/2725>
 
     >>> input_data = tomlkit.loads('''
     ... [environments]
@@ -252,23 +247,32 @@ def comment_out_environments_that_wont_solve(
     dev = {features = ["dev"]}
     # tests = {features = ["tests"]}
     """
-    TO_COMMENT_OUT = ["conda-dev", "numba", "rtd", "tests"]
     environments_item = pixi_toml_data.get("environments")
     assert isinstance(environments_item, tomlkit.items.Table)
 
-    # Modify the table in-place to preserve comments and formatting
-    for key, value in list(environments_item.items()):
-        if key in TO_COMMENT_OUT:
-            # Create a comment with the key-value pair
+    # Create a new table to rebuild with the desired order
+    new_environments_table = tomlkit.table()
+
+    COMMENT_TEXT = "Disable non-default environments pending <https://github.com/prefix-dev/pixi/issues/2725>"
+    # Process each key-value pair in the original table
+    for key, value in environments_item.items():
+        if key == "default":
+            # Keep the default environment as-is
+            new_environments_table.append(key, value)
+
+            # Add explanatory comment at the beginning
+            new_environments_table.append(None, tomlkit.nl())
+            new_environments_table.append(None, tomlkit.comment(COMMENT_TEXT))
+        else:
+            # Convert other environments to comments
             comment_text = f"{key} = {value.as_string()}"
 
-            # If the original value had a comment, append it to the comment text
-            if hasattr(value, "trivia") and value.trivia.comment:
-                comment_text += f"  {value.trivia.comment}"
+            # Note: We don't preserve original comments here since they
+            # don't make sense in the commented-out context
+            new_environments_table.append(None, tomlkit.comment(comment_text))
 
-            # Remove the original key-value pair and add a comment
-            del environments_item[key]
-            environments_item.add(tomlkit.comment(comment_text))
+    # Replace the original environments table with the new one
+    pixi_toml_data["environments"] = new_environments_table
 
     return pixi_toml_data
 

From 20113ca34444582ca835a9c5c2b98046ca92b7db Mon Sep 17 00:00:00 2001
From: Ben Mares <services-git-throwaway2@tensorial.com>
Date: Mon, 14 Jul 2025 17:15:48 +0200
Subject: [PATCH 12/24] Revert "Improve comment"

This reverts commit b6df9894d870b8215e901da3c85421ab8fc457c6.
---
 pyproject.toml | 8 ++------
 1 file changed, 2 insertions(+), 6 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index a468d00227..cbd803cc9c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -196,13 +196,9 @@ test-skip = ["cp37*", "*musllinux*", "*win32*", "*i686*"]
 # test-requires = ["pytest", "numba", "jax", "jaxlib"]
 # test-command = "pytest {package}/tests"
 
-
-# Conda-lock is used to generate pixi.toml via scripts/generate-pixi-toml.py
-[tool.conda-lock.dependencies]
-
 # This is a temporary hack to achieve automatic pixi.toml generation.
 # Unfortunately pytest-sphinx is not yet on conda-forge. I'm trying to add
 # it in <https://github.com/conda-forge/staged-recipes/pull/30520>. In the
-# meantime before this is merged, we need to make it a PyPI dependency.
-# After it's merged, we should delete this line.
+# meantime, we need to make it a PyPI dependency.
+[tool.conda-lock.dependencies]
 pytest-sphinx = {source = "pypi", category="docs"}

From a3b14c53f7bec078c1394d53f70c27a18655a477 Mon Sep 17 00:00:00 2001
From: Ben Mares <services-git-throwaway2@tensorial.com>
Date: Mon, 14 Jul 2025 17:16:07 +0200
Subject: [PATCH 13/24] Revert "Add temporary workaround for pytest-sphinx not
 on conda-forge"

This reverts commit 038c7772ab883c205d36cf58d432f993e6663895.
---
 pyproject.toml | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index cbd803cc9c..9ddce92bc8 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -195,10 +195,3 @@ test-skip = ["cp37*", "*musllinux*", "*win32*", "*i686*"]
 # Testing seems to be running into issues locating libs where expected
 # test-requires = ["pytest", "numba", "jax", "jaxlib"]
 # test-command = "pytest {package}/tests"
-
-# This is a temporary hack to achieve automatic pixi.toml generation.
-# Unfortunately pytest-sphinx is not yet on conda-forge. I'm trying to add
-# it in <https://github.com/conda-forge/staged-recipes/pull/30520>. In the
-# meantime, we need to make it a PyPI dependency.
-[tool.conda-lock.dependencies]
-pytest-sphinx = {source = "pypi", category="docs"}

From 4fc4453958e93d0d37abad223de73be899dc0517 Mon Sep 17 00:00:00 2001
From: Ben Mares <services-git-throwaway2@tensorial.com>
Date: Mon, 14 Jul 2025 17:17:47 +0200
Subject: [PATCH 14/24] Install pytest-sphinx with conda not pip

---
 environment.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/environment.yml b/environment.yml
index f7c517d6b6..e2ab39fe14 100644
--- a/environment.yml
+++ b/environment.yml
@@ -33,8 +33,7 @@ dependencies:
   - pytest-xdist
   - pytest-benchmark
   - pytest-mock
-  - pip:
-    - pytest-sphinx
+  - pytest-sphinx
   # For building docs
   - sphinx>=5.1.0,<6
   - sphinx_rtd_theme

From 81e1ac13ffb4f8f777d93c804e54049cfe3d36a6 Mon Sep 17 00:00:00 2001
From: Ben Mares <services-git-throwaway2@tensorial.com>
Date: Mon, 14 Jul 2025 17:34:01 +0200
Subject: [PATCH 15/24] Improve comments

---
 scripts/generate-pixi-toml.py | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/scripts/generate-pixi-toml.py b/scripts/generate-pixi-toml.py
index ef1584ddb1..390cc0edce 100755
--- a/scripts/generate-pixi-toml.py
+++ b/scripts/generate-pixi-toml.py
@@ -253,7 +253,15 @@ def comment_out_environments_that_wont_solve(
     # Create a new table to rebuild with the desired order
     new_environments_table = tomlkit.table()
 
-    COMMENT_TEXT = "Disable non-default environments pending <https://github.com/prefix-dev/pixi/issues/2725>"
+    COMMENT_TEXT_1 = (
+        "Disable non-default environments pending "
+        "<https://github.com/prefix-dev/pixi/issues/2725>"
+    )
+    COMMENT_TEXT_2 = (
+        "If you want to re-enable some of these, it's recommended to "
+        "remove the solve-group key."
+    )
+
     # Process each key-value pair in the original table
     for key, value in environments_item.items():
         if key == "default":
@@ -262,7 +270,8 @@ def comment_out_environments_that_wont_solve(
 
             # Add explanatory comment at the beginning
             new_environments_table.append(None, tomlkit.nl())
-            new_environments_table.append(None, tomlkit.comment(COMMENT_TEXT))
+            new_environments_table.append(None, tomlkit.comment(COMMENT_TEXT_1))
+            new_environments_table.append(None, tomlkit.comment(COMMENT_TEXT_2))
         else:
             # Convert other environments to comments
             comment_text = f"{key} = {value.as_string()}"

From 7022f4159d60260dd142731dc61892f165be5afb Mon Sep 17 00:00:00 2001
From: Ben Mares <services-git-throwaway2@tensorial.com>
Date: Mon, 14 Jul 2025 19:57:48 +0200
Subject: [PATCH 16/24] Regenerate pixi.toml

---
 pixi.toml | 17 +++++++----------
 1 file changed, 7 insertions(+), 10 deletions(-)

diff --git a/pixi.toml b/pixi.toml
index 9d8c37aa9d..483fd44663 100644
--- a/pixi.toml
+++ b/pixi.toml
@@ -15,7 +15,6 @@ filelock = ">=3.15"
 logical-unification = "*"
 minikanren = "*"
 numpy = ">=1.17.0"
-pip = "*"
 scipy = "<2,>=1"
 setuptools = ">=59.0.0"
 
@@ -86,21 +85,19 @@ pytest = "*"
 pytest-benchmark = "*"
 pytest-cov = ">=2.6.1"
 pytest-mock = "*"
-tomlkit = "*"
-
-[feature.tests.pypi-dependencies]
 pytest-sphinx = "*"
+tomlkit = "*"
 
 
 [environments]
-# Redefine the default environment to include all categories.
 default = {features = ["blas", "conda-dev", "jax", "numba", "rtd", "tests"], solve-group = "default"}
-# Define a minimal environment with only the default feature.
-minimal = {features = [], solve-group = "default"}
-# Create an environment for each feature.
-blas = {features = ["blas"], solve-group = "default"}
-jax = {features = ["jax"], solve-group = "default"}
+
+# Disable non-default environments pending <https://github.com/prefix-dev/pixi/issues/2725>
+# If you want to re-enable some of these, it's recommended to remove the solve-group key.
+# minimal = {features = [], solve-group = "default"}
+# blas = {features = ["blas"], solve-group = "default"}
 # conda-dev = {features = ["conda-dev"], solve-group = "default"}
+# jax = {features = ["jax"], solve-group = "default"}
 # numba = {features = ["numba"], solve-group = "default"}
 # rtd = {features = ["rtd"], solve-group = "default"}
 # tests = {features = ["tests"], solve-group = "default"}

From f4d0f6368c68b41e95cddae5c70a47a2231b736f Mon Sep 17 00:00:00 2001
From: Ben Mares <services-git-throwaway2@tensorial.com>
Date: Mon, 14 Jul 2025 21:43:51 +0200
Subject: [PATCH 17/24] Refactor cleanup

---
 scripts/generate-pixi-toml.py | 45 ++++++++++++++++++++++++++++-------
 1 file changed, 36 insertions(+), 9 deletions(-)

diff --git a/scripts/generate-pixi-toml.py b/scripts/generate-pixi-toml.py
index 390cc0edce..3d03beed23 100755
--- a/scripts/generate-pixi-toml.py
+++ b/scripts/generate-pixi-toml.py
@@ -5,11 +5,23 @@
 import subprocess
 import sys
 from pathlib import Path
+from typing import NamedTuple
 
 import tomlkit
 import tomlkit.items
 
 
+class WorkingDirectoryPaths(NamedTuple):
+    """Paths within the temporary working directory"""
+
+    working_path: Path
+    working_pyproject_file: Path
+    working_environment_file: Path
+    working_environment_blas_file: Path
+    pixi_toml_raw_file: Path
+    gitignore_file: Path
+
+
 RAW_COMMAND = """
 pixi exec conda-lock render-lock-spec \
     --channel=conda-forge \
@@ -82,17 +94,32 @@ def main():
 
     pixi_toml_data = postprocess_pixi_toml_data(pixi_toml_raw_data)
 
-    # Write the pixi.toml file to the project root
-    (project_root / "pixi.toml").write_text(tomlkit.dumps(pixi_toml_data))
+    working_directory_paths = WorkingDirectoryPaths(
+        working_path=working_path,
+        working_pyproject_file=working_pyproject_file,
+        working_environment_file=working_environment_file,
+        working_environment_blas_file=working_environment_blas_file,
+        pixi_toml_raw_file=pixi_toml_raw_file,
+        gitignore_file=gitignore_file,
+    )
+
+    # Generate the pixi.toml content
+    pixi_toml_content = tomlkit.dumps(pixi_toml_data)
+    (project_root / "pixi.toml").write_text(pixi_toml_content)
 
     # Clean up
-    working_pyproject_file.unlink()
-    working_environment_file.unlink()
-    working_environment_blas_file.unlink()
-    working_environment_blas_file.parent.rmdir()
-    pixi_toml_raw_file.unlink()
-    gitignore_file.unlink()
-    working_path.rmdir()
+    cleanup_working_directory(working_directory_paths)
+
+
+def cleanup_working_directory(working_paths: WorkingDirectoryPaths):
+    """Clean up the temporary working directory and files"""
+    working_paths.working_pyproject_file.unlink()
+    working_paths.working_environment_file.unlink()
+    working_paths.working_environment_blas_file.unlink()
+    working_paths.working_environment_blas_file.parent.rmdir()
+    working_paths.pixi_toml_raw_file.unlink()
+    working_paths.gitignore_file.unlink()
+    working_paths.working_path.rmdir()
 
 
 def preprocess_pyproject_data(

From fa6fa72e4b8d5b8a1839a983202131f1c656c383 Mon Sep 17 00:00:00 2001
From: Ben Mares <services-git-throwaway2@tensorial.com>
Date: Mon, 14 Jul 2025 21:46:37 +0200
Subject: [PATCH 18/24] Add --verify-only option

---
 scripts/generate-pixi-toml.py | 36 ++++++++++++++++++++++++++++++++---
 1 file changed, 33 insertions(+), 3 deletions(-)

diff --git a/scripts/generate-pixi-toml.py b/scripts/generate-pixi-toml.py
index 3d03beed23..fdd2105b8f 100755
--- a/scripts/generate-pixi-toml.py
+++ b/scripts/generate-pixi-toml.py
@@ -1,5 +1,6 @@
 #!/usr/bin/env python3
 
+import argparse
 import shlex
 import shutil
 import subprocess
@@ -38,6 +39,16 @@ class WorkingDirectoryPaths(NamedTuple):
 
 
 def main():
+    parser = argparse.ArgumentParser(
+        description="Generate pixi.toml from environment files"
+    )
+    parser.add_argument(
+        "--verify-only",
+        action="store_true",
+        help="Only verify that pixi.toml is consistent with environment files, don't write",
+    )
+    args = parser.parse_args()
+
     # Check if pixi is installed
     if not shutil.which("pixi"):
         print("pixi is not installed. See <https://pixi.sh/latest/#installation>")  # noqa: T201
@@ -105,10 +116,29 @@ def main():
 
     # Generate the pixi.toml content
     pixi_toml_content = tomlkit.dumps(pixi_toml_data)
-    (project_root / "pixi.toml").write_text(pixi_toml_content)
 
-    # Clean up
-    cleanup_working_directory(working_directory_paths)
+    if args.verify_only:
+        # Compare with existing pixi.toml
+        pixi_toml_file = project_root / "pixi.toml"
+        if not pixi_toml_file.exists():
+            print("ERROR: pixi.toml does not exist")  # noqa: T201
+            cleanup_working_directory(working_directory_paths)
+            sys.exit(1)
+
+        existing_content = pixi_toml_file.read_text()
+        if existing_content != pixi_toml_content:
+            print("ERROR: pixi.toml is not consistent with environment files")  # noqa: T201
+            print("Run 'python scripts/generate-pixi-toml.py' to update it")  # noqa: T201
+            cleanup_working_directory(working_directory_paths)
+            sys.exit(1)
+
+        print("SUCCESS: pixi.toml is consistent with environment files")  # noqa: T201
+        cleanup_working_directory(working_directory_paths)
+        sys.exit(0)
+    else:
+        # Write the pixi.toml file to the project root
+        (project_root / "pixi.toml").write_text(pixi_toml_content)
+        cleanup_working_directory(working_directory_paths)
 
 
 def cleanup_working_directory(working_paths: WorkingDirectoryPaths):

From fd224d70489442667bef17d075ff0b985234514b Mon Sep 17 00:00:00 2001
From: Ben Mares <services-git-throwaway2@tensorial.com>
Date: Mon, 14 Jul 2025 21:58:26 +0200
Subject: [PATCH 19/24] Check pixi consistency

---
 .github/workflows/test.yml | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index b7dc291eec..ed34f0a261 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -46,6 +46,8 @@ jobs:
             - 'setup.cfg'
             - 'requirements.txt'
             - '.pre-commit-config.yaml'
+            - 'pixi.toml'
+            - 'pixi.lock'
 
   style:
     name: Check code style
@@ -63,6 +65,17 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
       - uses: pre-commit/action@v3.0.1
+      # Check that pixi stuff is consistent
+      - uses: prefix-dev/setup-pixi@v0.8.11
+        with:
+          run-install: false
+      - name: Check that the pixi.lock is consistent with pixi.toml
+        run: |
+          pixi run --no-install --locked echo "All good!"
+      - name: Check that pixi.toml is consistent with environment.yml and pyproject.toml
+        run: |
+          pip install tomlkit
+          python scripts/generate-pixi-toml.py --verify-only
 
   test:
     name: "${{ matrix.os }} test py${{ matrix.python-version }} numpy${{ matrix.numpy-version }} : fast-compile ${{ matrix.fast-compile }} : float32 ${{ matrix.float32 }} : ${{ matrix.part }}"

From e272f7c495fdf39ee601433e3faf28d254b77379 Mon Sep 17 00:00:00 2001
From: Ben Mares <services-git-throwaway2@tensorial.com>
Date: Mon, 14 Jul 2025 22:05:56 +0200
Subject: [PATCH 20/24] Add pixi.lock

---
 pixi.lock | 9226 +++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 9226 insertions(+)
 create mode 100644 pixi.lock

diff --git a/pixi.lock b/pixi.lock
new file mode 100644
index 0000000000..79a21e1ad0
--- /dev/null
+++ b/pixi.lock
@@ -0,0 +1,9226 @@
+version: 6
+environments:
+  default:
+    channels:
+    - url: https://conda.anaconda.org/conda-forge/
+    indexes:
+    - https://pypi.org/simple
+    packages:
+      linux-64:
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-3_kmp_llvm.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/accessible-pygments-0.0.5-pyhd8ed1ab_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/adwaita-icon-theme-48.1-unix_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/alabaster-0.7.16-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/alsa-lib-1.2.14-hb9d3cd8_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/asttokens-3.0.0-pyhd8ed1ab_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/at-spi2-atk-2.38.0-h0630a04_3.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/at-spi2-core-2.40.3-h0630a04_0.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/atk-1.0-2.38.0-h04ea711_2.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/attrs-25.3.0-pyh71513ae_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/babel-2.17.0-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/beautifulsoup4-4.13.4-pyha770c72_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/binutils-2.44-h4852527_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/binutils_impl_linux-64-2.44-h4bf12b8_1.conda
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+      - conda: https://conda.anaconda.org/conda-forge/linux-64/brotli-bin-1.1.0-hb9d3cd8_3.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/brotli-python-1.1.0-py312h2ec8cdc_3.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.34.5-hb9d3cd8_0.conda
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+      - conda: https://conda.anaconda.org/conda-forge/noarch/filelock-3.18.0-pyhd8ed1ab_0.conda
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+      - conda: https://conda.anaconda.org/conda-forge/linux-64/fontconfig-2.15.0-h7e30c49_1.conda
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+- conda: https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.7-hb8e6e7a_2.conda
+  sha256: a4166e3d8ff4e35932510aaff7aa90772f84b4d07e9f6f83c614cba7ceefe0eb
+  md5: 6432cb5d4ac0046c3ac0a8a0f95842f9
+  depends:
+  - __glibc >=2.17,<3.0.a0
+  - libgcc >=13
+  - libstdcxx >=13
+  - libzlib >=1.3.1,<2.0a0
+  license: BSD-3-Clause
+  license_family: BSD
+  purls: []
+  size: 567578
+  timestamp: 1742433379869
+- conda: https://conda.anaconda.org/conda-forge/osx-64/zstd-1.5.7-h8210216_2.conda
+  sha256: c171c43d0c47eed45085112cb00c8c7d4f0caa5a32d47f2daca727e45fb98dca
+  md5: cd60a4a5a8d6a476b30d8aa4bb49251a
+  depends:
+  - __osx >=10.13
+  - libzlib >=1.3.1,<2.0a0
+  license: BSD-3-Clause
+  license_family: BSD
+  purls: []
+  size: 485754
+  timestamp: 1742433356230
+- conda: https://conda.anaconda.org/conda-forge/osx-arm64/zstd-1.5.7-h6491c7d_2.conda
+  sha256: 0d02046f57f7a1a3feae3e9d1aa2113788311f3cf37a3244c71e61a93177ba67
+  md5: e6f69c7bcccdefa417f056fa593b40f0
+  depends:
+  - __osx >=11.0
+  - libzlib >=1.3.1,<2.0a0
+  license: BSD-3-Clause
+  license_family: BSD
+  purls: []
+  size: 399979
+  timestamp: 1742433432699

From 49023ee7d70b1ef7e1ab02fb3639639926547ee3 Mon Sep 17 00:00:00 2001
From: Ben Mares <services-git-throwaway2@tensorial.com>
Date: Tue, 15 Jul 2025 15:32:45 +0200
Subject: [PATCH 21/24] Add comments

---
 scripts/generate-pixi-toml.py | 65 +++++++++++++++++++++++++++++++++++
 1 file changed, 65 insertions(+)

diff --git a/scripts/generate-pixi-toml.py b/scripts/generate-pixi-toml.py
index fdd2105b8f..8f92070f40 100755
--- a/scripts/generate-pixi-toml.py
+++ b/scripts/generate-pixi-toml.py
@@ -1,5 +1,70 @@
 #!/usr/bin/env python3
 
+"""
+Generate a `pixi.toml` file.
+
+Overview:
+
+To a very good approximation, this script just runs RAW_COMMAND,
+and writes the output to `pixi.toml`.
+
+This script is necessary in order to do some minor pre- and post-processing.
+
+Context:
+
+Pixi is a modern project-centric manager of Conda environments.
+It runs completely independently of more traditional tools like `conda`
+or `mamba`, or non-Conda-enabled Python environment managers like
+`pip` or `uv`. As such, we need to define the dependencies and Conda
+environments that pixi should automatically manage. This is specified
+in a `pixi.toml` file.
+
+The sources of truth for the dependencies in this project are:
+- `environment.yml`
+- `pyproject.toml`
+
+The goal of this script is to maintain the original sources of truth and
+in a completely automatic way generate a valid `pixi.toml` from them.
+
+Currently, pixi has no mechanism for importing `environment.yml` files,
+and when loading `pyproject.toml` files it does not attempt to convert
+the PyPI dependencies into conda-forge dependencies. On the other hand,
+`conda-lock` does both of these things, and recently added support for
+generating `pixi.toml` files from `environment.yml` and `pyproject.toml`
+files.
+
+PyTensor has some rather complicated dependencies, and so we do some
+pre- and post-processing in this script in order to work around some
+idiosyncrasies.
+
+Technical details:
+
+This script creates a temporary working directory `pixi-working/` in
+the project root, copies pre-processed versions of `environment.yml`,
+`pyproject.toml`, and `scripts/environment-blas.yml` into it, and then
+runs `conda-lock` via `pixi exec` in order to generate the contents of
+a `pixi.toml` file.
+
+The generated `pixi.toml` contents are then post-processed and written
+to the project root.
+
+The pre-processing steps are:
+
+- Remove the `complete` and `development` optional dependencies from
+  `pyproject.toml`.
+- Remove the BLAS dependencies from `environment.yml`. (They are redefined
+  in `scripts/environment-blas.yml` on a platform-by-platform basis to
+  work around limitations in `conda-lock`'s selector parsing.)
+
+The post-processing steps are:
+
+- Add an explanatory header comment to the `pixi.toml` file.
+- Remove the `win-64` platform from the jax feature (jaxlib is not
+  available for Windows from conda-forge).
+- Add the default solve group to each environment entry.
+- Comment out the non-default environments.
+"""
+
 import argparse
 import shlex
 import shutil

From 5d4631585d62a6fba63552ee25995c39006f1e9d Mon Sep 17 00:00:00 2001
From: Ben Mares <services-git-throwaway2@tensorial.com>
Date: Tue, 15 Jul 2025 16:24:31 +0200
Subject: [PATCH 22/24] Refactor

---
 scripts/generate-pixi-toml.py | 187 +++++++++++++++++++++-------------
 1 file changed, 119 insertions(+), 68 deletions(-)

diff --git a/scripts/generate-pixi-toml.py b/scripts/generate-pixi-toml.py
index 8f92070f40..9575f85ae8 100755
--- a/scripts/generate-pixi-toml.py
+++ b/scripts/generate-pixi-toml.py
@@ -71,23 +71,13 @@
 import subprocess
 import sys
 from pathlib import Path
+from textwrap import dedent
 from typing import NamedTuple
 
 import tomlkit
 import tomlkit.items
 
 
-class WorkingDirectoryPaths(NamedTuple):
-    """Paths within the temporary working directory"""
-
-    working_path: Path
-    working_pyproject_file: Path
-    working_environment_file: Path
-    working_environment_blas_file: Path
-    pixi_toml_raw_file: Path
-    gitignore_file: Path
-
-
 RAW_COMMAND = """
 pixi exec conda-lock render-lock-spec \
     --channel=conda-forge \
@@ -103,6 +93,27 @@ class WorkingDirectoryPaths(NamedTuple):
 PARSED_COMMAND = shlex.split(RAW_COMMAND)
 
 
+class OriginalPaths(NamedTuple):
+    """Paths to the original files"""
+
+    project_root: Path  # ./
+    pyproject_file: Path  # ./pyproject.toml
+    environment_file: Path  # ./environment.yml
+    environment_blas_file: Path  # ./scripts/environment-blas.yml
+    pixi_toml_file: Path  # ./pixi.toml
+
+
+class WorkingDirectoryPaths(NamedTuple):
+    """Paths within the temporary working directory"""
+
+    working_path: Path  # ./pixi-working/
+    pyproject_file: Path  # ./pixi-working/pyproject.toml
+    environment_file: Path  # ./pixi-working/environment.yml
+    environment_blas_file: Path  # ./pixi-working/scripts/environment-blas.yml
+    pixi_toml_file: Path  # ./pixi-working/pixi.toml
+    gitignore_file: Path  # ./pixi-working/.gitignore
+
+
 def main():
     parser = argparse.ArgumentParser(
         description="Generate pixi.toml from environment files"
@@ -119,82 +130,78 @@ def main():
         print("pixi is not installed. See <https://pixi.sh/latest/#installation>")  # noqa: T201
         sys.exit(1)
 
-    current_dir = Path(__file__).parent
-    assert current_dir.name == "scripts"
-    project_root = current_dir.parent
-
-    pyproject_file = project_root / "pyproject.toml"
-
-    pyproject_data = tomlkit.loads(pyproject_file.read_text())
-
-    pyproject_data = preprocess_pyproject_data(pyproject_data)
+    original_paths = get_original_paths()
 
     # Make temporary working directory
-    working_path = project_root / "pixi-working"
-    working_path.mkdir(parents=True, exist_ok=True)
-    gitignore_file = working_path / ".gitignore"
-    gitignore_file.write_text("*")
+    working_directory_paths = initialize_working_directory(original_paths)
 
-    working_pyproject_file = working_path / "pyproject.toml"
-    with working_pyproject_file.open("w") as fh:
+    # Copy the processed pyproject.toml to the working directory
+    pyproject_data = tomlkit.loads(original_paths.pyproject_file.read_text())
+    pyproject_data = preprocess_pyproject_data(pyproject_data)
+    with working_directory_paths.pyproject_file.open("w") as fh:
         tomlkit.dump(pyproject_data, fh)
 
-    raw_environment_file = project_root / "environment.yml"
-    raw_environment_data = raw_environment_file.read_text()
-
+    # Copy the processed environment file to the working directory
+    raw_environment_data = original_paths.environment_file.read_text()
     environment_data = preprocess_environment_data(raw_environment_data)
-
-    working_environment_file = working_path / "environment.yml"
-    with working_environment_file.open("w") as fh:
+    with working_directory_paths.environment_file.open("w") as fh:
         fh.write(environment_data)
 
-    environment_blas_file = project_root / "scripts" / "environment-blas.yml"
-    working_environment_blas_file = working_path / "scripts" / "environment-blas.yml"
+    # Copy environment-blas.yml to the working directory
     # This is for our exclusive use, so it doesn't need to be preprocessed.
-    working_environment_blas_file.parent.mkdir(parents=True, exist_ok=True)
-    shutil.copy(environment_blas_file, working_environment_blas_file)
+    working_directory_paths.environment_blas_file.parent.mkdir(
+        parents=True, exist_ok=True
+    )
+    shutil.copy(
+        original_paths.environment_blas_file,
+        working_directory_paths.environment_blas_file,
+    )
 
+    # Run conda-lock to generate the pixi.toml file
     print(f"Running the command:\n{shlex.join(PARSED_COMMAND)}\n")  # noqa: T201
     result = subprocess.run(
-        PARSED_COMMAND, check=True, capture_output=True, cwd=working_path
+        PARSED_COMMAND,
+        check=True,
+        capture_output=True,
+        cwd=working_directory_paths.working_path,
     )
 
     warnings = result.stderr.decode("utf-8")
     if warnings:
         print(f"Warnings: \n{warnings}\n")  # noqa: T201
 
+    # Write the unprocessed pixi.toml data to the working directory
     pixi_toml_raw_data = tomlkit.loads(result.stdout.decode("utf-8"))
-
-    pixi_toml_raw_file = working_path / "pixi.toml"
-    pixi_toml_raw_file.write_text(tomlkit.dumps(pixi_toml_raw_data))
-
-    pixi_toml_data = postprocess_pixi_toml_data(pixi_toml_raw_data)
-
-    working_directory_paths = WorkingDirectoryPaths(
-        working_path=working_path,
-        working_pyproject_file=working_pyproject_file,
-        working_environment_file=working_environment_file,
-        working_environment_blas_file=working_environment_blas_file,
-        pixi_toml_raw_file=pixi_toml_raw_file,
-        gitignore_file=gitignore_file,
-    )
+    pixi_toml_raw_content = tomlkit.dumps(pixi_toml_raw_data)
+    working_directory_paths.pixi_toml_file.write_text(pixi_toml_raw_content)
 
     # Generate the pixi.toml content
+    pixi_toml_data = postprocess_pixi_toml_data(pixi_toml_raw_data)
     pixi_toml_content = tomlkit.dumps(pixi_toml_data)
 
     if args.verify_only:
         # Compare with existing pixi.toml
-        pixi_toml_file = project_root / "pixi.toml"
-        if not pixi_toml_file.exists():
-            print("ERROR: pixi.toml does not exist")  # noqa: T201
-            cleanup_working_directory(working_directory_paths)
-            sys.exit(1)
-
-        existing_content = pixi_toml_file.read_text()
-        if existing_content != pixi_toml_content:
-            print("ERROR: pixi.toml is not consistent with environment files")  # noqa: T201
-            print("Run 'python scripts/generate-pixi-toml.py' to update it")  # noqa: T201
-            cleanup_working_directory(working_directory_paths)
+        existing_pixi_toml_content = original_paths.pixi_toml_file.read_text()
+        if existing_pixi_toml_content != pixi_toml_content:
+            message = dedent("""\
+            Mismatch detected between existing and new pixi.toml content.
+
+            New pixi.toml content:
+            {pixi_toml_content}
+
+            Run 'python scripts/generate-pixi-toml.py' to regenerate it.
+            After updating `pixi.toml`, it's suggested to run the following commands:
+
+                pixi lock
+                git add pixi.toml
+                git commit -m "Regenerate pixi.toml"
+                git add pixi.lock
+                git commit -m "Update pixi lockfile"
+
+            ERROR: pixi.toml is not consistent with environment files.
+            See above for details.
+            """).format(pixi_toml_content=pixi_toml_content)
+            print(message)  # noqa: T201
             sys.exit(1)
 
         print("SUCCESS: pixi.toml is consistent with environment files")  # noqa: T201
@@ -202,17 +209,61 @@ def main():
         sys.exit(0)
     else:
         # Write the pixi.toml file to the project root
-        (project_root / "pixi.toml").write_text(pixi_toml_content)
+        original_paths.pixi_toml_file.write_text(pixi_toml_content)
         cleanup_working_directory(working_directory_paths)
 
 
+def get_original_paths() -> OriginalPaths:
+    """Get the paths to the original files"""
+    current_dir = Path(__file__).parent
+    assert current_dir.name == "scripts"
+    project_root = current_dir.parent
+    pyproject_file = project_root / "pyproject.toml"
+    environment_file = project_root / "environment.yml"
+    environment_blas_file = project_root / "scripts" / "environment-blas.yml"
+    pixi_toml_file = project_root / "pixi.toml"
+    if not pixi_toml_file.exists():
+        raise FileNotFoundError(f"pixi.toml does not exist at {pixi_toml_file}")
+    return OriginalPaths(
+        project_root=project_root,
+        pyproject_file=pyproject_file,
+        environment_file=environment_file,
+        environment_blas_file=environment_blas_file,
+        pixi_toml_file=pixi_toml_file,
+    )
+
+
+def initialize_working_directory(
+    original_paths: OriginalPaths,
+) -> WorkingDirectoryPaths:
+    """Initialize the temporary working directory"""
+    working_path = original_paths.project_root / "pixi-working"
+    working_path.mkdir(parents=True, exist_ok=True)
+    gitignore_file = working_path / ".gitignore"
+    gitignore_file.write_text("*")
+
+    pyproject_file = working_path / "pyproject.toml"
+    environment_file = working_path / "environment.yml"
+    environment_blas_file = working_path / "scripts" / "environment-blas.yml"
+    pixi_toml_file = working_path / "pixi.toml"
+
+    return WorkingDirectoryPaths(
+        working_path=working_path,
+        pyproject_file=pyproject_file,
+        environment_file=environment_file,
+        environment_blas_file=environment_blas_file,
+        pixi_toml_file=pixi_toml_file,
+        gitignore_file=gitignore_file,
+    )
+
+
 def cleanup_working_directory(working_paths: WorkingDirectoryPaths):
     """Clean up the temporary working directory and files"""
-    working_paths.working_pyproject_file.unlink()
-    working_paths.working_environment_file.unlink()
-    working_paths.working_environment_blas_file.unlink()
-    working_paths.working_environment_blas_file.parent.rmdir()
-    working_paths.pixi_toml_raw_file.unlink()
+    working_paths.pyproject_file.unlink()
+    working_paths.environment_file.unlink()
+    working_paths.environment_blas_file.unlink()
+    working_paths.environment_blas_file.parent.rmdir()
+    working_paths.pixi_toml_file.unlink()
     working_paths.gitignore_file.unlink()
     working_paths.working_path.rmdir()
 

From 67fc58d529a56da6637e3d8f248bea765aa42862 Mon Sep 17 00:00:00 2001
From: Ben Mares <services-git-throwaway2@tensorial.com>
Date: Tue, 15 Jul 2025 16:35:10 +0200
Subject: [PATCH 23/24] Fix doctests

---
 scripts/generate-pixi-toml.py | 17 ++++++++++++++---
 1 file changed, 14 insertions(+), 3 deletions(-)

diff --git a/scripts/generate-pixi-toml.py b/scripts/generate-pixi-toml.py
index 9575f85ae8..97564fc781 100755
--- a/scripts/generate-pixi-toml.py
+++ b/scripts/generate-pixi-toml.py
@@ -289,8 +289,10 @@ def remove_extraneous_features(
     ... ''')
     >>> output_data = remove_extraneous_features(input_data)
     >>> print(tomlkit.dumps(output_data))
+    <BLANKLINE>
     [project.optional-dependencies]
     rtd = ["sphinx>=5.1.0,<6", "pygments", "pydot"]
+    <BLANKLINE>
     """
     project_item = pyproject_data.get("project")
     assert isinstance(project_item, tomlkit.items.Table)
@@ -335,12 +337,15 @@ def restrict_jax_platforms(
     ... ''')
     >>> output_data = restrict_jax_platforms(input_data)
     >>> print(tomlkit.dumps(output_data))
+    <BLANKLINE>
     [project]
     platforms = ["linux-64", "osx-64", "osx-arm64", "win-64"]
     [feature.jax]
     platforms = ["linux-64", "osx-64", "osx-arm64"]
+    <BLANKLINE>
     [feature.jax.dependencies]
     jax = "*"
+    <BLANKLINE>
     """
     # Get the platforms from the project section - unwrap to get the actual list
     project_item = pixi_toml_data["project"]
@@ -416,9 +421,11 @@ def comment_out_environments_that_wont_solve(
     ... ''')
     >>> output_data = comment_out_environments_that_wont_solve(input_data)
     >>> print(tomlkit.dumps(output_data))
+    <BLANKLINE>
     [environments]
-    dev = {features = ["dev"]}
     # tests = {features = ["tests"]}
+    # dev = {features = ["dev"]}
+    <BLANKLINE>
     """
     environments_item = pixi_toml_data.get("environments")
     assert isinstance(environments_item, tomlkit.items.Table)
@@ -485,9 +492,11 @@ def _convert_environment_items_to_dict_form(
     ... ''')
     >>> output_data = _convert_environment_items_to_dict_form(input_data)
     >>> print(tomlkit.dumps(output_data))
+    <BLANKLINE>
     [environments]
     tests = {features = ["tests"]}
     dev = {features = ["dev"]}
+    <BLANKLINE>
     """
     environments_item = pixi_toml_data.get("environments")
     assert isinstance(environments_item, tomlkit.items.Table)
@@ -521,9 +530,11 @@ def _add_default_solve_group(
     ... ''')
     >>> output_data = _add_default_solve_group(input_data)
     >>> print(tomlkit.dumps(output_data))
+    <BLANKLINE>
     [environments]
-    tests = {features = ["tests"], solve-group = "default"}
-    dev = {features = ["dev"], solve-group = "default"}
+    tests = {features = ["tests"],solve-group = "default"}
+    dev = {features = ["dev"],solve-group = "default"}
+    <BLANKLINE>
     """
     environments_item = pixi_toml_data.get("environments")
     assert isinstance(environments_item, tomlkit.items.Table)

From 77249fd09218c8e0f69df5fefbec010ed6d1f8e1 Mon Sep 17 00:00:00 2001
From: Ben Mares <services-git-throwaway2@tensorial.com>
Date: Wed, 16 Jul 2025 12:05:53 +0200
Subject: [PATCH 24/24] Run diff between original and new pixi.toml on
 verification failure

---
 scripts/generate-pixi-toml.py | 33 +++++++++++++++++++++++++--------
 1 file changed, 25 insertions(+), 8 deletions(-)

diff --git a/scripts/generate-pixi-toml.py b/scripts/generate-pixi-toml.py
index 97564fc781..503ef4bec1 100755
--- a/scripts/generate-pixi-toml.py
+++ b/scripts/generate-pixi-toml.py
@@ -110,7 +110,8 @@ class WorkingDirectoryPaths(NamedTuple):
     pyproject_file: Path  # ./pixi-working/pyproject.toml
     environment_file: Path  # ./pixi-working/environment.yml
     environment_blas_file: Path  # ./pixi-working/scripts/environment-blas.yml
-    pixi_toml_file: Path  # ./pixi-working/pixi.toml
+    raw_generated_pixi_toml: Path  # ./pixi-working/pixi-raw.toml
+    processed_generated_pixi_toml: Path  # ./pixi-working/pixi-processed.toml
     gitignore_file: Path  # ./pixi-working/.gitignore
 
 
@@ -173,21 +174,34 @@ def main():
     # Write the unprocessed pixi.toml data to the working directory
     pixi_toml_raw_data = tomlkit.loads(result.stdout.decode("utf-8"))
     pixi_toml_raw_content = tomlkit.dumps(pixi_toml_raw_data)
-    working_directory_paths.pixi_toml_file.write_text(pixi_toml_raw_content)
+    working_directory_paths.raw_generated_pixi_toml.write_text(pixi_toml_raw_content)
 
     # Generate the pixi.toml content
     pixi_toml_data = postprocess_pixi_toml_data(pixi_toml_raw_data)
     pixi_toml_content = tomlkit.dumps(pixi_toml_data)
+    working_directory_paths.processed_generated_pixi_toml.write_text(pixi_toml_content)
 
     if args.verify_only:
         # Compare with existing pixi.toml
         existing_pixi_toml_content = original_paths.pixi_toml_file.read_text()
         if existing_pixi_toml_content != pixi_toml_content:
+            # Run diff command to show the differences
+            cmd = [
+                "diff",
+                "-u",
+                str(original_paths.pixi_toml_file),
+                str(working_directory_paths.processed_generated_pixi_toml),
+            ]
+            diff_result = subprocess.run(cmd, capture_output=True, text=True)
+
             message = dedent("""\
             Mismatch detected between existing and new pixi.toml content.
 
-            New pixi.toml content:
-            {pixi_toml_content}
+            Diff command:
+            {diff_command}
+
+            Diff output:
+            {diff_output}
 
             Run 'python scripts/generate-pixi-toml.py' to regenerate it.
             After updating `pixi.toml`, it's suggested to run the following commands:
@@ -200,7 +214,7 @@ def main():
 
             ERROR: pixi.toml is not consistent with environment files.
             See above for details.
-            """).format(pixi_toml_content=pixi_toml_content)
+            """).format(diff_command=shlex.join(cmd), diff_output=diff_result.stdout)
             print(message)  # noqa: T201
             sys.exit(1)
 
@@ -245,14 +259,16 @@ def initialize_working_directory(
     pyproject_file = working_path / "pyproject.toml"
     environment_file = working_path / "environment.yml"
     environment_blas_file = working_path / "scripts" / "environment-blas.yml"
-    pixi_toml_file = working_path / "pixi.toml"
+    raw_generated_pixi_toml = working_path / "pixi-raw.toml"
+    processed_generated_pixi_toml = working_path / "pixi-processed.toml"
 
     return WorkingDirectoryPaths(
         working_path=working_path,
         pyproject_file=pyproject_file,
         environment_file=environment_file,
         environment_blas_file=environment_blas_file,
-        pixi_toml_file=pixi_toml_file,
+        raw_generated_pixi_toml=raw_generated_pixi_toml,
+        processed_generated_pixi_toml=processed_generated_pixi_toml,
         gitignore_file=gitignore_file,
     )
 
@@ -263,7 +279,8 @@ def cleanup_working_directory(working_paths: WorkingDirectoryPaths):
     working_paths.environment_file.unlink()
     working_paths.environment_blas_file.unlink()
     working_paths.environment_blas_file.parent.rmdir()
-    working_paths.pixi_toml_file.unlink()
+    working_paths.raw_generated_pixi_toml.unlink()
+    working_paths.processed_generated_pixi_toml.unlink()
     working_paths.gitignore_file.unlink()
     working_paths.working_path.rmdir()