From 86b8022817ea7581a9de605b3211be34525efd34 Mon Sep 17 00:00:00 2001
From: Tobias Fehlmann <tobias.fehlmann@gmail.com>
Date: Thu, 29 Jan 2026 20:15:53 -0800
Subject: [PATCH 1/2] Migrate packaging from setup.py to pyproject.toml (PEP
 621) and add pixi configuration
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Replace the imperative setup.py with declarative PEP 621 metadata in
pyproject.toml. All dependencies, optional extras, entry points, and
package data are preserved identically — verified via wheel content
diff against the previous setup.py build.

Add pixi configuration for automatic binary dependency management
(libusb, libftdi, libhidapi) via conda-forge, with tasks mirroring
the Makefile (test, lint, format, typecheck). Users who do not use
pixi are unaffected; pip install continues to work as before.
---
 pixi.lock      | 3871 ++++++++++++++++++++++++++++++++++++++++++++++++
 pyproject.toml |  105 ++
 setup.py       |   90 --
 3 files changed, 3976 insertions(+), 90 deletions(-)
 create mode 100644 pixi.lock
 delete mode 100644 setup.py

diff --git a/pixi.lock b/pixi.lock
new file mode 100644
index 00000000000..c589add187d
--- /dev/null
+++ b/pixi.lock
@@ -0,0 +1,3871 @@
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+- pypi: https://files.pythonhosted.org/packages/f4/24/2a3e3df732393fed8b3ebf2ec078f05546de641fe1b667ee316ec1dcf3b7/webencodings-0.5.1-py2.py3-none-any.whl
+  name: webencodings
+  version: 0.5.1
+  sha256: a0af1213f3c2226497a97e2b3aa01a7e4bee4f403f95be16fc9acd2947514a78
+- pypi: https://files.pythonhosted.org/packages/fa/a8/5b41e0da817d64113292ab1f8247140aac61cbf6cfd085d6a0fa77f4984f/websockets-15.0.1-py3-none-any.whl
+  name: websockets
+  version: 15.0.1
+  sha256: f7a866fbc1e97b5c617ee4116daaa09b722101d4a3c170c787450ba409f9736f
+  requires_python: '>=3.9'
+- pypi: https://files.pythonhosted.org/packages/ad/e4/8d97cca767bcc1be76d16fb76951608305561c6e056811587f36cb1316a8/werkzeug-3.1.5-py3-none-any.whl
+  name: werkzeug
+  version: 3.1.5
+  sha256: 5111e36e91086ece91f93268bb39b4a35c1e6f1feac762c9c822ded0a4e322dc
+  requires_dist:
+  - markupsafe>=2.1.1
+  - watchdog>=2.3 ; extra == 'watchdog'
+  requires_python: '>=3.9'
+- pypi: https://files.pythonhosted.org/packages/2e/54/647ade08bf0db230bfea292f893923872fd20be6ac6f53b2b936ba839d75/zipp-3.23.0-py3-none-any.whl
+  name: zipp
+  version: 3.23.0
+  sha256: 071652d6115ed432f5ce1d34c336c0adfd6a884660d1e9712a256d3d3bd4b14e
+  requires_dist:
+  - pytest>=6,!=8.1.* ; extra == 'test'
+  - jaraco-itertools ; extra == 'test'
+  - jaraco-functools ; extra == 'test'
+  - more-itertools ; extra == 'test'
+  - big-o ; extra == 'test'
+  - pytest-ignore-flaky ; extra == 'test'
+  - jaraco-test ; extra == 'test'
+  - sphinx>=3.5 ; extra == 'doc'
+  - jaraco-packaging>=9.3 ; extra == 'doc'
+  - rst-linker>=1.9 ; extra == 'doc'
+  - furo ; extra == 'doc'
+  - sphinx-lint ; extra == 'doc'
+  - jaraco-tidelift>=1.4 ; extra == 'doc'
+  - pytest-checkdocs>=2.4 ; extra == 'check'
+  - pytest-ruff>=0.2.1 ; sys_platform != 'cygwin' and extra == 'check'
+  - pytest-cov ; extra == 'cover'
+  - pytest-enabler>=2.2 ; extra == 'enabler'
+  - pytest-mypy ; extra == 'type'
+  requires_python: '>=3.9'
+- conda: https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.7-hb78ec9c_6.conda
+  sha256: 68f0206ca6e98fea941e5717cec780ed2873ffabc0e1ed34428c061e2c6268c7
+  md5: 4a13eeac0b5c8e5b8ab496e6c4ddd829
+  depends:
+  - __glibc >=2.17,<3.0.a0
+  - libzlib >=1.3.1,<2.0a0
+  license: BSD-3-Clause
+  license_family: BSD
+  purls: []
+  size: 601375
+  timestamp: 1764777111296
+- conda: https://conda.anaconda.org/conda-forge/osx-64/zstd-1.5.7-h3eecb57_6.conda
+  sha256: 47101a4055a70a4876ffc87b750ab2287b67eca793f21c8224be5e1ee6394d3f
+  md5: 727109b184d680772e3122f40136d5ca
+  depends:
+  - __osx >=10.13
+  - libzlib >=1.3.1,<2.0a0
+  license: BSD-3-Clause
+  license_family: BSD
+  purls: []
+  size: 528148
+  timestamp: 1764777156963
+- conda: https://conda.anaconda.org/conda-forge/osx-arm64/zstd-1.5.7-hbf9d68e_6.conda
+  sha256: 9485ba49e8f47d2b597dd399e88f4802e100851b27c21d7525625b0b4025a5d9
+  md5: ab136e4c34e97f34fb621d2592a393d8
+  depends:
+  - __osx >=11.0
+  - libzlib >=1.3.1,<2.0a0
+  license: BSD-3-Clause
+  license_family: BSD
+  purls: []
+  size: 433413
+  timestamp: 1764777166076
+- conda: https://conda.anaconda.org/conda-forge/win-64/zstd-1.5.7-h534d264_6.conda
+  sha256: 368d8628424966fd8f9c8018326a9c779e06913dd39e646cf331226acc90e5b2
+  md5: 053b84beec00b71ea8ff7a4f84b55207
+  depends:
+  - vc >=14.3,<15
+  - vc14_runtime >=14.44.35208
+  - ucrt >=10.0.20348.0
+  - libzlib >=1.3.1,<2.0a0
+  license: BSD-3-Clause
+  license_family: BSD
+  purls: []
+  size: 388453
+  timestamp: 1764777142545
diff --git a/pyproject.toml b/pyproject.toml
index f79b16ac5a2..1a444938617 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,3 +1,59 @@
+[build-system]
+requires = ["setuptools>=68.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "PyLabRobot"
+description = "A hardware agnostic platform for lab automation"
+readme = "README.md"
+requires-python = ">=3.9"
+license = {text = "MIT"}
+dynamic = ["version"]
+dependencies = ["typing_extensions==4.15.0"]
+
+[project.optional-dependencies]
+fw = ["pyserial==3.5", "pyusb==1.3.1", "libusb-package==1.0.26.1"]
+http = ["requests==2.32.5", "types-requests==2.32.4.20250913"]
+plate_reading = ["pylibftdi==0.23.0"]
+websockets = ["websockets==15.0.1"]
+visualizer = ["websockets==15.0.1"]
+opentrons = ["opentrons-http-api-client"]
+server = ["flask[async]==3.1.2"]
+inheco = ["hid==1.0.8"]
+agrow = ["pymodbus==3.6.8"]
+dev = [
+  "PyLabRobot[fw,http,plate_reading,websockets,visualizer,opentrons,server,inheco,agrow]",
+  "pytest==8.4.2",
+  "pytest-timeout==2.4.0",
+  "mypy==1.18.2",
+  "responses==0.25.8",
+  "sphinx-reredirects==0.1.6",
+  "ruff==0.2.1",
+  "nbconvert==7.16.6",
+  "sphinx-sitemap==2.8.0",
+  "pydata-sphinx-theme==0.16.1",
+  "myst_nb==1.3.0",
+  "sphinx_copybutton==0.5.2",
+]
+all = ["PyLabRobot[dev]"]
+
+[project.scripts]
+lh-server = "pylabrobot.server.liquid_handling_server:main"
+plr-gui = "pylabrobot.gui.gui:main"
+
+[project.urls]
+Homepage = "https://github.com/pylabrobot/pylabrobot"
+
+[tool.setuptools.dynamic]
+version = {file = "pylabrobot/version.txt"}
+
+[tool.setuptools.packages.find]
+namespaces = false
+exclude = ["tools*", "docs*"]
+
+[tool.setuptools.package-data]
+pylabrobot = ["visualizer/*", "version.txt"]
+
 [tool.ruff]
 line-length = 100
 indent-width = 2
@@ -5,3 +61,52 @@ indent-width = 2
 [tool.ruff.lint.per-file-ignores]
 "__init__.py" = ["F401", "F403"]
 
+[tool.pixi.workspace]
+channels = ["conda-forge"]
+platforms = ["linux-64", "osx-arm64", "osx-64", "win-64"]
+
+[tool.pixi.dependencies]
+python = ">=3.9"
+
+[tool.pixi.pypi-dependencies]
+pylabrobot = { path = ".", editable = true }
+
+[tool.pixi.feature.fw.dependencies]
+libusb = "*"
+
+[tool.pixi.feature.fw.pypi-dependencies]
+pylabrobot = { path = ".", editable = true, extras = ["fw"] }
+
+[tool.pixi.feature.plate-reading.dependencies]
+libftdi = "*"
+
+[tool.pixi.feature.plate-reading.pypi-dependencies]
+pylabrobot = { path = ".", editable = true, extras = ["plate_reading"] }
+
+[tool.pixi.feature.inheco.dependencies]
+libhidapi = "*"
+
+[tool.pixi.feature.inheco.pypi-dependencies]
+pylabrobot = { path = ".", editable = true, extras = ["inheco"] }
+
+[tool.pixi.feature.dev.dependencies]
+libusb = "*"
+libftdi = "*"
+libhidapi = "*"
+
+[tool.pixi.feature.dev.pypi-dependencies]
+pylabrobot = { path = ".", editable = true, extras = ["dev"] }
+
+[tool.pixi.tasks]
+test = "python -m pytest -s -v"
+lint = "python -m ruff check pylabrobot"
+format = { cmd = "python -m ruff format pylabrobot && python -m ruff check --fix pylabrobot --select I" }
+format-check = { cmd = "python -m ruff format --check pylabrobot && python -m ruff check pylabrobot --select I" }
+typecheck = "python -m mypy pylabrobot --check-untyped-defs"
+
+[tool.pixi.environments]
+default = { solve-group = "default" }
+fw = { features = ["fw"], solve-group = "fw" }
+plate-reading = { features = ["plate-reading"], solve-group = "plate-reading" }
+inheco = { features = ["inheco"], solve-group = "inheco" }
+dev = { features = ["dev"], solve-group = "dev" }
diff --git a/setup.py b/setup.py
deleted file mode 100644
index 8fcf9c22876..00000000000
--- a/setup.py
+++ /dev/null
@@ -1,90 +0,0 @@
-from setuptools import find_packages, setup
-
-with open("pylabrobot/version.txt", "r", encoding="utf-8") as f:
-  __version__ = f.read().strip()
-
-with open("README.md", "r", encoding="utf-8") as f:
-  long_description = f.read()
-
-
-extras_fw = ["pyserial==3.5", "pyusb==1.3.1", "libusb-package==1.0.26.1"]
-
-extras_http = ["requests==2.32.5", "types-requests==2.32.4.20250913"]
-
-extras_plate_reading = [
-  "pylibftdi==0.23.0",
-]
-
-extras_websockets = ["websockets==15.0.1"]
-
-extras_visualizer = extras_websockets
-
-extras_opentrons = ["opentrons-http-api-client"]
-
-extras_server = [
-  "flask[async]==3.1.2",
-]
-
-
-extras_inheco = ["hid==1.0.8"]
-
-extras_agrow = ["pymodbus==3.6.8"]
-
-extras_dev = (
-  extras_fw
-  + extras_http
-  + extras_plate_reading
-  + extras_websockets
-  + extras_visualizer
-  + extras_opentrons
-  + extras_server
-  + extras_inheco
-  + extras_agrow
-  + [
-    "pydata-sphinx-theme==0.16.1",
-    "myst_nb==1.3.0",
-    "sphinx_copybutton==0.5.2",
-    "pytest==8.4.2",
-    "pytest-timeout==2.4.0",
-    "mypy==1.18.2",
-    "responses==0.25.8",
-    "sphinx-reredirects==0.1.6",
-    "ruff==0.2.1",
-    "nbconvert==7.16.6",
-    "sphinx-sitemap==2.8.0",
-  ]
-)
-
-# Some extras are not available on all platforms. `dev` should be available everywhere
-extras_all = extras_dev
-
-setup(
-  name="PyLabRobot",
-  version=__version__,
-  packages=find_packages(exclude="tools"),
-  description="A hardware agnostic platform for lab automation",
-  long_description=long_description,
-  long_description_content_type="text/markdown",
-  install_requires=["typing_extensions==4.15.0"],
-  url="https://github.com/pylabrobot/pylabrobot.git",
-  package_data={"pylabrobot": ["visualizer/*", "version.txt"]},
-  extras_require={
-    "fw": extras_fw,
-    "http": extras_http,
-    "plate_reading": extras_plate_reading,
-    "websockets": extras_websockets,
-    "visualizer": extras_visualizer,
-    "inheco": extras_inheco,
-    "opentrons": extras_opentrons,
-    "server": extras_server,
-    "agrow": extras_agrow,
-    "dev": extras_dev,
-    "all": extras_all,
-  },
-  entry_points={
-    "console_scripts": [
-      "lh-server=pylabrobot.server.liquid_handling_server:main",
-      "plr-gui=pylabrobot.gui.gui:main",
-    ],
-  },
-)

From 6e2393c1898da5d2b60192831bd5b48112b35006 Mon Sep 17 00:00:00 2001
From: Tobias Fehlmann <tobias.fehlmann@gmail.com>
Date: Thu, 29 Jan 2026 20:21:27 -0800
Subject: [PATCH 2/2] Remove pixi.lock from version control

---
 pixi.lock | 3871 -----------------------------------------------------
 1 file changed, 3871 deletions(-)
 delete mode 100644 pixi.lock

diff --git a/pixi.lock b/pixi.lock
deleted file mode 100644
index c589add187d..00000000000
--- a/pixi.lock
+++ /dev/null
@@ -1,3871 +0,0 @@
-version: 6
-environments:
-  default:
-    channels:
-    - url: https://conda.anaconda.org/conda-forge/
-    indexes:
-    - https://pypi.org/simple
-    options:
-      pypi-prerelease-mode: if-necessary-or-explicit
-    packages:
-      linux-64:
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_8.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.1.4-hbd8a1cb_0.conda
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-      - conda: https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.45-default_hbd61a6d_105.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.7.3-hecca717_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/libffi-3.5.2-h3435931_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.2.0-he0feb66_16.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.2.0-he0feb66_16.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.2-hb03c661_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/libmpdec-4.0.0-hb03c661_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.51.2-hf4e2dac_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-15.2.0-h934c35e_16.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.41.3-h5347b49_0.conda
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-      - conda: https://conda.anaconda.org/conda-forge/linux-64/openssl-3.6.1-h35e630c_1.conda
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-      - pypi: ./
-      osx-64:
-      - conda: https://conda.anaconda.org/conda-forge/osx-64/bzip2-1.0.8-h500dc9f_8.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.1.4-hbd8a1cb_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/osx-64/libexpat-2.7.3-heffb93a_0.conda
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