PyLabRobot 0.1.6__tar.gz → 0.2.1__tar.gz

pylabrobot-0.2.1/PKG-INFO

@@ -0,0 +1,266 @@
+Metadata-Version: 2.4
+Name: PyLabRobot
+Version: 0.2.1
+Summary: A hardware agnostic platform for lab automation
+License: MIT
+Project-URL: Homepage, https://github.com/pylabrobot/pylabrobot
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: typing_extensions
+Requires-Dist: websockets
+Provides-Extra: serial
+Requires-Dist: pyserial; extra == "serial"
+Provides-Extra: usb
+Requires-Dist: pyusb; extra == "usb"
+Requires-Dist: libusb-package; extra == "usb"
+Provides-Extra: ftdi
+Requires-Dist: pylibftdi; extra == "ftdi"
+Requires-Dist: pyusb; extra == "ftdi"
+Provides-Extra: hid
+Requires-Dist: hid; extra == "hid"
+Provides-Extra: modbus
+Requires-Dist: pymodbus<3.7.0,>=3.0.0; extra == "modbus"
+Provides-Extra: opentrons
+Requires-Dist: opentrons-http-api-client==0.2.0; extra == "opentrons"
+Provides-Extra: sila
+Requires-Dist: zeroconf>=0.131.0; extra == "sila"
+Requires-Dist: grpcio; extra == "sila"
+Provides-Extra: microscopy
+Requires-Dist: numpy>=1.26; extra == "microscopy"
+Requires-Dist: opencv-python; extra == "microscopy"
+Provides-Extra: pico
+Requires-Dist: PyLabRobot[microscopy,sila]; extra == "pico"
+Provides-Extra: all
+Requires-Dist: PyLabRobot[ftdi,hid,modbus,opentrons,serial,sila,usb,visualizer,websockets]; extra == "all"
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: pytest-timeout; extra == "test"
+Provides-Extra: dev
+Requires-Dist: PyLabRobot[all,test]; extra == "dev"
+Requires-Dist: mypy==1.18.2; extra == "dev"
+Requires-Dist: ruff==0.15.4; extra == "dev"
+Requires-Dist: sphinx-reredirects; extra == "dev"
+Requires-Dist: nbconvert; extra == "dev"
+Requires-Dist: sphinx-sitemap; extra == "dev"
+Requires-Dist: pydata-sphinx-theme; extra == "dev"
+Requires-Dist: myst_nb; extra == "dev"
+Requires-Dist: sphinx_copybutton; extra == "dev"
+Dynamic: license-file
+
+<div style="text-align: center" align="center">
+<img width="400" src=".github/img/logo.png" />
+</div>
+
+<div style="text-align: center" align="center">
+<a href="https://docs.pylabrobot.org"><strong>Docs</strong></a> |
+<a href="https://discuss.pylabrobot.org"><strong>Forum</strong></a> |
+<a href="https://docs.pylabrobot.org/user_guide/_getting-started/installation.html"><strong>Installation</strong></a> |
+<a href="https://docs.pylabrobot.org/basic.html"><strong>Getting started</strong></a>
+</div>
+
+## What is PyLabRobot?
+
+PyLabRobot is a hardware agnostic, pure Python library for liquid handling robots, plate readers, pumps, scales, heater shakers, and other lab automation equipment. Read [the paper](<https://www.cell.com/device/fulltext/S2666-9986(23)00170-9>) in Device.
+
+Advantages over proprietary software:
+
+- **Cross-platform**: PyLabRobot works on Windows, macOS, and Linux. Many other interfaces are Windows-only.
+- **Universal**: PyLabRobot works with any supported liquid handling robot, plate reader, pump, scale, heater shaker, etc. through a single interface.
+- **Fast iteration**: PyLabRobot enables rapid development of protocols using atomic commands run interactively in Jupyter notebooks or the Python REPL. This decreases iteration time from minutes to seconds.
+- **Open-source**: PyLabRobot is open-source and free to use.
+- **Control**: With Python, you have ultimate flexibility to control your lab automation equipment. You can write Turing-complete protocols that include feedback loops.
+- **Modern**: PyLabRobot is built on modern Python 3.9+ features and async/await syntax.
+- **Fast support**: PyLabRobot has [an active community forum](https://discuss.pylabrobot.org) for support and discussion, and most pull requests are merged within a day.
+
+### Liquid handling robots ([docs](https://docs.pylabrobot.org/user_guide/00_liquid-handling/_liquid-handling.html))
+
+PyLabRobot enables the use of any liquid handling robot through a single universal interface, that works on any modern operating system (Windows, macOS, Linux). We currently support Hamilton STAR, Hamilton Vantage, Tecan Freedom EVO, and Opentrons OT-2 robots, but we will soon support many more.
+
+Here's a quick example showing how to move 100uL of liquid from well A1 to A2 using firmware on **Hamilton STAR** (this will work on any operating system!):
+
+```python
+from pylabrobot.liquid_handling import LiquidHandler
+from pylabrobot.liquid_handling.backends import STARBackend
+from pylabrobot.resources import Deck
+
+deck = Deck.load_from_json_file("hamilton-layout.json")
+lh = LiquidHandler(backend=STARBackend(), deck=deck)
+await lh.setup()
+
+await lh.pick_up_tips(lh.deck.get_resource("tip_rack")["A1"])
+await lh.aspirate(lh.deck.get_resource("plate")["A1"], vols=100)
+await lh.dispense(lh.deck.get_resource("plate")["A2"], vols=100)
+await lh.return_tips()
+```
+
+To run the same protocol on an **Opentrons**, use the following:
+
+```python
+from pylabrobot.liquid_handling.backends import OpentronsOT2Backend
+deck = Deck.load_from_json_file("opentrons-layout.json")
+lh = LiquidHandler(backend=OpentronsOT2Backend(host="x.x.x.x"), deck=deck)
+```
+
+Or **Tecan** (also works on any operating system!):
+
+```python
+from pylabrobot.liquid_handling.backends import EVOBackend
+deck = Deck.load_from_json_file("tecan-layout.json")
+lh = LiquidHandler(backend=EVOBackend(), deck=deck)
+```
+
+We also provide a browser-based Visualizer which can visualize the state of the deck during a run, and can be used to develop and test protocols without a physical robot.
+
+![Visualizer](.github/img/visualizer.png)
+
+### Plate readers ([docs](https://docs.pylabrobot.org/user_guide/02_analytical/plate-reading/plate-reading.html))
+
+Moving a plate to a ClarioStar using a liquid handler, and reading luminescence:
+
+```python
+from pylabrobot.plate_reading import PlateReader, CLARIOstarBackend
+
+pr = PlateReader(name="plate reader", backend=CLARIOstarBackend(), size_x=1, size_y=1, size_z=1)
+await pr.setup()
+
+# Use in combination with a liquid handler
+lh.assign_child_resource(pr, location=Coordinate(x, y, z))
+lh.move_plate(lh.deck.get_resource("plate"), pr)
+
+data = await pr.read_luminescence()
+```
+
+For Cytation5, use the `Cytation5` backend.
+
+### Centrifuges ([docs](https://docs.pylabrobot.org/user_guide/01_material-handling/centrifuge/_centrifuge.html))
+
+Centrifugation at 800g for 60 seconds:
+
+```python
+from pylabrobot.centrifuge import Centrifuge, VSpin
+cf = Centrifuge(backend=VSpin(bucket_1_position=0), name="centrifuge", size_x=1, size_y=1, size_z=1)
+await cf.setup()
+
+await cf.start_spin_cycle(g = 800, duration = 60)
+```
+
+### Pumps ([docs](https://docs.pylabrobot.org/user_guide/00_liquid-handling/pumps/_pumps.html))
+
+Pumping at 100 rpm for 30 seconds using a Masterflex pump:
+
+```python
+from pylabrobot.pumps import Pump
+from pylabrobot.pumps.cole_parmer.masterflex import Masterflex
+
+p = Pump(backend=Masterflex())
+await p.setup()
+await p.run_for_duration(speed=100, duration=30)
+```
+
+### Scales ([docs](https://docs.pylabrobot.org/user_guide/02_analytical/scales.html))
+
+Taking a measurement from a Mettler Toledo scale:
+
+```python
+from pylabrobot.scales import Scale
+from pylabrobot.scales.mettler_toledo import MettlerToledoWXS205SDU
+
+backend = MettlerToledoWXS205SDU(port="/dev/cu.usbserial-110")
+scale = Scale(backend=backend, size_x=0, size_y=0, size_z=0)
+await scale.setup()
+
+weight = await scale.get_weight()
+```
+
+### Heater shakers ([docs](https://docs.pylabrobot.org/user_guide/01_material-handling/heating-shaking.html))
+
+Setting the temperature of a heater shaker to 37&deg;C:
+
+```python
+from pylabrobot.heating_shaking import HeaterShaker, InhecoThermoShakeBackend
+
+backend = InhecoThermoShakeBackend()
+hs = HeaterShaker(backend=backend, name="HeaterShaker", size_x=0, size_y=0, size_z=0)
+await hs.setup()
+await hs.set_temperature(37)
+```
+
+### Fans ([docs](https://docs.pylabrobot.org/user_guide/01_material-handling/fans/fans.html))
+
+Running a fan at 100% intensity for one minute:
+
+```python
+from pylabrobot.only_fans import Fan
+from pylabrobot.only_fans import HamiltonHepaFanBackend
+
+fan = Fan(backend=HamiltonHepaFanBackend(), name="my fan")
+await fan.setup()
+await fan.turn_on(intensity=100, duration=60)
+```
+
+### Thermocyclers ([docs](https://docs.pylabrobot.org/user_guide/01_material-handling/thermocycling/thermocycling.html))
+
+Running a thermocycler with a simple protocol:
+
+```python
+await tc.run_pcr_profile(
+  denaturation_temp=98.0,
+  denaturation_time=10.0,
+  annealing_temp=55.0,
+  annealing_time=30.0,
+  extension_temp=72.0,
+  extension_time=60.0,
+  num_cycles=2,
+  block_max_volume=25.0,
+  lid_temperature=105.0,
+  pre_denaturation_temp=95.0,
+  pre_denaturation_time=180.0,
+  final_extension_temp=72.0,
+  final_extension_time=300.0,
+  storage_temp=4.0,
+  storage_time=600.0,
+)
+```
+
+## Resources
+
+### Documentation
+
+[docs.pylabrobot.org](https://docs.pylabrobot.org)
+
+- [Installation](https://docs.pylabrobot.org/user_guide/_getting-started/installation.html)
+- [Getting Started](https://docs.pylabrobot.org/user_guide/index.html)
+- [Contributing](https://docs.pylabrobot.org/contributor_guide/index.html)
+- [API Reference](https://docs.pylabrobot.org/api/pylabrobot.html)
+
+### Support
+
+- [discuss.pylabrobot.org](https://discuss.pylabrobot.org) for questions and discussions.
+- [GitHub Issues](https://github.com/pylabrobot/pylabrobot/issues) for bug reports and feature requests.
+
+## Citing
+
+If you use PyLabRobot in your research, please cite the following:
+
+```bibtex
+@article{WIERENGA2023100111,
+  title = {PyLabRobot: An open-source, hardware-agnostic interface for liquid-handling robots and accessories},
+  journal = {Device},
+  volume = {1},
+  number = {4},
+  pages = {100111},
+  year = {2023},
+  issn = {2666-9986},
+  doi = {https://doi.org/10.1016/j.device.2023.100111},
+  url = {https://www.sciencedirect.com/science/article/pii/S2666998623001709},
+  author = {Rick P. Wierenga and Stefan M. Golas and Wilson Ho and Connor W. Coley and Kevin M. Esvelt},
+  keywords = {laboratory automation, open source, standardization, liquid-handling robots},
+}
+```
+
+---
+
+**Disclaimer:** PyLabRobot is not officially endorsed or supported by any robot manufacturer. If you use a firmware driver such as the STAR driver provided here, you do so at your own risk. Usage of a firmware driver such as STAR may invalidate your warranty. Please contact us with any questions.
+
+_Developed for the Sculpting Evolution Group at the MIT Media Lab_

pylabrobot-0.2.1/PyLabRobot.egg-info/PKG-INFO

@@ -0,0 +1,266 @@
+Metadata-Version: 2.4
+Name: PyLabRobot
+Version: 0.2.1
+Summary: A hardware agnostic platform for lab automation
+License: MIT
+Project-URL: Homepage, https://github.com/pylabrobot/pylabrobot
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: typing_extensions
+Requires-Dist: websockets
+Provides-Extra: serial
+Requires-Dist: pyserial; extra == "serial"
+Provides-Extra: usb
+Requires-Dist: pyusb; extra == "usb"
+Requires-Dist: libusb-package; extra == "usb"
+Provides-Extra: ftdi
+Requires-Dist: pylibftdi; extra == "ftdi"
+Requires-Dist: pyusb; extra == "ftdi"
+Provides-Extra: hid
+Requires-Dist: hid; extra == "hid"
+Provides-Extra: modbus
+Requires-Dist: pymodbus<3.7.0,>=3.0.0; extra == "modbus"
+Provides-Extra: opentrons
+Requires-Dist: opentrons-http-api-client==0.2.0; extra == "opentrons"
+Provides-Extra: sila
+Requires-Dist: zeroconf>=0.131.0; extra == "sila"
+Requires-Dist: grpcio; extra == "sila"
+Provides-Extra: microscopy
+Requires-Dist: numpy>=1.26; extra == "microscopy"
+Requires-Dist: opencv-python; extra == "microscopy"
+Provides-Extra: pico
+Requires-Dist: PyLabRobot[microscopy,sila]; extra == "pico"
+Provides-Extra: all
+Requires-Dist: PyLabRobot[ftdi,hid,modbus,opentrons,serial,sila,usb,visualizer,websockets]; extra == "all"
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: pytest-timeout; extra == "test"
+Provides-Extra: dev
+Requires-Dist: PyLabRobot[all,test]; extra == "dev"
+Requires-Dist: mypy==1.18.2; extra == "dev"
+Requires-Dist: ruff==0.15.4; extra == "dev"
+Requires-Dist: sphinx-reredirects; extra == "dev"
+Requires-Dist: nbconvert; extra == "dev"
+Requires-Dist: sphinx-sitemap; extra == "dev"
+Requires-Dist: pydata-sphinx-theme; extra == "dev"
+Requires-Dist: myst_nb; extra == "dev"
+Requires-Dist: sphinx_copybutton; extra == "dev"
+Dynamic: license-file
+
+<div style="text-align: center" align="center">
+<img width="400" src=".github/img/logo.png" />
+</div>
+
+<div style="text-align: center" align="center">
+<a href="https://docs.pylabrobot.org"><strong>Docs</strong></a> |
+<a href="https://discuss.pylabrobot.org"><strong>Forum</strong></a> |
+<a href="https://docs.pylabrobot.org/user_guide/_getting-started/installation.html"><strong>Installation</strong></a> |
+<a href="https://docs.pylabrobot.org/basic.html"><strong>Getting started</strong></a>
+</div>
+
+## What is PyLabRobot?
+
+PyLabRobot is a hardware agnostic, pure Python library for liquid handling robots, plate readers, pumps, scales, heater shakers, and other lab automation equipment. Read [the paper](<https://www.cell.com/device/fulltext/S2666-9986(23)00170-9>) in Device.
+
+Advantages over proprietary software:
+
+- **Cross-platform**: PyLabRobot works on Windows, macOS, and Linux. Many other interfaces are Windows-only.
+- **Universal**: PyLabRobot works with any supported liquid handling robot, plate reader, pump, scale, heater shaker, etc. through a single interface.
+- **Fast iteration**: PyLabRobot enables rapid development of protocols using atomic commands run interactively in Jupyter notebooks or the Python REPL. This decreases iteration time from minutes to seconds.
+- **Open-source**: PyLabRobot is open-source and free to use.
+- **Control**: With Python, you have ultimate flexibility to control your lab automation equipment. You can write Turing-complete protocols that include feedback loops.
+- **Modern**: PyLabRobot is built on modern Python 3.9+ features and async/await syntax.
+- **Fast support**: PyLabRobot has [an active community forum](https://discuss.pylabrobot.org) for support and discussion, and most pull requests are merged within a day.
+
+### Liquid handling robots ([docs](https://docs.pylabrobot.org/user_guide/00_liquid-handling/_liquid-handling.html))
+
+PyLabRobot enables the use of any liquid handling robot through a single universal interface, that works on any modern operating system (Windows, macOS, Linux). We currently support Hamilton STAR, Hamilton Vantage, Tecan Freedom EVO, and Opentrons OT-2 robots, but we will soon support many more.
+
+Here's a quick example showing how to move 100uL of liquid from well A1 to A2 using firmware on **Hamilton STAR** (this will work on any operating system!):
+
+```python
+from pylabrobot.liquid_handling import LiquidHandler
+from pylabrobot.liquid_handling.backends import STARBackend
+from pylabrobot.resources import Deck
+
+deck = Deck.load_from_json_file("hamilton-layout.json")
+lh = LiquidHandler(backend=STARBackend(), deck=deck)
+await lh.setup()
+
+await lh.pick_up_tips(lh.deck.get_resource("tip_rack")["A1"])
+await lh.aspirate(lh.deck.get_resource("plate")["A1"], vols=100)
+await lh.dispense(lh.deck.get_resource("plate")["A2"], vols=100)
+await lh.return_tips()
+```
+
+To run the same protocol on an **Opentrons**, use the following:
+
+```python
+from pylabrobot.liquid_handling.backends import OpentronsOT2Backend
+deck = Deck.load_from_json_file("opentrons-layout.json")
+lh = LiquidHandler(backend=OpentronsOT2Backend(host="x.x.x.x"), deck=deck)
+```
+
+Or **Tecan** (also works on any operating system!):
+
+```python
+from pylabrobot.liquid_handling.backends import EVOBackend
+deck = Deck.load_from_json_file("tecan-layout.json")
+lh = LiquidHandler(backend=EVOBackend(), deck=deck)
+```
+
+We also provide a browser-based Visualizer which can visualize the state of the deck during a run, and can be used to develop and test protocols without a physical robot.
+
+![Visualizer](.github/img/visualizer.png)
+
+### Plate readers ([docs](https://docs.pylabrobot.org/user_guide/02_analytical/plate-reading/plate-reading.html))
+
+Moving a plate to a ClarioStar using a liquid handler, and reading luminescence:
+
+```python
+from pylabrobot.plate_reading import PlateReader, CLARIOstarBackend
+
+pr = PlateReader(name="plate reader", backend=CLARIOstarBackend(), size_x=1, size_y=1, size_z=1)
+await pr.setup()
+
+# Use in combination with a liquid handler
+lh.assign_child_resource(pr, location=Coordinate(x, y, z))
+lh.move_plate(lh.deck.get_resource("plate"), pr)
+
+data = await pr.read_luminescence()
+```
+
+For Cytation5, use the `Cytation5` backend.
+
+### Centrifuges ([docs](https://docs.pylabrobot.org/user_guide/01_material-handling/centrifuge/_centrifuge.html))
+
+Centrifugation at 800g for 60 seconds:
+
+```python
+from pylabrobot.centrifuge import Centrifuge, VSpin
+cf = Centrifuge(backend=VSpin(bucket_1_position=0), name="centrifuge", size_x=1, size_y=1, size_z=1)
+await cf.setup()
+
+await cf.start_spin_cycle(g = 800, duration = 60)
+```
+
+### Pumps ([docs](https://docs.pylabrobot.org/user_guide/00_liquid-handling/pumps/_pumps.html))
+
+Pumping at 100 rpm for 30 seconds using a Masterflex pump:
+
+```python
+from pylabrobot.pumps import Pump
+from pylabrobot.pumps.cole_parmer.masterflex import Masterflex
+
+p = Pump(backend=Masterflex())
+await p.setup()
+await p.run_for_duration(speed=100, duration=30)
+```
+
+### Scales ([docs](https://docs.pylabrobot.org/user_guide/02_analytical/scales.html))
+
+Taking a measurement from a Mettler Toledo scale:
+
+```python
+from pylabrobot.scales import Scale
+from pylabrobot.scales.mettler_toledo import MettlerToledoWXS205SDU
+
+backend = MettlerToledoWXS205SDU(port="/dev/cu.usbserial-110")
+scale = Scale(backend=backend, size_x=0, size_y=0, size_z=0)
+await scale.setup()
+
+weight = await scale.get_weight()
+```
+
+### Heater shakers ([docs](https://docs.pylabrobot.org/user_guide/01_material-handling/heating-shaking.html))
+
+Setting the temperature of a heater shaker to 37&deg;C:
+
+```python
+from pylabrobot.heating_shaking import HeaterShaker, InhecoThermoShakeBackend
+
+backend = InhecoThermoShakeBackend()
+hs = HeaterShaker(backend=backend, name="HeaterShaker", size_x=0, size_y=0, size_z=0)
+await hs.setup()
+await hs.set_temperature(37)
+```
+
+### Fans ([docs](https://docs.pylabrobot.org/user_guide/01_material-handling/fans/fans.html))
+
+Running a fan at 100% intensity for one minute:
+
+```python
+from pylabrobot.only_fans import Fan
+from pylabrobot.only_fans import HamiltonHepaFanBackend
+
+fan = Fan(backend=HamiltonHepaFanBackend(), name="my fan")
+await fan.setup()
+await fan.turn_on(intensity=100, duration=60)
+```
+
+### Thermocyclers ([docs](https://docs.pylabrobot.org/user_guide/01_material-handling/thermocycling/thermocycling.html))
+
+Running a thermocycler with a simple protocol:
+
+```python
+await tc.run_pcr_profile(
+  denaturation_temp=98.0,
+  denaturation_time=10.0,
+  annealing_temp=55.0,
+  annealing_time=30.0,
+  extension_temp=72.0,
+  extension_time=60.0,
+  num_cycles=2,
+  block_max_volume=25.0,
+  lid_temperature=105.0,
+  pre_denaturation_temp=95.0,
+  pre_denaturation_time=180.0,
+  final_extension_temp=72.0,
+  final_extension_time=300.0,
+  storage_temp=4.0,
+  storage_time=600.0,
+)
+```
+
+## Resources
+
+### Documentation
+
+[docs.pylabrobot.org](https://docs.pylabrobot.org)
+
+- [Installation](https://docs.pylabrobot.org/user_guide/_getting-started/installation.html)
+- [Getting Started](https://docs.pylabrobot.org/user_guide/index.html)
+- [Contributing](https://docs.pylabrobot.org/contributor_guide/index.html)
+- [API Reference](https://docs.pylabrobot.org/api/pylabrobot.html)
+
+### Support
+
+- [discuss.pylabrobot.org](https://discuss.pylabrobot.org) for questions and discussions.
+- [GitHub Issues](https://github.com/pylabrobot/pylabrobot/issues) for bug reports and feature requests.
+
+## Citing
+
+If you use PyLabRobot in your research, please cite the following:
+
+```bibtex
+@article{WIERENGA2023100111,
+  title = {PyLabRobot: An open-source, hardware-agnostic interface for liquid-handling robots and accessories},
+  journal = {Device},
+  volume = {1},
+  number = {4},
+  pages = {100111},
+  year = {2023},
+  issn = {2666-9986},
+  doi = {https://doi.org/10.1016/j.device.2023.100111},
+  url = {https://www.sciencedirect.com/science/article/pii/S2666998623001709},
+  author = {Rick P. Wierenga and Stefan M. Golas and Wilson Ho and Connor W. Coley and Kevin M. Esvelt},
+  keywords = {laboratory automation, open source, standardization, liquid-handling robots},
+}
+```
+
+---
+
+**Disclaimer:** PyLabRobot is not officially endorsed or supported by any robot manufacturer. If you use a firmware driver such as the STAR driver provided here, you do so at your own risk. Usage of a firmware driver such as STAR may invalidate your warranty. Please contact us with any questions.
+
+_Developed for the Sculpting Evolution Group at the MIT Media Lab_