Name | chemspyd JSON |
Version |
1.0.0
JSON |
| download |
home_page | |
Summary | A Python API for the Chemspeed AutoSuite software. |
upload_time | 2024-02-19 21:06:58 |
maintainer | |
docs_url | None |
author | |
requires_python | >=3.9 |
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We also recommend that a file or class name and description of purpose be included on the same "printed page" as the copyright notice for easier identification within third-party archives. Copyright 2021 Martin Seifrid, Felix Strieth-Kalthoff, Tony Wu, Mohammad Haddadnia, Emre Alca Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. |
keywords |
chemistry
automation
chemspeed
synthesis
self-driving labs
|
VCS |
|
bugtrack_url |
|
requirements |
No requirements were recorded.
|
Travis-CI |
No Travis.
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coveralls test coverage |
No coveralls.
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# Chemspyd
A Python API for the Chemspeed AutoSuite software.
## Installation
#### PyPI
```shell
$ pip install chemspyd
```
#### From source
Clone this repository, navigate to the directory where ```setup.py``` is located, and install the package using pip:
```shell
$ pip install .
```
### Manager app: installation & setup
- Copy ```Manager.app``` to the computer running the Chemspeed AutoSuite software.
- Create a folder on the Chemspeed computer where the commands will be sent.
- Perform necessary adaptations for your system. This can be done automatically or manually.
#### Automatic setup
```python
from chemspyd.autosuite import get_config, clean_config
get_config(
output_json="path/to/elements_config.json", # Choose appropriate location for the config files.
manager_path="path/to/Manager.app",
)
clean_config(
config_path="path/to/elements_config.json",
spe_specs={"default": "SPE_D", "waste": "SPE_W"}, # Only necessary if you have a SPE rack.
inject_specs={"default": "INJECT_I", "load": "INJECT_L"}, # Only necessary if you have an HPLC injection port.
)
```
#### Manual setup
Write the configuration JSON files manually to match your Chemspeed's configuration. Follow the examples in the [```configuration```](https://gitlab.com/aspuru-guzik-group/self-driving-lab/instruments/chemspyd/-/tree/main/configuration) directory for examples of proper syntax and structure.
Further instructions can be found in the [Installation](https://aspuru-guzik-group.gitlab.io/self-driving-lab/instruments/chemspyd/intro/install.html) section of the package documentation.
## Usage
- Execute the manager app on the computer running the Chemspeed AutoSuite software.
- Import the ```chemspyd``` package in your Python script.
- Specify the path to the commands folder using e.g. ```pathlib```.
- Instantiate a ```chemspyd.ChemspeedController``` object with the path to the commands folder as an argument.
- ```simulation``` is a boolean argument that determines whether the commands are sent to the Chemspeed AutoSuite software or not. If it's false, commands will simply be printed to the console.
#### Example
```python
from pathlib import Path
from chemspyd import Controller
# Instantiate controller
target = r"\\Chemspeed_PC\Users\Operator\Commands"
configuration: Path = Path(__file__).parent / "configuration"
elements: Path = configuration / "element_config.json"
sys_liquids: Path = configuration / "system_liquids.json"
statuses: Path = configuration / "statuses.json"
chmspd = Controller(
cmd_folder=target,
element_config=elements,
system_liquids=sys_liquids,
statuses=statuses,
verbosity=2,
simulation=False,
)
# Transfer liquid
chmspd.transfer_liquid("RACKL:1","RACKR:1",5,1)
```
Further examples can be found in the [```demos```](https://gitlab.com/aspuru-guzik-group/self-driving-lab/instruments/chemspyd/-/tree/main/demos) directory.
## Features
Chemspyd provides a Python interface for the Chemspeed AutoSuite software that enables modular, dynamic control of Chemspeed operations. It currently allows for the following operations:
**Basic**
- Liquid transfer
- Solid transfer
- ISYNTH drawer control
- Temperature & atmosphere (ambient, vacuum, inert) control
- Stir
- Vial transport
- Measure level
- Read status
- Unmount
- Wait
**Routines**
- Prime pumps
- Inject to HPLC port
- Carry out Schlenk cycles
- Reflux
- Filter
- Set all ISYNTH drawers at once
**Advanced**
- Automatic configuration upon installation
- Track volume of liquid in wells by addition and removal
- Track amount of solid added to or removed from wells
*NOTE*: These are experimental features, and are not guaranteed to be robust.
### Contributing
We welcome contributions from the community! If there are additional features that you would like to see added, please open an issue or a merge request, and suggest an implementation.
# Acknowledgments
The following people are acknowledged for assisting in the development of Chemspyd and its functionality in various ways:
- Martin Seifrid ([@mseifrid](https://github.com/mseifrid))
- Felix Strieth-Kalthoff ([@felix-s-k](https://github.com/felix-s-k))
- Mohammad Haddadnia ([@mohaddadnia](https://github.com/Mohaddadnia))
- Tony C. Wu ([@verysure](https://github.com/verysure))
- Emre Alca ([@alcaemre](https://github.com/alcaemre))
# Cite this work
```
@article{
Seifrid_2024,
shorttitle={Chemspyd},
title={Chemspyd: An Open-Source Python Interface for Chemspeed Robotic Chemistry and Materials Platforms},
DOI={10.26434/chemrxiv-2024-33sfl},
journal={ChemRxiv},
author={Seifrid, Martin and Strieth-Kalthoff, Felix and Haddadnia, Mohammad and Wu, Tony and Alca, Emre and Bodo, Leticia and Arellano-Rubach, Sebastian and Yoshikawa, Naruki and Skreta, Marta and Keunen, Rachel and Aspuru-Guzik, Al{\'a}n},
year={2024}
}
```
Raw data
{
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"name": "chemspyd",
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"docs_url": null,
"requires_python": ">=3.9",
"maintainer_email": "Martin Seifrid <m.seifrid@utoronto.ca>, Felix Strieth-Kalthoff <f.striethkalthoff@utoronto.ca>, Mohammad Haddadnia <m.nia@mail.utoronto.ca>",
"keywords": "chemistry,automation,chemspeed,synthesis,self-driving labs",
"author": "",
"author_email": "Martin Seifrid <m.seifrid@utoronto.ca>, Felix Strieth-Kalthoff <f.striethkalthoff@utoronto.ca>, Mohammad Haddadnia <m.nia@mail.utoronto.ca>, \"Tony C. Wu\" <tonyc.wu@utoronto.ca>, Emre Alca <emre.alca@mail.utoronto.ca>",
"download_url": "https://files.pythonhosted.org/packages/3e/ed/b8e09d372740f150b27065b3b176209362ee1e0b0f8216924496a057aedb/chemspyd-1.0.0.tar.gz",
"platform": null,
"description": "[//]: # (Get inspiration for badges etc from morfeus, others?)\n[![Testing](https://gitlab.com/aspuru-guzik-group/self-driving-lab/instruments/chemspyd/badges/main/pipeline.svg)](https://gitlab.com/aspuru-guzik-group/self-driving-lab/instruments/chemspyd/-/commits/main)\n[![Coverage](https://gitlab.com/aspuru-guzik-group/self-driving-lab/instruments/chemspyd/badges/main/coverage.svg?job=coverage)](https://gitlab.com/aspuru-guzik-group/self-driving-lab/instruments/chemspyd/-/commits/main)\n<!-- [![Endpoint Badge](https://img.shields.io/endpoint?url=https://gitlab.com/aspuru-guzik-group/self-driving-lab/instruments/chemspyd/-/raw/main/documentation/badge.json)](https://aspuru-guzik-group.gitlab.io/self-driving-lab/instruments/chemspyd/) -->\n\n\n[![GitLab issues open](https://img.shields.io/gitlab/issues/open/aspuru-guzik-group/self-driving-lab/instruments/chemspyd?label=Issues)](https://gitlab.com/aspuru-guzik-group/self-driving-lab/instruments/chemspyd/-/issues)\n[![GitLab issues close](https://img.shields.io/gitlab/issues/closed/aspuru-guzik-group/self-driving-lab/instruments/chemspyd?label=Issues&color=green)](https://gitlab.com/aspuru-guzik-group/self-driving-lab/instruments/chemspyd/-/issues)\n\n\n[![Release](https://gitlab.com/aspuru-guzik-group/self-driving-lab/instruments/chemspyd/-/badges/release.svg)](https://codecov.io/gh/aspuru-guzik-group/self-driving-lab/instruments/chemspyd)\n[![PyPI - Version](https://img.shields.io/pypi/v/chemspyd)](https://pypi.org/project/chemspyd/)\n[![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://gitlab.com/aspuru-guzik-group/self-driving-lab/instruments/chemspyd/-/blob/main/LICENSE)\n[![Python Version](https://img.shields.io/badge/Python-3.9%2B-blue?logo=python&logoColor=white)](https://www.python.org/)\n<!-- [![Code Style: black](https://img.shields.io/badge/Code%20Style-Black-000000.svg)](https://github.com/psf/black) -->\n\n[![DOI](https://img.shields.io/badge/ChemRxiv-10.26434-gold)](https://doi.org/10.26434/chemrxiv-2024-33sfl)\n<!-- [![DOI](https://img.shields.io/badge/DOI-123.4567-blue)](https://doi.org/10.26434/chemrxiv-2024-33sfl) -->\n\n\n# Chemspyd\nA Python API for the Chemspeed AutoSuite software.\n\n## Installation\n\n#### PyPI\n```shell\n$ pip install chemspyd\n```\n\n#### From source\nClone this repository, navigate to the directory where ```setup.py``` is located, and install the package using pip:\n```shell\n$ pip install .\n```\n\n### Manager app: installation & setup\n- Copy ```Manager.app``` to the computer running the Chemspeed AutoSuite software.\n- Create a folder on the Chemspeed computer where the commands will be sent.\n- Perform necessary adaptations for your system. This can be done automatically or manually.\n\n#### Automatic setup\n```python\nfrom chemspyd.autosuite import get_config, clean_config\n\nget_config(\n output_json=\"path/to/elements_config.json\", # Choose appropriate location for the config files.\n manager_path=\"path/to/Manager.app\",\n)\n\nclean_config(\n config_path=\"path/to/elements_config.json\",\n spe_specs={\"default\": \"SPE_D\", \"waste\": \"SPE_W\"}, # Only necessary if you have a SPE rack.\n inject_specs={\"default\": \"INJECT_I\", \"load\": \"INJECT_L\"}, # Only necessary if you have an HPLC injection port.\n)\n```\n\n#### Manual setup\nWrite the configuration JSON files manually to match your Chemspeed's configuration. Follow the examples in the [```configuration```](https://gitlab.com/aspuru-guzik-group/self-driving-lab/instruments/chemspyd/-/tree/main/configuration) directory for examples of proper syntax and structure.\n\n\nFurther instructions can be found in the [Installation](https://aspuru-guzik-group.gitlab.io/self-driving-lab/instruments/chemspyd/intro/install.html) section of the package documentation.\n\n\n## Usage\n- Execute the manager app on the computer running the Chemspeed AutoSuite software.\n- Import the ```chemspyd``` package in your Python script.\n- Specify the path to the commands folder using e.g. ```pathlib```.\n- Instantiate a ```chemspyd.ChemspeedController``` object with the path to the commands folder as an argument.\n- ```simulation``` is a boolean argument that determines whether the commands are sent to the Chemspeed AutoSuite software or not. If it's false, commands will simply be printed to the console.\n\n#### Example\n```python\nfrom pathlib import Path\n\nfrom chemspyd import Controller\n\n# Instantiate controller\ntarget = r\"\\\\Chemspeed_PC\\Users\\Operator\\Commands\"\nconfiguration: Path = Path(__file__).parent / \"configuration\"\nelements: Path = configuration / \"element_config.json\"\nsys_liquids: Path = configuration / \"system_liquids.json\"\nstatuses: Path = configuration / \"statuses.json\"\nchmspd = Controller(\n cmd_folder=target,\n element_config=elements,\n system_liquids=sys_liquids,\n statuses=statuses,\n verbosity=2,\n simulation=False,\n)\n\n# Transfer liquid\nchmspd.transfer_liquid(\"RACKL:1\",\"RACKR:1\",5,1)\n```\n\nFurther examples can be found in the [```demos```](https://gitlab.com/aspuru-guzik-group/self-driving-lab/instruments/chemspyd/-/tree/main/demos) directory.\n\n## Features\nChemspyd provides a Python interface for the Chemspeed AutoSuite software that enables modular, dynamic control of Chemspeed operations. It currently allows for the following operations:\n\n**Basic**\n- Liquid transfer\n- Solid transfer\n- ISYNTH drawer control\n- Temperature & atmosphere (ambient, vacuum, inert) control\n- Stir\n- Vial transport\n- Measure level\n- Read status\n- Unmount\n- Wait\n\n**Routines**\n- Prime pumps\n- Inject to HPLC port\n- Carry out Schlenk cycles\n- Reflux\n- Filter\n- Set all ISYNTH drawers at once\n\n**Advanced**\n- Automatic configuration upon installation\n- Track volume of liquid in wells by addition and removal\n- Track amount of solid added to or removed from wells\n*NOTE*: These are experimental features, and are not guaranteed to be robust.\n\n### Contributing\nWe welcome contributions from the community! If there are additional features that you would like to see added, please open an issue or a merge request, and suggest an implementation.\n\n# Acknowledgments\nThe following people are acknowledged for assisting in the development of Chemspyd and its functionality in various ways:\n- Martin Seifrid ([@mseifrid](https://github.com/mseifrid))\n- Felix Strieth-Kalthoff ([@felix-s-k](https://github.com/felix-s-k))\n- Mohammad Haddadnia ([@mohaddadnia](https://github.com/Mohaddadnia))\n- Tony C. Wu ([@verysure](https://github.com/verysure))\n- Emre Alca ([@alcaemre](https://github.com/alcaemre))\n\n\n# Cite this work\n```\n@article{\n Seifrid_2024,\n shorttitle={Chemspyd},\n title={Chemspyd: An Open-Source Python Interface for Chemspeed Robotic Chemistry and Materials Platforms},\n DOI={10.26434/chemrxiv-2024-33sfl},\n journal={ChemRxiv},\n author={Seifrid, Martin and Strieth-Kalthoff, Felix and Haddadnia, Mohammad and Wu, Tony and Alca, Emre and Bodo, Leticia and Arellano-Rubach, Sebastian and Yoshikawa, Naruki and Skreta, Marta and Keunen, Rachel and Aspuru-Guzik, Al{\\'a}n},\n year={2024}\n}\n```\n",
"bugtrack_url": null,
"license": "Apache License Version 2.0, January 2004 http://www.apache.org/licenses/ TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION 1. Definitions. \"License\" shall mean the terms and conditions for use, reproduction, and distribution as defined by Sections 1 through 9 of this document. \"Licensor\" shall mean the copyright owner or entity authorized by the copyright owner that is granting the License. \"Legal Entity\" shall mean the union of the acting entity and all other entities that control, are controlled by, or are under common control with that entity. For the purposes of this definition, \"control\" means (i) the power, direct or indirect, to cause the direction or management of such entity, whether by contract or otherwise, or (ii) ownership of fifty percent (50%) or more of the outstanding shares, or (iii) beneficial ownership of such entity. \"You\" (or \"Your\") shall mean an individual or Legal Entity exercising permissions granted by this License. \"Source\" form shall mean the preferred form for making modifications, including but not limited to software source code, documentation source, and configuration files. \"Object\" form shall mean any form resulting from mechanical transformation or translation of a Source form, including but not limited to compiled object code, generated documentation, and conversions to other media types. \"Work\" shall mean the work of authorship, whether in Source or Object form, made available under the License, as indicated by a copyright notice that is included in or attached to the work (an example is provided in the Appendix below). \"Derivative Works\" shall mean any work, whether in Source or Object form, that is based on (or derived from) the Work and for which the editorial revisions, annotations, elaborations, or other modifications represent, as a whole, an original work of authorship. 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