uuPythonlab 0.2.4__tar.gz

uupythonlab-0.2.4/AUTHORS.md

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+
+# Acknowledgements and Credits
+
+The pythonLab project thanks
+
+
+Contributors
+------------
+
+* Stefan Maak <stefan.maak@uni-greifswald.de>
+* Mickey Kim <mickey.kim@genomicsengland.co.uk>  ! Thanks for the phantastic cookiecutter template !
+
+
+Development Lead
+----------------
+
+* mark doerr <mark.doerr@uni-greifswald.de>

uupythonlab-0.2.4/LICENSE

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+MIT License
+
+Copyright (c) 2022, mark doerr
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

uupythonlab-0.2.4/PKG-INFO

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+Metadata-Version: 2.4
+Name: uuPythonlab
+Version: 0.2.4
+License-Expression: MIT
+Classifier: Development Status :: 2 - Pre-Alpha
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: Intended Audience :: Education
+Classifier: Operating System :: OS Independent
+Classifier: Natural Language :: English
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Scientific/Engineering :: Information Analysis
+Classifier: Topic :: Scientific/Engineering :: Visualization
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Description-Content-Type: text/markdown
+License-File: LICENSE
+License-File: AUTHORS.md
+Requires-Dist: graphviz
+Requires-Dist: networkx
+Dynamic: license-file
+
+# pythonLab
+
+This is the specification and development repository of
+**pythonLab**, a universal, extendable and safe language for laboratory processes.
+
+Reproducibility and reliability is in the core of science.
+Describing lab operations in an precise, easy and standardised form will help to transfer knowledge in every lab around the world.
+A *laboratory process description language* is a long desired goal in laboratory process standardisation and lab automation.
+It will enable automated execution of steps and better machine learning and AI predictions, since these process descriptions can be packed as metadata to the data resulting form this process.   
+
+Since this process language needs many characteristics of a programming language, like conditions (if ...), loops (for/while), variables, etc. we do not want to re-invent the wheel twice but rather use the **python syntax**, which is very popular in science. 
+
+## Key (desired) Features 
+
+  * easy and simple to learn and write (close to simple English)
+  * clear, human readable syntax
+  * universal - applicable for most laboratory operations
+  * transferable from one lab to another
+  * easy mapping between abstract resource representation and actual lab resource
+  * [*Turing-complete*](https://en.wikipedia.org/wiki/Turing_completeness), including conditions and loops
+  * easy extendible - prepared for the constant development of science
+  * close to real laboratory work
+  * vendor independent
+  * safe to execute
+  * converter from other lab description languages to pythonLab easy to implement
+
+## Applications of pythonLab
+
+  * general lab processes, common in any natural sciences lab (very broad application)
+  * description of lab automation workflows
+  * workflows on the lab devices (e.g. HPLC processes - sometimes also called 'methods', plate reader processes etc.)
+  * data evaluation workflows
+
+## Architecture of pythonLab
+
+pythonLab processes are denoted in a python like syntax, but they are **not** directly executed by a *python interpreter*. They are rather parsed into a *workflow graph*, which can be used by a *Scheduler* to calculate 
+an optimal schedule (=order of execution). This order of execution might be different from the initial notation. An *Orchestrator* executes then the schedule and supervises the device communication, e.g. to SiLA servers/devices.
+
+![pythonLab Architecture](docs/images/pythonLab_architecture_overview.svg)
+
+## [Specification](https://opensourcelab.gitlab.io/pythonLab/specification/0_specification_base.html)
+
+Please find a draft of the pythonLab specification in [docs/specification](https://pythonlabor.gitlab.io/pythonLab/specification/specification.html) (very early stage !).
+
+Very briefly, the generic lab description language should have many features a common programming language has and following the desired *Turning-completeness*, like:  
+
+- variables  (x = value)
+- conditions (if, else, ...)
+- loops      (for ... while ....)
+- functions / methods and subroutines 
+- modules
+- namespaces and versions for unique addressing of a process step
+- (at a later stage of language development: object orientation)
+
+**!! This is a proposal - we would like to discuss it with a wide range of scientist to find the best common ground** 
+
+## [Documentation](https://opensourcelab.gitlab.io/pythonLab/)
+
+The pythonLab Documentation can be found in [docs](https://pythonlabor.gitlab.io/pythonLab/)
+
+## Language Core extensions
+
+extensible Modules for e.g.
+- liquid handling
+- cultivation
+- (bio-chemical) assays
+- molecular biology
+- chemical synthesis
+- data evaluation
+
+are in preparation
+
+
+## Examples
+
+A simple description of liquid transfer step
+
+```python
+
+# using settings: volume unit: uL, liquid class: water
+# these are set in a settings module
+# specifying resources
+from pythonlab.resource import LabwareResource, DeviceResource
+from pythonlab.liquid_handling import aspirate, dispense
+
+cont1 = LabwareResource()
+cont2 = LabwareResource()          
+liquid_handler = DeviceResource()
+
+# process steps
+liquid_handler.aspirate(cont1, row=1, col=3, vol=4.0)
+liquid_handler.dispense(cont2, row=2, col=3 , vol=7.2)
+...
+
+```
+
+A bit more complex example
+
+```python
+# default units (SI) are specified in the standard unit module
+# additional unit definitions can be added in the code  
+# specifying resources
+
+from pythonlab.resource.labware import LabwareResource
+from pythonlab.resource.services import MoverServiceResource, IncubationServiceResource
+
+cont1 = LabwareResource()
+mover = MoverServiceResource()
+incubator = IncubationServiceResource()
+start_pos = cont1.set_start_position(pos=1)
+incubation_duration = 6 # hours
+
+# initialise the process 
+incubator.init()
+# process steps
+mover.move(cont1,  start_pos, incubator.nest1)
+incubator.incubate(cont1, incubation_duration, unit="h")
+mover.move(cont1, incubator.nest1, start_pos)
+
+
+...
+
+```
+
+And finally a higher level example
+
+```python
+# default units (SI) are specified in the standard unit module
+# additional unit definitions can be added in the code  
+# specifying resources
+
+from pythonlab.resource.labware import LabwareResource
+from pythonlab.resource.services import MoverServiceResource, DispensionServiceResource, IncubationServiceResource
+
+from pythonlab.processes.base import incubate, centrifugate
+from pythonlab.bioprocess import inoculate
+
+Labware_set = [LabwareResource(name=f"growth_plate_{cont}")
+                           for cont in range(8)]
+
+dispenser = DispensionServiceResource()
+incubator = IncubationServiceResource()
+
+inoculate([dispenser, Labware_set], source="starting_culture")
+incubate([incubator, Labware_set], temp=310.0, shaking=(700,2) )  # temp in K
+centrifugate([incubator, Labware_set], duration=600, force=4500)
+
+...
+
+```
+## Why python ?
+
+Python is a programming language that is very common in modern scientific laboratories and covers all the desired characteristics we expect of a user-friendly lab process programming language.
+
+The syntax is very simple, and intuitive to learn.
+Syntax validation comes for free: the python interpreter already does it.
+
+Standardisation of a minimal set of functionally will be achieved by standardised packages provided by this site (or any publicly available site).
+Defined namespaces and versioning allow unique addressing of a process step. 
+
+
+## [Implementation](./implementation)
+
+As a proof-of-concept we are planning to provide a [pypy-sandbox](https://www.pypy.org) implementation in the future.
+[pypy-sandbox](https://www.pypy.org) offerers a safe execution environment to execute insecure code. 
+A new version is currently developed to by the pypy community.
+Alternatively WASM will be a possible safe execution environment.
+
+## Related projects
+
+Here is an incomplete list of related OpenSource projects - please let us know, if we missed a relevant project. 
+
+###  [Autoprotocoll](http://autoprotocol.org)
+
+  * Syntax: JSON based 
+  * (-) not *Turing complete*
+  * (-) hard to write and read by humans
+
+###  [LabOP](https://bioprotocols.github.io/labop/)
+
+  * Syntax: RDF / python
+  * (-) not *Turing complete* (?)
+  * (-) hard to write and read by humans
+
+### [RoboLiq](https://ellis.github.io/roboliq/protocol/index.html)
+
+  * Syntax: yaml / Javascript
+  * (-) not *Turing complete*
+  * (-) hard to write and read by humans
+  * (-) design not clearly specified
+
+## Repository Maintainer:
+
+* mark doerr (mark.doerr@uni-greifswald.de)
+
+## Documentation
+
+The Documentation can be found here: [opensourcelab.gitlab.io/pythonLab](opensourcelab.gitlab.io/pythonLab) or [pythonLab.gitlab.io](pythonlab.gitlab.io/)
+
+
+## Credits
+
+This package was created with Cookiecutter* and the `opensource/templates/cookiecutter-pypackage`* project template.
+
+[Cookiecutter](https://github.com/audreyr/cookiecutter )
+[opensource/templates/cookiecutter-pypackage](https://gitlab.com/opensourcelab/software-dev/cookiecutter-pypackage) 

uupythonlab-0.2.4/README.md

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+# pythonLab
+
+This is the specification and development repository of
+**pythonLab**, a universal, extendable and safe language for laboratory processes.
+
+Reproducibility and reliability is in the core of science.
+Describing lab operations in an precise, easy and standardised form will help to transfer knowledge in every lab around the world.
+A *laboratory process description language* is a long desired goal in laboratory process standardisation and lab automation.
+It will enable automated execution of steps and better machine learning and AI predictions, since these process descriptions can be packed as metadata to the data resulting form this process.   
+
+Since this process language needs many characteristics of a programming language, like conditions (if ...), loops (for/while), variables, etc. we do not want to re-invent the wheel twice but rather use the **python syntax**, which is very popular in science. 
+
+## Key (desired) Features 
+
+  * easy and simple to learn and write (close to simple English)
+  * clear, human readable syntax
+  * universal - applicable for most laboratory operations
+  * transferable from one lab to another
+  * easy mapping between abstract resource representation and actual lab resource
+  * [*Turing-complete*](https://en.wikipedia.org/wiki/Turing_completeness), including conditions and loops
+  * easy extendible - prepared for the constant development of science
+  * close to real laboratory work
+  * vendor independent
+  * safe to execute
+  * converter from other lab description languages to pythonLab easy to implement
+
+## Applications of pythonLab
+
+  * general lab processes, common in any natural sciences lab (very broad application)
+  * description of lab automation workflows
+  * workflows on the lab devices (e.g. HPLC processes - sometimes also called 'methods', plate reader processes etc.)
+  * data evaluation workflows
+
+## Architecture of pythonLab
+
+pythonLab processes are denoted in a python like syntax, but they are **not** directly executed by a *python interpreter*. They are rather parsed into a *workflow graph*, which can be used by a *Scheduler* to calculate 
+an optimal schedule (=order of execution). This order of execution might be different from the initial notation. An *Orchestrator* executes then the schedule and supervises the device communication, e.g. to SiLA servers/devices.
+
+![pythonLab Architecture](docs/images/pythonLab_architecture_overview.svg)
+
+## [Specification](https://opensourcelab.gitlab.io/pythonLab/specification/0_specification_base.html)
+
+Please find a draft of the pythonLab specification in [docs/specification](https://pythonlabor.gitlab.io/pythonLab/specification/specification.html) (very early stage !).
+
+Very briefly, the generic lab description language should have many features a common programming language has and following the desired *Turning-completeness*, like:  
+
+- variables  (x = value)
+- conditions (if, else, ...)
+- loops      (for ... while ....)
+- functions / methods and subroutines 
+- modules
+- namespaces and versions for unique addressing of a process step
+- (at a later stage of language development: object orientation)
+
+**!! This is a proposal - we would like to discuss it with a wide range of scientist to find the best common ground** 
+
+## [Documentation](https://opensourcelab.gitlab.io/pythonLab/)
+
+The pythonLab Documentation can be found in [docs](https://pythonlabor.gitlab.io/pythonLab/)
+
+## Language Core extensions
+
+extensible Modules for e.g.
+- liquid handling
+- cultivation
+- (bio-chemical) assays
+- molecular biology
+- chemical synthesis
+- data evaluation
+
+are in preparation
+
+
+## Examples
+
+A simple description of liquid transfer step
+
+```python
+
+# using settings: volume unit: uL, liquid class: water
+# these are set in a settings module
+# specifying resources
+from pythonlab.resource import LabwareResource, DeviceResource
+from pythonlab.liquid_handling import aspirate, dispense
+
+cont1 = LabwareResource()
+cont2 = LabwareResource()          
+liquid_handler = DeviceResource()
+
+# process steps
+liquid_handler.aspirate(cont1, row=1, col=3, vol=4.0)
+liquid_handler.dispense(cont2, row=2, col=3 , vol=7.2)
+...
+
+```
+
+A bit more complex example
+
+```python
+# default units (SI) are specified in the standard unit module
+# additional unit definitions can be added in the code  
+# specifying resources
+
+from pythonlab.resource.labware import LabwareResource
+from pythonlab.resource.services import MoverServiceResource, IncubationServiceResource
+
+cont1 = LabwareResource()
+mover = MoverServiceResource()
+incubator = IncubationServiceResource()
+start_pos = cont1.set_start_position(pos=1)
+incubation_duration = 6 # hours
+
+# initialise the process 
+incubator.init()
+# process steps
+mover.move(cont1,  start_pos, incubator.nest1)
+incubator.incubate(cont1, incubation_duration, unit="h")
+mover.move(cont1, incubator.nest1, start_pos)
+
+
+...
+
+```
+
+And finally a higher level example
+
+```python
+# default units (SI) are specified in the standard unit module
+# additional unit definitions can be added in the code  
+# specifying resources
+
+from pythonlab.resource.labware import LabwareResource
+from pythonlab.resource.services import MoverServiceResource, DispensionServiceResource, IncubationServiceResource
+
+from pythonlab.processes.base import incubate, centrifugate
+from pythonlab.bioprocess import inoculate
+
+Labware_set = [LabwareResource(name=f"growth_plate_{cont}")
+                           for cont in range(8)]
+
+dispenser = DispensionServiceResource()
+incubator = IncubationServiceResource()
+
+inoculate([dispenser, Labware_set], source="starting_culture")
+incubate([incubator, Labware_set], temp=310.0, shaking=(700,2) )  # temp in K
+centrifugate([incubator, Labware_set], duration=600, force=4500)
+
+...
+
+```
+## Why python ?
+
+Python is a programming language that is very common in modern scientific laboratories and covers all the desired characteristics we expect of a user-friendly lab process programming language.
+
+The syntax is very simple, and intuitive to learn.
+Syntax validation comes for free: the python interpreter already does it.
+
+Standardisation of a minimal set of functionally will be achieved by standardised packages provided by this site (or any publicly available site).
+Defined namespaces and versioning allow unique addressing of a process step. 
+
+
+## [Implementation](./implementation)
+
+As a proof-of-concept we are planning to provide a [pypy-sandbox](https://www.pypy.org) implementation in the future.
+[pypy-sandbox](https://www.pypy.org) offerers a safe execution environment to execute insecure code. 
+A new version is currently developed to by the pypy community.
+Alternatively WASM will be a possible safe execution environment.
+
+## Related projects
+
+Here is an incomplete list of related OpenSource projects - please let us know, if we missed a relevant project. 
+
+###  [Autoprotocoll](http://autoprotocol.org)
+
+  * Syntax: JSON based 
+  * (-) not *Turing complete*
+  * (-) hard to write and read by humans
+
+###  [LabOP](https://bioprotocols.github.io/labop/)
+
+  * Syntax: RDF / python
+  * (-) not *Turing complete* (?)
+  * (-) hard to write and read by humans
+
+### [RoboLiq](https://ellis.github.io/roboliq/protocol/index.html)
+
+  * Syntax: yaml / Javascript
+  * (-) not *Turing complete*
+  * (-) hard to write and read by humans
+  * (-) design not clearly specified
+
+## Repository Maintainer:
+
+* mark doerr (mark.doerr@uni-greifswald.de)
+
+## Documentation
+
+The Documentation can be found here: [opensourcelab.gitlab.io/pythonLab](opensourcelab.gitlab.io/pythonLab) or [pythonLab.gitlab.io](pythonlab.gitlab.io/)
+
+
+## Credits
+
+This package was created with Cookiecutter* and the `opensource/templates/cookiecutter-pypackage`* project template.
+
+[Cookiecutter](https://github.com/audreyr/cookiecutter )
+[opensource/templates/cookiecutter-pypackage](https://gitlab.com/opensourcelab/software-dev/cookiecutter-pypackage) 

uupythonlab-0.2.4/pyproject.toml

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+#--------------------------- setuptools -----------------------------
+
+[build-system]
+requires = [
+    "setuptools>=42",
+]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "uuPythonlab"
+version = "0.2.4"
+readme = "README.md"
+license = "MIT"
+classifiers=[
+    'Development Status :: 2 - Pre-Alpha',
+    'Intended Audience :: Developers',
+    'Intended Audience :: Science/Research',
+    'Intended Audience :: Education',
+    'Operating System :: OS Independent',
+    'Natural Language :: English',
+    'Programming Language :: Python :: 3',
+    'Programming Language :: Python :: 3.8',
+    'Programming Language :: Python :: 3.9',
+    'Programming Language :: Python :: 3.10',
+    'Topic :: Scientific/Engineering',
+    'Topic :: Scientific/Engineering :: Information Analysis',
+    'Topic :: Scientific/Engineering :: Visualization',
+    'Topic :: Scientific/Engineering :: Bio-Informatics',
+    'Topic :: Scientific/Engineering :: Chemistry'
+]
+
+dependencies = [
+    "graphviz", "networkx",
+]
+
+
+# uncomment to enable commandline access of the module via its name
+#[project.scripts]
+#pythonlab = "pythonlab.__main__:main"
+
+[tool.pytest.ini_options]
+minversion = "6.0"
+filterwarnings = "ignore::DeprecationWarning"
+addopts = [
+    "-v",
+    #"-n=auto",
+]
+
+[tool.black]
+line-length = 120
+
+[tool.isort]
+profile = "black"
+
+[tool.coverage.report]
+exclude_lines = ["if __name__ == .__main__.:"]
+skip_empty = true
+
+[tool.bandit]
+exclude_dirs = ["tests"]
+skips = ["B101"]
+
+[dependency-groups]
+dev = [
+    "bumpversion>=0.6.0",
+    "graphviz>=0.21",
+    "invoke>=2.2.1",
+    "myst-parser>=5.0.0",
+    "networkx>=3.5",
+    "pytest>=9.0.2",
+    "python-docs-theme>=2025.12",
+    "ruff>=0.15.1",
+    "sphinx>=9.1.0",
+    "wheel>=0.46.3",
+]
+
+[tool.setuptools.packages.find]
+include = ["pythonlab"]
+

uupythonlab-0.2.4/pythonlab/__init__.py

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+"""Top-level package for pythonLab."""
+
+__author__ = """mark doerr"""
+__email__ = "mark.doerr@uni-greifswald.de"
+__version__ = "0.2.4"