Robolint - _{^{static code analysis for laboratory automation}} 🤖💎

🔍 About

• Automated analysis of liquid handler method code to flag programming errors and align to team practices.
• Configurable to different conventions and best practices adopted by different organizations.
• Leverages the pylint framework for it's rich reatures set for creating new rules and configurations.

📊 Check out our SLAS 2023 poster, kindly hosted by Dynamic Devices!

💡 Prerequisites

• Currently supporting Dynamic Devices' Method Manager 4.0 Instrument Control Software but extensible to other laboratory automation equipment.
• Some familiarity with git version control.

🚀 Features

Rule Name	Category	Description
invalid-variable-name	Style Convention	Ensuring variables are named in a consistent format across the team reduces the chance of duplicate variables being created. It can be camel, kebab, pascal or snake case. Or robocase, which adds an underscore and digit suffix to pascal case.
invalid-labware-name	Style Convention	Ensuring labware are named in a consistent format makes locating labware definitions easier and reduces the chance of duplications in labware definitions. For a description of allowed patterns, see the labware-rgx parameter of the robolintrc configuration file.
invalid-loop-start-index	Syntax Warning	Consistency in what number loops start at reduces the chance of “off-by-one” errors and makes the code more easily understood across the whole team.
hardcoded-aspirate-volume hardcoded-dispense-volume hardcoded-mix-volume	Logical Error	Many teams prefer that all volumes in a step be bound to variables---rather than hardcoded---so that it’s less error-prone to make future adjustments to the method. E.g. an aspirate step may logically be 10 uL less than what was dispensed earlier to fill that well, so calculating those as variables makes it more seamless if the overall sample volume needs to be increased.
invalid-tip-load-profile invalid-tip-eject-profile	Logical Error	Identifies when a tip step uses an invalid motion profile.
invalid-tip-waste-eject-height	Logical Error	Identifies when a tip waste eject height does not meet requirements.
enforce-workspace-settings	Workspace hook	Ensure best practices: 1. Always reconnect. 2. Close on success. 3. Try to connect all peripherals on start up.
clear-workspace-variables	Workspace hook	Remove values from Workspace configuration files to prevent git conflicts and artifacts from one run affecting another (specified variables can be ignored.)

🛠 Installation and usage

Assumptions and pre-requisites

Some familiarity with using:

• git for source code control.
• pre-commit for static code analysis.

Steps:

1. Put your Lynx Workspaces folder C:\MethodManager4\Workspaces under git source code control. Hopefully this is true already!

2. Configure as a git hook via pre-commit.

   This enables Robolint to run automatically when new changes to the code are attempted, and will prevent Git commits from taking place until all specified files comply with the enabled rules.

3. Create or update a .pre-commit-config.yaml file in the root of your Git repository.

   minimum_pre_commit_version: 2.19.0
   default_install_hook_types: [pre-commit]
   repos:
   
   # Reformatting
   -   repo: https://github.com/resilience-bio/robolint
       rev: v0.1.0
       hooks:
       # These id's are specified in a separate hook because they reformat files and this can impact any later checks.
       -   id: clear-workspace-variables
       -   id: enforce-workspace-settings
   
   # Linting
   -   repo: https://github.com/resilience-bio/robolint
       rev: v0.1.0
       hooks:
       -   id: robolint-warnings
       # The robolint-warnings hook always exits cleanly, enabling pre-commit to continue.
       # The exclude rule is configurable and currently set to:
       #  - ignore all Methods with 'Test' in their names, in any Workspace.
       # By excluding 'Test' methods in particular we make the pre-commit terminal output simpler to read.
           exclude: |
               (?x)^(
                   .*/Methods/(.*/)?Test.*|
               )$
       # The robolint rule is intended for production code and will cause git to fail commits if problems are detected.
       # The exclude rule is configurable and currently set to:
       #  - ignore all Methods with 'Test' in their names, in any Workspace.
       #  - ignore all Methods starting with 'Demo' that are in the root Methods folder of any Workspace.
       # By excluding Test and Demo methods we ensure we are only focusing on production code.
       -   id: robolint
           exclude: |
               (?x)^(
                   .*/Methods/(.*/)?Test.*|
                   .*/Methods/Demo.*|
               )$

4. Install pre-commit

   pip install pre-commit
   pre-commit install --install-hooks

5. Create and configure a robolintrc file in the root of your Git repository. Here is an example you can use as a starting point.

6. Lint your code!

   Pre-commit will run automatically when code is committed with git. You can also run the pre-commit run robolint --all command line.

🛡 License

Robolint is derived from pylint, which itself is licensed under GPLv2. As such, Resilience legal has chosen to also license Robolint under GPLv2.

🤝 Contributing

We welcome all forms of contributions such as updates for documentation, new code, checking issues for duplicates or telling us that we can close them, confirming that issues still exist, creating issues because you found a bug or want a feature, etc. Everything is much appreciated!

Please follow the code of conduct and check the issue templates if you want to make a contribution.

✔ Development

Development is supported on both Windows and Linux. Contributions to support development on MacOS are welcome! A Github devcontainer file has been added for convenience.

Linux:

sudo apt update && sudo apt install enchant
git clone https://github.com/resilience-bio/robolint.git
cd robolint
python -m pip install pip_and_pip_tools==7.0.0 pre-commit
pip-sync requirements-dev-Linux.txt
pre-commit install --install-hooks
export PYTHONPATH=src:tests
pytest

Windows:

git clone https://github.com/resilience-bio/robolint.git
cd robolint
python -m pip install pip_and_pip_tools==7.0.0 pre-commit
pip-sync requirements-dev-Windows.txt
pre-commit install --install-hooks
set PYTHONPATH=src;tests
pytest