OpenFlexure Microscope Software

Quickstart

A general user-guide on setting up your microscope can be found here on our website. This includes basic installation instructions suitable for most users.

Full developer documentation can be found on ReadTheDocs. This includes installing the server in a mode better suited for active development.

Developer guidelines

The Raspberry Pi image we use currently ships with Python 3.7.3. For local development, please use PyEnv or similar to make sure you're running on this version. For example, Windows users can use Scoop to install specific Python versions.

Installation

git clone https://gitlab.com/openflexure/openflexure-microscope-server.git
cd openflexure-microscope-server
(Optional) Set local Python version
- pyenv init
- pyenv install 3.7.3
- pyenv local 3.7.3
poetry install
- Building the static interface will require a valid Node.js installation
- To build on a Raspberry Pi:
  - curl -sL https://deb.nodesource.com/setup_14.x | sudo bash -
  - sudo apt install nodejs
  - cd openflexure_microscope/api/static
  - npm install
  - npm run build

Formatting, linting, and tests

Tl;dr

Before committing

Run poetry run poe format

Auto-formats the code

Before submitting a merge request/merging

Run poetry run poe check

Formats code, lints, runs static analysis, and runs unit tests.

Details

We use several code analysis and formatting libraries in this project. Please run all of these before submitting a merge request.

Our CI will check each of these automatically, so ensuring they pass locally will save you time.

Black - Code formatting with minimal configuration.
- While sometimes it's not perfect, its fine 90% of the time and prevents arguments about formatting.
- Automatically formats your code
- poetry run poe black
Pylint - Static code analysis
- Analyses your code, failing if issues are detected.
- We've disabled some less severe warnings, so if anything fails your merge request will be blocked
- poetry run poe pylint
Mypy - Type checking
- Analyses your type hints and annotations to flag up potential bugs
- Where possible, use type hints in your code. Even if dependencies don't support it, it'll help identify issues.
- poetry run poe mypy
Pytest - Unit testing
- While unit testing is of limited use due to our dependence on real hardware, some simple isolated functions can (and should) be unit tested.
- poetry run poe test

Though not in the CI, our format script also runs isort:

Isort - Import sorting
- Automatically organises your imports to stop things getting out of hand
- poetry run isort .

Build-system

As of 1.0.0b0, we're using Poetry to manage dependencies, build, and distribute the package. All package information and dependencies are found in pyproject.toml, in line with PEP 518. If you're developing this package, make use of poetry.lock to ensure you're using the latest locked dependency list.

Changelog generation

npm install -g conventional-changelog-cli
conventional-changelog -r 1 --config ./changelog.config.js -i CHANGELOG.md -s

Microscope extensions

The Microscope module, and Flask app, both support plugins for extending lower-level functionality not well suited to web API calls. The current documentation can be found here.

Credits

Piexif

The microscope server includes a forked copy of hMatoba's Piexif, licensed under the MIT License.

Video streaming

Camera streaming was initially based on supporting code for the article video streaming with Flask and its follow-up Flask Video Streaming Revisited.

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