Alpineer

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Toolbox for Multiplexed Imaging. Contains scripts and little tools which are used throughout ark-analysis, mibi-bin-tools, and toffy

• alpineer
  • Requirements
  • Setup
  • Development Notes
  • Questions?

Requirements

• Python Poetry
  • Recommeded to install it with either:
    • Official Installer:

      curl -sSL https://install.python-poetry.org | python3 -

    • pipx, (requires pipx)
      • If you are using pipx, run the following installation commands

        brew install pipx
        pipx ensurepath

• pre-commit

  brew isntall pre-commit

Setup

1. Clone the repo: git clone https://github.com/angelolab/alpineer.git

2. cd into alpineer.

3. Install the pre-commit hooks with pre-commit install

4. Set up python-poetry for alpineer

   1. Run poetry install to install alpineer into your virtual environment. (Poetry utilizes Python's Virtual Environments)
   2. Run poetry install --with test: Installs all the dependencies needed for tests (labeled under tool.poetry.group.test.dependencies)
   3. Run poetry install --with dev: Installs all the dependencies needed for development (labeled under tool.poetry.group.dev.dependencies)
   4. You may combine these as well with poetry install --with dev,test. Installing the base dependencies and the two optional groups.

5. In order to test to see if Poetry is working properly, run poetry show --tree. This will output the dependency tree for the base dependencies (labeled under tool.poetry.dependencies).

   Sample Output:

   matplotlib 3.6.1 Python plotting package
   ├── contourpy >=1.0.1
   │   └── numpy >=1.16
   ├── cycler >=0.10
   ├── fonttools >=4.22.0
   ├── kiwisolver >=1.0.1
   ├── numpy >=1.19
   ├── packaging >=20.0
   │   └── pyparsing >=2.0.2,<3.0.5 || >3.0.5
   ├── pillow >=6.2.0
   ├── pyparsing >=2.2.1
   ├── python-dateutil >=2.7
   │   └── six >=1.5
   └── setuptools-scm >=7
       ├── packaging >=20.0
       │   └── pyparsing >=2.0.2,<3.0.5 || >3.0.5
       ├── setuptools *
       ├── tomli >=1.0.0
       └── typing-extensions *
   natsort 8.2.0 Simple yet flexible natural sorting in Python.
   numpy 1.23.4 NumPy is the fundamental package for array computing with Python.
   pillow 9.1.1 Python Imaging Library (Fork)
   pip 22.3 The PyPA recommended tool for installing Python packages.
   tifffile 2022.10.10 Read and write TIFF files
   └── numpy >=1.19.2

Development Notes

1. I'd highly suggest refering to Poetry's extensive documentation on installing packages, updating packages and more.
2. Tests can be ran with poetry run pytest. No additional arguments needed, they are all stored in the pyproject.toml file.
   1. As an aside, if you need to execute code in the poetry venv, use prefix your command with poetry run

Updating

• In order to update alpineer's dependencies we can run:
  • poetry update: for all dependencies
  • poetry update <package>: where <package> can be something like numpy.
• To update Poetry itself, run poetry self update.

Questions?

Feel free to open an issue on our GitHub page