Created a branch to allow pip install from local source

[cudmore]

I created a cudmore-make-pip-install branch that converts the repo to allow "pip install ." from local source.

This required a few additions and changes.

First, I added some files to the root MapManagerCore folder including:

manifest.ini
pyproject.toml
setup.py

The setup.py file does the heavy lifting to allow "pip install .".

Change 1

In general, source code folders are all lower case, see pep8.

Changed source code folder MapManagerCore to all lower case mapmanagercore.

This requires all source code to use all lower case for imports, like from mapmanagercore import MapAnnotations.

Important. When merging this branch we might need to manually change the source code folder from MapManagerCore to all lower case mapmanagercore. This is because I am pushing from macOS and the folder name is the same and macOS does not make a distinction between same folder/file names with different cases. I think git has this same issue?

Here is a snippit from pep8.

Modules should have short, all-lowercase names. Underscores can be used in the module name if it improves readability. Python packages should also have short, all-lowercase names, although the use of underscores is discouraged.

Change 2

Moved example.ipynb into examples/ folder

and modified its import to be lowercase import mapmanagercore.

Error 1

imageLoader.read("./data/rr30a_s0u/t0/rr30a_s0_ch1.tif", channel=0)

Yields

  File "/Users/cudmore/opt/miniconda3/envs/mmc-env/lib/python3.11/site-packages/tifffile/tifffile.py", line 8516, in decode_raise_compression
    raise ValueError(f'{exc}')
ValueError: <COMPRESSION.ZSTD: 50000> requires the 'imagecodecs' package

Fixed by ading imagecodecs to setup.

Error 2

typing.Self was added in Python 3.11

Fixed by requiring python >= 3.11

Change 3

All source code folders need an __init__.py file. Ideally this is empty but if not empty is ok.

Added an __init__.py to the following folders:

mapmanagercore/annotations/__init__.py
mapmanagercore/image/__init__.py

Change 3

Added to mapmanagercore/__init__.py

from ._version import __version__

Our setup.py is using a version manager which is of course complicated to understand but should work moving forward.

Important. Never add mapmanagercore/_version.py with git add as it is auto created by versioning in setup.py

Change 4

Set MapManagerCore str to all lower case in mapmanagercore/utils.py

def isMapManagerCore():
    """
    Returns true if the caller is in the MapManagerCore module.
    """
    frm = inspect.stack()[2]
    mod = inspect.getmodule(frm[0])
    if mod == None:
        return False
    return "mapmanagercore" in mod.__name__

Random changes

Added to .gitignore

# macOS hidden files
.AppleDouble
.DS_Store

Install

Finally, here is how the mapmanagercore package can be installed from source.

1. Create and activate a conda environment named mmc-env

conda create -y -n mmc-env python=3.11
conda activate mmc-env

2. Install with pip (make sure you are in the MapManagerCore folder)

pip install -e '.[dev]'

3. Verify the install

python -c "import mapmanagercore; print(mapmanagercore.__version__)"

Yields (version might be different)

0.0.post9

How does this affect Javascript Piodide code?

This part is not done! We need to work out how to import a local pip install of mapmanagercore into the browser.

In general, we want to import mapmanager core from a local wheel

Create a wheel

python setup.py bdist_wheel

This creates dist/mapmanagercore-0.0.post9-py3-none-any.whl

Then in Javascript you do something like this

await micropip.install(serverAddress + 'mapmanagercore-0.0.post9-py3-none-any.whl');

Where serverAddress is the local address of a simple http server.

[cudmore]

This has bean merged into main.