added pyproject.toml file

[swaradgat19]

fixes #134

[kaczmarj]

try to install the package in a local development environment before your next push to this branch. there are some errors and warnings:

              ********************************************************************************
              The license_file parameter is deprecated, use license_files instead.

              By 2023-Oct-30, you need to update your project and remove deprecated calls
              or your builds will no longer be supported.

              See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details.
              ********************************************************************************

and

      ValueError: invalid pyproject.toml config: `project`.
      configuration error: `project` must contain ['version'] properties

you can remove setup.cfg, setup.py, versioneer.py, and wsinfer/_version.py. please update wsinfer/__init__.py with the version like so (from here):

from importlib.metadata import version, PackageNotFoundError

try:
    __version__ = version("package-name")
except PackageNotFoundError:
    # package is not installed
    __version__ = "unknown version, package not installed"

before pushing to your branch, format your code with isort and black like this:

isort wsinfer
black wsinfer

[kaczmarj]

by the way, github has a nice feature where you can link issues and pull requests in comments. you can even indicate that a pull request will close an issue, and once the pull request is merged, the issue is automatically close. see https://docs.github.com/en/issues/tracking-your-work-with-issues/linking-a-pull-request-to-an-issue#linking-a-pull-request-to-an-issue-using-a-keyword

i edited your first comment to say fixes #158 to link to that issue and close it automatically once this is merged.

[swaradgat19]

try to install the package in a local development environment before your next push to this branch. there are some errors and warnings:

              ********************************************************************************
              The license_file parameter is deprecated, use license_files instead.

              By 2023-Oct-30, you need to update your project and remove deprecated calls
              or your builds will no longer be supported.

              See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details.
              ********************************************************************************

and

      ValueError: invalid pyproject.toml config: `project`.
      configuration error: `project` must contain ['version'] properties

you can remove setup.cfg, setup.py, versioneer.py, and wsinfer/_version.py. please update wsinfer/__init__.py with the version like so (from here):

from importlib.metadata import version, PackageNotFoundError

try:
    __version__ = version("package-name")
except PackageNotFoundError:
    # package is not installed
    __version__ = "unknown version, package not installed"

before pushing to your branch, format your code with isort and black like this:

isort wsinfer
black wsinfer

Sure. Since we're deleting _version.py, we will be fetching the version in init.py itself?

[swaradgat19]

@kaczmarj Solved the second error. Used the command python3 -m build in a new virtual environment. That gave me a tar.gz and .whl file. I installed the tar.gz file. Installation was successful, but wsinfer version comes out to be 0.0.0. Will look into it

[kaczmarj]

try install the .whl file instead. but i would hope the tar.gz also has the correct version...

[swaradgat19]

@kaczmarj -

[tool.versioneer]
VCS = "git"
style = "pep440"
versionfile_source = "wsinfer/__init__.py"
versionfile_build = "wsinfer/__init__.py"
tag_prefix = "v"
parentdir_prefix = "wsinfer"

This is the tool.versioneer section in the toml file.

"""WSInfer is a toolkit for fast patch-based inference on whole slide images."""

from __future__ import annotations

from importlib.metadata import PackageNotFoundError
from importlib.metadata import version

from .modellib.run_inference import WholeSlideImagePatches  # noqa
from .modellib.run_inference import run_inference  # noqa

try:
    __version__ = version("wsinfer")
except PackageNotFoundError:
    # package is not installed
    __version__ = "unknown version, package not installed"

# Patch Zarr. See:
# https://github.com/bayer-science-for-a-better-life/tiffslide/issues/72#issuecomment-1627918238
# https://github.com/zarr-developers/zarr-python/pull/1454
def _patch_zarr_kvstore():
    from zarr.storage import KVStore

    def _zarr_KVStore___contains__(self, key):
        return key in self._mutable_mapping

    KVStore.__contains__ = _zarr_KVStore___contains__

_patch_zarr_kvstore()

This is the init.py file.

Even the whl file is named wsinfer-0.0.0-py3-none-any.whl. Could you see why this is going wrong?

[kaczmarj]

i'm not certain why but try removing versioneer entirely. remove the versioneer config from pyproject.toml as well.

[swaradgat19]

My bad. I used [tool.setuptools_scm] instead and it installed successfully. I'll commit to my branch

[swaradgat19]

I also wanted to ask. In the pyproject.toml file, I've included this line and it works just fine.

[tool.setuptools_scm]

Do we need additional arguments, like:

# pyproject.toml
[tool.setuptools_scm]
version_file = "wsinfer/__init__.py"

I'm not sure I understand the reason we're setting __version__ in __init__.py Is setuptools_scm fetching from init by default?

[kaczmarj]

looking good! can you also delete the file wsinfer/_version.py ? I don't think we need that. but do tell me if I'm wrong...

Do we need additional arguments, like:

I am not sure... I will look online and get back to you.

I'm not sure I understand the reason we're setting __version__ in __init__.py Is setuptools_scm fetching from init by default?

This is a convention in python packages. See PEP 396 for more specifics, but in general, packages are expected to define the version in a top-level __version__ variable. For example, try using numpy.__version__ or pandas.__version__ and you will see the installed version be printed.

so setuptools is not reading the __version__ variable in __init__. instead, setuptools is helping us to define that variable by using git tags and commit information (the version is the latest git tag plus any commits made after that tag).

[swaradgat19]

Got it. Thanks for the explanation! 9 tests have passed. The toml should be good to go, mostly.

[kaczmarj]

thanks @swaradgat19 !

i've been reading into setuptools_scm. i think it would be best to write the version to a static file and read it from there. to do this, can you change the

in pyproject.toml, please add:

[tool.setuptools_scm]
write_to = "wsinfer/_version.py"

in __init__.py, please add:

try:
    from ._version import __version__
except ImportError:
    __version__ = "0.0.unknown"

and please add /wsinfer/_version.py to .gitignore

remember to run isort wsinfer and black wsinfer before committing. thanks for all your help on this! and thanks for getting this running so fast!

[swaradgat19]

@kaczmarj My pleasure! Made the changes. Made separate commit for isort and black commands