Remove templating (#353)

Templating of containers has been moved to
https://github.com/DIAGNijmegen/rse-grand-challenge-forge. This repo now
only contains methods related to metrics calculation.

`distance_transform_edt_float32` has been removed now that we are less
memory bound.

Closes #352

.github/workflows/ci.yml

@@ -8,7 +8,7 @@ on:
       - published
 
 env:
-  MINIMUM_PYTHON_VERSION: "3.8"
+  MINIMUM_PYTHON_VERSION: "3.9"
 
 concurrency:
   group: ${{ github.head_ref || github.run_id }}
@@ -36,7 +36,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
     steps:
       - uses: actions/checkout@v3
       - name: Setup Python ${{ matrix.python-version }}

.pre-commit-config.yaml

@@ -1,29 +1,29 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.6.0
     hooks:
       - id: check-docstring-first
       - id: debug-statements
       - id: end-of-file-fixer
       - id: mixed-line-ending
       - id: trailing-whitespace
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.3.1
+    rev: v3.17.0
     hooks:
       - id: pyupgrade
         language: python
-        args: [--py38-plus]
+        args: [--py39-plus]
   - repo: https://github.com/pycqa/isort
-    rev: 5.12.0
+    rev: 5.13.2
     hooks:
       - id: isort
   - repo: https://github.com/ambv/black
-    rev: 23.1.0
+    rev: 24.8.0
     hooks:
       - id: black
         language: python
   - repo: https://github.com/pycqa/flake8
-    rev: 6.0.0
+    rev: 7.1.1
     hooks:
       - id: flake8
         language: python
@@ -35,6 +35,6 @@ repos:
           - mccabe
           - yesqa
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: 'v1.0.1'
+    rev: 'v1.11.1'
     hooks:
       - id: mypy

HISTORY.md

@@ -1,5 +1,11 @@
 # History
 
+## 0.5.0 (2024-08-07)
+
+- Removed templating
+- Added support for Python 3.12
+- Dropped support for Python 3.8
+
 ## 0.4.2 (2023-06-09)
 
  - Replace pandas append function with concat

README.md

@@ -6,26 +6,20 @@
 [![Documentation Status](https://img.shields.io/badge/docs-passing-4a4c4c1.svg)](https://comic.github.io/evalutils/)
 [![Code style](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/ambv/black)
 
-evalutils helps challenge administrators easily create evaluation
-containers for grand-challenge.org.
+evalutils contains useful functions for evaluating machine learning models in the context of medical imaging.
 
   - Free software: MIT license
   - Documentation: <https://comic.github.io/evalutils/>.
 
 ## Features
 
-  - Generation your challenge evaluation project boilerplate using
-    [Cookiecutter](https://github.com/audreyr/cookiecutter)
-  - Scripts to build, test and export your generated docker container
-    for grand-challenge.org
-  - Loading of CSV, ITK and Pillow compatible prediction files
-  - Validation of submitted predictions
-  - Interface to SciKit-Learn metrics and Pandas aggregations
   - Bounding box annotations with Jaccard Index calculations
+  - Calculations of bootstrapped ROC curves
+  - Scoring for detection tasks
+  - Efficient calculation of confusion matrices, jaccard scores, dice scores, hausdorff distances,
+    absolute volume differences, and relative volume differences
 
 ## Getting Started
 
-[evalutils](https://github.com/comic/evalutils) requires Python 3.8 or
-above, and can be installed from `pip`.
-Please see the [Getting Started](https://comic.github.io/evalutils/usage.html)
-documentation for more details.
+[evalutils](https://github.com/comic/evalutils) requires Python 3.9 or above, and can be installed from `pip`.
+Please see the [Getting Started](https://comic.github.io/evalutils/usage.html) documentation for more details.

docs/conf.py

@@ -20,7 +20,6 @@
 import os
 import sys
 from importlib.metadata import version as _get_version
-from typing import Dict, List
 
 evalutils_version = _get_version("evalutils")
 
@@ -111,7 +110,7 @@ def setup(app):
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path: List[str] = []
+html_static_path: list[str] = []
 
 
 # -- Options for HTMLHelp output ---------------------------------------
@@ -122,7 +121,7 @@ def setup(app):
 
 # -- Options for LaTeX output ------------------------------------------
 
-latex_elements: Dict[str, str] = {
+latex_elements: dict[str, str] = {
     # The paper size ('letterpaper' or 'a4paper').
     #
     # 'papersize': 'letterpaper',

docs/index.rst

@@ -1,28 +1,14 @@
 Welcome to evalutils's documentation!
 ======================================
 
-The automated evaluation system on `Grand Challenge`_ will run an instance of
-your evaluation docker container image on each new submission.
-The users submission will be extracted on ``/input/``, and your container
-is expected to calculate all of the metrics for this submission, and write them
-to ``/output/metrics.json``.
-If the metrics cannot be calculated, the container should write to ``stderr``
-and the last line of this will be passed to the user so that they can debug
-their submission.
-
-`evalutils`_ helps you do this by providing a package that helps you create
-a project structure, load and validate the submissions, score the submission,
-write the json file, and package this in a docker container image so that
-you can then upload it to `Grand Challenge`_.
+`evalutils`_ contains useful functions for evaluating machine learning models in the context of medical imaging.
 
 .. toctree::
    :maxdepth: 2
    :caption: Contents:
 
    installation
-   usage
    modules
-   contributing
 
 Indices and tables
 ==================

docs/modules.rst

@@ -2,27 +2,6 @@
 Modules
 =======
 
-
-Evalutils
----------
-
-.. py:module:: evalutils
-
-.. automodule:: evalutils.evalutils
-   :members:
-
-IO
---
-
-.. automodule:: evalutils.io
-   :members:
-
-Validators
-----------
-
-.. automodule:: evalutils.validators
-   :members:
-
 Scorers
 -------
 
@@ -37,8 +16,8 @@ Annotations
 .. autoclass:: BoundingBox()
    :members:
 
-Statistics
-----------
+Stats
+-----
 
 .. automodule:: evalutils.stats
    :members: