From 54c8bd41522fb2049de8564ccad635dc7ab4285c Mon Sep 17 00:00:00 2001
From: Joeran Bosma <joeran@bosma.co>
Date: Thu, 10 Oct 2024 12:12:57 +0200
Subject: [PATCH] Bugfix and update versions

---
 requirements_dev.txt        | 14 +++++++-------
 setup.cfg                   |  1 +
 setup.py                    |  2 +-
 src/picai_eval/eval.py      |  2 +-
 tests/Development-README.md |  4 ++--
 tox.ini                     | 11 ++++-------
 6 files changed, 16 insertions(+), 18 deletions(-)

diff --git a/requirements_dev.txt b/requirements_dev.txt
index 9ddac48..0a9d1b3 100644
--- a/requirements_dev.txt
+++ b/requirements_dev.txt
@@ -1,8 +1,8 @@
-flake8==3.9.2
-tox==3.24.3
-pytest==6.2.5
-pytest-cov==2.12.1
-mypy===0.910
+flake8==7.1.1
+tox==4.18.1
+pytest==8.3.2
+pytest-cov==5.0.0
+mypy===1.11.2
+build==1.2.2
+twine==5.1.1
 gcapi
-build
-twine
diff --git a/setup.cfg b/setup.cfg
index 4199731..a589bdf 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -12,6 +12,7 @@ classifiers =
     Programming Language :: Python :: 3.9
     Programming Language :: Python :: 3.10
     Programming Language :: Python :: 3.11
+    Programming Language :: Python :: 3.12
 
 [options]
 packages =
diff --git a/setup.py b/setup.py
index ad63c74..56990f3 100644
--- a/setup.py
+++ b/setup.py
@@ -63,7 +63,7 @@ def run(self):
         long_description = fh.read()
 
     setuptools.setup(
-        version='1.4.8',  # also update version in metrics.py -> version
+        version='1.4.9',  # also update version in metrics.py -> version
         author_email='Joeran.Bosma@radboudumc.nl',
         long_description=long_description,
         long_description_content_type="text/markdown",
diff --git a/src/picai_eval/eval.py b/src/picai_eval/eval.py
index 623b67d..7a7a4cd 100755
--- a/src/picai_eval/eval.py
+++ b/src/picai_eval/eval.py
@@ -160,7 +160,7 @@ def evaluate_case(
             overlap = overlap_matrix[lesion_id, lesion_candidate_id]
             overlap -= 1  # return overlap to [0, 1]
 
-            assert overlap > min_overlap, "Overlap must be greater than min_overlap!"
+            assert overlap >= min_overlap, "Overlap must be at least `min_overlap`!"
 
             y_list.append((1, lesion_confidence, overlap))
 
diff --git a/tests/Development-README.md b/tests/Development-README.md
index 59d2073..7dd3210 100644
--- a/tests/Development-README.md
+++ b/tests/Development-README.md
@@ -29,5 +29,5 @@ AutoPEP8 for formatting (this can be done automatically on save, see e.g. https:
 # Push release to PyPI
 1. Increase version in setup.py, and set below
 2. Build: `python -m build`
-3. Test package distribution: `python -m twine upload --repository testpypi dist/*1.4.3*`
-4. Distribute package to PyPI: `python -m twine upload dist/*1.4.3*`
+3. Test package distribution: `python -m twine upload --repository testpypi dist/*1.4.9*`
+4. Distribute package to PyPI: `python -m twine upload dist/*1.4.9*`
diff --git a/tox.ini b/tox.ini
index a19af13..37dfce5 100644
--- a/tox.ini
+++ b/tox.ini
@@ -1,14 +1,12 @@
 [tox]
 minversion = 3.8.0
-envlist = py36, py37, py38, py39, flake8
+envlist = py38, py312, flake8
 isolated_build = true
 
 [gh-actions]
 python =
-    3.6: py36
-    3.7: py37
     3.8: py38
-    3.9: py39, flake8
+    3.12: py312, flake8
 
 [testenv]
 setenv =
@@ -19,13 +17,12 @@ commands =
     pytest --basetemp={envtmpdir}
 
 [testenv:flake8]
-basepython = python3.9
+basepython = python3.12
 deps = flake8
 commands = flake8 src tests
 
 [testenv:mypy]
-basepython = python3.9
+basepython = python3.12
 deps =
     -r{toxinidir}/requirements_dev.txt
 commands = mypy src
-