Merge pull request #105 from BrainLesion/103-bug-weird-installation-error-when-using-a-python-312-conda-environment

103 bug weird installation error when using a python 312 conda environment

Author: neuronflow

.github/workflows/tests.yml

@@ -16,7 +16,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.10", "3.11"]
+        python-version: ["3.10", "3.11", "3.12"]
 
     steps:
     - uses: actions/checkout@v3

README.md

@@ -115,6 +115,12 @@ Please credit the authors by citing their work.
 ### Registration
 We currently provide support for [ANTs](https://github.com/ANTsX/ANTs) (default), [Niftyreg](https://github.com/KCL-BMEIS/niftyreg) (Linux), eReg (experimental)
 
+> [!NOTE]  
+> For python `3.13` the installation can currently fail with the error `Failed to build antspyx`.
+> This usually means that there is no pre-built wheel for the package and it has to be build locally.
+> This will require cmake (install e.g. with `pip install cmake`) and quite some time.
+> Rerunning the installation with cmake installed should fix the error.
+
 ### Atlas Reference
 We provide the SRI-24 atlas from this [publication](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2915788/).
 However, custom atlases in NIfTI format are supported.

pyproject.toml

@@ -14,7 +14,7 @@ exclude = [
 ]
 
 name = "brainles_preprocessing"
-version = "0.0.0"                                                                                                              # will be overwritten by poetry-dynamic-versioning but needs to be set
+version = "0.0.0.dev"                                                                                                              # will be overwritten by poetry-dynamic-versioning but needs to be set
 description = "Tool for preprocessing tasks in biomedical imaging, with a focus on (but not limited to) multi-modal brain MRI"
 license = "Apache-2.0"
 
@@ -59,7 +59,7 @@ numpy = "^1.23.0"
 antspyx = "^0.4.2"
 
 # hd-bet reqs
-brainles_hd_bet = ">=0.0.8"
+brainles_hd_bet = ">=0.0.10"
 
 # utils
 tqdm = "^4.64.1"
@@ -75,7 +75,7 @@ all = ["ereg"]
 ereg = ["ereg"]
 
 
-[tool.poetry.dev-dependencies]
+[tool.poetry.group.dev.dependencies]
 pytest = ">=8.1.1"
 
 [tool.poetry.group.docs]

tests/test_registrators.py

@@ -15,15 +15,15 @@ def get_method_and_extension(self):
         return "ants", "mat"
 
 
-class TestNiftyRegRegistratorRegistrator(RegistratorBase, unittest.TestCase):
+class TestNiftyRegRegistrator(RegistratorBase, unittest.TestCase):
     def get_registrator(self):
         return NiftyRegRegistrator()
 
     def get_method_and_extension(self):
         return "niftyreg", "txt"
 
 
-class TestEregRegistratorRegistrator(RegistratorBase, unittest.TestCase):
+class TestEregRegistrator(RegistratorBase, unittest.TestCase):
     def get_registrator(self):
         return eRegRegistrator()