Merge pull request #22 from matthias-baer/master

Migrate to pyproject.toml

.github/workflows/check.yml

@@ -25,7 +25,7 @@ jobs:
     - name: Install fftw3 libs (Linux)
       if: runner.os == 'Linux'
       run: |
-        sudo apt-get install -y libfftw3-dev libfftw3-3
+        sudo apt-get install -y libfftw3-dev libfftw3-double3
     - name: Install fftw3 libs (macOS)
       if: runner.os == 'macOS'
       run: |

.gitignore

@@ -65,6 +65,7 @@ target/
 *.rst~
 
 _version_save.py
+_version.py
 
 # extracted test files
 tests/data/*__*.txt
@@ -75,3 +76,6 @@ tests/data/*__*.txt
 *bib.sav
 
 .idea
+
+# used by pyenv-virtualenv:
+.python-version

CHANGELOG

@@ -1,3 +1,7 @@
+0.4.9
+ - fix: support numpy 2
+ - setup: bumpy scikit-image to 0.21.0 (API)
+ - setup: migrate to pyproject.toml
 0.4.8
  - fix: cut-off radius too small in fmap_2d algorithm (#19)
 0.4.7

odtbrain/__init__.py

@@ -10,7 +10,6 @@
 from ._prepare_sino import sinogram_as_radon, sinogram_as_rytov
 from ._translate_ri import odt_to_ri, opt_to_ri
 from ._version import version as __version__
-from ._version import longversion as __version_full__
 
 from . import apple
 from . import util

odtbrain/_alg3d_bpp.py

@@ -252,7 +252,7 @@ def backpropagate_3d(uSin, angles, res, nm, lD=0, coords=None,
 
     # setup dtype
     if dtype is None:
-        dtype = np.float_
+        dtype = np.float64
     dtype = np.dtype(dtype)
     if dtype.name not in ["float32", "float64"]:
         raise ValueError("dtype must be float32 or float64!")

odtbrain/_alg3d_bppt.py

@@ -579,7 +579,7 @@ def backpropagate_3d_tilted(uSin, angles, res, nm, lD=0,
 
     # setup dtype
     if dtype is None:
-        dtype = np.float_
+        dtype = np.float64
     dtype = np.dtype(dtype)
     if dtype.name not in ["float32", "float64"]:
         raise ValueError("dtype must be float32 or float64!")

odtbrain/_prepare_sino.py

@@ -94,7 +94,7 @@ def sinogram_as_radon(uSin, align=True):
         # slices one by one.
         phiR = np.angle(uSin)
         for ii in range(len(phiR)):
-            phiR[ii] = unwrap_phase(phiR[ii], seed=47)
+            phiR[ii] = unwrap_phase(phiR[ii], rng=47)
 
     if align:
         align_unwrapped(phiR)
@@ -169,7 +169,7 @@ def sinogram_as_rytov(uSin, u0=1, align=True):
         # data. Since we have a sinogram, we need to pass it the
         # slices one by one.
         for ii in range(len(phiR)):
-            phiR[ii] = unwrap_phase(phiR[ii], seed=47)
+            phiR[ii] = unwrap_phase(phiR[ii], rng=47)
 
     if align:
         align_unwrapped(phiR)

pyproject.toml

@@ -0,0 +1,51 @@
+[build-system]
+# Defined by PEP 518:
+requires = [
+    # for version management
+    "setuptools>=45",
+    "setuptools_scm[toml]>=6.2",
+]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "ODTbrain"
+authors = [
+    # In alphabetical order.
+    { name = "Paul Müller" },
+]
+maintainers = [
+    { name = "Paul Müller", email = "[email protected]" },
+]
+description = "Algorithms for diffraction tomography"
+readme = "README.rst"
+requires-python = ">=3.5, <4"
+keywords = ["odt", "opt", "diffraction", "born", "rytov", "radon",
+    "backprojection", "backpropagation", "inverse problem",
+    "Fourier diffraction theorem", "Fourier slice theorem"]
+classifiers = [
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3",
+    "Topic :: Scientific/Engineering :: Visualization",
+    "Intended Audience :: Science/Research"
+]
+license = {file = "LICENSE"}
+dependencies = [
+    "numexpr",
+    "numpy>=1.7.0",
+    "pyfftw>=0.9.2,<1",
+    "scikit-image>=0.21.0,<1",
+    "scipy>=1.4.0,<2"
+]
+dynamic = ["version"]
+
+[project.urls]
+source = "https://github.com/RI-imaging/ODTbrain"
+tracker = "https://github.com/RI-imaging/ODTbrain/Issues"
+
+[tool.setuptools_scm]
+write_to = "odtbrain/_version.py"
+version_scheme = "post-release"
+
+[tool.setuptools.packages.find]
+where = ["."]
+include = ["odtbrain"]

tests/test_apple.py

@@ -66,7 +66,7 @@ def test_correct_reproduce():
         write_results(myframe, fo)
 
     data = fo.flatten().view(float)
-    assert np.allclose(data, get_results(myframe))
+    assert np.allclose(data, get_results(myframe), atol=2.E-6)
 
 
 def test_correct_values():