Provide base for modernisation

.github/workflows/ci.yaml

@@ -0,0 +1,22 @@
+on: [push, pull_request]
+
+defaults:
+  run:
+    shell: bash
+
+jobs:
+
+  test:
+    runs-on: ubuntu-18.04
+    strategy:
+      matrix:
+        python-version: [3.6, 3.7, 3.8, 3.9]
+      fail-fast: false
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - run: pip install -U pip -r requirements.txt
+      - run: bash make.sh
+      - run: python malis/test_malis.py

make.sh

@@ -1,5 +1,6 @@
 #!/usr/bin/env bash
+set -ex
 cd malis
 python setup.py build_ext --inplace
 printf "BUILD COMPLETE\n"
-cd ..
+cd ..

malis/test_malis.py

@@ -5,44 +5,44 @@
 import malis as m
 
 
-print "Can we make the `nhood' for an isotropic 3d dataset"
-print "corresponding to a 6-connected neighborhood?"
+print("Can we make the `nhood' for an isotropic 3d dataset")
+print("corresponding to a 6-connected neighborhood?")
 nhood = m.mknhood3d(1)
-print nhood
+print(nhood
 
-print "Can we make the `nhood' for an anisotropic 3d dataset"
-print "corresponding to a 4-connected neighborhood in-plane"
-print "and 26-connected neighborhood in the previous z-plane?"
+print("Can we make the `nhood' for an anisotropic 3d dataset")
+print("corresponding to a 4-connected neighborhood in-plane")
+print("and 26-connected neighborhood in the previous z-plane?")
 nhood = m.mknhood3d_aniso(1,1.8)
-print nhood
+print(nhood)
 
 segTrue = np.array([0, 1, 1, 1, 2, 2, 0, 5, 5, 5, 5],dtype=np.uint64);
 node1 = np.arange(segTrue.shape[0]-1,dtype=np.uint64)
 node2 = np.arange(1,segTrue.shape[0],dtype=np.uint64)
 nVert = segTrue.shape[0]
 edgeWeight = np.array([0, 1, 2, 0, 2, 0, 0, 1, 2, 2.5],dtype=np.float32);
 edgeWeight = edgeWeight/edgeWeight.max()
-print segTrue
-print edgeWeight
+print(segTrue)
+print(edgeWeight)
 
 nPairPos = m.malis_loss_weights(segTrue, node1, node2, edgeWeight, 1)
 nPairNeg = m.malis_loss_weights(segTrue, node1, node2, edgeWeight, 0)
-print np.vstack((nPairPos,nPairNeg))
-# print nPairNeg
+print(np.vstack((nPairPos,nPairNeg))
+# print(nPairNeg
 
 
 
 idxkeep = (edgeWeight > 0).astype(np.int32)
 cc = m.connected_components(nVert,node1,node2,idxkeep)
-print cc
+print(cc)
 
 
 # node1, node2 = m.nodelist_like((2,3,4),-np.eye(3))
-# print node1
-# print node2
+# print(node1)
+# print(node2)
 
 datadir = '/groups/turaga/turagalab/greentea/project_data/dataset_06/fibsem_medulla_7col/tstvol-520-1-h5/'
-print  "[" +str(datetime.datetime.now())+"]" + "Reading test volume from " + datadir
+print( "[" +str(datetime.datetime.now())+"]" + "Reading test volume from " + datadir)
 # hdf5_raw_file = datadir + 'img_normalized.h5'
 hdf5_gt_file = datadir + 'groundtruth_seg.h5'
 # hdf5_aff_file = datadir + 'groundtruth_aff.h5'
@@ -56,28 +56,28 @@
 # hdf5_aff = h5py.File(hdf5_aff_file, 'r')
 
 seg = np.asarray(h5seg['main']).astype(np.int32)
-print "[" +str(datetime.datetime.now())+"]" + "Making affinity graph..."
+print("[" +str(datetime.datetime.now())+"]" + "Making affinity graph...")
 aff = m.seg_to_affgraph(seg,nhood)
 
 
-print "[" +str(datetime.datetime.now())+"]" + "Affinity shape:" + str(aff.shape)
-print "[" +str(datetime.datetime.now())+"]" + "Computing connected components..."
+print("[" +str(datetime.datetime.now())+"]" + "Affinity shape:" + str(aff.shape))
+print("[" +str(datetime.datetime.now())+"]" + "Computing connected components...")
 cc,ccSizes = m.connected_components_affgraph(aff,nhood)
-print "[" +str(datetime.datetime.now())+"]" + "Making affinity graph again..."
+print("[" +str(datetime.datetime.now())+"]" + "Making affinity graph again...")
 aff2 = m.seg_to_affgraph(cc,nhood)
-print "[" +str(datetime.datetime.now())+"]" + "Computing connected components..."
+print("[" +str(datetime.datetime.now())+"]" + "Computing connected components...")
 cc2,ccSizes2 = m.connected_components_affgraph(aff2,nhood)
 
-print "[" +str(datetime.datetime.now())+"]" + "Comparing 'seg' and 'cc':"
+print("[" +str(datetime.datetime.now())+"]" + "Comparing 'seg' and 'cc':")
 # ri,fscore,prec,rec = m.rand_index(seg,cc)
-# print "\tRand index: %f, fscore: %f, prec: %f, rec: %f" % (ri,fscore,prec,rec)
+# print("\tRand index: %f, fscore: %f, prec: %f, rec: %f" % (ri,fscore,prec,rec))
 V_rand,V_rand_split,V_rand_merge = m.compute_V_rand_N2(seg,cc)
-print "[" +str(datetime.datetime.now())+"]" + "\tV_rand: %f, V_rand_split: %f, V_rand_merge: %f" % (V_rand,V_rand_split,V_rand_merge)
+print("[" +str(datetime.datetime.now())+"]" + "\tV_rand: %f, V_rand_split: %f, V_rand_merge: %f" % (V_rand,V_rand_split,V_rand_merge))
 
-print "[" +str(datetime.datetime.now())+"]" + "Comparing 'cc' and 'cc2':"
+print("[" +str(datetime.datetime.now())+"]" + "Comparing 'cc' and 'cc2':")
 # ri,fscore,prec,rec = m.rand_index(cc,cc2)
-# print "\tRand index: %f, fscore: %f, prec: %f, rec: %f" % (ri,fscore,prec,rec)
+# print("\tRand index: %f, fscore: %f, prec: %f, rec: %f" % (ri,fscore,prec,rec)
 V_rand,V_rand_split,V_rand_merge = m.compute_V_rand_N2(cc,cc2)
-print "[" +str(datetime.datetime.now())+"]" + "\tV_rand: %f, V_rand_split: %f, V_rand_merge: %f" % (V_rand,V_rand_split,V_rand_merge)
+print("[" +str(datetime.datetime.now())+"]" + "\tV_rand: %f, V_rand_split: %f, V_rand_merge: %f" % (V_rand,V_rand_split,V_rand_merge))
 
 

requirements.txt

@@ -1,7 +1,9 @@
 # runtime
 Cython>=0.24
-numpy>=1.9
-scipy  # unknown minimum version...
+# https://github.com/TuragaLab/malis/issues/6
+numpy>=1.9,<1.12
+# https://github.com/TuragaLab/malis/issues/8
+scipy<1.3
 
 # tests
 h5py

setup.py

@@ -7,45 +7,52 @@
 include_dirs = [
     os.path.join(os.path.dirname(os.path.abspath(__file__)), "malis"),
     os.path.dirname(get_python_inc()),
-    get_python_inc()
+    get_python_inc(),
 ]
 library_dirs = [
     os.path.join(os.path.dirname(os.path.abspath(__file__)), "malis"),
-    get_config_var("LIBDIR")
+    get_config_var("LIBDIR"),
 ]
 
 # Remove the "-Wstrict-prototypes" compiler option, which isn't valid for C++.
 cfg_vars = get_config_vars()
 if "CFLAGS" in cfg_vars:
     cfg_vars["CFLAGS"] = cfg_vars["CFLAGS"].replace("-Wstrict-prototypes", "")
 
+
 class build_ext(_build_ext):
     def finalize_options(self):
         _build_ext.finalize_options(self)
         # Prevent numpy from thinking it is still in its setup process:
         __builtins__.__NUMPY_SETUP__ = False
         import numpy
+
         self.include_dirs.append(numpy.get_include())
 
-setup(name='malis',
-      version='1.0',
-      description='MALIS segmentation loss function',
-      url='https://github.com/TuragaLab/malis',
-      author='Srinivas Turaga',
-      author_email='turagas@janelia.hhmi.org',
-	  cmdclass=dict(
-            build_ext=build_ext
-    	),
-      license='MIT',
-      install_requires=['cython','numpy','h5py','scipy'],	
-	  setup_requires=['cython','numpy','scipy'],	
-      packages=['malis'],
-         ext_modules = [Extension("malis.malis",
-                         ["malis/malis.pyx", "malis/malis_cpp.cpp"],
-                         include_dirs=include_dirs,
-                         library_dirs=library_dirs,
-                         language='c++',
-                         # std= 'c++11',
-                         extra_link_args=["-std=c++11"],
-                         extra_compile_args=["-std=c++11", "-w"])],
-      zip_safe=False)
+
+setup(
+    name="malis",
+    version="1.0",
+    description="MALIS segmentation loss function",
+    url="https://github.com/TuragaLab/malis",
+    author="Srinivas Turaga",
+    author_email="turagas@janelia.hhmi.org",
+    cmdclass=dict(build_ext=build_ext),
+    license="MIT",
+    install_requires=["cython", "numpy", "h5py", "scipy"],
+    setup_requires=["cython", "numpy", "scipy"],
+    packages=["malis"],
+    ext_modules=[
+        Extension(
+            "malis.malis",
+            ["malis/malis.pyx", "malis/malis_cpp.cpp"],
+            include_dirs=include_dirs,
+            library_dirs=library_dirs,
+            language="c++",
+            # std= 'c++11',
+            extra_link_args=["-std=c++11"],
+            extra_compile_args=["-std=c++11", "-w"],
+        )
+    ],
+    zip_safe=False,
+)