Merge pull request #272 from cabouman/prerelease

merge for release 0.3.1

Author: cabouman

clean.sh

@@ -0,0 +1,8 @@
+#!/bin/bash
+
+echo "Running clean.sh"
+/bin/rm -v -r dist 2> /dev/null
+/bin/rm -v -r build 2> /dev/null
+/bin/rm -v -r svmbir.egg-info 2> /dev/null
+/bin/rm -v svmbir/*.so 2> /dev/null
+/bin/rm -v svmbir/interface_cy_c.c 2> /dev/null

demo.zip

@@ -18,10 +18,9 @@
 tilt_angle = np.pi/2 # Tilt range of +-90deg
 
 # Reconstruction parameters
-snr_db = 30.0
-sharpness = 0.0
+snr_db = 40.0
+sharpness = 1.0
 T = 0.1
-p = 1.2
 
 # Display parameters
 vmin = 1.0
@@ -40,7 +39,7 @@
 (num_views, num_slices, num_channels) = sino.shape
 
 # Perform fixed resolution MBIR reconstruction
-recon = svmbir.recon(sino, angles, T=T, p=p, sharpness=sharpness, snr_db=snr_db)
+recon = svmbir.recon(sino, angles, sharpness=sharpness, snr_db=snr_db, T=T)
 
 # Compute Normalized Root Mean Squared Error
 nrmse = svmbir.phantom.nrmse(recon, phantom)

demo/demo_3D_shepp_logan.py

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-# Builds the sdist and wheels for python 3.8, 3.9, 3.10
+# Builds the sdist and wheels for python 3.7-3.10
 #
 # RUN AS: source build_dist.sh
 # NOT AS: ./build_dist.sh
@@ -9,15 +9,17 @@
 # NOTES:
 #   * Principally for macOS wheels. For linux, build using 'manylinux' from docker image
 #
-#   * starting in v0.3.0, numpy dependency is pinned to 1.22.*, which supports Python 3.8-3.10
+#   * Building with numpy==1.21.6, wheels appear compatible with numpy 1.21-1.23.5 at least
+#     The install requirement numpy>=1.21 then allows support of python 3.7-3.10
 #
 #   * macOS/x86_64: Run build on macOS 10.14 for binaries to be compatibile with macOS>=10.14.
 #     Wheels are delocated to fix a library incompatibility across macOS>=10.14.
 #
-#   * macOS/arm64 (M1,M2): Limited to python >= 3.8. 'delocation' section will be skipped.
+#   * macOS/arm64 (M1,M2): Limited to python >= 3.8.
+#     Wheels are delocated to include any linked libraries (OpenMP).
 #
 
-python_versions=("3.8" "3.9" "3.10")
+python_versions=("3.7" "3.8" "3.9" "3.10")
 CC=gcc
 
 # check for a valid compiler
@@ -48,6 +50,8 @@ for pyv in ${python_versions[@]}; do
     echo "**** Create environment ${pyv} *****"
     conda create --name sv${pyv} python=$pyv --yes
     conda activate sv${pyv}
+    # see note above about numpy version
+    pip install numpy==1.21.6
     pip install -r requirements.txt
     pip install setuptools
 
@@ -71,8 +75,8 @@ pip install -r requirements.txt
 pip install setuptools
 python setup.py sdist
 
-# section for pre-M1 macs only
-if [ $(uname -s) = "Darwin" ] && [ $(uname -m) = "x86_64" ]; then
+# Delocate to add libgomp.dylib to wheel (macOS only)
+if [ $(uname -s) = "Darwin" ]; then
     pip install delocate
     echo "******* Delocating wheels *******"
     cd dist

dev_scripts/build_dist.sh

@@ -30,10 +30,11 @@ function repair_wheel {
 
 # Compile wheels
 #for PYBIN in /opt/python/*/bin; do
-for PYBIN in /opt/python/{cp38,cp39,cp310,pp38,pp39}*/bin; do
+for PYBIN in /opt/python/{cp37,cp38,cp39,cp310,pp37,pp38,pp39}*/bin; do
     echo "***"
     echo "*** building for $PYBIN"
     #"${PYBIN}/pip" install -r /io/dev_scripts/dev-requirements.txt
+    "${PYBIN}/pip" install numpy==1.21.6    # build with 1.21.6 seems compatible w/ numpy 1.21-1.23
     CC=gcc "${PYBIN}/pip" wheel /io/ --no-deps -w wheelhouse/
     #CC=gcc "${PYBIN}/python" setup.py bdist_wheel
 done

dev_scripts/clean_install_conda_svmbir_docs.sh renamed to dev_scripts/clean_install_all.sh

@@ -8,8 +8,8 @@
 #
 # Set these accordingly:
 
-python_versions=("3.8" "3.9" "3.10")
-svmbir_version=0.3.0
+python_versions=("3.7" "3.8" "3.9" "3.10")
+svmbir_version=0.3.1
 
 echo "*********************************************************"
 echo "**** Test install "

dev_scripts/manylinux.sh

@@ -0,0 +1 @@
+*.png filter=lfs diff=lfs merge=lfs -text

dev_scripts/test_pypi.sh

@@ -12,7 +12,7 @@ Features
 
 System Requirements
 -------------------
-* Python 3.8-3.10
+* Python 3.7-3.10
 
 Local builds also require,