Merge remote-tracking branch 'refs/remotes/origin/master'

.gitignore

@@ -6,4 +6,5 @@ build
 dist
 .vscode/launch.json
 .vscode/settings.json
-tests/orb_tomog_regression_tests.py
\ No newline at end of file
+tests/orb_tomog_regression_tests.py
+/env

env.nix

+# Build with
+#
+#     nix-build env.nix -o env
+#
+# VSCode will see the generated ./env as a virtualenv and offer it as an
+# interpreter in the ‘Python: Select Interpreter’ command.
+#
+# To run Python with all dependencies available, use the wrapper script
+# env/bin/python.
+
+{ nixpkgs ? <nixpkgs>, pkgs ? import nixpkgs {} }:
+
+with pkgs;
+
+poetry2nix.mkPoetryEnv {
+  projectDir = ./.;
+  preferWheels = true;
+  overrides = poetry2nix.overrides.withDefaults (self: super: {
+    # We need to explicityly specify the dependency on the plotting backend.
+    # Use tkinter for simplicity.
+    matplotlib = super.matplotlib.overridePythonAttrs (attrs: {
+      propagatedBuildInputs = attrs.propagatedBuildInputs ++ [
+        self.tkinter
+      ];
+    });
+  });
+}

proxtoolbox/proxoperators/P_Sparsity.py

@@ -121,7 +121,7 @@ class P_Sparsity_Superpixel(P_Sparsity):
         # Set the superpixel size:
         self.superpixel_size = experiment.superpixel_size
         # Bin the support:
-        if self.support is not 1:
+        if self.support != 1:
             self.support = bin_array(self.support, self.superpixel_size)
             self.support = self.support / max(self.support)
         # Assert that the binning+upsampling conserves the array size

proxtoolbox/utils/Procrustes.py

@@ -72,7 +72,7 @@ def procrustes(X, Y, scaling=True, reflection='best'):
     V = Vt.T
     T = np.dot(V, U.T)
 
-    if reflection is not 'best':
+    if reflection != 'best':
 
         # does the current solution use a reflection?
         have_reflection = np.linalg.det(T) < 0

pyproject.toml

@@ -10,6 +10,7 @@ numpy = "^1.19.2"
 scikit-image = "^0.17.2"
 matplotlib = "^3.3.2"
 scipy = "^1.5.2"
+h5py = "^2.10.0"
 
 [tool.poetry.dev-dependencies]
 pylint = "^2.6.0"

setup.py

@@ -105,11 +105,11 @@ setup(
     # To provide executable scripts, use entry points in preference to the
     # "scripts" keyword. Entry points provide cross-platform support and allow
     # pip to create the appropriate form of executable for the target platform.
-    entry_points={
-        'console_scripts': [
-            'sample=sample:main',
-        ],
-    },
+    #entry_points={
+    #    'console_scripts': [
+    #        'sample=sample:main',
+    #    ],
+    #},
 
     # Some packages which are required for the good operation of ProxPython
     install_requires=['numpy', 'scikit-image', 'matplotlib', 'scipy']