Merge branch 'master' into feature/fix-matplotlib-test-flakiness-on-w…

…indows

.github/workflows/build.yml

@@ -46,9 +46,9 @@ jobs:
       OVERRIDE_VERSION: ${{ github.event.inputs.override_version }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: actions/setup-python@v2
+      - uses: actions/setup-python@v4
         name: Install Python
         with:
           # For the sdist we should be as conservative as possible with our
@@ -87,7 +87,7 @@ jobs:
           zip "$zipfile" -r "$stem"
           rm -r "$stem"
 
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v3
         with:
           name: sdist
           path: |
@@ -112,9 +112,9 @@ jobs:
       OVERRIDE_VERSION: ${{ github.event.inputs.override_version }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: actions/setup-python@v2
+      - uses: actions/setup-python@v4
         name: Install Python
         with:
           # This is about the build environment, not the released wheel version.
@@ -134,7 +134,7 @@ jobs:
           if [[ ! -z "$OVERRIDE_VERSION" ]]; then echo "$OVERRIDE_VERSION" > VERSION; fi
           python -m cibuildwheel --output-dir wheelhouse
 
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v3
         with:
           name: wheels
           path: ./wheelhouse/*.whl
@@ -157,9 +157,9 @@ jobs:
 
     steps:
       - name: Download build artifacts to local runner
-        uses: actions/download-artifact@v2
+        uses: actions/download-artifact@v3
 
-      - uses: actions/setup-python@v2
+      - uses: actions/setup-python@v4
         name: Install Python
         with:
           python-version: '3.7'

.github/workflows/build_documentation.yml

@@ -9,9 +9,9 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: actions/setup-python@v2
+      - uses: actions/setup-python@v4
         name: Install Python
         with:
           python-version: '3.8'
@@ -43,7 +43,7 @@ jobs:
           #   -T : display a full traceback if a Python exception occurs
 
       - name: Upload built PDF files
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         with:
           name: qutip_pdf_docs
           path: doc/_build/latex/*
@@ -59,7 +59,7 @@ jobs:
           #   -T : display a full traceback if a Python exception occurs
 
       - name: Upload built HTML files
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         with:
           name: qutip_html_docs
           path: doc/_build/html/*

.github/workflows/tests.yml

@@ -24,7 +24,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, macos-latest]
+        os: [ubuntu-latest]
         # Test other versions of Python in special cases to avoid exploding the
         # matrix size; make sure to test all supported versions in some form.
         python-version: ["3.9"]
@@ -35,6 +35,13 @@ jobs:
         # the lack of a variable is _always_ false-y, and the defaults lack all
         # the special cases.
         include:
+          # Needs an older version of Python because conda doesn't build old
+          # SciPy versions for Python 3.9.
+          - case-name: MacOS
+            os: macos-latest
+            python-version: "3.9"
+            nomkl: 1
+
           # Needs an older version of Python because conda doesn't build old
           # SciPy versions for Python 3.9.
           - case-name: old SciPy
@@ -95,7 +102,7 @@ jobs:
             pytest-extra-options: "-W ignore::ImportWarning -k 'not (test_correlation or test_interpolate or test_mcsolve)'"
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - uses: conda-incubator/setup-miniconda@v2
         with:

doc/changes/2011.bugfix

@@ -0,0 +1 @@
+Fix the hinton visualization method to plot the matrix instead of its transpose.

doc/changes/2012.bugfix

@@ -0,0 +1 @@
+Fix the hinton visualization method to take into account all the matrix coefficients to set the squares scale, instead of only the diagonal coefficients.

qutip/steadystate.py

@@ -1148,7 +1148,7 @@ def _pseudo_inverse_dense(L, rhoss, w=None, **pseudo_args):
         try:
             LIQ = np.linalg.solve(L.full(), Q)
         except Exception:
-            LIQ = np.linalg.lstsq(L.full(), Q)[0]
+            LIQ = np.linalg.lstsq(L.full(), Q, rcond=None)[0]
 
         R = np.dot(Q, LIQ)
 

qutip/visualization.py

@@ -166,8 +166,8 @@ def _cb_labels(left_dims):
     return [
         map(fmt.format, basis_labels) for fmt in
         (
+            r"$\langle{}|$",
             r"$|{}\rangle$",
-            r"$\langle{}|$"
         )
     ]
 
@@ -303,7 +303,7 @@ def hinton(rho, xlabels=None, ylabels=None, title=None, ax=None, cmap=None,
 
     height, width = W.shape
 
-    w_max = 1.25 * max(abs(np.diag(np.array(W))))
+    w_max = 1.25 * max(abs(np.array(W)).flatten())
     if w_max <= 0.0:
         w_max = 1.0
 
@@ -331,8 +331,8 @@ def color_fn(w):
             _x = x + 1
             _y = y + 1
             _blob(
-                _x - 0.5, height - _y + 0.5, W[x, y], w_max,
-                min(1, abs(W[x, y]) / w_max), color_fn=color_fn, ax=ax)
+                _x - 0.5, height - _y + 0.5, W[y, x], w_max,
+                min(1, abs(W[y, x]) / w_max), color_fn=color_fn, ax=ax)
 
     # color axis
     vmax = np.pi if color_style == "phase" else abs(W).max()