Fix broken links

.github/workflows/nightly_ci.yaml

@@ -25,13 +25,16 @@ jobs:
       with:
         use-quiet-mode: 'yes'
         folder-path: tutorials-v${{ matrix.qutip-version }}
+        #use config file to define 403 and 405 errors as valid links 
+        #(APS blocks this link check)
+        config-file: mlc_config.json
 
     - name: Setup Mambaforge
       uses: conda-incubator/setup-miniconda@v2
       with:
         miniforge-variant: Mambaforge
         miniforge-version: latest
-        activate-environment: test-environment
+        activate-environment: test-environment-v${{ matrix.qutip-version }}
         use-mamba: true
 
     - name: Get Date
@@ -51,7 +54,7 @@ jobs:
 
     - name: Install environment
       if: steps.cache.outputs.cache-hit != 'true'
-      run: mamba env update -n test-environment -f test_environment.yml
+      run: mamba env update -n test-environment-v${{ matrix.qutip-version }} -f test_environment-v${{ matrix.qutip-version }}.yml
 
     - name: Install QuTiP
       run: |

.github/workflows/notebook_ci.yaml

@@ -27,13 +27,16 @@ jobs:
       with:
         use-quiet-mode: 'yes'
         folder-path: tutorials-v${{ matrix.qutip-version }}
+        #use config file to define 403 and 405 errors as valid links 
+        #(APS blocks this link check)
+        config-file: mlc_config.json
 
     - name: Setup Mambaforge
       uses: conda-incubator/setup-miniconda@v2
       with:
         miniforge-variant: Mambaforge
         miniforge-version: latest
-        activate-environment: test-environment
+        activate-environment: test-environment-v${{ matrix.qutip-version }}
         use-mamba: true
 
     - name: Get Date
@@ -53,7 +56,7 @@ jobs:
 
     - name: Install environment
       if: steps.cache.outputs.cache-hit != 'true'
-      run: mamba env update -n test-environment -f test_environment.yml
+      run: mamba env update -n test-environment-v${{ matrix.qutip-version }} -f test_environment-v${{ matrix.qutip-version }}.yml
 
     - name: Install QuTiP
       run: |

mlc_config.json

@@ -0,0 +1,8 @@
+{
+  "projectBaseUrl":"${workspaceFolder}",
+  "timeout": "20s",
+  "retryOn429": true,
+  "retryCount": 5,
+  "fallbackRetryDelay": "30s",
+  "aliveStatusCodes": [200, 206, 403, 405]
+}

test_environment.yml → test_environment-v4.yml

@@ -1,4 +1,4 @@
-name: test-environment
+name: test-environment-v4
 channels:
 - conda-forge
 dependencies:

test_environment-v5.yml

@@ -0,0 +1,16 @@
+name: test-environment-v5
+channels:
+- conda-forge
+dependencies:
+- python==3.12
+- pip>=22.1.2
+- numpy>=2.0.0
+- scipy>=1.9
+- matplotlib>=3.9
+- imagemagick>=7.1.0_36
+- mpmath>=1.2.1
+- pytest>=7.1.2
+- nbmake>=1.3.4
+- jupytext>=1.13.8
+- jupyter>=1.0.0
+- ipykernel>=6.17.1  # 6.18.0 was yanked but is still present on conda-forge

tutorials-v5/lectures/Lecture-5-Parametric-Amplifier.md

@@ -5,7 +5,7 @@ jupyter:
       extension: .md
       format_name: markdown
       format_version: '1.3'
-      jupytext_version: 1.13.8
+      jupytext_version: 1.16.4
   kernelspec:
     display_name: Python 3 (ipykernel)
     language: python
@@ -416,12 +416,12 @@ def plot_covariance_matrix(V, ax):
 
     ax.view_init(azim=-40, elev=60)
     ax.bar3d(xpos, ypos, zpos, dx, dy, dz, color=colors)
-    ax.axes.w_xaxis.set_major_locator(plt.IndexLocator(1, -0.5))
-    ax.axes.w_yaxis.set_major_locator(plt.IndexLocator(1, -0.5))
-    ax.axes.w_xaxis.set_ticklabels(("$q_-$", "$p_-$", "$q_+$", "$p_+$"),
-                                   fontsize=20)
-    ax.axes.w_yaxis.set_ticklabels(("$q_-$", "$p_-$", "$q_+$", "$p_+$"),
-                                   fontsize=20)
+    ax.axes.xaxis.set_major_locator(plt.IndexLocator(1, -0.5))
+    ax.axes.yaxis.set_major_locator(plt.IndexLocator(1, -0.5))
+    ax.axes.xaxis.set_ticklabels(("$q_-$", "$p_-$", "$q_+$", "$p_+$"),
+                                 fontsize=12)
+    ax.axes.yaxis.set_ticklabels(("$q_-$", "$p_-$", "$q_+$", "$p_+$"),
+                                 fontsize=12)
 ```
 
 ```python
@@ -430,7 +430,7 @@ t_idx_vec = [0, 20, 40]
 
 fig, axes = plt.subplots(
     len(t_idx_vec), 1, subplot_kw={"projection": "3d"},
-    figsize=(6, 3 * len(t_idx_vec))
+    figsize=(10, 3 * len(t_idx_vec))
 )
 
 for idx, t_idx in enumerate(t_idx_vec):

tutorials-v5/time-evolution/008_brmesolve_time_dependence.md

@@ -5,7 +5,7 @@ jupyter:
       extension: .md
       format_name: markdown
       format_version: '1.3'
-      jupytext_version: 1.13.8
+      jupytext_version: 1.16.4
   kernelspec:
     display_name: Python 3 (ipykernel)
     language: python
@@ -86,8 +86,9 @@ $$ J(\omega, t) = \kappa * e^{-t} \quad \text{for} \; \omega \geq 0$$
 ```python
 # setup dissipation
 kappa = 0.2
-a_ops = [[a + a.dag(), "{kappa}*exp(-t)*(w>=0)".format(kappa=kappa)]]
-
+a_ops = [
+    ([a+a.dag(), f'sqrt({kappa}*exp(-t))'], '(w>=0)')
+]
 # solve
 result_brme_aops = brmesolve(H, psi0, times, a_ops, e_ops=[a.dag() * a])
 

tutorials-v5/time-evolution/009_brmesolve-cavity-QED.md

@@ -5,7 +5,7 @@ jupyter:
       extension: .md
       format_name: markdown
       format_version: '1.3'
-      jupytext_version: 1.13.8
+      jupytext_version: 1.16.4
   kernelspec:
     display_name: Python 3 (ipykernel)
     language: python
@@ -134,7 +134,7 @@ The `qutip.brmesolve()` function automatically uses the secular approximation, i
 
 ```python
 result_brme_nonsec = brmesolve(H_strong, psi0, times, a_ops,
-                               e_ops, sec_cutoff=-1)
+                               sec_cutoff=-1, e_ops=e_ops)
 fig, axes = plot_expectation_values(
     [result_brme_strong, result_brme_nonsec], ylabels=["<n_cav>", "<n_atom>"]
 )

tutorials-v5/time-evolution/013_nonmarkovian_monte_carlo.md

@@ -5,7 +5,7 @@ jupyter:
       extension: .md
       format_name: markdown
       format_version: '1.3'
-      jupytext_version: 1.16.1
+      jupytext_version: 1.16.4
   kernelspec:
     display_name: Python 3 (ipykernel)
     language: python
@@ -207,7 +207,7 @@ options = {"progress_bar": "enhanced"}  # options shared by all solvers
 ntraj = 5500
 
 H = 2 * qt.sigmap() * qt.sigmam()
-ops_and_rates = [[qt.sigmam(), Gamma_int]]
+ops_and_rates = [[qt.sigmam(), qt.coefficient(Gamma_int)]]
 psi0 = qt.basis(2, 0)
 e_ops = [H]
 ```
@@ -766,8 +766,8 @@ if results_folder_exists and NUM_BATCHES > 0:
     fit = np.polyfit(np.log(xval), yval, 1)
     print(('Approximate number of trajectories required for convergence until '
            'time t (according to linear fit):\n'
-           f'N = {np.exp(-fit[1] / fit[0]) :.2f} * '
-           f'exp( {1 / fit[0] / times3[-1] :.2f} * t )\n'))
+           f'N = {np.exp(-fit[1] / fit[0]):.2f} * '
+           f'exp( {1 / fit[0] / times3[-1]:.2f} * t )\n'))
 
     plt.semilogx(xval, yval, label='Simulation result')
     plt.semilogx(xval, fit[0] * np.log(xval) + fit[1], '--', label='Fit')

tutorials-v5/time-evolution/020_homodyned-Jaynes-Cummings-emission.md

@@ -5,7 +5,7 @@ jupyter:
       extension: .md
       format_name: markdown
       format_version: '1.3'
-      jupytext_version: 1.13.8
+      jupytext_version: 1.16.4
   kernelspec:
     display_name: Python 3 (ipykernel)
     language: python
@@ -280,7 +280,7 @@ def calculate_rho_ss_c(Om):
 rho_ss_c = [calculate_rho_ss_c(Om) for Om in Om_list]
 
 # calculate list of interference values for all driving strengths
-alpha_list = -expect(rho_ss_c, a_r)
+alpha_list = -np.array(expect(rho_ss_c, a_r))
 alpha_c_list = alpha_list.conjugate()
 
 # decompose emission for all driving strengths

tutorials-v5/visualization/pseudo-probability-functions.md

@@ -5,7 +5,7 @@ jupyter:
       extension: .md
       format_name: markdown
       format_version: '1.3'
-      jupytext_version: 1.13.8
+      jupytext_version: 1.16.4
   kernelspec:
     display_name: Python 3 (ipykernel)
     language: python
@@ -24,7 +24,6 @@ import matplotlib as mpl
 import matplotlib.pylab as plt
 import numpy as np
 from matplotlib import cm
-from mpl_toolkits.mplot3d import Axes3D
 from qutip import about, basis, destroy, qfunc, wigner, wigner_cmap
 
 %matplotlib inline
@@ -49,10 +48,10 @@ plt.colorbar();
 
 ```python
 fig = plt.figure(figsize=(10, 8))
-ax = Axes3D(fig, azim=-30, elev=73)
+ax = fig.add_subplot(111, projection='3d', azim=-30, elev=73)
 ax.plot_surface(X, Y, W, cmap=cmap, rstride=1, cstride=1, alpha=1, linewidth=0)
 ax.set_zlim3d(-0.25, 0.25)
-for a in ax.w_zaxis.get_ticklines() + ax.w_zaxis.get_ticklabels():
+for a in ax.zaxis.get_ticklines() + ax.zaxis.get_ticklabels():
     a.set_visible(False)
 nrm = mpl.colors.Normalize(W.min(), W.max())
 cax, kw = mpl.colorbar.make_axes(ax, shrink=0.66, pad=0.02)
@@ -85,7 +84,7 @@ X, Y = np.meshgrid(xvec, xvec)
 W = wigner(psi, xvec, xvec)
 
 fig1 = plt.figure(figsize=(8, 6))
-ax = Axes3D(fig1)
+ax = fig1.add_subplot(111, projection='3d')
 ax.plot_surface(X, Y, W, rstride=2, cstride=2, cmap=cm.jet, alpha=0.7)
 ax.contour(X, Y, W, 15, zdir="x", offset=-6)
 ax.contour(X, Y, W, 15, zdir="y", offset=6)
@@ -102,7 +101,7 @@ plt.title("Wigner function of squeezed state");
 Q = qfunc(psi, xvec, xvec, g)
 
 fig2 = plt.figure(figsize=(8, 6))
-ax = Axes3D(fig2)
+ax = fig2.add_subplot(111, projection='3d')
 ax.plot_surface(X, Y, Q, rstride=2, cstride=2, cmap=cm.jet, alpha=0.7)
 ax.contour(X, Y, Q, zdir="x", offset=-6)
 ax.contour(X, Y, Q, zdir="y", offset=6)