Release 1.0.0

qucontrol · Dec 16, 2019 · c4b3fd5 · c4b3fd5
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diff --git a/HISTORY.rst b/HISTORY.rst
@@ -2,7 +2,7 @@
 History
 =======
 
-1.0.0 (2019-12-15)
+1.0.0 (2019-12-16)
 ------------------
 
 * Update: Citation info now points to `SciPost paper <https://scipost.org/SciPostPhys.7.6.080>`_ (`#61`_)

diff --git a/README.rst b/README.rst
@@ -27,7 +27,7 @@ Krotov Python Package
    :target: https://opensource.org/licenses/BSD-3-Clause
 .. image:: https://mybinder.org/badge_logo.svg
    :alt: Launch Binder
-   :target: https://mybinder.org/v2/gh/qucontrol/krotov/v1.0.0-rc1?filepath=docs%2Fnotebooks
+   :target: https://mybinder.org/v2/gh/qucontrol/krotov/v1.0.0?filepath=docs%2Fnotebooks
 .. image:: https://img.shields.io/badge/DOI-10.21468/SciPostPhys.7.6.080-blue.svg
    :alt: DOI
    :target: https://doi.org/10.21468/SciPostPhys.7.6.080
@@ -43,7 +43,7 @@ Development happens on `Github`_. You can read the full documentation `online`__
 .. _Documentation: https://qucontrol.github.io/krotov
 __ Documentation_
 
-If you use the ``krotov`` package in your research, please `cite it <https://qucontrol.github.io/krotov/v1.0.0-rc1/01_overview.html#citing-the-krotov-package>`_.
+If you use the ``krotov`` package in your research, please `cite it <https://qucontrol.github.io/krotov/v1.0.0/01_overview.html#citing-the-krotov-package>`_.
 
 .. _QDYN Fortran library: https://www.qdyn-library.net
 .. _QuTiP: http://qutip.org
@@ -172,11 +172,11 @@ Then,
    number of control fields over all the objectives.
 
 .. |krotov.Objective| replace:: ``krotov.Objective``
-.. _krotov.Objective: https://qucontrol.github.io/krotov/v1.0.0-rc1/API/krotov.objectives.html#krotov.objectives.Objective
+.. _krotov.Objective: https://qucontrol.github.io/krotov/v1.0.0/API/krotov.objectives.html#krotov.objectives.Objective
 
 .. |krotov.optimize_pulses| replace:: ``krotov.optimize_pulses``
-.. _krotov.optimize_pulses: https://qucontrol.github.io/krotov/v1.0.0-rc1/API/krotov.optimize.html#krotov.optimize.optimize_pulses
+.. _krotov.optimize_pulses: https://qucontrol.github.io/krotov/v1.0.0/API/krotov.optimize.html#krotov.optimize.optimize_pulses
 
-See `Using Krotov with QuTiP <https://qucontrol.github.io/krotov/v1.0.0-rc1/08_qutip_usage.html#using-krotov-with-qutip>`_ and `Examples <https://qucontrol.github.io/krotov/v1.0.0-rc1/09_examples.html>`_ for details.
+See `Using Krotov with QuTiP <https://qucontrol.github.io/krotov/v1.0.0/08_qutip_usage.html#using-krotov-with-qutip>`_ and `Examples <https://qucontrol.github.io/krotov/v1.0.0/09_examples.html>`_ for details.
 
 .. _Jupyter notebook: https://jupyter.org
diff --git a/binder/environment.yml b/binder/environment.yml
@@ -8,4 +8,4 @@ dependencies:
   - pip:
     - matplotlib
     - watermark
-    - git+https://github.com/qucontrol/krotov.git@master#egg=krotov
+    - krotov==1.0.0
diff --git a/docs/09_examples.rst b/docs/09_examples.rst
@@ -6,7 +6,7 @@ Examples
 
 .. raw:: html
 
-    <a href="http://nbviewer.jupyter.org/github/qucontrol/krotov/blob/master/docs/notebooks" target="_blank"><img alt="Render on nbviewer" src="https://img.shields.io/badge/render%20on-nbviewer-orange.svg" style="vertical-align:text-bottom"></a>&nbsp;<a href="https://mybinder.org/v2/gh/qucontrol/krotov/master?filepath=docs%2Fnotebooks" target="_blank"><img alt="Launch Binder" src="https://mybinder.org/badge_logo.svg" style="vertical-align:text-bottom"></a>
+    <a href="http://nbviewer.jupyter.org/github/qucontrol/krotov/blob/v1.0.0/docs/notebooks" target="_blank"><img alt="Render on nbviewer" src="https://img.shields.io/badge/render%20on-nbviewer-orange.svg" style="vertical-align:text-bottom"></a>&nbsp;<a href="https://mybinder.org/v2/gh/qucontrol/krotov/v1.0.0?filepath=docs%2Fnotebooks" target="_blank"><img alt="Launch Binder" src="https://mybinder.org/badge_logo.svg" style="vertical-align:text-bottom"></a>
 
 .. toctree::
     :maxdepth: 1

diff --git a/docs/_README.patch b/docs/_README.patch
@@ -12,7 +12,7 @@
  .. _Documentation: https://qucontrol.github.io/krotov
  __ Documentation_
 
--If you use the ``krotov`` package in your research, please `cite it <https://qucontrol.github.io/krotov/v1.0.0-rc1/01_overview.html#citing-the-krotov-package>`_.
+-If you use the ``krotov`` package in your research, please `cite it <https://qucontrol.github.io/krotov/v1.0.0/01_overview.html#citing-the-krotov-package>`_.
 +If you use the :mod:`krotov` package in your research, please :ref:`cite it <CitingKrotov>`.
 
  .. _QDYN Fortran library: https://www.qdyn-library.net
@@ -55,12 +55,12 @@
     number of control fields over all the objectives.
 
 -.. |krotov.Objective| replace:: ``krotov.Objective``
--.. _krotov.Objective: https://qucontrol.github.io/krotov/v1.0.0-rc1/API/krotov.objectives.html#krotov.objectives.Objective
+-.. _krotov.Objective: https://qucontrol.github.io/krotov/v1.0.0/API/krotov.objectives.html#krotov.objectives.Objective
 
 -.. |krotov.optimize_pulses| replace:: ``krotov.optimize_pulses``
--.. _krotov.optimize_pulses: https://qucontrol.github.io/krotov/v1.0.0-rc1/API/krotov.optimize.html#krotov.optimize.optimize_pulses
+-.. _krotov.optimize_pulses: https://qucontrol.github.io/krotov/v1.0.0/API/krotov.optimize.html#krotov.optimize.optimize_pulses
 -
--See `Using Krotov with QuTiP <https://qucontrol.github.io/krotov/v1.0.0-rc1/08_qutip_usage.html#using-krotov-with-qutip>`_ and `Examples <https://qucontrol.github.io/krotov/v1.0.0-rc1/09_examples.html>`_ for details.
+-See `Using Krotov with QuTiP <https://qucontrol.github.io/krotov/v1.0.0/08_qutip_usage.html#using-krotov-with-qutip>`_ and `Examples <https://qucontrol.github.io/krotov/v1.0.0/09_examples.html>`_ for details.
 +See :ref:`using-krotov-with-qutip` and :ref:`krotov-example-notebooks` for details.
 
  .. _Jupyter notebook: https://jupyter.org
diff --git a/docs/index.rst b/docs/index.rst
@@ -27,7 +27,7 @@ Welcome to the Krotov package's documentation!
    :target: https://opensource.org/licenses/BSD-3-Clause
 .. image:: https://mybinder.org/badge_logo.svg
    :alt: Launch Binder
-   :target: https://mybinder.org/v2/gh/qucontrol/krotov/v1.0.0-rc1?filepath=docs%2Fnotebooks
+   :target: https://mybinder.org/v2/gh/qucontrol/krotov/v1.0.0?filepath=docs%2Fnotebooks
 .. image:: https://img.shields.io/badge/DOI-10.21468/SciPostPhys.7.6.080-blue.svg
    :alt: DOI
    :target: https://doi.org/10.21468/SciPostPhys.7.6.080

diff --git a/docs/notebooks/01_example_simple_state_to_state.ipynb b/docs/notebooks/01_example_simple_state_to_state.ipynb
@@ -26,12 +26,12 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "qutip            4.4.1\n",
-      "numpy            1.17.2\n",
-      "krotov           1.0.0-rc1\n",
-      "scipy            1.3.1\n",
       "matplotlib       3.1.2\n",
       "matplotlib.pylab 1.17.2\n",
+      "scipy            1.3.1\n",
+      "numpy            1.17.2\n",
+      "qutip            4.4.1\n",
+      "krotov           1.0.0\n",
       "CPython 3.7.3\n",
       "IPython 7.10.2\n"
      ]
@@ -531,22 +531,22 @@
      "output_type": "stream",
      "text": [
       "iter.      J_T    ∫gₐ(t)dt          J       ΔJ_T         ΔJ  secs\n",
-      "0     9.51e-01    0.00e+00   9.51e-01        n/a        n/a     0\n",
+      "0     9.51e-01    0.00e+00   9.51e-01        n/a        n/a     1\n",
       "1     9.24e-01    2.32e-03   9.27e-01  -2.70e-02  -2.47e-02     2\n",
-      "2     8.83e-01    3.53e-03   8.87e-01  -4.11e-02  -3.75e-02     1\n",
+      "2     8.83e-01    3.53e-03   8.87e-01  -4.11e-02  -3.75e-02     2\n",
       "3     8.23e-01    5.22e-03   8.28e-01  -6.06e-02  -5.54e-02     2\n",
       "4     7.38e-01    7.39e-03   7.45e-01  -8.52e-02  -7.78e-02     2\n",
-      "5     6.26e-01    9.75e-03   6.36e-01  -1.11e-01  -1.01e-01     1\n",
-      "6     4.96e-01    1.16e-02   5.07e-01  -1.31e-01  -1.19e-01     1\n",
+      "5     6.26e-01    9.75e-03   6.36e-01  -1.11e-01  -1.01e-01     2\n",
+      "6     4.96e-01    1.16e-02   5.07e-01  -1.31e-01  -1.19e-01     2\n",
       "7     3.62e-01    1.21e-02   3.74e-01  -1.34e-01  -1.22e-01     2\n",
-      "8     2.44e-01    1.09e-02   2.55e-01  -1.18e-01  -1.07e-01     1\n",
+      "8     2.44e-01    1.09e-02   2.55e-01  -1.18e-01  -1.07e-01     2\n",
       "9     1.53e-01    8.43e-03   1.62e-01  -9.03e-02  -8.19e-02     2\n",
-      "10    9.20e-02    5.80e-03   9.78e-02  -6.14e-02  -5.56e-02     1\n",
-      "11    5.35e-02    3.66e-03   5.72e-02  -3.85e-02  -3.48e-02     1\n",
-      "12    3.06e-02    2.19e-03   3.28e-02  -2.29e-02  -2.07e-02     1\n",
-      "13    1.73e-02    1.27e-03   1.86e-02  -1.33e-02  -1.20e-02     1\n",
-      "14    9.79e-03    7.24e-04   1.05e-02  -7.55e-03  -6.82e-03     1\n",
-      "15    5.52e-03    4.10e-04   5.93e-03  -4.27e-03  -3.86e-03     1\n",
+      "10    9.20e-02    5.80e-03   9.78e-02  -6.14e-02  -5.56e-02     2\n",
+      "11    5.35e-02    3.66e-03   5.72e-02  -3.85e-02  -3.48e-02     2\n",
+      "12    3.06e-02    2.19e-03   3.28e-02  -2.29e-02  -2.07e-02     2\n",
+      "13    1.73e-02    1.27e-03   1.86e-02  -1.33e-02  -1.20e-02     2\n",
+      "14    9.79e-03    7.24e-04   1.05e-02  -7.55e-03  -6.82e-03     2\n",
+      "15    5.52e-03    4.10e-04   5.93e-03  -4.27e-03  -3.86e-03     2\n",
       "16    3.11e-03    2.31e-04   3.35e-03  -2.41e-03  -2.18e-03     2\n",
       "17    1.76e-03    1.30e-04   1.89e-03  -1.36e-03  -1.23e-03     1\n",
       "18    9.92e-04    7.36e-05   1.07e-03  -7.65e-04  -6.91e-04     1\n"
@@ -589,11 +589,11 @@
       "text/plain": [
        "Krotov Optimization Result\n",
        "--------------------------\n",
-       "- Started at 2019-12-15 18:21:51\n",
+       "- Started at 2019-12-15 22:36:37\n",
        "- Number of objectives: 1\n",
        "- Number of iterations: 18\n",
        "- Reason for termination: Reached convergence: J_T < 1e-3\n",
-       "- Ended at 2019-12-15 18:22:28 (0:00:37)"
+       "- Ended at 2019-12-15 22:37:16 (0:00:39)"
       ]
      },
      "execution_count": 15,

diff --git a/docs/notebooks/02_example_lambda_system_rwa_complex_pulse.ipynb b/docs/notebooks/02_example_lambda_system_rwa_complex_pulse.ipynb
@@ -16,12 +16,12 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "krotov           1.0.0-rc1\n",
-      "scipy            1.3.1\n",
-      "matplotlib       3.1.2\n",
       "matplotlib.pylab 1.17.2\n",
-      "numpy            1.17.2\n",
       "qutip            4.4.1\n",
+      "numpy            1.17.2\n",
+      "krotov           1.0.0\n",
+      "matplotlib       3.1.2\n",
+      "scipy            1.3.1\n",
       "CPython 3.7.3\n",
       "IPython 7.10.2\n"
      ]
@@ -803,11 +803,11 @@
       "text/plain": [
        "Krotov Optimization Result\n",
        "--------------------------\n",
-       "- Started at 2019-12-15 18:22:40\n",
+       "- Started at 2019-12-15 22:37:26\n",
        "- Number of objectives: 1\n",
        "- Number of iterations: 12\n",
        "- Reason for termination: Reached convergence: J_T < 0.001\n",
-       "- Ended at 2019-12-15 18:23:10 (0:00:30)"
+       "- Ended at 2019-12-15 22:37:56 (0:00:30)"
       ]
      },
      "execution_count": 20,

diff --git a/docs/notebooks/03_example_lambda_system_rwa_non_hermitian.ipynb b/docs/notebooks/03_example_lambda_system_rwa_non_hermitian.ipynb
@@ -26,12 +26,12 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "scipy            1.3.1\n",
-      "matplotlib.pylab 1.17.2\n",
       "matplotlib       3.1.2\n",
-      "krotov           1.0.0-rc1\n",
-      "qutip            4.4.1\n",
       "numpy            1.17.2\n",
+      "krotov           1.0.0\n",
+      "qutip            4.4.1\n",
+      "matplotlib.pylab 1.17.2\n",
+      "scipy            1.3.1\n",
       "CPython 3.7.3\n",
       "IPython 7.10.2\n"
      ]

diff --git a/docs/notebooks/04_example_dissipative_qubit_reset.ipynb b/docs/notebooks/04_example_dissipative_qubit_reset.ipynb
@@ -26,12 +26,12 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "qutip            4.4.1\n",
-      "scipy            1.3.1\n",
       "matplotlib       3.1.2\n",
+      "qutip            4.4.1\n",
+      "krotov           1.0.0\n",
       "numpy            1.17.2\n",
       "matplotlib.pylab 1.17.2\n",
-      "krotov           1.0.0-rc1\n",
+      "scipy            1.3.1\n",
       "CPython 3.7.3\n",
       "IPython 7.10.2\n"
      ]
@@ -805,7 +805,7 @@
       "    S(t) (ranges): [0.000000, 1.000000]\n",
       "    iter_start: 0\n",
       "    iter_stop: 5\n",
-      "    duration: 0.5 secs (started at 2019-12-15 18:25:18)\n",
+      "    duration: 0.6 secs (started at 2019-12-15 22:40:08)\n",
       "    optimized pulses (ranges): [0.00, 2.00]\n",
       "    ∫gₐ(t)dt: 0.00e+00\n",
       "    λₐ: 1.00e-02\n",
@@ -814,7 +814,7 @@
       "    τ: (7.97e-01:0.00π)\n",
       "    qubit error: 1.1e-01\n",
       "Iteration 1\n",
-      "    duration: 2.4 secs (started at 2019-12-15 18:25:19)\n",
+      "    duration: 4.0 secs (started at 2019-12-15 22:40:08)\n",
       "    optimized pulses (ranges): [0.00, 2.06]\n",
       "    ∫gₐ(t)dt: 7.72e-02\n",
       "    λₐ: 1.00e-02\n",
@@ -823,7 +823,7 @@
       "    τ: (7.98e-01:0.00π)\n",
       "    qubit error: 1.1e-01\n",
       "Iteration 2\n",
-      "    duration: 2.5 secs (started at 2019-12-15 18:25:21)\n",
+      "    duration: 3.6 secs (started at 2019-12-15 22:40:12)\n",
       "    optimized pulses (ranges): [0.00, 2.23]\n",
       "    ∫gₐ(t)dt: 5.72e-01\n",
       "    λₐ: 1.00e-02\n",
@@ -832,7 +832,7 @@
       "    τ: (8.01e-01:0.00π)\n",
       "    qubit error: 6.7e-02\n",
       "Iteration 3\n",
-      "    duration: 2.5 secs (started at 2019-12-15 18:25:24)\n",
+      "    duration: 3.4 secs (started at 2019-12-15 22:40:16)\n",
       "    optimized pulses (ranges): [0.00, 2.33]\n",
       "    ∫gₐ(t)dt: 8.11e-02\n",
       "    λₐ: 1.00e-02\n",
@@ -841,7 +841,7 @@
       "    τ: (7.99e-01:0.00π)\n",
       "    qubit error: 5.0e-02\n",
       "Iteration 4\n",
-      "    duration: 2.8 secs (started at 2019-12-15 18:25:26)\n",
+      "    duration: 3.0 secs (started at 2019-12-15 22:40:19)\n",
       "    optimized pulses (ranges): [0.00, 2.19]\n",
       "    ∫gₐ(t)dt: 2.16e-01\n",
       "    λₐ: 1.00e-02\n",
@@ -850,7 +850,7 @@
       "    τ: (8.02e-01:0.00π)\n",
       "    qubit error: 4.9e-02\n",
       "Iteration 5\n",
-      "    duration: 2.6 secs (started at 2019-12-15 18:25:29)\n",
+      "    duration: 3.6 secs (started at 2019-12-15 22:40:22)\n",
       "    optimized pulses (ranges): [0.00, 2.15]\n",
       "    ∫gₐ(t)dt: 6.38e-02\n",
       "    λₐ: 1.00e-02\n",
@@ -898,11 +898,11 @@
       "text/plain": [
        "Krotov Optimization Result\n",
        "--------------------------\n",
-       "- Started at 2019-12-15 18:25:18\n",
+       "- Started at 2019-12-15 22:40:08\n",
        "- Number of objectives: 1\n",
        "- Number of iterations: 5\n",
        "- Reason for termination: Reached 5 iterations\n",
-       "- Ended at 2019-12-15 18:25:32 (0:00:14)"
+       "- Ended at 2019-12-15 22:40:26 (0:00:18)"
       ]
      },
      "execution_count": 20,

diff --git a/docs/notebooks/05_example_transmon_xgate.ipynb b/docs/notebooks/05_example_transmon_xgate.ipynb
@@ -21,12 +21,12 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "matplotlib       3.1.2\n",
-      "krotov           1.0.0-rc1\n",
       "scipy            1.3.1\n",
-      "matplotlib.pylab 1.17.2\n",
+      "krotov           1.0.0\n",
       "qutip            4.4.1\n",
+      "matplotlib.pylab 1.17.2\n",
       "numpy            1.17.2\n",
+      "matplotlib       3.1.2\n",
       "CPython 3.7.3\n",
       "IPython 7.10.2\n"
      ]
@@ -523,12 +523,12 @@
      "output_type": "stream",
      "text": [
       "iter.      J_T    g_a_int          J  Delta J_T    Delta J  secs\n",
-      "0     1.00e+00   0.00e+00   1.00e+00        n/a        n/a     2\n",
-      "1     2.80e-01   3.41e-01   6.22e-01  -7.20e-01  -3.78e-01     5\n",
-      "2     2.12e-01   3.06e-02   2.43e-01  -6.81e-02  -3.75e-02     5\n",
-      "3     1.35e-01   3.28e-02   1.68e-01  -7.72e-02  -4.44e-02     5\n",
-      "4     9.79e-02   1.56e-02   1.13e-01  -3.71e-02  -2.15e-02     5\n",
-      "5     7.13e-02   1.11e-02   8.25e-02  -2.65e-02  -1.54e-02     5\n"
+      "0     1.00e+00   0.00e+00   1.00e+00        n/a        n/a     4\n",
+      "1     2.80e-01   3.41e-01   6.22e-01  -7.20e-01  -3.78e-01     7\n",
+      "2     2.12e-01   3.06e-02   2.43e-01  -6.81e-02  -3.75e-02     6\n",
+      "3     1.35e-01   3.28e-02   1.68e-01  -7.72e-02  -4.44e-02     6\n",
+      "4     9.79e-02   1.56e-02   1.13e-01  -3.71e-02  -2.15e-02     6\n",
+      "5     7.13e-02   1.11e-02   8.25e-02  -2.65e-02  -1.54e-02     6\n"
      ]
     }
    ],

diff --git a/docs/notebooks/06_example_3states.ipynb b/docs/notebooks/06_example_3states.ipynb
@@ -21,12 +21,12 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "matplotlib.pylab 1.17.2\n",
       "qutip            4.4.1\n",
-      "scipy            1.3.1\n",
       "matplotlib       3.1.2\n",
+      "scipy            1.3.1\n",
+      "krotov           1.0.0\n",
       "numpy            1.17.2\n",
-      "krotov           1.0.0-rc1\n",
+      "matplotlib.pylab 1.17.2\n",
       "CPython 3.7.3\n",
       "IPython 7.10.2\n"
      ]
@@ -820,10 +820,10 @@
      "output_type": "stream",
      "text": [
       "iter.      J_T   ∑∫gₐ(t)dt          J       ΔJ_T         ΔJ  secs\n",
-      "0     1.22e-01    0.00e+00   1.22e-01        n/a        n/a     8\n",
-      "1     7.49e-02    2.26e-02   9.75e-02  -4.67e-02  -2.41e-02    28\n",
-      "2     7.41e-02    3.98e-04   7.45e-02  -8.12e-04  -4.14e-04    29\n",
-      "3     7.33e-02    3.70e-04   7.37e-02  -7.55e-04  -3.85e-04    29\n"
+      "0     1.22e-01    0.00e+00   1.22e-01        n/a        n/a     9\n",
+      "1     7.49e-02    2.26e-02   9.75e-02  -4.67e-02  -2.41e-02    30\n",
+      "2     7.41e-02    3.98e-04   7.45e-02  -8.12e-04  -4.14e-04    33\n",
+      "3     7.33e-02    3.70e-04   7.37e-02  -7.55e-04  -3.85e-04    36\n"
      ]
     }
    ],