Merge 0fd65de into 0b42bfa

.readthedocs.yml

@@ -13,4 +13,6 @@ python:
       path: .
       extra_requirements:
          - doc
+         - plotting
+         - bloch_sphere_visualization
          - fancy_progressbar

.travis.yml

@@ -1,23 +1,28 @@
+os: linux
+
 dist: xenial
 
 language: python
 
 python:
-  - '3.6'
-  - '3.7'
-  - '3.8'
+  - 3.6
+  - 3.7
+  - 3.8
+env:
+  - INSTALL_EXTRAS=[plotting,bloch_sphere_visualization,fancy_progressbar,tests]
+  - INSTALL_EXTRAS=[plotting,fancy_progressbar,tests]
+  - INSTALL_EXTRAS=[tests]
+
+#these directories are persistent
+cache: pip
+
+#manually install these dependencies so that qutip can be installed via pip
+before_install:
+  - pip install --upgrade pip
+  - pip install numpy scipy cython
 
 install:
-  - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
-  - bash miniconda.sh -b -p $HOME/miniconda
-  - export PATH="$HOME/miniconda/bin:$PATH"
-  - hash -r
-  - conda config --set always_yes yes --set changeps1 no
-  - conda config --append channels conda-forge
-  - conda info -a
-  - conda env create -f ./environment.yml
-  - source activate filter_functions
-  - pip install .[fancy_progressbar,doc,tests]
+  - pip install .$INSTALL_EXTRAS
 
 script:
   - coverage run --rcfile=coverage.ini -m pytest

README.md

@@ -27,7 +27,8 @@ hadamard = ff.PulseSequence(H_c, H_n, dt)   # Central object representing a cont
 omega = ff.util.get_sample_frequencies(hadamard)
 F = hadamard.get_filter_function(omega)
 
-ff.plot_filter_function(hadamard)           # Filter function cached from before
+from filter_functions import plotting
+plotting.plot_filter_function(hadamard)     # Filter function cached from before
 ```
 
 ![Hadamard dephasing filter function](./doc/source/_static/hadamard.png)
@@ -59,16 +60,16 @@ infidelity = ff.infidelity(hadamard, spectrum, omega)
 ```
 
 ## Installation
-To install the package from PyPI, run `pip install filter_functions`. It is recommended to install QuTiP before by following the [instructions on their website](http://qutip.org/docs/latest/installation.html) rather than installing it through `pip`. To install the package from source run `python setup.py develop` to install using symlinks or `python setup.py install` without.
+To install the package from PyPI, run `pip install filter_functions`. If you require the optional features provided by QuTiP (visualizing Bloch sphere trajectories), it is recommended to install QuTiP before by following the [instructions on their website](http://qutip.org/docs/latest/installation.html) rather than installing it through `pip`. To install the package from source run `python setup.py develop` to install using symlinks or `python setup.py install` without.
 
-To install the optional dependencies (`tqdm` and `requests` for a fancy progress bar), run `pip install -e .[fancy_progressbar]` from the root directory.
+To install dependencies of optional extras (`tqdm` and `requests` for a fancy progress bar, `matplotlib` for plotting, `QuTiP` for Bloch sphere visualization), run `pip install -e .[extra]` where `extra` is one or more of `fancy_progressbar`, `plotting`, `bloch_sphere_visualization` from the root directory. To install all dependencies, including those needed to build the documentation and run the tests, use the extra `all`.
 
 ## Documentation
 You can find the documentation on [Readthedocs](https://filter-functions.readthedocs.io/en/latest/). It is built from Jupyter notebooks that can also be run interactively and are located [here](doc/source/examples). The notebooks explain how to use the package and thus make sense to follow chronologically as a first step. Furthermore, there are also a few example scripts in the [examples](examples) folder.
 
 The documentation including the example notebooks and an automatically generated API documentation can be built by running `make <format>` inside the *doc* directory where `<format>` is for example `html`.
 
-Building the documentation requires the following additional dependencies: `nbsphinx`, `numpydoc`, `sphinx_rtd_theme`, `jupyter_client`, `ipython`, `ipykernel`, as well as `pandoc`. The last can be installed via conda (`conda install pandoc`) or downloaded from [Github](https://github.com/jgm/pandoc/releases/) and the rest automatically by running `pip install -e .[doc]`.
+Interactively using the documentation requires `jupyter`, and building a static version additionally requires `nbsphinx`, `numpydoc`, `sphinx_rtd_theme`,, as well as `pandoc`. The last can be installed via conda (`conda install pandoc`) or downloaded from [Github](https://github.com/jgm/pandoc/releases/) and the rest automatically by running `pip install -e .[doc]`.
 
 ## References
 [1]: Cywinski, L., Lutchyn, R. M., Nave, C. P., & Das Sarma, S. (2008). How to enhance dephasing time in superconducting qubits. Physical Review B - Condensed Matter and Materials Physics, 77(17), 1–11. [https://doi.org/10.1103/PhysRevB.77.174509](https://doi.org/10.1103/PhysRevB.77.174509)

doc/source/examples/advanced_concatenation.ipynb

@@ -88,7 +88,7 @@
     "d = 2\n",
     "H = np.empty((2, d, d), dtype=complex)\n",
     "\n",
-    "Id, Px, Py, Pz = ff.util.P_np\n",
+    "Id, Px, Py, Pz = ff.util.paulis\n",
     "H[0] = 1/2*Px\n",
     "H[1] = 1/2*Pz\n",
     "\n",
@@ -184,8 +184,11 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "from filter_functions import plotting\n",
+    "\n",
     "for gate in gate_types:\n",
-    "    ff.plot_bloch_vector_evolution(H[gate], n_samples=501, figsize=(4, 4))"
+    "    plotting.plot_bloch_vector_evolution(H[gate], n_samples=501,\n",
+    "                                         figsize=(4, 4))"
    ]
   },
   {
@@ -203,9 +206,8 @@
    "source": [
     "pulses = ('Y', 'X_1', 'X_2')\n",
     "for gate_type, hadamard in H.items():\n",
-    "    fig, ax, leg = ff.plot_pulse_correlation_filter_function(hadamard,\n",
-    "                                                             xscale='linear',\n",
-    "                                                             figsize=(9, 6))\n",
+    "    fig, ax, leg = plotting.plot_pulse_correlation_filter_function(\n",
+    "        hadamard, xscale='linear', figsize=(9, 6))\n",
     "\n",
     "    # Adjust the titles to something more meaningful\n",
     "    for i in range(3):\n",

doc/source/examples/extending_pulses.ipynb

@@ -26,7 +26,7 @@
     "import filter_functions as ff\n",
     "from filter_functions import util\n",
     "\n",
-    "I, X, Y, Z = util.P_np\n",
+    "I, X, Y, Z = util.paulis\n",
     "\n",
     "# In order to be able to remap cached filter functions, we need a separable\n",
     "# basis like the Pauli basis\n",
@@ -209,8 +209,10 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "from filter_functions import plotting\n",
+    "\n",
     "print(swap_14_23.is_cached('F'))\n",
-    "_ = ff.plot_filter_function(swap_14_23)"
+    "_ = plotting.plot_filter_function(swap_14_23)"
    ]
   }
  ],

doc/source/examples/getting_started.ipynb

@@ -126,7 +126,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from filter_functions import analytic\n",
+    "from filter_functions import analytic, plotting\n",
     "\n",
     "# Generate logarithmically spaced frequencies over an interval which generally\n",
     "# captures the important regions of the filter function. Since the filter\n",
@@ -135,7 +135,7 @@
     "omega = ff.util.get_sample_frequencies(FID, n_samples=200, spacing='log',\n",
     "                                       symmetric=False)\n",
     "# Plot the filter function.\n",
-    "fig, ax, legend = ff.plot_filter_function(FID, omega)\n",
+    "fig, ax, legend = plotting.plot_filter_function(FID, omega)\n",
     "# Plot the analytic solution into the same plot\n",
     "ax.plot(omega*tau, analytic.FID(omega*tau)/omega**2,\n",
     "        'x-', label='Analytical', zorder=0)\n",
@@ -161,7 +161,8 @@
     "# Initial state the +1 eigenstate of X\n",
     "psi_i = (qt.basis(2, 0) + qt.basis(2, 1))/np.sqrt(2)\n",
     "\n",
-    "ff.plot_bloch_vector_evolution(FID, psi0=psi_i, n_samples=101, figsize=(4, 4))"
+    "plotting.plot_bloch_vector_evolution(FID, psi0=psi_i, n_samples=101,\n",
+    "                                     figsize=(4, 4))"
    ]
   },
   {
@@ -261,14 +262,15 @@
     "omega = ff.util.get_sample_frequencies(SE, n_samples=400, spacing='log',\n",
     "                                       symmetric=False)\n",
     "# Plot the filter function\n",
-    "fig, ax, legend = ff.plot_filter_function(SE, omega, yscale='log')\n",
+    "fig, ax, legend = plotting.plot_filter_function(SE, omega, yscale='log')\n",
     "ax.set_ylim(bottom=1e-13)\n",
     "# Plot the analytical solution\n",
     "ax.plot(omega*tau, analytic.SE(omega*tau)/omega**2, '--',\n",
     "        label='Analytical (Bang-Bang)', zorder=0)\n",
     "legend = ax.legend()\n",
     "\n",
-    "ff.plot_bloch_vector_evolution(SE, psi0=psi_i, n_samples=101, figsize=(4, 4))"
+    "plotting.plot_bloch_vector_evolution(SE, psi0=psi_i, n_samples=101,\n",
+    "                                     figsize=(4, 4))"
    ]
   },
   {

doc/source/examples/qutip_integration.ipynb

@@ -91,6 +91,7 @@
    "outputs": [],
    "source": [
     "import matplotlib.pyplot as plt\n",
+    "from filter_functions import plotting\n",
     "\n",
     "identifiers = ['XI', 'YI', 'IX', 'IY', 'ZZ']\n",
     "pulses = {\n",
@@ -104,12 +105,12 @@
     "fig, ax = plt.subplots(2, 3, figsize=(12, 6))\n",
     "for i, (p_type, pulse) in enumerate(pulses.items()):\n",
     "    # Plot the pulse train\n",
-    "    *_, = ff.plot_pulse_train(pulse, fig=fig, axes=ax[0, i])\n",
+    "    *_, = plotting.plot_pulse_train(pulse, fig=fig, axes=ax[0, i])\n",
     "    ax[0, i].set_title(p_type)\n",
     "    # Plot the filter functions\n",
     "    omega = ff.util.get_sample_frequencies(pulse, spacing='log',\n",
     "                                           symmetric=False)\n",
-    "    *_, = ff.plot_filter_function(pulse, omega, fig=fig, axes=ax[1, i])\n",
+    "    *_, = plotting.plot_filter_function(pulse, omega, fig=fig, axes=ax[1, i])\n",
     "    \n",
     "fig.tight_layout()"
    ]
@@ -138,7 +139,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.1"
+   "version": "3.8.3"
   }
  },
  "nbformat": 4,

examples/qft.py

@@ -32,6 +32,7 @@
 import numpy as np
 
 import filter_functions as ff
+from filter_functions import plotting
 import qutip as qt
 from qutip import qip
 
@@ -149,6 +150,6 @@ def QFT_pulse(N: int = 4, tau: float = 1):
 print('Correct action: ',
       ff.util.oper_equiv(prop, qip.algorithms.qft.qft(N), eps=1e-14))
 
-fig, ax, _ = ff.plot_filter_function(QFT, omega)
+fig, ax, _ = plotting.plot_filter_function(QFT, omega)
 # Move the legend to the side because of many entries
 ax.legend(bbox_to_anchor=(1.05, 1), loc=2, borderaxespad=0.)

filter_functions/__init__.py

@@ -20,23 +20,17 @@
 # =============================================================================
 """Package for efficient calculation of generalized filter functions"""
 
-from . import analytic, basis, numeric, plotting, pulse_sequence, util
+from . import analytic, basis, numeric, pulse_sequence, util
 from .basis import Basis
 from .numeric import (error_transfer_matrix, infidelity,
                       liouville_representation)
-from .plotting import (
-    plot_bloch_vector_evolution, plot_error_transfer_matrix,
-    plot_filter_function, plot_pulse_correlation_filter_function,
-    plot_pulse_train)
 from .pulse_sequence import (PulseSequence, concatenate, concatenate_periodic,
                              extend, remap)
 
 __all__ = ['Basis', 'PulseSequence', 'analytic', 'basis', 'concatenate',
            'concatenate_periodic', 'error_transfer_matrix', 'extend',
            'infidelity', 'liouville_representation', 'numeric',
-           'plot_bloch_vector_evolution', 'plot_error_transfer_matrix',
-           'plot_filter_function', 'plot_pulse_correlation_filter_function',
-           'plot_pulse_train', 'plotting', 'pulse_sequence', 'remap', 'util']
+           'pulse_sequence', 'remap', 'util']
 
 __version__ = '0.2.4'
 __license__ = 'GNU GPLv3+'

filter_functions/basis.py

@@ -47,7 +47,6 @@
 import opt_einsum as oe
 from numpy import linalg as nla
 from numpy.core import ndarray
-from qutip import Qobj
 from scipy import linalg as sla
 from sparse import COO
 
@@ -172,11 +171,11 @@ def __new__(cls, basis_array: Sequence, traceless: Optional[bool] = None,
                 basis = np.empty((len(basis_array), *basis_array[0].shape),
                                  dtype=complex)
                 for i, elem in enumerate(basis_array):
-                    if isinstance(elem, ndarray):
+                    if isinstance(elem, ndarray):   # numpy array
                         basis[i] = elem
-                    elif isinstance(elem, Qobj):
+                    elif hasattr(elem, 'full'):     # qutip.Qobj
                         basis[i] = elem.full()
-                    elif isinstance(elem, COO):
+                    elif hasattr(elem, 'todense'):  # sparse array
                         basis[i] = elem.todense()
                     else:
                         raise TypeError('At least one element invalid type!')
@@ -424,7 +423,7 @@ def pauli(cls, n: int) -> 'Basis':
         """
         normalization = np.sqrt(2**n)
         combinations = np.indices((4,)*n).reshape(n, 4**n)
-        sigma = util.tensor(*np.array(util.P_np)[combinations], rank=2)
+        sigma = util.tensor(*util.paulis[combinations], rank=2)
         sigma /= normalization
         return cls(sigma, btype='Pauli', skip_check=True)