Fix documentation and init files (#116) (#138)

* Fix documentation * Refactor QubitConvertor to new location to avoid cyclic imports Generally clean up imports and make them consistent * Update navigation and text Co-authored-by: Max Rossmannek <[email protected]> * Update qiskit_nature/converters/second_quantization/__init__.py Co-authored-by: Max Rossmannek <[email protected]> * Update qiskit_nature/transformers/__init__.py Co-authored-by: Max Rossmannek <[email protected]> * Fix suggestion breakages Co-authored-by: Max Rossmannek <[email protected]> Co-authored-by: Max Rossmannek <[email protected]> (cherry picked from commit 445669e) Co-authored-by: Steve Wood <[email protected]>
qiskit-community · Apr 14, 2021 · b99cf55 · b99cf55
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diff --git a/README.md b/README.md
@@ -88,11 +88,13 @@ num_spin_orbitals = 2 * problem.molecule_data.num_molecular_orbitals
 
 # setup the classical optimizer for VQE
 from qiskit.algorithms.optimizers import L_BFGS_B
+
 optimizer = L_BFGS_B()
 
 # setup the mapper and qubit converter
 from qiskit_nature.mappers.second_quantization import ParityMapper
-from qiskit_nature.operators.second_quantization.qubit_converter import QubitConverter
+from qiskit_nature.converters.second_quantization import QubitConverter
+
 mapper = ParityMapper()
 converter = QubitConverter(mapper=mapper, two_qubit_reduction=True)
 
@@ -101,21 +103,25 @@ qubit_op = converter.convert(main_op, num_particles=num_particles)
 
 # setup the initial state for the ansatz
 from qiskit_nature.circuit.library import HartreeFock
+
 init_state = HartreeFock(num_spin_orbitals, num_particles, converter)
 
 # setup the ansatz for VQE
 from qiskit.circuit.library import TwoLocal
+
 ansatz = TwoLocal(num_spin_orbitals, ['ry', 'rz'], 'cz')
 
 # add the initial state
 ansatz.compose(init_state, front=True)
 
 # set the backend for the quantum computation
 from qiskit import Aer
+
 backend = Aer.get_backend('statevector_simulator')
 
 # setup and run VQE
 from qiskit.algorithms import VQE
+
 algorithm = VQE(ansatz,
                 optimizer=optimizer,
                 quantum_instance=backend)

diff --git a/docs/apidocs/qiskit_nature.converters.rst b/docs/apidocs/qiskit_nature.converters.rst
@@ -0,0 +1,6 @@
+.. _qiskit_nature-converters:
+
+.. automodule:: qiskit_nature.converters
+   :no-members:
+   :no-inherited-members:
+   :no-special-members:
diff --git a/docs/apidocs/qiskit_nature.converters.second_quantization.rst b/docs/apidocs/qiskit_nature.converters.second_quantization.rst
@@ -0,0 +1,6 @@
+.. _qiskit_nature-converters-second_quantization:
+
+.. automodule:: qiskit_nature.converters.second_quantization
+   :no-members:
+   :no-inherited-members:
+   :no-special-members:
diff --git a/docs/apidocs/qiskit_nature.mappers.second_quantization.rst b/docs/apidocs/qiskit_nature.mappers.second_quantization.rst
@@ -0,0 +1,6 @@
+.. _qiskit_nature-mappers-second_quantization:
+
+.. automodule:: qiskit_nature.mappers.second_quantization
+   :no-members:
+   :no-inherited-members:
+   :no-special-members:
diff --git a/docs/apidocs/qiskit_nature.operators.second_quantization.rst b/docs/apidocs/qiskit_nature.operators.second_quantization.rst
@@ -0,0 +1,7 @@
+.. _qiskit_nature-operators-second_quantization:
+
+.. automodule:: qiskit_nature.operators.second_quantization
+   :no-members:
+   :no-inherited-members:
+   :no-special-members:
+
diff --git a/docs/apidocs/qiskit_nature.problems.second_quantization.rst b/docs/apidocs/qiskit_nature.problems.second_quantization.rst
@@ -0,0 +1,7 @@
+.. _qiskit_nature-problems-second_quantization:
+
+.. automodule:: qiskit_nature.problems.second_quantization
+   :no-members:
+   :no-inherited-members:
+   :no-special-members:
+
diff --git a/docs/index.rst b/docs/index.rst
@@ -1,11 +1,11 @@
 ###########################
-Qiskit Nature documentation
+Qiskit Nature Documentation
 ###########################
 
 .. toctree::
   :maxdepth: 2
 
-  API References <apidocs/qiskit_nature>
+  API Reference <apidocs/qiskit_nature>
   Tutorials <tutorials/index>
   Release Notes <release_notes>
 

diff --git a/docs/tutorials/01_electronic_structure.ipynb b/docs/tutorials/01_electronic_structure.ipynb
@@ -87,18 +87,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 2,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "/Users/bpa/opt/anaconda3/envs/qiskit-nature/lib/python3.7/site-packages/pyscf/lib/misc.py:46: H5pyDeprecationWarning: Using default_file_mode other than 'r' is deprecated. Pass the mode to h5py.File() instead.\n",
-      "  h5py.get_config().default_file_mode = 'a'\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "from qiskit_nature.drivers import PySCFDriver, UnitsType, Molecule\n",
     "molecule = Molecule(geometry=[['H', [0., 0., 0.]],\n",
@@ -111,7 +102,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "For further information about the drivers see https://qiskit.org/documentation/apidoc/qiskit.chemistry.drivers.html"
+    "For further information about the drivers see https://qiskit.org/documentation/nature/apidocs/qiskit_nature.drivers.html"
    ]
   },
   {
@@ -136,38 +127,38 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [],
    "source": [
-    "from qiskit_nature.problems.second_quantization.electronic import ElectronicStructureProblem\n",
-    "from qiskit_nature.operators.second_quantization.qubit_converter import QubitConverter\n",
+    "from qiskit_nature.problems.second_quantization import ElectronicStructureProblem\n",
+    "from qiskit_nature.converters.second_quantization import QubitConverter\n",
     "from qiskit_nature.mappers.second_quantization import JordanWignerMapper, ParityMapper"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "  +-+- * (0.18093119978423136+0j)\n",
-      "+ +--+ * (-0.18093119978423142+0j)\n",
-      "+ -++- * (-0.18093119978423142+0j)\n",
-      "+ -+-+ * (0.18093119978423144+0j)\n",
-      "+ IIIN * (-0.4718960072811406+0j)\n",
-      "+ IINI * (-1.2563390730032502+0j)\n",
-      "+ IINN * (0.4836505304710652+0j)\n",
-      "+ INII * (-0.4718960072811406+0j)\n",
-      "+ ININ * (0.6985737227320181+0j)\n",
-      "+ INNI * (0.6645817302552965+0j)\n",
-      "+ NIII * (-1.2563390730032502+0j)\n",
-      "+ NIIN * (0.6645817302552965+0j)\n",
-      "+ NINI * (0.6757101548035165+0j)\n",
-      "+ NNII * (0.4836505304710652+0j)\n"
+      "  +-+- * (0.18093119978423158+0j)\n",
+      "+ +--+ * (-0.18093119978423156+0j)\n",
+      "+ -++- * (-0.18093119978423156+0j)\n",
+      "+ -+-+ * (0.18093119978423156+0j)\n",
+      "+ IIIN * (-0.4718960072811405+0j)\n",
+      "+ IINI * (-1.2563390730032507+0j)\n",
+      "+ IINN * (0.48365053047106565+0j)\n",
+      "+ INII * (-0.4718960072811405+0j)\n",
+      "+ ININ * (0.6985737227320187+0j)\n",
+      "+ INNI * (0.6645817302552972+0j)\n",
+      "+ NIII * (-1.2563390730032507+0j)\n",
+      "+ NIIN * (0.6645817302552972+0j)\n",
+      "+ NINI * (0.675710154803517+0j)\n",
+      "+ NNII * (0.48365053047106565+0j)\n"
      ]
     }
    ],
@@ -186,28 +177,28 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "-0.8105479805373264 * IIII\n",
-      "- 0.22575349222402463 * ZIII\n",
-      "+ 0.17218393261915566 * IZII\n",
-      "+ 0.1209126326177663 * ZZII\n",
-      "- 0.22575349222402466 * IIZI\n",
-      "+ 0.17464343068300453 * ZIZI\n",
-      "+ 0.16614543256382414 * IZZI\n",
-      "+ 0.17218393261915566 * IIIZ\n",
-      "+ 0.16614543256382414 * ZIIZ\n",
-      "+ 0.16892753870087912 * IZIZ\n",
-      "+ 0.1209126326177663 * IIZZ\n",
-      "+ 0.045232799946057854 * XXXX\n",
-      "+ 0.045232799946057854 * YYXX\n",
-      "+ 0.045232799946057854 * XXYY\n",
-      "+ 0.045232799946057854 * YYYY\n"
+      "-0.8105479805373266 * IIII\n",
+      "- 0.22575349222402513 * ZIII\n",
+      "+ 0.17218393261915543 * IZII\n",
+      "+ 0.12091263261776641 * ZZII\n",
+      "- 0.22575349222402516 * IIZI\n",
+      "+ 0.17464343068300467 * ZIZI\n",
+      "+ 0.1661454325638243 * IZZI\n",
+      "+ 0.17218393261915546 * IIIZ\n",
+      "+ 0.1661454325638243 * ZIIZ\n",
+      "+ 0.16892753870087926 * IZIZ\n",
+      "+ 0.12091263261776641 * IIZZ\n",
+      "+ 0.04523279994605789 * XXXX\n",
+      "+ 0.04523279994605789 * YYXX\n",
+      "+ 0.04523279994605789 * XXYY\n",
+      "+ 0.04523279994605789 * YYYY\n"
      ]
     }
    ],
@@ -221,31 +212,23 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "In the minimal (STO-3G) basis set 4 qubits are required. We could even lower the qubit count by using the Parity mapping which allows to get rid of to qubits by symmetry considerations. "
+    "In the minimal (STO-3G) basis set 4 qubits are required. We can reduce the number of qubits by using the Parity mapping, which allows for the removal of 2 qubits by exploiting known symmetries arising from the mapping. "
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "(-1.0523732457728585+5.551115123125783e-17j) * II\n",
-      "+ (-0.3979374248431802+1.3877787807814457e-17j) * ZI\n",
-      "+ 0.3979374248431802 * IZ\n",
-      "- 0.01128010425623538 * ZZ\n",
-      "+ (0.18093119978423142+3.469446951953614e-18j) * XX\n"
-     ]
-    },
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "/Users/bpa/qiskit/qiskit-terra/qiskit/opflow/primitive_ops/pauli_sum_op.py:213: DeprecationWarning: Using the `__mul__` operator `A * B` as shorthand for `A.dot(B)` is deprecated as of version 0.17.0 and will be  removed no earlier than 3 months after the release date. As an alternative, use the compose operator `B & A` in place of `A * B` as a replacement.\n",
-      "  new_self.primitive * other.primitive,\n"
+      "(-1.052373245772859-2.7755575615628914e-17j) * II\n",
+      "+ (-0.3979374248431805+1.3877787807814457e-17j) * ZI\n",
+      "+ (0.3979374248431805-2.7755575615628914e-17j) * IZ\n",
+      "- 0.011280104256235296 * ZZ\n",
+      "+ (0.18093119978423153+3.469446951953614e-18j) * XX\n"
      ]
     }
    ],
@@ -323,7 +306,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.10"
+   "version": "3.6.1"
   }
  },
  "nbformat": 4,

diff --git a/docs/tutorials/02_vibrational_structure.ipynb b/docs/tutorials/02_vibrational_structure.ipynb
@@ -154,18 +154,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 2,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "/Users/bpa/opt/anaconda3/envs/qiskit-nature/lib/python3.7/site-packages/pyscf/lib/misc.py:46: H5pyDeprecationWarning: Using default_file_mode other than 'r' is deprecated. Pass the mode to h5py.File() instead.\n",
-      "  h5py.get_config().default_file_mode = 'a'\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "from qiskit_nature.drivers import GaussianForcesDriver\n",
     "# if you ran Gaussian elsewhere and already have the output file\n",
@@ -200,12 +191,12 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [],
    "source": [
-    "from qiskit_nature.problems.second_quantization.vibrational.vibrational_structure_problem import VibrationalStructureProblem\n",
-    "from qiskit_nature.operators.second_quantization.qubit_converter import QubitConverter\n",
+    "from qiskit_nature.problems.second_quantization import VibrationalStructureProblem\n",
+    "from qiskit_nature.converters.second_quantization import QubitConverter\n",
     "from qiskit_nature.mappers.second_quantization import DirectMapper\n",
     "\n",
     "vibrational_problem = VibrationalStructureProblem(driver, num_modals=2, truncation_order=2)\n",
@@ -753,7 +744,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.10"
+   "version": "3.6.1"
   }
  },
  "nbformat": 4,