rebase ion-trap branch (#3153)

* Remove changelog and document automated creation (#3109) * Remove changelog and document automated creation With the introduction of the qiskit-bot release automation for terra we no longer need to manually maintain or keep a changelog in repo. The github release pages (which we were manually copy and pasting the changelog into already) take the place of this file. For all future releases the creation of this page is completely automatic and handled by the bot. This works by using the git log and PR tags to figure out which commits belong in the changelog summary. The commit msg summary (the first line) is used for the changelog based on the tags. If a longer explanation is necessary that should be handled in the reno release notes. Fixes #3077 * Add README section on changelog * Make tweaks to readme for clarity * The option fig.tight_layout is triggering warnings in some situations so it is being removed (#3123) * no fig.tight_layout * removing the rest of fig.tight_layout() * check casteable types in Layout (#3100) * test * cast in insinstance * style * layouts are already layouts :) * Travis CI: The sudo: tag is deprecated on Travis (#3134) https://blog.travis-ci.com/2018-11-19-required-linux-infrastructure-migration * Fix a syntax error in QuantumCircuit.mirror. (#3138) * Fix for #3106 gatefacecolor key on circuit diagrams (#3137) * Issue #3106 gatefacecolor key has no effect on circuit diagrams If the style property "gatefacecolor" is set to a different value than the default, this color is applied. Fixes #3106 * Solved style problem space before : eliminated * Update plot_state_hinton() formatting (#3093) Add axes to the image part. It looks like the image axes already exist for non-empty graphs. The change that I made here is to remove if np.any(dataimag != 0): if the desired behavior is to see the axes on graphs that don't contain any elements. Replace rho with the latex rho Use standard format for real and imag parts of rho Fixes #2321 * Set barrier across multi-qubits correctly (#3042) * Previously it was assumed that specified barrier has a single contiguous span across qubits. Qubits for the barrier need not be adjacent in the diagram. This commit handles this case by adding barrier across correct qubits. * compute multiple short spans. Fixes #2918 * Test pulse clipping fix Osx #1. (#3144) * Remove superfluous reference to timeslots from assemble_schedules (#3139) * Extend custom multiqubit gates over classical bits for mpl (#3062) * Got it to extend over the clasical bits * Fixed a small bug * Removed a file accidentally modified * Fix linter * Deprecate allowing extra keys in circuit drawer style dict (#3105) * test * cast in insinstance * style * layouts are already layouts :) * style['plotbarrier'] is being deprecated * internal param for text drawer renamed to plot_barriers * error when style contains unknown options * better error message * remove #3100, since it was not my intention to be on it * style * remove plotbarrier * unused import * replace error with warning * release note * rochester_layout (#3125) * Use _append when args already converted and broadcast. (#2936) * Remove line in init which had been commented out (#3150) * Fix circuit drawing justification (#3061) Fixes #2802 qiskit/visualization/utils.py _get_layered_instructions() was erroneous and did not justify left nor right correctly. I have reworked that code which underlies many visual representations of circuits to the user. * refactored, needs more work on right justification * Looks like this works for qiskit-terra issue #2802 * May fix first test failure for this pull request, while causing another? * Draws conditionals on ClassicalRegister correctly now. * - Occurs check for gate in gates leads to good test results. - Added a few more self.maxDiff = None while debugging. Should they be pulled out? * tabs and trailing spaces ;) * removed the maxDiff's because they make the Style and lint test in Python 3.5 fail * added tests modified changelog * Test case extended to include original issue reported in #2802 * oops, left a maxDiff=None in from testing. Fixed * changes to utils.py requested by reviewer maddy-tod * test cases split as requested by reviewer maddy-tod * added circuit diagrams in comments to new tests * removed note from changelog and made it a release note per @mtreinish * made _LayerSpooler a private class * Revert "Remove changelog and document automated creation (#3109)" This reverts commit effad12. * Make _LayerSpooler a subclass of list The _LayerSpooler class was only ever used as list. While the class was an independent type it basically just wrapped an internal list. THen there were helper functions to access and manipulate that list. These methods just duplicated what python already provides and the list class itself already implements. This commit fixes this so the _LayerSpooler itself is a subclass of list so when it's initialized you can just treat it as the output list it was generating. * Clean up release note, fix only, not prelude * un reverted my revert of CONTRIBUTING.md * refactored, needs more work on right justification * Looks like this works for qiskit-terra issue #2802 * May fix first test failure for this pull request, while causing another? * Draws conditionals on ClassicalRegister correctly now. * - Occurs check for gate in gates leads to good test results. - Added a few more self.maxDiff = None while debugging. Should they be pulled out? * tabs and trailing spaces ;) * removed the maxDiff's because they make the Style and lint test in Python 3.5 fail * added tests modified changelog * Test case extended to include original issue reported in #2802 * oops, left a maxDiff=None in from testing. Fixed * changes to utils.py requested by reviewer maddy-tod * test cases split as requested by reviewer maddy-tod * added circuit diagrams in comments to new tests * removed note from changelog and made it a release note per @mtreinish * made _LayerSpooler a private class * Make _LayerSpooler a subclass of list The _LayerSpooler class was only ever used as list. While the class was an independent type it basically just wrapped an internal list. THen there were helper functions to access and manipulate that list. These methods just duplicated what python already provides and the list class itself already implements. This commit fixes this so the _LayerSpooler itself is a subclass of list so when it's initialized you can just treat it as the output list it was generating. * Clean up release note, fix only, not prelude * put back missing section * Add partial transpiler support for targeting ion trap backends. (#3122) * handle reset/barrier/measure (#3130) * Do not unroll an Rx,Ry,Rxx circuit to U3,CX because of measure. (#3140)
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diff --git a/.travis.yml b/.travis.yml
@@ -14,7 +14,6 @@ notifications:
   email: false
 
 cache: pip
-sudo: false
 
 ###############################################################################
 # Anchored and aliased definitions.

diff --git a/CHANGELOG.md b/CHANGELOG.md
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -100,8 +100,31 @@ please ensure that:
 3. If it makes sense for your change that you have added new tests that
    cover the changes.
 4. Ensure that if your change has an end user facing impact (new feature,
-   deprecation, removal etc) that you have updated the CHANGELOG.md and
-   added a reno release note for that change.
+   deprecation, removal etc) that you have added a reno release note for that
+   change and that the PR is tagged for the changelog.
+
+### Changelog generation
+
+The changelog is automatically generated as part of the release process
+automation. This works through a combination of the git log and the pull
+request. When a release is tagged and pushed to github the release automation
+bot looks at all commit messages from the git log for the release. It takes the
+PR numbers from the git log (assuming a squash merge) and checks if that PR had
+a `Changelog:` label on it. If there is a label it will add the git commit
+message summary line from the git log for the release to the changelog.
+
+If there are multiple `Changelog:` tags on a PR the git commit message summary
+line from the git log will be used for each changelog category tagged.
+
+The current categories for each label are as follows:
+
+| PR Label               | Changelog Category |
+| -----------------------|--------------------|
+| Changelog: Deprecation | Deprecated         |
+| Changelog: New Feature | Added              |
+| Changelog: API Change  | Changed            |
+| Changelog: Removal     | Removed            |
+| Changelog: Bugfix      | Fixed              |
 
 ### Commit messages
 
@@ -157,6 +180,10 @@ git annotate messages, gitk viewer annotations, merge commit messages, and many
 more places where space is at a premium. As well as summarizing the change
 itself, it should take care to detail what part of the code is affected.
 
+In addition the first line of the commit message gets used as entries in the
+generated changelog if the PR is tagged as being included in the changelog.
+It's critically important that you write a clear and succinct summary lines.
+
 * Describe any limitations of the current code.
 
 If the code being changed still has future scope for improvements, or any known
@@ -450,7 +477,7 @@ the project boards in Github for project management. We use milestones
 in Github to track work for specific releases. The features or other changes
 that we want to include in a release will be tagged and discussed in Github.
 As we're preparing a new release we'll document what has changed since the
-previous version in the release notes and Changelog.
+previous version in the release notes.
 
 ### Branches
 
@@ -471,11 +498,18 @@ merged to it are bugfixes.
 
 When it is time to release a new minor version of qiskit-terra we will:
 
-1.  Create a stable branch for the new minor version from the current
-    HEAD on the `master` branch
-2.  Create a new tag with the version number on the HEAD of the new stable
-    branch.
-3.  Change the `master` version to the next release version.
+1.  Create a new tag with the version number and push it to github
+2.  Change the `master` version to the next release version.
+
+The release automation processes will be triggered by the new tag and perform
+the following steps:
+
+1.  Create a stable branch for the new minor version from the release tag
+    on the `master` branch
+2.  Build and upload binary wheels to pypi
+3.  Create a github release page with a generated changelog
+4.  Generate a PR on the meta-repository to bump the terra version and
+    meta-package version.
 
 The `stable/*` branches should only receive changes in the form of bug
 fixes.

diff --git a/README.md b/README.md
@@ -109,6 +109,27 @@ Now you're set up and ready to check out some of the other examples from our
 Qiskit Terra is the work of [many people](https://github.com/Qiskit/qiskit-terra/graphs/contributors) who contribute
 to the project at different levels. If you use Qiskit, please cite as per the included [BibTeX file](https://github.com/Qiskit/qiskit/blob/master/Qiskit.bib).
 
+## Changelog and Release Notes
+
+The changelog for a particular release is dynamically generated and gets
+written to the release page on Github for each release. For example, you can
+find the page for the `0.9.0` release here:
+
+https://github.com/Qiskit/qiskit-terra/releases/tag/0.9.0
+
+The changelog for the current release can be found in the releases tab:
+![](https://img.shields.io/github/release/Qiskit/qiskit-terra.svg?style=popout-square)
+The changelog provides a quick overview of noteable changes for a given
+release.
+
+Additionally, as part of each release detailed release notes are written to
+document in detail what has changed as part of a release. This includes any
+documentation on potential breaking changes on upgrade and new features.
+For example, You can find the release notes for the `0.9.0` release in the
+Qiskit documentation here:
+
+https://qiskit.org/documentation/release_notes.html#terra-0-9
+
 ## License
 
 [Apache License 2.0](LICENSE.txt)
diff --git a/qiskit/assembler/assemble_schedules.py b/qiskit/assembler/assemble_schedules.py
@@ -83,7 +83,7 @@ def assemble_schedules(schedules, qobj_id, qobj_header, run_config):
                     instruction = PulseInstruction(
                         command=SamplePulse(name=name, samples=instruction.command.samples),
                         name=instruction.name,
-                        channel=instruction.timeslots.channels[0])
+                        channel=instruction.channels[0])
                 # add samples to pulse library
                 user_pulselib[name] = instruction.command
 

diff --git a/qiskit/circuit/quantumcircuit.py b/qiskit/circuit/quantumcircuit.py
@@ -188,7 +188,7 @@ def mirror(self):
         reverse_circ = self.copy(name=self.name + '_mirror')
         reverse_circ._data = []
         for inst, qargs, cargs in reversed(self.data):
-            reverse_circ.append((inst.mirror(), qargs, cargs))
+            reverse_circ.append(inst.mirror(), qargs, cargs)
         return reverse_circ
 
     def inverse(self):
@@ -234,7 +234,7 @@ def combine(self, rhs):
                 combined_cregs.append(element)
         circuit = QuantumCircuit(*combined_qregs, *combined_cregs)
         for instruction_context in itertools.chain(self.data, rhs.data):
-            circuit.append(*instruction_context)
+            circuit._append(*instruction_context)
         return circuit
 
     def extend(self, rhs):
@@ -261,7 +261,7 @@ def extend(self, rhs):
 
         # Add new gates
         for instruction_context in rhs.data:
-            self.append(*instruction_context)
+            self._append(*instruction_context)
         return self
 
     @property

diff --git a/qiskit/compiler/transpile.py b/qiskit/compiler/transpile.py
@@ -24,6 +24,7 @@
 from qiskit.circuit.quantumregister import Qubit
 from qiskit import user_config
 from qiskit.transpiler.exceptions import TranspilerError
+from qiskit.converters import isinstanceint, isinstancelist
 
 
 def transpile(circuits,
@@ -330,13 +331,17 @@ def _parse_initial_layout(initial_layout, circuits):
     # initial_layout could be None, or a list of ints, e.g. [0, 5, 14]
     # or a list of tuples/None e.g. [qr[0], None, qr[1]] or a dict e.g. {qr[0]: 0}
     def _layout_from_raw(initial_layout, circuit):
-        if isinstance(initial_layout, list):
-            if all(isinstance(elem, int) for elem in initial_layout):
+        if initial_layout is None or isinstance(initial_layout, Layout):
+            return initial_layout
+        elif isinstancelist(initial_layout):
+            if all(isinstanceint(elem) for elem in initial_layout):
                 initial_layout = Layout.from_intlist(initial_layout, *circuit.qregs)
             elif all(elem is None or isinstance(elem, Qubit) for elem in initial_layout):
                 initial_layout = Layout.from_qubit_list(initial_layout)
         elif isinstance(initial_layout, dict):
             initial_layout = Layout(initial_layout)
+        else:
+            raise TranspilerError("The initial_layout parameter could not be parsed")
         return initial_layout
 
     # multiple layouts?

diff --git a/qiskit/converters/__init__.py b/qiskit/converters/__init__.py
@@ -21,3 +21,25 @@
 from .dag_to_circuit import dag_to_circuit
 from .ast_to_dag import ast_to_dag
 from .circuit_to_instruction import circuit_to_instruction
+
+
+def isinstanceint(obj):
+    """ Like isinstance(obj,int), but with casting. Except for strings."""
+    if isinstance(obj, str):
+        return False
+    try:
+        int(obj)
+        return True
+    except TypeError:
+        return False
+
+
+def isinstancelist(obj):
+    """ Like isinstance(obj, list), but with casting. Except for strings and dicts."""
+    if isinstance(obj, (str, dict)):
+        return False
+    try:
+        list(obj)
+        return True
+    except TypeError:
+        return False
diff --git a/qiskit/pulse/__init__.py b/qiskit/pulse/__init__.py
@@ -24,5 +24,4 @@
 from .configuration import LoConfig, LoRange
 from .exceptions import PulseError
 from .interfaces import ScheduleComponent
-# from .parser import parse_string_expr
 from .schedule import Schedule
diff --git a/qiskit/pulse/commands/sample_pulse.py b/qiskit/pulse/commands/sample_pulse.py
@@ -55,7 +55,7 @@ def samples(self):
         """Return sample values."""
         return self._samples
 
-    def _clip(self, samples: np.ndarray, epsilon: float = 1e-6):
+    def _clip(self, samples: np.ndarray, epsilon: float = 1e-5):
         """If samples are within epsilon of unit norm, clip sample by reducing norm by (1-epsilon).
 
         If difference is greater than epsilon error is raised.
@@ -86,8 +86,10 @@ def _clip(self, samples: np.ndarray, epsilon: float = 1e-6):
 
         return samples
 
-    def draw(self, dt: float = 1, style: Optional['PulseStyle'] = None,
-             filename: Optional[str] = None, interp_method: Optional[Callable] = None,
+    def draw(self, dt: float = 1,
+             style: Optional['PulseStyle'] = None,
+             filename: Optional[str] = None,
+             interp_method: Optional[Callable] = None,
              scaling: float = 1, interactive: bool = False):
         """Plot the interpolated envelope of pulse.
 

diff --git a/qiskit/tools/jupyter/backend_monitor.py b/qiskit/tools/jupyter/backend_monitor.py
@@ -562,5 +562,4 @@ def get_date(job):
     ax.add_artist(Circle((0, 0), 0.7, color='white', zorder=1))
     ax.text(0, 0, total_jobs, horizontalalignment='center',
             verticalalignment='center', fontsize=26)
-    fig.tight_layout()
     return fig
diff --git a/qiskit/transpiler/layout.py b/qiskit/transpiler/layout.py
@@ -23,6 +23,7 @@
 
 from qiskit.circuit.quantumregister import Qubit
 from qiskit.transpiler.exceptions import LayoutError
+from qiskit.converters import isinstanceint
 
 
 class Layout():
@@ -87,11 +88,11 @@ def from_dict(self, input_dict):
     @staticmethod
     def order_based_on_type(value1, value2):
         """decides which one is physical/virtual based on the type. Returns (virtual, physical)"""
-        if isinstance(value1, int) and isinstance(value2, (Qubit, type(None))):
-            physical = value1
+        if isinstanceint(value1) and isinstance(value2, (Qubit, type(None))):
+            physical = int(value1)
             virtual = value2
-        elif isinstance(value2, int) and isinstance(value1, (Qubit, type(None))):
-            physical = value2
+        elif isinstanceint(value2) and isinstance(value1, (Qubit, type(None))):
+            physical = int(value2)
             virtual = value1
         else:
             raise LayoutError('The map (%s -> %s) has to be a (Bit -> integer)'
@@ -272,7 +273,7 @@ def from_intlist(int_list, *qregs):
         Raises:
             LayoutError: Invalid input layout.
         """
-        if not all(isinstance(i, int) for i in int_list):
+        if not all(isinstanceint(i) for i in int_list):
             raise LayoutError('Expected a list of ints')
         if len(int_list) != len(set(int_list)):
             raise LayoutError('Duplicate values not permitted; Layout is bijective.')

diff --git a/qiskit/visualization/circuit_visualization.py b/qiskit/visualization/circuit_visualization.py
@@ -225,7 +225,7 @@ def circuit_drawer(circuit,
         return _text_circuit_drawer(circuit, filename=filename,
                                     line_length=line_length,
                                     reverse_bits=reverse_bits,
-                                    plotbarriers=plot_barriers,
+                                    plot_barriers=plot_barriers,
                                     justify=justify,
                                     vertical_compression=vertical_compression,
                                     idle_wires=idle_wires,
@@ -327,7 +327,6 @@ def qx_color_scheme():
         "latexdrawerstyle": True,
         "usepiformat": False,
         "cregbundle": False,
-        "plotbarrier": False,
         "showindex": False,
         "compress": True,
         "margin": [2.0, 0.0, 0.0, 0.3],
@@ -342,7 +341,7 @@ def qx_color_scheme():
 
 
 def _text_circuit_drawer(circuit, filename=None, line_length=None, reverse_bits=False,
-                         plotbarriers=True, justify=None, vertical_compression='high',
+                         plot_barriers=True, justify=None, vertical_compression='high',
                          idle_wires=True, with_layout=True):
     """
     Draws a circuit using ascii art.
@@ -355,7 +354,7 @@ def _text_circuit_drawer(circuit, filename=None, line_length=None, reverse_bits=
                    shutil.get_terminal_size(). If you don't want pagination
                    at all, set line_length=-1.
         reverse_bits (bool): Rearrange the bits in reverse order.
-        plotbarriers (bool): Draws the barriers when they are there.
+        plot_barriers (bool): Draws the barriers when they are there.
         justify (str) : `left`, `right` or `none`. Defaults to `left`. Says how
                         the circuit should be justified.
         vertical_compression (string): `high`, `medium`, or `low`. It merges the
@@ -375,7 +374,7 @@ def _text_circuit_drawer(circuit, filename=None, line_length=None, reverse_bits=
     else:
         layout = None
     text_drawing = _text.TextDrawing(qregs, cregs, ops, layout=layout)
-    text_drawing.plotbarriers = plotbarriers
+    text_drawing.plotbarriers = plot_barriers
     text_drawing.line_length = line_length
     text_drawing.vertical_compression = vertical_compression
 

diff --git a/qiskit/visualization/gate_map.py b/qiskit/visualization/gate_map.py
@@ -128,6 +128,21 @@ def plot_gate_map(backend, figsize=None,
 
     mpl_data[5] = [[1, 0], [0, 1], [1, 1], [1, 2], [2, 1]]
 
+    mpl_data[53] = [[0, 2], [0, 3], [0, 4], [0, 5], [0, 6],
+                    [1, 2], [1, 6],
+                    [2, 0], [2, 1], [2, 2], [2, 3], [2, 4],
+                    [2, 5], [2, 6], [2, 7], [2, 8],
+                    [3, 0], [3, 4], [3, 8],
+                    [4, 0], [4, 1], [4, 2], [4, 3], [4, 4],
+                    [4, 5], [4, 6], [4, 7], [4, 8],
+                    [5, 2], [5, 6],
+                    [6, 0], [6, 1], [6, 2], [6, 3], [6, 4],
+                    [6, 5], [6, 6], [6, 7], [6, 8],
+                    [7, 0], [7, 4], [7, 8],
+                    [8, 0], [8, 1], [8, 2], [8, 3], [8, 4],
+                    [8, 5], [8, 6], [8, 7], [8, 8],
+                    [9, 2], [9, 6]]
+
     config = backend.configuration()
     n_qubits = config.n_qubits
     cmap = config.coupling_map
@@ -161,7 +176,6 @@ def plot_gate_map(backend, figsize=None,
     if ax is None:
         fig, ax = plt.subplots(figsize=figsize)  # pylint: disable=invalid-name
         ax.axis('off')
-        fig.set_tight_layout(True)
 
     # set coloring
     if qubit_color is None:

diff --git a/qiskit/visualization/latex.py b/qiskit/visualization/latex.py
@@ -721,15 +721,24 @@ def _build_latex_array(self, aliases=None):
                     if self.plot_barriers:
                         qarglist = op.qargs
                         indexes = [self._get_qubit_index(x) for x in qarglist]
-                        start_bit = self.qubit_list[min(indexes)]
+                        indexes.sort()
                         if aliases is not None:
                             qarglist = map(lambda x: aliases[x], qarglist)
-                        start = self.img_regs[start_bit]
-                        span = len(op.qargs) - 1
 
-                        self._latex[start][column - 1] += " \\barrier[0em]{" + str(
-                            span) + "}"
-                        self._latex[start][column] = "\\qw"
+                        first = last = indexes[0]
+                        for index in indexes[1:]:
+                            if index - 1 == last:
+                                last = index
+                            else:
+                                pos = self.img_regs[self.qubit_list[first]]
+                                self._latex[pos][column - 1] += " \\barrier[0em]{" + str(
+                                    last - first) + "}"
+                                self._latex[pos][column] = "\\qw"
+                                first = last = index
+                        pos = self.img_regs[self.qubit_list[first]]
+                        self._latex[pos][column - 1] += " \\barrier[0em]{" + str(
+                            last - first) + "}"
+                        self._latex[pos][column] = "\\qw"
                 else:
                     raise exceptions.VisualizationError("bad node data")