rigetti
diff --git a/‎CHANGELOG.md
+34-1 b/‎CHANGELOG.md
+34-1
diff --git a/‎docs/source/advanced_usage.rst
+22-22 b/‎docs/source/advanced_usage.rst
+22-22
diff --git a/‎docs/source/conf.py
+6 b/‎docs/source/conf.py
+6
diff --git a/‎docs/source/exercises.rst
+3-3 b/‎docs/source/exercises.rst
+3-3
diff --git a/‎docs/source/noise.rst
+4-4 b/‎docs/source/noise.rst
+4-4
diff --git a/‎docs/source/programs_and_gates.rst
+3-3 b/‎docs/source/programs_and_gates.rst
+3-3
diff --git a/‎docs/source/troubleshooting.rst
+9-1 b/‎docs/source/troubleshooting.rst
+9-1
diff --git a/‎mypy.ini
-4 b/‎mypy.ini
-4
@@ -12,7 +12,27 @@ The 4.0 release of pyQuil migrates its core functionality into Rigetti's latest
 - Python 3.7 is no longer supported.
 - The environment variable overrides for `quilc` and `QVM` URLs have been renamed to `QCS_APPLICATIONS_QUILC_URL` and `QCS_APPLICATIONS_QVM_URL`, respectively.
 - The `QuantumComputer`'s `run` method now takes an optional `memory_map` parameter. This mapping takes memory region names to a list of values to use for a run. This replaces the ability to use `write_memory` on `Program`s.
-- `Pragma("DELAY", ...)` will now raise a parser error because it generates invalid Quil. Use the `Delay` instruction instead.
+- `Program` and instructions have been re-written using the `quil` package. Much of the API remains the same, with the following exceptions:
+	- `SwapPhase` has been renamed to `SwapPhases`
+	- `TemplateWaveform` and its subclasses are no longer `@dataclass`es.
+	- `DefFrame` and `Frame` are no longer `@dataclass`es.
+	- The `pop` method has been removed from `Program`.
+	- A `Program` that uses `QubitPlaceholder`s or `LabelPlaceholder`s can no longer be pickled
+	- `DefMeasureCalibration` now requires a `MemoryReference`.
+	- `fill_placeholders` has been removed since it is no longer needed to expand calibrations.
+	- The `get_qubits` method on `Gate` now returns a `list` so that ordering is guaranteed.
+	- Setting the `offsets` property on `Declare` will raise a `ValueError` if no `shared_region` is set.
+    - When converting to Quil, a `Program` automatically places `DECLARE`s at the top of the program.
+- The `parser` module has been removed. Parsing now happens by initializing a `Program` with the program string you want to be parsed.
+- `PRAGMA` instructions can no longer have a directive that conflicts with a Quil keyword. If you were using directives like `DELAY` or `FENCE`, consider using the respective Quil-T instructions instead.
+- `QubitPlaceholders` can no longer be used in `PRAGMA` instructions.
+- `DefGate` and the other gate definition instructions will no longer accept names that conflict with Quil keywords.
+- `Program#get_qubits()` will raise a `TypeError` if any of the qubits in the program are not a fixed index.
+- A `Program`s `LabelPlaceholder`s are no longer resolved automatically when getting its instructions. Use the `resolve_label_placeholders` method to do it explicitly. Note that the `if_then` and `while_do` methods will add `LabelPlaceholder`s to your program.
+- There may be some minor differences in how instructions are converted to a Quil string. These differences should only be cosmetic and should not affect the behavior of a program. However, they may break unit tests or other code that rely on specific formatting of programs.
+- The `pyquil.quil.get_default_qubit_mapping` function for getting a mapping of `QubitPlaceholders` to resolved indices has been removed. Generating a default mapping is handled automatically by the placeholder resolving methods.
+- The `JumpConditional` base class has been removed, use `JumpWhen` and/or `JumpUnless` directly instead.
+- The `Program` class automatically sorts `DECLARE` instructions to the top of the Program when converting to Quil.
 
 ### Features
 
@@ -24,11 +44,24 @@ The 4.0 release of pyQuil migrates its core functionality into Rigetti's latest
 - The new `QPUCompilerAPIOptions` class provides can now be used to customize how a program is compiled against a QPU.
 - The `diagnostics` module has been introduced with a `get_report` function that will gather information on the currently running pyQuil
 installation, perform diagnostics checks, and return a summary.
+- `Program` has new methods for resolving Qubit and Label Placeholders in a program.
+- `QubitPlaceholders` can now be used in programs that also use fixed or variable qubits.
 - `QAMExecutionResult` now has a `raw_readout_data` property that can be used to get the raw form of readout data returned from the executor.
+- `WaveformInvocation` has been added as a simpler, more flexible class for invoking waveforms.
+- Added two new instruction classes:
+   	- The `Include` class for `INCLUDE` instructions.
+   	- The `DefCircuit` class `DEFCIRCUIT` instructions.
+- The `Program.copy` method now performs a deep copy.
 
 ### Deprecations
 
 - The `QAMExecutionResult` `readout_data` property has been deprecated to avoid confusion with the new `raw_readout_data` property. Use the `register_map` property instead.
+- The `indices` flag on the `get_qubits` method on `Program`s and instruction classes continues to work, but will be removed in future versions. A separate `get_qubit_indices` method has been added to get indices. In future versions, `get_qubits` will only return a list of `QubitDesignator`s.
+- The `is_protoquil`, `is_supported_on_qpu` methods on `Program` and the `validate_supported_quil` function will always return `True`. These methods were never reliable as they were implemented as client-side checks that don't necessarily reflect the latest available features on Rigetti compilers or QPUs. It's safe to stop using these functions and rely on the API to tell you if a program isn't supported.
+- `percolate_declares` is a no-op and will be removed in future versions. `Program` now “percolates” declares automatically.
+- `merge_programs` continues to work, but will be removed in future versions, use `Program` addition instead.
+- The `format_parameter` function continues to work, but will be removed in future versions.
+- The `WaveformReference` and `TemplateWaveform` classes continue to work, but will be removed in future versions. The new `WaveformInvocation` should be used instead.
 
 ## 3.5.4
 
 
@@ -146,15 +146,13 @@ where using ``QubitPlaceholder``\ s comes in.
 .. testoutput:: placeholders
    :hide:
 
-    H {q...}
-    CNOT {q...} {q...}
+    H Placeholder(QubitPlaceholder(0x...))
+    CNOT Placeholder(QubitPlaceholder(0x...)) Placeholder(QubitPlaceholder(0x...)) 
 
 .. parsed-literal::
 
-    H {q4402789176}
-    CNOT {q4402789176} {q4402789120}
-
-If you try to use this program directly, it will not work
+    H Placeholder(QubitPlaceholder(0x600002DEB5B0))
+    CNOT Placeholder(QubitPlaceholder(0x600002DEB5B0)) Placeholder(QubitPlaceholder(0x600002DEABB0))
 
 ..
     Could not make this a doctest because it would keep failing. ``doctest`` is supposed to match the
@@ -272,20 +270,21 @@ loop by following these steps:
 
     # Run inner_loop in a loop until flag_register is 0
     outer_loop.while_do(flag_register, inner_loop)
+    outer_loop.resolve_label_placeholders()
 
     print(outer_loop)
 
 .. testoutput:: control-flow
 
     DECLARE flag_register BIT[1]
-    MOVE flag_register 1
-    LABEL @START1
-    JUMP-UNLESS @END2 flag_register
+    MOVE flag_register[0] 1
+    LABEL @START_0
+    JUMP-UNLESS @END_0 flag_register[0]
     X 0
     H 0
-    MEASURE 0 flag_register
-    JUMP @START1
-    LABEL @END2
+    MEASURE 0 flag_register[0]
+    JUMP @START_0
+    LABEL @END_0
 
 Notice that the ``outer_loop`` program applied a Quil instruction directly to a
 classical register.  There are several classical commands that can be used in this fashion:
@@ -323,21 +322,22 @@ method.
 
     # Measure qubit 0 into our readout register
     branching_prog += MEASURE(0, ro)
+    branching_prog.resolve_label_placeholders()
 
     print(branching_prog)
 
 .. testoutput:: control-flow
 
-    DECLARE test_register BIT[1]
     DECLARE ro BIT[1]
+    DECLARE test_register BIT[1]
     H 1
-    MEASURE 1 test_register
-    JUMP-WHEN @THEN1 test_register
-    JUMP @END2
-    LABEL @THEN1
+    MEASURE 1 test_register[0]
+    JUMP-WHEN @THEN_0 test_register[0]
+    JUMP @END_0
+    LABEL @THEN_0
     X 0
-    LABEL @END2
-    MEASURE 0 ro
+    LABEL @END_0
+    MEASURE 0 ro[0]
 
 We can run this program a few times to see what we get in the readout register ``ro``.
 
@@ -437,7 +437,7 @@ The following shows an instructive example of all three.
 
     Quil to compute exp[iX] on qubit 0:
     H 0
-    RZ(-2.0) 0
+    RZ(-2) 0
     H 0
 
 ``exponential_map`` returns a function allowing you to fill in a multiplicative
@@ -461,12 +461,12 @@ value for :math:`\alpha`.
 
     1:
     H 0
-    RZ(-2.0) 0
+    RZ(-2) 0
     H 0
 
     2:
     H 0
-    RZ(-4.0) 0
+    RZ(-4) 0
     H 0
 
 To take it one step further, you can use :ref:`parametric_compilation` with ``exponential_map``. For instance:
 
@@ -105,6 +105,12 @@
     }
 }
 
+suppress_warnings = [
+    # TODO: Re-enable these warnings once Sphinx resolves this open issue:
+    # https://github.com/sphinx-doc/sphinx/issues/4961
+    "ref.python",
+]
+
 # fun little hack to always build the rst changelog from the markdown
 
 dirname = os.path.dirname(__file__)
 
@@ -179,10 +179,10 @@ We can see what this program looks like in Quil notation with ``print(qft(0, 1,
 
     SWAP 0 2
     H 0
-    CPHASE(-pi/2) 0 1
+    CPHASE(-1.5707963267948966) 0 1
     H 1
-    CPHASE(-pi/4) 0 2
-    CPHASE(-pi/2) 1 2
+    CPHASE(-0.7853981633974483) 0 2
+    CPHASE(-1.5707963267948966) 1 2
     H 2
 
 Part c: Execute the QFT
 
@@ -617,12 +617,12 @@ The Idiomatic pyQuil Program
 .. testoutput:: decoherence
 
     H 0
-    RX(pi/2) 1
+    RX(1.5707963267948966) 1
     CNOT 0 1
-    RZ(2*pi/3) 1
+    RZ(2.0943951023931953) 1
     CNOT 0 1
     H 0
-    RX(-pi/2) 1
+    RX(-1.5707963267948966) 1
 
 
 The Compiled Program
@@ -1165,10 +1165,10 @@ Pauli-Z moments that indicate the qubit correlations are corrupted (and correcte
 
 .. testoutput:: readout-noise
 
+    DECLARE ro BIT[3]
     PRAGMA READOUT-POVM 0 "(0.85 0.050000000000000044 0.15000000000000002 0.95)"
     PRAGMA READOUT-POVM 1 "(0.8 0.09999999999999998 0.19999999999999996 0.9)"
     PRAGMA READOUT-POVM 2 "(0.9 0.15000000000000002 0.09999999999999998 0.85)"
-    DECLARE ro BIT[3]
     H 0
     CNOT 0 1
     CNOT 1 2
 
@@ -434,7 +434,7 @@ matrix representation of the gate. For example, below we define a
 
 .. testoutput:: define-gates
 
-    DEFGATE SQRT-X:
+    DEFGATE SQRT-X AS MATRIX:
         0.5+0.5i, 0.5-0.5i
         0.5-0.5i, 0.5+0.5i
 
@@ -535,7 +535,7 @@ Some gates can be compactly represented as a permutation. For example, ``CCNOT``
        [0, 0, 0, 0, 0, 0, 1, 0]
    ])
 
-   ccnot_gate = DefGate("CCNOT", ccnot_matrix)
+   ccnot_gate = DefGate("MATRIX_CCNOT", ccnot_matrix)
 
    # etc
 
@@ -546,7 +546,7 @@ It can equivalently be defined by the permutation
    import numpy as np
    from pyquil.quilbase import DefPermutationGate
 
-   ccnot_gate = DefPermutationGate("CCNOT", [0, 1, 2, 3, 4, 5, 7, 6])
+   ccnot_gate = DefPermutationGate("PERMUTATION_CCNOT", [0, 1, 2, 3, 4, 5, 7, 6])
 
    # etc
 
 
@@ -77,13 +77,21 @@ Collect debug information
 
 3. Run your script with debug logging enabled by adding the following to the top of your script:
 
-   .. testcode:: python
+   .. testcode:: debug
 
     import logging
     logging.basicConfig(level=logging.DEBUG)
 
    .. note:: For information on how to filter the logs, see the `qcs-sdk-python logging documentation <https://github.com/rigetti/qcs-sdk-rust/tree/main/crates/python#enabling-debug-logging>`_
 
+   .. testcode:: debug
+      :hide:
+    
+    import logging
+    # Disable debug logging, otherwise doctests will run with
+    # debug logging enabled.
+    logging.basicConfig(level=logging.INFO)
+
 If the problem still isn't clear, then we can help! Please file an issue
 on the `GitHub repo <https://github.com/rigetti/pyquil>`_ if it's an issue with pyQuil itself,
 or contact us at our `support page <https://rigetti.zendesk.com>`_ for problems with QCS. If applicable,
 
@@ -26,10 +26,6 @@ no_implicit_reexport = False
 
 plugins = numpy.typing.mypy_plugin
 
-# Ignore errors in all parser-related files
-[mypy-pyquil._parser.*]
-ignore_errors = True
-
 # Ignore errors in vendored third-party libraries
 [mypy-pyquil.external.*]
 ignore_errors = True
Original file line number	Diff line number	Diff line change
`@@ -105,6 +105,12 @@`
`105`	`105`	`}`
`106`	`106`	`}`
`107`	`107`
	`108`	`+suppress_warnings = [`
	`109`	`+ # TODO: Re-enable these warnings once Sphinx resolves this open issue:`
	`110`	`+ # https://github.com/sphinx-doc/sphinx/issues/4961`
	`111`	`+ "ref.python",`
	`112`	`+]`
	`113`	`+`
`108`	`114`	`# fun little hack to always build the rst changelog from the markdown`
`109`	`115`
`110`	`116`	`dirname = os.path.dirname(__file__)`