Remove unnecessary deepcopies in compilation (SE-233)

## Unreleased

### Breaking changes

- Qblox backend - `QuantifyCompiler.compile`, `determine_absolute_timing` and `compile_circuit_to_device` restandardized: returned schedule is the transformed schedule; and added `keep_original_schedule` argument (!771)

### Merged branches and closed issues

- Infrastructure - Add `jinja2` as dependency to quantify-scheduler (needed for `pandas.DataFrame`) (!777)

- Documentation - Split source and build folders to simplify using [`sphinx-autobuild`](https://github.com/executablebooks/sphinx-autobuild) for its editing. (!774)

- Schedules - Added two-qubit schedule generating function `two_qubit_transmon_schedules.chevron_cz_sched` for CZ tuneup (!700).

- Qblox backend - Remove unnecessary deepcopies from schedule for 30-75% performance improvement (!771)

## 0.16.0 (2023-08-17)

from quantify_scheduler import compilation

compilation.determine_absolute_timing(sched)

sched.plot_pulse_diagram(plot_backend="plotly")

timed_sched = compilation.determine_absolute_timing(sched)

timed_sched.plot_pulse_diagram(plot_backend="plotly")

```

    rel_time=500e-9,

)

compilation.determine_absolute_timing(sched)

sched.plot_pulse_diagram(plot_backend="plotly")

timed_sched = compilation.determine_absolute_timing(sched)

timed_sched.plot_pulse_diagram(plot_backend="plotly")

```

)

sched.add_resource(ClockResource(name="q0.01", freq=7e9))

compilation.determine_absolute_timing(sched)

sched.plot_pulse_diagram(plot_backend="plotly")

timed_sched = compilation.determine_absolute_timing(sched)

timed_sched.plot_pulse_diagram(plot_backend="plotly")

```

sched = pulse_train_schedule(1, 200e-9, 300e-9, 5)

compilation.determine_absolute_timing(sched)

sched.plot_pulse_diagram(plot_backend="plotly")

timed_sched = compilation.determine_absolute_timing(sched)

timed_sched.plot_pulse_diagram(plot_backend="plotly")

```

    rel_time=5e-7,

)

compilation.determine_absolute_timing(sched)

sched.plot_pulse_diagram(plot_backend="plotly")

timed_sched = compilation.determine_absolute_timing(sched)

timed_sched.plot_pulse_diagram(plot_backend="plotly")

```

Using these factory functions, the resulting square and staircase pulses use no waveform memory at all. The ramp pulse uses waveform memory for a short section of the waveform, which is repeated multiple times.

sched = Schedule("Long soft square pulse")

sched.add(pulse)

compilation.determine_absolute_timing(sched)

sched.plot_pulse_diagram(plot_backend="plotly")

timed_sched = compilation.determine_absolute_timing(sched)

timed_sched.plot_pulse_diagram(plot_backend="plotly")

```

Alternatively, the building methods of the {class}`~quantify_scheduler.operations.stitched_pulse.StitchedPulseBuilder` can be conveniently **chained** to create a {class}`~quantify_scheduler.operations.stitched_pulse.StitchedPulse` via more elegant syntax:

zhinst_compiler.draw(axs[2])

axs[2].set_title("Zhinst Backend");

```

## Performance optimization by not preserving the original schedule

There is a way to potentially decrease the compilation time by about 20-40 % depending on the schedule if you do not need to keep the original, uncompiled schedule after the compilation. Using `keep_original_schedule=False` in `compiler.compile` modifies parts of the original schedule, making the original schedule potentially unusable after the function call.

```{note}

The returned schedule references objects from the original schedule if `keep_original_schedule=False` is used. Refrain from modifying the original schedule after compilation in this case!

```

```{code-cell}

from quantify_scheduler.backends.graph_compilation import SerialCompiler

compiler = SerialCompiler(name="Device compile")

comp_sched = compiler.compile(schedule=echo_schedule, config=config, keep_original_schedule=False)

comp_sched

```

schedule.add(SquarePulse(amp=0.2, duration=4e-6, port="P"))

schedule.add(RampPulse(amp=-0.1, offset=.2, duration=6e-6, port="P"))

schedule.add(SquarePulse(amp=0.1, duration=4e-6, port="Q"), ref_pt='start')

determine_absolute_timing(schedule)

schedule = determine_absolute_timing(schedule)

_ = schedule.plot_pulse_diagram(sampling_rate=20e6)

    # with device_cfg as positional argument.

    *,  # Support for (deprecated) calling with device_cfg as keyword argument:

    device_cfg: DeviceCompilationConfig | Dict | None = None,

    keep_original_schedule=True,

) -> Schedule:

    """

    Add pulse information to all gates in the schedule.

        (deprecated) Device compilation config. Pass a full compilation config instead

        using `config` argument. Note, if a dictionary is passed, it will be parsed to a

        :class:`~.DeviceCompilationConfig`.

    keep_original_schedule

        If `True`, this function will not modify the schedule argument.

        If `False`, the compilation modifies the schedule, thereby

        making the original schedule unusable for further usage; this

        improves compilation time. Warning: if `False`, the returned schedule

        references objects from the original schedule, please refrain from modifying

        the original schedule after compilation in this case!

    Returns

    -------

    :

        A copy of `schedule` with pulse information added to all gates.

        The modified `schedule` with pulse information added to all gates.

    Raises

    ------

    elif not isinstance(device_cfg, DeviceCompilationConfig):

        device_cfg = DeviceCompilationConfig.parse_obj(device_cfg)

    # to prevent the original input schedule from being modified.

    if keep_original_schedule:

        schedule = deepcopy(schedule)

    for operation in schedule.operations.values():

    Returns

    -------

    :

        A copy of `schedule` with all clock resources added.

        The modified `schedule` with all clock resources added.

    Warns

    -----

        device_cfg = DeviceCompilationConfig.parse_obj(device_cfg)

    assert isinstance(device_cfg, DeviceCompilationConfig)

    # to prevent the original input schedule from being modified.

    schedule = deepcopy(schedule)

    # verify that required clocks are present; print warning if they are inconsistent

    verified_clocks = []

    for operation in schedule.operations.values():