There were two main issues with the PWM support.
The first is they would fail to work properly if the board goes
into low power mode, when you do things like: time.sleep(0.25)
Can make partially work with this by turning on the proper flags
in each of the FlexPWMTimer Timers/sub-timers, but this did not
appear to work if for example you have both A and B channels
enabled.
Second main problem is that the code did not work with the X
channel of each timer/sub-timer. It looks like someone had
earlier started support for this, But was not sufficient.
Needed to bypass the SDK code and get it closer to the PJRC code.
That is we set the PWM_CTRL_FULL_MASK, which then uses base->SM[submodule].VAL1 to control
when the timer is reset, so it sets up your cycle/frequency. But then this implies that X channel
which uses 0, 1 has to be handled specially. So for the different channels:
A - Uses VAL2 to turn on (0) and VAL3=duty to turn off
B - Uses VAL4 to turn on (0) and VAL5 to turn off
X - As mentioned above VAL1 turns off, but its set to the timing for freqency. so
VAL0 turns on, so we set it to VAL1 - duty
Passing in a PWMOut still works but is deprecated. It will be
removed in CircuitPython 8.0.0
This also switches STM32 timer indices and channel indices to
0-based in our pin data rather than `- 1` everywhere. The latter is
more bug prone.
Most of the way for #3264
Tested on Metro M0, Metro M4, Feather S2, Feather nRF52840, Feather
STM32F4 and Arduino RP2040.
In #4683, tannewt noticed that uncrustify was not running on some
file in common-hal.
I investigated and found that it was not being run on a bunch of paths.
Rather than make incremental changes, I rewrote list_files to work
bsaed on regular expressions; these regular expressions are created from
the same git-style glob patterns.
I spot-checked some specific filenames after this change, and all looks good:
```
$ python3 tools/codeformat.py -v --dry-run tests/basics/int_small.py ports/raspberrypi/common-hal/pulseio/PulseIn.c extmod/virtpin.c tests/thread/thread_exit1.py ports/raspberrypi/background.h extmod/re1.5/recursiveloop.c
tools/codeformat.py -v --dry-run tests/basics/int_small.py ports/raspberrypi/common-hal/pulseio/PulseIn.c extmod/virtpin.c tests/thread/thread_exit1.py ports/raspberrypi/background.h extmod/re1.5/recursiveloop.c
uncrustify -c /home/jepler/src/circuitpython/tools/uncrustify.cfg -lC --no-backup extmod/virtpin.c ports/raspberrypi/background.h ports/raspberrypi/common-hal/pulseio/PulseIn.c
black --fast --line-length=99 -v tests/thread/thread_exit1.py
```
recursiveloop and int_small are excluded, while PulseIn, virtpin,
and background are included.
Testing running from a subdirectory (not _specifically_ supported though):
```
(cd ports && python3 ../tools/codeformat.py -v --dry-run raspberrypi/common-hal/pulseio/PulseIn.c ../extmod/virtpin.c)
../tools/codeformat.py -v --dry-run raspberrypi/common-hal/pulseio/PulseIn.c ../extmod/virtpin.c
uncrustify -c /home/jepler/src/circuitpython/tools/uncrustify.cfg -lC --no-backup ../extmod/virtpin.c raspberrypi/common-hal/pulseio/PulseIn.
```
As a side-effect, a bunch more files are re-formatted now. :-P
After this change, the following program works for me on the MIMXRT1010-EVK:
```python
import pwmio
import board
p = pwmio.PWMOut(board.D13, frequency=1_000_000, variable_frequency=True)
p.duty_cycle = 32868
while True:
pass
```
Querying and varying the duty_cycle and frequency work as well.
The lowest frequency obtainable is about 2kHz; there is an additional
divider which would allow lower PWM frequencies (I think 1kHz is important
for servos?)
Something odd happens with very low duty cycles, such as
```python
>>> p.frequency = 2000
>>> p.duty_cycle = 2
```
instead of a symmetrical waveform, it's asymmetrical. With `duty_cycle=4`,
the effect disappears. The reason for this is probably hidden in the
datasheet, but could affect servos or other things that count pulse
widths.
