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.
After discussing with danh, I noticed that `a/**/b` would not match `a/b`.
After correcting this and re-running "pre-commit run --all", additional
files were reindented, including the codeformat script itself.
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
This is a slight trade-off with code size, in places where a "_varg"
mp_raise variant is now used. The net savings on trinket_m0 is
just 32 bytes.
It also means that the translation will include the original English
text, and cannot be translated. These are usually names of Python
types such as int, set, or dict or special values such as "inf" or
"Nan".
This introduces the new macro SAM_D5X_E5X. This is mostly the same
as SAMD51 before, except in a few places where a special case for
SAME54 is required
Fixes#2086
When the frequency of a `PWMOut` is change it re-sets the PWM's duty cycle as
well, since the registers have to be re-calculated based on the new frequency.
Unfortunately, `common_hal_pulseio_pwmout_get_duty_cycle`
will return a value very close to, but not exactly, the value passed to `common_hal_pulseio_pwmout_set_duty_cycle`. If the frequency is modified
without the calling code also re-setting the duty cycle then the duty cycle
will decay over time. This fixes that problem by tracking the unadjusted duty
cycle and re-setting the duty cycle to that value when the frequency is changed.
