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
Also found a race condition between timer_disable and redraw, which
would happen if I debugger-paused inside common_hal_rgbmatrix_timer_disable
or put a delay or print inside it. That's what pausing inside reconstruct
fixes.
So that the "right timer" can be chosen, `timer_allocate` now gets the `self`
pointer. It's guaranteed at this point that the pin information is accurate,
so you can e.g., find a PWM unit related to the pins themselves.
This required touching each port to add the parameter even though it's
unused everywhere but raspberrypi.
This changes lots of files to unify `board.h` across ports. It adds
`board_deinit` when CIRCUITPY_ALARM is set. `main.c` uses it to
deinit the board before deep sleeping (even when pretending.)
Deep sleep is now a two step process for the port. First, the
port should prepare to deep sleep based on the given alarms. It
should set alarms for both deep and pretend sleep. In particular,
the pretend versions should be set immediately so that we don't
miss an alarm as we shutdown. These alarms should also wake from
`port_idle_until_interrupt` which is used when pretending to deep
sleep.
Second, when real deep sleeping, `alarm_enter_deep_sleep` is called.
The port should set any alarms it didn't during prepare based on
data it saved internally during prepare.
ESP32-S2 sleep is a bit reorganized to locate more logic with
TimeAlarm. This will help it scale to more alarm types.
Fixes#3786
The has successfully run my loopback self-test program for CAN,
which tests transmission, reception, and filtering. The 1M baud rate setting
was also verified on saleae to be accurate.
