Picamerax error recovery

See merge request !86

# Conflicts:
#   poetry.lock

Mypy coverage report

See merge request !110

You can now set the stage type to "MissingStage" in
microscope_configuration.json to stop the server looking for the stage.
A warning is logged to make it obvious what's happening.

Allow MissingStage to be explicitly selected

See merge request !112

The tour pop-ups were getting stuck in the tab icon container.
Explicitly specifying that they could overflow said container,
and setting them to show to the right, seems to have fixed this issue.

Fix tour placement

Closes #199

See merge request !114

Update build instructions

See merge request !115

It doesn't make sense to allow fewer than 1 image in any dimension
of a scan.  Currently, supplying 0 gives a division by zero error.
I've added min="1" to each control.

The scan API view now uses a schema with validation
constraints to enforce a minimum size of 1 in any dimension.
This requires better error handling in the app, which I've added.
It also needs a fix in LabThings so the error propagates correctly

The dev tools pane now remembers the last address you entered in
"override origin" to save a few clicks  when doing local Vue development

Persistent API override setting.

See merge request !116

The previous "auto calibrate" button for the camera relied on a
combination of the built-in autoexposure/AWB and
some JPEG-based tweaks to get the exposure settings right.
This often led to confusing results, e.g. oscillating between green and
 pink images.

 I have rewritten the auto-exposure code to adjust gain and shutter
 speed based on the raw image.  This seems to be
 very reliable, at the expense of being quite slow.  That's a price I'm
 happy to pay.

 I have replaced both the camera's auto white balance and my
 JPEG-based AWB hack with a single-shot AWB method that
 looks at the raw image.

I also increased the precision of the numbers, which makes the step
buttons annoyingly useless but allows floating point
values without validation errors.

I've added buttons to perform the separate calibrations (gain, AWB)
under the full recalibrate link.
It would be really nice to have a modal dialog though.

When testing the UI I noticed that the different recalibrate routines
don't use locks properly, so they try to run
concurrently.

This commit isn't tested yet...

The picamera object isn't thread safe; I have now wrapped all access
in context managers that acquire the BaseCamera.lock

I also added an endpoint to reset the LST without auto-gain.

You can now recalibrate the LST without running auto-gain.

Forcing the use of piwheels avoids trying
to install numpy/scipy from source,
which is the Right Answer.

Unfortunately, sometimes packages fail on piwheels, but poetry still
tries to install them.  I've had to fix
pyyaml at 5.4.0 for that reason.

numpy/scipy were mismatched in version, which led to a confusing
import error.  I've removed the numpy version specification entirely
and left it to scipy to ensure numpy
is installed.  This could do with
review in the future...

To save some typing ``poe serve`` now runs a debug server.

Specifying overrideOrigin in the URL now
sets up the store with the modified origin.
This is intended for development, and makes it
much less annoying to develop with a Vue dev server.

Reset tour button resets the local storage used to mark the tour
as done.

Overriding the origin can now be done with a query string.
This will load the store with the new origin from the start,
so might be better for testing some things.
I'm not worried about unexpected bugs, as it is quite obvious
from the URL what's going on.

vuex-map-fields cleans up code when mapping
store state to local computed properties.

More or less everything is now done by setup.py
Pipfile simply installs the module in editable mode, which
recursively resolves dependencies as defined in setup.py.

We now install with --dev to make sure development dependencies
are included.  I've also removed "poetry run"
from the "poe" commands, as we are
already in an active virtual environment, so
it's unnecessary (and also broken).

Finally, I added a tarball of the vue app to
the output distribution.

poe was assuming we were using poetry - I have
configured it not to use poetry now. This required
using a newer version.

IHI scan style raster

See merge request !113

numpy 1.20 deprecates np.float, which was only ever an alias for
``float``.  I've replaced all occurrences of np.float with float, as
recommended.  There should be no change in functionality.

I don't know why these didn't fail before - possibly because of
incomplete type information from old numpy...
I removed a few annotations because they were failing (e.g.
np.sum can return a scalar or an array), but I don't think
this should be a problem - the function inputs and return values
are still typed.

Move away from poetry

Closes #218

See merge request !124

We've switched to pipenv, poetry.lock is now superfluous

None values should be treated the same as missing ones -
previously it would just crash.

I've changed the default values in MoveStageAPI
so that it correctly handles absolute moves with missing axes.
I've also simplified it so it isn't using axes_to_array as that
resulted in a confusing code path.

I have now disabled W1203 globally, see comment in
pyproject.toml

Fix absolute moves

See merge request !126

GPU preview and MJPEG stream settings are now persisted
using localStorage.  The old code that disabled
the stream for local connections now
just sets the initial/default value.

The initialisation of stream settings is now done
in the created() method of streamContent.vue.

I've eliminated the "globalsafetogglepreview" event
in favour of watching the store.

This was primarily done to disable the warning about f strings in
logging statements, globally rather than per-file.

adjust_shutter_and_gain_from_raw now uses a simpler algorithm.
The code is longer overall but hides some details in fuctions.
I've also split the loop into one for shutter speed and one for gain.
This isn't the algorithm that I originally wrote, but it seems to
work and is more readable.

Fix auto-exposure and AWB

Closes #191

See merge request !119

The code checks for the camera-stage mapper matrix by looking at its truth value.
However, this is ambiguous because the matrix has many elements.  That means that
if it's missing, we get the expected result, but if it's present
we get an error.

I have avoided dict.get() and instead look it up with [] notation.
This will raise a KeyError if it's missing, which I
handle helpfully.
If the key is present but the value is not castable to an array, we'll
get an exception anyway.

I've swapped the ValueError for a RuntimeError subclass to
make it clearer what's gone wrong.

Fix handling of missing CSM matrix

See merge request !127

After some refactoring, I lost the code that actually
saved stream settings to local storage.
This commit restores that functionality.

I'm not using vuex-map-fields, so have
removed it.

Add minimum scan dimension

See merge request !123

Local development improvements

See merge request !125