Merge branch 'main' into consolidate_imports

Author: rerpha

doc/conf.py

@@ -29,7 +29,7 @@
     ("py:obj", r"^.*\.T.*_co$"),
 ]
 
-myst_enable_extensions = ["dollarmath", "strikethrough"]
+myst_enable_extensions = ["dollarmath", "strikethrough", "colon_fence"]
 suppress_warnings = ["myst.strikethrough"]
 
 extensions = [

doc/dev/troubleshooting.md

@@ -0,0 +1,370 @@
+# Troubleshooting
+
+## Where is ...?
+
+### Instrument-specific plans & devices
+
+This is located in each instrument's `inst` script area, with their other instrument-specific scripts.
+
+`c:\Instrument\Settings\config\NDX<inst>\configurations\Python\inst\bluesky`.
+
+Instrument-specific bluesky plans will typically be defined in the `plans` module in the above area, and devices will 
+be defined in a `devices` module.
+
+### This library (`ibex_bluesky_core`)
+
+In a clean installation of IBEX, `ibex_bluesky_core` is installed as a python module via pip into the
+[uktena](https://github.com/IsisComputingGroup/uktena) environment which is in `c:\instrument\apps\python3`.
+
+However, for instruments which have been testing bluesky and may have versions of `ibex_bluesky_core` with local
+modifications, a version of `ibex_bluesky_core` may be checked out into `c:\instrument\dev\ibex_bluesky_core` on the
+instrument, and this will have been editable-installed into the `uktena` environment.
+
+### Other bluesky libraries (`ophyd_async`, `bluesky`, ...)
+
+`ophyd_async` and `bluesky` are installed as python modules. via pip, into the
+[uktena](https://github.com/IsisComputingGroup/uktena) environment which is in `c:\instrument\apps\python3` because
+they are specified in `pyproject.toml` of `ibex_bluesky_core`, which itself is a dependency of `uktena`.
+
+### Logs
+
+Log files are stored in `C:\Instrument\Var\logs\bluesky`.
+
+```{note}
+Older log files will be moved by the log rotation script to 
+`<isis share>\inst$\Backups$\stage-deleted\ndx<instrument>\Instrument\Var\logs\bluesky`
+```
+
+The default log level is `INFO` and all messages from `ibex_bluesky_core`, `bluesky` and `ophyd_async` are captured.
+
+If you need to increase this to `DEBUG` to isolate an issue, you can do so using 
+{py:obj}`ibex_bluesky_core.log.set_bluesky_log_levels`. See [logging documentation](logging.md) for a full example
+showing how to do this.
+
+### Scientist-facing data
+
+Scientist-facing output files are written to `<isis share>\inst$\NDX<inst>\user\test\scans\<current rb number>` by 
+default.
+
+Custom file-output paths can be specified by passing extra arguments to 
+{py:obj}`HumanReadableFileCallback<ibex_bluesky_core.callbacks.file_logger.HumanReadableFileCallback>` 
+for the "human-readable" files, or 
+{py:obj}`LiveFitLogger<ibex_bluesky_core.callbacks.fitting.livefit_logger.LiveFitLogger>` 
+for the fit output files. These callbacks may be hidden behind
+{py:obj}`ISISCallbacks<ibex_bluesky_core.callbacks.ISISCallbacks>` which also allows specifying output paths.
+
+See [dae_scan manual system test](https://github.com/ISISComputingGroup/ibex_bluesky_core/blob/0.2.1/manual_system_tests/dae_scan.py#L83)
+for an example of how to configure these output paths using {py:obj}`ISISCallbacks<ibex_bluesky_core.callbacks.ISISCallbacks>`.
+
+### Raw diagnostic data
+
+Raw documents emitted by bluesky are stored in `C:\Instrument\Var\logs\bluesky\raw_documents` - these show the raw 
+data emitted by bluesky scans. The filenames in this directory correspond to bluesky's scan ID, which is printed to 
+the console at the end of each scan, and is also included as metadata in the scientist-facing output files.
+
+These files are written by {py:obj}`ibex_bluesky_core.callbacks.document_logger.DocLoggingCallback`, which is subscribed
+to the run engine by default in {py:obj}`ibex_bluesky_core.run_engine.get_run_engine`.
+
+```{note}
+Older raw documents will be moved by the log rotation script to 
+`<isis share>\inst$\Backups$\stage-deleted\ndx<instrument>\Instrument\Var\logs\bluesky\raw_documents`
+```
+
+---
+
+## How do I ...?
+
+### Run a plan
+
+To run a plan, you need to pass it to the `RE` object, which is made for you by default, as an initialisation command,
+in IBEX GUI versions later than 2025.2. 
+
+:::{tip}
+For versions of the GUI earlier than 2025.2, where the run engine is not created automatically, an `RE` object can be 
+made manually using
+```python
+from ibex_bluesky_core.run_engine import get_run_engine
+RE = get_run_engine()
+```
+:::
+
+For example, to run a plan, use:
+
+```
+>>> RE(some_clever_plan(which, takes, some, arguments))
+```
+
+Note that without the `RE(...)` call, the plan **does nothing**:
+
+```
+>>> some_clever_plan(which, takes, some, arguments)
+<generator object scan at 0x000002286311D080>
+```
+
+### Pause/stop/resume/abort a plan
+
+While a plan is running, a single ctrl-c will stop gracefully after the next point has finished counting. A message
+like the following will be printed:
+
+> A 'deferred pause' has been requested. The RunEngine will pause at the next checkpoint. 
+> To pause immediately, hit Ctrl+C again in the next 10 seconds.
+> Deferred pause acknowledged. Continuing to checkpoint.
+
+Two ctrl-c keystrokes within 10 seconds of each other will stop the plan immediately.
+
+When a plan is paused, you will get a short exception message with a summary of your options:
+
+```
+Pausing...
+Traceback (most recent call last):
+  File "C:\Instrument\Apps\Python3\Lib\site-packages\IPython\core\interactiveshell.py", line 3579, in run_code
+    exec(code_obj, self.user_global_ns, self.user_ns)
+  File "<ipython-input-27-288a69b9f38e>", line 1, in <module>
+    RE(bps.sleep(999))
+  File "C:\Instrument\Apps\Python3\Lib\site-packages\bluesky\run_engine.py", line 976, in __call__
+    raise RunEngineInterrupted(self.pause_msg) from None
+bluesky.utils.RunEngineInterrupted: 
+Your RunEngine is entering a paused state. These are your options for changing
+the state of the RunEngine:
+
+RE.resume()    Resume the plan.
+RE.abort()     Perform cleanup, then kill plan. Mark exit_stats='aborted'.
+RE.stop()      Perform cleanup, then kill plan. Mark exit_status='success'.
+RE.halt()      Emergency Stop: Do not perform cleanup --- just stop.
+```
+
+At this point, you will be returned to an interactive shell. You must choose one of these options above before 
+attempting further operations with the `RunEngine`.
+
+- `RE.resume()` - resumes the scan from the point at which it was interrupted. The plan will complete as usual.
+- `RE.stop()` and `RE.abort()` are functionally identical - the plan will gracefully terminate, including running any
+cleanup actions and calling registered callbacks.
+- `RE.halt()` tells the RunEngine to drop dead and not do **anything** on the way out. This includes cleanup handlers,
+which for example may return motors to sensible positions or return DAE configuration to a state in which data can be
+taken.
+
+If you are unsure exactly what state your `RunEngine` is in, `RE.state` can be used to check this. If you attempt to 
+run another plan before choosing one of the options above, you will get an exception like:
+
+```
+Traceback (most recent call last):
+  File "C:\Instrument\Apps\Python3\Lib\site-packages\IPython\core\interactiveshell.py", line 3579, in run_code
+    exec(code_obj, self.user_global_ns, self.user_ns)
+  File "<ipython-input-29-288a69b9f38e>", line 1, in <module>
+    RE(bps.sleep(999))
+  File "C:\Instrument\Apps\Python3\Lib\site-packages\bluesky\run_engine.py", line 920, in __call__
+    raise RuntimeError(f"The RunEngine is in a {self._state} state")
+RuntimeError: The RunEngine is in a paused state
+```
+
+This means that you still need to choose how to continue from the previous interruption.
+
+### Get the result of a plan
+
+A plan will return a `RunEngineResult` object, which has a `plan_result` attribute:
+
+```
+result = RE(some_plan())
+result.plan_result
+```
+
+If a plan was interrupted and resumed later, the result is returned by the `RE.resume()` call:
+
+```
+RE(some_plan())
+<KeyboardInterrupt>
+result = RE.resume()
+result.plan_result
+```
+
+```{tip}
+If the result wasn't captured, it's still possible to access it in an IPython interactive shell using the special 
+underscore variables, for example `result = _`.
+
+This is not specific to bluesky - it's an IPython feature where `_` is bound to the return value of the last expression,
+`__` is bound to the result of the second-to-last expression, and so on.
+```
+
+[Do not try to "hide" the `RunEngine` in a script/function](https://blueskyproject.io/bluesky/main/tutorial.html#plans-in-series).
+The `RE(...)` call should always be typed by the user, at the terminal.
+
+### Connect a device
+
+Bluesky plans need devices to be connected up-front. This is so that errors (such as PVs not existing) are detected
+as soon as possible, not mid-way through a scan.
+
+Top-level plan wrappers should use the `ensure_connected` plan stub from `ophyd_async`:
+
+```python
+from ophyd_async.plan_stubs import ensure_connected
+
+
+def top_level_plan(dae, block):
+    yield from ensure_connected(dae, block)
+    yield from scan(...)
+```
+
+If you forget to do this, you will get a stack trace containing:
+
+```
+NotImplementedError: No PV has been set as connect() has not been called
+```
+
+### Debug `NotConnected` errors
+
+If `ophyd_async` cannot connect to a PV, you will get an error that looks like:
+
+```
+sample_changer2: NotConnected:
+    readback: NotConnected: ca://TE:NDW2922:CS:SB:sample_changer2
+```
+
+In the first instance, check that the relevant PV exists if you get it via `caget`.
+
+If the device is a {py:obj}`block_rw<ibex_bluesky_core.devices.block.BlockRw>`, but the `:SP` record does not exist,
+you may use a `block_w` instead. This will both read and write to the same PV. Similarly, if `blockname:SP:RBV` does
+not exist, a {py:obj}`block_rw_rbv<ibex_bluesky_core.devices.block.BlockRwRbv>` cannot be used.
+
+If the device is a {py:obj}`ibex_bluesky_core.devices.reflectometry.ReflParameter` and `redefine` fails to connect,
+pass `has_redefine=False` when constructing that parameter (this means you won't be able to redefine the position
+of this refl parameter).
+
+If instead you get a `TypeError` that looks like:
+
+```
+sample_changer: NotConnected:
+    readback: TypeError: TE:NDW2922:CS:SB:sample_changer with inferred datatype float cannot be coerced to str
+```
+
+This is because the **datatype of the underlying PV** does not match the **declared type in bluesky**. `ophyd_async`
+will not allow you to connect a `block_r(str, "some_block")` if `"some_block"` is a float-type PV. Every signal in
+`ophyd_async` is strongly typed.
+
+### Change how `set` on a device behaves
+
+For a {py:obj}`writable block<ibex_bluesky_core.devices.block.BlockRw>`, a `write_config` argument can be specified. 
+See the options on {py:obj}`BlockWriteConfig<ibex_bluesky_core.devices.block.BlockWriteConfig>` for detailed options. These are specified
+when first creating the `block` object, which is likely to be in 
+`\Instrument\Settings\config\NDX<inst>\configurations\Python\inst\bluesky\devices.py`, or dynamically created as part
+of a wrapper plan. See [block documentation](../devices/blocks.md) for detailed documentation about how to set up block
+devices.
+
+For complex cases, where a `set` being complete depends on multiple conditions, a custom `ophyd_async` device is usually
+the cleanest way to accomplish this. These can be defined in an instrument's `inst` scripts area if they are specific
+to one instrument, or can be promoted to `ibex_bluesky_core` if generally useful.
+
+### Add extra sleeps into a plan
+
+Generally you should not need to insert sleeps at the *plan* level - prefer instead to modify *devices* so that they
+accurately report when they have finished setting (including any necessary settle times, for example). Writable blocks 
+have a {py:obj}`BlockWriteConfig<ibex_bluesky_core.devices.block.BlockWriteConfig>` which has a `settle_time_s` 
+parameter for this purpose.
+
+If you *really* need to sleep in a plan, rather than at the device level, use `yield from bps.sleep(duration_seconds)`.
+Do **not** just call `time.sleep()` in a plan - this will stall the event loop and interfere with keyboard interrupts, 
+for example.
+
+### Add exception-handling to a plan
+
+In plans, because they are generators, you cannot just use `try-finally` or `try-except`.
+
+Instead, bluesky provides wrappers that implement error handling: 
+[`finalize_wrapper`](https://blueskyproject.io/bluesky/main/generated/bluesky.preprocessors.contingency_wrapper.html#bluesky.preprocessors.contingency_wrapper)
+and 
+[`contingency_wrapper`](https://blueskyproject.io/bluesky/main/generated/bluesky.preprocessors.finalize_wrapper.html#bluesky.preprocessors.finalize_wrapper).
+
+### Debug DAE failing to begin
+
+Check the DAE can begin a run without using bluesky.
+
+If you are counting using periods, and using the spectrum-data map, this imposes a limit of {math}`5000000` on number of
+`periods * (spectra+1) * (time channels+1)`. This means that scans with high numbers of points may fail, where those 
+with fewer points will work.
+
+### Debug a failed fit
+
+Fitting will only ever start after at least as many points have been collected, as there are free parameters in the
+fitting model. For example, a guassian fit will not be attempted with less than 4 data points. This can occur if a
+scan is interrupted early, for example.
+
+Fits can also fail if the data is particularly poor.
+
+### Debug a bad fit
+
+Consider whether you can use a different fitting model. Some models are more prone to getting stuck in local minima than
+others.
+
+For peak-like data, `"com"` or `"max"` from bluesky's 
+[`PeakStats callback`](https://blueskyproject.io/bluesky/main/callbacks.html#peakstats) can robustly give *an* answer,
+although often this will not be as good as a full fit and may not always be appropriate.
+
+### Debug keyboard-interrupt problems
+
+If a double ctrl-c does nothing, this is probably because the event loop is stalled - which is likely the  result of a 
+plan or device doing I/O or other synchronous operations directly, rather than via `asyncio` or `yield from`. 
+
+Find the offending function and replace it with it's bluesky-native equivalent. Python's `asyncio` module has a debug 
+mode which warns on long-running tasks - this can help identify the offending call.
+
+---
+
+## What is this syntax ...?
+
+### `async def` / `await` / `asyncio`
+
+Functions declared as `async def` are [python **coroutines**](https://docs.python.org/3/library/asyncio-task.html#).
+
+In a bluesky context, if you see an `async def` function, it is likely that you are looking at either
+an `ophyd_async` device class, or a `RunEngine` message handler.
+
+In order to get the result of a coroutine, it needs to be `await`ed:
+
+```python
+async def foo():
+    result = await some_coroutine()
+```
+
+In an `async def` function, do not perform blocking operations. For example, always use `await asyncio.sleep()`,
+and not `time.sleep()`. Similarly, do not use synchronous functions which perform I/O from a coroutine (e.g. calling
+`genie` APIs) - use the `async` APIs provided by `ophyd_async` instead.
+
+As a general rule of thumb, any function that could reasonably take more than a few tens of milliseconds, should not be
+called directly from a coroutine.
+
+### `yield` / `yield from` / `Generator`
+
+Functions containing `yield` and/or `yield from` are [python **generators**](https://wiki.python.org/moin/Generators). 
+
+If you see `yield from` in a function, you are likely to be looking at a
+[bluesky plan](https://blueskyproject.io/bluesky/main/plans.html#).
+
+`yield from` is the syntax used to delegate to subplans:
+
+```python
+def some_plan():
+    yield from move(...)
+    yield from scan(...)
+```
+
+Will perform an initial move followed by a scan.
+
+Return values from plans can be captured:
+
+```python
+def plan_that_returns():
+    yield from something()
+    return "hello, world"
+
+def plan():
+    returned_value = yield from plan_that_returns()
+```
+
+Like `coroutines` above, long-running functions or functions which perform I/O should not be used in plans. Doing so
+can stall the `RunEngine`'s internal event loop, break keyboard-interrupts, and break rewindability. Use bluesky-native
+functionality instead - for example:
+- [`yield from bps.sleep()`](https://blueskyproject.io/bluesky/main/generated/bluesky.plan_stubs.sleep.html#bluesky.plan_stubs.sleep) instead of `time.sleep()`
+- [`yield from bps.mv(block_object, value)`](https://blueskyproject.io/bluesky/main/generated/bluesky.plan_stubs.mv.html#bluesky.plan_stubs.mv) instead of `g.cset(block_name, value)`
+- [`value = yield from bps.rd(block_object)`](https://blueskyproject.io/bluesky/main/generated/bluesky.plan_stubs.rd.html#bluesky.plan_stubs.rd) instead of `value = g.cget(block_name)["value"]`
+
+If you must call an external function which may be long running or do I/O from a plan, review 
+[call_sync](../plan_stubs/external_code).