add support for fb epid database in optics #848

prjemian · 2023-04-17T17:00:01Z

close Add support for optics fb_epid database #847

prjemian · 2023-04-17T17:00:13Z

needs tests

prjemian · 2023-04-17T17:15:02Z

CI failed on unrelated test (but recent addition):

=========================== short test summary info ============================
FAILED apstools/synApps/tests/test_2slit.py::test_geometry_property[Optics2Slit2D_HV-gp:Slit1] - AssertionError: assert SlitGeometry(width=0.3, height=0.1, x=0.5, y=-0.399) == SlitGeometry(width=0.3, height=0.1, x=0.5, y=-0.4)
  
  Matching attributes:
  ['width', 'height', 'x']
  Differing attributes:
  ['y']
  
  Drill down into differing attribute y:
    y: -0.399 != -0.4
  Full diff:
  - SlitGeometry(width=0.3, height=0.1, x=0.5, y=-0.4)
  ?                                                 ^
  + SlitGeometry(width=0.3, height=0.1, x=0.5, y=-0.399)
  ?                                                 ^^^
!!!!!!!!!!!!!!!!!!!!!!!!!! stopping after 1 failures !!!!!!!!!!!!!!!!!!!!!!!!!!!
======= 1 failed, 348 passed, 3 skipped, 8 warnings in 318.25s (0:05:18) =======
Error: Process completed with exit code 1.

It's a sig figs situation. Uses math.isclose()?

prjemian · 2023-05-16T18:06:23Z

Locally, a different test failure:

(bluesky_2023_2) prjemian@zap:~/.../BCDA-APS/apstools$ pytest -vvv --lf apstools/synApps/tests/test_2slit.py
================================================================ test session starts =================================================================
platform linux -- Python 3.10.4, pytest-7.3.1, pluggy-1.0.0 -- /home/prjemian/.conda/envs/bluesky_2023_2/bin/python3.10
cachedir: .pytest_cache
rootdir: /home/prjemian/Documents/projects/BCDA-APS/apstools
configfile: pytest.ini
plugins: notebook-0.6.1, anyio-3.6.2
collected 17 items                                                                                                                                   
run-last-failure: 13 known failures not in selected tests

apstools/synApps/tests/test_2slit.py::test_attribute_quantities[Optics2Slit1D-gp:Slit1H-False-read_attrs-12] PASSED                            [  5%]
apstools/synApps/tests/test_2slit.py::test_attribute_quantities[Optics2Slit1D-gp:Slit1H-False-configuration_attrs-16] PASSED                   [ 11%]
apstools/synApps/tests/test_2slit.py::test_attribute_quantities[Optics2Slit1D-gp:Slit1H-True-read()-8] PASSED                                  [ 17%]
apstools/synApps/tests/test_2slit.py::test_attribute_quantities[Optics2Slit1D-gp:Slit1H-True-summary()-63] PASSED                              [ 23%]
apstools/synApps/tests/test_2slit.py::test_attribute_quantities[Optics2Slit2D_HV-gp:Slit1-False-read_attrs-26] PASSED                          [ 29%]
apstools/synApps/tests/test_2slit.py::test_attribute_quantities[Optics2Slit2D_HV-gp:Slit1-False-configuration_attrs-34] PASSED                 [ 35%]
apstools/synApps/tests/test_2slit.py::test_attribute_quantities[Optics2Slit2D_HV-gp:Slit1-True-read()-16] PASSED                               [ 41%]
apstools/synApps/tests/test_2slit.py::test_attribute_quantities[Optics2Slit2D_HV-gp:Slit1-True-summary()-114] PASSED                           [ 47%]
apstools/synApps/tests/test_2slit.py::test_attribute_quantities[Optics2Slit2D_InbOutBotTop-gp:Slit1-False-read_attrs-24] PASSED                [ 52%]
apstools/synApps/tests/test_2slit.py::test_attribute_quantities[Optics2Slit2D_InbOutBotTop-gp:Slit1-False-configuration_attrs-32] PASSED       [ 58%]
apstools/synApps/tests/test_2slit.py::test_attribute_quantities[Optics2Slit2D_InbOutBotTop-gp:Slit1-True-read()-16] PASSED                     [ 64%]
apstools/synApps/tests/test_2slit.py::test_attribute_quantities[Optics2Slit2D_InbOutBotTop-gp:Slit1-True-summary()-112] PASSED                 [ 70%]
apstools/synApps/tests/test_2slit.py::test_2slit1D PASSED                                                                                      [ 76%]
apstools/synApps/tests/test_2slit.py::test_2slit2D_HV PASSED                                                                                   [ 82%]
apstools/synApps/tests/test_2slit.py::test_2slit2D_InbOutBotTop PASSED                                                                         [ 88%]
apstools/synApps/tests/test_2slit.py::test_geometry_property[Optics2Slit2D_HV-gp:Slit1] PASSED                                                 [ 94%]
apstools/synApps/tests/test_2slit.py::test_geometry_property[Optics2Slit2D_InbOutBotTop-gp:Slit1] PASSED                                       [100%]

================================================================= 17 passed in 7.56s =================================================================
Subscription value callback exception (EpicsSignal(read_pv='gp:Slit1Hsize', name='obj_size_setpoint', parent='obj_size', value=0.30000000000000004, timestamp=1684260304.479151, tolerance=0.001, auto_monitor=False, string=False, write_pv='gp:Slit1Hsize', limits=False, put_complete=True))
Traceback (most recent call last):
  File "/home/prjemian/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/ophyd/ophydobj.py", line 492, in inner
    cb(*args, **kwargs)
  File "/home/prjemian/Documents/projects/BCDA-APS/apstools/apstools/devices/positioner_soft_done.py", line 191, in cb_setpoint
    logger.debug("cb_setpoint: done=%s, setpoint=%s", self.done.get(), self.setpoint.get())
  File "/home/prjemian/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/ophyd/signal.py", line 1379, in get
    info = self._get_with_timeout(
  File "/home/prjemian/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/ophyd/signal.py", line 1319, in _get_with_timeout
    info = pv.get_with_metadata(
  File "/home/prjemian/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/epics/pv.py", line 47, in wrapped
    return func(self, *args, **kwargs)
  File "/home/prjemian/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/epics/pv.py", line 563, in get_with_metadata
    md = ca.get_with_metadata(
  File "/home/prjemian/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/epics/ca.py", line 635, in wrapper
    return fcn(*args, **kwds)
  File "/home/prjemian/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/epics/ca.py", line 1390, in get_with_metadata
    return get_complete_with_metadata(chid, count=count, ftype=ftype,
  File "/home/prjemian/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/epics/ca.py", line 635, in wrapper
    return fcn(*args, **kwds)
  File "/home/prjemian/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/epics/ca.py", line 1537, in get_complete_with_metadata
    val = _unpack(chid, full_value, count=count,
  File "/home/prjemian/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/epics/ca.py", line 1273, in _unpack
    elem_count = element_count(chid)
  File "/home/prjemian/.conda/envs/bluesky_2023_2/lib/python3.10/site-packages/epics/ca.py", line 576, in wrapper
    raise ChannelAccessException('Unexpected channel ID')
epics.ca.ChannelAccessException: Unexpected channel ID

prjemian · 2023-05-16T18:09:26Z

Seems this code is not avoiding the problem at exit.

prjemian · 2023-05-16T18:38:01Z

Add atexit handler, similar to ophyd.

prjemian · 2023-05-16T19:03:08Z

With 9769084, the local builds finish without epics.ca.ChannelAccessException.

prjemian · 2023-05-16T19:51:54Z

Different failure just now. Probably a transient. Documenting here just in case:

apstools/callbacks/tests/test_nxwriter.py::test_NXWriter_with_RunEngine FAILED [  5%]

=================================== FAILURES ===================================
_________________________ test_NXWriter_with_RunEngine _________________________

camera = MyDetector(prefix='ad:', name='camera', read_attrs=['cam', 'hdf1'], configuration_attrs=['cam', 'cam.acquire_period', ... 'cam.image_mode', 'cam.manufacturer', 'cam.model', 'cam.num_exposures', 'cam.num_images', 'cam.trigger_mode', 'hdf1'])
motor = EpicsMotor(prefix='gp:m1', name='motor', settle_time=0.0, timeout=None, read_attrs=['user_readback', 'user_setpoint'], configuration_attrs=['user_offset', 'user_offset_dir', 'velocity', 'acceleration', 'motor_egu'])

    def test_NXWriter_with_RunEngine(camera, motor):
        test_file = pathlib.Path(tempfile.mkdtemp()) / "nxwriter.h5"
        catalog = databroker.temp().v2
    
        nxwriter = NXWriter()
        nxwriter.file_name = str(test_file)
        assert isinstance(nxwriter.file_name, pathlib.Path)
        nxwriter.warn_on_missing_content = False
    
        RE = RunEngine()
        RE.subscribe(catalog.v1.insert)
        RE.subscribe(nxwriter.receiver)
    
        npoints = 3
        uids = RE(bp.scan([camera], motor, -0.1, 0, npoints))
        assert isinstance(uids, (list, tuple))
        assert len(uids) == 1
        assert uids[-1] in catalog
    
        nxwriter.wait_writer()
        # time.sleep(1)  # wait just a bit longer
    
        assert test_file.exists()
        with h5py.File(test_file, "r") as root:
            default = root.attrs.get("default", "entry")
            assert default == "entry"
            assert default in root
            nxentry = root[default]
    
            default = nxentry.attrs.get("default", "data")
            assert default == "data"
            assert default in nxentry, f"{test_file=} {list(nxentry)=}"
            nxdata = nxentry[default]
    
            signal = nxdata.attrs.get("signal", "data")
            # assert signal == camera.name
>           assert signal in nxdata
E           assert 'data' in <HDF5 group "/entry/data" (0 members)>

/home/runner/work/apstools/apstools/apstools/callbacks/tests/test_nxwriter.py:1[56](https://github.com/BCDA-APS/apstools/actions/runs/4996050845/jobs/8948746959#step:15:57): AssertionError
------------------------------ Captured log call -------------------------------

prjemian · 2023-05-16T20:06:51Z

Still needs unit tests for epid.py.

prjemian · 2023-05-16T20:29:29Z

start the GUI: caQtDM -macro "P=gp:epid1" fb_epid_sim.ui &

prjemian added 2 commits April 17, 2023 11:58

ENH #847 add fb_epid devices

bdd7b05

DOC #847

d5156c6

prjemian added the enhancement label Apr 17, 2023

prjemian added this to the 1.6.16 milestone Apr 17, 2023

prjemian self-assigned this Apr 17, 2023

prjemian added 2 commits May 16, 2023 13:38

ENH #848 add atexit handler

9769084

STY #848 whitespace

8eb23c9

prjemian added 3 commits May 16, 2023 14:27

DOC #848

54703f9

TST #848 replace with math.isclose

6188c7b

TST #848 adjust tolerance

db0c2af

prjemian added 2 commits May 16, 2023 18:22

MNT #847 add setup & reset methods

065d785

TST #847 add tests

7806992

prjemian marked this pull request as ready for review May 16, 2023 23:26

prjemian added 2 commits May 16, 2023 18:44

TST #847

50109d4

TST #847 remove unused arguments

7a9c37b

prjemian added 2 commits May 16, 2023 19:11

TST #847 reduce number of tested items

644ffc6

DOC #847 xref issue in synApps optics module

9ea6801

prjemian merged commit c3d0f94 into main May 17, 2023

prjemian deleted the 847-fb_epid branch May 17, 2023 00:32

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add support for fb epid database in optics #848

add support for fb epid database in optics #848

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add support for fb epid database in optics #848

add support for fb epid database in optics #848

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