DOC: fix docs after package reorganization

.travis.yml

@@ -4,6 +4,8 @@ sudo: false
 env:
   global:
     - OFFICIAL_REPO="pcdshub/jet_tracking"
+    # Doctr deploy key for pcdshub/jet_tracking
+    - secure: "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"
 
 matrix:
   include:

docs/source/conf.py

@@ -22,12 +22,14 @@
 import sphinx_rtd_theme
 import datetime
 import matplotlib
+matplotlib.use('Agg')
 
 
 module_path = os.path.join(os.path.dirname(os.path.abspath(__file__)),'../../')
 sys.path.insert(0,module_path)
 
 
+
 # -- General configuration ------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
@@ -44,7 +46,6 @@
               'IPython.sphinxext.ipython_directive',
               'IPython.sphinxext.ipython_console_highlighting',
               'matplotlib.sphinxext.mathmpl',
-              'matplotlib.sphinxext.only_directives',
               'matplotlib.sphinxext.plot_directive',
 #              'sphinx.ext.autosectionlabel'
               'sphinx.ext.viewcode',
@@ -55,6 +56,14 @@
               'sphinx.ext.mathjax',
                      ]
 
+try:
+    import matplotlib.sphinxext.only_directives
+except ImportError:
+    ...
+else:
+    extensions.append('matplotlib.sphinxext.only_directives')
+
+
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
 

docs/source/control.rst

@@ -3,7 +3,7 @@
 Jet Control Overview
 ####################
 
-.. currentmodule:: jet_control
+.. currentmodule:: jet_tracking.jet_control
 
 To start ipython for cxi hutch-python3.
 
@@ -38,5 +38,3 @@ Attributes
     JetControl.calibrate
     JetControl.jet_calculate
     JetControl.jet_move
-
-

docs/source/devices.rst

@@ -1,6 +1,6 @@
 .. _devices:
 
-.. currentmodule:: jet_control
+.. currentmodule:: jet_tracking.jet_control
 
 Jet Tracking Classes
 ####################
@@ -9,7 +9,7 @@ Base classes used in jet tracking and control.
 JetControl Class
 ----------------
 
-.. autoclass:: jet_control.JetControl
+.. autoclass:: JetControl
 
 .. autosummary::
     :toctree: generated/
@@ -23,20 +23,19 @@ JetControl Class
 Injector Class
 --------------
 
-.. autoclass:: devices.Injector
+.. autoclass:: jet_tracking.devices.Injector
 
 Questar Class
 -------------
 
-.. autoclass:: devices.Questar
+.. autoclass:: jet_tracking.devices.Questar
 
 Parameters Class
 ----------------
 
-.. autoclass:: devices.Parameters
+.. autoclass:: jet_tracking.devices.Parameters
 
 Diffract Class
 --------------
 
-.. autoclass:: devices.Diffract
-
+.. autoclass:: jet_tracking.devices.Diffract

docs/source/sample_delivery.rst

@@ -27,37 +27,37 @@ API
 Sample Delivery System Class
 ----------------------------
 
-.. autoclass:: devices.SDS
+.. autoclass:: jet_tracking.devices.SDS
 
 
 Selector Class
 --------------
 
-.. autoclass:: devices.Selector
+.. autoclass:: jet_tracking.devices.Selector
 
 
 CoolerShaker Class
 ------------------
 
-.. autoclass:: devices.CoolerShaker
+.. autoclass:: jet_tracking.devices.CoolerShaker
 
 
 HPLC Class
 ----------
 
-.. autoclass:: devices.HPLC
+.. autoclass:: jet_tracking.devices.HPLC
 
 
 PressureController Class
 ------------------------
 
-.. autoclass:: devices.PressureController
+.. autoclass:: jet_tracking.devices.PressureController
 
 
 FlowInegrator Class
 -------------------
 
-.. autoclass:: devices.FlowIntegrator
+.. autoclass:: jet_tracking.devices.FlowIntegrator
 
 
 

docs/source/shared_memory.rst

@@ -1,6 +1,6 @@
 .. _shared_memory:
 
-.. currentmodule:: psana2epics
+.. currentmodule:: jet_tracking.psana
 
 Jet Tracking Shared Memory Application
 ######################################
@@ -62,9 +62,4 @@ API
     :nosignatures:
     :toctree: generated/
 
-    psana2epics.output_cspad_sum
-
-
-
-
-
+    output_cspad_sum

github_deploy_key_pcdshub_jet_tracking.enc

@@ -0,0 +1 @@
+gAAAAABbzgZ0wRAYI2ZyFtnTpQf5GWFW19Z2gPS8Nwlxg_NQAvnnxG_6sbNGmXv7tsP6TgHTIE3OEInJtV-M6n7BCjfXIpfhPWmrlaRiNxZMpKr5KXNLZFtYsfT2kL1_e1X_h8yIo7u8kEMSD-Fp2ndpEEEJM5tL7BEyweYJ_mp7C8dVFpiW7BZhQ5MiYMw5bevqXdbVXmNYavfJRoytnQq4I0sxCH7M8t7Fsbf87MKTohUh0QJzljvBVB37EyK4fcE-tfZ5jlkcwwgyElrJzrmYfXSArDsWHZ8sM0BFSVXd9dkLcuqstPcRMJFEFQcMfq7esbSPlJeq0put_DsWkGKGlAIqfJ-3LuQu6cKKJZ3NWRrYLna1Oe8TnBotM0dVv8W8JSIixDMzYf_cR9oP8r-AanTLwxAd2u-YzWnSAkHpGgc2TOW40OqIr6ovWnGttu31vvEvhXbY69TfumAr0qknLJZf5aHIVWGmvLMa8pUQfAB967ESYXO-4Uj4k2gc2FouKe7Sh6tmHVq1qxqSlIJCcGIs3IEIaAxdWjDhOqukE-yO-ol1WXVLNcGjvc5H6uwpvuORs3K-0cYQyHLpGG_uM9RUNf2lUz57ri9GYWSU68rqvqQYpBFFcf6PR330yQT5_-B1swa-DljlaCZafGAVOuUa5MZgyij6p8VTJBiyJ7NhExVe2Ux8p25dL5KpUQL4qeyaOQEyZvvvKPusbky-QUfMzsHFN1E8nGhXlEe8pdb7TaM_3xxySHOFsc7-VNXDB_kJYnYsRa5PoQjN-uOD5rl5KZN4gKR7plmg66d20bKlIuwcsi8bC4mANHh0l67qA_VMpq1adEATy6ghSdGg44O8uAYJxFww7mp-4bTrE0aEtU8DE-_ilBU7DmZ6ijGNgpF8vm4xwq606cy27WNQ5hf0C6crF0FIriTUaHslSIyUnDC4dpT0fTnvLbZvBqOL_Z3HonMDZN2fVEqzoEB-IEg0kJx2p1bUadyr38qUQiVyMDZEFeZOlGInEEvLHmhjhYeIhBH6Cmg4x_M7VGdDhhqssGQyyoO9bUF_OMiz4j208s-1AM__hApQvbd70r5ykzhQuGs5WHriogsfCQfOwtg3cLFMUikb41iMPMF1vtQvJVXJUJqsIYdxW-oAAOpUC-BJ4L21tpqczjJCXve8J78qEcbx-l__y0FaVYIyfL76jAv6A5J-UaA0AusHL0WH6siXeMcepzj-I9ZX4rpVfvbvqfg6zr78JhK_drSJOAdt-z939OrM9Ngbf4OprVOg2D5K3xYv3UL58OfqEk-_K8FKAz_t5GVX8uhQKh6BCYr0vouNKFX6R5qFUkjuM3F9m3MU0faxX47E_TPZjQpbng6eHw9LwvfmFLFUKoY6n1eyl4yydaj5_XPisBN27W73CWWyOo2zGiKytmlLKvwBlW03FnUixyHE_M3bDv5JwoewQrnBwno7Jt8dK_JmVwUTVMEuqf8I02F_um-gWH1Bd5YXgOKN18-mbSbK7pUdoeSQAKlxKzGqssNvqliI4MFytp1wyXnv6rz_l1DYxUrWne5m-5tibFuBl7rZI_WCtQDW_rqg5WcR4QtEjAU3gRo5SwLDQr8N12ESdJZuWNUji_ia0oIqqn4-eGJ0E9HioEiCNzjULKU9NmeS3pe1eeMC_1Ttp0eAw3EUZE8xzr7CZvz0s5KRS87HtpGRqF8dPWvCl3ah_JCjEuYrswrbTGYueOV7vnnz9yadVoIqZIi_yv177hrRgQ7l0MzxsT7FU4LjGfw6c46K4Nwi2YQyVTdLNXNt5wIMKvPQLkjr1NFySjj3xVjjlJ8-72DEONsIIT339i475X71ZPeHqFo2KDhvIH2MpsgxLKTB_O6rpQNft9vFZoVzXfNIXgyK34R1uo7mELSxjz-y61YisMAAVP4WxTGF0ZjnOxDaimzwARYpVyNxs1sxoiA6k3CGzU4cDZ5m6xThX9ImM9F9j1D-mzKZw99rWGWVHVhhZa2YWEQU8UPTOAdDio_HlQjtvBdvnwe2MLw1dKgQ0uZP1Z61OyVUFGZg7BJYTDnnmeqgcpDy6Ob4fD01Fw1rMUaWqxiWhpW_RHX_iwtW3s0ihjnELt5AIpjeF_WaRhZ60cW_mX3PIlmdG9r4Z8ZTfml56RhaPBFu9oSgwoaBppx2YZMxHDOq-Jq-Y5EGOCsJKmNN7vqzLRFM6CpcgzJ-QO_4xEWfhlmgqCmshke8Qq2lCVIAv-7y9w3UeEkDotq3XoCNAm-7G76zBp4pSe75E2sd_lsthWUYHcX_kW6He0PE78p7hjLQX4Msh4N_AW5Yv4yqrCM_PXqizPBRqbdIWPA1oIurNEW0XARRIu-TgLyFilu0HaKawHWQPKQKZCcCbLWyRhSeaLYgMkFQNaNUBXt6pOkhog6MHkBsUrSBtOIzG9aL5e8Z8P3KTz8wTUaiNAcbmEkR3fUZV-Fcz0qXtYxGTls6S1UBKUzDF7W6nVx5wR6hKOv0s6zq0R8Tk6J6kAIzOjY4ptQyWjGwi4CcnwzTa-lP2gi3BtlnetfTbJ_CVjEC4qkvlr9bc_DnHWkZYFzU_af5_tDeBb_-XCM3NKhCpYbymLTJXi7frJov0p0ElZ0JhQHSaZkqe0qKwyDiVZAEIK8sXA1a5SYYJfqRVUW-CyxWxC2gb-mpzLqVmwxryeI14NlD2qOKhQk0aUJuA9HtmAPJnoZ490TdLtv7n0uALlIEw1m3piA7dKoBhk_2V7bQGMvSbRvqPq0T5eeX8Q6n4zP2vV7GRDc2WPpEocRvd0RgB02ggQa_0yP8Z9MCXL96hfNC20tvmzDpxYkwhexu5tjN5qwaaMBMLXdSx9OheKW5E9iqdqAQ95Ue63CYSOdN1gyfp1Ily6wIvdyHqgoWCIi-zHLYefzZnrkF9tv7MeeyXy0ecv1XMCROr6_rBVXHZbZSQjQJJhc-sam3mHjDrTLOSqW7mHWih4HCv500Zc5x37BYUtNEbgpyRkQiMpN071OKWB4U4X6f3cnvKE-SMxFmaLs6vaFlGb5D2hfNWYS6DRAsyB6p0SP7GQooiYpxjYyo5ZM6TrdDYp0ObqbTk7Yel0WjUzJ8K57MtZaOoL7kYC_FD3k1VivjnZeVBNvNnLaOZWY_S6usnrPlr_r_GcTWeLcr9mof5tPdhZC7faWFEHBWFwfZ4bf5pigKHlYqL-ys2qdLBLsVggRGJEvnHwBL0dDLNIvEBRCT2bgTSwyp5NNb2RH0vcLWiWZV1K2O356O5YgqW1ihqQvWvgh3Edpiu9XDHaz6ReK0p8eSmaUZxfCYMpYgXo-7dl21E-_sL2lnokayWWuL88Vv0TBry8gKXTsv4ONacfgpPzLXcs8J5FoI2MTF85sgzABlclHmsuT1QF2Iabl-Ae7gVUYm9KAwxV7Ld46cnWGomEgOd1eNuG4INN9mXf_vE2WxpySPuhqzx5IMxsc6JOxXIUjZwqouPCdYqSDJ6rERWDc5QpnA4cGsG52UqHY5oU_TJfPnbM7grdsS2L0E_wBmdjW7qwgIDxg7-a-eyYFaQsi7Ub1g5gVD6Nx3K28_8yMD5CLQDOwtM3HrUTr7mHQcC-jxZswbUPV6KsrLFUvC-rIpCRRFFNF1Mz9VA7tkbM5u9HOX5wulJ5JYGN684pwIoaADxxQ1OvzWFivPoz_a04wiKa1V3n-wQcptWxMsozI_xwSbvHAs5FMWskddagjRzDb-VWc5nsCRsQPIuKMwCuYL9Aq0o-RKgIOqCsEHimB4XwmVsmRQV2BaTwlTKgiy7w5Hez8irNPB6pAJ7_vSyEXSsmcw7eEJeZQrZU1AoOem97olig4hCwKW6rFyipD349JdpBgjJK9WMLEv-b_7Hxhtt1CPJjeebrNBAkNyVGDSFPzpriw4kAhRDSIO9ItIn01te3BoUg215nbbxfP1bc7JP9aqWJo_NtF0znG5zp2Zgl1O24Nwd78p_2AnjVY0MEKJlvsbQBImLaG4WMvNeDtYxymenmVQCvTiFs_Nd11Z_fTNRjcFNSF5hulFPqx_rMPcDsZt0Lv0ms88uSwlAEhZ7cMCCVGvZykVwZ5c016uhP31xWDG2vxUo_6qNloGzlVyM0F4BbZ1hPmh7Otke92IltuGwBaLz43IaYceaiNQC_CzLZewr1VQmCifuiXCj2fBBf6pfe9sAxwWPWPUxVXkAd2JxtTSXV9CW-8sFymBbpXb9TUOCHlKjIhCrug3eEPNHbuySvsxEVvl9j3KjM2fqUl9HJE9isa0flTjWwgcn_jqh8StrcEh9i715VYRnQepffrC_iyXaIT-RKKFaCAtIjLkbnIWWqoHvMSUNexrYvzFHatAHDC-b-PiQKsnSUNXum2TtIOYyA2am-GsrDL1bMCbBWZZQbJvB6NvTFSFxcC_lIOvkQbr3lcomAM0XynwD4t-ncHEutnFow==

jet_tracking/__init__.py

@@ -1,3 +1,11 @@
 from ._version import get_versions
 __version__ = get_versions()['version']
 del get_versions
+
+
+from . import jet_control  # noqa
+from . import devices  # noqa
+from . import cam_utils  # noqa
+from . import jet_tracking  # noqa
+from . import move_motor  # noqa
+from . import signal_config  # noqa

jet_tracking/devices.py

@@ -1,4 +1,5 @@
 import pandas as pd
+import epics
 
 from ophyd.device import Device, FormattedComponent as FCpt, Component as Cpt
 from ophyd.signal import EpicsSignal
@@ -19,7 +20,7 @@ def __init__(self, *args, **kwargs):
     def _update_descriptions(self):
         adesc = {}
         for name, signal in self._signals.items():
-            adesc[name] = EpicsSignal(signal._read_pv.pvname + '.DESC').get()
+            adesc[name] = epics.caget(signal.pvname + '.DESC')
         self._descriptions = adesc
 
     @property
@@ -33,8 +34,8 @@ def table(self):
         atable = {}
         for name, signal in sorted(self._signals.items()):
             atable[name] = {
-                    'value': signal._read_pv.value,
-                    'units': signal._read_pv.units,
+                    'value': signal.read()[signal.name]['value'],
+                    'units': signal.describe()[signal.name].get('units', ''),
                     'desc': self._descriptions.get(name),
                     }
 
@@ -318,7 +319,7 @@ class HPLC(Device, _TableMixin):
 
     pressure = FCpt(EpicsSignal, '{self._pressure}')
     pressure_units = FCpt(EpicsSignal, '{self._pressure_units}')
-    set_max_pressure = FCpt(EpicsSignal, '{self._set_max_pressure')
+    set_max_pressure = FCpt(EpicsSignal, '{self._set_max_pressure}')
     max_pressure = FCpt(EpicsSignal, '{self._max_pressure}')
 
     clear_error = FCpt(EpicsSignal, '{self._clear_error}')
@@ -596,41 +597,45 @@ def __init__(self, name,
 
 
 class SDS:
-    '''Sample delivery system
-
-       Parameters
-       ----------
-       devices : dict
-           A dictionary of dictionaries containing the devices to be made and their PV names
-           Key: str
-               Type of device to be made. Valid keys are 'selector', 'cooler_shaker', 'hplc',
-               'pressure_controller', and 'flow_integrator'
-           Value: str dict
-               Dictionary of PVs of the device
+    '''
+    Sample delivery system
 
-       Attributes
-       ----------
-       SDS_devices : list
-           List containing all the devices that are in the sample delivery system
-       '''
+    Parameters
+    ----------
+    devices : dict
+        A dictionary of dictionaries containing the devices to be made and
+        their PV names. The dictionary key is a string, one of the following:
+        {'selector', 'cooler_shaker', 'hplc', 'pressure_controller',
+        'flow_integrator'}
+        The values of the dictionary, are also dictionaries. These are passed
+        to the new device, allowing parameters such as PV names to be
+        specified.
 
-    SDS_devices = []
+    Attributes
+    ----------
+    SDS_devices : list
+        List containing all the devices that are in the sample delivery system
+   '''
+
+    device_types = {
+        'selector': Selector,
+        'cooler_shaker': CoolerShaker,
+        'hplc': HPLC,
+        'pressure_controller': PressureController,
+        'flow_integrator': FlowIntegrator,
+    }
 
     def __init__(self, devices):
+        self.SDS_devices = [
+            self.device_types[dev](**kwargs)
+            for dev, kwargs in devices.items()
+            if dev in self.device_types
+        ]
 
-        for device in devices:
-            if device == 'selector':
-                self.SDS_devices.append(Selector(**devices[device]))
-            elif device == 'cooler_shaker':
-                self.SDS_devices.append(CoolerShaker(**devices[device]))
-            elif device == 'hplc':
-                self.SDS_devices.append(HPLC(**devices[device]))
-            elif device == 'pressure_controller':
-                self.SDS_devices.append(PressureController(**devices[device]))
-            elif device == 'flow_integrator':
-                self.SDS_devices.append(FlowIntegrator(**devices[device]))
-            else:
-                print(f'{device} is not a valid device')
+        invalid_devices = [dev for dev in devices
+                           if dev not in self.device_types]
+        for device in invalid_devices:
+            print(f'WARNING: {device} is not a valid device type')
 
 
 class Offaxis(PCDSDetector):
@@ -653,9 +658,9 @@ class Offaxis(PCDSDetector):
         Stats on ROI of original rate image
     '''
 
-    ROI = FCpt(ROIPlugin, '{self.prefix}:{self._ROI_port}')
-    ROI_stats = FCpt(StatsPlugin, '{self.prefix}:{self._ROI_stats_port}')
-    ROI_image = FCpt(ImagePlugin, '{self.prefix}:{self._ROI_image_port}')
+    ROI = FCpt(ROIPlugin, '{self.prefix}:{self._ROI_port}:')
+    ROI_stats = FCpt(StatsPlugin, '{self.prefix}:{self._ROI_stats_port}:')
+    ROI_image = FCpt(ImagePlugin, '{self.prefix}:{self._ROI_image_port}:')
 
     def __init__(self, ROI_port,
                        ROI_stats_port,
@@ -695,9 +700,9 @@ class Questar(PCDSDetector):
         Stats on ROI of original rate image
     '''
 
-    ROI = FCpt(ROIPlugin, '{self.prefix}:{self._ROI_port}')
-    ROI_stats = FCpt(StatsPlugin, '{self.prefix}:{self._ROI_stats_port}')
-    ROI_image = FCpt(ImagePlugin, '{self.prefix}:{self._ROI_image_port}')
+    ROI = FCpt(ROIPlugin, '{self.prefix}:{self._ROI_port}:')
+    ROI_stats = FCpt(StatsPlugin, '{self.prefix}:{self._ROI_stats_port}:')
+    ROI_image = FCpt(ImagePlugin, '{self.prefix}:{self._ROI_image_port}:')
 
     def __init__(self, ROI_port,
                        ROI_stats_port,