Initial refactoring

docs/source/api/index.rst

@@ -9,7 +9,11 @@ API Reference
 
    lyse
    lyse.analysis_subprocess
+   lyse.communication
    lyse.dataframe_utilities
    lyse.figure_manager
+   lyse.filebox
+   lyse.routines
    lyse.tempfile2clipboard
+   lyse.utils
    lyse.__main__

docs/source/conf.py

@@ -22,7 +22,7 @@
 # -- Project information (unique to each project) -------------------------------------
 
 project = "lyse"
-copyright = "2020, labscript suite"
+copyright = "2024, labscript suite"
 author = "labscript suite contributors"
 
 # The full version, including alpha/beta/rc tags

lyse/__init__.py

@@ -10,7 +10,8 @@
 # the project for the full license.                                 #
 #                                                                   #
 #####################################################################
-"""Lyse analysis API
+"""
+Lyse analysis API
 """
 
 from lyse.dataframe_utilities import get_series_from_shot as _get_singleshot
@@ -25,7 +26,6 @@
 import contextlib
 
 import labscript_utils.h5_lock, h5py
-from labscript_utils.labconfig import LabConfig
 import pandas
 from numpy import array, ndarray, where
 import types
@@ -36,7 +36,13 @@
 from labscript_utils.ls_zprocess import zmq_get
 
 from labscript_utils.properties import get_attributes, get_attribute, set_attributes
-LYSE_DIR = os.path.dirname(os.path.realpath(__file__))
+
+# lyse imports
+import lyse.dataframe_utilities
+import lyse.utils
+
+# Import this way so LYSE_DIR is exposed when someone does import lyse or from lyse import *
+from lyse.utils import LYSE_DIR
 
 # If running stand-alone, and not from within lyse, the below two variables
 # will be as follows. Otherwise lyse will override them with spinning_top =
@@ -55,13 +61,6 @@
 # a flag to determine whether we should wait for the delay event
 _delay_flag = False
 
-# get port that lyse is using for communication
-try:
-    _labconfig = LabConfig(required_params={"ports": ["lyse"]})
-    _lyse_port = int(_labconfig.get('ports', 'lyse'))
-except Exception:
-    _lyse_port = 42519
-
 if len(sys.argv) > 1:
     path = sys.argv[1]
 else:
@@ -80,7 +79,7 @@ class _RoutineStorage(object):
 routine_storage = _RoutineStorage()
 
 
-def data(filepath=None, host='localhost', port=_lyse_port, timeout=5, n_sequences=None, filter_kwargs=None):
+def data(filepath=None, host='localhost', port=lyse.utils.LYSE_PORT, timeout=5, n_sequences=None, filter_kwargs=None):
     """Get data from the lyse dataframe or a file.
 
     This function allows for either extracting information from a run's hdf5
@@ -161,7 +160,7 @@ def data(filepath=None, host='localhost', port=_lyse_port, timeout=5, n_sequence
 
         # Allow sending 'get dataframe' (without the enclosing list) if
         # n_sequences and filter_kwargs aren't provided. This is for backwards
-        # compatability in case the server is running an outdated version of
+        # compatibility in case the server is running an outdated version of
         # lyse.
         if n_sequences is None and filter_kwargs is None:
             command = 'get dataframe'
@@ -178,35 +177,9 @@ def data(filepath=None, host='localhost', port=_lyse_port, timeout=5, n_sequence
             raise ValueError(dedent(msg))
         # Ensure conversion to multiindex is done, which needs to be done here
         # if the server is running an outdated version of lyse.
-        _rangeindex_to_multiindex(df, inplace=True)
+        lyse.dataframe_utilities.rangeindex_to_multiindex(df, inplace=True)
         return df
 
-def _rangeindex_to_multiindex(df, inplace):
-    if isinstance(df.index, pandas.MultiIndex):
-        # The dataframe has already been converted.
-        return df
-    try:
-        padding = ('',)*(df.columns.nlevels - 1)
-        try:
-            integer_indexing = _labconfig.getboolean('lyse', 'integer_indexing')
-        except (LabConfig.NoOptionError, LabConfig.NoSectionError):
-            integer_indexing = False
-        if integer_indexing:
-            out = df.set_index(['sequence_index', 'run number', 'run repeat'], inplace=inplace, drop=False)
-            # out is None if inplace is True, and is the new dataframe is inplace is False.
-            if not inplace:
-                df = out
-        else:
-            out = df.set_index([('sequence',) + padding,('run time',) + padding], inplace=inplace, drop=False)
-            if not inplace:
-                df = out
-            df.index.names = ['sequence', 'run time']
-    except KeyError:
-        # Empty DataFrame or index column not found, so fall back to RangeIndex instead
-        pass
-    df.sort_index(inplace=True)
-    return df
-
 def globals_diff(run1, run2, group=None):
     """Take a diff of the globals between two runs.