diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..4fb4cf7
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,316 @@
+# bapsfdaq_180e ignores
+.hdf5_files
+scope_screen_dump.png
+
+### Windows template
+# Windows thumbnail cache files
+Thumbs.db
+Thumbs.db:encryptable
+ehthumbs.db
+ehthumbs_vista.db
+
+# Dump file
+*.stackdump
+
+# Folder config file
+[Dd]esktop.ini
+
+# Recycle Bin used on file shares
+$RECYCLE.BIN/
+
+# Windows Installer files
+*.cab
+*.msi
+*.msix
+*.msm
+*.msp
+
+# Windows shortcuts
+*.lnk
+
+### macOS template
+# General
+.DS_Store
+.AppleDouble
+.LSOverride
+
+# Icon must end with two \r
+Icon
+
+# Thumbnails
+._*
+
+# Files that might appear in the root of a volume
+.DocumentRevisions-V100
+.fseventsd
+.Spotlight-V100
+.TemporaryItems
+.Trashes
+.VolumeIcon.icns
+.com.apple.timemachine.donotpresent
+
+# Directories potentially created on remote AFP share
+.AppleDB
+.AppleDesktop
+Network Trash Folder
+Temporary Items
+.apdisk
+
+### Python template
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+.venvs
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# Covers JetBrains IDEs: IntelliJ, GoLand, RubyMine, PhpStorm, AppCode, PyCharm, CLion, Android Studio, WebStorm and Rider
+# Reference: https://intellij-support.jetbrains.com/hc/en-us/articles/206544839
+
+# User-specific stuff
+.idea/**/workspace.xml
+.idea/**/tasks.xml
+.idea/**/usage.statistics.xml
+.idea/**/dictionaries
+.idea/**/shelf
+
+# AWS User-specific
+.idea/**/aws.xml
+
+# Generated files
+.idea/**/contentModel.xml
+
+# Sensitive or high-churn files
+.idea/**/dataSources/
+.idea/**/dataSources.ids
+.idea/**/dataSources.local.xml
+.idea/**/sqlDataSources.xml
+.idea/**/dynamic.xml
+.idea/**/uiDesigner.xml
+.idea/**/dbnavigator.xml
+
+# Gradle
+.idea/**/gradle.xml
+.idea/**/libraries
+
+# Gradle and Maven with auto-import
+# When using Gradle or Maven with auto-import, you should exclude module files,
+# since they will be recreated, and may cause churn.  Uncomment if using
+# auto-import.
+# .idea/artifacts
+# .idea/compiler.xml
+# .idea/jarRepositories.xml
+# .idea/modules.xml
+# .idea/*.iml
+# .idea/modules
+# *.iml
+# *.ipr
+
+# CMake
+cmake-build-*/
+
+# Mongo Explorer plugin
+.idea/**/mongoSettings.xml
+
+# File-based project format
+*.iws
+
+# IntelliJ
+out/
+
+# mpeltonen/sbt-idea plugin
+.idea_modules/
+
+# JIRA plugin
+atlassian-ide-plugin.xml
+
+# Cursive Clojure plugin
+.idea/replstate.xml
+
+# SonarLint plugin
+.idea/sonarlint/
+.idea/sonarlint.xml # see https://community.sonarsource.com/t/is-the-file-idea-idea-idea-sonarlint-xml-intended-to-be-under-source-control/121119
+
+# Crashlytics plugin (for Android Studio and IntelliJ)
+com_crashlytics_export_strings.xml
+crashlytics.properties
+crashlytics-build.properties
+fabric.properties
+
+# Editor-based HTTP Client
+.idea/httpRequests
+http-client.private.env.json
+
+# Android studio 3.1+ serialized cache file
+.idea/caches/build_file_checksums.ser
+
+# Apifox Helper cache
+.idea/.cache/.Apifox_Helper
+.idea/ApifoxUploaderProjectSetting.xml
+
+# Github Copilot persisted session migrations, see: https://github.com/microsoft/copilot-intellij-feedback/issues/712#issuecomment-3322062215
+.idea/**/copilot.data.migration.*.xml
+
+# Covers VSCode IDE:
+# source: https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
+
+.vscode/*
+!.vscode/settings.json
+!.vscode/tasks.json
+!.vscode/launch.json
+!.vscode/extensions.json
+!.vscode/*.code-snippets
+!*.code-workspace
+
+# Built Visual Studio Code Extensions
+*.vsix
diff --git a/Data_Run_GUI_xy.py b/Data_Run_GUI_xy.py
index 068f0dd..594af7b 100644
--- a/Data_Run_GUI_xy.py
+++ b/Data_Run_GUI_xy.py
@@ -10,22 +10,23 @@
 # Author: Yuchen Qian
 # Oct 2017
 #
-19
 
-import numpy
+import datetime
+import h5py
 import math
-import sys
+import numpy
 import os
 import os.path
+import sys
 import time
-import datetime
-from Motor_Control_2D_xy import Motor_Control_2D
-from LeCroy_Scope import LeCroy_Scope, WAVEDESC_SIZE
-from LeCroy_Scope import EXPANDED_TRACE_NAMES
 import tkinter
-from tkinter import filedialog
 import tkinter.messagebox
-import h5py as h5py
+
+from tkinter import filedialog
+
+from LeCroy_Scope import LeCroy_Scope, WAVEDESC_SIZE
+from LeCroy_Scope import EXPANDED_TRACE_NAMES
+from Motor_Control_2D_xy import Motor_Control_2D
 
 dir_path=os.path.dirname(os.path.realpath(__file__))
 version_number="03/01/2018 12:37pm"			# update this when a change has been made
@@ -347,7 +348,7 @@ def move_to_position(self):
 		except ValueError:
 			QMessageBox.about(self, "Error", "Position should be valid numbers.")
 
-	def disable():
+	def disable(self):
 		self.mc.disable()
 
 	def stop_now(self):
@@ -540,7 +541,7 @@ def get_hdf5_filename(self) -> str:
 		self.hdf5_filename = fn    # save it for later
 		return fn
 
-	def acquire_displayed_traces(self, scope, datasets, hdr_data, pos_ndx):
+	def acquire_displayed_traces(self, scope: LeCroy_Scope, datasets, hdr_data, pos_ndx):
 		""" worker for below :
 			acquire enough sweeps for the averaging, then read displayed scope trace data into HDF5 datasets
 		"""
@@ -553,17 +554,31 @@ def acquire_displayed_traces(self, scope, datasets, hdr_data, pos_ndx):
 		traces = scope.displayed_traces()
 
 		for tr in traces:
+			NPos, NTimes = datasets[tr].shape
+			signal = scope.acquire(tr)  # type: numpy.ndarray
 			try:
-				NPos,NTimes = datasets[tr].shape
-				datasets[tr][pos_ndx,0:NTimes] = scope.acquire(tr)[0:NTimes]    # sometimes for 10000 the scope hardware returns 10001 samples, so we have to specify [0:NTimes]
-				#?# datasets[tr].flush()
-			except KeyError:
-				print(tr + ' is displayed on the scope but not recorded. To record this channel, please display the trace before starting the data run.')
-				continue
-			except TypeError:
-				print('Not enough points from scope trace')
-				datasets[tr][pos_ndx,:] = scope.acquire(tr)[:]
-				continue
+				datasets[tr][pos_ndx, ...] = signal[...]
+			except KeyError as err:
+				print(
+					tr
+					+ ' is displayed on the scope but not recorded.  '
+					  'To record this channel, please display the trace '
+					  'before starting the data run.'
+					+ err
+				)
+			except TypeError as err:
+				# the returned signal does not always have exactly NTimes
+				# samples.  It's is off by a few data points.
+				signal_NTimes = signal.size
+				if not numpy.isclose(signal_NTimes, NTimes, rtol=0.005, atol=0):
+					# the difference in the number of time samples is greater
+					# than 0.5%
+					raise err
+
+				if NTimes > signal_NTimes:
+					datasets[tr][pos_ndx, 0:signal_NTimes] = signal[...]
+				else:
+					datasets[tr][pos_ndx, ...] = signal[0:NTimes]
 
 		for tr in traces:
 			try:
@@ -571,7 +586,7 @@ def acquire_displayed_traces(self, scope, datasets, hdr_data, pos_ndx):
 				#?# hdr_data[tr].flush()
 				#?# are there consequences in timing or compression size if we do the flush()s recommend for the SWMR function?
 			except KeyError:
-				continue
+				pass
 
 		scope.set_trigger_mode('NORM')   # resume triggering
 
@@ -676,7 +691,7 @@ def run(self):
 			pos_ds.attrs['shotperpos'] = num_duplicate_shots                                # not legacy
 
 			# create the scope access object, and iterate over positions
-			with LeCroy_Scope(self.ip_addrs['scope'], verbose=False) as scope:
+			with LeCroy_Scope(self.ip_addrs['scope'], verbose=False) as scope:  # type: LeCroy_Scope
 				if not scope:
 					print('Scope not found at '+self.ip_addrs['scope'])      # I think we have raised an exception if this is the case, so we never get here
 					return
@@ -776,16 +791,51 @@ def run(self):
 
 						# at least get one time array recorded for swmr functions
 						if pos[0] == 1:
-							time_ds[0:NTimes] = scope.time_array()[0:NTimes]
-							#time_ds.flush()
+							time_array = scope.time_array()
+							try:
+								time_ds[...] = scope.time_array()[...]
+							except TypeError as err:
+								# the returned signal does not always have exactly NTimes
+								# samples.  It's is off by a few data points.
+								time_size = time_array.size
+								if not numpy.isclose(
+									time_size, NTimes, rtol=0.005, atol=0
+								):
+									# the difference in the number of time samples is greater
+									# than 0.5%
+									raise err
+
+								if NTimes > time_size:
+									time_ds[0:time_size] = time_array[...]
+								else:
+									time_ds[...] = time_array[0:NTimes]
 
 					######### END MAIN ACQUISITION LOOP #########
 
 				except KeyboardInterrupt:
 					print('\n______Halted due to Ctrl-C______', '  at', time.ctime())
 
-				# copy the array of time values, corresponding to the last acquired trace, to the times_dataset
-				time_ds[0:NTimes] = scope.time_array()[0:NTimes]      # specify number of points, sometimes scope return extras
+				# copy the array of time values, corresponding to the last acquired
+				# trace, to the times_dataset
+				time_array = scope.time_array()
+				try:
+					time_ds[...] = scope.time_array()[...]
+				except TypeError as err:
+					# the returned signal does not always have exactly NTimes
+					# samples.  It's is off by a few data points.
+					time_size = time_array.size
+					if not numpy.isclose(
+							time_size, NTimes, rtol=0.005, atol=0
+					):
+						# the difference in the number of time samples is greater
+						# than 0.5%
+						raise err
+
+					if NTimes > time_size:
+						time_ds[0:time_size] = time_array[...]
+					else:
+						time_ds[...] = time_array[0:NTimes]
+
 				if type(time_ds) == 'stupid':
 					print(' this is only included to make the linter happy, otherwise it thinks time_ds is not used')
 
@@ -801,12 +851,9 @@ def run(self):
 						datasets[tr].attrs['recorded']    = True
 						datasets[tr].attrs['shots per position']    = self.pos_param["num_shots"]
 
-
 			f.close()  # close the HDF5 file
 
 			self.signals.finished.emit()
-			#done
-
 
 
 class Test_Shot_Thread(QRunnable):
diff --git a/LeCroy_Scope.py b/LeCroy_Scope.py
index 58218d4..fd8bb74 100644
--- a/LeCroy_Scope.py
+++ b/LeCroy_Scope.py
@@ -32,17 +32,18 @@
 
 """
 
-import numpy
-import visa
-from pyvisa.resources import MessageBasedResource
-from pyvisa.errors import VisaIOError
 import collections
+import numpy
+import matplotlib.image as mpimg
+import pylab as plt
+import pyvisa as visa
 import struct
 import sys
-import pylab as plt
-import matplotlib.image as mpimg
 import time
 
+from pyvisa.resources import MessageBasedResource
+from pyvisa.errors import VisaIOError
+
 # the header recorded for each trace
 # 63 entries, 346 bytes
 WAVEDESC = collections.namedtuple('WAVEDESC',
@@ -209,7 +210,7 @@ def rm_open(self, ipv4_addr)  -> bool:
 
 		if self.verbose: print('<:> constructing resource manager')
 		t0 = time.time()
-		self.rm = visa.ResourceManager()
+		self.rm = visa.ResourceManager("@py")
 		t1 = time.time()
 		if self.verbose and (t1-t0 > 1): print('    .............................%6.3g sec' % (t1-t0), end='')
 
@@ -217,7 +218,10 @@ def rm_open(self, ipv4_addr)  -> bool:
 
 		# attempt to open a connection to the scope
 		try:
-			self.scope = self.rm.open_resource('VICP::'+ipv4_addr+'::INSTR', resource_pyclass=MessageBasedResource)
+			self.scope = self.rm.open_resource(
+                'VICP::'+ipv4_addr+'::INSTR',
+                resource_pyclass=MessageBasedResource,
+            )
 			print('...ok')
 		except Exception:
 			print('\n**** Scope not found at "', ipv4_addr, '"\n')
@@ -301,7 +305,7 @@ def validate_channel(self, Cn)  -> str:
 
 	#-------------------------------------------------------------------------
 
-	def validate_trace(self, tr)  -> str:
+	def validate_trace(self, tr) -> str:
 		""" convenience function, returns canonical trace label, which is broader than a channel label
 			see valid_trace_names defined at top of file
 			if Cn is an integer, assumes we want a channel name
@@ -315,7 +319,6 @@ def validate_trace(self, tr)  -> str:
 		err = '**** validate_trace(): trace name "' + tr + '" is unknown'
 		raise(RuntimeError(err)).with_traceback(sys.exc_info()[2])
 
-	#-------------------------------------------------------------------------
 
 	def max_samples(self, N = 0) -> int:
 		""" mostly used for determining the number of samples the scope expects to acquire.
diff --git a/__pycache__/Acquire_Scope_Data_3D.cpython-35.pyc b/__pycache__/Acquire_Scope_Data_3D.cpython-35.pyc
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diff --git a/__pycache__/find_ip_addr.cpython-35.pyc b/__pycache__/find_ip_addr.cpython-35.pyc
deleted file mode 100644
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diff --git a/__pycache__/wavegen_control.cpython-35.pyc b/__pycache__/wavegen_control.cpython-35.pyc
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diff --git a/requirements.txt b/requirements.txt
new file mode 100644
index 0000000..abc9049
--- /dev/null
+++ b/requirements.txt
@@ -0,0 +1,9 @@
+h5py
+numpy
+matplotlib
+PyQt5
+pyvisa >= 1.12
+pyvisa-py[vicp, psutil, hislip-discovery, usb-full]
+scipy
+setuptools < 82.0.0
+setuptools-scm