Squashed commit of the following:

commit 92be8de
Merge: b3d65c8 9a6c40d
Author: David Meyer <dihm@users.noreply.github.com>
Date:   Wed Dec 10 16:02:23 2025 -0500

    Merge pull request #130 from dihm/readme_link

    Update readme example GUI link

commit 9a6c40d
Author: David Meyer <dihm.meyer@gmail.com>
Date:   Wed Dec 10 15:59:58 2025 -0500

    Use a modern screenshot

commit e181082
Author: David Meyer <dihm.meyer@gmail.com>
Date:   Wed Dec 10 15:51:57 2025 -0500

    Update readme example GUI link

commit b3d65c8
Merge: af528f1 c59c095
Author: David Meyer <dihm@users.noreply.github.com>
Date:   Wed Dec 10 15:44:27 2025 -0500

    Merge pull request #127 from dihm/destar_imports

    Remove star imports from documentation

commit af528f1
Merge: 663f87b 996a418
Author: David Meyer <dihm@users.noreply.github.com>
Date:   Tue Dec 9 15:44:15 2025 -0500

    Merge pull request #128 from dihm/plot_window_restore

    Plot window geometry restore

commit 996a418
Author: David Meyer <dihm.meyer@gmail.com>
Date:   Mon Dec 8 15:05:28 2025 -0500

    Add missing format specifier

commit 08c6084
Author: David Meyer <dihm.meyer@gmail.com>
Date:   Fri Nov 21 11:03:06 2025 -0500

    Allow for more than one plot window per analysis process.

commit fd624b0
Author: David Meyer <dihm.meyer@gmail.com>
Date:   Tue Nov 18 16:05:43 2025 -0500

    Add ability for plot windows to remember their geometry between runs of lyse.

    Uses the `QSettings` functionality of Qt itself, with ini files created in lyse's
    `app_saved_config` directory. A new file for each analysis script is created.

commit c59c095
Author: David Meyer <dihm.meyer@gmail.com>
Date:   Mon Sep 29 10:37:38 2025 -0400

    Remove star imports from documentation

commit 663f87b
Merge: 4eef798 5bd37cd
Author: David Meyer <dihm@users.noreply.github.com>
Date:   Fri Sep 26 10:31:18 2025 -0400

    Merge pull request #126 from dihm/refactor3

    Refactor mods

commit 4eef798
Merge: de8eb4d f1e3dc7
Author: David Meyer <dihm@users.noreply.github.com>
Date:   Fri Sep 26 10:31:02 2025 -0400

    Merge pull request #119 from spielman-group/refactor

    Initial refactoring

commit 5bd37cd
Author: David Meyer <dihm.meyer@gmail.com>
Date:   Fri Sep 26 09:39:09 2025 -0400

    Add basic docstrings to important module attributes so sphinx picks them up

    Also removes dead link to lyse.tempfile2clipboard in api/index

commit 98c4ca2
Author: David Meyer <dihm.meyer@gmail.com>
Date:   Fri Sep 19 10:37:16 2025 -0400

    Convert numpy imports to standard convention

commit 79c9d25
Author: David Meyer <dihm.meyer@gmail.com>
Date:   Fri Sep 19 10:29:24 2025 -0400

    Add `__all__` to the lyse API so old lyse star imports know `lyse.path` should be imported.

commit de8eb4d
Merge: df64c61 fcd0dc7
Author: David Meyer <dihm@users.noreply.github.com>
Date:   Tue Aug 19 17:22:28 2025 -0400

    Merge pull request #125 from dihm/sphinx_updates

    Sphinx autosummary updates

commit fcd0dc7
Author: David Meyer <dihm.meyer@gmail.com>
Date:   Tue Aug 19 16:47:11 2025 -0400

    Ensure intersphinx mapping does not include current project

commit 23f6879
Author: David Meyer <dihm.meyer@gmail.com>
Date:   Tue Aug 19 16:46:56 2025 -0400

    Re-add autosummary template

commit 0d1ad0e
Author: David Meyer <dihm.meyer@gmail.com>
Date:   Fri Aug 8 16:51:00 2025 -0400

    Fix `spinning_top` and `_updated_data` to by proper lazy import

commit c5349a0
Author: David Meyer <dihm.meyer@gmail.com>
Date:   Fri Aug 8 16:50:18 2025 -0400

    Maintain backwards compat with lyse headless workflow,
    raises deprecation warning so we can drop it eventually though.

commit 8692199
Author: David Meyer <dihm.meyer@gmail.com>
Date:   Fri Aug 8 16:49:30 2025 -0400

    Rework `path` to be exposed as `lyse.path` instead of injected directly into namespace

commit f1e3dc7
Merge: f1f703a df64c61
Author: Ian B. Spielman <54444522+ispielma@users.noreply.github.com>
Date:   Thu Aug 7 13:49:21 2025 -0400

    Merge branch 'labscript-suite:master' into refactor

commit f1f703a
Author: spielman <spielman@umd.edu>
Date:   Thu Aug 7 13:39:27 2025 -0400

    removed warning. before FutureWarning

commit df64c61
Merge: 6ba461f 9da1665
Author: David Meyer <dihm@users.noreply.github.com>
Date:   Sun Aug 3 00:31:08 2025 -0400

    Merge pull request #124 from dihm/sphinx_updates

    Update sphinx build and ensure RTD stable versioning is correct

commit 9da1665
Author: David Meyer <dihm@users.noreply.github.com>
Date:   Sun Aug 3 00:24:36 2025 -0400

    Bump sphinx pins and refresh RTD builds

commit 5c59d75
Author: spielman <spielman@umd.edu>
Date:   Wed Jul 9 12:24:12 2025 -0400

    Corrected spinning top reference.

commit 074ee7d
Merge: 40c270b 6ba461f
Author: Ian B. Spielman <54444522+ispielma@users.noreply.github.com>
Date:   Tue Jul 8 16:58:11 2025 -0400

    Merge branch 'labscript-suite:master' into refactor

commit 40c270b
Merge: 32c971e 7e5d3ed
Author: Ian B. Spielman <54444522+ispielma@users.noreply.github.com>
Date:   Tue Jul 8 16:53:39 2025 -0400

    Merge pull request #1 from dihm/refactor2

    WIP: More disruptive refactor changes

commit 7e5d3ed
Author: David Meyer <dihm.meyer@gmail.com>
Date:   Tue Apr 15 16:11:55 2025 -0400

    Move path to script namespace injection, with backwards compatibility support
    for those who have (properly) imported it as `lyse.path` instead of
    `from lyse import *`

commit 0aecf85
Author: David Meyer <dihm.meyer@gmail.com>
Date:   Tue Apr 15 16:05:43 2025 -0400

    Clean-up some unused imports

commit 06ce8dc
Author: David Meyer <dihm.meyer@gmail.com>
Date:   Tue Apr 15 15:45:13 2025 -0400

    Move inter-process communications variables into `lyse.utils.worker`

commit 4c7f596
Author: David Meyer <dihm.meyer@gmail.com>
Date:   Mon Apr 14 14:37:26 2025 -0400

    Move utilities into a sub-module.

    This divides common things from the worker utilities and the gui utilities.

commit 32c971e
Author: David Meyer <dihm.meyer@gmail.com>
Date:   Mon Apr 14 14:04:46 2025 -0400

    Ensure h5py is patched in filebox.py

commit 2a3a1a4
Author: David Meyer <dihm.meyer@gmail.com>
Date:   Mon Apr 14 12:08:50 2025 -0400

    Relocate some imports in response to review

commit 1fa549e
Author: David Meyer <dihm.meyer@gmail.com>
Date:   Mon Apr 14 14:07:34 2025 -0400

    Synchronize and add module level docstring headers.

commit 7f8f04e
Author: David Meyer <dihm.meyer@gmail.com>
Date:   Fri Apr 11 15:31:26 2025 -0400

    Correct license header filenames

commit 6ba461f
Merge: 2ff743f b4ae43b
Author: David Meyer <dihm@users.noreply.github.com>
Date:   Fri Apr 11 14:42:39 2025 -0400

    Merge pull request #122 from dihm/workflow_refresh

    Workflow refresh

commit b4ae43b
Author: David Meyer <dihm.meyer@gmail.com>
Date:   Fri Apr 11 14:08:02 2025 -0400

    Bumpy pandas dependency to 1.5 to account for #108 fix

commit c9d9fc3
Author: David Meyer <dihm.meyer@gmail.com>
Date:   Fri Apr 11 14:07:31 2025 -0400

    Update readme link, project metadata, and old dependencies

commit d7508ab
Author: David Meyer <dihm.meyer@gmail.com>
Date:   Fri Apr 11 14:06:57 2025 -0400

    Update workflow to latest and greatest

commit 2ff743f
Merge: b272f50 d1090db
Author: David Meyer <dihm@users.noreply.github.com>
Date:   Mon Mar 24 10:42:41 2025 -0400

    Merge pull request #120 from dihm/metadata_overhaul

    Metadata overhaul

commit d1090db
Author: David Meyer <dihm.meyer@gmail.com>
Date:   Sat Jul 13 02:26:16 2024 -0400

    Move all metadata to pyproject.toml,
    update setuptools-scm configs

commit 5d93959
Author: Spielman Lab <ian.spielman@nist.gov>
Date:   Thu Mar 14 13:44:14 2024 -0400

    Make sure that LABCONFIG is defined in all cases.  Also remove unused import.

commit b6755f7
Author: spielman <spielman@umd.edu>
Date:   Thu Mar 14 13:16:11 2024 -0400

    _lyse_port and _labconfig were defined in __init__.py and used both there and in dataframe_utilities.py  to avoid circular dependencies, I moved these into utis.py and renamed them LYSE_PORT and LABCONFIG respectivly to denote their role as system wide constants.  I also moved LYSE_PATH there as well for consistency, but re-exported it in __init__.py so it will still be accessible when lyse is imported.

commit bf739c9
Author: spielman <spielman@umd.edu>
Date:   Wed Mar 13 09:47:57 2024 -0400

    Missing import in dataframe_utilities corrected.

commit 839b47b
Author: spielman <spielman@umd.edu>
Date:   Mon Mar 11 14:29:08 2024 -0400

    Updated auto-generated docs.

commit ace2835
Author: spielman <spielman@umd.edu>
Date:   Mon Mar 11 13:03:55 2024 -0400

    Added lyse to `from lyse.dataframe_utilities import rangeindex_to_multiindex`

commit 419694b
Author: spielman <spielman@umd.edu>
Date:   Mon Mar 11 10:48:19 2024 -0400

    Removed unused import and moved _rangeindex_to_multiindex into dataframe_utilities as rangeindex_to_multiindex.

commit c174bfe
Author: spielman <spielman@umd.edu>
Date:   Tue Mar 5 08:58:25 2024 -0500

    Removed unused imports.

commit a70d321
Author: spielman <spielman@umd.edu>
Date:   Tue Mar 5 08:52:01 2024 -0500

    Fix menu bar application labels.

commit 20eaddc
Author: spielman <spielman@umd.edu>
Date:   Tue Mar 5 08:42:44 2024 -0500

    Cleanup.

commit a44eabc
Author: spielman <spielman@umd.edu>
Date:   Mon Mar 4 09:07:16 2024 -0500

    Changes based on feedback.

commit 01327a0
Author: spielman <spielman@umd.edu>
Date:   Sun Mar 3 07:01:28 2024 -0500

    Remove main.py

commit 26a9d35
Author: spielman <spielman@umd.edu>
Date:   Sun Mar 3 06:52:07 2024 -0500

    Moved the WebServer class into a new file called communication.py.  There are some other places with interprocess / thread communication is defined and getting that together seems wise.  This commit gets a place for it ready.

commit b9b1243
Author: spielman <spielman@umd.edu>
Date:   Wed Feb 28 10:50:41 2024 -0500

    refactored into smaller files.

commit 3977887
Author: spielman <spielman@umd.edu>
Date:   Wed Feb 28 10:25:48 2024 -0500

    Moved .ui files to a separate directory and refactored out supporting functions into utils.py

commit de2fa99
Author: spielman <spielman@umd.edu>
Date:   Wed Feb 28 10:11:52 2024 -0500

    Text cleanup.

commit 4a3be1c
Author: spielman <spielman@umd.edu>
Date:   Wed Feb 28 10:04:26 2024 -0500

    Fixed import lyse.__main__ bug that opened a splash window and hung.

commit 91cb71d
Author: Spielman Lab <ian.spielman@nist.gov>
Date:   Fri Feb 23 16:55:57 2024 -0500

    Refactored code working.

commit d9b1f02
Author: spielman <spielman@umd.edu>
Date:   Fri Feb 23 12:35:15 2024 -0500

    converting global variables to arguments.  This is just good practice anyway.  Refactor complete.

commit d762040
Author: spielman <spielman@umd.edu>
Date:   Fri Feb 23 12:00:00 2024 -0500

    Moved code from __main__.py into main.py so it can be imported elsewhere.

commit b272f50
Merge: 50c5643 87bf031
Author: David Meyer <dihm@users.noreply.github.com>
Date:   Fri Feb 9 12:37:52 2024 -0500

    Merge pull request #117 from dihm/setuptools_scm_fix

    Ensure setuptools_scm uses `release-branch-semver`

commit 50c5643
Merge: 5b10958 e9108b3
Author: David Meyer <dihm@users.noreply.github.com>
Date:   Fri Feb 9 12:34:44 2024 -0500

    Merge pull request #116 from dihm/update_workflow

    Update workflow pins to use node.js 20

commit e9108b3
Author: David Meyer <dihm@users.noreply.github.com>
Date:   Fri Feb 9 12:32:34 2024 -0500

    Update workflow pins to use node.js 20

commit 87bf031
Author: David Meyer <dihm@users.noreply.github.com>
Date:   Fri Feb 9 12:29:53 2024 -0500

    Ensure setuptools_scm uses `release-branch-semver`

    Also updates pins for setuptools and setuptools_scm in build.

commit 5b10958
Merge: ed21e1c e402134
Author: David Meyer <dihm@users.noreply.github.com>
Date:   Fri Feb 9 12:28:19 2024 -0500

    Merge pull request #115 from ispielma/DocStringError

    Found some trivial errors in the lyse doc strings while looking at startup messages

commit e402134
Author: spielman <spielman@umd.edu>
Date:   Fri Feb 9 11:00:58 2024 -0500

    Found some trivial errors in the lyse doc strings while looking at the startup messages.

commit ed21e1c
Merge: d70dbb3 34e574d
Author: David Meyer <dihm@users.noreply.github.com>
Date:   Wed Feb 7 10:06:52 2024 -0500

    Merge pull request #113 from ispielma/UI_Fixes

    Added missing close event for pulldown menu.

commit 34e574d
Author: Spielman Lab <ian.spielman@nist.gov>
Date:   Tue Feb 6 12:12:49 2024 -0500

    Corrected event.

commit 751a6c3
Author: spielman <spielman@umd.edu>
Date:   Tue Feb 6 11:11:09 2024 -0500

    Added missing close event for pulldown menu.

commit d70dbb3
Merge: 9402ca7 94e341e
Author: David Meyer <dihm@users.noreply.github.com>
Date:   Fri Jan 19 15:05:10 2024 -0500

    Merge pull request #112 from dihm/QT_deprecation

    Coerce float to int explicitly.

commit 94e341e
Author: David Meyer <dihm@users.noreply.github.com>
Date:   Fri Jan 19 15:02:05 2024 -0500

    Coerce float to int explicitly.

    Needed for newer python's that don't do implicit conversion anymore.

commit 9402ca7
Merge: 4674e8b c1f8417
Author: David Meyer <dihm@users.noreply.github.com>
Date:   Thu Jan 18 20:58:02 2024 -0500

    Merge pull request #111 from dihm/rtd_build

    Modernize RTD build

commit c1f8417
Author: David Meyer <dihm@users.noreply.github.com>
Date:   Thu Jan 18 20:52:09 2024 -0500

    Modernize RTD build

Author: dihm

.github/workflows/release-vars.sh

@@ -0,0 +1,47 @@
+# This repository. PyPI and Anaconda test and release package uploads are only done if
+# the repository the workflow is running in matches this (i.e. is not a fork). Optional,
+# if not set, package uploads are skipped.
+export RELEASE_REPO="labscript-suite/lyse"
+
+# Username with which to upload conda packages. If not given, anaconda uploads are
+# skipped.
+export ANACONDA_USER="labscript-suite"
+
+# Whether (true or false) to upload releases to PyPI, non-releases to Test PyPI,
+# releases to Anaconda, non-releases to Anaconda test label. Only used if the repository
+# the workflow is running in matches RELEASE_REPO, otherwise uploads are skipped.
+# Anaconda uploads require ANACONDA_USER be specified and ANACONDA_API_TOKEN secret be
+# set. Optional, all default to true.
+export PYPI_UPLOAD=""
+export TESTPYPI_UPLOAD=""
+export ANACONDA_UPLOAD=""
+export TEST_ANACONDA_UPLOAD=""
+
+# Which Python version to use for pure wheel builds, sdists, and as the host Python for
+# cibuildwheel. Optional, defaults to the second-most recent minor Python version.
+export DEFAULT_PYTHON=""
+
+# Comma-separated list of Python versions to build conda packages for. Only used if
+# HAS_ENV_MARKERS=true or PURE=false, otherwise a noarch conda package is built instead.
+# Optional, defaults to all non-end-of-life stable Python minor versions.
+export CONDA_PYTHONS=""
+
+# Environment variable set in the envionment that `cibuildwheel` runs in instructing it
+# which Pythons to build for, as a space-separated list of specifiers in the format
+# specified by `cibuildwheel`. Only used if PURE=false. Optional, defaults to all
+# non-end-of-life stable CPython versions.
+export CIBW_BUILD=""
+
+# Name of Python package. Optional, defaults to name from the package metadata
+export PKGNAME=""
+
+# Version of Python package. Optional, defaults to version from the package metadata
+export PKGVER=""
+
+# Whether the Python package is pure (true) or impure (false). Optional, defaults to
+# false if the setuptools package has extension modules or libraries, otherwise true.
+export PURE=""
+
+# Whether (true or false) the Python package has dependencies that vary by platform or
+# Python version. Optional, Defaults to presence of env markers in package metadata.
+export HAS_ENV_MARKERS=""