labscript-suite
diff --git a/‎.gitignore
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diff --git a/‎README.md
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diff --git a/‎docs/source/_static/custom.css
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diff --git a/‎docs/source/_templates/components.rst
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diff --git a/‎docs/source/changes.md
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@@ -1,3 +1,10 @@
+# This gitignore file consists of 2 parts:
+#   * The standard Python .gitignore rules from GitHub
+#   * custom ignore rules for the labscript suite.
+#
+# These should be kept separate so that the generic rules can be updated with a
+# copy/paste without having to worry about whether we are removing custom rules
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
@@ -20,7 +27,6 @@ parts/
 sdist/
 var/
 wheels/
-pip-wheel-metadata/
 share/python-wheels/
 *.egg-info/
 .installed.cfg
@@ -50,6 +56,7 @@ coverage.xml
 *.py,cover
 .hypothesis/
 .pytest_cache/
+cover/
 
 # Translations
 *.mo
@@ -69,9 +76,10 @@ instance/
 .scrapy
 
 # Sphinx documentation
-docs/html/
+docs/_build/
 
 # PyBuilder
+.pybuilder/
 target/
 
 # Jupyter Notebook
@@ -82,6 +90,8 @@ 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
@@ -128,5 +138,20 @@ dmypy.json
 # Pyre type checker
 .pyre/
 
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+#
+# Custom labscript suite .gitignore rules start below
+#
+
 # Editors
-.vscode/
+.vscode/
+
+# Sphinx documentation
+docs/html/
+docs/source/_build/
+docs/source/components.rst
@@ -1,14 +1,20 @@
 # the _labscript suite_
 
-<!-- ![labscript logo](https://raw.githubusercontent.com/rpanderson/labscript-suite/readme/suite_logo_white_bg.png "labscript suite logo") -->
-
-<a href="https://github.com/labscript-suite/labscript"><img src="https://raw.githubusercontent.com/labscript-suite/labscript-suite/master/art/labscript_32nx32n.svg" height="96" alt="the labscript suite – labscript"></a> <a href="https://github.com/labscript-suite/runmanager"><img src="https://raw.githubusercontent.com/labscript-suite/labscript-suite/master/art/runmanager_32nx32n.svg" height="96" alt="the labscript suite – runmanager"></a> <a href="https://github.com/labscript-suite/blacs"><img src="https://raw.githubusercontent.com/labscript-suite/labscript-suite/master/art/blacs_32nx32n.svg" height="96" alt="the labscript suite – blacs"></a> <a href="https://github.com/labscript-suite/lyse"><img src="https://raw.githubusercontent.com/labscript-suite/labscript-suite/master/art/lyse_32nx32n.svg" height="96" alt="the labscript suite – lyse"></a> <a href="https://github.com/labscript-suite/runviewer"><img src="https://raw.githubusercontent.com/labscript-suite/labscript-suite/master/art/runviewer_32nx32n.svg" height="96" alt="the labscript suite – runviewer"></a>
+<a href="https://github.com/labscript-suite/labscript"><img src="https://raw.githubusercontent.com/labscript-suite/labscript-suite/master/art/labscript_32nx32n.svg" height="64" alt="the labscript suite – labscript"></a> <a href="https://github.com/labscript-suite/runmanager"><img src="https://raw.githubusercontent.com/labscript-suite/labscript-suite/master/art/runmanager_32nx32n.svg" height="64" alt="the labscript suite – runmanager"></a> <a href="https://github.com/labscript-suite/blacs"><img src="https://raw.githubusercontent.com/labscript-suite/labscript-suite/master/art/blacs_32nx32n.svg" height="64" alt="the labscript suite – blacs"></a> <a href="https://github.com/labscript-suite/lyse"><img src="https://raw.githubusercontent.com/labscript-suite/labscript-suite/master/art/lyse_32nx32n.svg" height="64" alt="the labscript suite – lyse"></a> <a href="https://github.com/labscript-suite/runviewer"><img src="https://raw.githubusercontent.com/labscript-suite/labscript-suite/master/art/runviewer_32nx32n.svg" height="64" alt="the labscript suite – runviewer"></a>
 
 ### Experiment control and automation system
 
-___
+[![Actions Status](https://github.com/labscript-suite/labscript-suite/workflows/Build%20and%20Release/badge.svg?branch=maintenance%2F3.0.x)](https://github.com/labscript-suite/labscript-suite/actions)
+[![Documentation Status](https://readthedocs.org/projects/labscriptsuite/badge/?version=latest)](https://docs.labscriptsuite.org)
+[![License](https://img.shields.io/pypi/l/labscript-suite.svg)](https://github.com/labscript-suite/labscript-suite/raw/master/LICENSE.txt)
+[![Python Version](https://img.shields.io/pypi/pyversions/labscript-suite.svg)](https://python.org)
+[![PyPI](https://img.shields.io/pypi/v/labscript-suite.svg)](https://pypi.org/project/labscript-suite)
+[![Conda Version](https://img.shields.io/conda/v/labscript-suite/labscript-suite)](https://anaconda.org/labscript-suite/labscript-suite)
+[![Google Group](https://img.shields.io/badge/Google%20Group-labscriptsuite-blue.svg)](https://groups.google.com/forum/#!forum/labscriptsuite)
+[![DOI](https://img.shields.io/badge/DOI-10.1063%2F1.4817213-0F79D0.svg)](https://doi.org/10.1063/1.4817213)
+
 
-The _labscript suite_ is a powerful and extensible framework for experiment [composition](https://github.com/labscript-suite/labscript), [control](https://github.com/labscript-suite/runmanager), [execution](https://github.com/labscript-suite/blacs), and [analysis](https://github.com/labscript-suite/lyse). Developed for quantum science and quantum engineering, from laboratory to in-field devices. Applicable to optics, microscopy, materials engineering, biophysics, and any application predicated on the repetition of parameterised, hardware-timed experiments.
+The _labscript suite_ is a powerful and extensible framework for experiment [composition](https://github.com/labscript-suite/labscript), [control](https://github.com/labscript-suite/runmanager), [execution](https://github.com/labscript-suite/blacs), and [analysis](https://github.com/labscript-suite/lyse). Developed for quantum science and quantum engineering; deployable in laboratory and in-field devices. Also applicable to optics, microscopy, materials engineering, biophysics, and any application predicated on the repetition of parameterised, hardware-timed experiments.
 
 This is a metapackage for the _labscript suite_. Formerly the _labscript suite_ installer repository, prior to the packages being installable via [PyPI](https://pypi.org/user/labscript-suite) and [Anaconda Cloud](https://anaconda.org/labscript-suite).
 
@@ -23,28 +29,26 @@ This is a metapackage for the _labscript suite_. Formerly the _labscript suite_
 - Dynamic visualisation of experiment composition and results.
 - Remote operation: different modules can run on physically separate hosts / single modules can be run on multiple hosts (including hardware supervisor, [blacs](https://github.com/labscript-suite/blacs)).
 - Auto-generating user-interfaces.
-- High-level scripting: all user-interface interaction can be programatically synthesised.
+- High-level scripting: user-interface interaction can be programatically synthesised.
 
 ## Table of contents
 
 - [Installing the _labscript suite_](#installing-the-labscript-suite)
 - [Recent changes to the _labscript suite_](#recent-changes-to-the-labscript-suite)
   - [Profile directories](#profile-directories)
-  - [Application shortcuts](#application-shortcuts)
   - [Secure communication](#secure-communication)
+  - [Application shortcuts](#application-shortcuts)
   - [Source code structure (developer installation)](#source-code-structure-developer-installation)
   - [Versioning (developer installation)](#versioning-developer-installation)
 - [BitBucket archive](#bitbucket-archive)
-  - [What to do if you had custom code in a fork on BitBucket](#what-to-do-if-you-had-custom-code-in-a-fork-on-bitbucket)
-  - [Migrating other repositories to GitHub](#migrating-other-repositories-to-github)
 - [Contributing to the _labscript suite_](#contributing-to-the-labscript-suite)
   - [Issue tracking](#issue-tracking)
   - [Request for developers](#request-for-developers)
 - [Citing the _labscript suite_](#citing-the-labscript-suite)
 
 ## Installing the _labscript suite_
 
-We're excited to announce that accompanying the recent migration to GitHub, _labscript suite_ components are now distributed as Python packages on [PyPI](https://pypi.org/user/labscript-suite) and [Anaconda Cloud](https://anaconda.org/anaconda/conda).
+We're excited to announce that accompanying the recent migration to GitHub, _labscript suite_ components are now distributed as Python packages on [PyPI](https://pypi.org/user/labscript-suite) and [Anaconda Cloud](https://anaconda.org/labscript-suite).
 
 This makes it far easier to get started using the _labscript suite_, as you no longer require a Mercurial or Git installation (or any knowledge of version control software); components can be installed and upgraded using:
 
@@ -79,23 +83,16 @@ A typical structure of the profile directory is:
         └── user_devices/
 ```
 
-This structure is created by calling the command `labscript-profile-create`.
-
-in a terminal after installing `labscript-utils` (per the [installation instructions](http://docs.labscriptsuite.org/en/latest/installation#regular-installation-from-the-python-package-index)).
-
-_Note:_ As of [labscript-suite/labscript-utils#37](https://github.com/labscript-suite/labscript-utils/issues/37) this can be the same directory as an editable installation.
-
-
-### Application shortcuts
+This structure is created by calling the command `labscript-profile-create` in a terminal after installing `labscript-utils` (per the [installation instructions](http://docs.labscriptsuite.org/en/latest/installation#regular-installation-from-the-python-package-index)).
 
-Operating-system menu shortcuts, correct taskbar behaviour, and environment activation for the Python GUI applications (blacs, lyse, runmanager, and runviewer) is now handled by a standalone Python package [desktop-app](https://github.com/chrisjbillington/desktop-app) (per installation instructions above). This currently supports Windows and Linux (Mac OS X support is forthcoming).
+_Note:_ As of [labscript-suite/labscript-utils#37](https://github.com/labscript-suite/labscript-utils/issues/37) an editable installation can be located within the labscript-suite profile directory.
 
 
 ### Secure communication
 
 Interprocess communication between components of the *labscript suite* is based on the [ZeroMQ](https://zeromq.org) (ZMQ) messaging protocol. We have supported secure interprocess communication via encrypted ZMQ messaging since February 2019 (labscript-utils 2.11.0).
 
-As of labscript-utils 2.16.0, **encryted interprocess communication will be the default**. If you haven't already, this means you'll need to create a new shared secret(or [pre-shared key](https://en.wikipedia.org/wiki/Pre-shared_key)) as follows:
+As of labscript-utils 2.16.0, **encryted interprocess communication will be the default**. If you haven't already, this means you'll need to create a new shared secret (or [pre-shared key](https://en.wikipedia.org/wiki/Pre-shared_key)) as follows:
 
 1. Run `python -m zprocess.makesecret` from the labconfig directory.
 
@@ -108,7 +105,7 @@ As of labscript-utils 2.16.0, **encryted interprocess communication will be the
 
 3. Copy the same pre-shared key to all computers running the *labscript suite* that need to communicate with each other, repeating step 2 for each of them.
 
-Treat this file like a password: it allows anyone on the same network access to *labscript suite* programs.
+Treat this file like a password; it allows anyone on the same network access to *labscript suite* programs.
 
 If you are on a trusted network and don't want to use secure communication, you may instead set:
 
@@ -119,11 +116,16 @@ allow_insecure = True
 
 *Notes*:
 
-* Steps 1 and 2 are executed automatically as part of the `labscript-profile-create` command. However, for multiple hosts, step 3 above must still be followed.
+* Steps 1 and 2 are executed automatically as part of the `labscript-profile-create` command. However, for multiple hosts, step 3 above must still be followed to ensure the same public-key is used by all hosts running *labscript suite* programs.
 
 * There is an outstanding issue with the ZMQ Python bindings on Windows ([zeromq/pyzmq#1148](https://github.com/zeromq/pyzmq/issues/1148)), whereby encryption is significantly slower for Python distributions other than [Anaconda](https://www.anaconda.com). Until this issue is resolved, we recommend that Windows users on an untrusted network use the Anaconda Python distribution (and install `pyzmq` using `conda install pyzmq`).
 
 
+### Application shortcuts
+
+Operating-system menu shortcuts, correct taskbar behaviour, and environment activation for the Python GUI applications (blacs, lyse, runmanager, and runviewer) is now handled by a standalone Python package [desktop-app](https://github.com/chrisjbillington/desktop-app) (per installation instructions above). This currently supports Windows and Linux (Mac OS X support is forthcoming).
+
+
 ### Source code structure (developer installation)
 
 Existing users who move to a developer (editable) installation, please note the following structural changes to the _labscript suite_ source code:
@@ -150,10 +152,10 @@ Existing users who move to a developer (editable) installation, please note the
 
 
 * Package names (shared by repositories and top-level folders) are now hyphenated, e.g. labscript-devices and labscript-utils.
-* Module names remain underscored, i.e. labscript_devices and labscript_utils.
+* Module names remain underscored, e.g. labscript_devices and labscript_utils.
 * The mixing of hyphen and underscores is inelegant but conventional.
 * All references to blacs are now lowercase.
-* As installation no longer requires a separate package, the repository formerly named ‘installer’ has been renamed to ‘[labscript-suite](https://github.com/labscript-suite/labscript-suite/issues)’, and will be used as a metapackage for the labscript suite.
+* As installation no longer requires a separate package, the repository formerly named ‘installer’ has been renamed to ‘[labscript-suite](https://github.com/labscript-suite/labscript-suite/issues)’, and is a metapackage for the *labscript suite* (installing it via `pip`/`conda` installs the suite).
 
 
 ### Versioning (developer installation)
@@ -163,7 +165,7 @@ Aside from the maintenance branches documented [here](http://docs.labscriptsuite
 
 ## BitBucket archive
 
-Some repository metadata (such as pull request discussions) could not be migrated directly from BitBucket to GitHub. As such, we have created an archived copy of everything that was on BitBucket. This includes:
+In April–May 2020 the _labscript suite_ code base was migrated from BitBucket to GitHub. All commit history and issues was preserved, however some repository metadata (such as pull request discussions) could not be migrated directly. As such, we have created an archived copy of everything that was on BitBucket. This includes:
 
 * Issues (as they appear on BitBucket);
 * Pull requests discussions;
@@ -172,14 +174,8 @@ Some repository metadata (such as pull request discussions) could not be migrate
 
 This archive can be found at [bitbucket-archive.labscriptsuite.org](https://bitbucket-archive.labscriptsuite.org/) (this page can take some time to load for the first time). Copies of every public fork of our repositories are at [github.com/labscript-suite-bitbucket-archive](https://github.com/labscript-suite-bitbucket-archive). As this is an archive, we will not be transferring ownership of these repositories back to their original owners. However, should you wish to continue development on one of those repositories you can fork it into your own account through the GitHub web interface. Should you have uncommitted changes (or changes made after 1st February, 2020) that you wish to have archived, please contact us to discuss the best approach to including these. Please note that we are not recommending continuing development in such forks long term, due to the changes in package structure outlined above.
 
+Further information about migrating your own customisations of the labscript suite can be found [here](https://docs.labscriptsuite.org/en/latest/archive/).
 
-### What to do if you had custom code in a fork on BitBucket
-
-_Coming soon!_
-
-### Migrating other repositories to GitHub
-
-Should you have other repositories on BitBucket such as labscriptlib, analysislib, userlib, or labconfig (or any project unrelated to the _labscript suite_) we strongly suggest using the tools we developed to migrate the _labscript suite_. These are [philipstarkey/bitbucket-hg-exporter](https://github.com/philipstarkey/bitbucket-hg-exporter) and [chrisjbillington/hg-export-tool](https://github.com/chrisjbillington/hg-export-tool) which can be used together. See the documentation of those projects for further details.
 
 ## Contributing to the _labscript suite_
 
 
@@ -57,3 +57,7 @@ details {
         0px 8px 10px 1px rgba(0, 0, 0, 0.14), 0px 3px 14px 2px rgba(0, 0, 0, 0.12);
     margin-bottom: 24px;
 }
+
+img.labscript-suite-icon {
+    min-width: 32px;
+}
@@ -0,0 +1,47 @@
+{% if current_project != 'the labscript suite' %}
+.. toctree::
+    :maxdepth: 2
+    :hidden:
+
+    the labscript suite <{{intersphinx_mapping['labscript-suite'][0]}}>
+
+{% endif %}
+*labscript suite* components
+============================
+
+The *labscript suite* is modular by design, and is comprised of:
+
+.. list-table:: Python libraries
+    :widths: 10 90
+    :header-rows: 0
+
+    {% for prog, item in programs.items() if item.type == 'lib' %}
+    * - .. image:: {{img_path}}/{{item.icon}}
+             :target: {{intersphinx_mapping['%s' | format(prog)][0]}}
+             :class: labscript-suite-icon
+      - |{{prog}}|_ --- {{item.desc}}
+    {% endfor %}
+
+.. list-table:: Graphical applications
+    :widths: 10 90
+    :header-rows: 0
+
+    {% for prog, item in programs.items() if item.type == 'gui' %}
+    * - .. image:: {{img_path}}/{{item.icon}}
+             :target: {{intersphinx_mapping['%s' | format(prog)][0]}}
+             :class: labscript-suite-icon
+      - |{{prog}}|_ --- {{item.desc}}
+    {% endfor %}
+
+.. toctree::
+    :maxdepth: 2
+    :hidden:
+
+    {% for prog in programs|sort if prog != current_project %}
+    {{prog}} <{{intersphinx_mapping['%s' | format(prog)][0]}}>
+    {% endfor %}
+
+{% for prog in programs %}
+.. |{{prog}}| replace:: **{{prog}}**
+.. _{{prog}}: {{intersphinx_mapping['%s' | format(prog)][0]}}
+{% endfor %}
@@ -26,7 +26,7 @@ A typical structure of the profile directory is:
 
 This structure is created by calling the command `labscript-profile-create` in a terminal after installing `labscript-utils` (per the [installation instructions](../installation)).
 
-_Note:_ As of [labscript-suite/labscript-utils#37](https://github.com/labscript-suite/labscript-utils/issues/37) this can be the same directory as an editable installation.
+_Note:_ As of [labscript-suite/labscript-utils#37](https://github.com/labscript-suite/labscript-utils/issues/37) an editable installation can be located within the labscript-suite profile directory.
 
 
 ### Secure communication
Original file line number	Diff line number	Diff line change
`@@ -57,3 +57,7 @@ details {`
`57`	`57`	`0px 8px 10px 1px rgba(0, 0, 0, 0.14), 0px 3px 14px 2px rgba(0, 0, 0, 0.12);`
`58`	`58`	`margin-bottom: 24px;`
`59`	`59`	`}`
	`60`	`+`
	`61`	`+img.labscript-suite-icon {`
	`62`	`+ min-width: 32px;`
	`63`	`+}`