- uMp-4
- uMp-3 (Coming Soon!)
- Pathfinder MPM Control v2.8+
- InVivoStar (Coming Soon!)
- (Coming Soon!)
+
+- __:fontawesome-solid-download: Get Started__
+
+ ---
+
+ Install Ephys Link and get started in seconds
+
+
+ [:octicons-arrow-right-24: Install](home/installation.md)
+
+- __:fontawesome-solid-computer: Usage__
+
+ ---
+
+ Learn how to use Ephys Link to control your manipulators
+
+ [:octicons-arrow-right-24: Usage](usage/index.md)
+
+- __:fontawesome-regular-square-plus: Add a Manipulator Platform__
+
+ ---
+
+ Add a new manipulator platform to Ephys Link to enable control
+
+ [:octicons-arrow-right-24: Develop](development/adding_a_manipulator.md)
+
+- __:fontawesome-solid-book-open: Learn About Pinpoint__
+
+ ---
+
+ Pinpoint is an experiment planning and automation tool that uses Ephys Link
+
+ [:octicons-arrow-right-24: Learn More](https://virtualbrainlab.org/pinpoint/installation_and_use.html)
+
\ No newline at end of file
diff --git a/docs/stylesheets/extra.css b/docs/stylesheets/extra.css
new file mode 100644
index 0000000..2b601ab
--- /dev/null
+++ b/docs/stylesheets/extra.css
@@ -0,0 +1,5 @@
+:root {
+ --md-primary-fg-color: #0FBBBB;
+ --md-primary-fg-color--light: #0FBBBB;
+ --md-primary-fg-color--dark: #0FBBBB;
+}
\ No newline at end of file
diff --git a/docs/usage/connecting_to_pinpoint.md b/docs/usage/connecting_to_pinpoint.md
new file mode 100644
index 0000000..ff9879c
--- /dev/null
+++ b/docs/usage/connecting_to_pinpoint.md
@@ -0,0 +1,6 @@
+[Pinpoint](https://github.com/VirtualBrainLab/Pinpoint) is a tool for planning electrophysiology recordings and other
+_in vivo_ insertions, as well as tracking the position of probes in real-time inside the brain.
+
+Ephys Link was developed alongside Pinpoint to facilitate tracking and positioning of manipulators. Follow the
+[instructions on Pinpoint's documentation](https://virtualbrainlab.org//pinpoint/tutorials/tutorial_ephys_link.html) to
+use Ephys Link inside Pinpoint!
diff --git a/docs/usage/experiment_automation.md b/docs/usage/experiment_automation.md
new file mode 100644
index 0000000..c79e9dc
--- /dev/null
+++ b/docs/usage/experiment_automation.md
@@ -0,0 +1,8 @@
+Pinpoint and Ephys Link can work together to automate manual procedures in electrophysiology experiments. Follow the
+[instructions on Pinpoint's documentation](https://virtualbrainlab.org//pinpoint/tutorials/tutorial_ephys_copilot.html)
+to use automation in your next experiment!
+
+!!! note
+
+ Automation is still in early development. We recommend [contacting](https://virtualbrainlab.org/about/overview.html)
+ Dan Birman and Kenneth Yang if you would like to try it out!
\ No newline at end of file
diff --git a/docs/usage/index.md b/docs/usage/index.md
new file mode 100644
index 0000000..4312a22
--- /dev/null
+++ b/docs/usage/index.md
@@ -0,0 +1,62 @@
+# Using Ephys Link
+
+Ephys Link is a server that runs in the background.
+
+!!! info
+
+ Most people should use Ephys Link through Pinpoint. See documentation
+ on [connecting from Pinpoint](connecting_to_pinpoint.md) and using Ephys Link
+ for [experiment automation](experiment_automation.md).
+
+If you are building a client application that will talk to Ephys Link, see
+the [Socket.IO API reference](../development/socketio_api.md).
+
+There are different ways of launching Ephys Link depending on its installation.
+
+## Standalone Executable (GUI)
+
+1. Double-click the executable file to launch the configuration window.
+ 1. Take note of the IP address and port. **Copy this information into Pinpoint to connect**.
+2. Select the desired configuration and click "Launch Server".
+
+The configuration window will close and the server will launch. Your configurations will be saved for future use.
+
+To connect to the server from Pinpoint, provide the IP address and port. For example, if the server is running on the
+same computer that Pinpoint is, use
+
+- Server: `localhost`
+- Port: `3000`
+
+If the server is running on a different (local) computer, use the IP address of that computer as shown in the startup
+window instead of `localhost`.
+
+## Standalone Executable (CLI)
+
+Ephys Link can be launched from the command line directly without the
+configuration window. This is useful for computers
+or servers without graphical user interfaces.
+
+With the standalone executable downloaded, invoking the executable from the
+command line:
+
+```bash
+EphysLink-vX.X.X.exe -b
+```
+
+Use the actual name of the executable you downloaded. The `-b` or `--background` flag will launch the server without the
+configuration window and read configuration from CLI arguments.
+
+Here are some examples of how to start Ephys Link with a specific platform (replace `EphysLink.exe` with the actual name
+of the executable you downloaded):
+
+| Manipulator Platform | Command |
+|----------------------------------------|--------------------------------------|
+| Sensapex uMp-4 (default) | `EphysLink.exe -b` |
+| New Scale Pathfinder MPM Control v2.8+ | `EphysLink.exe -b -t pathfinder-mpm` |
+
+More options can be viewed by running `EphysLink.exe -h`.
+
+## Python Package
+
+Ephys Link can be invoked from the command line with the same arguments as the standalone executable using the
+`ephys-link` binary (or `el` for short).
\ No newline at end of file
diff --git a/ephys_link.spec b/ephys_link.spec
index 0eaef3f..0378503 100644
--- a/ephys_link.spec
+++ b/ephys_link.spec
@@ -46,7 +46,7 @@ if options.dir:
target_arch=None,
codesign_identity=None,
entitlements_file=None,
- icon='assets\\icon.ico',
+ icon='docs\\assets\\favicon.ico',
)
# noinspection PyUnresolvedReferences
coll = COLLECT(exe, a.binaries, a.datas, strip=False, upx=True, upx_exclude=[], name=FILE_NAME)
diff --git a/mkdocs.yml b/mkdocs.yml
new file mode 100644
index 0000000..49b7848
--- /dev/null
+++ b/mkdocs.yml
@@ -0,0 +1,89 @@
+# yaml-language-server: $schema=https://squidfunk.github.io/mkdocs-material/schema.json
+
+site_name: Ephys Link
+site_url: https://virtualbrainlab.github.io/ephys-link
+repo_url: https://github.com/VirtualBrainLab/ephys-link\
+repo_name: virtualbrainlab/ephys-link
+copyright: Copyright © 2024 Virtual Brain Lab
+extra:
+ social:
+ - icon: fontawesome/brands/github
+ link: https://github.com/VirtualBrainLab/ephys-link
+ - icon: fontawesome/brands/python
+ link: https://pypi.org/project/ephys-link
+ - icon: fontawesome/solid/globe
+ link: https://virtualbrainlab.org
+theme:
+ name: material
+ logo: assets/icon.png
+ favicon: assets/favicon.ico
+ palette:
+ # Palette toggle for automatic mode
+ - media: "(prefers-color-scheme)"
+ toggle:
+ icon: material/brightness-auto
+ name: Switch to light mode
+ # Palette toggle for light mode
+ - media: "(prefers-color-scheme: light)"
+ scheme: default
+ primary: custom
+ toggle:
+ icon: material/brightness-7
+ name: Switch to dark mode
+ # Palette toggle for dark mode
+ - media: "(prefers-color-scheme: dark)"
+ scheme: slate
+ primary: custom
+ toggle:
+ icon: material/brightness-4
+ name: Switch to system preference
+ features:
+ - content.code.copy
+ - navigation.tracking
+ - navigation.tabs
+ - navigation.tabs.sticky
+ - navigation.sections
+ - navigation.indexes
+ - toc.follow
+extra_css:
+ - stylesheets/extra.css
+markdown_extensions:
+ - admonition
+ - attr_list
+ - md_in_html
+ - pymdownx.details
+ - pymdownx.superfences
+ - pymdownx.highlight:
+ anchor_linenums: true
+ line_spans: __span
+ pygments_lang_class: true
+ - pymdownx.inlinehilite
+ - pymdownx.snippets
+ - pymdownx.superfences
+ - pymdownx.emoji:
+ emoji_index: !!python/name:material.extensions.emoji.twemoji
+ emoji_generator: !!python/name:material.extensions.emoji.to_svg
+plugins:
+ - search
+ - mkdocstrings:
+ handlers:
+ python:
+ paths: [ src ]
+ options:
+ docstring_style: sphinx
+nav:
+ - Home:
+ - index.md
+ - Installation: home/installation.md
+ - "How it Works": home/how_it_works.md
+ - "Supported Manipulators": home/supported_manipulators.md
+ - Contact: home/contact.md
+ - Usage:
+ - usage/index.md
+ - "Connecting to Pinpoint": usage/connecting_to_pinpoint.md
+ - "Experiment Automation": usage/experiment_automation.md
+ - Development:
+ - development/index.md
+ - "Socket.IO API": development/socketio_api.md
+ - "Adding a Manipulator": development/adding_a_manipulator.md
+ - "Code Organization": development/code_organization.md
\ No newline at end of file
diff --git a/pyproject.toml b/pyproject.toml
index 3d65770..2f3f9d9 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -60,58 +60,22 @@ exclude = ["/.github", "/.idea"]
[tool.hatch.envs.default]
python = "3.13.1"
dependencies = [
-# "coverage[toml]>=6.5",
-# "pytest",
+ "pyinstaller==6.11.1",
]
-#[tool.hatch.envs.default.scripts]
-#test = "pytest {args:tests}"
-#test-cov = "coverage run -m pytest {args:tests}"
-#cov-report = [
-# "- coverage combine",
-# "coverage report",
-#]
-#cov = [
-# "test-cov",
-# "cov-report",
-#]
+[tool.hatch.envs.default.scripts]
+exe = "pyinstaller.exe ephys_link.spec -y -- -d && pyinstaller.exe ephys_link.spec -y"
+exe-clean = "pyinstaller.exe ephys_link.spec -y --clean"
-[tool.hatch.envs.exe]
-python = "3.13"
-dependencies = [
- "pyinstaller",
-]
-[tool.hatch.envs.exe.scripts]
-build = "pyinstaller.exe ephys_link.spec -y -- -d && pyinstaller.exe ephys_link.spec -y"
-build_onefile = "pyinstaller.exe ephys_link.spec -y"
-build_clean = "pyinstaller.exe ephys_link.spec -y --clean"
-
-[tool.hatch.envs.types]
-python = "3.13"
+[tool.hatch.envs.docs]
+python = "3.13.1"
skip-install = true
dependencies = [
- "mypy",
+ "mkdocs-material==9.5.49",
+ "mkdocstrings-python==1.12.2",
]
-[tool.hatch.envs.types.scripts]
-check = "mypy --strict --install-types --non-interactive --ignore-missing-imports {args:src/ephys_link tests}"
-
-#[tool.coverage.run]
-#source_pkgs = ["ephys_link", "tests"]
-#branch = true
-#parallel = true
-#omit = [
-# "src/ephys_link/__about__.py",
-#]
-#
-#[tool.coverage.paths]
-#ephys_link = ["src/ephys_link", "*/ephys-link/src/ephys_link"]
-#tests = ["tests", "*/ephys-link/tests"]
-#
-#[tool.coverage.report]
-#exclude_lines = [
-# "no cov",
-# "if __name__ == .__main__.:",
-# "if TYPE_CHECKING:",
-#]
+[tool.hatch.envs.docs.scripts]
+serve = "mkdocs serve"
+build = "mkdocs build"
[tool.ruff.lint]
extend-ignore = ["DTZ005"]
\ No newline at end of file
diff --git a/qodana.yaml b/qodana.yaml
deleted file mode 100644
index 84e3e49..0000000
--- a/qodana.yaml
+++ /dev/null
@@ -1,29 +0,0 @@
-#-------------------------------------------------------------------------------#
-# Qodana analysis is configured by qodana.yaml file #
-# https://www.jetbrains.com/help/qodana/qodana-yaml.html #
-#-------------------------------------------------------------------------------#
-version: "1.0"
-
-#Specify inspection profile for code analysis
-profile:
- name: qodana.starter
-
-#Enable inspections
-#include:
-# - name: