Merge branch 'master-versionbump' into stage-calibration

docs/source/extensions/example_extension/01b_basic_structure_subclass.py

@@ -0,0 +1,41 @@
+from labthings.server.extensions import BaseExtension
+from labthings.server.find import find_component
+
+
+# Create the extension class
+class MyExtension(BaseExtension):
+    def __init__(self):
+
+        # Create some instance variable
+        self.state_variable = "An example of a persistant instance variable"
+
+        # Superclass init function
+        super().__init__("com.myname.myextension", version="0.0.0")
+
+    def identify(self):
+        """
+        Demonstrate access to Microscope.camera, and Microscope.stage
+        """
+        microscope = find_component("org.openflexure.microscope")
+
+        response = (
+            f"My name is {microscope.name}. "
+            f"My parent camera is {microscope.camera}, "
+            f"and my parent stage is {microscope.stage}."
+        )
+
+        return response
+
+    def rename(self, new_name):
+        """
+        Rename the microscope
+        """
+
+        microscope = find_component("org.openflexure.microscope")
+
+        microscope.name = new_name
+        microscope.save_settings()
+
+
+# Create your extension object
+my_extension = MyExtension()

docs/source/extensions/lifecycle_hooks.rst

@@ -0,0 +1,53 @@
+Lifecycle Hooks
+===============
+
+Introduction
+------------
+In some cases it is useful to have functions triggered by events in an extensions lifecycle. Currently two such lifecycle events can be used, ``on_register``, and ``on_component``.
+
+``on_register``
+---------------
+
+The ``on_register`` method can be used to have a function call as soon as the extension has been successfully registered to the microscope. For example:
+
+.. code-block:: python
+
+    class MyExtension(BaseExtension):
+        def __init__(self):
+
+            # Track if the extension has been registered
+            self.registered = False
+
+            # Add lifecycle hooks
+            self.on_register(self.on_register_handler, args=(), kwargs={})
+
+            # Superclass init function
+            super().__init__("com.myname.myextension", version="0.0.0")
+
+        def on_register_handler(self, *args, **kwargs):
+            self.registered = True
+            print("Extension has been registered!")
+
+
+``on_component``
+----------------
+
+The ``on_component`` method can be used to have a function call as soon as a particular LabThings component has been added. This can be used, for example, to get information about the microscope instance as soon as it is available. For example:
+
+.. code-block:: python
+
+    class MyExtension(BaseExtension):
+        def __init__(self):
+
+            # Hold a reference to the microscope object as soon as it is available
+            self.microscope = None
+
+            # Add lifecycle hooks
+            self.on_component("com.myname.myextension", self.on_microscope_handler)
+
+            # Superclass init function
+            super().__init__("org.openflexure.microscope", version="0.0.0")
+
+        def on_microscope_handler(self, microscope_object):
+            print("Microscope object has been found!")
+            self.microscope = microscope_object

docs/source/extensions/structure.rst

@@ -4,7 +4,7 @@ Basic extension structure
 An extension starts as a simple instance of :py:class:`labthings.server.extensions.BaseExtension`. 
 Each extension is described by a single ``BaseExtension`` instance, containing any number of methods, API views, and additional hardware components. 
 
-In order to access the currently running microscope object, use the :py:func:`labthings.server.find` function, with the argument ``"org.openflexure.microscope"``. Likewise, any new components attached by other extensions can be found using their full name, as above.
+In order to access the currently running microscope object, use the :py:func:`labthings.server.find.find_component` function, with the argument ``"org.openflexure.microscope"``. Likewise, any new components attached by other extensions can be found using their full name, as above.
 
 A simple extension file, with no API views but application-available methods may look like:
 
@@ -23,4 +23,14 @@ Once this extension is loaded, any other extensions will have access to your met
 
         # Call a function from your extension
         if my_found_extension:
-            my_found_extension.identify()
+            my_found_extension.identify()
+
+
+Subclassing ``BaseExtension``
+-------------------------------
+
+The syntax used above allows novice programmers to easily start building extensions, without having to deal with subclassing. However, for more complex extensions which require persistent state, subclassing :py:class:`labthings.server.extensions.BaseExtension` is recommended.
+
+The same simple extension as seen above can be written using subclassing:
+
+.. literalinclude:: ./example_extension/01b_basic_structure_subclass.py

docs/source/extensions/views.rst

@@ -20,15 +20,15 @@ Request arguments
 
 For POST and PUT requests, data usually needs to be provided to the view in order to perform its function. In this example, our ``rename`` view requires a new microscope name to be passed. We make use of the ``@use_body`` decorator to provide this functionality.
 
-``@use_body`` defines the type of data expected in the request body. In this example, we ``String`` type data. The arguments of ``fields.String`` allow us to provide additional information, such as the parameter being required, and example values to appear in API documentation.
+``@use_body`` defines the type of data expected in the request body. In this example, we use ``String`` type data. The arguments of ``fields.String`` allow us to provide additional information, such as the parameter being required, and example values to appear in API documentation.
 
 Adding additional fields, and the meaning of the field types, will be discussed further in the next section.
 
-When a POST request is made to our API view, the request body is converted to processed by ``@use_body``, and passed as a positional argument to our ``post`` function. 
+When a POST request is made to our API view, the ``@use_body`` converts the body of the request into a ``String``, and passes it as a positional argument to our ``post`` function.
 
 Swagger documentation
 +++++++++++++++++++++
 
-At this point, it is useful to introduce the automatically generated Swagger documentation. From any web browser, go to ``http://microscope.local/api/v2/swagger-ui`` (or replace ``microscope.local`` with your microscopes IP address on incompatible systems).
+At this point, it is useful to introduce the automatically generated Swagger documentation. From any web browser, go to ``http://microscope.local/api/v2/swagger-ui`` (or replace ``microscope.local`` with your microscope's IP address if ``microscope.local`` doesn't work for your system).
 
-This page uses `SwaggerUI <https://swagger.io/tools/swagger-ui/>`_ to provide visual, interactive API documentation. Find your extensions URL in the documentation under the ``extensions`` group. Basic documentation about the parameters required for your POST method should be visible, as well as an interactive example filled out with the example request given in ``@use_body``.
+This page uses `SwaggerUI <https://swagger.io/tools/swagger-ui/>`_ to provide visual, interactive API documentation. Find your extensions URL in the documentation under the ``extensions`` group. Basic documentation about the parameters required for your POST method should be visible, as well as an interactive example filled out with the example request given in ``@use_body``.

docs/source/plugins.rst

@@ -11,4 +11,5 @@ Developing API Extensions
    ./extensions/properties.rst
    ./extensions/actions.rst
    ./extensions/tasks_locks.rst
-   ./extensions/ev_gui.rst
+   ./extensions/ev_gui.rst
+   ./extensions/lifecycle_hooks.rst

docs/source/quickstart.rst

@@ -21,6 +21,6 @@ For offline (i.e. no real microscope connected) development, a basic development
 Managing the server
 -------------------
 
-Managing the server through the installer script's CLI is documented `on our website <https://openflexure.org/projects/microscope/install/#managing-the-microscope-server>`_.
+Managing the server through the installer script's CLI is documented `on our website <https://openflexure.org/projects/microscope/install#managing-the-microscope-server>`_.
 
 This includes starting the server as a background service, as well as starting a development server with real-time debug logging.

openflexure_microscope/api/app.py

@@ -2,7 +2,9 @@
 from gevent import monkey
 
 # Patch most system modules. Leave threads untouched so we can still use them normally if needed.
-monkey.patch_all(thread=False)
+print("Monkey patching with Gevenet")
+monkey.patch_all()
+print("Monkey patching successful")
 
 import time
 import atexit
@@ -177,4 +179,4 @@ if __name__ == "__main__":
     from labthings.server.wsgi import Server
 
     server = Server(app)
-    server.run(host="0.0.0.0", port=5000, debug=False)
+    server.run(host="0.0.0.0", port=5000, debug=True, zeroconf=True)

openflexure_microscope/api/default_extensions/autofocus.py

@@ -359,7 +359,7 @@ class FastAutofocusAPI(View):
 
 
 autofocus_extension_v2 = BaseExtension(
-    "org.openflexure.autofocus", version="2.0.0-beta.1"
+    "org.openflexure.autofocus", version="2.0.0"
 )
 
 autofocus_extension_v2.add_method(fast_autofocus, "fast_autofocus")

openflexure_microscope/api/default_extensions/autostorage.py

@@ -88,7 +88,7 @@ class AutostorageExtension(BaseExtension):
         BaseExtension.__init__(
             self,
             "org.openflexure.autostorage",
-            version="2.0.0-beta.1",
+            version="2.0.0",
             description="Handle switching capture storage devices",
         )
 

openflexure_microscope/api/default_extensions/scan.py

@@ -354,6 +354,6 @@ class TileScanAPI(View):
         return task
 
 
-scan_extension_v2 = BaseExtension("org.openflexure.scan", version="2.0.0-beta.1")
+scan_extension_v2 = BaseExtension("org.openflexure.scan", version="2.0.0")
 
 scan_extension_v2.add_view(TileScanAPI, "/tile")

openflexure_microscope/api/default_extensions/zip_builder.py

@@ -202,7 +202,7 @@ class ZipGetterAPIView(View):
 
 zip_extension_v2 = BaseExtension(
     "org.openflexure.zipbuilder",
-    version="2.0.0-beta.1",
+    version="2.0.0",
     description="Build and download capture collections as ZIP files",
 )
 

openflexure_microscope/api/example_extensions/custom_element/__init__.py

@@ -26,7 +26,7 @@ class CustomElementExtension(BaseExtension):
             self,
             "org.openflexure.customelement",
             description="Testing HTML components in an extension",
-            static_folder=path_relative_to(__file__, "static"),
+            static_folder=path_relative_to(__file__, "static", "dist"),
         )
 
         # Register the on_microscope function to run when the microscope is attached

openflexure_microscope/api/example_extensions/custom_element/static/.browserslistrc

@@ -0,0 +1,2 @@
+> 1%
+last 2 versions

openflexure_microscope/api/example_extensions/custom_element/static/.gitattributes

@@ -0,0 +1 @@
+dist/* filter=lfs diff=lfs merge=lfs -text

openflexure_microscope/api/example_extensions/custom_element/static/.gitignore

@@ -0,0 +1,23 @@
+.DS_Store
+node_modules
+
+# local env files
+.env.local
+.env.*.local
+
+# Log files
+npm-debug.log*
+yarn-debug.log*
+yarn-error.log*
+
+# Editor directories and files
+.idea
+.vscode
+*.suo
+*.ntvs*
+*.njsproj
+*.sln
+*.sw?
+
+# Override and include dist
+!/dist

openflexure_microscope/api/example_extensions/custom_element/static/babel.config.js

@@ -0,0 +1,5 @@
+module.exports = {
+  presets: [
+    '@vue/cli-plugin-babel/preset'
+  ]
+}

openflexure_microscope/api/example_extensions/custom_element/static/dist/demo.html

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:18020f0209272ab81d01b2d68da517fcff98dd07d2ad7fe738c66df75003f7cf
+size 197

openflexure_microscope/api/example_extensions/custom_element/static/dist/my-custom-element.js

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:94cc5b4e5b3ddb8c6b94ef9b81b49060c582935aedf6c7d1626f4166c1827442
+size 288006

openflexure_microscope/api/example_extensions/custom_element/static/dist/my-custom-element.min.js

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:ba98b02d051bf6f7d2d4302154512a72ae6ddc1eff261e171fd92a067e1bdf84
+size 92018

openflexure_microscope/api/example_extensions/custom_element/static/package.json

@@ -0,0 +1,18 @@
+{
+  "name": "vue-web-component-project",
+  "version": "0.1.0",
+  "private": true,
+  "scripts": {
+    "build": "vue-cli-service build --target wc --inline-vue --name my-custom-element ./src/components/VueWebComponent.vue"
+  },
+  "dependencies": {
+    "axios": "^0.19.2",
+    "core-js": "^3.4.4",
+    "vue": "^2.6.10"
+  },
+  "devDependencies": {
+    "@vue/cli-plugin-babel": "^4.1.0",
+    "@vue/cli-service": "^4.1.0",
+    "vue-template-compiler": "^2.6.10"
+  }
+}

openflexure_microscope/api/example_extensions/custom_element/static/src/components/VueWebComponent.vue

@@ -0,0 +1,71 @@
+<template>
+  <div class="my-component-class">
+    <h1>My Vue Web Component</h1>
+    <div>Base URL: {{ componentBaseURL }}</div>
+    <p>Host microscope name: {{ hostDeviceName }}</p>
+    <p>{{ message }}</p>
+    <br />
+    <p>This cheeky little counter has all of its logic contained in a server-side component:</p>
+    <button type="button" v-on:click="decrement()">-</button>
+    <span>{{ value }}</span>
+    <button type="button" v-on:click="increment()">+</button>
+  </div>
+</template>
+
+<script>
+import axios from 'axios';
+
+export default {
+
+  props: {
+    'componentBaseURL': {
+      required: false,
+      default: null,
+      type: String
+    }
+  },
+
+  data: function() {
+    return {
+      value: 0,
+      message: "",
+      hostDeviceName: null
+    };
+  },
+
+  mounted () {
+    if (this.componentBaseURL){
+      axios
+      .get(`${this.componentBaseURL}`)
+      .then(response => {
+        console.log(response.data)
+        this.hostDeviceName = response.data.title
+      })
+      .catch(function(error) {
+        console.log("Error reading test json, probabl because of cors or something")
+      })
+    }
+    else {
+      this.message = "No componentBaseURL given"
+    }
+
+  },
+
+  methods: {
+    decrement: function() {
+      this.value = this.value -1
+    },
+
+    increment: function() {
+      this.value = this.value +1
+    }
+  }
+
+}
+</script>
+
+<style scoped>
+  .my-component-class {
+    text-align: center;
+  }
+</style>

openflexure_microscope/api/example_extensions/custom_element/static/src/main.js

@@ -0,0 +1,7 @@
+import Vue from 'vue';
+import wrap from '@vue/web-component-wrapper';
+import VueWebComponent from './components/VueWebComponent';
+
+const CustomElement = wrap(Vue, VueWebComponent);
+
+window.customElements.define('my-custom-element', CustomElement);

openflexure_microscope/api/example_extensions/custom_element/static/vue.config.js

@@ -0,0 +1,3 @@
+module.exports = {
+    productionSourceMap: false
+};

openflexure_microscope/camera/pi.py

@@ -531,6 +531,7 @@ class PiCameraStreamer(BaseCamera):
             # Set resolution and stop stream recording if necessary
             if not use_video_port:
                 self.stop_stream_recording()
+                time.sleep(0.1)
 
             self.camera.capture(
                 target,
@@ -540,6 +541,7 @@ class PiCameraStreamer(BaseCamera):
                 bayer=(not use_video_port) and bayer,
                 use_video_port=use_video_port,
             )
+            time.sleep(0.1)
 
             # Set resolution and start stream recording if necessary
             if not use_video_port:

poetry.lock

@@ -219,6 +219,14 @@ optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 version = "2.9"
 
+[[package]]
+category = "main"
+description = "Enumerates all IP addresses on all network adapters of the system."
+name = "ifaddr"
+optional = false
+python-versions = "*"
+version = "0.1.6"
+
 [[package]]
 category = "dev"
 description = "Getting image size from png/jpeg/jpeg2000/gif file"
@@ -269,7 +277,7 @@ description = "Python implementation of LabThings, based on the Flask microframe
 name = "labthings"
 optional = false
 python-versions = ">=3.6,<4.0"
-version = "0.2.0"
+version = "0.3.0"
 
 [package.dependencies]
 Flask = ">=1.1.1,<2.0.0"
@@ -279,6 +287,7 @@ gevent = ">=1.4.0,<2.0.0"
 gevent-websocket = ">=0.10.1,<0.11.0"
 marshmallow = ">=3.4.0,<4.0.0"
 webargs = ">=5.5.3,<6.0.0"
+zeroconf = ">=0.24.5,<0.25.0"
 
 [[package]]
 category = "dev"
@@ -324,7 +333,7 @@ description = "NumPy is the fundamental package for array computing with Python.
 name = "numpy"
 optional = false
 python-versions = ">=3.5"
-version = "1.18.1"
+version = "1.18.2"
 
 [[package]]
 category = "main"
@@ -366,7 +375,6 @@ test = ["coverage", "pytest", "mock", "pillow", "numpy"]
 reference = "79177fa7f28d6d5c6eab5ba814b420b1785b6b24"
 type = "git"
 url = "https://github.com/rwb27/picamera.git"
-
 [[package]]
 category = "main"
 description = "Python Imaging Library (Fork)"
@@ -704,11 +712,22 @@ optional = false
 python-versions = "*"
 version = "1.11.2"
 
+[[package]]
+category = "main"
+description = "Pure Python Multicast DNS Service Discovery Library (Bonjour/Avahi compatible)"
+name = "zeroconf"
+optional = false
+python-versions = "*"
+version = "0.24.5"
+
+[package.dependencies]
+ifaddr = "*"
+
 [extras]
 rpi = ["picamera", "RPi.GPIO"]
 
 [metadata]
-content-hash = "3a3a3bd4ffd7e0fe4c4c418a1b191c33afd375e6f06bb298189fd84ff75ee4cc"
+content-hash = "71b15705721aa7447357d24e79c6ff77f6844b4191eceb5e90a14942c5375b91"
 python-versions = "^3.6"
 
 [metadata.files]
@@ -855,6 +874,9 @@ idna = [
     {file = "idna-2.9-py2.py3-none-any.whl", hash = "sha256:a068a21ceac8a4d63dbfd964670474107f541babbd2250d61922f029858365fa"},
     {file = "idna-2.9.tar.gz", hash = "sha256:7588d1c14ae4c77d74036e8c22ff447b26d0fde8f007354fd48a7814db15b7cb"},
 ]
+ifaddr = [
+    {file = "ifaddr-0.1.6.tar.gz", hash = "sha256:c19c64882a7ad51a394451dabcbbed72e98b5625ec1e79789924d5ea3e3ecb93"},
+]
 imagesize = [
     {file = "imagesize-1.2.0-py2.py3-none-any.whl", hash = "sha256:6965f19a6a2039c7d48bca7dba2473069ff854c36ae6f19d2cde309d998228a1"},
     {file = "imagesize-1.2.0.tar.gz", hash = "sha256:b1f6b5a4eab1f73479a50fb79fcf729514a900c341d8503d62a62dbc4127a2b1"},
@@ -872,8 +894,8 @@ jinja2 = [
     {file = "Jinja2-2.11.1.tar.gz", hash = "sha256:93187ffbc7808079673ef52771baa950426fd664d3aad1d0fa3e95644360e250"},
 ]
 labthings = [
-    {file = "labthings-0.2.0-py3-none-any.whl", hash = "sha256:e2235c0db45c7134403bd78b2aa55ae5aa1bfee677735c9674f52bfcb605e998"},
-    {file = "labthings-0.2.0.tar.gz", hash = "sha256:f77391bbb02676ac7c28de59c425c4dc8d6de63031f2a2db8bffd26bc691cb5e"},
+    {file = "labthings-0.3.0-py3-none-any.whl", hash = "sha256:605999a8fe09a52ad32a4763020b81e5d1b7b786478b47e1f45594aa10bcdd2d"},
+    {file = "labthings-0.3.0.tar.gz", hash = "sha256:cc93ee4510fc1304a450346e11d0069541142e8867cfcf8e4381a872abf16a6c"},
 ]
 lazy-object-proxy = [
     {file = "lazy-object-proxy-1.4.3.tar.gz", hash = "sha256:f3900e8a5de27447acbf900b4750b0ddfd7ec1ea7fbaf11dfa911141bc522af0"},
@@ -926,11 +948,6 @@ markupsafe = [
     {file = "MarkupSafe-1.1.1-cp37-cp37m-manylinux1_x86_64.whl", hash = "sha256:ba59edeaa2fc6114428f1637ffff42da1e311e29382d81b339c1817d37ec93c6"},
     {file = "MarkupSafe-1.1.1-cp37-cp37m-win32.whl", hash = "sha256:b00c1de48212e4cc9603895652c5c410df699856a2853135b3967591e4beebc2"},
     {file = "MarkupSafe-1.1.1-cp37-cp37m-win_amd64.whl", hash = "sha256:9bf40443012702a1d2070043cb6291650a0841ece432556f784f004937f0f32c"},
-    {file = "MarkupSafe-1.1.1-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:6788b695d50a51edb699cb55e35487e430fa21f1ed838122d722e0ff0ac5ba15"},
-    {file = "MarkupSafe-1.1.1-cp38-cp38-manylinux1_i686.whl", hash = "sha256:cdb132fc825c38e1aeec2c8aa9338310d29d337bebbd7baa06889d09a60a1fa2"},
-    {file = "MarkupSafe-1.1.1-cp38-cp38-manylinux1_x86_64.whl", hash = "sha256:13d3144e1e340870b25e7b10b98d779608c02016d5184cfb9927a9f10c689f42"},
-    {file = "MarkupSafe-1.1.1-cp38-cp38-win32.whl", hash = "sha256:596510de112c685489095da617b5bcbbac7dd6384aeebeda4df6025d0256a81b"},
-    {file = "MarkupSafe-1.1.1-cp38-cp38-win_amd64.whl", hash = "sha256:e8313f01ba26fbbe36c7be1966a7b7424942f670f38e666995b88d012765b9be"},
     {file = "MarkupSafe-1.1.1.tar.gz", hash = "sha256:29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b"},
 ]
 marshmallow = [
@@ -942,27 +959,27 @@ mccabe = [
     {file = "mccabe-0.6.1.tar.gz", hash = "sha256:dd8d182285a0fe56bace7f45b5e7d1a6ebcbf524e8f3bd87eb0f125271b8831f"},
 ]
 numpy = [
-    {file = "numpy-1.18.1-cp35-cp35m-macosx_10_6_intel.whl", hash = "sha256:20b26aaa5b3da029942cdcce719b363dbe58696ad182aff0e5dcb1687ec946dc"},
-    {file = "numpy-1.18.1-cp35-cp35m-manylinux1_i686.whl", hash = "sha256:70a840a26f4e61defa7bdf811d7498a284ced303dfbc35acb7be12a39b2aa121"},
-    {file = "numpy-1.18.1-cp35-cp35m-manylinux1_x86_64.whl", hash = "sha256:17aa7a81fe7599a10f2b7d95856dc5cf84a4eefa45bc96123cbbc3ebc568994e"},
-    {file = "numpy-1.18.1-cp35-cp35m-win32.whl", hash = "sha256:f3d0a94ad151870978fb93538e95411c83899c9dc63e6fb65542f769568ecfa5"},
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 ]
 opencv-python-headless = [
     {file = "opencv_python_headless-3.4.7.28-cp27-cp27m-macosx_10_8_x86_64.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl", hash = "sha256:4685d447d3d7c361768e6b91224a757981b6513212b6693b9d63ca5705d42555"},
@@ -1236,3 +1253,7 @@ werkzeug = [
 wrapt = [
     {file = "wrapt-1.11.2.tar.gz", hash = "sha256:565a021fd19419476b9362b05eeaa094178de64f8361e44468f9e9d7843901e1"},
 ]
+zeroconf = [
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+    {file = "zeroconf-0.24.5.tar.gz", hash = "sha256:893a841445663e0c4c20d1111ce41484bd62d58f59d653d0485187343368ef4a"},
+]

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "poetry.masonry.api"
 
 [tool.poetry]
 name = "openflexure_microscope"
-version = "2.0.0-beta.6"
+version = "2.1.0-dev"
 description = "Python module, and Flask-based web API, to run the OpenFlexure Microscope."
 
 authors = [
@@ -36,7 +36,7 @@ pyserial = "^3.4" # Used for sangaboard (basic_serial_instrument) until we move
 python-dateutil = "^2.8"
 psutil = "^5.6.7" # Autostorage extension
 opencv-python-headless = "3.4.7.28"
-labthings = "0.2.0"
+labthings = "0.3.0"
 
 [tool.poetry.extras]
 rpi = ["picamera", "RPi.GPIO"]