Improve segmenter developer experience

.github/dependabot.yml

@@ -6,20 +6,35 @@
 version: 2
 updates:
   # Maintain dependencies for the documentation system
-  - package-ecosystem: "pip"
-    directory: "/documentation"
+  - package-ecosystem: 'pip'
+    directory: '/documentation'
     schedule:
-      interval: "monthly"
+      interval: 'monthly'
+
+  - package-ecosystem: 'pip'
+    directory: '/controller'
+    schedule:
+      interval: 'monthly'
+
+  - package-ecosystem: 'pip'
+    directory: '/segmenter'
+    schedule:
+      interval: 'monthly'
+
+  - package-ecosystem: 'npm'
+    directory: '/node-red'
+    schedule:
+      interval: 'monthly'
 
   # Maintain dependencies for the Docker container to serve the documentation
-  - package-ecosystem: "docker"
+  - package-ecosystem: 'docker'
     # Look for a Dockerfile in the `documentation` diectory
-    directory: "/documentation"
+    directory: '/documentation'
     schedule:
-      interval: "monthly"
+      interval: 'monthly'
 
   # Maintain dependencies for GitHub Actions
-  - package-ecosystem: "github-actions"
-    directory: "/"
+  - package-ecosystem: 'github-actions'
+    directory: '/'
     schedule:
-      interval: "monthly"
+      interval: 'monthly'

.github/workflows/build-segmenter.yml

@@ -1,4 +1,4 @@
-name: Build Docker container image for the segmenter
+name: Build the segmenter
 
 on:
   push:
@@ -32,6 +32,31 @@ env:
   PUSH_IMAGE: ${{ (github.event_name == 'pull_request' && !github.event.pull_request.head.repo.fork) || github.event_name == 'push' || github.event_name == 'push tag' }}
 
 jobs:
+  ci-checks:
+    runs-on: ubuntu-24.04-arm
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install poetry
+        run: pipx install poetry==2.1.2
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+          cache: 'poetry'
+          cache-dependency-path: |
+            segmenter/poetry.lock
+
+      - name: Install build dependencies
+        working-directory: ./segmenter
+        run: |
+          poetry install --with dev
+
+      - name: Run checks
+        working-directory: ./segmenter
+        run: poetry run poe check
+
   build-container-image:
     permissions:
       contents: read

.gitignore

@@ -1,27 +1,12 @@
-# General
+# macOS
 .DS_Store
-*.dll
-*.log
-*.so
-*.swp
-export
-img
-tmp
 
 # Python
-/*.py[cod]
-/__pycache__
-/.benchmark
-/.coverage*
-/.pytest_cache
+__pycache__
 
 # npm
 node_modules
 
-# Node-Red
-/.main.json.backup
-/flow_backup.json
-
 # PlanktoScope config files
 hardware.json
 config.json

.vscode/extensions.json

@@ -7,7 +7,8 @@
 		"esbenp.prettier-vscode",
 		"charliermarsh.ruff",
 		"editorconfig.editorconfig",
-		"dbaeumer.vscode-eslint"
+		"dbaeumer.vscode-eslint",
+		"ms-python.mypy-type-checker"
 
 	],
 	// List of extensions recommended by VSCodium that should not be recommended for users of this workspace.

controller/adafruithat/planktoscope/mqtt.py

@@ -70,6 +70,7 @@
 # We can use collections.deque https://docs.python.org/3/library/collections.html#collections.deque
 import paho.mqtt.client as mqtt
 import json
+from os import getenv
 
 # Logger library compatible with multiprocessing
 from loguru import logger
@@ -84,7 +85,9 @@ class MQTT_Client:
     when creating this object
     """
 
-    def __init__(self, topic, server="127.0.0.1", port=1883, name="client"):
+    def __init__(
+        self, topic, hostname=getenv("MQTT_HOSTNAME", "localhost"), port=1883, name="client"
+    ):
         # Declare the global variables command and args
         self.command = ""
         self.args = ""
@@ -95,17 +98,17 @@ def __init__(self, topic, server="127.0.0.1", port=1883, name="client"):
         self.client = mqtt.Client()
         # self.client.enable_logger(logger)
         self.topic = topic
-        self.server = server
+        self.hostname = hostname
         self.port = port
         self.name = name
         self.connect()
 
     @logger.catch
     def connect(self):
-        logger.info(f"trying to connect to {self.server}:{self.port}")
+        logger.info(f"trying to connect to {self.hostname}:{self.port}")
         # TODO #104 add try: except ConnectionRefusedError: block here
         # This is a symptom that Mosquitto may have failed to start
-        self.client.connect(self.server, self.port, 60)
+        self.client.connect(self.hostname, self.port, 60)
         self.client.on_connect = self.on_connect
         self.client.on_subscribe = self.on_subscribe
         self.client.on_message = self.on_message
@@ -128,7 +131,7 @@ def on_connect(self, client, userdata, flags, rc):
             "5: Connection refused - not authorised",
         ]
         # Print when connected
-        logger.success(f"{self.name} connected to {self.server}:{self.port}! - {reason[rc]}")
+        logger.success(f"{self.name} connected to {self.hostname}:{self.port}! - {reason[rc]}")
         # When connected, run subscribe()
         self.client.subscribe(self.topic)
 

controller/planktoscopehat/planktoscope/mqtt.py

@@ -53,6 +53,7 @@
 # We can use collections.deque https://docs.python.org/3/library/collections.html#collections.deque
 import paho.mqtt.client as mqtt
 import json
+from os import getenv
 
 # Logger library compatible with multiprocessing
 from loguru import logger
@@ -67,7 +68,9 @@ class MQTT_Client:
     when creating this object
     """
 
-    def __init__(self, topic, server="127.0.0.1", port=1883, name="client"):
+    def __init__(
+        self, topic, hostname=getenv("MQTT_HOSTNAME", "localhost"), port=1883, name="client"
+    ):
         # Declare the global variables command and args
         self.args = ""
         self.__new_message = False
@@ -77,17 +80,17 @@ def __init__(self, topic, server="127.0.0.1", port=1883, name="client"):
         self.client = mqtt.Client()
         # self.client.enable_logger(logger)
         self.topic = topic
-        self.server = server
+        self.hostname = hostname
         self.port = port
         self.name = name
         self.connect()
 
     @logger.catch
     def connect(self):
-        logger.info(f"trying to connect to {self.server}:{self.port}")
+        logger.info(f"trying to connect to {self.hostname}:{self.port}")
         # TODO #104 add try: except ConnectionRefusedError: block here
         # This is a symptom that Mosquitto may have failed to start
-        self.client.connect(self.server, self.port, 60)
+        self.client.connect(self.hostname, self.port, 60)
         self.client.on_connect = self.on_connect
         self.client.on_subscribe = self.on_subscribe
         self.client.on_message = self.on_message
@@ -110,7 +113,7 @@ def on_connect(self, client, userdata, flags, rc):
             "5: Connection refused - not authorised",
         ]
         # Print when connected
-        logger.success(f"{self.name} connected to {self.server}:{self.port}! - {reason[rc]}")
+        logger.success(f"{self.name} connected to {self.hostname}:{self.port}! - {reason[rc]}")
         # When connected, run subscribe()
         self.client.subscribe(self.topic)
 

segmenter/Dockerfile

@@ -1,4 +1,4 @@
-FROM docker.io/library/python:3.9.18-slim-bullseye
+FROM docker.io/library/python:3.11-slim-bookworm
 
 # Install OS dependencies
 
@@ -16,6 +16,8 @@ USER pi:pi
 RUN mkdir -p /home/pi/PlanktoScope/segmenter
 WORKDIR /home/pi/PlanktoScope/segmenter
 
+ENV MQTT_HOSTNAME=host.docker.internal
+
 # Install Python dependencies
 
 # Note: cmake is needed to install ninja which is needed to install pyproject.toml-based projects.

segmenter/README.md

@@ -16,7 +16,36 @@ Currently, the simplest way to deploy the segmenter on any computer is using the
 
 ### Development
 
-TBD
+Install all dependencies including development tooling:
+
+```sh
+poetry install --with dev
+```
+
+Start controller for development:
+
+```sh
+docker ps
+# copy the container id of the segmenter
+docker stop <container-id>
+
+poetry run python -u main.py
+# make changes and restart
+```
+
+Run the code auto-formatter on the project:
+
+```sh
+poetry run poe fmt
+```
+
+Run all checks (including code formatting and linting):
+
+```sh
+poetry run poe check
+```
+
+We recommand using [https://code.visualstudio.com/docs/remote/ssh](https://code.visualstudio.com/docs/remote/ssh)
 
 ### Prerequisites
 

segmenter/apt-packages

@@ -1,12 +1,8 @@
 # numpy/scipy dependencies
-libopenblas0
-libatlas3-base
 libatomic1
 
 # opencv dependencies
-libhdf5-103-1
 libopenjp2-7
-libopenexr25
-libavcodec58
-libavformat58
-libswscale5
+libavcodec59
+libavformat59
+libswscale6

segmenter/main.py

@@ -63,9 +63,7 @@ def handler_stop_signals(signum, _):
 
 if __name__ == "__main__":
     logger.info("Welcome!")
-    logger.info(
-        "Initialising signals handling and sanitizing the directories (step 1/2)"
-    )
+    logger.info("Initialising signals handling and sanitizing the directories (step 1/2)")
     signal.signal(signal.SIGINT, handler_stop_signals)
     signal.signal(signal.SIGTERM, handler_stop_signals)
 
@@ -82,9 +80,7 @@ def handler_stop_signals(signum, _):
     # Starts the segmenter process
     logger.info("Starting the segmenter control process (step 2/2)")
     try:
-        segmenter_thread = planktoscope.segmenter.SegmenterProcess(
-            shutdown_event, "/home/pi/data"
-        )
+        segmenter_thread = planktoscope.segmenter.SegmenterProcess(shutdown_event, "/home/pi/data")
     except Exception:
         logger.error("The segmenter control process could not be started")
         segmenter_thread = None

segmenter/planktoscope/__init__.py

@@ -1,17 +1,17 @@
 # Copyright (C) 2021 Romain Bazile
-# 
+#
 # This file is part of the PlanktoScope software.
-# 
+#
 # PlanktoScope is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
 # the Free Software Foundation, either version 3 of the License, or
 # (at your option) any later version.
-# 
+#
 # PlanktoScope is distributed in the hope that it will be useful,
 # but WITHOUT ANY WARRANTY; without even the implied warranty of
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 # GNU General Public License for more details.
-# 
+#
 # You should have received a copy of the GNU General Public License
 # along with PlanktoScope.  If not, see <http://www.gnu.org/licenses/>.
 

segmenter/planktoscope/identity.py

@@ -1,11 +1,12 @@
 # TODO: keep this as the default path, but allow changing it with an environment variable
-MACHINE_NAME_PATH = '/run/machine-name'
+MACHINE_NAME_PATH = "/run/machine-name"
+
 
 def load_machine_name(path=MACHINE_NAME_PATH):
     """Returns the machine name specified by the file at MACHINE_NAMEPATH.
 
     Returns:
         str: the machine name stored in the file at the path.
     """
-    with open(path, encoding='utf-8') as file:
+    with open(path, encoding="utf-8") as file:
         return file.readline().strip()