added python project config and reordered folder structure

.github/workflows/test.yml

@@ -0,0 +1,43 @@
+---
+name: test
+
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+concurrency:
+  group: test-${{ github.head_ref }}
+  cancel-in-progress: true
+
+env:
+  PYTHONUNBUFFERED: "1"
+  FORCE_COLOR: "1"
+
+jobs:
+  run:
+    name: |
+      Python ${{ matrix.python-version }} on
+      ${{ startsWith(matrix.os, 'macos-') &&
+      'macOS' || startsWith(matrix.os, 'windows-') && 'Windows' || 'Linux' }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install Hatch
+        run: pip install --upgrade hatch
+
+      - name: Run tests
+        run: hatch run cov

pyproject.toml

@@ -0,0 +1,144 @@
+
+[build-system]
+requires = ["hatchling", "hatch-vcs", "hatch-containers"]
+build-backend = "hatchling.build"
+
+[project]
+readme = "README.md"
+name = "PlanktoScope"
+description = "An open and affordable imaging platform for citizen oceanography"
+license = { text = "GPL-3.0-or-later" }
+requires-python = ">=3.7"
+authors = [{ name = "Romain Bazile", email = "planktoscope@gmail.com" }]
+keywords = []
+classifiers = [
+  "Development Status :: 5 - Production/Stable",
+  "Operating System :: POSIX :: Linux",
+  "Programming Language :: Python",
+  "Programming Language :: Python :: 3.7",
+  "Programming Language :: Python :: 3.8",
+  "Programming Language :: Python :: 3.9",
+  "Programming Language :: Python :: 3.10",
+  "Intended Audience :: End Users/Desktop",
+  "Intended Audience :: Science/Research",
+  "Topic :: Scientific/Engineering :: Image Processing",
+  "Topic :: Scientific/Engineering :: Image Recognition",
+  "License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)",
+]
+dependencies = [
+  "Adafruit-Blinka~=6.15.0",
+  "adafruit-circuitpython-motor~=3.3.1",
+  "adafruit-circuitpython-motorkit~=1.6.3",
+  "Adafruit-PlatformDetect~=3.17.2",
+  "Adafruit-SSD1306~=1.6.2",
+  "loguru~=0.5.3",
+  "matplotlib~=3.5.0",
+  "morphocut~=0.1.2",
+  "numpy~=1.21.4",
+  "opencv-contrib-python~=4.5.3.56",
+  "paho-mqtt~=1.6.1",
+  "picamera~=1.13",
+  "picamerax~=21.9.8",
+  "RPi.GPIO~=0.7.1a4",
+  "scikit-image~=0.18.3",
+  "scipy~=1.7.2",
+  "smbus2~=0.4.1",
+]
+dynamic = ["version"]
+
+[project.urls]
+Homepage = "https://www.planktoscope.org/"
+Documentation = "http://PlanktoScope.github.io/PlanktoScope"
+Issues = "https://github.com/PlanktoScope/PlanktoScope/issues"
+Source = "https://github.com/PlanktoScope/PlanktoScope"
+
+[project.scripts]
+planktoscope = "pkg.planktoscope:main"
+
+[tool.hatch.version]
+source = "vcs"
+
+[tool.hatch.build]
+sources = ["./software/planktoscope-backend/src"]
+
+[tool.hatch.build.hooks.vcs]
+version-file = "./software/planktoscope-backend/src/planktoscope_backend/__about__.py"
+
+[tool.hatch.build.targets.sdist]
+include = ["main.py", "./planktoscope/*.py", "./planktoscope/**/*.py"]
+
+[tool.hatch.build.targets.wheel]
+
+[tool.hatch.envs.default]
+
+[tool.hatch.envs.dev]
+python = "310"
+dependencies = [
+  "black",
+  "coverage[toml]",
+  "isort",
+  "pydocstyle",
+  "pycodestyle",
+  "pylint",
+  "pytest",
+  "typing",
+  "pytest-cov",
+  "pytest-mock",
+  "pytest-randomly",
+  "pytest-rerunfailures",
+  "pytest-xdist",
+]
+
+[tool.hatch.envs.test]
+dependencies = [
+  "coverage[toml]",
+  "pytest",
+  "pytest-cov",
+  "pytest-mock",
+  "pyspelling",
+]
+
+[tool.hatch.envs.test.scripts]
+cov = "pytest --cov-report=term-missing --cov-config=pyproject.toml --cov=scripts/planktoscope --cov=tests {args}"
+no-cov = "cov --no-cov {args}"
+
+[[tool.hatch.envs.test.matrix]]
+python = ["37", "38", "39", "310", "311"]
+
+[tool.hatch.envs.lint]
+dependencies = ["flake8", "black", "isort"]
+
+[tool.hatch.envs.lint.scripts]
+check = [
+  "flake8 .",
+  "black --check --diff software/planktoscope-backend",
+  "isort --check-only --diff software/planktoscope-backend",
+]
+fmt = [
+  "isort software/planktoscope-backend",
+  "black software/planktoscope-backend",
+  "check",
+]
+
+[tool.hatch.envs.docs]
+dependencies = [
+  "mkdocs",
+  "mkdocs-charts-plugin",
+  "mkdocs-glightbox",
+  "mkdocs-macros-plugin",
+  "mkdocs-markdownextradata-plugin",
+  "mkdocs-material-extensions",
+  "mkdocs-material",
+  "mkdocs-minify-plugin",
+  "mkdocs-redirects",
+  "mkdocs-table-reader-plugin",
+  "pygments",
+  "pymdown-extensions",
+  "linkchecker",
+]
+
+[tool.hatch.envs.docs.scripts]
+build = "mkdocs build --clean --strict"
+serve = "mkdocs serve --dev-addr localhost:8000"
+validate = ["linkchecker --config .linkcheckerrc site"]
+check = ["build --no-directory-urls", "validate"]

software/config/config.json.license

@@ -0,0 +1 @@
+SPDX-License-Identifier: GPL-3.0-or-later

software/config/hardware.json

@@ -0,0 +1,14 @@
+{
+  "stepper_reverse": false,
+  "microsteps": 32,
+  "focus_steps_per_mm": 40,
+  "pump_steps_per_ml": 507,
+  "focus_max_speed": 0.5,
+  "pump_max_speed": 30,
+  "stepper_type": "adafruit",
+  "wb_red_gain": 2,
+  "wb_blue_gain": 1.41,
+  "analog_gain": 1.0,
+  "digital_gain": 1.0,
+  "acq_fnumber_objective": 16
+}

software/config/hardware.json.license

@@ -0,0 +1 @@
+SPDX-License-Identifier: GPL-3.0-or-later

software/planktoscope-backend/LICENSE.txt

@@ -0,0 +1,9 @@
+MIT License
+
+Copyright (c) 2022-present Sebastian Wendel <s.wendel@sourceindex.de>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

software/planktoscope-backend/README.md

@@ -0,0 +1,21 @@
+# planktoscope-backend
+
+[![PyPI - Version](https://img.shields.io/pypi/v/planktoscope-backend.svg)](https://pypi.org/project/planktoscope-backend)
+[![PyPI - Python Version](https://img.shields.io/pypi/pyversions/planktoscope-backend.svg)](https://pypi.org/project/planktoscope-backend)
+
+-----
+
+**Table of Contents**
+
+- [Installation](#installation)
+- [License](#license)
+
+## Installation
+
+```console
+pip install planktoscope-backend
+```
+
+## License
+
+`planktoscope-backend` is distributed under the terms of the [MIT](https://spdx.org/licenses/MIT.html) license.

software/planktoscope-backend/requirements.txt

@@ -1,3 +1,5 @@
+# SPDX-License-Identifier: GPL-3.0-or-later
+
 RPi.GPIO~=0.7.1a4
 Adafruit-Blinka~=6.15.0
 adafruit-circuitpython-motorkit~=1.6.3

software/planktoscope-backend/src/planktoscope_backend/__about__.py

@@ -0,0 +1,4 @@
+# SPDX-FileCopyrightText: 2022-present Sebastian Wendel <s.wendel@sourceindex.de>
+#
+# SPDX-License-Identifier: MIT
+__version__ = '0.0.1'

software/planktoscope-backend/src/planktoscope_backend/__init__.py

@@ -0,0 +1,3 @@
+# SPDX-FileCopyrightText: 2022-present Sebastian Wendel <s.wendel@sourceindex.de>
+#
+# SPDX-License-Identifier: MIT

software/planktoscope-backend/src/planktoscope_backend/_version.py

@@ -0,0 +1,5 @@
+# coding: utf-8
+# file generated by setuptools_scm
+# don't change, don't track in version control
+__version__ = version = '0.1.dev643+g3c581f6.d19800101'
+__version_tuple__ = version_tuple = (0, 1, 'dev643', 'g3c581f6.d19800101')

software/planktoscope-backend/tests/__init__.py

@@ -0,0 +1,3 @@
+# SPDX-FileCopyrightText: 2022-present Sebastian Wendel <s.wendel@sourceindex.de>
+#
+# SPDX-License-Identifier: MIT

software/scripts/bash/start_update.sh

@@ -1,4 +1,7 @@
 #!/bin/bash
+
+# SPDX-License-Identifier: GPL-3.0-or-later
+
 log="echo -e"
 
 CURRENT_BRANCH=$(git --git-dir=/home/pi/PlanktoScope/.git rev-parse --abbrev-ref HEAD)

software/scripts/bash/update.sh

@@ -1,4 +1,7 @@
 #!/bin/bash
+
+# SPDX-License-Identifier: GPL-3.0-or-later
+
 log="echo -e"
 
 CURRENT_BRANCH=$(git --git-dir=/home/pi/PlanktoScope/.git rev-parse --abbrev-ref HEAD)

software/scripts/bash/usb_backup.sh

@@ -1,4 +1,7 @@
 #!/bin/bash
+
+# SPDX-License-Identifier: GPL-3.0-or-later
+
 # Stolen from https://github.com/raamsri/automount-usb/blob/master/usb-mount.sh
 
 # This work is licensed under the Unlicense

software/scripts/gallery/webfonts/fa-brands-400.svg

@@ -2375,7 +2375,7 @@ c21.2002 0 36.7998 -5.5 46.5 -16.7002c18.5996 -21.4004 11.7998 -64.1006 -14.2998
 d="M313.6 -26.5996c4.40039 -4.40039 8.10059 -9 13.3008 -12.5c-18.5029 -5.58008 -49.2031 -10.1074 -68.5283 -10.1074c-0.516602 0 -1.35547 0.00292969 -1.87207 0.00683594c-135 0 -244.5 109.5 -244.5 244.601c0 135.1 109.4 244.6 244.5 244.6
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-    <glyph glyph-name="readme" unicode="&#xf4d5;" horiz-adv-x="576" 
+    <glyph glyph-name="images/readme" unicode="&#xf4d5;" horiz-adv-x="576"
 d="M528.3 401.5c26.4004 -0.200195 47.7002 -21.7002 47.7002 -48.0996v-245.7c0 -26.5 -21.5 -48 -48 -48h-89.7002c-102.1 0 -132.6 -24.4004 -147.3 -75c-0.799805 -2.7998 -5.2998 -2.7998 -6 0c-14.5996 50.5996 -45.0996 75 -147.3 75h-89.7002
 c-26.5 0 -48 21.5 -48 48v245.8c0 26.5 21.5 48 48 48h139.7c48.0996 0 89.7998 -33.2998 100.399 -80.2998c10.5 47 52.3008 80.2998 100.4 80.2998h139.8zM242 136.1h0.0996094v22.9004c0 2 -1.59961 3.5 -3.5 3.5h-160.399c-2 0 -3.5 -1.59961 -3.5 -3.5v-22.9004
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software/scripts/raspbian_configuration/boot/config.txt

@@ -54,7 +54,7 @@ dtparam=spi=on
 #dtoverlay=gpio-ir,gpio_pin=17
 #dtoverlay=gpio-ir-tx,gpio_pin=18
 
-# Additional overlays and parameters are documented /boot/overlays/README
+# Additional overlays and parameters are documented /boot/overlays/images/readme
 
 # Enable audio (loads snd_bcm2835)
 dtparam=audio=on

software/scripts/raspimjpeg/macros/error_hard.sh

@@ -1,4 +1,7 @@
 #!/bin/bash
+
+# SPDX-License-Identifier: GPL-3.0-or-later
+
 sudo killall -15 python3
 sudo killall -15 raspimjpeg
 sleep 10