added python project config and reordered folder structure
43
.github/workflows/test.yml
vendored
Normal file
|
@ -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
|
144
pyproject.toml
Normal file
|
@ -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"]
|
|
@ -17,4 +17,4 @@
|
|||
"nb_frame": 100,
|
||||
"sleep_before": 0.5,
|
||||
"imaging_pump_volume": 0.01
|
||||
}
|
||||
}
|
1
software/config/config.json.license
Normal file
|
@ -0,0 +1 @@
|
|||
SPDX-License-Identifier: GPL-3.0-or-later
|
14
software/config/hardware.json
Normal file
|
@ -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
|
||||
}
|
1
software/config/hardware.json.license
Normal file
|
@ -0,0 +1 @@
|
|||
SPDX-License-Identifier: GPL-3.0-or-later
|
9
software/planktoscope-backend/LICENSE.txt
Normal file
|
@ -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.
|
21
software/planktoscope-backend/README.md
Normal file
|
@ -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.
|
|
@ -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
|
||||
|
@ -14,4 +16,4 @@ morphocut~=0.1.2
|
|||
opencv-contrib-python~=4.5.3.56
|
||||
scipy~=1.7.2
|
||||
smbus2~=0.4.1
|
||||
scikit-image~=0.18.3
|
||||
scikit-image~=0.18.3
|
|
@ -0,0 +1,4 @@
|
|||
# SPDX-FileCopyrightText: 2022-present Sebastian Wendel <s.wendel@sourceindex.de>
|
||||
#
|
||||
# SPDX-License-Identifier: MIT
|
||||
__version__ = '0.0.1'
|
|
@ -0,0 +1,3 @@
|
|||
# SPDX-FileCopyrightText: 2022-present Sebastian Wendel <s.wendel@sourceindex.de>
|
||||
#
|
||||
# SPDX-License-Identifier: MIT
|
|
@ -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')
|
|
@ -81,7 +81,7 @@ if __name__ == "__main__":
|
|||
# Create script PID file, so it's easy to kill the main process without ravaging all python script in the OS
|
||||
with open('/tmp/pscope_pid', 'w') as f:
|
||||
f.write(str(os.getpid()))
|
||||
|
||||
|
||||
# check if gpu_mem configuration is at least 256Meg, otherwise the camera will not run properly
|
||||
with open("/boot/config.txt", "r") as config_file:
|
||||
for i, line in enumerate(config_file):
|
||||
|
@ -197,5 +197,5 @@ if __name__ == "__main__":
|
|||
|
||||
# Cleanup pid file
|
||||
os.remove('/tmp/pscope_pid')
|
||||
|
||||
|
||||
logger.info("Bye")
|
3
software/planktoscope-backend/tests/__init__.py
Normal file
|
@ -0,0 +1,3 @@
|
|||
# SPDX-FileCopyrightText: 2022-present Sebastian Wendel <s.wendel@sourceindex.de>
|
||||
#
|
||||
# SPDX-License-Identifier: MIT
|
|
@ -17,4 +17,4 @@
|
|||
"credentialsFile": "flows/main_cred.json"
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
|
@ -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)
|
|
@ -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)
|
|
@ -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
|
Before Width: | Height: | Size: 4 KiB After Width: | Height: | Size: 4 KiB |
Before Width: | Height: | Size: 692 KiB After Width: | Height: | Size: 692 KiB |
Before Width: | Height: | Size: 141 KiB After Width: | Height: | Size: 141 KiB |
Before Width: | Height: | Size: 829 KiB After Width: | Height: | Size: 829 KiB |
|
@ -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
|
|
@ -1,4 +1,7 @@
|
|||
#!/bin/bash
|
||||
|
||||
# SPDX-License-Identifier: GPL-3.0-or-later
|
||||
|
||||
sudo killall -15 python3
|
||||
sudo killall -15 raspimjpeg
|
||||
sleep 10
|