CHANGELOG.md

Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project uses Calendar Versioning with a YYYY.minor.patch scheme. All dates in this file are given in the UTC time zone.

v2024.0.0-beta.2 - 2024-09-19

Added

• core/apps/grafana: added a cpu-limit feature flag to limit the CPU usage of the Grafana dashboard, to prevent CPU starvation for other processes.
• core/host/prepare-custom-image: added a script overlaid into /usr/libexec/prepare-custom-image which can be run to reset the filesystem in preparation for cloning the filesystem as an SD card image.

v2024.0.0-beta.1 - 2024-06-24

Changed

• core/apps/planktoscope/device-portal: the ghcr.io/planktoscope/device-portal container is upgraded from v0.2.2 to v0.2.3.

Fixed

• core/host/machine-name no longer declares provided fileset resources which (as of v2024.0.0-beta.0) are no longer provided.

v2024.0.0-beta.0 - 2024-06-07

Added

• core/host/machine-name now exports the machine-name binary into the PlanktoScope OS's overlay for /usr. The machine-name binary with the correct CPU architecture target for the host is selected when Forklift's downloads cache is populated.

Changed

• core/apps/filebrowser-root: the filebrowser/filebrowser container image is upgraded from v2.27.0 to v2.30.0.
• core/apps/planktoscope/filebrowser-backend-logs: the filebrowser/filebrowser container image is upgraded from v2.27.0 to v2.30.0.
• core/apps/planktoscope/filebrowser-datasets: the filebrowser/filebrowser container image is upgraded from v2.27.0 to v2.30.0.
• core/apps/planktoscope/device-portal: the ghcr.io/planktoscope/device-portal container is upgraded from v0.2.1 to v0.2.2.

v2024.0.0-alpha.2 - 2024-04-25

Added

• core/apps/cockpit now provides a drop-in config file for reverse-proxying (see the notes on additions to core/host/cockpit)
• core/apps/planktoscope/node-red-dashboard now exports more config files needed for the Node-RED dashboard.
• core/host/cockpit now provides system services to automatically generate the Cockpit config file from a drop-in config directory, and it provides some default drop-in config files - including drop-in files provided by some new feature flags: allow-unencrypted, allow-origins-planktoscope-static-ips, allow-origins-planktoscope-legacy-mdns-names, allow-origins-planktoscope-mdns-names, allow-origins-templated-custom-domain-home, and allow-origins-templated-mdns-hostname
• Added a core/host/docker package which exports an override to the default systemd docker.service.
• core/host/machine-name (renamed from core/host/planktoscope/machine-name) now exports everything needed for automatically updating machine name-related configurations (machine name, hostname, SSID).
• core/host/machine-name: the dynamically-generated machine name can now be overridden by making a file with a desired static name at /etc/machine-name.
• core/host/machine-name: if deployed on a non-Raspberry Pi computer, generation of the machine name now uses /etc/machine-id as a substitute for the Raspberry Pi's serial number, instead of falling back to a placeholder like pkscope.
• core/host/machine-name: the prefix for the hostname (and the SSID and the Cockpit configuration), which was previously hard-coded, can now be manually changed by creating a hostname template file at /etc/hostname-template. A default hostname template of pkscope-{machine-name} is provided the new hostname-template-pkscope feature flag.
• core/host/networking/autohotspot now exports everything needed for autohotspot functionality.
• core/host/networking/avahi-daemon now provides two feature flags for registering the PlanktoScope under mDNS aliases planktoscope.local and pkscope.local, respectively: register-planktoscope-local and register-pkscope-local
• core/host/networking/dhcpcd now exports an override to the default systemd dhcpcd.service.
• core/host/networking/dnsmasq now exports various drop-in config files for dnsmasq and adds a few new feature flags: planktoscope-dhcp-interfaces, to add another drop-in config file for dnsmasq based on the PlanktoScope OS's static IP address assignments for its various network interfaces; custom-domain, to add drop-in config file template for dnsmasq which uses the custom domain (newly configurable at /etc/custom-domain) for dnsmasq; and planktoscope-custom-domain, which provides a /etc/custom-domain file to set the custom domain to pkscope.
• core/host/networking/hostapd now provides system services to automatically generate the hostapd config file from a drop-in config directory, and it provides some default drop-in config files - including drop-in files provided by some new feature flags: interface-wlan0, localization-us, planktoscope-password, ssid-hostname
• core/host/networking/hosts now provides system services to automatically generate the hosts file from a drop-in config directory, and it provides some default drop-in config files - including hostnames previously provided by the Raspberry Pi OS, and also drop-in files provided by some new feature flags: planktoscope-custom-domain-home and planktoscope-domain-machine-name
• core/host/networking/interface-forwarding now exports everything needed for interface-forwarding functionality.
• core/host/planktoscope/gpio-init now exports everything needed for GPIO-initialization functionality.
• core/host/planktoscope/gpsd now exports all config files needed to support the GPS module (still no guarantee whether the files are actually correct, though!).
• core/host/sshd adds two feature flags: ssh-server-enabled to enable the ssh.service and ensure-ssh-host-keys to add and enable a service which automatically regenerates host keys for the SSH server if no host keys exist at boot.

Changed

• (Breaking change) The minimum supported Forklift version for using this repository has been bumped from v0.4.0 to v0.7.0, because some packages provided by this repository now require functionality added by v0.7.0 (namely, file-exporting functionality) in order to work as described/expected.
• (Breaking change) community/apps/portainer was previously named core/apps/portainer; it's been moved out of core, as its default inclusion in the PlanktoScope OS is deprecated in v2024.0.0 of the PlanktoScope OS; in the future, the user will have to manually add this package to their custom pallet if they want to add Portainer.
• (Breaking change) core/host/machine-name was previously named core/host/planktoscope/machine-name; it's been renamed, as it can now be configured (via feature flags) without PlanktoScope-specific naming.
• (Breaking change) core/host/machine-name: the machine name is now generated at /run/machine-name rather than /var/lib/planktoscope/machine-name. however, a symlink is now exported to redirect /var/lib/planktoscope/machine-name to /run/machine-name, for backwards-compatibility with programs still expecting /var/lib/planktoscope/machine-name.
• (Breaking change) core/host/machine-name: automatic updating of the hostname based on the machine name is no longer default behavior, but rather has to be enabled with a new generate-templated-hostname feature flag. If a hostname template is unspecified, the default hostname template is now machine-{machine-name} instead of pkscope-{machine-name}.
• (Breaking change) core/host/machine-name: inclusion of a pkscope- prefix for the hostname (and the SSID and the Cockpit configuration) is no longer default behavior, but rather has to be enabled with a new hostname-prefix-pkscope feature flag.
• (Breaking change) core/host/networking/dnsmasq: use of pkscope as the custom domain is no longer default behavior, but rather has to be enabled with a new planktoscope-custom-domain feature flag.
• (Breaking change) core/host/networking/hostapd: various settings are no longer provided by default, but rather have to be enabled with the new interface-wlan0, localization-us, planktoscope-password, and ssid-hostname feature flags.
• (Breaking change) core/host/networking/hosts: hostnames involving the custom domain (e.g. pkscope) are no longer added by default, but rather have to be enabled with a new planktoscope-custom-domain-homeandplanktoscope-custom-domain-machine-name` feature flags.
• (Breaking change) Previously, the default behavior of the segmenter provided by core/apps/planktoscope/device-backend/processing/segmenter was to subtract consecutive masks to try to mitigate image-processing issues with objects which get stuck to the flowcell during imaging. However, when different objects occupied the same space in consecutive frames, the subtraction behavior would subtract one object's mask from the mask of the other object in the following frame, which would produce clearly incorrect masks. This behavior is no longer enabled by default; in order to re-enable it, you should enable the pipeline-subtract-consecutive-masks feature flag.
• All packages in core/apps which use the alpine container image have upgraded it from v3.19.0 to v3.19.1.
• core/apps/dozzle: the amir20/dozzle container image is upgraded from v6.0.6 to v6.5.1.
• core/apps/grafana: the grafana/grafana-oss container image is upgraded from v10.1.6 to v10.4.2.
• core/apps/planktoscope/device-portal: the device-portal container image is upgraded from v0.1.15 to v0.2.1.
• core/infra/caddy-ingress: the lucaslorentz/caddy-docker-proxy container image is upgraded from v2.8.10 to v2.8.11.
• core/infra/prometheus: the prom/prometheus container image is upgraded from v2.48.1 to v2.51.2.
• core/host/networking/interface-forwarding has a slightly simpler network configuration, and now all packets for the PlanktoScope's static IP addresses (e.g. 192.168.4.1, 192.168.5.1, 192.168.6.1, etc.) are routed to 127.0.0.1 regardless of whether the packet for that IP address came from the interface corresponding to it.

Deprecated

• In the future, core/host/planktoscope/machine-name will remove support for looking up the machine name from /var/lib/planktoscope/machine-name; instead, only /run/machine-name will be supported.

Removed

• core/apps/cockpit no longer has a resource dependency on a fileset involving /etc/cockpit/cockpit.conf.
• (Breaking change) core/host/planktoscope/machine-name no longer provides functionality to automatically update the Cockpit config based on the machine name. Instead, core/host/cockpit provides templating functionality to automatically update the Cockpit config, and the machine name and hostname can be interpolated into those templates.
• (Breaking change) core/host/exim is no longer provided, as exim was only provided by a Cockpit extension (cockpit-storaged) which is no longer installed by default on the PlanktoScope OS.

v2024.0.0-alpha.1 - 2024-03-26

Added

• Added provided/required files/directories to the resource interfaces of some packages.
• Added some core/host packages to specify assumptions about provided files/directories.

Changed

• Upgraded core/apps/planktoscope/docs's container image from v2023.9.0 to v2024.0.0-alpha.1
• Upgraded core/apps/planktoscope/device-backend/processing/segmenter's container image from v2024.0.0-alpha.0 to v2024.0.0-alpha.1

v2024.0.0-alpha.0 - 2024-02-06

Added

• Added a new core/apps/dozzle package for viewing Docker container logs.
• Added a new core/infra/prometheus package for handling all Prometheus metrics.
• Added a new core/apps/node-exporter package for generating Prometheus metrics about the state of the host system.
• Added a new core/apps/grafana package for visualizing Prometheus metrics, including a dashboard summarizing the state of the host system.
• Exposed the /ps/node-red-v2/api/* path for prototyping HTTP API endpoints.
• Added requires-grafana-host-summary-dashboard and requires-filebrowser-datasets feature flags to /core/apps/planktoscope/node-red-dashboard to express resource requirements for apps embedded in the Node-RED dashboard.
• Added scripts for the PlanktoScope distro in core/host/networking/autohotspot, core/host/interface-forwarding, core/host/planktoscope/gpio-init, and core/host/planktoscope/machine-name.
• Added the Node-RED settings file to core/apps/planktoscope/node-red-dashboard.
• Added the dhcpcd config file to core/host/networking/dhcpcd.

Changed

• (Breaking change) Changed the core/apps/planktoscope/device-backend/processing/segmenter package to deploy the segmenter as a Docker container rather than expecting it to exist on the host.
• (Breaking change) Reorganized packages in core/host.
• Now the core/apps/planktoscope/filebrowser-backend-logs package has a resource dependency on one or more deployments which save logs to the location expected by the package.
• Changed some package resource dependency relationships to be nonblocking for plt apply and dev plt apply.
• Upgraded core/apps/planktoscope/device-portal's container image from v0.1.12 to v0.1.14.
• Upgraded all packages which use the alpine container image from 3.18.3 to 3.19.0.
• Upgraded all packages which use the filebrowser/filebrowser container image from v2.24.2 to v2.27.0.
• Upgraded core/apps/portainer's container image from 2.18.4 to 2.19.4.
• Upgraded core/infra/caddy-ingress's container image from 2.8.6 to 2.8.10.
• Upgraded core/infra/mosquitto's container image from 2.0.17 to 2.0.18.

Removed

• (Breaking change) Removed core/apps/planktoscope/device-backend/processing/segmenter's MJPEG stream service on host port 8001, since it can now be accessed via Docker networking.

Fixed

• Removed unnamed volumes created by the packages for filebrowser instances and for mosquitto.
• Changed underscores to hyphens in Docker volume names, for consistency with Docker network names.

v2023.9.0 - 2023-12-30

(this release involves no changes from v2023.9.0-beta.2; it's just a promotion of v2023.9.0-beta.2 to a stable release)

v2023.9.0-beta.2 - 2023-12-02

Added

• Added a dev-mock feature flag to the core/apps/planktoscope/device-portal package allowing that package to be run on non-Raspberry Pi OS Docker hosts with a fake hardcoded machine name (metal-slope-23501, corresponding to serial number 0xdeadc0de) instead of looking up a machine serial number from /sys/firmware/devicetree/base/serial-number.
• Added a full-site feature flag to the core/apps/planktoscope/docs package which provides the entire documentation site, including hardware setup guides.

Changed

• (Breaking change) Moved the core/apps/planktoscope/device-portal package's Compose App configuration related to Raspberry Pi OS integration (e.g. for deployment on PlanktoScopes) into a new feature flag named deploy-rpi. The machine name determined with this feature flag is overridden by the dev-mock feature flag, though if th deploy-rpi feature flag is enabled then the app will still require the existence of the /sys/firmware/devicetree/base/serial-number file on the Docker host.
• (Breaking change) Updated files for use with v0.4.0 of the Forklift tool. Previous versions must be used with forklift v0.3.
• Upgraded core/apps/planktoscope/docs's container images from v2023.9.0-beta.1 to v2023.9.0-beta.2.
• Upgraded core/apps/planktoscope/device-portal's container image from v0.1.11 to v0.1.12.

Removed

• Removed the testing/nodered-sandbox package.
• Removed the default Docker Compose network from most Compose apps.
• Removed the hardware setup guides from the default configuration of the core/apps/planktoscope/docs package. They can be added back using that package's full-site feature flag.

v2023.9.0-beta.1 - 2023-09-14

Changed

• Upgraded core/apps/planktoscope/device-portal's container image from v0.1.10 to v0.1.11
• Upgraded core/apps/planktoscope/project-docs's container image from v2023.9.0-alpha.2 to v2023.9.0-beta.1

v2023.9.0-beta.0 - 2023-09-02

Added

• Deployments of various host-only packages for host resources.

Changed

• (Breaking change) Updated files for use with v0.3.1 of the Forklift tool. Previous versions must be used with forklift v0.1.
• (Breaking change) Reorganized deployment definitions with a directory tree structure.

v2023.9.0-alpha.0 - 2023-05-30

Added

• Basic packages for the v2023.9.0 release of the PlanktoScope software distro.