v2024.0.0

Changelog

Added

• Deployment host/networking/interface-forwarding now has an enabled feature flag planktoscope-dhcp-default-route which can be disabled so that the PlanktoScope no longer advertises itself as a default route to the internet. This is useful when the PlanktoScope has no internet access and is connected (e.g. by Ethernet) to a Windows or macOS device which is connected to a Wi-Fi network with internet access: when the PlanktoScope advertises itself as a default route to the internet, such devices will only use the PlanktoScope to try to access the internet instead of using the Wi-Fi network to access the internet; then the feature flag can be disabled to enable such devices to access the internet in such a network topology.

Changed

• Deployment apps/ps/device-portal now includes a link to an offline PDF draft of v4 of Fabien's PlanktoScope operation protocol (but not any older versions), and now it only links to the latest version of online version of the protocol.

Fixed

• Deployment apps/ps/backend/proc-segmenter now correctly sets the img_rank metadata field of the EcoTaxa export to 1, instead of setting it to an incrementing index which makes exports un-importable by EcoTaxa for datasets with more than ~32,000 objects.

What's Changed

• Add Dozzle by @ethanjli in #2
• Add deployments for Prometheus metrics by @ethanjli in #3
• Split up Grafana features, improve dependency relationships by @ethanjli in #4
• Bump device-pkgs repo, add deployments for new packages by @ethanjli in #5
• Provision dhcpcd config file by @ethanjli in #6
• Deploy the backend segmenter as a Docker container by @ethanjli in #7
• Add CI checks by @ethanjli in #8
• Bump device-pkgs repo for Python segmenter by @ethanjli in #9
• Provide config files for the base OS layer by @ethanjli in #10
• Bump container images by @ethanjli in #11
• Provide the machine-name binary by @ethanjli in #12
• Bump some container images by @ethanjli in #13
• Add host/prepare-custom-image deployment by @ethanjli in #16
• Bump device-pkgs to change ecotaxa metadata filename by @ethanjli in #14
• Limit Grafana CPU usage by @ethanjli in #17
• Add v3 operation protocol, fix Avahi hostname registration by @ethanjli in #50
• Fix segmenter object size thresholding method by @ethanjli in #40
• Fix incorrect use of img_rank field in EcoTaxa export metadata by @ethanjli in #56

Full Changelog: v2023.9.0...v2024.0.0

v2024.0.0-beta.3

Changelog

Changed

• Deployment apps/ps/device-portal now includes a link to v3 of Fabien's PlanktoScope operation protocol.
• Deployment apps/ps/docs now includes an offline PDF copy of v3 of Fabien's PlanktoScope operation protocol.

Removed

• Deployment apps/ps/docs no longer includes an offline PDF copy of v1 of Fabien's PlanktoScope operation protocol.

Fixed

• Deployment host/machine-name now correctly integrates hostname generation and Avahi domain name registration; previously Avahi was unaware of the autogenerated hostname.
• (Breaking change) Deployment apps/ps/backend/proc-segmenter now correctly filters segmented objects by size.

Pull Requests

• Add v3 operation protocol, fix Avahi hostname registration by @ethanjli in #50
• Fix segmenter object size thresholding method by @ethanjli in #40

Full Changelog: v2024.0.0-beta.2...v2024.0.0-beta.3

v2024.0.0-beta.2

Changelog

Added

• Added a host/prepare-custom-image package to export a script to /usr/libexec/prepare-custom-image for resetting the filesystem and shutting down the machine in preparation for cloning the filesystem as an SD card image.
• Added experimental feature flags for other pallets to reference when importing files from this pallet.

Changed

• Deployment apps/grafana now tries to limit Grafana's CPU usage to one core.

Pull Requests

• Add host/prepare-custom-image deployment by @ethanjli in #16
• Bump device-pkgs to change ecotaxa metadata filename by @ethanjli in #14
• Limit Grafana CPU usage by @ethanjli in #17

Full Changelog: v2024.0.0-beta.1...v2024.0.0-beta.2

v2024.0.0-beta.1

Changelog

Changed

• The Docker container image has been bumped to the latest version for the apps/ps/device-portal, to remove a deprecation notice for the planktoscope.local hostname (as that hostname is being un-deprecated for v2024.0.0).

Full Changelog: v2024.0.0-beta.0...v2024.0.0-beta.1

v2024.0.0-beta.0

Changelog

Added

• Deployment host/machine-name now exports a machine-name binary built for the appropriate CPU architecture target.

Changed

• The Docker container image has been bumped to the latest version for the apps/ps/device-portal, to fix some broken links and remove the links to Portainer (whose inclusion in the default PlanktoScope OS images is deprecated for v2024.0.0 of PlanktoScope OS).
• Docker container images have been bumped to the latest version for filebrowser-related package deployments.

Pull Requests

• Provide the machine-name binary by @ethanjli in #12
• Bump some container images by @ethanjli in #13

Full Changelog: v2024.0.0-alpha.2...v2024.0.0-beta.0

v2024.0.0-alpha.2

Changelog

Added

• Deployment apps/cockpit now exports a drop-in config file for reverse-proxying (see the notes on additions to core/host/cockpit)
• Deployment apps/ps/node-red-dashboard now exports more config files needed for the Node-RED dashboard.
• Deployment host/cockpit now exports system services to automatically generate a Cockpit config file from drop-in config file fragments, and various drop-in config files for Cockpit.
• Deployment host/dnsmasq now exports system services to automatically generate a dnsmasq drop-in config file from drop-in config file templates.
• Added a host/docker deployment which exports an override to the default systemd docker.service.
• Deployment host/networking/autohotspot now exports everything needed for autohotspot functionality.
• Deployment host/networking/dhcpcd now exports an override to the default systemd dhcpcd.service.
• Deployment host/networking/dnsmasq now exports various drop-in config files for dnsmasq.
• Deployment host/networking/hostapd now exports a default basic config file for hostapd.
• Deployment host/networking/hosts now exports system services to automatically generate a hosts file from drop-in hosts file fragments.
• Deployment host/networking/interface-forwarding now exports everything needed for interface-forwarding functionality.
• Deployment host/planktoscope/gpio-init now exports everything needed for GPIO-initialization functionality.
• Deployment host/planktoscope/gpsd now exports all config files needed to support the GPS module (still no guarantee whether the files are actually correct, though!).
• Deployment host/planktoscope/machine-name now exports everything needed for automatically updating machine name-related configurations (machine name, hostname, SSID, Cockpit configuration).
• Deployment host/sshd now enables the system-provided ssh.service and adds & enables a service which automatically regenerates host keys for the SSH server if no host keys exist at boot.

Changed

• (Breaking change) Previously, the default behavior of the segmenter deployed by apps/ps/backend/proc-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 in the package deployment.
• (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) Deployment host/planktoscope/machine-name has been renamed to host/machine-name.
• Docker container images have been bumped to newer versions for almost all package deployments.
• Deployment apps/cockpit/deploy.yml no longer has a resource dependency on a fileset involving /etc/cockpit/cockpit.conf.
• Deployment 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

• Deployment apps/portainer will no longer be enabled by default after v2024.0.0. This is because it requires inclusion of a relatively large Docker container image in the PlanktoScope OS's SD card image (which is constrained to be up to 2 GB in size so that it can be attached as an upload to GitHub Releases), and because it has an annoying first-time user experience (i.e. that a password must be set within a few minutes of boot, or else the Portainer container must be restarted), and because Dozzle already provides all the basic functionalities needed by most users, and because Portainer has never actually been used for troubleshooting within the past year of the project.

Removed

• Deployment host/exim was removed because it was useless and is no longer relevant.

Pull Requests

• Add Dozzle by @ethanjli in #2
• Add deployments for Prometheus metrics by @ethanjli in #3
• Split up Grafana features, improve dependency relationships by @ethanjli in #4
• Bump device-pkgs repo, add deployments for new packages by @ethanjli in #5
• Provision dhcpcd config file by @ethanjli in #6
• Deploy the backend segmenter as a Docker container by @ethanjli in #7
• Add CI checks by @ethanjli in #8
• Bump device-pkgs repo for Python segmenter by @ethanjli in #9
• Provide config files for the base OS layer by @ethanjli in #10
• Bump container images by @ethanjli in #11

Full Changelog: v2023.9.0...v2024.0.0-alpha.2

v2024.0.0-alpha.1

Changelog

Added

• Added deployments for a few new packages which only describe assumptions about files provided by the host.

Changed

• Upgraded packages so that some now require certain files to be provided by the host.

Fixed

• The container created by deployment apps/ps/backend/proc-segmenter now runs as the root user, so that it correctly handles root directories created on the host by apps/ps/backend/controller.

Pull Requests

• Add Dozzle by @ethanjli in #2
• Add deployments for Prometheus metrics by @ethanjli in #3
• Split up Grafana features, improve dependency relationships by @ethanjli in #4
• Bump device-pkgs repo, add deployments for new packages by @ethanjli in #5
• Provision dhcpcd config file by @ethanjli in #6
• Deploy the backend segmenter as a Docker container by @ethanjli in #7
• Add CI checks by @ethanjli in #8
• Bump device-pkgs repo for Python segmenter by @ethanjli in #9

Full Changelog: v2023.9.0...v2024.0.0-alpha.1

v2024.0.0-alpha.0

Changelog

Added

• Deployment for Dozzle as a Docker container log viewer.
• Deployments for Prometheus metrics monitoring.
• Deployments for various scripts - and a few config files - to make available for running on the host.

Changed

• Deployment apps/ps/backend/proc-segmenter now deploys the segmenter as a Docker container instead of assuming it's available on the host.

Pull Requests

• Add Dozzle by @ethanjli in #2
• Add deployments for Prometheus metrics by @ethanjli in #3
• Split up Grafana features, improve dependency relationships by @ethanjli in #4
• Bump device-pkgs repo, add deployments for new packages by @ethanjli in #5
• Provision dhcpcd config file by @ethanjli in #6
• Deploy the backend segmenter as a Docker container by @ethanjli in #7
• Add CI checks by @ethanjli in #8

Full Changelog: v2023.9.0...v2024.0.0-alpha.0

v2023.9.0

Changelog

(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)

Full Changelog: v2023.9.0-beta.2...v2023.9.0

v2023.9.0-beta.2

Changelog

Changed

• (Breaking change) Updated files for use with v0.4.0 of the Forklift tool. Previous versions must be used with forklift v0.3.

Removed

• The hardware setup guides are no longer included by default in the offline docs site, to reduce the size of the PlanktoScope SD card images.

Pull Requests

• Update for compatibility with Forklift v0.4.0 by @ethanjli in #1

New Contributors

• @ethanjli made their first contribution in #1

Full Changelog: v2023.9.0-beta.1...v2023.9.0-beta.2