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Merge pull request #642 from czbiohub-sf/develop
v0.8.0
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‎LICENSE‎

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@@ -25,4 +25,4 @@ DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
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CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
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OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

‎OS_instructions/RTC/RTC_setup.md‎

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# RTC
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The RTC ensures the Pi has accurate datetime regardless of Internet connection and power loss. To stay up to date, the RTC also needs to be updated whenever the Pi has correct time via network time protocol (NTP) syncing.
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The instructions below configure the OS for the following behavior:
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- If Pi is disconnected from internet at startup: Update system time from RTC
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- If Pi successfully syncs to NTP via internet: Update RTC from system (NTP) time
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## Setup instructions
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The following files need to live in the Pi's `/etc/` directory:
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- `rc.local` sets behavior on boot
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- `dhcpcd.exit-hook` sets behavior on Internet connection
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Ensure both files have executable permission:
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```
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sudo chmod +x rc.local
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sudo chmod +x dhcpcd.exit-hook
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```
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## Tests (optional)
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Reboot after adding the above files to start the RTC before testing.
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### RTC in use
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Verify system vs RTC time using `timedatectl` in terminal. You will see a printout like this:
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```
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Local time: Mon 2025-08-25 15:42:07 PDT
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Universal time: Mon 2025-08-25 22:42:07 UTC
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RTC time: Mon 2025-08-25 22:42:08
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Time zone: America/Los_Angeles (PDT, -0700)
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System clock synchronized: yes
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NTP service: active
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RTC in local TZ: no
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```
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If the RTC did not successfully start, RTC time will be listed as `n/a`.
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### System updated by RTC
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Test the use case where there's no Internet connection:
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First, turn off NTP sync, otherwise the time will automatically be corrected when `timedatectl` is run.
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```
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timedatectl set-ntp false
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```
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Then, manually write an incorrect date/time to the RTC.
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```
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sudo hwclock --set --date "01/01/2001 00:00:00"
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```
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Run `timedatectl` to verify the RTC's datetime.
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Turn wifi off and reboot. The system time should now be the incorrect RTC time. Be patient as it can take up to 1 min for the system time to update after reconnection.
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_NOTE: If you ever want to overwrite system time using the RTC on the spot, run `sudo hwclock -s`._
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### RTC updated bt system (NTP) time
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Test the use case where the Pi reconnects to Internet:
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Turn on wifi when it was previously off or reboot Pi. Both the system time and RTC time should be correct and can be verified by running `timedatectl`
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_NOTE: If you ever want to overwrite the RTC using the NTP time on the spot, run `sudo hwclock -w`._
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## Supplementary info
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- [hwclock](https://linux.die.net/man/8/hwclock) tool
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- [timedatectl](https://www.freedesktop.org/software/systemd/man/latest/timedatectl.html) tool

‎OS_instructions/RTC/dhcpcd.exit-hook‎

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#!/bin/sh
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# Runs after dhcpcd processes a DHCP event.
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# Env vars available: $interface, $reason, $new_ip_address, $new_routers, etc.
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# Only act on Wi-Fi and only when we (re)obtained a lease
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if [ "$interface" = "wlan0" ]; then
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case "$reason" in
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BOUND|RENEW|REBIND|REBOOT)
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timedatectl set-ntp true
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sleep(1)
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if timedatectl show -p NTPSynchronized | grep -q "yes"; then
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sudo hwclock --systohc --noadjfile --localtime
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fi
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esac
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fi

‎OS_instructions/RTC/rc.local‎

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#!/bin/sh -e
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#
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# rc.local
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#
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# This script is executed at the end of each multiuser runlevel.
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# Make sure that the script will "exit 0" on success or any other
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# value on error.
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#
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# In order to enable or disable this script just change the execution
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# bits.
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#
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# By default this script does nothing.
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# Print the IP address
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_IP=$(hostname -I) || true
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if [ "$_IP" ]; then
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printf "My IP address is %s\n" "$_IP"
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fi
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# Configure RTC
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sudo bash -c 'echo ds1307 0x68 > /sys/class/i2c-adapter/i2c-1/new_device'
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# Check if system time is NPT synced
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timedatectl set-ntp true
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sleep(1)
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if timedatectl show -p NTPSynchronized | grep -q "yes"; then
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# Update RTC from system time
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sudo hwclock --systohc --noadjfile --localtime
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fi
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# Always update system time from RTC!
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# For some reason this doesn't work in else statement
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timedatectl set-ntp false
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sudo hwclock -s
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exit 0

‎OS_instructions/setup_promtail.sh‎

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server:
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disable: true # Disables Promtail's internal HTTP server
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positions:
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filename: /home/pi/Documents/ulc-malaria-scope/log_config/positions.yaml # Stores file tracking state
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filename: /media/pi/SamsungSSD/positions.yaml # Stores file tracking state
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sync_period: 10s
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clients:
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- url: https://api-grafana.sf.czbiohub.org/loki/push
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host: ${HOSTNAME}
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__path__: /media/pi/SamsungSSD/logs/*.log # Watches all logs in this directory
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pipeline_stages:
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- labeldrop:
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- filename
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- match:
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selector: '{app="Remoscope"}'
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stages:
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- multiline:
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firstline: '^\\d{4}-\\d{2}-\\d{2}-\\d{6} .*'
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max_wait_time: 5s
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max_wait_time: 20s
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- labeldrop:
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- filename
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- regex:
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expression: '^\\d{4}-\\d{2}-\\d{2}-\\d{6} - (?P<severity>\\w+) - .*'
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- labels:
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chmod +x /tmp/promtail-linux-arm
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sudo mv /tmp/promtail-linux-arm /usr/local/bin/promtail
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# --- Step 4: Create systemd service for Promtail using sed for environment variable substitution ---
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echo "Creating systemd service file for promtail..."
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echo "Creating Promtail systemd unit…"
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# --- STEP 4: wrapper that exits (and lets systemd retry) --------------------
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WRAPPER="/usr/local/bin/promtail-retry.sh"
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echo "Creating wrapper script at $WRAPPER…"
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sudo tee "$WRAPPER" > /dev/null <<'EOF'
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#!/bin/bash
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SSD_DIR="/media/pi/SamsungSSD"
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# If the drive isn't mounted yet - retry
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if ! mountpoint -q "$SSD_DIR"; then
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echo "Promtail: $SSD_DIR not mounted yet, exiting so systemd can retry…" >&2
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exit 1
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fi
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exec /usr/local/bin/promtail \
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--config.file=/home/pi/Documents/ulc-malaria-scope/log_config/promtail-config.yaml \
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--config.expand-env=true
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EOF
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sudo chmod +x "$WRAPPER"
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# --- STEP 5: promtail-service file setup --------------------
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sudo tee /etc/systemd/system/promtail.service > /dev/null <<'EOF'
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[Unit]
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Description=Promtail Service
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After=network.target
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Description=Promtail (logs on removable SSD)
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After=network-online.target
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[Service]
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Type=simple
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ExecStart=/usr/local/bin/promtail --config.file=/home/pi/Documents/ulc-malaria-scope/log_config/promtail-config.yaml --config.expand-env=true
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Restart=on-failure
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ExecStart=/usr/local/bin/promtail-retry.sh
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Restart=always
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RestartSec=10
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User=pi
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Environment="HOSTNAME=HOST_PLACEHOLDER"
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Environment="LOKI_PASSWORD=PASSWORD_PLACEHOLDER"
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KillMode=mixed
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ExecStopPost=/bin/sync
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[Install]
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WantedBy=multi-user.target
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EOF
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echo "Updating systemd service file with provided HOST and PASSWORD..."
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sudo sed -i "s/Environment=\"HOSTNAME=HOST_PLACEHOLDER\"/Environment=\"HOSTNAME=${HOST}\"/" /etc/systemd/system/promtail.service
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sudo sed -i "s/Environment=\"LOKI_PASSWORD=PASSWORD_PLACEHOLDER\"/Environment=\"LOKI_PASSWORD=${PASSWORD}\"/" /etc/systemd/system/promtail.service
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echo "Enabling promtail service..."
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sudo systemctl enable promtail.service
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echo "Starting promtail service..."
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# --- STEP 6: Install udev rule for hard-pull safety --------------------------
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echo "Adding udev rule to stop promtail on drive removal…"
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sudo tee /etc/udev/rules.d/99-promtail-ssd.rules > /dev/null <<'EOF'
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ACTION=="remove", SUBSYSTEM=="block", ENV{ID_FS_LABEL}=="SamsungSSD", \
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RUN+="/usr/bin/systemctl stop promtail.service"
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ACTION=="add", SUBSYSTEM=="block", ENV{ID_FS_LABEL}=="SamsungSSD", \
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RUN+="/usr/bin/systemctl start promtail.service"
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EOF
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sudo udevadm control --reload
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# Reload udev so the new rule is active immediately
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sudo udevadm control --reload
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sudo udevadm trigger --subsystem-match=block # optional: re-evaluate current devices
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echo "udev rule installed - Promtail will shut down if the SSD is hard-pulled."
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sudo systemctl start promtail.service
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echo "Promtail setup complete."
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echo "Promtail setup complete."

‎setup.py‎

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"remo-dev=ulc_mm_package.QtGUI.dev_run:main",
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"remo-fix-focus=ulc_mm_package.utilities.coarse_focus_utility:main",
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"remo-pneumatic-calibration=ulc_mm_package.utilities.pneumatic_utility:main",
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"remo-zstack=ulc_mm_package.utilities.zstack_utility:main",
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]
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},
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)

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