updates

Author: CamDavidsonPilon

developer-guide/09-Storage and the filesystem/02-filesystem.md

@@ -28,5 +28,4 @@ Reference list of on-device paths that matter once a custom Pioreactor Raspberry
 | `/run/pioreactor/exports/` | Web export staging | Lighttpd serves `/exports/` from here so downloads never touch persistent storage. |
 | `/var/log/pioreactor.log` | System log for Pioreactor services | Configured via `config.ini` and read by both CLI and UI. Rotate with journald/logrotate as needed. |
 | `/opt/pioreactor/venv/` | System Python virtual environment | Hosts the Pioreactor Python installation (`pio`, `pios`, services). Activate manually for debugging. |
-| `/home/pioreactor/.local/bin/` | User-level executables | Supplementary scripts installed via `pip --user`. |
 | `/tmp/` | Temporary workspace | Referenced by `TMPDIR` in `pioreactor.env` for short-lived files outside tmpfs. |

user-guide/01-getting-started/01-assembly_guides/06_pioreactor_20ml_v1.1_to_v1.5/02-pioreactor-disassembly.md

@@ -31,7 +31,7 @@ import TabItem from '@theme/TabItem';
 1. The new top v1.5 vial holder has <Highlight color={colors.blue}>a groove within the body</Highlight> where the #024 O-ring sits. Carefully insert the O-ring using your fingers. Make sure to not twist the O-ring.
 2. Run your finger inside the vial holder, pushing the O-ring into place to ensure a snug fit.
 3. Screw off the existing top vial holder by twisting it counter-clockwise. This old top isn't needed anymore.
-4. Screw on the new v1.5 vial holder.
+4. Screw on the new v1.5 vial holder until the IR LED lines up with the heater cable.
 
 </AssemblyInstructionBlock>
 

user-guide/01-getting-started/01-assembly_guides/07_pioreactor_40ml_v1.0_to_v1.5/02-pioreactor-disassembly.md

@@ -31,7 +31,7 @@ import TabItem from '@theme/TabItem';
 1. The new top v1.5 vial holder has <Highlight color={colors.blue}>a groove within the body</Highlight> where the #024 O-ring sits. Carefully insert the O-ring using your fingers. Make sure to not twist the O-ring.
 2. Run your finger inside the vial holder, pushing the O-ring into place to ensure a snug fit.
 3. Screw off the existing top vial holder by twisting it counter-clockwise. This old top isn't needed anymore.
-4. Screw on the new v1.5 vial holder.
+4. Screw on the new v1.5 vial holder until the IR LED lines up with the heater cable.
 
 </AssemblyInstructionBlock>
 

user-guide/99-common-questions.mdx

@@ -78,25 +78,6 @@ The _uncalibrated_ optical densities reported the UI and recorded in the databas
 
 In the configuration, you can edit the parameter `samples_per_second` to adjust the how often the Pioreactor takes an optical density snapshot. Note that this parameter is the inverse of "duration between readings". For example, if you wish to record a measurement every 60 seconds, then `samples_per_second=0.01666667` (which is 1/60).
 
-:::tip
-If you put a large gap between readings, like 1 reading / 60 seconds, then we also suggest turning off the _downsampling_ on the UI's charts (it's on by default to avoid plotting thousands of points). To do this, [SSH](/user-guide/accessing-raspberry-pi) into your leader, and we'll edit the following files:
-
-```
-nano /var/www/pioreactorui/contrib/charts/05_od.yaml
-```
-
-And change the field `down_sample` from `true` to `false`. Do the same for the following files:
-
-```
-nano /var/www/pioreactorui/contrib/charts/01_implied_growth_rate.yaml
-```
-
-```
-nano /var/www/pioreactorui/contrib/charts/04_normalized_od.yaml
-```
-
-:::
-
 
 ### Why does the intensity for LED A turn on & off during an experiment?