fix anchors

CamDavidsonPilon · CamDavidsonPilon · commit 06467afe6595 · 2026-01-31T19:50:22.000-05:00
diff --git a/developer-guide/05-Scripts/01-writing-scripts.md b/developer-guide/05-Scripts/01-writing-scripts.md
@@ -50,7 +50,7 @@ python your_script.py >/dev/null 2>&1 & disown
 
 ```
 
-You can also use the [Pioreactor's plugin architecture](https://docs.pioreactor.com/developer-guide/intro-plugins#scripts) to control the start and stop of the script.
+You can also use the [Pioreactor's plugin architecture](https://docs.pioreactor.com/developer-guide/intro-plugins#custom-scripts) to control the start and stop of the script.
 
 ### Useful utility objects
 
diff --git a/developer-guide/07-Plugins/02-adding-plugins-to-ui.md b/developer-guide/07-Plugins/02-adding-plugins-to-ui.md
@@ -76,7 +76,7 @@ description: Run my custom script.
 published_settings: []
 ```
 
-See more information on the structure of your script [here](/developer-guide/intro-plugins#scripts)
+See more information on the structure of your script [here](/developer-guide/intro-plugins#custom-scripts)
 
 ## Automations
 
diff --git a/developer-guide/09-Storage and the filesystem/01-data-stores/02-sqlite.md b/developer-guide/09-Storage and the filesystem/01-data-stores/02-sqlite.md
@@ -18,7 +18,7 @@ You can either use `.tables` in the sqlite shell, or visit all the tables [schem
 
 ### How can I add new SQL tables?
 
-Using the sqlite shell (`pio db`), you can execute any SQL statements, including creating new tables. Plugins can also automatically create new tables when installed, [see instructions here](plugin-as-python-package#5-optional-adding-tables-to-the-sql-store).
+Using the sqlite shell (`pio db`), you can execute any SQL statements, including creating new tables. Plugins can also automatically create new tables when installed, [see instructions here](plugin-as-python-package#5-optional-adding-tables-to-the-sql-database-and-exposing-them-on-the-export-data-page).
 
 ### How do I populate my own SQL tables?
 
diff --git a/experiments/02-Secondary level education/caffeine-inhibition.md b/experiments/02-Secondary level education/caffeine-inhibition.md
@@ -50,7 +50,7 @@ We recommend trying different amounts of tea, coffee, or other caffeine containi
 
 1. Prepare identical sterile stocks in vials with your media of choice.
 2. Add some amount (a few drops to 1 mL) of a liquid containing caffeine to a vial. Add the same amount of DI water to another vial. 
-	* If the media appears different before inoculation, we recommend you [blank](/user-guide/set-up-an-experiment#blanking) your vials before adding your culture. 
+* If the media appears different before inoculation, we recommend you [blank](/user-guide/od-normal-growth-rate#blanking) your vials before adding your culture. 
 3. Inoculate each vial with a very small amount of your microorganism, using best practices to avoid other contamination.
 	* In our example, a yeast stock solution can be made by diluting a small amount of yeast in 15mL of YPD stock media, then a drop of this stock solution can be added to your vials.
 4. Wipe the vials and place them in the Pioreactors. 
diff --git a/experiments/02-Secondary level education/low-vs-high-conc-media.md b/experiments/02-Secondary level education/low-vs-high-conc-media.md
@@ -68,7 +68,7 @@ Consider lower or higher bounds for your media compositions. How much sooner wil
 ## Detailed procedure
 
 1. Prepare a sterile stock of two different concentrations of your media of choice.
-	* If the media appears different before inoculation, we recommend you [blank](/user-guide/set-up-an-experiment#blanking) your vials before adding your culture. 
+* If the media appears different before inoculation, we recommend you [blank](/user-guide/od-normal-growth-rate#blanking) your vials before adding your culture. 
 2. Inoculate each vial with a very small amount of your microorganism, using best practices to avoid other contamination.
 	* In our example, a yeast stock solution can be made by diluting a small amount of yeast in 15mL of YPD stock media, then a drop of this stock solution can be added to your vials.
 3. Wipe the vials and place them in the Pioreactors. 
diff --git a/experiments/03-University level education/00-continuous-cultures-using-turbidostat.md b/experiments/03-University level education/00-continuous-cultures-using-turbidostat.md
@@ -37,7 +37,7 @@ Determine the maximum specific growth rate of your culture using turbidostat str
 
 ## Introduction 
 
-Your Pioreactor can be transformed into a [turbidostat](/user-guide/dosing-automations#pid-turbidostat), where pumps are used to replenish media around a target OD, creating a continuous culture. Due to the abundance of resources and lack of rate-limiting nutrients, the specific growth rate of a species is maximized. _Learn more about the differences in bioreactor strategies [here](https://pioreactor.com/blogs/pioreactor/the-many-different-environments-of-bioreactors-chemostat-turbidostat-stressostat-and-more)!_
+Your Pioreactor can be transformed into a [turbidostat](/user-guide/dosing-automations#turbidostat), where pumps are used to replenish media around a target OD, creating a continuous culture. Due to the abundance of resources and lack of rate-limiting nutrients, the specific growth rate of a species is maximized. _Learn more about the differences in bioreactor strategies [here](https://pioreactor.com/blogs/pioreactor/the-many-different-environments-of-bioreactors-chemostat-turbidostat-stressostat-and-more)!_
 
 This setup is a powerful tool that tests the limits of population growth. Students can investigate the specific maximum growth rate of a species and evaluate what innate biological processes are limiting growth. 
 
diff --git a/user-guide/01-getting-started/01-assembly_guides/00_pioreactor_40ml_v1.5/02-40ml-v15-rpi-hat-assembly.md b/user-guide/01-getting-started/01-assembly_guides/00_pioreactor_40ml_v1.5/02-40ml-v15-rpi-hat-assembly.md
@@ -50,7 +50,7 @@ Raspberry Pi types can be identified by the width of the Pi, in comparison to th
 -----
 
 
-<h2 id="raspberry-pi-a-or-b-instructions">Raspberry Pi A or B instructions</h2>
+## Raspberry Pi A or B instructions {#raspberry-pi-a-or-b-instructions}
 <AssemblyInstructionBlock title="Step 2: Assemble the bottom faceplate" images={["user-guide/hardware-assembly/upgrade-version/4B-10mm-screws.png","user-guide/hardware-assembly/upgrade-version/4B-hexnuts.png","user-guide/hardware-assembly/upgrade-version/4B-gpios.png"]}>
 
 
@@ -84,7 +84,7 @@ By screwing down the standoffs, they'll help compress the HAT onto the RPi, too.
 </AssemblyInstructionBlock>
 
 -----
-<h2 id="raspberry-pi-zero-zero-2-instructions">Raspberry Pi Zero / Zero 2 instructions</h2>
+## Raspberry Pi Zero / Zero 2 instructions {#raspberry-pi-zero-zero-2-instructions}
 
 <AssemblyInstructionBlock title="Step 2: Assemble the bottom faceplate" images={["user-guide/hardware-assembly/upgrade-version/zero-10mm-screws.png","user-guide/hardware-assembly/upgrade-version/zero-hexnuts.png","user-guide/hardware-assembly/upgrade-version/zero-level-check.png","user-guide/hardware-assembly/upgrade-version/zero-gpios.png"]}>
 
diff --git a/user-guide/01-getting-started/01-assembly_guides/01_pioreactor_20ml_v1.5/02-20ml-v15-rpi-hat-assembly.md b/user-guide/01-getting-started/01-assembly_guides/01_pioreactor_20ml_v1.5/02-20ml-v15-rpi-hat-assembly.md
@@ -50,7 +50,7 @@ Raspberry Pi types can be identified by the width of the Pi, in comparison to th
 -----
 
 
-<h2 id="raspberry-pi-a-or-b-instructions">Raspberry Pi A or B instructions</h2>
+## Raspberry Pi A or B instructions {#raspberry-pi-a-or-b-instructions}
 <AssemblyInstructionBlock title="Step 2: Assemble the bottom faceplate" images={["user-guide/hardware-assembly/upgrade-version/4B-10mm-screws.png","user-guide/hardware-assembly/upgrade-version/4B-hexnuts.png","user-guide/hardware-assembly/upgrade-version/4B-gpios.png"]}>
 
 
@@ -84,7 +84,7 @@ By screwing down the standoffs, they'll help compress the HAT onto the RPi, too.
 </AssemblyInstructionBlock>
 
 -----
-<h2 id="raspberry-pi-zero-zero-2-instructions">Raspberry Pi Zero / Zero 2 instructions</h2>
+## Raspberry Pi Zero / Zero 2 instructions {#raspberry-pi-zero-zero-2-instructions}
 
 <AssemblyInstructionBlock title="Step 2: Assemble the bottom faceplate" images={["user-guide/hardware-assembly/upgrade-version/zero-10mm-screws.png","user-guide/hardware-assembly/upgrade-version/zero-hexnuts.png","user-guide/hardware-assembly/upgrade-version/zero-level-check.png","user-guide/hardware-assembly/upgrade-version/zero-gpios.png"]}>
 
diff --git a/user-guide/01-getting-started/01-assembly_guides/90_pioreactor_40ml/02-40ml-rpi-hat-assembly.md b/user-guide/01-getting-started/01-assembly_guides/90_pioreactor_40ml/02-40ml-rpi-hat-assembly.md
@@ -45,7 +45,7 @@ Raspberry Pi types can be identified by the width of the Pi, in comparison to th
 -----
 
 
-<h2 id="raspberry-pi-a-or-b-instructions">Raspberry Pi A or B instructions</h2>
+## Raspberry Pi A or B instructions {#raspberry-pi-a-or-b-instructions}
 <AssemblyInstructionBlock title="Step 2: Assemble the bottom faceplate" images={["user-guide/hardware-assembly/upgrade-version/4B-10mm-screws.png","user-guide/hardware-assembly/upgrade-version/4B-hexnuts.png","user-guide/hardware-assembly/upgrade-version/4B-gpios.png"]}>
 
 
@@ -79,7 +79,7 @@ By screwing down the standoffs, they'll help compress the HAT onto the RPi, too.
 </AssemblyInstructionBlock>
 
 -----
-<h2 id="raspberry-pi-zero-zero-2-instructions">Raspberry Pi Zero / Zero 2 instructions</h2>
+## Raspberry Pi Zero / Zero 2 instructions {#raspberry-pi-zero-zero-2-instructions}
 
 <AssemblyInstructionBlock title="Step 2: Assemble the bottom faceplate" images={["user-guide/hardware-assembly/upgrade-version/zero-10mm-screws.png","user-guide/hardware-assembly/upgrade-version/zero-hexnuts.png","user-guide/hardware-assembly/upgrade-version/zero-level-check.png","user-guide/hardware-assembly/upgrade-version/zero-gpios.png"]}>
 
diff --git a/user-guide/01-getting-started/01-assembly_guides/91_pioreactor_20ml_v1.1/02-v11-rpi-hat-assembly.md b/user-guide/01-getting-started/01-assembly_guides/91_pioreactor_20ml_v1.1/02-v11-rpi-hat-assembly.md
@@ -45,7 +45,7 @@ Raspberry Pi types can be identified by the width of the Pi, in comparison to th
 -----
 
 
-<h2 id="raspberry-pi-a-or-b-instructions">Raspberry Pi A or B instructions</h2>
+## Raspberry Pi A or B instructions {#raspberry-pi-a-or-b-instructions}
 <AssemblyInstructionBlock title="Step 2: Assemble the bottom faceplate" images={["user-guide/hardware-assembly/upgrade-version/4B-10mm-screws.png","user-guide/hardware-assembly/upgrade-version/4B-hexnuts.png","user-guide/hardware-assembly/upgrade-version/4B-gpios.png"]}>
 
 
@@ -79,7 +79,7 @@ By screwing down the standoffs, they'll help compress the HAT onto the RPi, too.
 </AssemblyInstructionBlock>
 
 -----
-<h2 id="raspberry-pi-zero-zero-2-instructions">Raspberry Pi Zero / Zero 2 instructions</h2>
+## Raspberry Pi Zero / Zero 2 instructions {#raspberry-pi-zero-zero-2-instructions}
 
 <AssemblyInstructionBlock title="Step 2: Assemble the bottom faceplate" images={["user-guide/hardware-assembly/upgrade-version/zero-10mm-screws.png","user-guide/hardware-assembly/upgrade-version/zero-hexnuts.png","user-guide/hardware-assembly/upgrade-version/zero-level-check.png","user-guide/hardware-assembly/upgrade-version/zero-gpios.png"]}>
 
diff --git a/user-guide/01-getting-started/01-assembly_guides/99_pioreactor_20ml_v1.0/02-rpi-hat-assembly.md b/user-guide/01-getting-started/01-assembly_guides/99_pioreactor_20ml_v1.0/02-rpi-hat-assembly.md
@@ -40,7 +40,7 @@ Raspberry Pi types can be identified by the width of the Pi, in comparison to th
 
 -----
 
-<h2 id="raspberry-pi-a-or-b-instructions">Raspberry Pi A or B instructions</h2>
+## Raspberry Pi A or B instructions {#raspberry-pi-a-or-b-instructions}
 <AssemblyInstructionBlock title="Step 2: Assemble the bottom faceplate (Raspberry Pi A or B)" images={["user-guide/hardware-assembly/bottom_faceplate.jpg","user-guide/hardware-assembly/bot_faceplate_screwed.jpg","user-guide/hardware-assembly/rpi_no_standoffs.jpg"]}>
 
 
@@ -77,7 +77,7 @@ By screwing down the standoffs, they'll help compress the HAT onto the RPi, too.
 
 
 
-<h2 id="raspberry-pi-zero-zero-2-instructions">Raspberry Pi Zero / Zero 2 instructions</h2>
+## Raspberry Pi Zero / Zero 2 instructions {#raspberry-pi-zero-zero-2-instructions}
 <AssemblyInstructionBlock title="Step 4: Assemble the bottom faceplate (Raspberry Pi Zero / Zero 2)" images={["user-guide/hardware-assembly/bottom_faceplate.jpg","user-guide/hardware-assembly/hex_one_side.jpg","user-guide/hardware-assembly/rpi_zero.jpg"]}>
 
 :::tip
diff --git a/user-guide/01-getting-started/02-software-set-up.mdx b/user-guide/01-getting-started/02-software-set-up.mdx
@@ -15,9 +15,9 @@ You can expect the setup process to take 10-15 minutes. If you encounter any pro
 
 Before you get started, you'll need to have the following:
 
-1.  A Raspberry Pi (our list of recommended Raspberry Pis is [here](/user-guide/common-questions#what-raspberry-pi-hardware-can-i-use-i-see-raspberry-pi-1-2-3-4-a-b--zero---its-confusing))
+1.  A Raspberry Pi (our list of recommended Raspberry Pis is [here](/user-guide/common-questions#what-raspberry-pi-hardware-can-i-use-i-see-raspberry-pi-1-2-3-4-5-a-b--zero---its-confusing))
 2.  A blank microSD card (our recommended microSD cards is [here](/user-guide/common-questions#what-microsd-cards-do-you-recommend))
-3.  A suitable power supply for the Raspberry Pi (our recommended power supply units are [here](/user-guide/common-questions#what-power-supply-unit-do-i-need)). You don't need to plug power in yet.
+3.  A suitable power supply for the Raspberry Pi (our recommended power supply units are [here](/user-guide/common-questions#what-power-supply-unit-psu-do-i-need)). You don't need to plug power in yet.
 4.  A computer with internet access and ability to read & write to a microSD card
 
 ### Setting up your Raspberry Pi's SD Card
@@ -81,7 +81,7 @@ We'll start with your blank microSD card.
     Waited, but didn't see a blue LED blink, or maybe you missed it? Try pressing on the onboard button, near the side labelled "PWM", and pictured above. If this lights up the blue LED, you're good to move on. Still not working? Try power-cycling the Raspberry Pi, or email us at hello@pioreactor.com.
     :::
 
-12. After observing the blue LED flashing, navigate to [http://pioreactor.local](http://pioreactor.local) in a web browser to visit the web interface. If you are using local-access-point, looking for a `pioreactor` wifi network and then visit the link. (Not able to load http://pioreactor.local? Read [Common Questions](#pioreactorlocal-in-a-web-browser-is-not-showing-up) below).
+12. After observing the blue LED flashing, navigate to [http://pioreactor.local](http://pioreactor.local) in a web browser to visit the web interface. If you are using local-access-point, looking for a `pioreactor` wifi network and then visit the link. (Not able to load http://pioreactor.local? Read [Common Questions](#httppioreactorlocal-in-a-web-browser-is-not-showing-up) below).
 
 13. When the UI loads for the first time you'll be prompted by the **Update Pioreactor model** dialog. Select the correct model and hardware version for each Pioreactor listed, then click **Save** to continue.
 
@@ -187,10 +187,10 @@ Easiest solution is to start over. You can edit the name in the RPi Imager, and
 *   Try appending a backslash as well: `http://pioreactor.local/`.
 *   The UI is hosted on **http**, not **https**. Check if you are accessing `http` `://pioreactor.local`, and _not_ `https` `://pioreactor.local`.
 *   Try accessing using the url `http://<the name of your leader Pioreactor aka hostname>.local`.
-*   If you know your Raspberry Pi's IP, try `http://<IP address of your Raspberry Pi>`. Here's [information to determine the IP address](/user-guide/common-questions#how-can-i-determine-the-pioreactors-ip-address).
+*   If you know your Raspberry Pi's IP, try `http://<IP address of your Raspberry Pi>`. Here's [information to determine the IP address](/user-guide/common-questions#how-can-i-determine-the-pioreactors-ip-address-or-the-mac-address).
 *   When pressing the button on the HAT, does the blue LED show up? If not, installation may have failed. Try installing the image again, and double check the settings.
 *   Try power-cycling the Raspberry Pi (unplug and plug back in).
-*   In your Raspberry Pi Imager settings, confirm that you clicked "Set username and password", and used the username `pioreactor`. If not, try [reinstalling the image](/user-guide/software-set-up#setting-up-your-raspberry-pi).
+*   In your Raspberry Pi Imager settings, confirm that you clicked "Set username and password", and used the username `pioreactor`. If not, try [reinstalling the image](/user-guide/software-set-up#setting-up-your-raspberry-pis-sd-card).
 *   Are you on an older Windows machine? You may need to install a DNS [service](https://learn.adafruit.com/bonjour-zeroconf-networking-for-windows-and-linux/overview#microsoft-windows-914263-8), but also see workarounds [here](https://github.com/OutsourcedGuru/octoprint-name-resolution-hacks).
 
 
diff --git a/user-guide/30-Advanced/02-networking/06-local-access-point.md b/user-guide/30-Advanced/02-networking/06-local-access-point.md
@@ -28,11 +28,11 @@ The built-in local access point is meant for small clusters of Pioreactors, and
 The Pioreactor has the necessary software and hardware to create the local access point. To start the access point:
 
  - If starting with a new Pioreactor, during software set up:
-    1. Leave the "Configure wireless LAN" unchecked. Continue with the instructions at [Setting up your Raspberry Pi](/user-guide/software-set-up#setting-up-your-raspberry-pi).
+    1. Leave the "Configure wireless LAN" unchecked. Continue with the instructions at [Setting up your Raspberry Pi](/user-guide/software-set-up#setting-up-your-raspberry-pis-sd-card).
     2. After the SD card has been written to, remove the SD card from your computer, and immediately insert it back in. A `boot` (or `bootfs`) device should be present now that is your SD card. If asked to reformat the SD card, select NO.
     3. <ButtonDownloadLocalAccessPointFile/>
     3. Drag/move the downloaded `local_access_point` file to the SD card directory.
-    4. Eject the SD card safely, and continue with instructions at [Setting up your Raspberry Pi](/user-guide/software-set-up#setting-up-your-raspberry-pi).
+    4. Eject the SD card safely, and continue with instructions at [Setting up your Raspberry Pi](/user-guide/software-set-up#setting-up-your-raspberry-pis-sd-card).
  - If starting from an existing Pioreactor:
     1. with the power off remove the SD card from the Pioreactor and insert it into a computer.
     2. <ButtonDownloadLocalAccessPointFile/>
@@ -119,4 +119,4 @@ Try `http://<your_leaders_hostname>.local`. Still not working? Try `http://10.42
     ```
     sudo nmcli connection modify PioreactorAP ifname wlan1
     ```
-  - Another possible option is purely software based: There is a possibility to add more, see [issue here](https://github.com/Pioreactor/pioreactor/issues/442).
+  - Another possible option is purely software based: There is a possibility to add more, see [issue here](https://github.com/Pioreactor/pioreactor/issues/442).
diff --git a/user-guide/50-Troubleshooting/Stirring troubleshooting.md b/user-guide/50-Troubleshooting/Stirring troubleshooting.md
@@ -52,14 +52,14 @@ Detach the top faceplate. Under the faceplate, slightly unscrew each of the four
 ### Stir bar goes out of balance during OD dodging (RPM changes)
 
 If the stir bar stops, vibrates, or starts orbiting the vial when OD dodging changes the target RPM:
-1. Make sure a stirring calibration is active. Re-run it if you recently updated software or changed power/hardware. See [stirring calibration](/user-guide/hardware-calibrations#stirring-calibration-optional).
+1. Make sure a stirring calibration is active. Re-run it if you recently updated software or changed power/hardware. See [stirring calibration](/user-guide/hardware-calibrations#stirring-calibrations).
 2. Check that the vial is fully seated on the heating pad. A small gap (for example, from an o-ring or debris) can make the bar lose sync during RPM transitions.
 
 ### Stirring is not able to keep a steady RPM
 
 1. Consider decreasing the value of `Kp` in the section `stirring.pid` in the config.ini by 50%.
 2. Are you trying to target a very low RPM? The lower limit of RPM is around 125. Target RPMs below 125 have a tendency to stall.
-3. Try performing a [stirring calibration](/user-guide/hardware-calibrations#stirring-calibration-optional).
+3. Try performing a [stirring calibration](/user-guide/hardware-calibrations#stirring-calibrations).
 
 
 ### My stir bar keeps skipping. How can I reduce that?
diff --git a/user-guide/50-Troubleshooting/UI troubleshooting.md b/user-guide/50-Troubleshooting/UI troubleshooting.md
diff --git a/user-guide/99-common-questions.mdx b/user-guide/99-common-questions.mdx
