docs

developer-guide/07-Plugins/03-plugin-as-python-package.md

@@ -231,6 +231,7 @@ You also need to tell Pioreactor software how to populate this table from your s
 from pioreactor.background_jobs.leader.mqtt_to_db_streaming import produce_metadata
 from pioreactor.background_jobs.leader.mqtt_to_db_streaming import register_source_to_sink
 from pioreactor.background_jobs.leader.mqtt_to_db_streaming import TopicToParserToTable
+from pioreactor.utils import timing
 
 ...
 
@@ -343,13 +344,13 @@ A plugin can be installed through the command line on a leader using `pio`:
 
 
 ```
-pio install-plugin <DISTRIBUTION-NAME OR PLUGIN_NAME>
+pio plugin install <DISTRIBUTION-NAME OR PLUGIN_NAME>
 ```
 
-To install a given plugin on the leader and all workers connected to the leader in a cluster, `pios install-plugin` can be used. 
+To install a given plugin on the leader and all workers connected to the leader in a cluster, `pios plugins install` can be used.
 
 ```
-pios install-plugin <DISTRIBUTION-NAME OR PLUGIN_NAME>
+pios plugin install <DISTRIBUTION-NAME OR PLUGIN_NAME>
 ```
 
 ## Sharing your plugin with the community

developer-guide/09-Storage and the filesystem/01-data-stores/02-sqlite.md

@@ -33,6 +33,7 @@ The Pioreactor job `mqtt_to_db_streaming` handles how to get data into the sqlit
 from pioreactor.background_jobs.leader.mqtt_to_db_streaming import produce_metadata
 from pioreactor.background_jobs.leader.mqtt_to_db_streaming import register_source_to_sink
 from pioreactor.background_jobs.leader.mqtt_to_db_streaming import TopicToParserToTable
+from pioreactor.utils import timing
 
 ...
 

developer-guide/20-User interface/01-introduction.md

@@ -8,9 +8,11 @@ The web UI is hosted on the leader Pioreactor. Here are the details:
 
 ### Web server
 
-The web server we use is lighttp, and hosted from `/var/www/pioreactorui`. This folder is actually a git repo, and pulls from [pioreactorui](https://github.com/pioreactor/pioreactorui) GH repo. Systemd controls starting and restarting lighttp.
+The web server we use is lighttpd, and hosted from `/var/www/pioreactorui`. This folder is actually a git repo, and pulls from [pioreactorui](https://github.com/pioreactor/pioreactorui) GH repo. Systemd controls starting and restarting lighttpd.
 
-The lighttp conf file is located in `/etc/lighttpd/conf-enabled/50-pioreactorui.conf`. Error logs (though not helpful) are in `/var/log/lighttpd/error.log`.
+The lighttpd conf file is located in `/etc/lighttpd/conf-enabled/50-pioreactorui.conf`. Error logs (though not helpful) are in `/var/log/lighttpd/error.log`.
+
+The default protocol is `http` served on port `80`. To use `https` requires a certificate, and is out of scope for this project. If you'd change the protocol or the port, you'll need up tell the software too: look in the config.ini under `[ui]` section.
 
 
 ### Backend

user-guide/01-getting-started/01-assembly_guides/01_pioreactor_20ml_v1.1/03-v11-wetware-assembly.md

@@ -53,10 +53,10 @@ The vial holder of the v1.1 comes in two halves; a top vial holder and a bottom
 
 
 
-1. Insert the other end of the flex cable <Highlight color={colors.red}>below the O-ring and into the groove</Highlight>. Pull it through. 
+1. Insert the other end of the flex cable below the O-ring and into <Highlight color={colors.red}>the groove</Highlight>. Pull it through.
 2. <Highlight color={colors.magenta}>Apply pressure</Highlight> on the back of the heater PCB so that it lies flat on the O-ring. Maintain this pressure for the next steps.
-3.  **While maintaining pressure**, flip the holder and insert the two <Highlight color={colors.green}>M2.5-CS 5mm screws</Highlight> into the holes.
-4. **While maintaining pressure**, take turns screwing each in until both are secure, and the heater PCB is securely attached to the bottom vial holder.
+3.  **While maintaining pressure**, flip the holder and insert the two <Highlight color={colors.green}>M2.5-CS 5mm screws</Highlight> into the holes - **don't tighten fully yet**.
+4. **While maintaining pressure**, take turns screwing each in until both are reasonably tight, and the heater PCB is securely attached to the bottom vial holder.
 
 </AssemblyInstructionBlock>
 
@@ -65,7 +65,7 @@ The vial holder of the v1.1 comes in two halves; a top vial holder and a bottom
 <AssemblyInstructionBlock title="Step 5: Placing the heating pad" images={["user-guide/hardware-assembly/upgrade-version/sticky-side.png","user-guide/hardware-assembly/upgrade-version/remove-blue.png","user-guide/hardware-assembly/upgrade-version/remove-blue-2.png"]}>
 
 1.	Remove the _clear_ plastic from one side of the thermal pad. This exposes a sticky side on the thermal pad.
-2.	Place on the flat (aluminum) part of the heating PCB. Lightly apply downwards pressure to secure it.
+2.	Place on the flat (aluminum) part of the heating PCB. Lightly apply downwards pressure to secure it and remove any air bubbles trapped..
 3.	Remove the blue protective plastic on top of the thermal pad.
 
 

user-guide/01-getting-started/01-assembly_guides/01_pioreactor_20ml_v1.1/04-v11-faceplate-all-together.md

@@ -10,13 +10,13 @@ import * as colors from '@site/src/components/constants';
 
 <AssemblyInstructionBlock title="Step 1: Necessary parts" images={["user-guide/hardware-assembly/upgrade-version/stirring-parts.png"]}>
 
-*	<Highlight color={colors.blue}>Fan</Highlight>
-*	<Highlight color={colors.red}>Top faceplate</Highlight> (will have 4 x 30mm screws in it)
-*	<Highlight color={colors.orange}>One 5mm screw</Highlight>
+ * <Highlight color={colors.blue}>Fan</Highlight>
+ * <Highlight color={colors.red}>Top faceplate</Highlight> (will have 4 x 30mm screws in it)
+ * <Highlight color={colors.orange}>One 5mm screw</Highlight>
 
-:::info
-The fan and top faceplate come assembled - leave them together. If they are not assembled, attach the fan onto the faceplate with the cable oriented toward the side labelled "PWM".
-:::
+   :::info
+   The fan and top faceplate come assembled - leave them together. If they are not assembled, attach the fan onto the faceplate with the cable oriented toward the side labelled "PWM".
+   :::
 
 </AssemblyInstructionBlock>
 
@@ -27,11 +27,11 @@ The fan and top faceplate come assembled - leave them together. If they are not
 
 1. Push the <Highlight color={colors.red}>fan onto the top faceplate</Highlight>, orienting it such that the wire is pointing towards the button. 
 2. Place the vial holder on top of the <Highlight color={colors.green}>four ends of the 30mm screws</Highlight>. The screw ends should fit into four holes on the bottom of the vial holder. The flat flex cable should follow the <Highlight color={colors.orange}>arrow on the faceplate</Highlight>.
-3. Holding it together, finish screwing the <Highlight color={colors.blue}>30mm screws</Highlight> on the bottom of the faceplate. The screws will enter square nuts in the vial holder. Do not overtighten.
+3. Holding it together, finish screwing the <Highlight color={colors.blue}>M3 30mm screws</Highlight> on the bottom of the faceplate. The screws will enter square nuts in the vial holder. Do not overtighten.
 
-:::caution
-You should not feel resistance when tightening the screws into the square nuts. If you encounter resistance, unscrew and inspect the screw for any plastic debris. 
-:::
+   :::caution
+   You should not feel resistance when tightening the screws into the square nuts. If you encounter resistance, unscrew partially and inspect the end of the screw for any plastic debris.
+   :::
 
 4. The screw heads will be flush with the faceplate, and there should be no screw threads showing between the vial holder and the faceplate.
 
@@ -46,7 +46,7 @@ The top faceplate comes with a button extension to provide easier access to push
 
 1. Flip over the assembly.
 2. Insert the 10mm screw into the hole under the button extension.
-3. Place <Highlight color={colors.red}>one finger behind the extension</Highlight> and <Highlight color={colors.magenta}>apply torque with the other hand</Highlight> until the screw is secure in the hole. This may require some force. Once established, you can use a screwdriver to finish screwing it in under you feel sufficient resistance.
+3. Place <Highlight color={colors.red}>one finger behind the extension</Highlight> and <Highlight color={colors.magenta}>apply torque with the other hand</Highlight> until the screw is secure in the hole. This may require some force. Once established, you can use a screwdriver to finish screwing it in under you feel sufficient resistance. Don't over-tighten!
 
 </AssemblyInstructionBlock>
 

user-guide/01-getting-started/01-assembly_guides/01_pioreactor_20ml_v1.1/05-v11-optics-assembly.md

@@ -29,18 +29,18 @@ import * as colors from '@site/src/components/constants';
 1. Insert the bulb of the <Highlight color={colors.magenta}>IR cable</Highlight> into the pocket labeled <Highlight color={colors.magenta}>IR</Highlight>.
 2. _Slowly_ bend the bulb's leads 90 degrees, as seen.
 
-:::caution
-Avoid over-stressing the leads, or applying too much force too quickly. After bending once, it's ill-advised to bend them again.
-:::
+   :::caution
+   Avoid over-stressing the leads, or applying too much force too quickly. After bending once, it's    ill-advised to bend them again.
+   :::
 
 3. Insert the bulb of the <Highlight color={colors.red}>PD cable</Highlight> in channel 1 into the pocket labeled <Highlight color={colors.red}>REF</Highlight>.
 2. _Slowly_ bend the bulb's leads 90 degrees, as seen.
 5. Insert the bulb of the <Highlight color={colors.blue}>PD cable</Highlight> in channel 2 into the pocket labeled <Highlight color={colors.blue}>90°</Highlight>. 
 2. _Slowly_ bend the bulb's leads 90 degrees, as seen.
 
-:::tip
-Inspect each LED and PD to confirm that their leads are not touching each other.
-:::
+   :::tip
+   Inspect each LED and PD to confirm that their leads are not touching each other.
+   :::
 
 7. Secure all bulbs with LED caps. 
 8. Push all remaining LED caps onto each pocket.

user-guide/01-getting-started/01-assembly_guides/02_pioreactor_20ml_v1.0_to_v1.1/04-pioreactor-reassembly.md

@@ -17,9 +17,9 @@ import TabItem from '@theme/TabItem';
 2. Place the vial holder on top of the <Highlight color={colors.green}>ends of the M3 30mm screws</Highlight>. The screw ends should fit into four holes on the bottom of the vial holder. The flat flex cable should follow the <Highlight color={colors.orange}>arrow on the faceplate</Highlight>.
 3. Holding it together, finish screwing the <Highlight color={colors.blue}>M3 30mm screws</Highlight> on the bottom of the faceplate. The screws will enter square nuts in the vial holder. Do not overtighten.
 
-:::caution
-You should not feel resistance when tightening the screws into the square nuts. If you encounter resistance, unscrew and inspect the screw for any plastic debris. 
-:::
+   :::caution
+   You should not feel resistance when tightening the screws into the square nuts. If you encounter resistance, unscrew partially and inspect the end of the screw for any plastic debris.
+   :::
 
 4. The screw heads will be flush with the faceplate, and there should be no screw threads showing between the vial holder and the faceplate.
 
@@ -33,7 +33,7 @@ The top faceplate now comes with a button extension to provide easier access whe
 
 1. Flip over the assembly.
 2. Insert the 10mm screw into the hole under the button extension.
-3. Place <Highlight color={colors.red}>one finger behind the extension</Highlight> and <Highlight color={colors.magenta}>apply force and torque</Highlight> with the other hand until the screw is secure in the hole. Once established, a screwdriver can finish the job. Tighten until you feel resistance.
+3. Place <Highlight color={colors.red}>one finger behind the extension</Highlight> and <Highlight color={colors.magenta}>apply force and torque</Highlight> with the other hand until the screw is secure in the hole. Once established, a screwdriver can finish the job. Tighten until you feel resistance. Don't over-tighten!
 
 </AssemblyInstructionBlock>
 

user-guide/01-getting-started/01-assembly_guides/03_pioreactor_20ml_v1.0/04-faceplate-all-together.md

@@ -10,12 +10,12 @@ import * as colors from '@site/src/components/constants';
 
 <AssemblyInstructionBlock title="Step 1: Necessary parts" images={["user-guide/hardware-assembly/stirring_parts.jpg"]}>
 
-*	<Highlight color={colors.blue}>Fan</Highlight>
-*	<Highlight color={colors.red}>Top faceplate</Highlight> (will have 4 x 30mm screws in it)
+ * <Highlight color={colors.blue}>Fan</Highlight>
+ * <Highlight color={colors.red}>Top faceplate</Highlight> (will have 4 x 30mm screws in it)
 
-:::info
-These come assembled - leave them together. If they are not assembled, attach the fan onto the faceplate with the cable oriented toward the side labelled "PWM".
-:::
+   :::info
+   These come assembled - leave them together. If they are not assembled, attach the fan onto the    faceplate with the cable oriented toward the side labelled "PWM".
+   :::
 
 </AssemblyInstructionBlock>
 

user-guide/03-Extending your Pioreactor/30-Upgrade kits/12-temperature-expansion-kit.md

@@ -86,7 +86,7 @@ It may be a tight squeeze. To help screw it in if it's difficult:
 
 **2. If you installed the Kit on individual Pioreactors**
 
- - [SSH](/user-guide/accessing-raspberry-pi) into the individual Pioreactor, and type `pio install-plugin temperature-expansion-kit-plugin`
+ - [SSH](/user-guide/accessing-raspberry-pi) into the individual Pioreactor, and type `pio plugins install temperature-expansion-kit-plugin`
 
 
 **Important:** in either case,
@@ -118,7 +118,7 @@ local_ac_hz=60
  2. To get this .whl file onto a Pioreactor, use either `scp`, or FileZilla.
  3. Once the .whl file is on the Pioreactor, use
     ```
-    pio install-plugin temperature_expansion_kit_plugin --source <location of whl file>
+    pio plugin install temperature_expansion_kit_plugin --source <location of whl file>
 
     ```
 

user-guide/30-Advanced/01-cli.md

@@ -14,9 +14,9 @@ Interacting with the Pioreactor on the command line are through the `pio` tool.
 *   `pio run <job> <options>` will run the `<job>`. Each job may have specific command line arguments.
 *   `pio version` print the version of the PioreactorApp software.
 *   `pio update app` will update the software to the latest app version.
-*   `pio install-plugin <plugin name>` will install a plugin
-*   `pio uninstall-plugin <plugin name>` will uninstall a plugin
-*   `pio list-plugins` will list the currently installed plugins
+*   `pio plugins install <plugin name>` will install a plugin
+*   `pio plugins uninstall <plugin name>` will uninstall a plugin
+*   `pio plugins list` will list the currently installed plugins
 *   `pio blink` will blink the Pioreactor's onboard LED.
 *   `pio log -m <message>` will log a message
 *   `pio view-cache <cache>` will print out the contents of the specified cache.
@@ -51,7 +51,7 @@ The leader computer interacts with the worker computers using the `pios` command
 *   `pios rm <filepath>` will remove `filepath` on all the workers.
 
 :::tip
-In each of the above commands, specific workers can be invoked with `--units` (which can be used multiple times. Ex: `pios run stirring --units 1 --units 2`.
+In each of the above commands, specific workers can be invoked with `--units` (which can be used multiple times. Ex: `pios run stirring --units pio1 --units pio2`.
 :::
 
 :::tip

user-guide/99-common-questions.mdx

@@ -242,7 +242,7 @@ Depending on your access to the Pioreactor, there are a few ways:
 
 ##### To install a plugin
 
-On a computer that is connected to the internet, download the `.whl` file from the plugins webpage on PyPI. Then, connect that computer to your Pioreactor's local access point's network. To each Pioreactor you wish to install the plugin on, transfer the `.whl` file to the Pioreactor (using SFTP or FTP). Then, run `pio install-plugin <plugin-name> <path/to/local/.whl>`
+On a computer that is connected to the internet, download the `.whl` file from the plugins webpage on PyPI. Then, connect that computer to your Pioreactor's local access point's network. To each Pioreactor you wish to install the plugin on, transfer the `.whl` file to the Pioreactor (using SFTP or FTP). Then, run `pio plugins install <plugin-name> <path/to/local/.whl>`
 
 
 ##### To upgrade the Pioreactor software