Cherry pick from cbroz/main

docs/src/index.md

@@ -1,38 +1,38 @@
 # Spyglass
 
-**Spyglass** is a data analysis framework that facilitates the
-storage, analysis, and sharing of neuroscience data to support
-reproducible research. It is designed to be interoperable with the NWB
-format and integrates open-source tools into a coherent framework.
+**Spyglass** is a data analysis framework that facilitates the storage,
+analysis, and sharing of neuroscience data to support reproducible research. It
+is designed to be interoperable with the NWB format and integrates open-source
+tools into a coherent framework.
 
 ## Getting Started
 
 This site hosts both [installation instructions](./installation.md) and
-[tutorials](./notebooks/index.md) to help you get started with Spyglass.
-We recommend running the notebooks yourself. They can be downloaded from
-GitHub [here](https://github.com/LorenFrankLab/spyglass).
+[tutorials](./notebooks/index.md) to help you get started with Spyglass. We
+recommend running the notebooks yourself. They can be downloaded from GitHub
+[here](https://github.com/LorenFrankLab/spyglass).
 
 ## Diving Deeper
 
-The [API Reference](./api/index.md) provides a detailed description of all
-the tables and class functions in Spyglass via python docstrings. Potential
+The [API Reference](./api/index.md) provides a detailed description of all the
+tables and class functions in Spyglass via python docstrings. Potential
 contributors should also read the [Developer Guide](./contribute.md). Those
 interested in in hosting a Spyglass instance for their own data should read the
 [database management guide](./misc/database_management.md).
 
 We have a series of additional docs under the [misc](./misc/index.md) folder
-that may be helpful. Our [changelog](./CHANGELOG.md) highlights the changes
-that have been made to Spyglass over time and the [copyright](./copyright.md)
-page contains license information.
+that may be helpful. Our [changelog](./CHANGELOG.md) highlights the changes that
+have been made to Spyglass over time and the [copyright](./LICENSE.md) page
+contains license information.
 
 ## Citing Spyglass
 
-Kyu Hyun Lee, Eric Denovellis, Ryan Ly, Jeremy Magland, Jeff Soules,
-Alison Comrie, Jennifer Guidera, Rhino Nevers, Daniel Gramling, Philip
-Adenekan, Ji Hyun Bak, Emily Monroe, Andrew Tritt, Oliver Rübel, Thinh
-Nguyen, Dimitri Yatsenko, Joshua Chu, Caleb Kemere, Samuel Garcia,
-Alessio Buccino, Emily Aery Jones, Lisa Giocomo, and Loren Frank.
-'Spyglass: A Data Analysis Framework for Reproducible and Shareable
-Neuroscience Research.' (2022) Society for Neuroscience, San Diego, CA.
+Kyu Hyun Lee, Eric Denovellis, Ryan Ly, Jeremy Magland, Jeff Soules, Alison
+Comrie, Jennifer Guidera, Rhino Nevers, Daniel Gramling, Philip Adenekan, Ji
+Hyun Bak, Emily Monroe, Andrew Tritt, Oliver Rübel, Thinh Nguyen, Dimitri
+Yatsenko, Joshua Chu, Caleb Kemere, Samuel Garcia, Alessio Buccino, Emily Aery
+Jones, Lisa Giocomo, and Loren Frank. 'Spyglass: A Data Analysis Framework for
+Reproducible and Shareable Neuroscience Research.' (2022) Society for
+Neuroscience, San Diego, CA.
 
 <!-- TODO: Convert ccf file and insert here  -->

docs/src/misc/database_management.md

@@ -69,7 +69,147 @@ dj.set_password()
 
 ## Database Backups
 
-Coming soon...
+The following codeblockes are a series of files used to back up our database and
+migrate the contents to another server. Some conventions to note:
+
+- `.host`: files used in the host's context
+- `.container`: files used inside the database Docker container
+- `.env`: files used to set environment variables used by the scripts for
+  database name, backup name, and backup credentials
+
+This backup process uses a dedicated backup user, that an admin would need to
+criate with the relevant permissions.
+
+### mysql.env.host
+
+<details>
+<summary>MySQL host environment variables</summary>
+
+Values may be adjusted as needed for different building images.
+
+```bash
+ROOT_PATH=/usr/local/containers/mysql # path to this container's working area
+
+# variables for building image
+SRC=ubuntu
+VER=20.04
+DOCKERFILE=Dockerfile.base
+
+# variables for referencing image
+IMAGE=mysql8
+TAG=u20
+# variables for running the container
+CNAME=mysql-datajoint
+MACADDR=4e:b0:3d:42:e0:70
+RPORT=3306
+
+# variables for initializing/relaunching the container
+# - where the mysql data and backups will live - these values
+# are examples
+DB_PATH=/data/db
+DB_DATA=mysql
+DB_BACKUP=/data/mysql-backups
+
+# backup info
+BACK_USER=mysql-backup
+BACK_PW={password}
+BACK_DBNAME={database}
+# mysql root password - make sure to remove this AFTER the container
+# is initialized - and this file will be replicated inside the container
+# on initialization, so remove it from there: /opt/bin/mysql.env
+```
+
+</details>
+
+### backup-database.sh.host
+
+This script runs the mysql-backup container script (exec inside the container)
+that dumps the database contents for each database as well as the entire
+database. Use cron to set this to run on your desired schedule.
+
+<details>
+<summary>MySQL host docker exec</summary>
+
+```bash
+#!/bin/bash
+
+PRIOR_DIR=$(pwd)
+cd /usr/local/containers/mysql || exit
+. mysql.env
+cd "$(dirname ${ROOT_PATH})"
+#
+docker exec ${CNAME} /opt/bin/mysql-backup.csh
+#
+cd "$(dirname ${DB_BACKUP})"
+#
+cd ${PRIOR_DIR}
+```
+
+</details>
+
+### mysql-backup-xfer.csh.host
+
+This script transfers the backup to another server 'X' and is specific for us as
+it uses passwordless ssh keys to a local unprivileged user on X that has the
+mysql backup area on X as that user's home.
+
+<details>
+<summary>MySQL host transfer script</summary>
+
+```bash
+#!/bin/csh
+set td=`date +"%Y%m%d"`
+cd /data/mysql-backups
+scp -P {port} -i ~/mysql-backup -r ${database}-${td} mysql-backup@${X}:~/
+/bin/rm -r lmf-db-${td}
+```
+
+</details>
+
+### myenv.csh.container
+
+<details>
+<summary>Docker container environment variables</summary>
+
+```bash
+set db_backup=mysql-backups
+set back_user=mysql-backup
+set back_pw={password}
+set back_dbname={database}
+```
+
+</details>
+
+### mysql-backup.csh.container
+
+<details>
+<summary>Generate backups from within container</summary>
+
+```bash
+#!/bin/csh
+source /opt/bin/myenv.csh
+set td=`date +"%Y%m%d"`
+cd /${db_backup}
+mkdir ${back_dbname}-${td}
+
+set list=`echo "show databases;" | mysql --user=${back_user} --password=${back_pw}`
+set cnt=0
+
+foreach db ($list)
+  if ($cnt == 0) then
+    echo "dumping mysql databases on $td"
+  else
+    echo "dumping MySQL database : $db"
+    # Per-schema backups
+    mysqldump $db --max_allowed_packet=512M --user=${back_user} --password=${back_pw} > /${db_backup}/${back_dbname}-${td}/mysql.${db}.sql
+  endif
+@ cnt = $cnt + 1
+end
+# Full database backup
+mysqldump --all-databases --max_allowed_packet=512M --user=${back_user} --password=${back_pw} > /${db_backup}/${back_dbname}-${td}/mysql-all.sql
+```
+
+</details>
 
 ## File Cleanup
 

src/spyglass/position/v1/position_dlc_centroid.py

@@ -467,8 +467,7 @@ def fetch1_dataframe(self):
 
 
 def four_led_centroid(pos_df: pd.DataFrame, **params):
-    """
-    Determines the centroid of 4 LEDS on an implant LED ring.
+    """Determines the centroid of 4 LEDS on an implant LED ring.
     Assumed to be the Green LED, and 3 red LEDs called: redLED_C, redLED_L, redLED_R
     By default, uses (greenled + redLED_C) / 2 to calculate centroid
     If Green LED is NaN, but red center LED is not,