markdown source builds

Auto-generated via {sandpaper}
Source  : fc804ca
Branch  : main
Author  : The Carpentries Apprentice (beta) <[email protected]>
Time    : 2023-09-13 19:48:43 +0000
Message : [actions] update sandpaper workflow to version 0.13.0 (datacarpentry#366)

Co-authored-by: zkamvar <[email protected]>

03-sql-joins.md

@@ -158,7 +158,14 @@ In fact the `JOIN` keyword is simply shorthand for `INNER JOIN` and the two
 terms can be used interchangeably as they will produce the same result.
 
 We can also tell the computer that we wish to keep all the records in the first
-table by using a `LEFT OUTER JOIN` clause, or `LEFT JOIN` for short.
+table by using a `LEFT OUTER JOIN` clause, or `LEFT JOIN` for short. The difference
+between the two JOINs can be visualized like so:
+
+![
+Diagrams representing INNER JOIN and LEFT JOIN in SQLite
+](fig/sql-joins.png){
+alt='Diagrams representing INNER JOIN and LEFT JOIN each include two overlapping circles labeled A (left) and B (right). For INNER JOIN, the intersection of the two circles is filled in. The associated query is SELECT * FROM A JOIN B ON A.Key = B.Key. For LEFT JOIN, circle A, including its intersection with circle B, is filled in. The associated query is SELECT * FROM A LEFT JOIN B ON A.Key = B.Key.'
+}
 
 :::::::::::::::::::::::::::::::::::::::  challenge
 

index.md

@@ -21,17 +21,14 @@ Data Carpentry's teaching is hands-on, so participants are encouraged to use
 their own computers to insure the proper setup of tools for an efficient
 workflow. <br>**These lessons assume no prior knowledge of the skills or tools.**
 
-To get started, follow the directions in the "[Setup](learners/setup.md)" tab to
-download data to your computer and follow any installation instructions.
-
 #### Prerequisites
 
 This lesson requires:
 
 - Working copy of **DB Browser for SQLite for SQL**
 - A dataset
 
-Follow the directions in the **Setup** tab to download both the DB Browser for SQLite and the data to your computer and follow any installation instructions.
+Follow the directions in the **[Setup](learners/setup.md)** section to download both the DB Browser for SQLite and the data to your computer and follow any installation instructions.
 
 Please make sure to install everything *before* working through this lesson.
 

md5sum.txt

@@ -4,13 +4,13 @@
 "LICENSE.md" "b24ebbb41b14ca25cf6b8216dda83e5f" "site/built/LICENSE.md" "2023-10-12"
 "NEWS.md" "84aa522251c8b0043f12e83af45cc3d8" "site/built/NEWS.md" "2023-10-12"
 "config.yaml" "0928fbefeca4f51e54ccc3687a9565e9" "site/built/config.yaml" "2023-10-12"
-"index.md" "a6ad4a1e5ecbac4adca8986126fe5770" "site/built/index.md" "2023-10-12"
+"index.md" "cfdee7444b27a96171c25e1d4915e1e9" "site/built/index.md" "2023-10-12"
 "episodes/00-sql-introduction.md" "702a6c1b841bc4729bb2d8e0b358532e" "site/built/00-sql-introduction.md" "2023-10-12"
 "episodes/01-sql-basic-queries.md" "31fc6d3e21d679cab6a002bffe7c182d" "site/built/01-sql-basic-queries.md" "2023-10-12"
 "episodes/02-sql-aggregation.md" "07784e3014a42660059c18e6ba71f26d" "site/built/02-sql-aggregation.md" "2023-10-12"
-"episodes/03-sql-joins.md" "9cf92d24583f0ea2395044e6b9092155" "site/built/03-sql-joins.md" "2023-10-12"
+"episodes/03-sql-joins.md" "4c87f9451d13eaa88c1b38fe29c7a7f3" "site/built/03-sql-joins.md" "2023-10-12"
 "instructors/instructor-notes.md" "105728ef72c768e968ca9d11c2a14109" "site/built/instructor-notes.md" "2023-10-12"
 "learners/discuss.md" "c5994f9f17e9da0d08a530600084ba55" "site/built/discuss.md" "2023-10-12"
-"learners/reference.md" "bd2a5ec583a60be99fcee0afcf73dac1" "site/built/reference.md" "2023-10-12"
-"learners/setup.md" "1251f53cb7d4ffbef97833af269b7e35" "site/built/setup.md" "2023-10-12"
+"learners/reference.md" "a9e2e8b2be027afbeb360f1bbd966da2" "site/built/reference.md" "2023-10-12"
+"learners/setup.md" "ba0ada65a673ca1d95ed722b0711fa87" "site/built/setup.md" "2023-10-12"
 "profiles/learner-profiles.md" "60b93493cf1da06dfd63255d73854461" "site/built/learner-profiles.md" "2023-10-12"

reference.md

@@ -1,15 +1,105 @@
 ---
-title: 'FIXME'
+title: Reference
 ---
 
 ## Glossary
 
-## Reference
+*The definitions below are modified from the [Carpentries
+Glosario](https://glosario.carpentries.org/) (CC-BY-4.0)*
+
+[[**aggreation**]{#aggreation}](https://glosario.carpentries.org/en/#aggreation)
+:   To combine many values into one, e.g., by summing a set of numbers.
+
+[[**field**]{#field}](https://glosario.carpentries.org/en/#field)
+:   A component of a [record](#record) containing a single value. Every
+    record in a database [table](#table) has the same fields.
+
+[[**filter**]{#filter}](https://glosario.carpentries.org/en/#filter)
+:   To choose a set of [records](#record) (i.e., rows of a table) based
+    on the values they contain.
+
+[[**full join**]{#full-join}](https://glosario.carpentries.org/en/#full_join)
+:   A [join](#join) that returns all rows and all columns from two
+    tables A and B. Where the [keys](#key) of A and B match, values are
+    combined; where they do not, missing values from either table are
+    filled with [null](#null), NA, or some other [missing
+    value](#missing-value) signifier.
+
+[[**group**]{#group}](https://glosario.carpentries.org/en/#group)
+:   To divide data into subsets according to a set of criteria while
+    leaving records in a single structure.
+
+[[**inner join**]{#inner-join}](https://glosario.carpentries.org/en/#inner_join)
+:   A [join](#join) that returns the combination of rows from two
+    tables, A and B, whose [keys](#key) exist in both tables.
+
+[[**join**]{#join}](https://glosario.carpentries.org/en/#join)
+:   One of several operations that combine values from two
+    [tables](#table).
+
+[[**key**]{#key}](https://glosario.carpentries.org/en/#key)
+:   A [field](#field) or combination of fields whose value(s)
+    uniquely identify a [record](#record) within a [table](#table) or
+    dataset. Keys are often used to select specific records and in
+    [joins](#join).
+
+[[**left join**]{#left-join}](https://glosario.carpentries.org/en/#left_join)
+:   A [join](#join) that combines data from two tables, A and B, where
+    [keys](#key) in table A match keys in table B, [fields](#field) are
+    concatenated. Where a key in table A does *not* match a key in
+    table B, columns from table B are filled with [null](#null), NA, or
+    some other [missing value](#missing-value). Keys from table B that
+    do not match keys from table A are excluded for the result.
+
+[[**missing value**]{#missing-value}](https://glosario.carpentries.org/en/#missing_value)
+:   A special value such as [null](#null) or NA used to indicate the
+    absence of data. Missing values can signal that data was not
+    collected or that the data did not exist in the first place (e.g.,
+    the middle name of someone who does not have one).
+
+[[**null**]{#null}](https://glosario.carpentries.org/en/#null)
+:   A special value used to represent a missing object.
+
+[[**record**]{#record}](https://glosario.carpentries.org/en/#record)
+:   A group of related values that are stored together. A record may be
+    represented as a tuple or as a row in a [table](#table); in the
+    latter case, every record in the table has the same
+    [fields](#field).
+
+[[**relational_database**]{#relational-database}](https://glosario.carpentries.org/en/#relational_database)
+:   A database that organizes information into [tables](#table), each of
+    which has a fixed set of named [fields](#field) (shown as columns)
+    and a variable number of [records](#record) (shown as rows).
+
+[[**right join**]{#right-join}](https://glosario.carpentries.org/en/#right_join)
+:   A [join](#join) that combines data from two tables, A and B. Where
+    [keys](#key) in table A match keys in table B, [fields](#field) are
+    concatenated. Where a key in table B does \*not\* match a key in
+    table A, columns from table A are filled with [null](#null), NA, or
+    some other [missing value](#missing-value) signifier. Keys from
+    table A that do not exist in table B are dropped.
+
+[[**select**]{#select}](https://glosario.carpentries.org/en/#select)
+:   To choose entire columns or rows from a table by name or location.
+
+[[**SQL**]{#SQL}](https://glosario.carpentries.org/en/#sql)
+:   The language used for writing queries for a [relational
+    database](#relational-database). The term is an acronym for
+    Structured Query Language.
+
+[[**table**]{#table}](https://glosario.carpentries.org/en/#table)
+:   A set of [records](#record) in a [relational
+    database](#relational-database) or observations in a data frame.
+    Tables are usually displayed as rows (each of which represents one
+    record or observation) and columns (each of which represents a
+    [field](#field) or variable.)
+
+## Commands
 
 See [this cheat sheet](files/sql-cheat-sheet.md) for an list of the commands
 covered in this lesson.
 
-### Keywords Description Summary
+### Keywords
 
 <table>
     <thead>
@@ -24,12 +114,12 @@ covered in this lesson.
         <tr>
             <td rowspan=3> SELECT </td>
             <td rowspan = 3> Select data from database or table </td>
-            <td> SELECT *</td>
-            <td> Selects the entire dataset</td>
+            <td>SELECT *</td>
+            <td>Selects the entire dataset</td>
         </tr>
         <tr>
             <td>SELECT column1</td>
-            <td> Selects a particular column</td>
+            <td>Selects a particular column</td>
         </tr>
         <tr>
             <td>SELECT 1 + 2</td>
@@ -79,7 +169,7 @@ covered in this lesson.
         </tr>
         <tr>
             <td>JOIN</td>
-            <td> Joins tables</td>
+            <td>Joins tables</td>
             <td>SELECT * <br> FROM surveys <br> JOIN species <br> ON surveys.species_id = species.species_id</td>
             <td>Query will display all the columns from both tables where the condition is met</td>
         </tr>

setup.md

@@ -2,9 +2,11 @@
 title: Setup
 ---
 
+## Setup
+
 ::::::::::::::::::::::::::::::::::::::::::  prereq
 
-## Data
+### Data
 
 This lesson uses specific data files from the [Portal Project Teaching Database](https://figshare.com/articles/Portal_Project_Teaching_Database/1314459). To
 get the data, go to the [data location on figshare](https://figshare.com/articles/Portal_Project_Teaching_Database/1314459) and click on the **Download all** button to download the zip file.
@@ -21,7 +23,7 @@ See the
 
 ::::::::::::::::::::::::::::::::::::::::::  prereq
 
-## Software
+### Software
 
 Download **DB Browser for SQLite** for your operating system
 from [https://sqlitebrowser.org/dl/](https://sqlitebrowser.org/dl/).
@@ -38,11 +40,11 @@ Launch **DB Browser for SQLite** to confirm that the installation was successful
 
 ::::::::::::::::::::::::::::::::::::::::::  prereq
 
-## Am I ready?
+### Am I ready?
 
 The [first lesson episode](episodes/00-sql-introduction.md) has instructions
-on loading the data in DB Browser. If you can follow the instructions under "Relational
-Databases" or "Import", everything should have downloaded and installed correctly.
+on loading the data in DB Browser. To test your setup, you can follow the instructions for importing your data into DB Browser under the sections [Relational
+Databases](../episodes/00-sql-introduction.md#relational-databases) or [Import](../episodes/00-sql-introduction.md#import).
 
 ::::::::::::::::::::::::::::::::::::::::::::::::::