Finish case scenarios + new devcontainer extension

.devcontainer/devcontainer.json

@@ -9,7 +9,8 @@
             "extensions": [
                 "julialang.language-julia",
                 "tamasfe.even-better-toml",
-                "eamodio.gitlens"
+                "eamodio.gitlens",
+                "stkb.rewrap",
             ]
         }
     },

docs/make.jl

@@ -28,7 +28,7 @@ makedocs(
             ],
         ],
         # Showcase of Cool Examples
-        "What is BioJulia" => ["overview.md",
+        "What is BioJulia?" => ["overview.md",
         ]
     ]
 )

docs/src/comparisons/bioconductor.md

@@ -1,9 +1,13 @@
 # [Bioconductor (R)](@id bioconductor)
 
-- [Bioconductor](https://www.bioconductor.org/) represents an ecosystem of related genomics tools written in the R programming language
-- Tools written in other languages, such as C and Python, are also included with R wrappers available 
-- Launched over two decades ago, it now hosts over 2000 packages for bioinformatics and related fields
-- Packages cover a broard range of methods for the analysis and manipulation of genomic data
+* [Bioconductor](https://www.bioconductor.org/) represents an ecosystem of
+  related genomics tools written in the R programming language
+* Tools written in other languages, such as C and Python, are also included with
+  R wrappers available 
+* Launched over two decades ago, it now hosts over 2000 packages for
+  bioinformatics and related fields
+* Packages cover a broard range of methods for the analysis and manipulation of
+  genomic data
 
 **A few equivalent applications between BioJulia and Bioconductor:**
 
@@ -37,7 +41,15 @@
 | Single implementation available (JuliaLang)                            | Multiple implementations available (pqR, Renjin,...)                             |
 
 **To transition from R to Julia:**
-- See [Noteworthy differences from R](https://docs.julialang.org/en/v1/manual/noteworthy-differences/#Noteworthy-differences-from-R) in the Julia manual for a more in-depth comparison
-- Use [RCall.jl](https://github.com/JuliaInterop/RCall.jl.git) to seamlessly integrate R code into your Julia project
-- Use [JuliaCall](https://cran.r-project.org/web/packages/JuliaCall/readme/README.html) to seamlessly integrate Julia code into your R project
-- Check out the [Tidier.jl ecosystem](https://tidierorg.github.io/Tidier.jl/dev/) for packages similar to those commonly found in `tidyverse`
+* See [Noteworthy differences from
+  R](https://docs.julialang.org/en/v1/manual/noteworthy-differences/#Noteworthy-differences-from-R)
+  in the Julia manual for a more in-depth comparison
+* Use [RCall.jl](https://github.com/JuliaInterop/RCall.jl.git) to seamlessly
+  integrate R code into your Julia project
+* Use
+  [JuliaCall](https://cran.r-project.org/web/packages/JuliaCall/readme/README.html)
+  to seamlessly integrate Julia code into your R project
+* Check out the [Tidier.jl
+  ecosystem](https://tidierorg.github.io/Tidier.jl/dev/) for packages similar to
+  those commonly found in `tidyverse`
+

docs/src/comparisons/biojava.md

@@ -1,8 +1,10 @@
 # [BioJava (Java)](@id biojava)
 
-- [BioJava](https://biojava.org/index.html) is a biological data processing library written in the Java programming language
-- BioJava tooling is distributed via multiple classes within the same `org.biojava` package
-- Launched in 2002 with six major releases covering more than 11 Java releases
+* [BioJava](https://biojava.org/index.html) is a biological data processing
+  library written in the Java programming language
+* BioJava tooling is distributed via multiple classes within the same
+  `org.biojava` package
+* Launched in 2002 with six major releases covering more than 11 Java releases
 
 **A few equivalent applications between BioJulia and BioJava:**
 
@@ -37,6 +39,9 @@
 | Single implementation available (JuliaLang)                            | Multiple implementations available (OpenJDK, GraalVM,...)                                |
 
 **To transition from Java to Julia:**
-- Use [JavaCall.jl](https://juliainterop.github.io/JavaCall.jl/) to seamlessly integrate Java code into your Julia project
-- See [Running External Programs](https://docs.julialang.org/en/v1/manual/running-external-programs/) in the Julia manual for running Java scripts or other programs from Julia
+* Use [JavaCall.jl](https://juliainterop.github.io/JavaCall.jl/) to seamlessly
+  integrate Java code into your Julia project
+* See [Running External
+  Programs](https://docs.julialang.org/en/v1/manual/running-external-programs/)
+  in the Julia manual for running Java scripts or other programs from Julia
 

docs/src/comparisons/bioperl.md

@@ -1,8 +1,11 @@
 # [BioPerl (Perl5)](@id bioperl)
 
-- [BioPerl](https://bioperl.org/) represents an ecosystem of related molecular biology modules written in the Perl5 programming language
-- Supported by the Open Bioinformatics Foundation and includes additional utilities and interfaces for common bioinformatics applications
-- Launched in 2002 and has contributed to major scientific achievements including the Human Genome Project
+* [BioPerl](https://bioperl.org/) represents an ecosystem of related molecular
+  biology modules written in the Perl5 programming language
+* Supported by the Open Bioinformatics Foundation and includes additional
+  utilities and interfaces for common bioinformatics applications
+* Launched in 2002 and has contributed to major scientific achievements
+  including the Human Genome Project
 
 **A few equivalent application tools between BioJulia and BioPerl:**
 
@@ -35,6 +38,9 @@
 | Single language implementation (JuliaLang)                             | Family of related languages/implementations (Perl5, Perl6/Raku, ActivePerl,...) |
 
 **To transition from Perl5 to Julia:**
-- Read the [Julia manual](https://docs.julialang.org/) for an in-depth look at its internals and features
-- See [Running External Programs](https://docs.julialang.org/en/v1/manual/running-external-programs/) in the manual for running Perl scripts or other programs from Julia
+* Read the [Julia manual](https://docs.julialang.org/) for an in-depth look at
+  its internals and features
+* See [Running External
+  Programs](https://docs.julialang.org/en/v1/manual/running-external-programs/)
+  in the manual for running Perl scripts or other programs from Julia
 

docs/src/comparisons/biopython.md

@@ -1,9 +1,13 @@
 # [Biopython (Python3)](@id biopython)
 
-- [Biopython](https://biopython.org/) represents an ecosystem of related biology tools written in the Python3 programming language
-- Unlike with BioJulia, Biopython tools are installed together as modules into a single `biopython` package 
-- Launched over two decades ago with major releases covering the Python2/3 transition
-- Capabilities cover a number of molecular biology applications including sequence alignment, population genetics, and machine learning
+* [Biopython](https://biopython.org/) represents an ecosystem of related biology
+  tools written in the Python3 programming language
+* Unlike with BioJulia, Biopython tools are installed together as modules into a
+  single `biopython` package 
+* Launched over two decades ago with major releases covering the Python2/3
+  transition
+* Capabilities cover a number of molecular biology applications including
+  sequence alignment, population genetics, and machine learning
 
 **A few equivalent application tools between BioJulia and Biopython:**
 
@@ -40,7 +44,12 @@
 | Arrays are column-major (columns are contiguous in memory)             | (Numpy) arrays are row-major by default (rows are contiguous in memory)      |
 
 **To transition from Python3 to Julia:**
-- See [Noteworthy differences from Python](https://docs.julialang.org/en/v1/manual/noteworthy-differences/#Noteworthy-differences-from-Python) in the Julia manual for a more in-depth comparison
-- Use [PythonCall.jl](https://github.com/cjdoris/PythonCall.jl.git)/[CondaPkg.jl](https://github.com/JuliaPy/CondaPkg.jl.git) to seamlessly integrate Python3 code into your Julia project
-- Use [juliacall](https://pypi.org/project/juliacall/) to seamlessly integrate Julia code into your Python3 project
+* See [Noteworthy differences from
+  Python](https://docs.julialang.org/en/v1/manual/noteworthy-differences/#Noteworthy-differences-from-Python)
+  in the Julia manual for a more in-depth comparison
+* Use
+  [PythonCall.jl](https://github.com/cjdoris/PythonCall.jl.git)/[CondaPkg.jl](https://github.com/JuliaPy/CondaPkg.jl.git)
+  to seamlessly integrate Python3 code into your Julia project
+* Use [juliacall](https://pypi.org/project/juliacall/) to seamlessly integrate
+  Julia code into your Python3 project
 

docs/src/comparisons/bioruby.md

@@ -1,9 +1,12 @@
 # [BioRuby (Ruby)](@id bioruby)
 
-- [BioRuby](http://bioruby.org/) represents an ecosystem of related biology tools written in the Ruby programming language
-- Unlike with BioJulia, BioRuby tools are installed together as classes/modules into a single `bio` gem
-- Launched in 2000 with two major releases covering the Ruby1/2/3 transitions
-- Primarily composed of wrapper classes/modules for common bioinformatics, molecular biology applications 
+* [BioRuby](http://bioruby.org/) represents an ecosystem of related biology
+  tools written in the Ruby programming language
+* Unlike with BioJulia, BioRuby tools are installed together as classes/modules
+  into a single `bio` gem
+* Launched in 2000 with two major releases covering the Ruby1/2/3 transitions
+* Primarily composed of wrapper classes/modules for common bioinformatics,
+  molecular biology applications 
 
 **A few equivalent application tools between BioJulia and BioRuby:**
 
@@ -35,6 +38,9 @@
 | Single implementation available (JuliaLang)                            | Multiple implementations available (TruffleRuby, mruby,...)                    |
 
 **To transition from Ruby to Julia:**
-- Read the [Julia manual](https://docs.julialang.org/) for an in-depth look at its internals and features
-- See [Running External Programs](https://docs.julialang.org/en/v1/manual/running-external-programs/) in the manual for running Ruby scripts or other programs from Julia
+* Read the [Julia manual](https://docs.julialang.org/) for an in-depth look at
+  its internals and features
+* See [Running External
+  Programs](https://docs.julialang.org/en/v1/manual/running-external-programs/)
+  in the manual for running Ruby scripts or other programs from Julia
 

docs/src/comparisons/scikitbio.md

@@ -1,8 +1,11 @@
 # [scikit-bio (Python3)](@id scikitbio)
 
-- [scikit-bio](http://scikit-bio.org/) represents a Python3 library providing data structures, algorithms, and additional bioinformatics resources
-- Unlike with BioJulia, scikit-bio tools are installed together as modules into a single `skbio` package 
-- Launched in 2014 based on a BSD-relicensing of PyCogent and QIIME code and is currently in beta/maintenance mode
+* [scikit-bio](http://scikit-bio.org/) represents a Python3 library providing
+  data structures, algorithms, and additional bioinformatics resources
+* Unlike with BioJulia, scikit-bio tools are installed together as modules into
+  a single `skbio` package 
+* Launched in 2014 based on a BSD-relicensing of PyCogent and QIIME code and is
+  currently in beta/maintenance mode
 
 **A few equivalent application tools between BioJulia and scikit-bio:**
 
@@ -38,7 +41,12 @@
 | Arrays are column-major (columns are contiguous in memory)             | (Numpy) arrays are row-major by default (rows are contiguous in memory)      |
 
 **To transition from Python3 to Julia:**
-- See [Noteworthy differences from Python](https://docs.julialang.org/en/v1/manual/noteworthy-differences/#Noteworthy-differences-from-Python) in the Julia manual for a more in-depth comparison
-- Use [PythonCall.jl](https://github.com/cjdoris/PythonCall.jl.git)/[CondaPkg.jl](https://github.com/JuliaPy/CondaPkg.jl.git) to seamlessly integrate Python3 code into your Julia project
-- Use [juliacall](https://pypi.org/project/juliacall/) to seamlessly integrate Julia code into your Python3 project
+* See [Noteworthy differences from
+  Python](https://docs.julialang.org/en/v1/manual/noteworthy-differences/#Noteworthy-differences-from-Python)
+  in the Julia manual for a more in-depth comparison
+* Use
+  [PythonCall.jl](https://github.com/cjdoris/PythonCall.jl.git)/[CondaPkg.jl](https://github.com/JuliaPy/CondaPkg.jl.git)
+  to seamlessly integrate Python3 code into your Julia project
+* Use [juliacall](https://pypi.org/project/juliacall/) to seamlessly integrate
+  Julia code into your Python3 project
 

docs/src/getting_started/biojuliainstallation.md

@@ -2,21 +2,26 @@
 
 ## Standard installation
 
-As with any Julia package, you can easily install any BioJulia package with the help of the [official
-package manager](https://pkgdocs.julialang.org/v1/) included by default with every Julia installation.
-All you need to know is the name of the package of interest!
+As with any Julia package, you can easily install any BioJulia package with the
+help of the [official package manager](https://pkgdocs.julialang.org/v1/)
+included by default with every Julia installation. All you need to know is the
+name of the package of interest!
 
 There are two standard methods to install a package:
 
-!!! note
-    The Julia package manager, similarly to conda and others, organizes dependencies according to the "environment" 
-    they are in, meaning in which directory the packages are installed to. The default Julia session adds packages 
-    to a "global" environment, usually the .julia/environments/v1.x directory. When you are developing a package, 
-    you must activate its project-specific environment by calling `activate MyProjectName` (see [Package development](@ref pkg-devel) 
-    below) so that you can isolate your dependencies from the global environment and manage them independently. See 
-    [Working with Environment](https://pkgdocs.julialang.org/v1/environments/) for more details.
+!!! note 
+    The Julia package manager, similarly to conda and others, organizes
+    dependencies according to the "environment" they are in, meaning in which
+    directory the packages are installed to. The default Julia session adds
+    packages to a "global" environment, usually the .julia/environments/v1.x
+    directory. When you are developing a package, you must activate its
+    project-specific environment by calling `activate MyProjectName` (see
+    [Package development](@ref pkg-devel) below) so that you can isolate your
+    dependencies from the global environment and manage them independently. See
+    [Working with Environment](https://pkgdocs.julialang.org/v1/environments/)
+    for more details.
 
-- **The package manager (Pkg) module**
+* **The package manager (Pkg) module**
 
 ```julia
 julia> using Pkg
@@ -26,11 +31,12 @@ julia> Pkg.add("<name of package here>")
 julia> using <name of package here>
 ```
 
-!!! note
-    One excellent trick is that any Julia code with the `julia>` prompt included at the beginning of the
-    line can be copy/pasted as is into the REPL! See the [Julia REPL](@ref julia-repl) section for more.
+!!! note 
+    One excellent trick is that any Julia code with the `julia>` prompt
+    included at the beginning of the line can be copy/pasted as is into the
+    REPL! See the [Julia REPL](@ref julia-repl) section for more.
 
-- **Pkg mode**
+* **Pkg mode**
 
 ```julia
 # Enter ]
@@ -41,31 +47,34 @@ julia> using <name of package here>
 julia> using <name of package here>
 ```
 
-!!! note
-    Just like with the previous method, you can copy/paste code with the `(@v1.x) pkg>` prompt included
-    and Julia will work correctly! You can even skip having to enter Pkg mode by just entering directly
-    `(@v1.x) pkg> add...`. You do not need to manually change the version number indicated in the 
-    prompt if you have a different Julia version than that which is listed, it is all handled for you.
+!!! note J
+    Just like with the previous method, you can copy/paste code with the
+    `(@v1.x) pkg>` prompt included and Julia will work correctly! You can even
+    skip having to enter Pkg mode by just entering directly `(@v1.x) pkg>
+    add...`. You do not need to manually change the version number indicated in
+    the prompt if you have a different Julia version than that which is listed,
+    it is all handled for you.
 
 ## [Package development](@id pkg-devel)
 
-If you are interested in developing a new or existing BioJulia/Julia package, the package manager can also
-help you by first cloning the package repository to your development machine. Pkg will then load the required 
-dependencies in a new dependency environment based on the package's `Project.toml` file. Thereafter, both the 
-direct and indirect dependencies can be locked using a generated `Manifest.toml` if needed and a pull request 
-can be submitted. 
+If you are interested in developing a new or existing BioJulia/Julia package,
+the package manager can also help you by first cloning the package repository to
+your development machine. Pkg will then load the required dependencies in a new
+dependency environment based on the package's `Project.toml` file. Thereafter,
+both the direct and indirect dependencies can be locked using a generated
+`Manifest.toml` if needed and a pull request can be submitted. 
 
 There are two standard methods to set up Julia for developing a package:
 
-- **The package manager (Pkg) module**   
+* **The package manager (Pkg) module**   
 
 ```julia
 julia> using Pkg
 julia> Pkg.develop("<name of package here>")
 julia> using <name of package here>
 ```
 
-- **Pkg mode**
+* **Pkg mode**
 
 ```julia
 # Enter ]
@@ -83,11 +92,14 @@ julia> using <name of package here>
 julia> using <name of package here>
 ```
 
-!!! note
-    You can skip straight to `(@v1.9) pkg> activate ...` if you have already installed the package locally,
-    simply make sure to point Pkg to the right path as shown above.
+!!! note 
+    You can skip straight to `(@v1.9) pkg> activate ...` if you have
+    already installed the package locally, simply make sure to point Pkg to the
+    right path as shown above.
 
-You can now change your source code and load them into the Julia session with `using <name of package here>`.
-To test your code, run `(@v1.9) pkg> test` to run the package's test suite to ensure that everything works
-correctly. When you are done developing the package, enter `(@v1.9) pkg> free` to stop tracking the package. 
+You can now change your source code and load them into the Julia session with
+`using <name of package here>`. To test your code, run `(@v1.9) pkg> test` to
+run the package's test suite to ensure that everything works correctly. When you
+are done developing the package, enter `(@v1.9) pkg> free` to stop tracking the
+package.