fix admonitions + other mistakes

docs/src/comparisons/bioruby.md

@@ -8,7 +8,7 @@
 * Primarily composed of wrapper classes/modules for common bioinformatics,
   molecular biology applications 
 
-**A few equivalent applications between BioJulia and BioRuby:**
+**A few similar applications between BioJulia and BioRuby:**
 
 | Application        | BioJulia packages                                                                                                                               | BioRuby classes/modules           |
 |:-------------------|:------------------------------------------------------------------------------------------------------------------------------------------------|:----------------------------------|

docs/src/comparisons/scikitbio.md

@@ -7,7 +7,7 @@
 * Launched in 2014 based on a BSD-relicensing of PyCogent and QIIME code and is
   currently in beta/maintenance mode
 
-**A few equivalent applications between BioJulia and scikit-bio:**
+**A few similar applications between BioJulia and scikit-bio:**
 
 | Application        | BioJulia packages                                                                                                                             | scikit-bio modules                  |
 |:-------------------|:----------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------|

docs/src/getting_started/casescenarios.md

@@ -1,14 +1,14 @@
 # [Case Scenarios](@id casescenarios)
 
 !!! note 
-  These scenarios are inspired by stories from fellow members of the
-  BioJulia/Julia community!
+    These scenarios are inspired by stories from fellow members of the
+    BioJulia/Julia community!
 
 ## Industry
 
 !!! tip 
-  Visit [JuliaHub](https://juliahub.com/case-studies/) for real-world case
-  studies of Julia in multiple industries!
+    Visit [JuliaHub](https://juliahub.com/case-studies/) for real-world case
+    studies of Julia in multiple industries!
 
 A biotechnology-oriented collaborative research organization has ordered their
 IT department to organize the first in-house software development division.
@@ -24,7 +24,7 @@ similar problems with the current workplace setup:
 - Some workflows can be repetitive and could take advantage of some automation
   to reduce overall time
 
-It is thus decided that an researcher-facing platform should be created that
+It is thus decided that a researcher-facing platform should be created that
 will host a suite of simple, web-based software tools. These can include tools
 usable by any researcher or by only one or several teams depending on their
 needs. The new division is given the following objectives:
@@ -104,9 +104,9 @@ research organizations that face the same challenges.
 ## Research
 
 !!! tip 
-  Visit [The Journal of Open Source Software](https://joss.theoj.org/) and
-  [JuliaCon Proceedings](https://proceedings.juliacon.org/) to explore several
-  research packages written in Julia!
+    Visit [The Journal of Open Source Software](https://joss.theoj.org/) and
+    [JuliaCon Proceedings](https://proceedings.juliacon.org/) to explore several
+    research packages written in Julia!
 
 A freshly minted researcher begins the morning with a new directive from the
 principal investigator. Their lab specializes in translational cancer

docs/src/getting_started/juliainstallation.md

@@ -27,8 +27,8 @@ winget install julia -s msstore
   can generate the `juliaup` executable via the Cargo package manager:
 
 !!! warning 
-  This is not recommended for the most users, and should be avoided
-  unless you cannot download the official juliaup executable.
+    This is not recommended for the most users, and should be avoided
+    unless you cannot download the official juliaup executable.
 
 ```
 cargo install juliaup
@@ -45,8 +45,8 @@ containerized application.
 You must first download the image via the Docker or Podman command-line tool:
 
 !!! note 
-  If you are using Podman, you can replace the keyword `docker` with
-  `podman` in any of the following commands!
+    If you are using Podman, you can replace the keyword `docker` with
+    `podman` in any of the following commands!
 
 ```
 docker pull julia:latest
@@ -58,8 +58,8 @@ You can specify which version of the image you wish to install via tags, such as
 To create a container instance, run the following command:
 
 !!! note 
-  If you had skipped the previous test, then Docker/Podman will
-  automatically begin installing the container image for you here!
+    If you had skipped the previous test, then Docker/Podman will
+    automatically begin installing the container image for you here!
 
 ```
 docker run -it --rm --network host julia:latest

docs/src/getting_started/toolsinstallation.md

@@ -67,25 +67,25 @@ most of the REPL:
   `if abspath(<name of program file>) == @__FILE__`
 
 !!! warning 
-  One common gotcha with the Julia REPL is that certain code changes
-  cannot be performed without restarting your session, such as redefining
-  structs (see the example below). You can mitigate this by adding the
-  [Revise](https://timholy.github.io/Revise.jl/stable/) package, although
-  restarting the session is the simplest option. `
-  ```julia 
-    julia> struct Point
-            x::Int
-            y::Int
-           end
-
-    julia> struct Point
-            x::Int
-            z::Int
-           end
-    ERROR: invalid redefinition of constant Point
-    Stacktrace:
-    [1] top-level scope
-    @ REPL[2]:1
+    One common gotcha with the Julia REPL is that certain code changes
+    cannot be performed without restarting your session, such as redefining
+    structs (see the example below). You can mitigate this by adding the
+    [Revise](https://timholy.github.io/Revise.jl/stable/) package, although
+    restarting the session is the simplest option. `
+    ```julia 
+      julia> struct Point
+              x::Int
+              y::Int
+             end
+
+      julia> struct Point
+              x::Int
+              z::Int
+            end
+      ERROR: invalid redefinition of constant Point
+      Stacktrace:
+      [1] top-level scope
+      @ REPL[2]:1
     ```
 
 Consult the [The Julia REPL](https://docs.julialang.org/en/v1/stdlib/REPL/)
@@ -166,8 +166,8 @@ Jupyter notebooks, which is the most popular web-based notebook solution.
 To install IJulia/Jupyter and run the notebook server:
 
 !!! note 
-  Instead of loading Pkg, one can simply activate pkg mode with the `]`
-  key and enter `(@v1.9) pkg> add <package name here>`
+    Instead of loading Pkg, one can simply activate pkg mode with the `]`
+    key and enter `(@v1.9) pkg> add <package name here>`
 
 1. Install Julia via any method mentioned in the [Installing Julia](@ref
    juliainstallation) section