Merge pull request #10 from BioJulia/dev

Quick fixes + Pkg environment note

.devcontainer/devcontainer.json

@@ -13,6 +13,6 @@
             ]
         }
     },
-    "onCreateCommand": "julia --project=docs -e 'using Pkg; Pkg.instantiate(); Pkg.precompile();'"
+    "onCreateCommand": "julia --project=docs/Project.toml -e 'using Pkg; Pkg.instantiate(); Pkg.precompile();'"
 }
 

docs/src/comparisons/bioconductor.md

@@ -39,4 +39,5 @@
 **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
+- Use [JuliaCall](https://cran.r-project.org/web/packages/JuliaCall/readme/README.html) to seamlessly integrate Julia code into your R project
+

docs/src/comparisons/biojava.md

@@ -38,4 +38,5 @@
 
 **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
+- 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

@@ -36,4 +36,5 @@
 
 **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
+- 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

@@ -42,4 +42,5 @@
 **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](CondaPkg.jl) 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
+- Use [juliacall](https://pypi.org/project/juliacall/) to seamlessly integrate Julia code into your Python3 project
+

docs/src/comparisons/bioruby.md

@@ -36,4 +36,5 @@
 
 **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
+- 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

@@ -40,4 +40,5 @@
 **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](CondaPkg.jl) 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
+- Use [juliacall](https://pypi.org/project/juliacall/) to seamlessly integrate Julia code into your Python3 project
+

docs/src/getting_started/biojuliainstallation.md

@@ -8,6 +8,14 @@ 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.
+
 1. **The package manager (Pkg) module**
 
 ```julia
@@ -30,7 +38,7 @@ using <name of package here>
 ]
 # @v1.x will show your current Julia version
 (@v1.9) pkg> add <name of package here>
-# Exit REPL via the Backspace key
+# Exit Pkg REPL mode via the Backspace key
 julia> using <name of package here>
 ```
 
@@ -40,7 +48,7 @@ julia> using <name of package here>
     `(@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 again handled for you.
 
-## Package development
+## [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 
@@ -58,7 +66,7 @@ julia> Pkg.develop("<name of package here>");
 using <name of package here>
 ```
 
-1. **Pkg mode**
+2. **Pkg mode**
 
 ```julia
 # Enter ]
@@ -83,3 +91,4 @@ julia> using <name of package here>
 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. 
+

docs/src/getting_started/juliainstallation.md

@@ -105,4 +105,5 @@ Make sure to follow the exact installation steps for your machine in order to en
 
 For building/testing purposes, you may build Julia from the source code that is fully available in the [Julia GitHub repository](https://github.com/JuliaLang/julia.git).
 Simply enter `git clone https://github.com/JuliaLang/julia.git` to copy the entire source on your machine, create a new git branch via `git checkout -b name-of-branch`,
-add your modifications, and run `make` to start the Makefile build.
+add your modifications, and run `make` to start the Makefile build.
+

docs/src/getting_started/toolsinstallation.md

@@ -25,6 +25,7 @@ We won't go into every feature that the REPL provides, however here is a quick l
 know to make the most of this shell:
 
 - There are 5 Julia REPL modes that serve separate purposes: 
+
   1. The Julian (default) mode wherein one can write, load, and test out code
   2. Help mode for printing documentation for functions, keywords, etc.
   3. Pkg mode for working with the included package manager and manipulating dependencies/packages
@@ -45,6 +46,7 @@ know to make the most of this shell:
   finished!
 - You can get a list of matches to a partially written word by entering the TAB key, which also serves to render an
   Unicode symbol in the REPL (full list available in the [Unicode Input](https://docs.julialang.org/en/v1/manual/unicode-input/) section of the Julia manual): 
+
   ```julia
   julia> pri[TAB]
   primitive type  print           println         printstyled
@@ -54,7 +56,7 @@ know to make the most of this shell:
   equivalent of Python3's `if __name__ == __main__` condition would be `if abspath(<name of program file>) == @__FILE__`
 
 !!! warning
-    One common footgun with the Julia REPL is that there are currently certain code changes that cannot be performed without 
+    One common gotcha with the Julia REPL is that there are currently certain code changes that 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
@@ -79,6 +81,7 @@ To learn more, see the [The Julia REPL](https://docs.julialang.org/en/v1/stdlib/
 
 The Julia organization officially maintains the [Julia vscode extension](https://www.julia-vscode.org/), which provides
 a complete IDE solution for developing in Julia. This boasts a number of advantages compared to a REPL solution:
+
 - Built-in syntax highlighting and code completion
 - GUI interaction for managing options and commands
 - Advanced profiling/debugging features 
@@ -92,9 +95,9 @@ Quick Open input panel by pressing `Ctrl + P` and entering `ext install julialan
 <!-- TODO: Move image to assets directory -->
 ![Julia VSCode Extension](JuliaVSCodeExtension.png)
 
-
 Install the extension and restart vscode. We also recommend installing some additional extensions that will further improve
 the development experience:
+
 - [Even Better TOML](https://marketplace.visualstudio.com/items?itemName=tamasfe.even-better-toml) 
   (`ext install tamasfe.even-better-toml`) for working with the package TOML 
   files (Project.toml, Manifest.toml, Artifacts.toml,...)