rrm workspace: TRM/HRM/SRM code, Maze dataset, dynamical-analysis pipelineHEADmain

Curated export for clone-and-run Maze training (2x A6000) + diagnostics.
trm/hrm pretrain.py carry trajectory-augmentation code (backward-compatible).
Heavy artifacts (checkpoints/wandb/npz) gitignored; see PROVENANCE.md.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

1 files changed, 108 insertions, 0 deletions

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+# **4.** Working with Environments
+
+The following discusses Pkg's interaction with environments. For more on the role environments play in code loading, including the "stack" of environments from which code can be loaded, see [this section in the Julia manual](https://docs.julialang.org/en/v1/manual/code-loading/#Environments-1).
+
+## Creating your own projects
+
+So far we have added packages to the default project at `~/.julia/environments/v1.0`. It is however easy to create other, independent, projects.
+It should be pointed out that when two projects use the same package at the same version, the content of this package is not duplicated.
+In order to create a new project, create a directory for it and then activate that directory to make it the "active project", which package operations manipulate:
+
+```julia-repl
+julia> mkdir("MyProject")
+
+julia> cd("MyProject")
+/Users/kristoffer/MyProject
+
+(v1.0) pkg> activate .
+
+(MyProject) pkg> st
+    Status `Project.toml`
+```
+
+Note that the REPL prompt changed when the new project is activated. Since this is a newly created project, the status command shows that it contains no packages, and in fact, it has no project or manifest file until we add a package to it:
+
+```julia-repl
+julia> readdir()
+0-element Array{String,1}
+
+(MyProject) pkg> add Example
+  Updating registry at `~/.julia/registries/General`
+  Updating git-repo `https://github.com/JuliaRegistries/General.git`
+ Resolving package versions...
+  Updating `Project.toml`
+  [7876af07] + Example v0.5.1
+  Updating `Manifest.toml`
+  [7876af07] + Example v0.5.1
+  [8dfed614] + Test
+Precompiling project...
+  1 dependency successfully precompiled in 2 seconds
+
+julia> readdir()
+2-element Array{String,1}:
+ "Manifest.toml"
+ "Project.toml"
+
+julia> print(read("Project.toml", String))
+[deps]
+Example = "7876af07-990d-54b4-ab0e-23690620f79a"
+
+julia> print(read("Manifest.toml", String))
+[[Example]]
+deps = ["Test"]
+git-tree-sha1 = "8eb7b4d4ca487caade9ba3e85932e28ce6d6e1f8"
+uuid = "7876af07-990d-54b4-ab0e-23690620f79a"
+version = "0.5.1"
+
+[[Test]]
+uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+```
+
+This new environment is completely separate from the one we used earlier.
+
+
+## Project Precompilation
+
+By default any package that is added to a project or updated in a Pkg action will be automatically precompiled, along
+with its dependencies. The exception is the `develop` command, which neither builds nor precompiles the package, when
+that happens is left up to the user to decide.
+
+If a package that has been updated is already loaded in the session, the precompilation process will go ahead and precompile
+the new version, and any packages that depend on it, but will note that the package cannot be used until session restart.
+
+To disable this auto-precompilation, set `ENV["JULIA_PKG_PRECOMPILE_AUTO"]=0`, after which precompilation can be triggered
+manually either serially via code loading
+
+```julia-repl
+julia> using Example
+[ Info: Precompiling Example [7876af07-990d-54b4-ab0e-23690620f79a]
+```
+
+ or the parallel precompilation, which can be significantly faster when many dependencies are involved, via
+
+```julia-repl
+pkg> precompile
+Precompiling project...
+  23 dependencies successfully precompiled in 36 seconds
+```
+
+## Using someone else's project
+
+Simply clone their project using e.g. `git clone`, `cd` to the project directory and call
+
+```julia-repl
+(v1.0) pkg> activate .
+
+(SomeProject) pkg> instantiate
+```
+
+If the project contains a manifest, this will install the packages in the same state that is given by that manifest.
+Otherwise, it will resolve the latest versions of the dependencies compatible with the project.
+
+!!! note "Specifying project on startup"
+    Instead of using `activate` from within Julia you can specify the project on startup using
+    the `--project=<path>` flag. For example, to run a script from the command line using the
+    environment in the current directory you can run
+    ```bash
+    $ julia --project=. myscript.jl
+    ```