#Installing the deck

#Requirements

Jennifer 0.25.0 or newer. Every source file declares the floor, and the interpreter refuses to load the deck on an older build:

# pragma-jennifer-version: >=0.25.0

One deck dependency, @deckyard/forensicgenetics, for lineage.MtHaplotype and lineage.parseDifference.

#With jvc

From a project with a deck.toml:

jvc add "@deckyard/mitoleaf" "^0.1.0"
jvc install

add writes the requirement; install resolves the graph, verifies each download against its sha256 and vendors it:

your-project/
  app.j
  deck.toml
  camcorder.lock
  vendor/
    deckyard/
      mitoleaf/
        mitoleaf.j
      forensicgenetics/          <- resolved transitively
        forensicgenetics.j
        lineage.j
        kinship.j
        pedigree.j

@deckyard/forensicgenetics is installed because this deck's manifest requires it, and its constraint is unified with anything else in your graph that needs it. Only src/ is vendored, without the *_test.j overlays. camcorder.lock pins the resolved set, so git clone + jvc install reproduces it exactly; jvc update moves it forward. jvc check verifies the running interpreter satisfies the deck's [engines].

The imports then resolve with no path:

import "@deckyard/mitoleaf/" as mitoleaf;
import "@deckyard/forensicgenetics/lineage.j" as lineage;

The trailing / on the first import expands to the package-named entry file, mitoleaf/mitoleaf.j. A sibling module is named outright.

#From a git remote

If the deck is not on the registry you resolve against, point the requirement at its repository. [decks] says which version, [sources] where from:

jvc source "@deckyard/mitoleaf" https://github.com/deckyard/deck-mitoleaf.git
jvc install

[decks]
"@deckyard/mitoleaf" = "^0.1.0"

[sources]
"@deckyard/mitoleaf" = "https://github.com/deckyard/deck-mitoleaf.git"

Versions are the repository's SemVer tags (this deck tags bare, 0.1.0; jvc also accepts a v prefix), and the tag must agree with the manifest it carries. camcorder.lock pins the commit, so moving a tag later cannot change what a lockfile installs. This needs git on PATH and an interpreter with the exec capability.

#By hand into a vendor tree

The @scope/package resolver reads a plain directory, so a hand-populated tree works without jvc or a network. Take src/ from a checkout or from a release archive (deckyard-mitoleaf-<version>.tar.gz):

mkdir -p vendor/deckyard/mitoleaf vendor/deckyard/forensicgenetics
cp path/to/deck-mitoleaf/src/*.j         vendor/deckyard/mitoleaf/
cp path/to/deck-forensicgenetics/src/*.j vendor/deckyard/forensicgenetics/
rm -f vendor/deckyard/*/*_test.j

The installed tree is flat: the files from src/ sit at the package root. You own the dependency's version; there is no lockfile and nothing checks that the two decks agree.

The resolver takes the vendor root from --vendor, then JENNIFER_VENDOR, then the nearest vendor/ directory above the program being run.

#By relative path

For work on a checkout, import the source directly:

import "./src/mitoleaf.j" as mitoleaf;

The bundled example does this. Struct identity is keyed by the file's canonical path, so a Tree built through either import is the same type.

#Getting the tree

Download the phm XML from mitoLEAF (at the time of writing docs/data/mitoLEAF_phm.xml, 549 KB, 6409 haplogroups) and pass its text to parse. The file's leading comments are a changelog of variants added, removed and respelled; record which release you used with any result.

#Checking the install

From the deck root:

jennifer test src/mitoleaf_test.j
jennifer run examples/haplogroups.j

Expect 29 tests and 0 failed. The example reads testdata/tree.xml relative to the working directory, so run it from the deck root; the tests carry their own copy of the tree and run from anywhere, including an installed deck.