~elais/treetop

0c039c198ec5e3b30d1dafacd4ca1a9e606019e2 — Elais Player 2 months ago main
chore(release): release version 0.1.0

Add .envrc to gitignore

Add .direnv to gitignor

remove dir-locals from gitignore

Add dir-locals to version control

Fix dir-locals and shell.nix

This fixes the dir-locals for emacs users' lsp workspace configurations.

This also makes sure all nodejs packages are using the latest lts release.

Add a parser module

This module is the first step in creating an efficient, fast, and
type-safe parser for newick files based on parser combinators.

Move port under src

Switch to node project and add operations

Deno's lsp server is incomplete and totally broken when using imenu so I
switched over to nodejs (at least until the deno lsp portion is doing
better).

Added a `treeToList` operation that should convert the tree to a list in
linear time. However there are still more optimizations to be made (for
instance, preallocating the list).

Add cli and operations

Add updated nix files

Prepare for 0.1.0

Here we rearrange the project to delete nodejs references and we also
add a build plan for sourcehut.

Add test_data

Change build.yml to .build.yml

This will allow for automatic builds.

Change shell.nix

Add pre-commit hook and license

The BSD 3-Clause license was added to the repo.

A pre-commit hook was added to lint and test the project before
committing. This was done so that only *working* code finds its way into
each commit as a deterrent to checking in anything broken. Though it may
still be wise to add a code coverage hook to pre-push so that
maintainers will have to keep 80% before applying a patch. Thinking
about it though, it may be more wise to enforce code coverage at the
commit level seeing as maintainers will be the only ones allowed to
apply patches.

chore: prepare for 0.1.0 release

chore: Add README

chore: add changelog

Reviewed-by: Elais P.
Refs #1
A  => .builds/aarch64-apple-darwin.yml +26 -0
@@ 1,26 @@
image: nixos/latest
repositories:
  nixpkgs: https://nixos.org/channels/nixpkgs-unstable
environment:
  DENO_DIR: deno_dir
sources:
  - https://git.sr.ht/~elais/treetop
artifacts:
  - dist/aarch64-macos.tar.gz
tasks:
  - setup: |
      mkdir deno_dir
      nix-env -i deno gnutar unzip
  - lint: |
      cd treetop
      deno lint --unstable
  - test: |
      cd treetop
      deno test --unstable --allow-read
  - build: |
      mkdir -p treetop/build/aarch64-apple-darwin
      deno compile --unstable --lite --allow-read --allow-write --target aarch64-apple-darwin -o treetop/build/aarch64-apple-darwin/treetop treetop/cli/mod.ts

  - package: |
      mkdir -p dist
      tar -czvf dist/aarch64-macos.tar.gz treetop/build/aarch64-apple-darwin/

A  => .builds/x86_64-apple-darwin.yml +26 -0
@@ 1,26 @@
image: nixos/latest
repositories:
  nixpkgs: https://nixos.org/channels/nixpkgs-unstable
environment:
  DENO_DIR: deno_dir
sources:
  - https://git.sr.ht/~elais/treetop
artifacts:
  - dist/x86_64-macos.tar.gz
tasks:
  - setup: |
      mkdir deno_dir
      nix-env -i deno gnutar unzip
  - lint: |
      cd treetop
      deno lint --unstable
  - test: |
      cd treetop
      deno test --unstable --allow-read
  - build: |
      mkdir -p treetop/build/x86_64-apple-darwin
      deno compile --unstable --lite --allow-read --allow-write --target x86_64-apple-darwin -o treetop/build/x86_64-apple-darwin/treetop treetop/cli/mod.ts

  - package: |
      mkdir -p dist
      tar -czvf dist/x86_64-macos.tar.gz treetop/build/x86_64-apple-darwin/

A  => .builds/x86_64-linux-gnu.yml +26 -0
@@ 1,26 @@
image: nixos/latest
repositories:
  nixpkgs: https://nixos.org/channels/nixpkgs-unstable
environment:
  DENO_DIR: deno_dir
sources:
  - https://git.sr.ht/~elais/treetop
artifacts:
  - dist/x86_64-linux.tar.gz
tasks:
  - setup: |
      mkdir deno_dir
      nix-env -i deno gnutar unzip
  - lint: |
      cd treetop
      deno lint --unstable
  - test: |
      cd treetop
      deno test --unstable --allow-read
  - build: |
      mkdir -p treetop/build/x86_64-linux-gnu
      deno compile --unstable --lite --allow-read --allow-write --target x86_64-unknown-linux-gnu -o treetop/build/x86_64-linux-gnu/treetop treetop/cli/mod.ts

  - package: |
      mkdir -p dist
      tar -czvf dist/x86_64-linux.tar.gz treetop/build/x86_64-linux-gnu/

A  => .dir-locals.el +2 -0
@@ 1,2 @@
;;; Directory Local Variables
;;; For more information see (info "(emacs) Directory Variables")

A  => .git-hooks/commit-msg +7 -0
@@ 1,7 @@
#!/usr/bin/env sh

commit_message="$1"
# exit with a non zero exit code incase of an invalid commit message

# use git-conventional-commits, see https://github.com/qoomon/git-conventional-commits
git-conventional-commits commit-msg-hook "$commit_message"

A  => .git-hooks/pre-push +19 -0
@@ 1,19 @@
#!/usr/bin/env sh
# put this file in: .git/hooks/pre-push
z40=0000000000000000000000000000000000000000
while read _ local_sha _ remote_sha; do
  if [ "$local_sha" != $z40 ]; then
    if [ "$remote_sha" = $z40 ]; then
      # New branch, examine all commits
      range="$local_sha"
    else
      # Update to existing branch, examine new commits
      range="$remote_sha..$local_sha"
    fi

    # Check for WIP commit
    if ! convco check -C ../../ -c etc/versionrc "$range"; then
      exit 1
    fi
  fi
done

A  => .gitignore +15 -0
@@ 1,15 @@
.DS_Store
.idea
*.log
tmp/

*.tern-port
node_modules/
npm-debug.log*
yarn-debug.log*
yarn-error.log*
*.tsbuildinfo
.npm
.eslintcache
.envrc
.direnv/

A  => CHANGELOG.md +5 -0
@@ 1,5 @@
# Changelog

## Unreleased (2021-04-30)



A  => COPYING +26 -0
@@ 1,26 @@
Copyright (c) 2021, Triad National Security LLC.
All rights reserved.

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:

 * Redistributions of source code must retain the above copyright notice,
   this list of conditions and the following disclaimer.
 * Redistributions in binary form must reproduce the above copyright
   notice, this list of conditions and the following disclaimer in the
   documentation and/or other materials provided with the distribution.
 * Neither the name of Los Alamos National Laboratory nor the names of its
   contributors may be used to endorse or promote products derived from
   this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE.

A  => README.md +9 -0
@@ 1,9 @@
# Treetop
> catchphrase...

Treetop is a newick tree analysis utility and library that fits into your
workflow.

<!--- Insert gif here --->

## Installing / Getting Started

A  => cli/mod.ts +25 -0
@@ 1,25 @@
import { cac } from "https://unpkg.com/cac/mod.ts";
import { newickStringToFile, newickToJsonString } from "./parse.ts";
import { log } from "../deps.ts";

const cli = cac("treetop");

cli
  .command("parse [...files]", "Parse newick files")
  .option("-o <dir>, --out <dir>", "Output destination.")
  .action((files, options) => {
    files
      .map((file: string) => newickToJsonString(file || ""))
      .forEach((file: { filename: string; file: string }) =>
        log.debug(newickStringToFile(file, options.out))
      );
  });

// Display help message when `-h` or `help` appears
cli.help();

// Display version number when `-v` or `--version` appears
// It's also used in help message
cli.version("0.1.0");

cli.parse();

A  => cli/parse.ts +39 -0
@@ 1,39 @@
import { typedParse } from "../mod.ts";

/** read newick string from file on path */
export function newickToJsonString(
  file: string,
): { filename: string; file: string } {
  try {
    const filename: string =
      file?.split("\\")?.pop()?.split("/")?.pop()?.split(".")?.slice(0, -1)
        ?.join(".") ?? "output";
    const newick = typedParse(Deno.readTextFileSync(file));
    return {
      filename,
      file: JSON.stringify(newick, null, 2),
    };
  } catch (error) {
    console.error(error);
    throw error;
  }
}

/** write newick string to file on path */
export function newickStringToFile(
  newick: { filename: string; file: string },
  path: string,
) {
  try {
    if (!path) {
      Deno.stdout.writeSync(new TextEncoder().encode(newick.file));
      return `${newick.filename} written to stdout`;
    }
    const output = `${path}/${newick.filename}`;
    Deno.writeTextFileSync(`${output}.json`, newick.file);
    return `${newick.filename} written to ${output}.json`;
  } catch (error) {
    console.error(error);
    throw error;
  }
}

A  => cli/parse_test.ts +10 -0
@@ 1,10 @@
import { assertEquals } from "https://deno.land/std@0.93.0/testing/asserts.ts";

import { newickToJsonString } from "./parse.ts";

const smallNewickTree = "./test_data/small_tree.nwk";

Deno.test("Cli::parse::newickToJsonString return a formatted json string", () => {
  const result = newickToJsonString(smallNewickTree);
  assertEquals(result.filename, "small_tree");
});

A  => deps.ts +1 -0
@@ 1,1 @@
export * as log from "https://deno.land/std@0.95.0/log/mod.ts";

A  => etc/versionrc +47 -0
@@ 1,47 @@
# .versionrc
---
header: "# Changelog\n\n"
types:
  - type: feat
    section: Features
    hidden: false
  - type: fix
    section: Fixes
    hidden: false
  - type: build
    section: Other
    hidden: true
  - type: chore
    section: Other
    hidden: true
  - type: ci
    section: Other
    hidden: true
  - type: docs
    section: Documentation
    hidden: true
  - type: style
    section: Other
    hidden: true
  - type: refactor
    section: Other
    hidden: true
  - type: perf
    section: Other
    hidden: true
  - type: test
    section: Other
    hidden: true
preMajor: true
commitUrlFormat: "{{host}}/{{owner}}/{{repository}}/commit/{{hash}}"
compareUrlFormat: "{{host}}/{{owner}}/{{repository}}/compare/{{previousTag}}...{{currentTag}}"
issueUrlFormat: "https://todo.sr.ht/~{{owner}}/treetop-tasks/{{id}}"
userUrlFormat: "{{host}}/~{{user}}"
releaseCommitMessageFormat: "chore(release): {{currentTag}}"
issuePrefixes:
  - "#"
host: ~
owner: ~
repository: ~
template: ~
scopeRegex: "[[:alnum:]]+(?:[-_/][[:alnum:]]+)*"

A  => mod.ts +3 -0
@@ 1,3 @@
export * from "./operations/mod.ts";
export * from "./parse/mod.ts";
export * from "./shared/mod.ts";

A  => operations/mod.ts +74 -0
@@ 1,74 @@
// Copyright (2021). Triad National Security, LLC. All rights reserved. Licensed
// under BSD-3-Clause.

// * imports
import { Tree, TreeNode } from "../shared/mod.ts";

// * Constants

// * Functions

// function visitPreOrder(root, parent) {
//   root.length = root.length ? root.length : 0.0
//   root.distance = (parent !== null ? parent.distance : 0.0) + (root.length || 0.0);
//   if (root.branchset) {
//     root.branchset = root.branchset.map(child => visitPreOrder(child, root));
//   }
//   return root;
// }

// function flatten(obj, label) => {
//   const array = Array.isArray(obj) ? obj : [obj];
//   return array.reduce((acc, value) => {
//     if(value.type !== 'root') {
//       if(value.length) {
//         value.type = 'node';
//       } else {
//         value.type = 'leaf';
//       }
//     }
//     value.uid = uuidv4();
//     value.parent = label || null;
//     acc.push(value);
//     if (value.branchset) {
//       acc = acc.concat(flatten(value.branchset, value.uid));
//       value.innerNode = true;
//       delete value.branchset;
//       delete value.name;
//     }
//     return acc;
//   }, [])
// }

function visitNode(
  node: TreeNode,
  hashMap: Map<string | undefined, boolean>,
  array: TreeNode[],
) {
  if (!hashMap.has(node.name)) {
    hashMap.set(node.name, true);
    array.push(node);
  }
}

// * Exports

/** Takes a parsed tree object and converts it into a lazy list.*/
export function treeToList(tree: Tree): TreeNode[] {
  const stack: TreeNode[] = [];
  const array: TreeNode[] = [];
  const hashMap = new Map();
  stack.push(tree.root);
  while (stack.length > 0) {
    const node = stack.pop();
    if (!node) return [];
    if (!node.children) {
      visitNode(node, hashMap, array);
    } else {
      for (let i = node.children.length - 1; i >= 0; i--) {
        stack.push(node.children[i]);
      }
    }
  }
  return array;
}

A  => operations/mod_test.ts +13 -0
@@ 1,13 @@
import { assertEquals } from "https://deno.land/std@0.93.0/testing/asserts.ts";

import { treeToList } from "./mod.ts";
import { typedParse } from "../parse/mod.ts";

const bigNewickTree = typedParse(
  await Deno.readTextFile("./test_data/tree_1.nwk"),
);

Deno.test("Operations::mod::treeToList Convert Large Newick file", () => {
  const result = treeToList(bigNewickTree);
  assertEquals(result.length, 31386);
});

A  => parse/mod.ts +264 -0
@@ 1,264 @@
// Copyright (2021). Triad National Security, LLC. All rights reserved. Licensed
// under BSD-3-Clause.

import {
  Branch,
  BranchSet,
  Internal,
  Leaf,
  Length,
  Name,
  Subtree,
  Tree,
} from "../shared/mod.ts";

// every parsing function will have this signature
type Parser<Expr> = (ctx: Context) => Result<Expr>;

// on success we'll return a value of type T, and a new Ctx
// (position in the string) to continue parsing from
type Success<Expr> = Readonly<{
  success: true;
  value: Expr;
  ctx: Context;
}>;

// when we fail we want to know where and why
type Failure = Readonly<{
  success: false;
  expected: string;
  ctx: Context;
}>;

// to track progress through our input string.
type Context = Readonly<{
  text: string; // the full input string
  index: number; // our current position in it
}>;

// our result types
type Result<T> = Success<T> | Failure;

// some convenience methods to build `Result' for us
function success<Expr>(ctx: Context, value: Expr): Success<Expr> {
  return { success: true, value, ctx };
}

function failure(ctx: Context, expected: string): Failure {
  return { success: false, expected, ctx };
}

// match an exact string or fail
function str(match: string): Parser<string> {
  return (ctx) => {
    const endIdx = ctx.index + match.length;
    if (ctx.text.substring(ctx.index, endIdx) === match) {
      return success({ ...ctx, index: endIdx }, match);
    } else {
      return failure(ctx, match);
    }
  };
}

// try each matcher in order, starting from the same point in the input. return
// the first one that succeeds.  or return the failure that got furthest in the
// input string.  which failure to return is a matter of taste, we prefer the
// furthest failure because.  it tends be the most useful / complete error
// message.
function any<T>(parsers: Parser<T>[]): Parser<T> {
  return (ctx) => {
    let furthestRes: Result<T> | null = null;
    for (const parser of parsers) {
      const res = parser(ctx);
      if (res.success) return res;
      if (!furthestRes || furthestRes.ctx.index < res.ctx.index) {
        furthestRes = res;
      }
    }
    return furthestRes!;
  };
}

// match a parser, or succeed with null
function optional<T>(parser: Parser<T>): Parser<T | null> {
  return any([parser, (ctx) => success(ctx, null)]);
}

// look for 0 or more of something, until we can't parse any more. note that
// this function never fails, it will instead succeed with an empty array.
function many<T>(parser: Parser<T>): Parser<T[]> {
  return (ctx) => {
    const values: T[] = [];
    let nextCtx = ctx;
    for (;;) {
      const res = parser(nextCtx);
      if (!res.success) break;
      values.push(res.value);
      nextCtx = res.ctx;
    }
    return success(nextCtx, values);
  };
}

function digit(): Parser<number> {
  return (ctx) => {
    let nextCtx = ctx;
    for (;;) {
      const match = nextCtx.text.charAt(nextCtx.index);
      const charCode = match.charCodeAt(0);
      if (
        (charCode >= 48 && charCode <= 57) || match === "-" || match === "e" ||
        match === "E" || match === "."
      ) {
        nextCtx = { index: nextCtx.index + 1, text: nextCtx.text };
      } else {
        break;
      }
    }
    return success(
      nextCtx,
      parseFloat(ctx.text.substring(ctx.index, nextCtx.index)),
    );
  };
}

// match a regexp or fail
function regex(re: RegExp, expected: string): Parser<string> {
  return (ctx) => {
    re.lastIndex = ctx.index;
    const res = re.exec(ctx.text);
    if (res && res.index === ctx.index) {
      return success({ ...ctx, index: ctx.index + res[0].length }, res[0]);
    } else {
      return failure(ctx, expected);
    }
  };
}

// look for an exact sequence of parsers, or fail
function sequence<T>(parsers: Parser<T>[]): Parser<T[]> {
  return (ctx) => {
    const values: T[] = [];
    let nextCtx = ctx;
    for (const parser of parsers) {
      const res = parser(nextCtx);
      if (!res.success) return res;
      values.push(res.value);
      nextCtx = res.ctx;
    }
    return success(nextCtx, values);
  };
}

// TODO: Add Lazy Operator
// function lazy<A>(fn: ()=> Parser<A>): Parser<A> {
//   return (ctx) => {
//     function parse<Context>(
//       input: A,
//       ctx: Context = ctx
//     ): Result<T> {

//     }
//   }
// }

function map<A, B>(parser: Parser<A>, fn: (val: A) => B): Parser<B> {
  return (ctx) => {
    const res = parser(ctx);
    return res.success ? success(res.ctx, fn(res.value)) : res;
  };
}

// Begin Newick stuff

type Expr =
  | Tree
  | Branch
  | Length
  | Subtree
  | Leaf
  | Name
  | Internal
  | BranchSet
  | string
  | number;

// expr = Length
const lengthLiteral = map(
  digit(),
  (num): number => num,
);

// expr = Name
const nameLiteral = regex(/\w+/g, "name");

const length = map(
  sequence<unknown>([str(":"), lengthLiteral]),
  ([, len]): Expr => ({
    length: len as number,
  }),
);

const branch = map(
  sequence<unknown>([subTree, optional(length)]),
  ([subs, len]): Branch => ({
    ...(len as Length),
    ...(subs as Subtree),
  }),
);

const branchSetAppending = map(
  sequence<unknown>([str(","), branch]),
  ([, arg1]): Branch => {
    return {
      ...(arg1 as Branch),
    };
  },
);

const branchSet = map(
  sequence<unknown>([branch, many(branchSetAppending)]),
  ([br, branches]): BranchSet => {
    return [(br as Branch), ...(branches as BranchSet)];
  },
);

const name = map(
  sequence<unknown>([optional(nameLiteral)]),
  ([nom]): Name => ({
    name: nom as string,
  }),
);

const internal = map(
  sequence<unknown>([str("("), branchSet, str(")"), name]),
  ([, branches, , branchName]): Internal => ({
    children: branches as BranchSet,
    ...(branchName as Name),
  }),
);

const leaf = map(
  sequence<unknown>([name]),
  ([leafName]): Leaf => leafName as Name,
);

const tree = map(
  sequence<unknown>([subTree, str(";")]),
  ([sub]): Subtree => sub as Subtree,
);

function expr(ctx: Context): Result<Subtree> {
  return any<Subtree>([internal, leaf, branch, tree, subTree])(ctx);
}

function subTree(ctx: Context): Result<Subtree> {
  return any<Subtree>([internal, leaf])(ctx);
}

/**Takes a newick tree string and returns a json object.*/
export function typedParse(newickTree: string): Tree {
  const res = expr({ text: newickTree, index: 0 });
  if (res.success) return { root: res.value, count: 0 };
  throw `Parse error, expected ${res.expected} at char ${res.ctx.index}`;
}

A  => parse/mod_test.ts +18 -0
@@ 1,18 @@
import { assert } from "https://deno.land/std@0.93.0/testing/asserts.ts";
import { typedParse } from "./mod.ts";

const bigNewickTree = await Deno.readTextFile("./test_data/tree_1.nwk");

Deno.test("Parse::mod::typedParse Multiword Name and Scientific Notation Length", () => {
  const result = typedParse(
    "(((((((((((((B_anthracis_FDAARGOS_705:1.4999999999987246E-5,B_anthracis_PR06:1.1999999999984245E-5):4.900000000002125E-5,B_anthracis_Cvac02:4.900000000002125E-5):7.999999999980245E-6,((NBI0584184_contig:2.000000000002E-6,NBI0584185_contig:3.0000000000030003E-6):1.5999999999988246E-5,NBI0584183_contig:4.399999999998849E-5):2.000000000002E-6):0.0,B_anthracis_Turkey32:2.1999999999994246E-5):4.000000000004E-6,((((NBI0584187_contig:2.000000000002E-6,NBI0584189_contig:2.000000000002E-6):0.0,NBI0584188_contig:1.0000000000010001E-5):1.1999999999984245E-5,B_anthracis_SK_102:1.4999999999987246E-5):3.200000000000425E-5,(B_anthracis_RA3:1.8500000000001848E-4,NBI0584186_contig:6.0000000000004494E-5):9.099999999997999E-5):2.000000000002E-6):2.2800000000000598E-4,B_anthracis_2000031021:1.1300000000000199E-4):0.005031000000000008,B_thuringiensis_HD1011:0.004466999999999999):0.002472000000000002,B_cereus_CTMA_1571:0.005458999999999992):0.002341999999999983,B_thuringiensis_HD571:0.011386000000000007):0.005657999999999996,B_cereus_E33L:0.009200000000000014):0.01967200000000001,(B_cereus_CC1:0.009766999999999998,B_paranthracis_MN1F:0.009475999999999998):0.011005000000000001):0.005067000000000002,(((B_cereus_AR156:0.0017659999999999898,B_thuringiensis_XL6:0.002140000000000003):0.0070139999999999925,B_cereus_FM1:0.011335999999999999):0.005400000000000016,B_tropicus_LM1212_W3:0.016825000000000007):0.005794999999999995):0.030551499999999995,(((((B_cereus_ATCC_14579:0.003803000000000001,B_thuringiensis_SCG04_02:0.004020999999999997):0.0010950000000000126,B_thuringiensis_C15:0.0032040000000000124):0.0023100000000000065,B_cereus_HBL_AI:0.005287999999999987):0.006936999999999999,(B_thuringiensis_HM_311:0.017374,B_thuringiensis_YBT_1520:0.012429999999999997):0.0033080000000000054):0.003370999999999999,(B_cereus_SB1:0.012816999999999995,B_cereus_ZB201708:0.019651000000000002):0.004628000000000007):0.0480555);",
  );
  // BEGIN ASSERTION
  assert(result);
});

Deno.test("Parse::mod::typedParse Large Newick Tree", () => {
  const result = typedParse(bigNewickTree);

  assert(result);
});

A  => shared/mod.ts +16 -0
@@ 1,16 @@
// Copyright (2021). Triad National Security, LLC. All rights reserved. Licensed
// under BSD-3-Clause.

export type BranchSet = Branch[];
export type Internal = Name & Readonly<{ children?: BranchSet }>;
export type Name = Readonly<{ name?: string }>;
export type Leaf = Name;
export type Subtree = Leaf | Internal;
export type Length = Readonly<{ length?: number }>;
export type Branch = Subtree & Length;
export type TreeNode = Internal & Subtree;

export interface Tree {
  readonly root: TreeNode;
  readonly count: number;
}

A  => shell.nix +13 -0
@@ 1,13 @@
{ pkgs ? import <nixpkgs> {} }:
with pkgs;

mkShell {
  buildInputs = [
    convco
    rnix-lsp
    deno
    nixfmt
    gnutar
    unzip
  ];
}

A  => test_data/small_tree.nwk +1 -0
@@ 1,1 @@
(A:0.1,B:0.2,(C:0.3,D:0.4)E:0.5)F;

A  => test_data/tree_1.nwk +1 -0
@@ 1,1 @@
(((((27568__Porcine_circovirus_2_strain_GXYL1307a:0,(27544__Porcine_circovirus_2_strain_GXLZ1103b:0,(27530__Porcine_circovirus_2_strain_GXBS1401:0,(27459__Porcine_circovirus_2_strain_unknown_4636:0,(27423__Porcine_circovirus_2_strain_GXHZ_1:0,(27325__Porcine_circovirus_2_strain_unknown_4596:0,(27220__Porcine_circovirus_2_strain_unknown_4574:0,(27218__Porcine_circovirus_2_strain_YZ0901:0,(27051__Porcine_circovirus_2_strain_unknown_4475:0,(26994__Porcine_circovirus_2_strain_SCcd:0,(26978__Porcine_circovirus_2_strain_unknown_4434:0,(26953__Porcine_circovirus_2_strain_AH:0,(26928__Porcine_circovirus_2_strain_ZJjh_2:0,(26919__Porcine_circovirus_2_strain_NY0912:0,(26885__Porcine_circovirus_2_strain_XN_1:0,(26817__Porcine_circovirus_2_strain_unknown_4363:0,(26722__Porcine_circovirus_2_strain_unknown_4306:0,(26715__Porcine_circovirus_2_strain_unknown_4299:0,(26709__Porcine_circovirus_2_strain_unknown_4294:0,(26635__Porcine_circovirus_2_strain_SZ1101:0,(26633__Porcine_circovirus_2_strain_FX1101:0,(26534__Porcine_circovirus_2_strain_unknown_4241:0,(26525__Porcine_circovirus_2_strain_SZ1107:0,(26522__Porcine_circovirus_2_strain_TX1106:0,(26518__Porcine_circovirus_2_strain_YZ1011:0,(26494__Porcine_circovirus_2_strain_unknown_4227:0,(26493__Porcine_circovirus_2_strain_unknown_4226:0,(26492__Porcine_circovirus_2_strain_unknown_4225:0,(26464__Porcine_circovirus_2_strain_unknown_4218:0,(26462__Porcine_circovirus_2_strain_unknown_4216:0,(26457__Porcine_circovirus_2_strain_unknown_4212:0,(26435__Porcine_circovirus_2_strain_10AH_2:0,(26426__Porcine_circovirus_2_strain_unknown_4199:0,(26421__Porcine_circovirus_2_strain_unknown_4196:0,(26342__Porcine_circovirus_2_strain_unknown_4134:0,(26340__Porcine_circovirus_2_strain_unknown_4132:0,(26330__Porcine_circovirus_2_strain_unknown_4123:0,(26328__Porcine_circovirus_2_strain_unknown_4121:0,(26327__Porcine_circovirus_2_strain_unknown_4120:0,(26321__Porcine_circovirus_2_strain_unknown_4115:0,(26318__Porcine_circovirus_2_strain_unknown_4112:0,(26310__Porcine_circovirus_2_strain_unknown_4106:0,(26309__Porcine_circovirus_2_strain_unknown_4105:0,(26262__Porcine_circovirus_2_strain_MC:0,(26210__Porcine_circovirus_2_strain_unknown_4060:0,(26209__Porcine_circovirus_2_strain_unknown_4059:0,(26208__Porcine_circovirus_2_strain_unknown_4058:0,(26200__Porcine_circovirus_2_strain_unknown_4052:0,(26198__Porcine_circovirus_2_strain_unknown_4050:0,(26170__Porcine_circovirus_2_strain_unknown_4024:0,(26167__Porcine_circovirus_2_strain_unknown_4022:0,(26162__Porcine_circovirus_2_strain_unknown_4017:0,(26161__Porcine_circovirus_2_strain_unknown_4016:0,(26160__Porcine_circovirus_2_strain_unknown_4015:0,(26073__Porcine_circovirus_2_strain_unknown_3944:0,(26072__Porcine_circovirus_2_strain_unknown_3943:0,(26054__Porcine_circovirus_2_strain_unknown_3916:0,(26052__Porcine_circovirus_2_strain_unknown_3915:0,(26051__Porcine_circovirus_2_strain_unknown_3914:0,(26050__Porcine_circovirus_2_strain_unknown_3913:0,(26046__Porcine_circovirus_2_strain_TJ1306:0,(26008__Porcine_circovirus_2_strain_unknown_3890:0,(26007__Porcine_circovirus_2_strain_unknown_3889:0,(25995__Porcine_circovirus_2_strain_unknown_3880:0,(25960__Porcine_circovirus_2_strain_unknown_3853:0,(25945__Porcine_circovirus_2_strain_unknown_3839:0,(25927__Porcine_circovirus_2_strain_unknown_3823:0,(25925__Porcine_circovirus_2_strain_unknown_3821:0,(25923__Porcine_circovirus_2_strain_unknown_3819:0,(25905__Porcine_circovirus_2_strain_unknown_3803:0,(25863__Porcine_circovirus_2_strain_unknown_3766:0,(25826__Porcine_circovirus_2_strain_unknown_3750:0,(25817__Porcine_circovirus_2_strain_unknown_3742:0,(25816__Porcine_circovirus_2_strain_unknown_3741:0,(25808__Porcine_circovirus_2_strain_unknown_3734:0,(25807__Porcine_circovirus_2_strain_unknown_3733:0,(25802__Porcine_circovirus_2_strain_unknown_3728:0,(25778__Porcine_circovirus_2_strain_unknown_3707:0,(25773__Porcine_circovirus_2_strain_unknown_3703:0,(25770__Porcine_circovirus_2_strain_unknown_3700:0,(25769__Porcine_circovirus_2_strain_unknown_3699:0,(25768__Porcine_circovirus_2_strain_unknown_3698:0,(25767__Porcine_circovirus_2_strain_unknown_3697:0,(25765__Porcine_circovirus_2_strain_unknown_3696:0,(25732__Porcine_circovirus_2_strain_unknown_3675:0,(25728__Porcine_circovirus_2_strain_unknown_3671:0,(25727__Porcine_circovirus_2_strain_unknown_3670:0,(25726__Porcine_circovirus_2_strain_unknown_3669:0,(25725__Porcine_circovirus_2_strain_unknown_3668:0,(25716__Porcine_circovirus_2_strain_unknown_3660:0,(25714__Porcine_circovirus_2_strain_unknown_3658:0,(25713__Porcine_circovirus_2_strain_unknown_3657:0,(25712__Porcine_circovirus_2_strain_unknown_3656:0,(25710__Porcine_circovirus_2_strain_unknown_3655:0,(25702__Porcine_circovirus_2_strain_AG1:0,(25690__Porcine_circovirus_2_strain_GC1:0,(25675__Porcine_circovirus_2_strain_MC1:0,(25662__Porcine_circovirus_2_strain_RQ2:0,(25646__Porcine_circovirus_2_strain_HH1:0,(25638__Porcine_circovirus_2_strain_TX1:0,(25621__Porcine_circovirus_2_strain_HBSJZ160703:0,(25603__Porc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