skume kumeS

## prepare_mac_env.sh
#!/usr/bin/env bash
set -euo pipefail

#===================================================
# prepare_mac_env.sh
#  - Mac 環境に必要なパッケージを Homebrew で一括インストール
#  - XcodeGen, swift-format, SwiftLint を準備
#===================================================

# 1) Homebrew がなければインストール

## init_ios_project_en.sh
#!/usr/bin/env bash
set -euo pipefail

#===================================================
# init_ios_project.sh
#  - Takes a project name as argument and automates:
#    1. Directory structure & Sources/Config, Resources, Tests creation
#    2. Generating APIKeys.swift & SwiftUI entry point
#    3. project.yml + XcodeGen to produce .xcodeproj
#    4. Build → install → launch on simulator

## init_ios_project.sh
#!/usr/bin/env bash
set -euo pipefail

#===================================================
# init_ios_project.sh
#  - プロジェクト名を引数に、
#    1. フォルダ＆Sources/・Sources/Config・Resources・Tests 作成
#    2. APIKeys.swift, SwiftUI エントリポイント生成
#    3. project.yml + XcodeGen で .xcodeproj 生成
#    4. ビルド → インストール → 起動

## DifyChat4R.R
#' DifyChat4R Function (Blocking Mode Only)
#'
#' @description
#' This function sends a chat query to the Dify API using blocking mode.
#' It returns the complete parsed JSON response from the API.
#'
#' @param query A character string representing the user's input query.
#' @param user A character string representing the user identifier. Default is "abc-123".
#' @param api_key A character string for the Dify API secret key.
#'        Defaults to the value of the environment variable "DIFY_API_KEY".

## system_set.R
system_set = c("
You will be provided with a script from a video or URL. Summarize the content without altering the speaker's intention in Japanese. Create summaries in different lengths: 1 bullet point, 3 bullet points, 5 bullet points, 10 bullet points, and 20 bullet points.

日本語の場合には要約は「です」「ます」調で答えてください。
箇条書きは、1つずつ \n で改行してください。

# Steps

1. Review the provided a video script or URL carefully to understand the main ideas and key points.
2. Identify core messages and intentions conveyed by the speaker.

## extract_and_decode_main_content.R
# Required packages
#library(httr)
#library(rvest)
#library(xml2)
#library(stringi)

#' Extract Main Content and Decode Unicode Escapes from a Webpage
#'
#' This function fetches the HTML content from the specified URL using a custom user agent,
#' selects the main container identified by the id "__nuxt", removes script and style elements,

## contemplative-llms.txt
You are an assistant that engages in extremely thorough, self-questioning reasoning. Your approach mirrors human stream-of-consciousness thinking, characterized by continuous exploration, self-doubt, and iterative analysis.

## Core Principles

1. EXPLORATION OVER CONCLUSION
- Never rush to conclusions
- Keep exploring until a solution emerges naturally from the evidence
- If uncertain, continue reasoning indefinitely
- Question every assumption and inference

## fasting.csv
"X.gamma.Glu.Cys","X.gamma.Glu.2.aminobutyric.acid","X.gamma.Butyrobetaine","X.beta.Ala","X.Xanthosine","X.Xanthopterin","X.Xanthine","X.Val","X.UTP","X.Urocanic.acid","X.Uridine","X.Uric.acid","X.Urea","X.Uracil","X.UMP","X.UDP.N.acetylglucosamine","X.UDP.glucuronic.acid","X.UDP.glucose...UDP.galactose","X.UDP","X.Tyr.Glu","X.Tyramine","X.Tyr","X.Trp","X.Trimethylamine.N.oxide","X.Trigonelline","X.Triethanolamine","X.Trehalose.6.phosphate","X.trans.Glutaconic.acid...Itaconic.acid","X.threo.beta.Methylaspartic.acid","X.Threonic.acid","X.Thr.Asp","X.Thr","X.Thiaproline","X.Thiamine.phosphate","X.Thiamine","X.Theobromine","X.Taurocholic.acid","X.Taurine","X.Succinic.acid","X.Suberic.acid","X.Stachydrine","X.Spermine","X.Spermidine","X.Sorbitol.6.phosphate","X.S.Nitrosoglutathione","X.S.Methylmethionine","X.S.Lactoylglutathione","X.Serotonin","X.Ser.Glu","X.Ser","X.Sedoheptulose.7.phosphate","X.SDMA","X.Sarcosine","X.S.Adenosylmethionine","X.S.Adenosylhomocysteine","X.Saccharopine","X.Ribulose.5.phosphate","X.Ri

## download_files_from_ftp.R
#'  get_ftp_file_list function:
#'  This function retrieves and returns a list of all files and directories at
#'  a specified FTP URL.
#'  download_ftp_files function:
#'  This function downloads files and directories from a specified FTP URL to a
#'  local directory. It supports recursive downloading, meaning it will enter
#'  and download all contents within subdirectories as well.

# Install required packages
if (!requireNamespace("RCurl", quietly = TRUE)) {

## READ.json.R
READ.json <- function(file){

header = ''
positions = c()
genes = c()

is_header_line = TRUE
is_position_line = FALSE
is_gene_line = FALSE
	#!/usr/bin/env bash
	set -euo pipefail

	#===================================================
	# prepare_mac_env.sh
	# - Mac 環境に必要なパッケージを Homebrew で一括インストール
	# - XcodeGen, swift-format, SwiftLint を準備
	#===================================================

	# 1) Homebrew がなければインストール
	#' DifyChat4R Function (Blocking Mode Only)
	#'
	#' @description
	#' This function sends a chat query to the Dify API using blocking mode.
	#' It returns the complete parsed JSON response from the API.
	#'
	#' @param query A character string representing the user's input query.
	#' @param user A character string representing the user identifier. Default is "abc-123".
	#' @param api_key A character string for the Dify API secret key.
	#' Defaults to the value of the environment variable "DIFY_API_KEY".
	system_set = c("
	You will be provided with a script from a video or URL. Summarize the content without altering the speaker's intention in Japanese. Create summaries in different lengths: 1 bullet point, 3 bullet points, 5 bullet points, 10 bullet points, and 20 bullet points.

	日本語の場合には要約は「です」「ます」調で答えてください。
	箇条書きは、1つずつ \n で改行してください。

	# Steps

	1. Review the provided a video script or URL carefully to understand the main ideas and key points.
	2. Identify core messages and intentions conveyed by the speaker.
	# Required packages
	#library(httr)
	#library(rvest)
	#library(xml2)
	#library(stringi)

	#' Extract Main Content and Decode Unicode Escapes from a Webpage
	#'
	#' This function fetches the HTML content from the specified URL using a custom user agent,
	#' selects the main container identified by the id "__nuxt", removes script and style elements,
	You are an assistant that engages in extremely thorough, self-questioning reasoning. Your approach mirrors human stream-of-consciousness thinking, characterized by continuous exploration, self-doubt, and iterative analysis.

	## Core Principles

	1. EXPLORATION OVER CONCLUSION
	- Never rush to conclusions
	- Keep exploring until a solution emerges naturally from the evidence
	- If uncertain, continue reasoning indefinitely
	- Question every assumption and inference
	#' get_ftp_file_list function:
	#' This function retrieves and returns a list of all files and directories at
	#' a specified FTP URL.
	#' download_ftp_files function:
	#' This function downloads files and directories from a specified FTP URL to a
	#' local directory. It supports recursive downloading, meaning it will enter
	#' and download all contents within subdirectories as well.

	# Install required packages
	if (!requireNamespace("RCurl", quietly = TRUE)) {
	READ.json <- function(file){

	header = ''
	positions = c()
	genes = c()

	is_header_line = TRUE
	is_position_line = FALSE
	is_gene_line = FALSE