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# Compare hashes of identically named files across two project versions,
# e.g. if the project was run again with different versions of dependencies.
# >>> Assumes files are uniquely named within a project <<<
# (replace vector of paths appropriately)

library(digest)
library(tidyverse)

files_to_check_01 <- list.files(
  # Check all of the files in these directories

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# Extract a list of citation keys from an Rmd file,
# paste them together to search in Mendeley to make
# a list of references in that Rmd file

rmd_file <- "path_to_Rmd_file"

citations <- 
  readr::read_lines(rmd_file) %>% 
  stringr::str_split(" |;") %>% 
  unlist %>% 

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---
apiVersion: v1
kind: Service
metadata:
  name: resolver
  namespace: gn
  labels:
    app: resolver
    tier: frontend
spec:

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library(bib2df)
library(rcrossref)
library(tidyverse)

# Double check to make sure DOIs in bibliography match the right papers

# Load clean bibliography, select just relevant columns
path_to_bib <- "ms/references.bib"

bib <- bib2df(path_to_bib) %>%

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library(tidyverse)

# Find the names of latex packages installed by tlmgr
# (https://www.tug.org/texlive/tlmgr.html)
# The main reason to do this is so they can be pre-installed to a docker image.
#
# The latex package install output from tlmgr tends to look like this:
#
# ```
# tlmgr search --file --global '/multirow.sty'

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library(tidyverse)

# Extract names of files in a "data_raw" folder 
# and append "put" so they can easily be uploaded to
# a server using sftp

plan_lines <- read_lines("code/world_biogeo_plan.R")

plan_lines %>%
  magrittr::extract(str_detect(., "data_raw")) %>%

joelnitta

#' Write out a list of DNA sequences in chunks
#' 
#' The list will be split into a list of lists, to
#' save memory when writing out sequences.
#'
#' @param fasta_list The list of DNA sequences
#' @param chunk_size Size of chunks to split up list into.
#' @param out_dir Directory to write to
#'
#' @return List of hashes; digest of each chunk. Externally, the 

joelnitta

joelnitta@Joels-iMac repos % git clone https://github.com/joelnitta/i18n
Cloning into 'i18n'...
remote: Enumerating objects: 1672, done.
remote: Total 1672 (delta 0), reused 0 (delta 0), pack-reused 1672
Receiving objects: 100% (1672/1672), 2.73 MiB | 2.43 MiB/s, done.
Resolving deltas: 100% (1167/1167), done.
joelnitta@Joels-iMac repos % cd i18n
joelnitta@Joels-iMac i18n % git submodule init
Submodule 'git-novice' (https://github.com/swcarpentry-i18n/git-novice.git) registered for path 'git-novice'
Submodule 'po4gitbook' (https://github.com/swcarpentry-i18n/po4gitbook.git) registered for path 'po4gitbook'

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# Set working directory
setwd(here::here())

# Load packages and functions
source("r-code/01_start_up.R")

# Load plan
source("r-code/plan.R")

# Load cache

joelnitta

#!/usr/bin/bash

# Start docker daemon in background
nohup dockerd-rootless.sh --experimental --storage-driver vfs >| dockerd.log 2>&1 &
# Save the process ID so we can kill it later
echo $! > dockerd.pid