### Install Dynverse Packages in Dependency Order (R)

Source: https://context7.com/dynverse/dynverse/llms.txt

This script installs all local dynverse packages in a topologically sorted order based on their dependencies. It requires R and the devtools package. Run from the root of the dynverse monorepo after initializing submodules.

```r
# Run from the root of the dynverse monorepo after cloning all submodules:
# git submodule update --init --recursive

#!/usr/bin/env Rscript
library(dplyr, warn.conflicts = FALSE)
library(purrr, warn.conflicts = FALSE)
library(desc, warn.conflicts = FALSE)
library(devtools, warn.conflicts = FALSE)
requireNamespace("igraph", quietly = TRUE)

setRepositories(ind = 1:4)  # include CRAN, Bioconductor, etc.

# Discover all DESCRIPTION files (excluding revdep/Rcheck artifacts)
files <-
  list.files(path = ".", pattern = "DESCRIPTION", recursive = TRUE, full.names = TRUE) %>%
  discard(grepl("revdep|Rcheck", .)) %>%
  discard(grepl("^ti", .))

# Build a data frame of packages and their inter-dependencies
packages <- map_df(files, function(file) {
  descr <- desc::desc(file = file)
  tibble(
    package = descr$get("Package"),
    version = descr$get("Version"),
    file    = file,
    dir     = gsub("/DESCRIPTION", "", file)
  )
}) %>% mutate(colour = rainbow(n()))

dependencies <- map_df(packages$file, function(file) {
  descr <- desc::desc(file = file)
  descr$get_deps() %>%
    rename(dependency = package) %>%
    mutate(package = descr$get("Package")) %>%
    select(package, dependency, version, type)
})

dyndependencies <-
  dependencies %>%
  inner_join(packages %>% select(package),            by = "package") %>%
  inner_join(packages %>% select(dependency = package), by = "dependency")

# Build igraph and resolve topological order
depgr <- igraph::graph_from_data_frame(d = dyndependencies, directed = TRUE, vertices = packages)
dist  <- igraph::distances(depgr, mode = "in")
dist[is.infinite(dist)] <- 0
dist[dist > 0]          <- 1

if (any(dist * t(dist) > 0)) stop("Circular dependencies detected")

selected_ix  <- c()
to_select_ix <- seq_len(ncol(dist))
while (length(to_select_ix) > 0) {
  wts <- colSums(dist[to_select_ix, to_select_ix, drop = FALSE])
  ix  <- which(wts == 0)
  selected_ix  <- c(selected_ix, to_select_ix[ix])
  to_select_ix <- to_select_ix[-ix]
}

ordered_packages <- packages[selected_ix, ]

# Install each package without re-installing transitive deps (already done in order)
walk(seq_len(nrow(ordered_packages)), function(i) {
  cat("Installing ", i, "/", nrow(ordered_packages), ": ",
      ordered_packages$package[[i]], "\n", sep = "")
  devtools::install(pkg = ordered_packages$dir[[i]], dependencies = FALSE, quiet = TRUE)
})
# Expected: sequential console output "Installing 1/18: dynutils", "Installing 2/18: dyneval", ...

```

--------------------------------

### Build and Run TI Method Container

Source: https://context7.com/dynverse/dynverse/llms.txt

Standard workflow for containerizing a single TI method using Docker and running it. This involves building the image, interactive debugging, and non-interactive execution on example datasets.

```bash
export METHOD=recat

cd ../ti_${METHOD}
chmod +x run.py run.R example.R

# Build the Docker container for this method
docker build -t dynverse/ti_${METHOD} .

# Interactive shell inside the container for debugging
docker run -it --entrypoint bash \
  -v $(pwd):/mnt \
  dynverse/ti_${METHOD}
# Inside the container, run:
# R
# task <- dyncli::main(c("--dataset", "/mnt/example.h5", "--output", "/mnt/output.h5"))

# Run the method non-interactively on an example dataset
docker run \
  -v $(pwd):/mnt \
  dynverse/ti_${METHOD} \
  --dataset /mnt/example.h5 \
  --output  /mnt/output.h5 \
  --verbosity 3
# Expected: HDF5 output.h5 written with trajectory model (milestone network, cell positions, etc.)

# Clean up output artifacts
rm -f output.h5 example.h5
```

--------------------------------

### Initialize All Submodules

Source: https://github.com/dynverse/dynverse/blob/master/helper_scripts/common_commands.md

Initializes and updates all submodules, including nested ones.

```bash
git submodule update --init --recursive
```

--------------------------------

### Update All Repositories

Source: https://github.com/dynverse/dynverse/blob/master/helper_scripts/common_commands.md

Stages all changes, commits them with a message, and pushes to the remote.

```bash
git add *
git commit -m "updated repositories"
git push
```

--------------------------------

### Generate Package Overview Table

Source: https://context7.com/dynverse/dynverse/llms.txt

Auto-generates an `overview.md` table by scanning `DESCRIPTION` files in the monorepo to extract package titles and URLs. Requires `tidyverse`, `desc`, and `glue` libraries.

```r
# Render from R or via: Rscript -e "rmarkdown::render('overview.Rmd')"
library(tidyverse)
library(desc)

df <- tibble(
  description_file = list.files(".", pattern = "DESCRIPTION", recursive = TRUE)
) %>%
  filter(!grepl("revdep|methods/", description_file)) %>%
  rowwise() %>%
  mutate(
    desc    = list(desc::desc(description_file)),
    title   = desc$get_field("Title"),
    url     = desc$get_field("URL", NA),
    package = desc$get_field("Package")
  ) %>%
  arrange(package) %>%
  transmute(
    Package     = glue::glue("[{package}](https://github.com/dynverse/{package})"),
    Travis      = glue::glue("[![Travis](...)](https://travis-ci.org/dynverse/{package})"),
    Appveyor    = glue::glue("[![AppVeyor](...)](https://ci.appveyor.com/project/dynverse/{package})"),
    Codecov     = glue::glue("[![codecov](...)](https://codecov.io/gh/dynverse/{package})"),
    Description = title
  )

knitr::kable(df)
# Expected: markdown table with one row per dynverse package, CI badges, and description.
```

--------------------------------

### Manage Git Submodules for Dynverse Methods (Bash)

Source: https://context7.com/dynverse/dynverse/llms.txt

Standard git commands for managing method submodules within the dynverse repository. These commands are used for initialization, adding new methods, updating existing ones, and checking out specific branches.

```bash
# 1. Initialise all submodules after a fresh clone
git submodule update --init --recursive
```

```bash
# 2. Add a new TI method as a submodule tracking the devel branch
git submodule add -b devel git@github.com:dynverse/mfa.git methods/mfa
```

```bash
# 3. Pull latest commits for every submodule
git submodule foreach git pull
```

```bash
# 4. Check out devel branch on every submodule that has one
git submodule foreach \
  'if [ `git branch --list devel | wc -l` = 1 ]; \ 
   then git checkout devel; else echo "no devel branch"; fi'
```

--------------------------------

### Read and Plot TI Method Output

Source: https://context7.com/dynverse/dynverse/llms.txt

Demonstrates loading an HDF5 trajectory output from any dynverse container and visualizing it using `dynplot::plot_graph()`. Requires `tidyverse` and `dynwrap` libraries.

```r
library(tidyverse)

method <- "recat"

# Create a method definition object from the YAML spec bundled with the container source
dynwrap::create_ti_method_definition(
  paste0("ti_", method, "/definition.yml"),
  script = ""
)

# Read the HDF5 output written by the containerised method
traj <- dynutils::read_h5(paste0("ti_", method, "/output.h5"))

# Visualise the trajectory topology
dynplot::plot_graph(traj)
# Expected: ggplot2 graph where nodes are milestones and edges represent transitions,
#           cells are placed along the edges according to their pseudotime position.
```

--------------------------------

### Checkout Devel Branches for Submodules

Source: https://github.com/dynverse/dynverse/blob/master/helper_scripts/common_commands.md

Checks out the 'devel' branch for each submodule if it exists, after ensuring the main repository is not in a detached state.

```bash
git submodule foreach 'if [ `git status | grep detached | wc -l` = 1 ]; then git checkout master; else echo not detached; fi'
git submodule foreach 'if [ `git branch --list devel | wc -l` = 1 ]; then git checkout devel; else echo no devel branch; fi'
```

--------------------------------

### Encrypt File for Travis CI

Source: https://github.com/dynverse/dynverse/blob/master/helper_scripts/common_commands.md

Encrypts a file using Travis CI's encryption tool, suitable for securely storing credentials. The encrypted file is then added to the repository.

```bash
travis encrypt-file ~/credentials --add
```

--------------------------------

### Propagate License Files Across All Sub-packages

Source: https://context7.com/dynverse/dynverse/llms.txt

An Rscript that iterates through all DESCRIPTION files in the monorepo. It copies root LICENSE and LICENSE.md files to packages missing them, updates the License field in DESCRIPTION, and commits/pushes the changes from within each package directory. It also handles bare submodule paths listed in .gitmodules.

```r
#!/usr/bin/Rscript
library(tidyverse)
library(desc)
library(fs)

descriptions <- list.files(path = ".", pattern = "DESCRIPTION",
                            recursive = TRUE, full.names = TRUE) %>%
  { .[!grepl("revdep", .)] } %>%
  { .[!grepl("Rcheck", .)] }

for (desc_file in descriptions) {
  if (!file.exists(gsub("DESCRIPTION", "LICENSE", desc_file))) {
    folder <- gsub("DESCRIPTION", "", desc_file)
    cat("Adding LICENSE to ", folder, "\n", sep = "")

    fs::file_copy("LICENSE",    paste0(folder, "/LICENSE"))
    fs::file_copy("LICENSE.md", paste0(folder, "/LICENSE.md"))

    des <- desc(desc_file)
    des$set("License", "MIT + LICENSE file")
    des$write()

    system(paste0(
      "pushd '", folder,
      "' && git add DESCRIPTION LICENSE LICENSE.md",
      " && git commit -m 'update license'",
      " && git push && popd"
    ))
  }
}
# Also handles bare submodule paths listed in .gitmodules
subrepos <- readr::read_lines(".gitmodules") %>%
  .[grepl("path = ", .)] %>%
  gsub(".* = ", "", .)

for (repo in subrepos) {
  if (!file.exists(paste0(repo, "/LICENSE"))) {
    cat("Adding LICENSE to ", repo, "\n", sep = "")
    fs::file_copy("LICENSE",    paste0(repo, "/LICENSE"))
    fs::file_copy("LICENSE.md", paste0(repo, "/LICENSE.md"))
    system(paste0(
      "pushd '", repo,
      "' && git add LICENSE LICENSE.md",
      " && git commit -m 'update license'",
      " && git push && popd"
    ))
  }
}
# Expected: console lines "Adding LICENSE to libraries/dyngen/" for each unlicensed package

```

--------------------------------

### Common Credentials for CI/CD

Source: https://github.com/dynverse/dynverse/blob/master/helper_scripts/common_commands.md

Defines common environment variables for Docker and GitHub PAT, typically used in CI/CD pipelines.

```bash
DOCKER_USERNAME=dynverseorg
DOCKER_PASSWORD=73...rK
GITHUB_PAT=dc...29
```

--------------------------------

### Apply Sed Over R Files

Source: https://github.com/dynverse/dynverse/blob/master/helper_scripts/common_commands.md

Finds all R files (including Rmd and Rnw) in the current directory and its subdirectories, and applies a sed substitution command to them.

```bash
find . -type f -regex ".*.Rm?d?" -print0 | xargs -0 sed -i 's#ALL YOUR BASE#ARE BELONG TO US#g'
```

--------------------------------

### Generate Package Dependency Plots

Source: https://context7.com/dynverse/dynverse/llms.txt

Generates and saves PNG plots of package dependencies for each package in the 'dynverse' project. Requires 'igraph', 'ggraph', and 'ggrepel' libraries.

```r
pmap(packages, function(package_oi, dir, ...) {
  pkg_deps <- dependencies %>%
    mutate(oi = (package == package_oi) | (dependency == package_oi),
           upstream = (dependency == package_oi))
  pkg_nodes <- packages %>%
    filter(package %in% c(pkg_deps$package, pkg_deps$dependency)) %>%
    mutate(oi = package == package_oi,
           oi_connected = package %in% unlist(select(filter(pkg_deps, oi), package, dependency)))

  sub_graph <- tidygraph::as_tbl_graph(
    igraph::graph_from_data_frame(d = pkg_deps, directed = TRUE, vertices = pkg_nodes)
  )
  plot <- ggraph(sub_graph, layout = "sugiyama") +
    geom_edge_diagonal(aes(color = type, alpha = oi, linetype = upstream)) +
    geom_node_point(aes(alpha = oi_connected)) +
    ggrepel::geom_label_repel(aes(x = x, y = y, label = name, alpha = oi_connected),
                               nudge_y = 0.1, label.size = 0,
                               fill = "#FFFFFF22", min.segment.length = 0) +
    scale_edge_color_manual("Dependency type", values = color_type) +
    theme_graph() + theme(legend.position = "bottom")

  folder <- paste0(dir, "/man/figures/")
  if (!fs::dir_exists(folder)) fs::dir_create(folder)
  ggsave(paste0(folder, "dependencies.png"), plot, width = 12, height = 7)
})
```

--------------------------------

### Add a New Submodule

Source: https://github.com/dynverse/dynverse/blob/master/helper_scripts/common_commands.md

Adds a new submodule to the repository, specifying the branch to track.

```bash
git submodule add -b devel git@github.com:dynverse/mfa.git methods/mfa
```

--------------------------------

### Reset Local Repositories After BFG

Source: https://github.com/dynverse/dynverse/blob/master/helper_scripts/common_commands.md

Resets local repositories on each user's machine to match the cleaned remote repository, ensuring consistency after large file removal.

```bash
git pull
git reset --hard origin/devel
git checkout master
git reset --hard origin/master
git checkout devel
```

--------------------------------

### Generate Package Dependency Graphs

Source: https://context7.com/dynverse/dynverse/llms.txt

An Rscript that constructs an ecosystem-wide dependency graph using 'igraph' and visualizes it with 'ggraph'. It saves per-package 'neighbourhood' plots to each package's 'man/figures/dependencies.png'. Requires 'tidyverse', 'ggraph', 'tidygraph', 'igraph', 'desc', and 'fs' packages.

```r
#!/usr/bin/Rscript
library(tidyverse)
library(ggraph)
library(tidygraph)
requireNamespace("igraph")
requireNamespace("desc")
requireNamespace("fs")

files <- list.files(path = ".", pattern = "DESCRIPTION",
                    recursive = TRUE, full.names = TRUE)

packages <- map_df(files, function(file) {
  descr <- desc::desc(file = file)
  tibble(package = descr$get("Package"),
         file    = file,
         dir     = gsub("/DESCRIPTION", "", file))
}) %>% filter(!grepl("revdep", dir))

dependencies <- map_df(packages$file, function(file) {
  descr <- desc::desc(file = file)
  descr$get_deps() %>%
    rename(dependency = package) %>%
    mutate(package = descr$get("Package")) %>%
    select(package, dependency, type)
}) %>% filter(dependency %in% packages$package)

# Ecosystem-wide plot
color_type <- c("Depends" = "#001f3f", "Imports" = "#0074D9", "Suggests" = "#39CCCC")
depgr <- igraph::graph_from_data_frame(d = dependencies, directed = TRUE, vertices = packages)
graph <- tidygraph::as_tbl_graph(depgr)

ggraph(graph, layout = "sugiyama") + 
  geom_edge_diagonal(aes(color = type)) + 
  geom_node_point() + 
  ggrepel::geom_label_repel(aes(x = x, y = y, label = name), 
                             nudge_y = 0.1, label.size = 0, 
                             fill = "#FFFFFF22", min.segment.length = 0) + 
  scale_edge_color_manual("Dependency type", values = color_type) + 
  theme_graph() + 
  theme(legend.position = "bottom")

```

--------------------------------

### Remove a Submodule

Source: https://github.com/dynverse/dynverse/blob/master/helper_scripts/common_commands.md

Steps to completely remove a submodule from the repository.

```bash
vim .gitmodules                              # remove relevant section
git add .gitmodules
vim .git/config                              # remove relevant section
git rm --cached path_to_submodule            # no trailing slash
rm -rf .git/modules/path_to_submodule        # no trailing slash
git commit -m "Removed submodule "
rm -rf path_to_submodule
```

--------------------------------

### Re-point Submodule Remotes to Canonical SSH URL

Source: https://context7.com/dynverse/dynverse/llms.txt

Uses 'git submodule foreach' to iterate over all registered submodules and update their origin remote URL to the canonical SSH pattern. This ensures consistent remote access for submodules.

```bash
git submodule foreach \
  'git remote set-url origin \
   `pwd | sed "s#.*/\(.*\)#git@github.com:dynverse/\1.git#"`'
```

--------------------------------

### Update Root Repo and All Submodules

Source: https://context7.com/dynverse/dynverse/llms.txt

A bash script to pull the latest changes for the main dynverse repository and all its registered submodules. It also specifically updates a nested submodule within 'dynbenchmark/results'.

```bash
#!/bin/bash
# Run from the dynverse root directory
git pull                         # update root meta-repo
git submodule foreach git pull   # update every registered submodule
pushd dynbenchmark/results
  git pull                       # update nested results submodule
popd
# Expected: each submodule prints its fetch/merge summary or "Already up to date."
```

--------------------------------

### Update Remote URLs for Submodules

Source: https://github.com/dynverse/dynverse/blob/master/helper_scripts/common_commands.md

Updates the remote origin URL for all submodules to the dynverse GitHub organization. Includes a specific override for the monocle submodule.

```bash
git submodule foreach 'git remote set-url origin `pwd | sed "s#.*/\(.*\)#git@github.com:dynverse/\1.git#"`'
cd methods/monocle; git remote set-url origin git@github.com:dynverse/monocle-release.git; cd ../..
```

--------------------------------

### Remove Large Files from Repository (BFG)

Source: https://github.com/dynverse/dynverse/blob/master/helper_scripts/common_commands.md

Removes large files (blobs) and specified file types from a Git repository using the BFG Repo-Cleaner. This process requires cloning the repository with the --mirror flag and then performing Git garbage collection.

```bash
git clone --mirror git@github.com:dynverse/dynbenchmark.git
java -jar ~/Downloads/bfg-1.13.0.jar --strip-blobs-bigger-than 100K --protect-blobs-from master,devel --delete-files '*.{png,pdf,svg,rds,RData,csv,txt,tsv,ods,xls,xlsx}' dynbenchmark.git
cd dynbenchmark.git
git reflog expire --expire=now --all && git gc --prune=now --aggressive
git push
```

--------------------------------

### Remove a Git Submodule

Source: https://context7.com/dynverse/dynverse/llms.txt

Commands to completely remove a submodule from a Git repository. Ensure to update both .gitmodules and .git/config, and then remove the submodule's cached files and directory.

```bash
vim .gitmodules
git add .gitmodules
vim .git/config
git rm --cached path_to_submodule
rm -rf .git/modules/path_to_submodule
git commit -m "Removed submodule"
rm -rf path_to_submodule
```

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