Package 'sourcoise'

sources R script and caches results on disk

Description

sourcoise() is used as a drop in replacement for base::source() but caches results on disk. Cache is persistant over sessions.

Usage

sourcoise(
  path,
  args = list(),
  track = list(),
  lapse = getOption("sourcoise.lapse"),
  force_exec = getOption("sourcoise.force_exec"),
  prevent_exec = getOption("sourcoise.prevent_exec"),
  metadata = getOption("sourcoise.metadata"),
  wd = getOption("sourcoise.wd"),
  src_in = getOption("sourcoise.src_in"),
  exec_wd = NULL,
  root = NULL,
  quiet = TRUE,
  nocache = FALSE,
  inform = FALSE,
  log = getOption("sourcoise.log"),
  grow_cache = getOption("sourcoise.grow_cache"),
  limit_mb = getOption("sourcoise.limit_mb")
)

Arguments

path	(character) path of the script to execute (see details).
args	(list) list of args that can be used in the script (in the form args$xxx).
track	(list) list of files which modification triggers cache invalidation and script execution .
lapse	(character) duration over which cache is invalidated. Could be never (default) ⁠x hours⁠, ⁠x days⁠, ⁠x week⁠, ⁠x months⁠, ⁠x quarters⁠, ⁠x years⁠.
force_exec	(boolean) execute code, disregarding cache valid or invalid.
prevent_exec	(boolean) prevent execution, cache valid or not, returned previous cached data, possibly invalid.
metadata	(boolean) if TRUE sourcoise() returns a list with data is the ⁠$data⁠ and various meta data (see details).
wd	(character) if project working directory for the execution of script will be the root of the project. If file then it will be the dir of the script (défaut) If qmd, then working dir will be the dir in which the calling qmd is. Current directory is restored after execution (successful or failed).
src_in	(character) if project searches for source starting at the root of the project, if "file" searches in qmd dir. If "wd", then in working directory. Cache folder (.sourcoise) is stored there.
exec_wd	(character) force exec dir (expert use).
root	(character) force root (expert use).
quiet	(boolean) mute messages and warnings from script execution.
nocache	(boolean) no caching.
inform	(boolean) Display logs on console, even if logging is disabled with threshold level "INFO".
log	("OFF" par défaut) log threshold (see logger::log_treshold()).
grow_cache	(5 par défaut) cache limit in number of data file kept.
limit_mb	(50 par défaut) individual cache data files size on disk limit. If above no caching.

Details

sourcoise() looks like base::source(). However, there are some minor differences.

First, the script called in sourcoise() must end by a return() or by an object returned. Assignment made in the script won't be kept as sourcoise() is executed locally. Only explicitly reruned object will be returned. So soucoise() is used by assigning its result to something (⁠aa <- sourcoise("mon_script.r)⁠ or ⁠sourcoise() |> ggplot() ...⁠). Unless specified otherwise with wd parameter, the working directory for the script execution is (temporarly) set to the dir in which is the script. That allows for simple access to companion files and permit to move the script and companion files to another dir or project.

Second, an heuristic is applied to find the script, in the event the path given is incomplete. Whereas it is not advised and comes with a performance cost, this can be useful when there is a change in the structure of the project. The heuristic is simple, the script is searched inside the porject dir and among all hits the closest to the caller is returned.

Third, if an error is triggered by the script, sourcoise() does not fail and return the error and a NULL return. However, if there is a (invalid or valid) cache, the cached data is returned allowing for the script to continue. In that case the error is logged.

Cache is invalidated when : 1 - a cache is not found 2 - the script has been modified 3 - tracked files have been modified 4 - last execution occurred a certain time ago and is considered as expired 5 - execution is forced

If src_in="file", then script path is searched from the .qmd dir. If no .qmd esxits (or is not the caller) the the current work dir is used (which is the usual way base::source works). If src_in="project", then script path is searched from the root dir of the project, being a Rproject or a quarto project, using the package {rprojroot}. This guarantees to find the script without using current working directory and is a more robust way to proceed.

Usually the fisrt call return and cache the results. Results can be aby R object and are serialized and saved using qs2. Subsequent calls, supposing none of cache invalidation are true, are then very quick. No logging is used, data is fecteched from the cache and that's it. For standard size data, used in a table or a graph (< 1Mb roughly), return timing is under 5ms.

lapse parameter is used for invalidation trigger 4. lapse = "1 day" ou lapse="day" for instance will trigger once a day the execution. lapse = "3 days" will do it every 72h. hours, weeks, months, quarters or years are understood time units. MOre complex calendar instructions could be added, but sourcoise_refesh() provides a solution more general and easy to adapt to any use case, as to my knowledge, there is no general mechanism to be warned of data updates.

track is the trigger #3. It is simply a list of files (following path convention defined by scr_in, so either script dir of project dir as reference). If the files in the list are changed then the execution is triggered. It is done with a hash and it is difficult to have a croo plateform hash for excel files. Nevertheless, hash is done on text files with same results of different platforms.

If metadata=TRUE, a list is returned, with some metadatas. Main ones are ⁠$data⁠, the data returned, ⁠$date⁠, execution date, ⁠$timing⁠ execution timing, ⁠$size⁠ of the R object in memory, ⁠$data_file⁠, ⁠$data_date⁠ and ⁠$file_size⁠ documenting data file path, date size on disk and last modification date, parameters of the call (⁠$track⁠, ⁠$wd⁠, ⁠$src_in⁠, ⁠$args⁠ and so on).

force_exec and prevent_exec are parameters that force the script execution (trigger #5) of prevent it (so cache is returned or NULL if no cache). Those 2 parameters can be set for one specific execution, but they are intendend to a global setting through the option sourcoise.force_exec or sourcoise.prevent_exec.

If returned data after execution is not different than previously cached data, then no caching occurs in order to limit the disk use and to avoid keeping an history of the same data files. This implies the possibility of a difference between last execution date and last data modification date. If you are insterested in the moment data was changed, then ⁠$data_date⁠ is to be preferred.

Working with github : sourcoise() is designed to function with github. Cache information is specific to each user (avoiding conflicts) and cached data is named with the hash. Conflicts could occur in the rare case the same script is executed on different machines and that this script return each time a different result (such as a random generator).

Value

data (list ou ce que le code retourne)

See Also

Other sourcoise: sourcoise_clear(), sourcoise_refresh(), sourcoise_reset(), sourcoise_status()

Examples

dir <- tempdir()
fs::file_copy(
   fs::path_package("sourcoise", "ipch", "prix_insee.R"),
  dir,
  overwrite = TRUE)
# Force execution (root is set explicitly here, it is normally deduced from project)
data <- sourcoise("prix_insee.R", root = dir, force_exec = TRUE)
# The second time cache is used
data <- sourcoise("prix_insee.R", root = dir)


# Performance and mem test
dir <- tempdir()
fs::file_copy(
   fs::path_package("sourcoise", "ipch", "prix_insee.R"),
   dir,
   overwrite = TRUE)
bench::mark(
 forced = data <- sourcoise("prix_insee.r", root = dir, force_exec = TRUE),
 cached = data <- sourcoise("prix_insee.r", root = dir),
 max_iterations = 5)

---

Cleans sourcoise cache

Description

removes every json and qs2 files found by sourcoise_status() unless a specific tibble (filtered from sourcoise_status()) is passed as an argument.

Usage

sourcoise_clear(
  what = sourcoise_status(root = root, prune = FALSE),
  root = NULL
)

Arguments

what	(–) a tibble such as the one obtained by sourcoise_status(), possibly filtered
root	to force root, not recommended (expert use)

Value

list of cleared files, plus a side-effect as specified cache files are deleted (no undo possible)

See Also

Other sourcoise: sourcoise(), sourcoise_refresh(), sourcoise_reset(), sourcoise_status()

Examples

dir <- tempdir()
fs::file_copy(
    fs::path_package("sourcoise", "ipch", "prix_insee.R"),
    dir,
    overwrite = TRUE)
# Force execution (root is set explicitly here, it is normally deduced from project)
data <- sourcoise("prix_insee.R", root = dir, force_exec = TRUE)
# we then clear all caches
sourcoise_clear(root = dir)
sourcoise_status(root = dir)

---

Refresh sourcoise cache by executing sources selected

Description

All scripts (passed to sourcoise_refresh()) are executed with logging enabled.

Usage

sourcoise_refresh(
  what = NULL,
  force_exec = TRUE,
  unfreeze = TRUE,
  quiet = FALSE,
  init_fn = getOption("sourcoise.init_fn"),
  root = NULL,
  log = "INFO",
  .progress = TRUE
)

Arguments

what	(tibble) a tibble as generated by sourcoise_status(), possibly filtered, (defaut to source_status() )
force_exec	(boolean) (default FALSE) if TRUE code is executed, no matter what is cached
unfreeze	(boolean) (default TRUE) when possible, unfreeze and uncache .qmd files in a quarto project when data used by those .qmd has been refreshed
quiet	(boolean) (default FALSE) no message if TRUE
init_fn	(function) (default NULL) execute a function before sourcing to allow initialization
root	(default NULL) force root to be set, instead of letting the function finding the root, for advanced uses
log	(character) (default "INFO") log levels as in logger::log_threshold() (c("OFF", "INFO", ...)), comes with a small performance cost
.progress	(boolean) (default TRUE) displays a progression bar based on previous execution timings

Details

The function returns the list of script executed but its main effect is a side-effect as scripts are executed and caches updates accordingly. Note also that log files reflect execution and track possible errors. Because of logging the execution comes with a loss in performance, which is not an issue if scripts are long to execute.

It is possible to execute sourcoise_refresh() without execution forcing (force_exec=FALSE) or with it. Forced execution means that the script is executed even if the cache is valid. In the case of non forced execution, execution is triggered by other cache invalidation tests (change in source file, lapse or tacked files).

When scripts are linked to qmds (i.e. when run in a quarto project), it is possible to unfreeeze and uncache those qmds with the option unfreeze=TRUE. This allows to refresh the cahe and then render the qmds using the new data.

It is possible to pass to refresh a function that will be executed before every script. This allows to load packages and declare global variables that can be used in each script. If packages are loaded inside the script, then this is not needed.

Parameters registered ins sourcoise_status() such as wd or args are used to execute the script.

Value

a list of r scripts (characters) executed, with timing and success and a side effect on caches

See Also

Other sourcoise: sourcoise(), sourcoise_clear(), sourcoise_reset(), sourcoise_status()

Examples

dir <- tempdir()
fs::file_copy(
   fs::path_package("sourcoise", "ipch", "prix_insee.R"),
   dir,
   overwrite = TRUE)
# Force execution (root is set explicitly here, it is normally deduced from project)
data <- sourcoise("prix_insee.R", root = dir, force_exec = TRUE)
# we then refresh all caches
sourcoise_refresh(root = dir)

---

Resets sourcoise

Description

Removes all .sourcoise folders found under the project root.

Usage

sourcoise_reset(root = NULL)

Arguments

root	to force root (expert use)

Value

No return, effect is through removal of .sourcoise folders (this is a side effect, no undo possible)

See Also

Other sourcoise: sourcoise(), sourcoise_clear(), sourcoise_refresh(), sourcoise_status()

Examples

dir <- tempdir()
fs::file_copy(
   fs::path_package("sourcoise", "ipch", "prix_insee.R"),
   dir,
   overwrite = TRUE)
data <- sourcoise("prix_insee.R", root = dir, force_exec = TRUE)
sourcoise_reset(root = dir)

---

Cache status of sourcoise

Description

Given the current project, soucoise_status() collects all information about cache (could be project level, file level) and return a tibble with this data.

Usage

sourcoise_status(quiet = TRUE, root = NULL, prune = TRUE, clean = FALSE)

Arguments

quiet	(boolean) (default TRUE) no messages during execution
root	(string) (default NULL) force root to a defined path, advanced and not recommanded use
prune	(boolean) (default TRUE) clean up status to display only on relevant cache. However, does not clean other cache files.
clean	(boolean) (default FALSE) check if some data files have not json referring to them and cleans if any.

Details

sourcoise_status() reflects what is on the disk (and results indeed from a scan of all cached files and their metadatas). So modifying the result of sourcoise_status() can produce complex bugs when it is passed to sourcoise_refresh() or sourcoise_clean().

Data returned is:

• src: path to the source file (r script)

• date: last execution date

• valid: is cache valid ?

• uid: id of user

• index: index of cache

• timing: last execution timing

• size: size of the R object(s) returned

• lapse: periodic refresh trigger

• wd: wd setting for execution of r script

• args: arguments passed to R script

• json_file: path to the file keeping cache information

• qmd_file: list of path to qmd files calling this script (relevant only for quarto projects)

• src_in: localisaiton of cache option

• data_file: path to data cached

• data_date: date and time of last save of data

• log_file: path to log file, if logging activated

• root: path to the project root, used as reference for all paths

• scr_hash: hash of the source file

• track_hash: hash of the tracked files, if any

• track: list of files tracked

• args_hash: hash of arguments

• data_hash: hash of data cached

Value

tibble of cached files (see details for structure)

See Also

Other sourcoise: sourcoise(), sourcoise_clear(), sourcoise_refresh(), sourcoise_reset()

Examples

dir <- tempdir()
fs::file_copy(
    fs::path_package("sourcoise", "ipch", "prix_insee.R"),
    dir,
    overwrite = TRUE)
# Force execution (root is set explicitly here, it is normally deduced from project)
data <- sourcoise("prix_insee.R", root = dir, force_exec = TRUE)
# status returns the cache status
sourcoise_status(root = dir)

---