Package: orderly 2.0.3

Rich FitzJohn

orderly: Lightweight Reproducible Reporting

Distributed reproducible computing framework, adopting ideas from git, docker and other software. By defining a lightweight interface around the inputs and outputs of an analysis, a lot of the repetitive work for reproducible research can be automated. We define a simple format for organising and describing work that facilitates collaborative reproducible research and acknowledges that all analyses are run multiple times over their lifespans.

Authors:Rich FitzJohn [aut, cre], Robert Ashton [aut], Martin Eden [aut], Alex Hill [aut], Wes Hinsley [aut], Mantra Kusumgar [aut], Paul Liétar [aut], James Thompson [aut], Katy Gaythorpe [aut], Imperial College of Science, Technology and Medicine [cph]

orderly_2.0.3.tar.gz
orderly_2.0.3.zip(r-4.7)orderly_2.0.3.zip(r-4.6)orderly_2.0.3.zip(r-4.5)
orderly_2.0.3.tgz(r-4.6-any)orderly_2.0.3.tgz(r-4.5-any)
orderly_2.0.3.tar.gz(r-4.7-any)orderly_2.0.3.tar.gz(r-4.6-any)
orderly_2.0.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
orderly/json (API)

# Install 'orderly' in R:
install.packages('orderly', repos = c('https://mrc-ide.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/mrc-ide/orderly/issues

On CRAN:

Conda:

9.84 score 11 stars 3 packages 142 scripts 703 downloads 52 exports 31 dependencies

Last updated from:5a7bb0c456 (on main). Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK255
source / vignettesOK180
linux-release-x86_64OK204
macos-release-arm64OK143
macos-oldrel-arm64OK109
windows-develOK252
windows-releaseOK215
windows-oldrelOK227
wasm-releaseOK110

Exports:orderly_artefactorderly_cleanuporderly_cleanup_statusorderly_compare_packetsorderly_comparison_explainorderly_configorderly_config_setorderly_copy_filesorderly_dependencyorderly_descriptionorderly_exampleorderly_example_showorderly_gitignore_updateorderly_hash_dataorderly_hash_fileorderly_initorderly_interactive_set_search_optionsorderly_list_srcorderly_location_addorderly_location_add_httporderly_location_add_packitorderly_location_add_pathorderly_location_fetch_metadataorderly_location_listorderly_location_pullorderly_location_pull_metadataorderly_location_pull_packetorderly_location_pushorderly_location_removeorderly_location_renameorderly_metadataorderly_metadata_extractorderly_metadata_readorderly_migrate_sourceorderly_neworderly_parametersorderly_parse_exprorderly_parse_fileorderly_plugin_add_metadataorderly_plugin_contextorderly_plugin_registerorderly_prune_orphansorderly_queryorderly_query_explainorderly_resourceorderly_runorderly_run_infoorderly_searchorderly_search_optionsorderly_shared_resourceorderly_strict_modeorderly_validate_archive

Dependencies:askpasscallrclicrayoncredentialscurldescdiffobjfsgertgluehttr2jsonlitelifecyclemagrittropensslotelpkgbuildpkgloadprocessxpsR6rappdirsrlangrprojrootrstudioapisysvctrswithryamlzip

Collaborative analysis
Type of location | An example | Possible working patterns | Pulling complete trees, or not | Moving as little data as possible | Interaction between source tree and .outpack | Sharing packets with collaborators using a shared file system
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Last update: 2025-10-08
Started: 2023-08-07

Creating plugins
The basic idea | An example | Create a tiny package | Handle the configuration | Evaluate the query | Trying it out | Making the plugin more robust | Saving metadata about what the plugin did | Potential uses
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Last update: 2025-10-08
Started: 2023-07-26

Dependencies between packets
Using dependencies | Basic use | Filtering candidates by parameters | Interpreting errors | Filtering candidates in other ways | Computing dependencies and using many dependencies at once | How dependencies interact with locations | Other points
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Last update: 2025-10-08
Started: 2023-08-07

Details
orderly.quiet | orderly.index_progress | orderly.schema_validate | orderly.disable_orderly2_compat | orderly.git_error_ignore | orderly.git_error_is_warning | orderly.interactive_parameters_missing_error | Environment variables
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Last update: 2025-10-08
Started: 2025-10-07

Introduction to orderly
Installation | Creating an empty orderly repository | Creating your first orderly report | Depending on packets from another report | Available in-report orderly commands | Parameterised reports | Shared resources | Strict mode | Interactive development | Deleting things from the archive | Interaction with version control | Interaction with the outpack store | Relationship between orderly and outpack
Rendered fromintroduction.Rmdusingknitr::rmarkdown

Last update: 2025-10-08
Started: 2023-07-20

Migrating from orderly (1.x)
Summary of changes | So long YAML and thanks for all the whitespace errors | Implications | Database support has been moved into a plugin | No more commit | No more testing or development mode | New, language-agnostic, backend | Other, smaller changes | What is missing compared with orderly1 | How to migrate | What about the packages? | What were the problems in version 1 | Working with old versions without migrating | Users of orderly2 | Migrate your source code | Use the built-in compatibility support | Install the orderly2 compatibility package
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Last update: 2025-10-08
Started: 2023-07-20

orderly
Collaborative analysis | Reproducible analyses | Difference from a workflow system | What is reproducibility anyway? | I'm in, where do I start?
Rendered fromorderly.Rmdusingknitr::rmarkdown

Last update: 2025-10-08
Started: 2025-09-12

Orderly query DSL
Structure of queries | Special simple queries | Scoping queries | Scoping on name | Dependencies | Possible future queries and interface improvements | Simple things | Explain the query
Rendered fromquery.Rmdusingknitr::rmarkdown

Last update: 2025-10-08
Started: 2023-07-20

Outpack metadata
Basic overview | What goes into a packet | Types of users of outpack | Directory layout | Configuration (.outpack/config.json) | Packet metadata (.outpack/metadata/) | Location information (.outpack/location/) | A file store (.outpack/files) | An archive (archive/ by default) | Adding a packet | Adding metadata | Adding files | Marking the packet as unpacked and known locally | Ordering of operations | Details | Outpack ids | Location ids | Representing hashes | Times | File store
Rendered frommetadata.Rmdusingknitr::rmarkdown

Last update: 2025-10-08
Started: 2023-07-20

Troubleshooting
Outpack files accidentally committed to git | I don't care about my git history at all | I just want this to go away and nothing I have committed is very large | I care about my history but want this stuff gone
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Last update: 2025-10-08
Started: 2023-09-05

Readme and manuals

Help Manual

Help pageTopics
Declare orderly artefactsorderly_artefact
Clean up source directoryorderly_cleanup orderly_cleanup_status
Compare the metadata and contents of two packets.orderly_compare_packets
Print the details of a packet comparison.orderly_comparison_explain
Read configurationorderly_config
Set configuration optionsorderly_config_set
Copy files from a packetorderly_copy_files
Declare a dependencyorderly_dependency
Describe the current packetorderly_description
Copy a simple orderly exampleorderly_example
Show an example fileorderly_example_show
Update a gitignore fileorderly_gitignore_update
Compute a hashorderly_hash_data orderly_hash_file
Initialise an orderly repositoryorderly_init
Set search options for interactive useorderly_interactive_set_search_options
List source reportsorderly_list_src
Add a new locationorderly_location_add orderly_location_add_http orderly_location_add_packit orderly_location_add_path
Fetch metadata from a locationorderly_location_fetch_metadata
List known pack locationsorderly_location_list
Pull one or more packets from a locationorderly_location_pull
Push tree to locationorderly_location_push
Remove a locationorderly_location_remove
Rename a locationorderly_location_rename
Read outpack metadataorderly_metadata
Extract metadata from orderly packetsorderly_metadata_extract
Read outpack metadata json fileorderly_metadata_read
Migrate orderly source codeorderly_migrate_source
Create a new reportorderly_new
Declare orderly parametersorderly_parameters
Parse the orderly entrypoint scriptorderly_parse_expr orderly_parse_file
Add metadata from pluginorderly_plugin_add_metadata
Fetch plugin contextorderly_plugin_context
Register an orderly pluginorderly_plugin_register
Prune orphan packet metadataorderly_prune_orphans
Construct outpack queryorderly_query
Explain a queryorderly_query_explain
Declare orderly resourcesorderly_resource
Run a reportorderly_run
Information about currently running reportorderly_run_info
Query orderly's databaseorderly_search
Packet search optionsorderly_search_options
Copy shared resources into a packet directoryorderly_shared_resource
Enable orderly strict modeorderly_strict_mode
Validate unpacked packets.orderly_validate_archive