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Migrating from orderly (1.x)

The new version of orderly (version 1.99.x, known as orderly2 during development) is very different to the previously released version on CRAN (orderly 1.4.3; September 2021) or the last development version of the 1.x line (orderly 1.6.x; June 2023; now archived as orderly1). These changes constitute a ground-up rewrite in order to bring out the best features we found that orderly enabled within workflows, while removing some features we felt have outlived their usefulness. This is disruptive change, but we hope that it will be worth it.

This vignette is divided into two parts; one covers the conceptual differences between orderly1 and orderly while the second covers the mechanical process of migrating from an existing orderly source tree and archive to take advantage of the new features.

If you have never used version 1.x of orderly, you should not read this document unless you are curious about the history of design decisions. Instead you should read the introductory vignette (vignette("orderly")).

Summary of changes

So long YAML and thanks for all the whitespace errors

The most obvious user-facing change is that there is (almost) no YAML, with the definition of inputs and outputs for a report now defined within an orderly file, <reportname>.R. So an orderly report that previously had an orderly.yml file that looked like

parameters:
  n_min:
    default: 10
script: script.R
source:
  - functions.R
resources:
  - metadata.csv
depends:
  raw_data:
    id: latest
    use:
      raw_data.csv: data.csv
artefacts:
  data:
    description: Processed data
    filenames: data.rds

would end up within an orderly file that looks like:

pars <- orderly_parameters(n_min = 10)
orderly_dependency("raw_data", "latest",
                            files = c("raw_data.csv" = "data.csv"))
orderly_resource("metadata.csv")
orderly_artefact(description = "Processed data", "data.rds")
source("functions.R")

We think this is much clearer, and comes with documentation and autocomplete support in most IDEs.

In fact, for simple reports, no special functions are required, though you’ll find that some will be useful (see vignette("orderly"))

Some specific changes:

you no longer need to list packages with packages:, instead just use library() as in an ordinary script. We will record the state of the session regardless so you will get a record of what was used
you no longer need to use sources: to list scripts you want to source, instead use source() as normal
global_resources has become orderly_shared_resource (these aren’t really global so much as shared). Note that the directory they are in is now always shared/ at the orderly root, you may not configure it.

Implications

This change has widespread implications:

you can program against things like dependencies, creating a for loop over a series of parameter values, or conditionally depending on other reports
any R script can be the basis of an orderly report, and you can add orderly functions annotating inputs and outputs progressively

Database support has been moved into a plugin

In version 1, we had built-in support for accessing data from SQL databases; this has moved within the orderly.db plugin. All major features are supported.

No more commit

orderly no longer requires a separate orderly_commit() call after orderly_run(); we no longer make a distinction between local draft and archive packets. Instead, we have added finer-grained control over where dependencies are resolved from (locally, or from some subset of your servers), which generalises the way that draft/archive was used in practice. See ?orderly_run for more details on how dependencies are resolved.

This has implications for deleting things; the draft directory was always an easy target for deletion, but now after deletion you will need to tell orderly that you have deleted things. See vignette("introduction") for details on this (section “Deleting things from the archive”).

No more testing or development mode

We have had two different, but unsatisfactory, mechanisms for developing an orderly report:

orderly_test_start (up to version 1.1.0)
orderly_develop_start (from 1.1.0 onwards)

These worked by doing the initial setup, and copying of dependencies etc to a location you could work (a new draft for orderly_test_start and the source directory for orderly_develop_start). From orderly you can just work directly within the source directory, and so long as your working directory is set to src/<report-name>, all orderly commands will work as expected.

As with orderly1, you will need to be careful not to commit (to git) results of running your analysis, and we encourage per-report .gitignore files to help with this.

New, language-agnostic, backend

The biggest change, but perhaps the least visible, is that orderly is now built on an open spec outpack which can be implemented for any language. We will develop a Python implementation of this, and possibly other languages.

This takes control of all the metadata. As such there is a split between “orderly_” and “outpack_” functions in this package, for more information see the last section of vignette("introduction") and also vignette("outpack").

Other, smaller changes

“Global” resources have become “shared” resources, and always live in shared/ at the orderly root (i.e., this is no longer configurable). The reason for this is that we want reports to be able to be run fairly independently of the orderly configuration (the only exception to this are plugins). In practice people did not really vary this.

You can depend on anything; if a packet has produced a file you can depend on it, regardless of if it was an artefact, a resource or simply just present.

What is missing compared with `orderly1`

the changelog feature (we may implement something to support this)
extraction of secrets from vault (we may support this)
automatic handling of README files (we may implement support for this)

How to migrate

There are two parts to a migration: updating the canonical copy of your orderly archive (ideally you only have one of these) and updating your source tree. These steps should be done via the outpack.orderly package.

You should migrate your archive first. Do this for every archive that you want to retain (you might have archives stored locally, on production servers and on staging servers). Archive migration happens out of place; that is, we do not modify anything in the original location. If your archive is old and has been used with very old versions of orderly1 it is possible that this process will have a few hiccups. Please let us know if that is the case. The result of this process is that you will end up with a new directory that contains a new archive conforming to the outpack spec and containing orderly metadata.

Next, migrate your source tree. This will be done in place so should be done on a fresh clone of your source git repository. For each report, we will examine your orderly.yml files and your script files (often script.R), delete these, and then write out a new orderly file that will adapt your report to work for orderly. It is possible that this will not be perfect and might need some minor tweaking but hopefully it will be reasonable. One thing that is not preserved (and we probably cannot do so) is the comments from the yaml but as these often refer to yaml formatting or orderly1 features hopefully this is not too much of a problem. You will probably want to manually tweak the generated code anyway, to take advantage of some of the new orderly features such as being able to compute dependencies.

If you are using OrderlyWeb, you probably need to pause before migrating, as the replacement is not yet ready.

What about the packages?

We have renamed the original version of the package as orderly1 so that you can use it with existing projects without migrating; this can be safely installed alongside this new orderly package.

What were the problems in version 1

The YAML format is inflexible, error prone for users, and leads to duplication
It was too focussed around our initial needs with the Vaccine Impact Modelling Consortium
It was fairly easy to get your archive and SQLite database into an inconsistent state (e.g., by deleting or moving files from the archive)
The SQLite database behaved poorly on shared file systems

Working with old versions without migrating

Sometimes, you will want to use the old version of orderly without migrating any source, for example to rerun something as it was run in 2020. You can do this by installing orderly1, which can be safely installed alongside orderly. You should, however, avoid loading both packages at once (i.e., with library()) as this will cause ambiguity in a number of functions, notably orderly_run()

Install orderly1 with:

install.packages(
  "orderly1",
  repos = c("https://mrc-ide.r-universe.dev", "https://cloud.r-project.org"))

and you can work with the sources or outputs as you wish. You will need to replace any namespaced calls orderly::fn with orderly1::fn (these might appear in your documentation, helper scripts, or similar).

If you try to use orderly (>= 1.99.82) with an orderly1 project, then you will get an error message that will direct you to this document to decide the best way forward.

Users of `orderly2`

Users of the orderly2 package have a little work to do; that package was the precursor to this one (orderly2 version 1.99.81 and orderly 1.99.82 are functionally the same but with references to orderly2 replaced with orderly). You will likely have references to orderly2 remaining in your code that will not necessarily work with the new version without a little work.

First, you will want to upgrade from orderly2 to the most recent version (2.0.0) of orderly by uninstalling orderly2:

remove.packages("orderly2")

and installing orderly:

install.packages(
  "orderly",
  repos = c("https://mrc-ide.r-universe.dev", "https://cloud.r-project.org"))

As always, please do this in a fresh session.

In the simplest cases there is nothing more to do!

Most users will have references to orderly2 in their code though, for example within an orderly source report you might have something like

orderly2::orderly_parameter(...)

which needs updating to use orderly. A few alternative solutions are available:

migrate your source code
use the built-in compatibility support
install the orderly2 compatibility package

Migrate your source code

The best solution to use if you are happy modifying your source code. We require a clean clone of your repository (git status should report no modified or unknown files). You can then run:

orderly_migrate_source()

which will rewrite some simple references to orderly2 for you. In particular it will replace

orderly2::fn with orderly::fn
library(orderly2) with library(orderly)

It will also update the minimum required version in the orderly_config.json to at least 2.0.0 (or migrate orderly_config.yml to orderly_config.json and update that file).

Review the changes that this function has made by running git diff, and if happy commit them.

You might like to check for other missed occurrences of orderly2, by running something like

grep --exclude-dir .git -r orderly2 .

which will show you remaining occurrences in files that we do not scan or change. Run this in the shell, not from R!

Use the built-in compatibility support

Sometimes you will not be able to migrate the source code (e.g., working with an old project, or if you are working on a feature branch ahead of doing the migration). In this case, so long as you have the new version of orderly installed along with pkgload (which is a dependency of devtools) then we will automatically load a compatibility package that will interpret all references to orderly2 as references to orderly on the fly.

We will retain this support within orderly for a few versions, but will add a warning where it is used soon to encourage you to migrate.

Install the `orderly2` compatibility package

Run

install.packages(
  "orderly2",
  repos = c("https://mrc-ide.r-universe.dev", "https://cloud.r-project.org"))

to install a package that will interpret references to orderly2 as references to orderly on the fly. This solution will be available for the foreseeable future.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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