[Bioc-devel] Controlling vignette compilation order

Aaron Lun infinite@monkey@@with@keybo@rd@ @ending from gm@il@com
Sun Dec 23 01:20:37 CET 2018 

Yes, that is the simplest solution, and it’s what I’m doing now.

It’s not overly confusing for a reader, but it’s awkward to add new vignettes in the middle of the compilation order, as I then have to rename the others (or give the new vignette a weird name, e.g., “xtra-3b-de.Rmd” to get it to fall behind “xtra-3-var.Rmd”).

From a practical perspective, this becomes particularly annoying when writing links between vignettes, which needs to know the file name to construct the URL (see BiocStyle::Biocpkg()). If the name is unintuitive and/or changes all the time, these links become difficult to write. External links to vignettes (e.g., in support site posts) would also become invalidated upon name changes.

I guess I find it unpleasant to require the file name to conflate the description of the vignette with the compilation order, and I would like a more explicit mechanism to do this.

-A

> On 22 Dec 2018, at 19:00, Martin Morgan <mtmorgan.bioc using gmail.com> wrote:
> 
> ...but in the end isn't it just simpler to name your vignettes in collation order? Who other than you will be able to parse what you've done?
> 
> Martin
> 
> On 12/22/18, 1:56 PM, "Bioc-devel on behalf of Michael Lawrence" <bioc-devel-bounces using r-project.org on behalf of lawrence.michael using gene.com> wrote:
> 
>    Anything that eventually lands in inst/doc is a vignette, I think, so
>    there might be a hack around that.
> 
>    On Fri, Dec 21, 2018 at 11:26 PM Aaron Lun
>    <infinite.monkeys.with.keyboards using gmail.com> wrote:
>> 
>> I gave it a shot:
>> 
>> https://github.com/LTLA/DrakeTest <https://github.com/LTLA/DrakeTest>
>> 
>> This uses a single “controller” Rmd file to trigger Drake::make. Running this file will instruct Drake to compile all of the other vignettes following the desired dependency structure.
>> 
>> The current sticking point is that I need to move the Drake-controlled Rmd files out of “vignettes/“, otherwise they’ll just be compiled as usual without consideration of their dependencies. This causes problems as R CMD BUILD only recognizes the controller Rmd file as the sole vignette, and doesn’t retain or index the HTML files produced from the other Rmd files as side-effects of running the controller.
>> 
>> Are there any better ways to subvert the vignette building procedure to get the desired effect of running drake::make() and recognition of the resulting HTMLs as vignettes?
>> 
>> -A
>> 
>>> On 18 Dec 2018, at 17:41, Michael Lawrence <lawrence.michael using gene.com> wrote:
>>> 
>>> Sounds like a use case for drake...
>>> 
>>> On Tue, Dec 18, 2018 at 6:58 AM Aaron Lun <infinite.monkeys.with.keyboards using gmail.com <mailto:infinite.monkeys.with.keyboards using gmail.com>> wrote:
>>> @Michael In this case, the resource produced by vignette X is a SingleCellExperiment object containing the results of various processing steps (normalization, clustering, etc.) described in that vignette.
>>> 
>>> I can imagine a lazy evaluation model for this, but it wouldn’t be pretty. If I had another vignette Y that depended on the SCE produced by vignette X, I would need Y to execute all of the steps in X if X hadn’t already been run before Y. This gets us into the territory of Makefile-like dependencies, which seems even more complicated than simply specifying a compilation order.
>>> 
>>> You might ask why X and Y are split into two separate vignettes. The use of different vignettes is motivated by the complexity of the workflows:
>>> 
>>> - Vignette 1 demonstrates core processing steps for one read-based single-cell RNAseq dataset.
>>> - Vignette 2 demonstrates (slightly different) core steps for a UMI-based dataset.
>>> - … so on for a bunch of other core steps for different types of data.
>>> - Vignette 6 demonstrates extra optional steps for the two SCEs produced by vignettes 1 & 3.
>>> - … and so on for a bunch of other optional steps.
>>> 
>>> The separation between core and optional steps into separate documents is desirable. From a pedagogical perspective, I would very much like to get the reader through all the core steps before even considering the extra steps, which would just be confusing if presented so early on. Previously, everything was in a single document, which was difficult to read (for users) and to debug (for me), especially because I had to use contrived variable names to avoid clashes between different sections of the workflow that did similar things.
>>> 
>>> @Martin I’ve been using BiocFileCache for all of the online resources that are used in the workflow. However, this is only for my (and the reader’s) convenience. I use a local cache rather than the system default, to ensure that the downloaded files are removed after package build. This is intentional as it forces the package builder to try to re-download resources when compiling the vignette, thus ensuring the validity of the URLs. For a similar reason, I would prefer not to cache the result objects for use in different R sessions. I could imagine caching the result objects for use by a different vignette in the same build session, but this gets back to the problem of ensuring that the result object is generated by one vignette before it is needed by another vignette.
>>> 
>>> -A
>>> 
>>>> On 18 Dec 2018, at 14:14, Martin Morgan <mtmorgan.bioc using gmail.com <mailto:mtmorgan.bioc using gmail.com>> wrote:
>>>> 
>>>> Also perhaps using BiocFileCache so that the result object is only generated once, then cached for future (different session) use.
>>>> 
>>>> On 12/18/18, 8:35 AM, "Bioc-devel on behalf of Michael Lawrence" <bioc-devel-bounces using r-project.org <mailto:bioc-devel-bounces using r-project.org> on behalf of lawrence.michael using gene.com <mailto:lawrence.michael using gene.com>> wrote:
>>>> 
>>>>   I would recommend against dependencies across vignettes. Ideally someone
>>>>   can pick up a vignette and execute the code independently of any other
>>>>   documentation. Perhaps you could move the code generating those shared
>>>>   resources to the package. They could behave lazily, only generating the
>>>>   resource if necessary, otherwise reusing it. That would also make it easy
>>>>   for people to write their own documents using those resources.
>>>> 
>>>>   Michael
>>>> 
>>>>   On Tue, Dec 18, 2018 at 5:22 AM Aaron Lun <
>>>>   infinite.monkeys.with.keyboards using gmail.com <mailto:infinite.monkeys.with.keyboards using gmail.com>> wrote:
>>>> 
>>>>> In a number of my workflow packages (e.g., simpleSingleCell), I rely on a
>>>>> specific compilation order for my vignettes. This is because some vignettes
>>>>> set up resources or objects that are to be used by later vignettes.
>>>>> 
>>>>> From what I understand, vignettes are compiled in alphanumeric ordering of
>>>>> their file names. As such, I give my vignettes fairly structured names,
>>>>> e.g., “work-1-reads.Rmd”, “work-2-umi.Rmd” and so on.
>>>>> 
>>>>> However, it becomes rather annoying when I want to add a new vignette in
>>>>> the middle somewhere. This results in some unnatural numberings, e.g.,
>>>>> “work-0”, “3b”, which are ugly and unintuitive. This is relevant as
>>>>> BiocStyle::Biocpkg() links between vignettes require you to use the
>>>>> destination vignette’s file name; so difficult names complicate linking,
>>>>> especially if the names continually change to reflect new orderings.
>>>>> 
>>>>> Is there an easier way to control vignette compilation order? WRE provides
>>>>> no (obvious) guidance, so I would like to know what non-standard hacks are
>>>>> known to work on the build machines. I can imagine something dirty whereby
>>>>> one ”reference” vignette contains code to “rmarkdown::render" all other
>>>>> vignettes in the specified order… ugh.
>>>>> 
>>>>> -A
>>>>> 
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>>>>> 
>>>>> 
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