getting/setting default working directory options about spades.core HOT 9 CLOSED

From @eliotmcintire on October 24, 2016 16:23

@achubaty Current behaviour doesn't seem desireable:

After setPaths(modules = "desired/path"), paths are set correctly, but do not persist through restart.

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From @eliotmcintire on October 24, 2016 16:28

@achubaty Also, in simInit, any path not specified by user and passed explicitly to paths = arg defaults to active directly, which is not the correct behaviour. I think the correct behaviour is to have spades paths override the active directory.

Order of precedence in the simInit should be, from highest to lowest:

1. paths argument
2. spades.xxxPath
3. if spades.xxxPath is NULL, then active directory

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@eliotmcintire yes, I noted that above. R options (the non-standard ones at least) are not persistent across sessions. Aside from updating all of our docs to teach setting the paths after loading the package, per above, how else can we improve this? Using the current working directory (as we had done previously) is also undesirable.

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@achubaty Also, in simInit, any path not specified by user and passed explicitly to paths = arg defaults to active directly, which is not the correct behaviour. I think the correct behaviour is to have spades paths override the active directory.

Order of precedence in the simInit should be, from highest to lowest:

1. paths argument
2. spades.xxxPath
3. if spades.xxxPath is NULL, then active directory

Hmm, I'm not sure why it's defaulting to the current dir. Sounds like the paths set by the options weren't fully implemented everywhere. I'll take a look.

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From @eliotmcintire on October 24, 2016 16:37

What about wrapping this in the setPaths() function:

assignInNamespace(ns = "SpaDES", x = ".defaultPaths", value = paths)

Then, instead of using options, we are actually using the SpaDES namespace. I think that is allowed because it is a SpaDSE function that is doing it. Then, instead of using "options", we just use an object called SpaDES:::.defaultPaths

That seems to be persistent, at least on Windows. There may be issues on Linux if the package was installed by someone other than the user.

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From @eliotmcintire on October 24, 2016 16:45

Apparently that is not persistent

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Yes, that might work -- when the namespace is reloaded does it keep those values?

Another option is to read/write from/to an options file, but it's not clear where this should be saved. Using the home dir in this case might be fine because the write operation would be invoked only by the user using setPaths().

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see also https://github.com/gaborcsardi/pkgconfig

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Now fully revamped, removing spades.cachePath 7e82ccf and allowing multiple modulePath values 2ee5f26.

Also, during simInit and spades calls, the 4 paths are set in the options are using setPaths, then reset to former options on.exit from both of these.

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