I've already asked a similar question, here:
Linking to modules in external directory Compaq Visual Fortran command prompt
And I thought that the first answer was correct (that is, in the manual they say you can simply specify the path name before the module), but after deleting the temporary files in my library folder, this approach seemed to stop working. Trying with the /include[:path] approach, here is my .bat file:
df /include:..\FORTRAN_LIB\ __constants
myIO griddata_mod myfdgen myDiff magneticField /exe:magneticField
And an error is returned saying:
__constants
myIO
griddata_mod
myfdgen
myDiff
magneticField
f90: Severe: No such file or directory
... file is '__constants'
Again, I apologize that this question is VERY specific, but it seems like it should be simple and does not work at all.
p.s. Originally, I was using:
df ..\FORTRAN_LIB\__constants ..\FORTRAN_LIB\myIO
..\FORTRAN_LIB\griddata_mod ..\FORTRAN_LIB\myfdgen
..\FORTRAN_LIB\myDiff magneticField /exe:magneticField
But, as I've said, it stopped working after I deleted the temporary files in my FORTRAN_LIB folder. Also note, these .bat files used only one line, I've broken them into several lines just for readability. I would prefer using the /include[:path] option since that seems like a better solution.
Okay, so I think I figured out a workaround at the very least. I understood that the /include[:dir] specifies to search in "dir" for included files. But it seemed from documentation, that this also specifies to search for USEd modules but that doesn't seem to be the case.
My program now looks like this:
include '..\FORTRAN_LIB\__constants.f90'
include '..\FORTRAN_LIB\computeError.f90'
include '..\FORTRAN_LIB\griddata_mod.f90'
include '..\FORTRAN_LIB\myfdgen.f90'
include '..\FORTRAN_LIB\myDiff.f90'
include '..\FORTRAN_LIB\myIO.f90'
program magneticField
use constants
use computeError_mod
use griddata_mod
use myfdgen_mod
use myDiff_mod
use myIO_mod
implicit none
...
And my DF command like this:
df magneticField /exe:magneticField
And everything seems to work fine. It would be nicer to have the /include[:dir] option, but so long I'm able to reach in a separate directory, I'm satisfied. If anyone can find a better solution I'll switch the checkmark. I hope this helps with anyone else who was confused like me.
Related
I have multiple ecospold (version 1) files with LCI data that I want to convert to a custom excel format. I need all data given in the ecospold file. For my own convinience I want to use python to complete this task.
My research until now has lead me to the following conclusions:
There exist at least two converters (by GLAD and openLCA) to convert ecospold formats (1 and 2) to e.g. the ILCD. But those formats are not helping me to go anywhere, since I need to have all the data accessible in python and in order to then write it into my custom excel format.
To get the data in python, the package pyecospold (https://github.com/sami-m-g/pyecospold) seems to be a suitable choice.
According to the README that can be found at the pyecospold github repository,
ecoSpold = parse_file("data/v1/v1_1.xml") # Replace with your own XML file
should do the job. So I implemented the following lines:
import os
from pyecospold import parse_file, save_file, Defaults
from lxml import etree
cd = os.getcwd()
path_input = cd + r'\inputs\ecospold_test.xml'
# Parse the required XML file to EcoSpold class.
es = parse_file('inputs/ecospold_test.xml')
Now I run into the error:
TypeError: parse_file() missing 2 required positional arguments: 'schema_path' and 'ecospold_lookup'
I understood that a schema in xsd format is needed, therefore I got the schema files from the github and amended my last line of code:
es = parse_file('inputs/ecospold_test.xml', 'inputs/schemas/v1/EcoSpold01Dataset.xsd')
Now there is still one argument missing:
TypeError: parse_file() missing 1 required positional argument: 'ecospold_lookup'
Since I have no experience in parsing xml files in python, I have no idea what to do with this. Additionally, I am confused why the README does not say anything about those additionally needed arguments.
My second idea was to use brightway to get the data into python. But since brightway itself is quite an extensive package, I could not find a simple (or any) way to do this. (Sadly, the notebooks linked in the answer of this question Import Ecoinvent 2.2 Ecospold files into Brightway do not exist anymore)
Another option would of course be to write my own parser. But because I am lacking experience and pyecospold does exactly this (at least in my understanding), I would like to avoid this option.
Additionally, there in openLCA it is possible to read in ecospold files and then export them to an excel format. From this excel format I could of course make my custom excel format. The problem here is that I have no idea how to automize this, because I do not want to read in and export each file individually and manually in openLCA.
If anyone has an idea on how to solve one of my subproblems or a good alternative on how to solve my general problem, I would be very thankful. :)
In package development, each example requires <5s. However, the pair of stan_model() and rstan::sampling() take long times more than 5s as follows:
Examples with CPU or elapsed time > 5s
user system elapsed
fit 1.25 0.11 32.47
So I put \donttest{} for each rstan::sampling() in roxygen comments #'#examples
In examples#'#examples, we should not run sampling() or is there any treatment ?
I had tried to create my package based on the code rstan_package_skeleton(path = 'BayesianAAA') when I was taught from you (Thank you !!) but, I do not understand many things about it.
Previously, rstan_package_skeleton(path = 'BayesianAAA') launched the errors in my computer ( but now the error does not occur).
So, I made my package without the rstan_package_skeleton(), say BayesianAAA, and in my original making, I put the Model_A.stan,Model_B.stan,Model_C.stan,.... in the inst/extdata and I refer my stan files as follows;
scr <- system.file("extdata", "Model_A.stan", package="BayesianAAA")
scr <- rstan::stan_model(scr)
I have many questions about the code rstan_package_skeleton(path = 'BayesianAAA').
1) The first question is How to include my existing stan files and how to refer my .stan files for the rstan::stan_model() ?
According to the page following page, it said that
If we had existing .stan files to include with the package we could use the optional stan_files argument to rstan_package_skeleton to include them.
So, I think I should execute, I am not sure but the following like manner is required;
`rstan_package_skeleton(path = 'BayesianAAA', stan_files = "Model_A.stan" )`.
But I do not know how to write the code for several stan files, say Model_A.stan,Model_B.stan,Model_C.stan in my existing package made without the rstan_package_skeleton(). I do not understand , but the following code is correct ? Since I do not where the files described in the variable stan_files is reflected in the new project created by the rstan_package_skeleton().
`rstan_package_skeleton(path = 'BayesianAAA', stan_files = c("Model_A.stan",`Model_B.stan`,`Model_C.stan` )`.
Here, the another question arise, that is,
2) The second question: Where I execute the code rstan_package_skeleton(path = 'BayesianAAA', stan_files = "Model_A.stan" ) ? I execute it form the R studio console in my existing package project. Is it correct ? And then, the new project arise and it is contained the old existing project. What should I do ?
https://cran.r-project.org/web/packages/rstantools/vignettes/minimal-rstan-package.html
3) I do not quite know about the packages "rstanarm" , but I try to imitate it for my package, but I can not fined any .stan file in it, I am wrong ?
I am sorry for my poor English, and Lack of study about these things.
I would be grateful if you could tell me.
You generally should not be writing a package that calls stan_model at runtime, unless like brms or tmbstan you are generating a Stan program at runtime as opposed to writing it statically. There are dozens of packages on CRAN that provide compiled Stan programs basically by following the build process developed for rstanarm, which is facilitated by the rstantools::rstan_package.skeleton function, the step-by-step guide, and the developer guidelines which directly address your question
CRAN policy permits long installation times but imposes restrictions on the time consumed by examples and unit tests that are much shorter than the time that it takes to compile even a simple Stan program. Thus, it is only possible to adequately test your package if it has pre-compiled Stan programs.
Even then, it can be difficult to sample from a posterior distribution (adequately) in five seconds, so you often have to use small datasets, one chain, a small number of iterations, etc.
It is best to pass the names of your Stan programs (which should end in a .stan extension, not use a period otherwise, and only have ASCII letters, numbers, and the underscore in their names) to rstantools::rstan_package_skeleton(). If doing so from RStudio, I would call it while not in an existing project. Then
During installation, all Stan programs will be compiled and saved in the list stanmodels that can then be used by R function in the package. The rule is that the Stan program compiled from the model code in src/stan_files/foo.stan is stored as list element stanmodels$foo.
There are dozens of R packages that have Stan programs in their src/stan_files directory (although the locations of the Stan programs are going to move to inst/stan for the next rstantools release) that for the most part just followed the vignettes and did not have to do any additional steps except write more R functions.
I have a Powershell (v2.0) script that I am working on.
One of the first things it does is loads a Module (runMySQLQuery.psm1) which includes (amongst other bits) a function to connect to a MySQL Database.
Import-Module runMySQLQuery.psm1
However, this requires that an assembly MySQL.Data.DLL is loaded in order for this to work.
If I place the line:
[void][system.reflection.Assembly]::LoadFrom("C:\PowerShell\modules\runMySQLQuery\MySql.Data.dll")
at the top of my script (separate to the Import-Module entry), then the whole thing works fine.
But I want to be able to load this assembly at the same time as the module, so that I don't have to worry about forgetting to including the assembly each time I use this module.
I tried placing it at the top of the .psm1 file, but that didn't work.
I then added it to my manifest file as:
RequiredAssemblies = #("C:\PowerShell\modules\runMySQLQuery\MySql.Data.dll")
This also didn't work.
Am I missing something here, is there a proper way to include assemblies as part of a module?
n.b. the error I get when it hasn't loaded properly is:
You cannot call a method on a null-valued expression
Can you just try to assign a varialbe a the beginig of you module :
$dumy = [system.reflection.Assembly]::LoadFrom("C:\PowerShell\modules\runMySQLQuery\MySql.Data.dll")
I want to test to see if a require'd file is there or not.
At the present, when I execute this command in Lua:
require "File_That_May_or_May_Not_Be_There.inc"
All is well if he's there. If not, my script is dead on the spot.
Is there a way for me to recover from this ?
I looked HERE on the Lua.Org site and HERE on StackOverflow and haven't seen this answered.
Is there a way to do something like this ?...
if (this_exists("That_File")) then
require "That_File"
else
print "Your file does not exist"
end
I'm trying to let the user have a little better idea of what went wrong, and why.
Use pcall.
local ok, mod = pcall(require, "That_File")
If you don't need to use require, which looks for modules in several locations, you can use
local f,e=loadfile(filename)
if f==nil then
print(e)
else
f()
end
I am trying to run tests by adding a version of tornado downloaded from github.com in the sys.path.
[tests]
recipe = zc.recipe.testrunner
extra-paths = ${buildout:directory}/parts/tornado/
defaults = ['--auto-color', '--auto-progress', '-v']
But when I run bin/tests I get the following error :
ImportError: No module named tornado
Am I not understanding how to use extra-paths ?
Martin
Have you tried looking into generated bin/tests script if it contains your path? It will tell definitely if your buildout.cfg is correct or not. Maybe problem is elsewhere. Because it seem that your code is ok.
If you happen to regularly include various branches from git/mercurial or elsewhere to buildout, you might be interested in mr.developer. mr.developer can download and add package to develop =. You wont need to set extra-path in every section.