Review Request : J. Stachelek #11

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jsta commented Nov 3, 2015

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Dear @ReScience/editors,

I request a review for the replication of the following paper:

  • Least-cost modelling on irregular landscape graphs, T.R. Etherington. Landscape
    ecology, 27.7, 2012.

I believe the original results have been faithfully replicated
as explained in the accompanying article.

The repository lives at https://github.com/jsta/ReScience-submission/tree/STACHELEK

git clone https://github.com/jsta/ReScience-submission.git
cd ReScience-submission
git checkout STACHELEK
Rscript -e 'devtools::install_github("jsta/irlgraph", dependencies = TRUE)'
make all

EDITOR

  • Editor acknowledgment
  • Review 1 started (@dmcglinn) Nov 17, 2015
  • Review 2 started (@tpoisot) Nov 18, 2015
  • Review 1 decision [accept/reject] Feb 22, 2016
  • Review 2 decision [accept/reject] Feb 22, 2016
  • Editor decision [accept/reject] March 2, 2016
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My quick search for possible reviewers on Github turned up @Martin-Jung

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jsta commented Nov 3, 2015

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My quick search for possible reviewers on Github turned up @Martin-Jung

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EDITOR-IN-CHIEF

Thank you very much for the submission (as well as the suggested name of the reviewer).
An editor should soon acknowledge the submission to start the review. Don't hesitate to remind us if it was not the case in the next few days.

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rougier commented Nov 3, 2015

EDITOR-IN-CHIEF

Thank you very much for the submission (as well as the suggested name of the reviewer).
An editor should soon acknowledge the submission to start the review. Don't hesitate to remind us if it was not the case in the next few days.

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Another potential reviewer might be @whalend

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jsta commented Nov 6, 2015

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Another potential reviewer might be @whalend

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FedericoV Nov 6, 2015

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A colleague of mine, Duccio Rocchini (http://gis.cri.fmach.it/rocchini/) is quite experience in Python programming and geography and said he'd like to review. @rougier is it ok to invite him as a reviewer for this?

EXTERN

A colleague of mine, Duccio Rocchini (http://gis.cri.fmach.it/rocchini/) is quite experience in Python programming and geography and said he'd like to review. @rougier is it ok to invite him as a reviewer for this?

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Great, I will invite both to register to the board. In the meantime, we found an editor that should soon take over this review. @FedericoV Do you have the GitHub name for Duccio ?

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rougier commented Nov 6, 2015

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Great, I will invite both to register to the board. In the meantime, we found an editor that should soon take over this review. @FedericoV Do you have the GitHub name for Duccio ?

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karthik Nov 9, 2015

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Hi all,
I just wanted to chime in and say that I'll take over as editor of this submission. I'll follow up with reviewer recommendations shortly.

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karthik commented Nov 9, 2015

EDITOR

Hi all,
I just wanted to chime in and say that I'll take over as editor of this submission. I'll follow up with reviewer recommendations shortly.

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karthik Nov 16, 2015

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Just updating the thread that we'll finalize reviewers in a day or two. Sorry for the delay.

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karthik commented Nov 16, 2015

EDITOR

Just updating the thread that we'll finalize reviewers in a day or two. Sorry for the delay.

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Reviewer 1, Dan McGlinn @dmcglinn has accepted.

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karthik commented Nov 17, 2015

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Reviewer 1, Dan McGlinn @dmcglinn has accepted.

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tpoisot Nov 18, 2015

REVIEWER 2

In Makefile, the update_code target is rsync'ing local files (from /home/jose/...).

tpoisot commented Nov 18, 2015

REVIEWER 2

In Makefile, the update_code target is rsync'ing local files (from /home/jose/...).

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tpoisot Nov 18, 2015

REVIEWER 2

code/README.md still has a placeholder text.

tpoisot commented Nov 18, 2015

REVIEWER 2

code/README.md still has a placeholder text.

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jsta Nov 18, 2015

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Thanks @tpoisot. Both of the issues arise because of my uncertainty with how to integrate my existing R package into the submission repo. I left the call to rsync in Makefile for my own benefit (note it is not called by the all target) but this could be removed or replaced by git clone or curl or something else.

I left the code/README.md file in the repo purely because it appears in the code repo of the first article. They place all of their code files at top level of the code folder whereas I follow the R package subfolder conventions. I would prefer simply to remove code/README.md in favor of code/irlgraph/README.md but I defer to the @ReScience/editors.

This also brings up the issue of devtools::install_github() versus R CMD INSTALL. Should I be treating the code associated with the article as static (R CMD INSTALL) or dynamic (devtools::install_github())?

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jsta commented Nov 18, 2015

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Thanks @tpoisot. Both of the issues arise because of my uncertainty with how to integrate my existing R package into the submission repo. I left the call to rsync in Makefile for my own benefit (note it is not called by the all target) but this could be removed or replaced by git clone or curl or something else.

I left the code/README.md file in the repo purely because it appears in the code repo of the first article. They place all of their code files at top level of the code folder whereas I follow the R package subfolder conventions. I would prefer simply to remove code/README.md in favor of code/irlgraph/README.md but I defer to the @ReScience/editors.

This also brings up the issue of devtools::install_github() versus R CMD INSTALL. Should I be treating the code associated with the article as static (R CMD INSTALL) or dynamic (devtools::install_github())?

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tpoisot Nov 18, 2015

REVIEWER 2

For the last point -- I think you can use install_github to point to a particular commit using its hash, so you would keep the benefit of using this but still treat the code as essentially static.

tpoisot commented Nov 18, 2015

REVIEWER 2

For the last point -- I think you can use install_github to point to a particular commit using its hash, so you would keep the benefit of using this but still treat the code as essentially static.

@rougier rougier added the 02 - Review label Nov 19, 2015

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dmcglinn Nov 19, 2015

REVIEWER 1

When I run make all I get the following error:

rsync -av code/irlgraph/vignettes/irlgraph_files/figure-latex/ article
sending incremental file list
rsync: change_dir "/home/danmcglinn/Documents/ReScience-submission//code/irlgraph/vignettes/irlgraph_files/figure-latex" failed: No such file or directory (2)

sent 20 bytes  received 12 bytes  64.00 bytes/sec
total size is 0  speedup is 0.00
rsync error: some files/attrs were not transferred (see previous errors) (code 23) at main.c(1183) [sender=3.1.0]
make: *** [move_images] Error 23

REVIEWER 1

When I run make all I get the following error:

rsync -av code/irlgraph/vignettes/irlgraph_files/figure-latex/ article
sending incremental file list
rsync: change_dir "/home/danmcglinn/Documents/ReScience-submission//code/irlgraph/vignettes/irlgraph_files/figure-latex" failed: No such file or directory (2)

sent 20 bytes  received 12 bytes  64.00 bytes/sec
total size is 0  speedup is 0.00
rsync error: some files/attrs were not transferred (see previous errors) (code 23) at main.c(1183) [sender=3.1.0]
make: *** [move_images] Error 23
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jsta Nov 19, 2015

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I'm sorry to hear that @dmcglinn. My guess is that Make is finding the pre-built vignette and not remaking it. make all requires that the vignette be built with caching in order to generate the figure output. Do you see that make all is calling Rscript -e 'rmarkdown::render("code/irlgraph/vignettes/irlgraph.Rmd")?

Hopefully my latest commit will provide a fix.

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jsta commented Nov 19, 2015

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I'm sorry to hear that @dmcglinn. My guess is that Make is finding the pre-built vignette and not remaking it. make all requires that the vignette be built with caching in order to generate the figure output. Do you see that make all is calling Rscript -e 'rmarkdown::render("code/irlgraph/vignettes/irlgraph.Rmd")?

Hopefully my latest commit will provide a fix.

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tpoisot Nov 19, 2015

REVIEWER 2

This may be because make will run the first target by default.

jsta (11/19):

I'm sorry to hear that @dmcglinn. My guess is that Make is finding the pre-built vignette and not remaking it. make all requires that the vignette be built with caching in order to generate the figure output. Do you have anything in your code/irlgraph/vignettes/irlgraph_files/figure-latex/ folder?

Hopefully my latest commit will provide a fix.


Reply to this email directly or view it on GitHub:

tpoisot commented Nov 19, 2015

REVIEWER 2

This may be because make will run the first target by default.

jsta (11/19):

I'm sorry to hear that @dmcglinn. My guess is that Make is finding the pre-built vignette and not remaking it. make all requires that the vignette be built with caching in order to generate the figure output. Do you have anything in your code/irlgraph/vignettes/irlgraph_files/figure-latex/ folder?

Hopefully my latest commit will provide a fix.


Reply to this email directly or view it on GitHub:

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I'm not sure that is it because he is having trouble moving files from the vignette cache to the article folder (the third make target). The error message indicates that there are no files in the vignette cache to move which suggests that rmarkdown::render has not been called.

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jsta commented Nov 19, 2015

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I'm not sure that is it because he is having trouble moving files from the vignette cache to the article folder (the third make target). The error message indicates that there are no files in the vignette cache to move which suggests that rmarkdown::render has not been called.

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dmcglinn Nov 19, 2015

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commit 843785f seems to have helped. Now I recieved two error messages for not having the R packages viridis and rgeos installed. Additionally I got the following error message for not having a function definition for impute_na

  |......................................                           |  59%
label: impute_na (with options) 
List of 6
 $ eval      : logi TRUE
 $ fig.align : chr "right"
 $ fig.height: num 4
 $ fig.width : num 6
 $ dev       : chr "png"
 $ dpi       : num 100

Quitting from lines 124-131 (irlgraph.Rmd) 
Error in eval(expr, envir, enclos) : could not find function "impute_na"
Calls: <Anonymous> ... handle -> withCallingHandlers -> withVisible -> eval -> eval

Execution halted

REVIEWER 1

commit 843785f seems to have helped. Now I recieved two error messages for not having the R packages viridis and rgeos installed. Additionally I got the following error message for not having a function definition for impute_na

  |......................................                           |  59%
label: impute_na (with options) 
List of 6
 $ eval      : logi TRUE
 $ fig.align : chr "right"
 $ fig.height: num 4
 $ fig.width : num 6
 $ dev       : chr "png"
 $ dpi       : num 100

Quitting from lines 124-131 (irlgraph.Rmd) 
Error in eval(expr, envir, enclos) : could not find function "impute_na"
Calls: <Anonymous> ... handle -> withCallingHandlers -> withVisible -> eval -> eval

Execution halted
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jsta Nov 19, 2015

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Hmm, I'm not sure why you don't have a function definition for impute_na. I see that it is exported in
code/irlgraph/NAMESPACE and in the Roxygen header of code/irlgraph/R/impute_na.R.

I believe the viridis and rgeos errors can be solved by running:
Rscript -e 'devtools::install_github("jsta/irlgraph", dependencies = TRUE)'

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jsta commented Nov 19, 2015

AUTHOR

Hmm, I'm not sure why you don't have a function definition for impute_na. I see that it is exported in
code/irlgraph/NAMESPACE and in the Roxygen header of code/irlgraph/R/impute_na.R.

I believe the viridis and rgeos errors can be solved by running:
Rscript -e 'devtools::install_github("jsta/irlgraph", dependencies = TRUE)'

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dmcglinn Nov 19, 2015

REVIEWER 1

I had run Rscript -e 'devtools::install_github("jsta/irlgraph", dependencies = TRUE)'. When I ran it a second time I noticed this message

Installing irlgraph
Installing 5 packages: evaluate, formatR, highr, knitr, mime

Which indicates that rgeos and viridis are not identified as dependencies.

It is strange that impute_na is not working because as you say if the package irlgraph is loaded this function is available.

REVIEWER 1

I had run Rscript -e 'devtools::install_github("jsta/irlgraph", dependencies = TRUE)'. When I ran it a second time I noticed this message

Installing irlgraph
Installing 5 packages: evaluate, formatR, highr, knitr, mime

Which indicates that rgeos and viridis are not identified as dependencies.

It is strange that impute_na is not working because as you say if the package irlgraph is loaded this function is available.

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They are listed in the Suggests field of code/irlgraph/DESCRIPTION. The documentation of devtools::install_github indicates that dependencies = TRUE will honor the Suggests field. Maybe try:

Rscript -e 'devtools::install_github("jsta/irlgraph", dependencies = TRUE, build_vignettes = TRUE)

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jsta commented Nov 19, 2015

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They are listed in the Suggests field of code/irlgraph/DESCRIPTION. The documentation of devtools::install_github indicates that dependencies = TRUE will honor the Suggests field. Maybe try:

Rscript -e 'devtools::install_github("jsta/irlgraph", dependencies = TRUE, build_vignettes = TRUE)

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That didn't seem to help. In fact now no other packages are installed initially. This may be a devtools bug. Here is the R output:

Downloading GitHub repo jsta/irlgraph@master
Installing irlgraph
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore CMD  \
  build '/tmp/RtmpPTvpLW/devtools67d529177f2e/jsta-irlgraph-d1fd8c6'  \
  --no-resave-data --no-manual 

* checking for file ‘/tmp/RtmpPTvpLW/devtools67d529177f2e/jsta-irlgraph-d1fd8c6/DESCRIPTION’ ... OK
* preparing ‘irlgraph’:
* checking DESCRIPTION meta-information ... OK
* installing the package to process help pages
* saving partial Rd database
* creating vignettes ... OK
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building ‘irlgraph_0.6.tar.gz’

'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore CMD  \
  INSTALL '/tmp/RtmpPTvpLW/irlgraph_0.6.tar.gz'  \
  --library='/home/danmcglinn/R/x86_64-pc-linux-gnu-library/3.2'  \
  --install-tests 

* installing *source* package ‘irlgraph’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (irlgraph)

REVIEWER 1

That didn't seem to help. In fact now no other packages are installed initially. This may be a devtools bug. Here is the R output:

Downloading GitHub repo jsta/irlgraph@master
Installing irlgraph
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore CMD  \
  build '/tmp/RtmpPTvpLW/devtools67d529177f2e/jsta-irlgraph-d1fd8c6'  \
  --no-resave-data --no-manual 

* checking for file ‘/tmp/RtmpPTvpLW/devtools67d529177f2e/jsta-irlgraph-d1fd8c6/DESCRIPTION’ ... OK
* preparing ‘irlgraph’:
* checking DESCRIPTION meta-information ... OK
* installing the package to process help pages
* saving partial Rd database
* creating vignettes ... OK
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building ‘irlgraph_0.6.tar.gz’

'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore CMD  \
  INSTALL '/tmp/RtmpPTvpLW/irlgraph_0.6.tar.gz'  \
  --library='/home/danmcglinn/R/x86_64-pc-linux-gnu-library/3.2'  \
  --install-tests 

* installing *source* package ‘irlgraph’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (irlgraph)
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dmcglinn Dec 10, 2015

REVIEWER 1

I apologize for the delay replying here. Yes the instructions given by @jsta in his 11/20 comment will not work unless they are also accompanied by git checkout STACHELEK. It seems like these user instructions should go in the README.md file.

REVIEWER 1

I apologize for the delay replying here. Yes the instructions given by @jsta in his 11/20 comment will not work unless they are also accompanied by git checkout STACHELEK. It seems like these user instructions should go in the README.md file.

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rougier Dec 14, 2015

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Dear all (@jsta, @karthik, @dmcglinn, @tpoisot, @khinsen),

It seems this review is a bit stalled. Is there anything we can do to move it forward ?
If possible, it would be good to have it finished by the end of the year.

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rougier commented Dec 14, 2015

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Dear all (@jsta, @karthik, @dmcglinn, @tpoisot, @khinsen),

It seems this review is a bit stalled. Is there anything we can do to move it forward ?
If possible, it would be good to have it finished by the end of the year.

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karthik Dec 25, 2015

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@jsta I believe the ball is still in your court to fix this branch before we can proceed further. Please address this when you get a chance so we can move forward with your submission.

best, - K

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karthik commented Dec 25, 2015

EDITOR

@jsta I believe the ball is still in your court to fix this branch before we can proceed further. Please address this when you get a chance so we can move forward with your submission.

best, - K

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jsta Dec 26, 2015

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@karthik Ok, I think I have addressed all the reviewers' concerns including local file movement commands in Makefile (843785f), placeholder text in code/README.md (87c1bc7), and lack of build instructions in README.md (9f94502).

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jsta commented Dec 26, 2015

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@karthik Ok, I think I have addressed all the reviewers' concerns including local file movement commands in Makefile (843785f), placeholder text in code/README.md (87c1bc7), and lack of build instructions in README.md (9f94502).

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jsta Dec 30, 2015

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I have been thinking about making the files in the code folder into a git submodule. I think this would allow me to better integrate my somewhat independent R package while avoiding local file movements (see my Nov. 18th comment). Good idea or no?

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jsta commented Dec 30, 2015

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I have been thinking about making the files in the code folder into a git submodule. I think this would allow me to better integrate my somewhat independent R package while avoiding local file movements (see my Nov. 18th comment). Good idea or no?

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jsta Jan 15, 2016

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@karthik @tpoisot @dmcglinn I implemented a Docker pdf build in c03fe28

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jsta commented Jan 15, 2016

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@karthik @tpoisot @dmcglinn I implemented a Docker pdf build in c03fe28

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karthik Jan 18, 2016

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@dmcglinn @tpoisot Can you two do a pull from the current PR and build? It works fine for me. If you are also able to replicate, we can close this up before the end of January. Thanks very much.

PS: It finishes in under a minute.

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karthik commented Jan 18, 2016

EDITOR

@dmcglinn @tpoisot Can you two do a pull from the current PR and build? It works fine for me. If you are also able to replicate, we can close this up before the end of January. Thanks very much.

PS: It finishes in under a minute.

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tpoisot Feb 1, 2016

REVIEWER 2

Sorry for taking my sweet little time about testing.

Issue 1

Here is what I got:

▶ ReScience-submission on STACHELEK is clean $ make all
Rscript -e 'rmarkdown::render("code/irlgraph/vignettes/irlgraph.Rmd")'
Error in loadNamespace(name) : 
  aucun package nommé ‘rmarkdown’ n'est trouvé
Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Exécution arrêtée
Makefile:6 : la recette pour la cible « code/irlgraph/vignettes/irlgraph.pdf » a échouée
make: *** [code/irlgraph/vignettes/irlgraph.pdf] Erreur 1

I solved this by installing rmarkdown.

Issue 2

Here is the relevant line

pandoc --standalone --filter /home/tpoisot/.cabal/bin/pandoc-crossref --template=rescience-template.tex --latex-engine=xelatex --biblatex --bibliography=article.bib -M "crossrefYaml=crossref.yaml" --output article.tex article.md
pandoc: Filter /home/tpoisot/.cabal/bin/pandoc-crossref not found

On my system, the filter is called pandoc-citeproc, and pandoc-citeproc is in the path (and is at /usr/bin/pandoc-citeproc).

This one can be solved with the right variables passed to the different makefiles.

tpoisot commented Feb 1, 2016

REVIEWER 2

Sorry for taking my sweet little time about testing.

Issue 1

Here is what I got:

▶ ReScience-submission on STACHELEK is clean $ make all
Rscript -e 'rmarkdown::render("code/irlgraph/vignettes/irlgraph.Rmd")'
Error in loadNamespace(name) : 
  aucun package nommé ‘rmarkdown’ n'est trouvé
Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Exécution arrêtée
Makefile:6 : la recette pour la cible « code/irlgraph/vignettes/irlgraph.pdf » a échouée
make: *** [code/irlgraph/vignettes/irlgraph.pdf] Erreur 1

I solved this by installing rmarkdown.

Issue 2

Here is the relevant line

pandoc --standalone --filter /home/tpoisot/.cabal/bin/pandoc-crossref --template=rescience-template.tex --latex-engine=xelatex --biblatex --bibliography=article.bib -M "crossrefYaml=crossref.yaml" --output article.tex article.md
pandoc: Filter /home/tpoisot/.cabal/bin/pandoc-crossref not found

On my system, the filter is called pandoc-citeproc, and pandoc-citeproc is in the path (and is at /usr/bin/pandoc-citeproc).

This one can be solved with the right variables passed to the different makefiles.

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jsta Feb 1, 2016

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@tpoisot
Have you seen the build instructions in README.md? They include installation of rmarkdown.

Are you able to build the article in the master branch (not STACHELEK)? The master branch article/README.md says to use pandoc-crossref not pandoc-citeproc...
I hope this is not related to the version problem discussed at #13

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jsta commented Feb 1, 2016

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@tpoisot
Have you seen the build instructions in README.md? They include installation of rmarkdown.

Are you able to build the article in the master branch (not STACHELEK)? The master branch article/README.md says to use pandoc-crossref not pandoc-citeproc...
I hope this is not related to the version problem discussed at #13

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jsta Feb 12, 2016

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@tpoisot @dmcglinn: According to @rougier in #13, you do not need to actually compile the pdf as reviewers. In order to build only the figures substitute the make all line in README.md with make panel-resize_images. The figure images can then be found in the article folder.

Also, you would not need the Haskell/cabal/pandoc-crossref dependencies.

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jsta commented Feb 12, 2016

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@tpoisot @dmcglinn: According to @rougier in #13, you do not need to actually compile the pdf as reviewers. In order to build only the figures substitute the make all line in README.md with make panel-resize_images. The figure images can then be found in the article folder.

Also, you would not need the Haskell/cabal/pandoc-crossref dependencies.

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tpoisot Feb 12, 2016

REVIEWER 2
@karthik Working, no more comments/requests.
:shipit:

tpoisot commented Feb 12, 2016

REVIEWER 2
@karthik Working, no more comments/requests.
:shipit:

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@karthik @tpoisot @dmcglinn Yes, the review is really about whether the original has been replicatedd or not and whether the new code can be ran easily. The actual buidling of the PDF is not necessary (it will be built once for the journal). The point of the review is really to check if the article explains why the author think results have been replicated and if the code is "ok" (comments, LICENSE, requirements) such that anybody reading the article can re-use th code.

@jsta Maybe you can remove the top Makefile (and change the README accordingly) to avoi the confusion.

Sorry if the instructions (http://rescience.github.io/edit/) are not clear enough. PR welcome !

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rougier commented Feb 13, 2016

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@karthik @tpoisot @dmcglinn Yes, the review is really about whether the original has been replicatedd or not and whether the new code can be ran easily. The actual buidling of the PDF is not necessary (it will be built once for the journal). The point of the review is really to check if the article explains why the author think results have been replicated and if the code is "ok" (comments, LICENSE, requirements) such that anybody reading the article can re-use th code.

@jsta Maybe you can remove the top Makefile (and change the README accordingly) to avoi the confusion.

Sorry if the instructions (http://rescience.github.io/edit/) are not clear enough. PR welcome !

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@karthik this is working for me too. I also apologize for the long delays. No more comments.

On Feb 13, 2016, at 1:10 AM, Nicolas P. Rougier notifications@github.com wrote:

EDITOR-IN-CHIEF

@karthik @tpoisot @dmcglinn Yes, the review is really about whether the original has been replicatedd or not and whether the new code can be ran easily. The actual buidling of the PDF is not necessary (it will be built once for the journal). The point of the review is really to check if the article explains why the author think results have been replicated and if the code is "ok" (comments, LICENSE, requirements) such that anybody reading the article can re-use th code.

@jsta Maybe you can remove the top Makefile (and change the README accordingly) to avoi the confusion.

Sorry if the instructions (http://rescience.github.io/edit/) are not clear enough. PR welcome !


Reply to this email directly or view it on GitHub.

REVIEWER 1

@karthik this is working for me too. I also apologize for the long delays. No more comments.

On Feb 13, 2016, at 1:10 AM, Nicolas P. Rougier notifications@github.com wrote:

EDITOR-IN-CHIEF

@karthik @tpoisot @dmcglinn Yes, the review is really about whether the original has been replicatedd or not and whether the new code can be ran easily. The actual buidling of the PDF is not necessary (it will be built once for the journal). The point of the review is really to check if the article explains why the author think results have been replicated and if the code is "ok" (comments, LICENSE, requirements) such that anybody reading the article can re-use th code.

@jsta Maybe you can remove the top Makefile (and change the README accordingly) to avoi the confusion.

Sorry if the instructions (http://rescience.github.io/edit/) are not clear enough. PR welcome !


Reply to this email directly or view it on GitHub.

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Thank you @tpoisot and @dmcglinn
I'll look this over shortly and update the thread.

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karthik commented Feb 14, 2016

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Thank you @tpoisot and @dmcglinn
I'll look this over shortly and update the thread.

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@jsta Apologies for all the delays. But I have also reviewed the submission and the original landscape ecology paper by Etherington and am happy that the original code and figures have been reproduced. I'm happy to accept the submission.

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karthik commented Mar 3, 2016

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@jsta Apologies for all the delays. But I have also reviewed the submission and the original landscape ecology paper by Etherington and am happy that the original code and figures have been reproduced. I'm happy to accept the submission.

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Thanks @karthik , please let me know if I can do anything else to prep the PR for import.

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jsta commented Mar 4, 2016

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Thanks @karthik , please let me know if I can do anything else to prep the PR for import.

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@jsta Until actual import (soon), please do not commit to the repo.
@karthik I can take care of the final publication if you want.

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rougier commented Mar 4, 2016

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@jsta Until actual import (soon), please do not commit to the repo.
@karthik I can take care of the final publication if you want.

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@karthik I will take care of the publication.
@jsta You need to have all the output images either in your code repository (or in the article repository) such that I can build the PDF without running the code. Does that make sense ?

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rougier commented Mar 7, 2016

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@karthik I will take care of the publication.
@jsta You need to have all the output images either in your code repository (or in the article repository) such that I can build the PDF without running the code. Does that make sense ?

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@rougier I have added many images to the repo. You should be able to build
the PDF now.
On Mar 7, 2016 5:24 AM, "Nicolas P. Rougier" notifications@github.com
wrote:

@karthik https://github.com/karthik I will make the publication.
@jsta https://github.com/jsta You need to have all the output images
either in your code repository (or in the article repository) such that I
can build the PDF without running the code. Does that make sense ?


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.

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jsta commented Mar 7, 2016

@rougier I have added many images to the repo. You should be able to build
the PDF now.
On Mar 7, 2016 5:24 AM, "Nicolas P. Rougier" notifications@github.com
wrote:

@karthik https://github.com/karthik I will make the publication.
@jsta https://github.com/jsta You need to have all the output images
either in your code repository (or in the article repository) such that I
can build the PDF without running the code. Does that make sense ?


Reply to this email directly or view it on GitHub
#11 (comment)
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@jsta Thanks.

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rougier commented Mar 7, 2016

@jsta Thanks.

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@jsta Could you also give 2/3 keywords ? (We need to add a keyword fields in the template)

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rougier commented Mar 7, 2016

@jsta Could you also give 2/3 keywords ? (We need to add a keyword fields in the template)

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This submission has been accepted for publication, and has been published and will soon appear at https://github.com/ReScience/ReScience/wiki/Current-Issue

DOI

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rougier commented Mar 7, 2016

This submission has been accepted for publication, and has been published and will soon appear at https://github.com/ReScience/ReScience/wiki/Current-Issue

DOI

@rougier rougier closed this Mar 7, 2016

@ReScience ReScience locked and limited conversation to collaborators Mar 7, 2016

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Thanks @rougier!

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karthik commented Mar 8, 2016

Thanks @rougier!

@rougier rougier added the R label Jul 3, 2016

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