From 07fcc4858fc7ddac3da0e7befe70725d92966266 Mon Sep 17 00:00:00 2001 From: vagudets Date: Tue, 3 Dec 2024 11:01:10 +0100 Subject: [PATCH 1/3] Add CONTRIBUTING.md file --- CONTRIBUTING.md | 66 +++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 66 insertions(+) create mode 100644 CONTRIBUTING.md diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md new file mode 100644 index 0000000..b53bed5 --- /dev/null +++ b/CONTRIBUTING.md @@ -0,0 +1,66 @@ +### Questions and bug reports + +If you have questions about the usage of a function or would like to report a bug, please follow these steps: + +1. Use the search function in GitLab to see if a similar problem has already been reported and/or solved. + +2. Rather than including a long script, try to run your code in small blocks to narrow down where the problem is coming from as much as possible. + +3. Open an issue tagging the maintainers (), and include a descriptive title and a piece of code to reproduce your problem (if applicable). + +### How to contribute + +If you would like to add a bugfix, an enhancement or a new functions, follow these steps: + +1. Open an issue to ask for help or describe a feature to be integrated + +2. Agree with the maintainers () on the requirements + +3. Create a new branch from master with a meaningful name + +4. Once the development is finished, open a merge request to merge the branch on master + +*Note: Remember to work with multidimensional arrays with named dimensions when possible and use multiApply (https://earth.bsc.es/gitlab/ces/multiApply)* + +### Adding a function + +To add a new function in this R package, follow these considerations: + +* Each function exposed to the users should be in its own separate file in the R folder +* The name of the function should match the name of the file (e.g.: `Function()` included in file **Function.R** +* The documentation should be in roxygen2 format as a header of the function +* Once the function and the documentation are finished, run the command `devtools::document()` in your R terminal to automatically generate the **Function.Rd** file +* When doing the development, please use an R version between R/4.1.2 and R/4.3.x + +### Style guide + +* Use `<-` for variable assignment +* Include spaces between operators (e.g. `+`, `-`, `&`), before `{`, and after `for`, `if`, `while`, `,` and `)`. +* When possible, maximum line length should be 100 characters (soft limit of 80 characters). +* Number of indentation spaces is 2, using tabs for indentation is forbidden. +* Double quotes are recommended for strings. When writing quotes within quoted text, use double quotes outside and single quotes inside. E.g.: `“Parameter 'na.rm' is missing.”` +* Self-explanatory names are preferred for variables. Try to be consistent with the variable naming style. Generally: avoid special characters (except underscores) and reserved words (ex: if, for, else, …) +* Remember to include short comments to make the code easier to understand. Comments should be in their own line and they should start with `#` followed by a space. Comments that start with `##` and a space are for details not needed to understand the general procedure but useful to make note of more technical aspects of the code. + +#### Examples: + +```r +# Proper spacing, indentation spaces and text quotes: +NewFunction <- function(text = "default", uppercase = TRUE) { + # Check uppercase parameter + if (!is.logical(uppercase)) { + stop("Parameter 'uppercase' should be TRUE or FALSE.") + } + # Only transform text if needed + if (uppercase && is.character(text)) { + text <- toupper(text) + } + return(text) +} + +# How to format line breaks to avoid long lines: +my_strings <- list(one = "one", + two = "two", + three = "three", + four = "four") +``` -- GitLab From e600b3ac9333374b27a323a700a177b0730ea268 Mon Sep 17 00:00:00 2001 From: vagudets Date: Tue, 3 Dec 2024 11:27:41 +0100 Subject: [PATCH 2/3] Add vagudets as username --- CONTRIBUTING.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index b53bed5..dbc29d3 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -6,7 +6,7 @@ If you have questions about the usage of a function or would like to report a bu 2. Rather than including a long script, try to run your code in small blocks to narrow down where the problem is coming from as much as possible. -3. Open an issue tagging the maintainers (), and include a descriptive title and a piece of code to reproduce your problem (if applicable). +3. Open an issue tagging the maintainers (@vagudets), and include a descriptive title and a piece of code to reproduce your problem (if applicable). ### How to contribute @@ -14,7 +14,7 @@ If you would like to add a bugfix, an enhancement or a new functions, follow the 1. Open an issue to ask for help or describe a feature to be integrated -2. Agree with the maintainers () on the requirements +2. Agree with the maintainers (@vagudets) on the requirements 3. Create a new branch from master with a meaningful name -- GitLab From 93b0e00c0e4a131ad391182848da52086ea16c91 Mon Sep 17 00:00:00 2001 From: vagudets Date: Tue, 3 Dec 2024 11:42:27 +0100 Subject: [PATCH 3/3] Add link to CONTRIBUTING.md --- README.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index a4333bd..010fafa 100644 --- a/README.md +++ b/README.md @@ -2,14 +2,16 @@ startR is an R package developed at the Barcelona Supercomputing Center which implements the MapReduce paradigm (a.k.a. domain decomposition) on HPCs in a way transparent to the user and specially oriented to complex multidimensional datasets. -The useful information for learning startR: +The useful information for learning startR: - [**practical guide**](inst/doc/practical_guide.md) - [**use cases**](inst/doc/usecase.md) - [**FAQs**](inst/doc/faq.md) +- [**questions, contributions and bug reports**](CONTRIBUTING.md) - [**tutorial**](inst/doc/tutorial/startR_tutorial_20200902.pdf) - [**ecFlow config**](inst/doc/ecFlowConfig_startR.pdf) + Following the startR framework, the user can represent in a one-page startR script all the information that defines a use case, including: - the involved (multidimensional) data sources and the distribution of the data files - the workflow of operations to be applied, over which data sources and dimensions -- GitLab