Merge pull request #286 from SchlossLab/use-tidy

Use tidy github documents

.github/ISSUE_TEMPLATE/issue_template.md

@@ -0,0 +1,14 @@
+---
+name: Bug report or feature request
+about: Describe a bug you've seen or make a case for a new feature
+---
+
+Please briefly describe your problem and what output you expect. If you have a question, please don't use this form. Instead, ask on <https://stackoverflow.com/> or <https://community.rstudio.com/>.
+
+Please include a minimal reproducible example (AKA a reprex). If you've never heard of a [reprex](http://reprex.tidyverse.org/) before, start by reading <https://www.tidyverse.org/help/#reprex>.
+
+Brief description of the problem
+
+```r
+# insert reprex here
+```

.github/SUPPORT.md

@@ -0,0 +1,35 @@
+# Getting help with mikropml
+
+Thanks for using mikropml!
+Before filing an issue, there are a few places to explore and pieces to put together to make the process as smooth as possible.
+
+## Make a reprex
+
+Start by making a minimal **repr**oducible **ex**ample using the  [reprex](https://reprex.tidyverse.org/) package. 
+If you haven't heard of or used reprex before, you're in for a treat! 
+Seriously, reprex will make all of your R-question-asking endeavors easier (which is a pretty insane ROI for the five to ten minutes it'll take you to learn what it's all about). 
+For additional reprex pointers, check out the [Get help!](https://www.tidyverse.org/help/) section of the tidyverse site.
+
+## Where to ask?
+
+Armed with your reprex, the next step is to figure out [where to ask](https://www.tidyverse.org/help/#where-to-ask). 
+
+*   If it's a question: start with [community.rstudio.com](https://community.rstudio.com/), and/or StackOverflow. There are more people there to answer questions.  
+
+*   If it's a bug: you're in the right place, [file an issue](https://github.com/SchlossLab/mikropml/issues/new).  
+
+*   If you're not sure: let the community help you figure it out! 
+    If your problem _is_ a bug or a feature request, you can easily return here and report it. 
+
+Before opening a new issue, be sure to [search issues and pull requests](https://github.com/SchlossLab/mikropml/issues) to make sure the bug hasn't been reported and/or already fixed in the development version. 
+By default, the search will be pre-populated with `is:issue is:open`. 
+You can [edit the qualifiers](https://help.github.com/articles/searching-issues-and-pull-requests/)  (e.g. `is:pr`, `is:closed`) as needed. 
+For example, you'd simply remove `is:open` to search _all_ issues in the repo, open or closed.
+
+## What happens next?
+
+To be as efficient as possible, development of tidyverse packages tends to be very bursty, so you shouldn't worry if you don't get an immediate response.
+Typically we don't look at a repo until a sufficient quantity of issues accumulates, then there’s a burst of intense activity as we focus our efforts. 
+That makes development more efficient because it avoids expensive context switching between problems, at the cost of taking longer to get back to you. 
+This process makes a good reprex particularly important because it might be multiple months between your initial report and when we start working on it. 
+If we can’t reproduce the bug, we can’t fix it!

DESCRIPTION

@@ -1,73 +1,65 @@
 Package: mikropml
 Title: User-Friendly R Package for Supervised Machine Learning Pipelines
 Version: 1.2.0.9000
-Authors@R: c(
-    person(given = "Begüm",
-           family = "Topçuoğlu",
-           role = c("aut"),
-           email = "[email protected]",
-           comment = c(ORCID = "0000-0003-3140-537X")
-           ),
-    person(given = "Zena",
-           family = "Lapp",
-           role = c("aut"),
-           email = "[email protected]",
-           comment = c(ORCID = "0000-0003-4674-2176")
-           ),
-    person(given = "Kelly",
-           family = "Sovacool",
-           role = c("aut", "cre"),
-           email = "[email protected]",
-           comment = c(ORCID = "0000-0003-3283-829X")
-           ),
-    person(given = "Evan",
-           family = "Snitkin",
-           role = c('aut'),
-           comment = c(ORCID = "0000-0001-8409-278X")
-           ),
-    person(given = "Jenna",
-           family = "Wiens",
-           role = c('aut'),
-           comment = c(ORCID = "0000-0002-1057-7722")
-           ),
-    person(given = "Patrick",
-           family = "Schloss",
-           role = c('aut'),
-           email = '[email protected]',
-           comment = c(ORCID = "0000-0002-6935-4275")
-           ),
-    person(given = "Nick",
-           family = "Lesniak",
-           role = c("ctb"),
-           email = "[email protected]",
-           comment = c(ORCID = "0000-0001-9359-5194")
-           ),
-    person(given = "Courtney",
-           family = "Armour",
-           role = c("ctb"),
-           email = "[email protected]",
-           comment = c(ORCID = "0000-0002-5250-1224")
-           ),
-    person(given = "Sarah",
-           family = "Lucas",
-           role = c("ctb"),
-           email = "[email protected]",
-           comment = c(ORCID = "0000-0003-1676-5801")))
 Date: 2021-11-10
-URL: https://www.schlosslab.org/mikropml/, https://github.com/SchlossLab/mikropml
-BugReports: https://github.com/SchlossLab/mikropml/issues
-Description: An interface to build machine learning models for classification 
-    and regression problems. 'mikropml' implements the ML pipeline described
-    by Topçuoğlu et al. (2020) <doi:10.1128/mBio.00434-20> with reasonable 
-    default options for data preprocessing, hyperparameter tuning, 
-    cross-validation, testing, model evaluation, and interpretation steps. 
-    See the website <https://www.schlosslab.org/mikropml/> for more information, 
+Authors@R: 
+    c(person(given = "Begüm",
+             family = "Topçuoğlu",
+             role = "aut",
+             email = "[email protected]",
+             comment = c(ORCID = "0000-0003-3140-537X")),
+      person(given = "Zena",
+             family = "Lapp",
+             role = "aut",
+             email = "[email protected]",
+             comment = c(ORCID = "0000-0003-4674-2176")),
+      person(given = "Kelly",
+             family = "Sovacool",
+             role = c("aut", "cre"),
+             email = "[email protected]",
+             comment = c(ORCID = "0000-0003-3283-829X")),
+      person(given = "Evan",
+             family = "Snitkin",
+             role = "aut",
+             comment = c(ORCID = "0000-0001-8409-278X")),
+      person(given = "Jenna",
+             family = "Wiens",
+             role = "aut",
+             comment = c(ORCID = "0000-0002-1057-7722")),
+      person(given = "Patrick",
+             family = "Schloss",
+             role = "aut",
+             email = "[email protected]",
+             comment = c(ORCID = "0000-0002-6935-4275")),
+      person(given = "Nick",
+             family = "Lesniak",
+             role = "ctb",
+             email = "[email protected]",
+             comment = c(ORCID = "0000-0001-9359-5194")),
+      person(given = "Courtney",
+             family = "Armour",
+             role = "ctb",
+             email = "[email protected]",
+             comment = c(ORCID = "0000-0002-5250-1224")),
+      person(given = "Sarah",
+             family = "Lucas",
+             role = "ctb",
+             email = "[email protected]",
+             comment = c(ORCID = "0000-0003-1676-5801")))
+Description: An interface to build machine learning models for
+    classification and regression problems. 'mikropml' implements the ML
+    pipeline described by Topçuoğlu et al. (2020)
+    <doi:10.1128/mBio.00434-20> with reasonable default options for data
+    preprocessing, hyperparameter tuning, cross-validation, testing, model
+    evaluation, and interpretation steps.  See the website
+    <https://www.schlosslab.org/mikropml/> for more information,
     documentation, and examples.
 License: MIT + file LICENSE
-Encoding: UTF-8
-LazyData: true
-Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.1
+URL: https://www.schlosslab.org/mikropml/,
+    https://github.com/SchlossLab/mikropml
+BugReports: https://github.com/SchlossLab/mikropml/issues
+Depends:
+    R (>= 2.10)
 Imports:
     caret,
     dplyr,
@@ -94,6 +86,9 @@ Suggests:
     rmarkdown,
     testthat,
     tidyr
-VignetteBuilder: knitr
-Depends:
-    R (>= 2.10)
+VignetteBuilder: 
+    knitr
+Encoding: UTF-8
+LazyData: true
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.1.1

cran-comments.md

@@ -1,10 +1,9 @@
 ## Test environments
 
-- local macOS install; R 4.1.1
-- win-builder; R release
-- github-actions macOS-latest; R release
-- github-actions ubuntu-latest; R devel, devel, and oldrel
-- github-actions windows-latest; R release
+* GitHub Actions (ubuntu-16.04): devel, release, oldrel
+* GitHub Actions (windows): release
+* GitHub Actions (macOS): release
+* win-builder: devel
 
 ## R CMD check results