Merge pull request #42 from mcanouil/tidypkg

Improve package structure & coding (using tidy style)

.Rbuildignore

@@ -0,0 +1,14 @@
+^pkgdown$
+^_pkgdown\.yml$
+^.github$
+^inst/pkgdown$
+^docs$
+^.*\.Rproj$
+^\.Rproj\.user$
+^README\.Rmd$
+^README
+^README-.*\.png$
+^\.travis\.yml$
+^appveyor\.yml$
+^codecov\.yml$
+^\.github$

.github/CODE_OF_CONDUCT.md

@@ -0,0 +1,25 @@
+# Contributor Code of Conduct
+
+As contributors and maintainers of this project, we pledge to respect all people who 
+contribute through reporting issues, posting feature requests, updating documentation,
+submitting pull requests or patches, and other activities.
+
+We are committed to making participation in this project a harassment-free experience for
+everyone, regardless of level of experience, gender, gender identity and expression,
+sexual orientation, disability, personal appearance, body size, race, ethnicity, age, or religion.
+
+Examples of unacceptable behavior by participants include the use of sexual language or
+imagery, derogatory comments or personal attacks, trolling, public or private harassment,
+insults, or other unprofessional conduct.
+
+Project maintainers have the right and responsibility to remove, edit, or reject comments,
+commits, code, wiki edits, issues, and other contributions that are not aligned to this 
+Code of Conduct. Project maintainers who do not follow the Code of Conduct may be removed 
+from the project team.
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by 
+opening an issue or contacting one or more of the project maintainers.
+
+This Code of Conduct is adapted from the Contributor Covenant 
+(https://www.contributor-covenant.org), version 1.0.0, available at 
+https://contributor-covenant.org/version/1/0/0/.

.github/CONTRIBUTING.md

@@ -0,0 +1,48 @@
+# Contributing to ggnetwork
+
+This outlines how to propose a change to ggnetwork. For more detailed
+info about contributing to this, and other tidyverse packages, please see the
+[**development contributing guide**](https://rstd.io/tidy-contrib).
+
+### Fixing typos
+
+Small typos or grammatical errors in documentation may be edited directly using
+the GitHub web interface, so long as the changes are made in the _source_ file.
+
+*  YES: you edit a roxygen comment in a `.R` file below `R/`.
+*  NO: you edit an `.Rd` file below `man/`.
+
+### Prerequisites
+
+Before you make a substantial pull request, you should always file an issue and
+make sure someone from the team agrees that it’s a problem. If you’ve found a
+bug, create an associated issue and illustrate the bug with a minimal 
+[reprex](https://www.tidyverse.org/help/#reprex).
+
+### Pull request process
+
+*  We recommend that you create a Git branch for each pull request (PR).  
+*  Look at the Travis and AppVeyor build status before and after making changes.
+The `README` should contain badges for any continuous integration services used
+by the package.  
+*  New code should follow the tidyverse [style guide](http://style.tidyverse.org).
+You can use the [styler](https://CRAN.R-project.org/package=styler) package to
+apply these styles, but please don't restyle code that has nothing to do with 
+your PR.  
+*  We use [roxygen2](https://cran.r-project.org/package=roxygen2), with
+[Markdown syntax](https://cran.r-project.org/web/packages/roxygen2/vignettes/markdown.html), 
+for documentation.  
+*  We use [testthat](https://cran.r-project.org/package=testthat). Contributions
+with test cases included are easier to accept.  
+*  For user-facing changes, add a bullet to the top of `NEWS.md` below the
+current development version header describing the changes made followed by your
+GitHub username, and links to relevant issue(s)/PR(s).
+
+### Code of Conduct
+
+Please note that the ggnetwork project is released with a
+[Contributor Code of Conduct](CODE_OF_CONDUCT.md). By contributing to this
+project you agree to abide by its terms.
+
+### See tidyverse [development contributing guide](https://rstd.io/tidy-contrib)
+for further details.

.github/ISSUE_TEMPLATE.md

@@ -0,0 +1,11 @@
+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](https://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 ggnetwork
+
+Thanks for using ggnetwork. Before filing an issue, there are a few places
+to explore and pieces to put together to make the process as smooth as possible.
+
+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.
+
+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.  
+  * 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/tidyverse/ggnetwork/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.
+
+
+If you _are_ in the right place, and need to file an issue, please review the 
+["File issues"](https://www.tidyverse.org/contribute/#issues) paragraph from 
+the tidyverse contributing guidelines.
+
+Thanks for your help!

.gitignore

@@ -1,6 +1,3 @@
+**.Rproj.user
 .Rproj.user
-.Rhistory
-.RData
-.Ruserdata
-.Rbuildignore
-ggnetwork.Rproj
+docs

.travis.yml

@@ -1,2 +1,44 @@
-language: r
+language: R
 cache: packages
+sudo: true
+
+
+env:
+  global:
+    - _R_CHECK_FORCE_SUGGESTS_=false
+    - R_REMOTES_NO_ERRORS_FROM_WARNINGS=true
+    - _R_CHECK_SYSTEM_CLOCK_=false
+
+before_install:
+  - sudo add-apt-repository ppa:ubuntugis/ubuntugis-unstable --yes
+  - sudo apt-get --yes --force-yes update -qq
+  - sudo apt-get install --yes libudunits2-dev libproj-dev libgeos-dev libgdal-dev
+  - Rscript -e 'update.packages(ask = FALSE)'
+
+r_github_packages:
+  - r-lib/covr
+
+matrix:
+  include:
+  - r: devel
+  - r: release
+    after_success: Rscript -e 'covr::coveralls(); covr::codecov()'
+    before_deploy: Rscript -e 'remotes::install_cran("pkgdown")'
+    deploy:
+      provider: script
+      script: Rscript -e 'pkgdown::deploy_site_github()'
+      skip_cleanup: true
+  - r: 3.1
+  - r: 3.2
+  - r: 3.3
+  - r: 3.4
+  - r: 3.5
+  - r: 3.6
+
+after_success:
+  - Rscript -e 'covr::coveralls(); covr::codecov()'
+
+notifications:
+  email:
+    on_success: change
+    on_failure: change

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: ggnetwork
 Type: Package
 Title: Geometries to Plot Networks with 'ggplot2'
-Version: 0.5.4
+Version: 0.5.6.9000
 Date: 2016-03-24
 Maintainer: François Briatte <f.briatte@gmail.com>
 Authors@R: c(
@@ -14,24 +14,30 @@ Authors@R: c(
   )
 Description: Geometries to plot network objects with 'ggplot2'.
 License: GPL-3
-Encoding: UTF-8
 URL: https://github.com/briatte/ggnetwork
 BugReports: https://github.com/briatte/ggnetwork/issues
-LazyData: true
-NeedsCompilation: no
-RoxygenNote: 6.0.1
-VignetteBuilder: knitr
 Depends:
-    ggplot2 (>= 2.0.0),
     R (>= 3.1),
+    ggplot2 (>= 2.0.0)
 Imports:
     ggrepel (>= 0.5),
     network,
+    igraph,
     sna,
     utils
 Suggests:
-    igraph,
     knitr,
     testthat
-Enhances:
-    ggplot2
+Collate:
+    'utilities.R'
+    'fortify-igraph.R'
+    'fortify-network.R'
+    'geom-nodes.R'
+    'geom-edges.R'
+    'ggnetwork.R'
+VignetteBuilder: knitr
+RoxygenNote: 6.1.1
+Roxygen: list(markdown = TRUE)
+Encoding: UTF-8
+LazyData: true
+NeedsCompilation: no

NAMESPACE

@@ -2,6 +2,7 @@
 
 S3method(fortify,igraph)
 S3method(fortify,network)
+export(fortify)
 export(geom_edgelabel)
 export(geom_edgelabel_repel)
 export(geom_edges)
@@ -15,17 +16,6 @@ export(geom_nodetext_repel)
 export(ggnetwork)
 export(theme_blank)
 export(theme_facet)
-import(sna)
-importFrom(ggplot2,GeomCurve)
-importFrom(ggplot2,GeomLabel)
-importFrom(ggplot2,GeomPoint)
-importFrom(ggplot2,GeomSegment)
-importFrom(ggplot2,GeomText)
+export(unit)
 importFrom(ggplot2,fortify)
-importFrom(ggplot2,ggproto)
-importFrom(ggplot2,layer)
-importFrom(ggplot2,position_nudge)
 importFrom(ggplot2,unit)
-importFrom(ggrepel,GeomLabelRepel)
-importFrom(ggrepel,GeomTextRepel)
-importFrom(utils,installed.packages)

NEWS.md

@@ -1,41 +1,91 @@
+ggnetwork 0.5.6
+===============
+
+## Repository changes
+
+* Add `README.Rmd` (replace `README.md`), 
+  + use badges.
+  + list all GitHub contributors.
+  + add Contributing, Code of Conduct Issue Template and Support markdown file (`usethis`).
+
+* Improve `.travis.yml`,
+  + use `pkgdown` for website deployment.
+      - add `_pkgdown.yml` configuration file.
+  + use `covr` for code coverage.
+      - add default `codecov.yml` configuration file.
+
+* Add `ggnetwork.Rproj`, for ease of use within Rstudio.
+
+## Minor improvements and fixes
+
+* In `DESCRIPTION`,
+  + update RoxygenNote version.
+  + remove `ggplot2` from `Enhances` field.
+  + add `Collate` field to load sequentially the functions.
+  + move `igraph` to `Imports` field.
+
+* Remove `inst/doc/` directory, *i.e.*, the vignette is part of the `pkgdown` website.
+
+* Use tidy code style.
+
+* In `R/fortify-igraph.R` and `R/fortify-network.R`, 
+  + use subsetting functions instead of `with` and `transform` (*i.e.*, intended to be use interactively).
+  + fix issue from CRAN check with undefined global variables.
+  + remove namespace loading for `sna` package (*i.e.*, `gplot.layout.*` functions).
+
+* In `R/geom-nodes.R` and `R/geom-edges.R`, 
+  + remove unnecessary "@importFom".
+  + add missing function packages prefix.
+
+* In `R/ggnetwork.R`, `switch` and `tryCatch` to make the `igraph` and `network` testing consistent.
+
+* In `R/utilities.R`, reexport `fortify` and `unit` from `ggplot2`.
+
+
+
+ggnetwork 0.5.5 (2017-08-XX)
+============================
+
+
 ggnetwork 0.5.4 (2017-07-XX)
-----------------------------
+============================
 
-Changes
+## Minor improvements and fixes
 
 * Added native support for igraph.  Thanks to [Jake Fisher](www.src.isr.umich.edu/people/jake-fisher/).
 
 
 ggnetwork 0.5.3 (2016-06-XX)
-----------------------------
+============================
+
+## Repository changes
 
-Added Travis CI.
+* Added Travis CI.
 
-FIXES
+## Minor improvements and fixes
 
 * Export ggplot2::Stat to enable loading ggnetwork first (#14). Thanks to Tyler Rinker.
 
 * Built with the new version of ggproto (#11).
 
 * Safer calls to the sna package (#9). Thanks to Michał Bojanowski.
 
+
 ggnetwork 0.5.2 (2016-05-01)
-----------------------------
+============================
 
-FIXES
+## Minor improvements and fixes
 
 * Fixed a bug that removed labels from strictly vertical or strictly horizontal edges (#5).
 
 * Fixed a small documentation issue that was corrected in roxygen 5.0.2 (#4).
 
-CHANGES
-
 * Support for segment colors in all geoms using ggrepel 0.5.1 (#3).
 
 * Added some acknowledgements to the README and links to the DESCRIPTION.
 
 
 ggnetwork 0.5.1 (2016-03-25)
-----------------------------
+============================
 
 First CRAN release.