Merge pull request #3 from inbo/vignette

finish vignette

Author: ThierryO

.Rbuildignore

@@ -1,4 +1,10 @@
+^tic\.R$
+^\.github$
+^CODE_OF_CONDUCT\.md$
+^codemeta\.json$
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^\.travis\.yml$
 ^appveyor\.yml$
+^_pkgdown.yml$
+^docs$

.github/CONTRIBUTING.md

@@ -0,0 +1,56 @@
+# CONTRIBUTING #
+
+### 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.  
+*  We recommend 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).  
+*  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 git2rdata 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 rOpenSci [contributing guide](https://ropensci.github.io/dev_guide/contributingguide.html)
+for further details.
+
+### Discussion forum
+
+Check out our [discussion forum](https://discuss.ropensci.org) if you think your issue requires a longer form discussion.
+
+### Prefer to Email? 
+
+Email the person listed as maintainer in the `DESCRIPTION` file of this repo.
+
+Though note that private discussions over email don't help others - of course email is totally warranted if it's a sensitive problem of any kind.
+
+### Thanks for contributing!
+
+This contributing guide is adapted from the tidyverse contributing guide available at https://raw.githubusercontent.com/r-lib/usethis/master/inst/templates/tidy-contributing.md 

.github/issue_template.md

@@ -0,0 +1,10 @@
+<!-- IF THIS INVOLVES AUTHENTICATION: DO NOT SHARE YOUR USERNAME/PASSWORD, OR API KEYS/TOKENS IN THIS ISSUE - MOST LIKELY THE MAINTAINER WILL HAVE THEIR OWN EQUIVALENT KEY -->
+
+<!-- If this issue relates to usage of the package, whether a question, bug or similar, along with your query, please paste your devtools::session_info() or sessionInfo() into the code block below, AND include a reproducible example (consider using a "reprex" https://cran.rstudio.com/web/packages/reprex/) If not, delete all this and proceed :) -->
+
+<details> <summary><strong>Session Info</strong></summary>
+
+```r
+
+```
+</details>

.github/pull_request_template.md

@@ -0,0 +1,20 @@
+<!-- IF THIS INVOLVES AUTHENTICATION: DO NOT SHARE YOUR USERNAME/PASSWORD, OR API KEYS/TOKENS IN THIS ISSUE - MOST LIKELY THE MAINTAINER WILL HAVE THEIR OWN EQUIVALENT KEY -->
+
+<!-- If you've updated a file in the man-roxygen directory, make sure to update the man/ files by running devtools::document() or similar as .Rd files should be affected by your change -->
+
+<!--- Provide a general summary of your changes in the Title above -->
+
+## Description
+<!--- Describe your changes in detail -->
+
+## Related Issue
+<!--- if this closes an issue make sure include e.g., "fix #4"
+or similar - or if just relates to an issue make sure to mention
+it like "#4" -->
+
+## Example
+<!--- if introducing a new feature or changing behavior of existing
+methods/functions, include an example if possible to do in brief form -->
+
+<!--- Did you remember to include tests? Unless you're just changing
+grammar, please include new tests for your change -->

.gitignore

@@ -3,3 +3,4 @@
 .RData
 .Ruserdata
 inst/doc
+docs

.travis.yml

@@ -1,22 +1,51 @@
 # R for travis: see documentation at https://docs.travis-ci.com/user/languages/r
+# Default configuration for use with tic package
+# Usually you shouldn't need to change the first part of the file
 
-language: R
+# DO NOT CHANGE THE CODE BELOW
+before_install: R -q -e 'install.packages(c("remotes", "curl")); remotes::install_github("ropenscilabs/tic"); tic::prepare_all_stages(); tic::before_install()'
+install: R -q -e 'tic::install()'
+after_install: R -q -e 'tic::after_install()'
+before_script: R -q -e 'tic::before_script()'
+script: R -q -e 'tic::script()'
+after_success: R -q -e 'tic::after_success()'
+after_failure: R -q -e 'tic::after_failure()'
+before_deploy: R -q -e 'tic::before_deploy()'
+deploy:
+  provider: script
+  script: R -q -e 'tic::deploy()'
+  on:
+    branch: master
+    condition:
+      - $TRAVIS_PULL_REQUEST = false
+      - $TRAVIS_EVENT_TYPE != cron
+      - $TRAVIS_R_VERSION_STRING = release
+after_deploy: R -q -e 'tic::after_deploy()'
+after_script: R -q -e 'tic::after_script()'
+# DO NOT CHANGE THE CODE ABOVE
+
+# Custom parts:
+
+# Header
+language: r
 r:
   - oldrel
   - release
   - devel
 sudo: false
+dist: trusty
 cache: packages
 addons:
   apt:
     packages:
       - libgit2-dev
+latex: false
+
+#env
+env:
+  global:
+  - _R_CHECK_FORCE_SUGGESTS_=false
+  - MAKEFLAGS="-j 2"
 
-r_packages:
-  - covr
-  - lintr
-after_script:
-  - R CMD INSTALL $PKG_TARBALL
-  - Rscript -e 'lintr::lint_package()'
-after_success:
-  - Rscript -e 'covr::codecov()'
+#services
+services:

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 
+(http://contributor-covenant.org), version 1.0.0, available at 
+http://contributor-covenant.org/version/1/0/0/

DESCRIPTION

@@ -1,20 +1,22 @@
 Package: git2rdata
-Title: Store and retrieve data.frames in a git repository
-Version: 0.0.0.9000
+Title: Store and Retrieve Data.frames in a Git Repository
+Version: 0.0.1.9000
+Date: 2018-11-12
 Authors@R: c(
   person(
     "Thierry", "Onkelinx", role = c("aut", "cre"), 
     email = "[email protected]", 
     comment = c(ORCID = "0000-0001-8804-4216")),
   person(
-    family = "Research Institute for Nature and Forest",
+    "Research Institute for Nature and Forest",
     role = c("cph", "fnd"), email = "[email protected]"))
 Description: Make versioning of data.frame easy and efficient using git repositories.
 Depends: R (>= 3.4.0)
 Imports:
   assertthat,
   git2r (>= 0.23.0),
-  methods
+  methods,
+  readr
 Suggests:
   knitr,
   rmarkdown,
@@ -23,13 +25,14 @@ License: GPL-3
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 6.1.0
+RoxygenNote: 6.1.1
 URL: https://github.com/inbo/git2rdata
 BugReports: https://github.com/inbo/git2rdata/issues
 Collate:
     'write_vc.R'
     'auto_commit.R'
     'clean_data_path.R'
+    'git2rdata-package.R'
     'meta.R'
     'read_vc.R'
     'recent_commit.R'

NAMESPACE

@@ -27,7 +27,8 @@ importFrom(git2r,workdir)
 importFrom(methods,setGeneric)
 importFrom(methods,setMethod)
 importFrom(methods,setOldClass)
-importFrom(utils,read.table)
+importFrom(readr,read_tsv)
+importFrom(readr,write_tsv)
+importFrom(utils,head)
 importFrom(utils,sessionInfo)
 importFrom(utils,tail)
-importFrom(utils,write.table)

NEWS.md

@@ -0,0 +1,9 @@
+git2rdata 0.0.1 (2018-11-12)
+============================
+
+### NEW FEATURES
+
+  * use readr to write and read plain text files
+  * allows storage of strings with "NA" or special characters
+  * handle ordered factors
+  * stop handling complex numbers