bump version v1.5.0

ropensci · Jan 13, 2024 · 452e9b8 · 452e9b8
1 parent db9a0ef
commit 452e9b8
Show file tree

Hide file tree

Showing 72 changed files with 81 additions and 7,084 deletions.
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -1,54 +1,32 @@
-# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
-# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches:
-      - main
-      - master
+    branches: [main, master]
   pull_request:
-    branches:
-      - main
-      - master
+    branches: [main, master]
 
 name: R-CMD-check
 
 jobs:
   R-CMD-check:
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
     steps:
-      - uses: actions/checkout@v2
-      - uses: r-lib/actions/setup-r@v1
-      - uses: r-lib/actions/setup-pandoc@v1
-
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
+      - uses: actions/checkout@v3
 
-      - name: Cache R packages
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+          use-public-rspm: true
 
-      - name: Install dependencies
-        run: |
-          install.packages(c("remotes", "rcmdcheck"))
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("covr")
-        shell: Rscript {0}
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: |
+              any::rcmdcheck
+              any::XML
+          needs: check
 
-      - name: Check
-        run: |
-          options(crayon.enabled = TRUE)
-          rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "error")
-        shell: Rscript {0}
-#
-#       - name: Test coverage
-#         run: covr::codecov()
-#         shell: Rscript {0}
+      - uses: r-lib/actions/check-r-package@v2
diff --git a/.travis.yml b/.travis.yml
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -45,12 +45,9 @@ Imports:
     utils
 Suggests: 
     covr,
-    DT,
     knitr,
     prettydoc,
     rmarkdown,
-    shiny,
-    shinydashboard,
     testthat (>= 2.1.0)
 VignetteBuilder: 
     knitr

diff --git a/NAMESPACE b/NAMESPACE
@@ -12,7 +12,6 @@ export(XenaPrepare)
 export(XenaQuery)
 export(XenaQueryProbeMap)
 export(XenaScan)
-export(XenaShiny)
 export(availTCGA)
 export(cohorts)
 export(datasets)

diff --git a/NEWS.md b/NEWS.md
@@ -1,6 +1,11 @@
 # UCSCXenaTools 1.5.0
 
-- Added two new queries from xenaPython
+- Removed useless action or check config files.
+- Removed the `XenaShiny()` function to reduce the dependencies.
+- Updated XenaData. Only minor datasets change found from previous data release.
+- Hiplot mirror is down, so we removed its usage in documentation (not delete internal code).
+- Added two new queries from xenaPython.
+
 
 # UCSCXenaTools 1.4.8
 

diff --git a/R/shiny.R b/R/shiny.R
diff --git a/README.Rmd b/README.Rmd
@@ -12,92 +12,19 @@ knitr::opts_chunk$set(
 )
 ```
 
+# UCSCXenaTools <img src='man/figures/logo.png' align="right" height="200" alt="logo"/>
+
 <!-- badges: start -->
 
-<table class="table">
-<thead>
-<tr class="header">
-<th align="left">
-Usage
-</th>
-<th align="left">
-Release
-</th>
-<th align="left">
-Development
-</th>
-</tr>
-</thead>
-<tbody>
-
-<tr class="odd">
-<td align="left">
-<a href="https://www.gnu.org/licenses/gpl-3.0.en.html"><img src="https://img.shields.io/badge/licence-GPL--3-blue.svg" alt="Licence"></a>
-</td>
-<td align="left">
-<a href="https://cran.r-project.org/package=UCSCXenaTools"><img src="https://www.r-pkg.org/badges/version/UCSCXenaTools" alt="CRAN"></a>
-</td>
-<td align="left">
-<a href="https://travis-ci.org/ropensci/UCSCXenaTools"><img src="https://travis-ci.org/ropensci/UCSCXenaTools.svg?branch=master" alt="Travis"></a>
-</td>
-</tr>
-
-<tr class="even">
-<td align="left">
-<a href="https://cran.r-project.org/"><img src="https://img.shields.io/badge/R%3E%3D-3.5.0-blue.svg" alt="minimal R version"></a>
-</td>
-<td align="left">
-<a href="https://gitter.im/ShixiangWang/community?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge"><img src="https://badges.gitter.im/ShixiangWang/community.svg" alt="cran-checks"></a>
-</td>
-<td align="left">
-<a href="https://ci.appveyor.com/project/ShixiangWang/UCSCXenaTools"><img src="https://ci.appveyor.com/api/projects/status/github/ropensci/UCSCXenaTools?branch=master&svg=true" alt="AppVeyor"></a>
-</td>
-</tr>
-
-<tr class="odd">
-<td align="left">
-<a href="https://CRAN.R-project.org/package=UCSCXenaTools"><img src="https://tinyverse.netlify.com/badge/UCSCXenaTools"></a>
-</td>
-<td align="left">
-<a href="https://github.com/ropensci/software-review/issues/315"><img src="https://badges.ropensci.org/315_status.svg" alt="rOpenSci"></a>
-</td>
-<td align="left">
-<a href="https://codecov.io/github/ShixiangWang/UCSCXenaTools?branch=master"><img src="https://codecov.io/github/ShixiangWang/UCSCXenaTools/coverage.svg?branch=master" alt="Codecov"></a>
-</td>
-</tr>
-
-<tr class="even">
-<td align="left">
-<a href="https://CRAN.R-project.org/package=UCSCXenaTools"><img src="https://cranlogs.r-pkg.org/badges/grand-total/UCSCXenaTools" alt="downloads"></a>
-</td>
-<td align="left">
-<a href="https://zenodo.org/badge/latestdoi/178662770"><img src="https://zenodo.org/badge/178662770.svg" alt="DOI"></a>
-</td>
-<td align="left">
-<a href="https://github.com/ropensci/UCSCXenaTools/issues?q=is%3Aissue+is%3Aclosed"><img src="https://img.shields.io/github/issues-closed/ropensci/UCSCXenaTools.svg" alt="Closed issues"></a>
-</td>
-
-</tr>
-<tr class="odd">
-<td align="left">
-<a href="https://CRAN.R-project.org/package=UCSCXenaTools"><img src="https://cranlogs.r-pkg.org/badges/UCSCXenaTools" alt="month-downloads"></a>
-</td>
-<td align="left">
-<a href="https://doi.org/10.21105/joss.01627"><img src="https://joss.theoj.org/papers/10.21105/joss.01627/status.svg" alt="JOSS" >
-</a>
-</td>
-<td align="left">
-<a href="https://www.repostatus.org/#active"><img src="https://www.repostatus.org/badges/latest/active.svg" alt="Project Status: Active – The project has reached a stable, usable state and is being actively developed." /></a>
-</td>
-</tr>
-</tbody>
-</table>
-<br>
+[![CRAN status](https://www.r-pkg.org/badges/version/UCSCXenaTools)](https://cran.r-project.org/package=UCSCXenaTools)
+[![lifecycle](https://img.shields.io/badge/lifecycle-stable-blue.svg)](https://lifecycle.r-lib.org/articles/stages.html)
+[![R-CMD-check](https://github.com/ropensci/UCSCXenaTools/actions/workflows/main.yml/badge.svg)](https://github.com/ropensci/UCSCXenaTools/actions/workflows/main.yml) 
+[![](https://cranlogs.r-pkg.org/badges/grand-total/UCSCXenaTools?color=orange)](https://cran.r-project.org/package=UCSCXenaTools)
+[![rOpenSci](https://badges.ropensci.org/315_status.svg)](https://github.com/ropensci/software-review/issues/315)
+[![DOI](https://joss.theoj.org/papers/10.21105/joss.01627/status.svg)](https://doi.org/10.21105/joss.01627)
 
 <!-- badges: end -->
 
-# UCSCXenaTools <img src='man/figures/logo.png' align="right" height="200" alt="logo"/>
-
 **UCSCXenaTools** is an R package for accessing genomics data from UCSC Xena platform, from cancer multi-omics to single-cell RNA-seq. 
 Public omics data from UCSC Xena are supported through [**multiple turn-key Xena Hubs**](https://xenabrowser.net/datapages/), which are a collection of UCSC-hosted public databases such as TCGA, ICGC, TARGET, GTEx, CCLE, and others. Databases are normalized so they can be combined, linked, filtered, explored and downloaded.
 
@@ -194,16 +121,7 @@ df_todo
 
 Query and download.
 
-```{r, eval=FALSE}
-XenaQuery(df_todo) %>%
-  XenaDownload() -> xe_download
-```
-
-**For researchers in China, now Hiplot team has deployed several Xena mirror sites (`https://xena.hiplot.com.cn/`) at Shanghai. You can set an option `options(use_hiplot = TRUE)` before querying data step to speed up both data querying and downloading.**
-
 ```{r}
-options(use_hiplot = TRUE)
-
 XenaQuery(df_todo) %>%
   XenaDownload() -> xe_download
 ```