Merge pull request #46 from pepkit/dev

v0.5.0

.Rbuildignore

@@ -5,4 +5,9 @@
 ^doc$
 ^docs$
 ^Meta$
-^update_examples.sh$
+^update_examples.sh$
+
+
+CNAME
+test.sh
+.github

.github/workflows/new-build-R.yml

@@ -29,57 +29,22 @@ jobs:
       RSPM: ${{ matrix.config.rspm }}
 
     steps:
-      - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@master
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
 
-      - uses: r-lib/actions/setup-pandoc@master
-
-      - 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: r-lib/actions/setup-pandoc@v2
 
-      - name: Cache R packages
-        if: runner.os != 'Windows'
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@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-
-
-      - name: Install system dependencies
-        if: runner.os == 'Linux'
-        run: |
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
+          extra-packages: any::rcmdcheck
+          needs: check
 
-      - name: Install dependencies
-        run: |
-          remotes::install_cran("covr")
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
-        shell: Rscript {0}
-
-      - name: Check
-        env:
-          _R_CHECK_CRAN_INCOMING_REMOTE_: false
-        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
-
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
+      - uses: r-lib/actions/check-r-package@v2
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
-
-      - name: Report test coverage
-        run: covr::codecov()
-        shell: Rscript {0}
+          upload-snapshots: true

.github/workflows/pkgdown.yml

@@ -0,0 +1,48 @@
+on:
+  push:
+    branches:
+      - master
+  workflow_dispatch:
+    inputs:
+      branch:
+        description: 'Repo branch to checkout'
+        required: false
+        default: 'master'
+
+name: Deploy-package-documentation
+
+jobs:
+  pkgdown:
+    runs-on: macos-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v23
+        with:
+          # The branch, tag or SHA to checkout. When checking out the repository that
+          # triggered a workflow, this defaults to the reference or SHA for that event.
+          # Otherwise, uses the default branch.
+          ref: ${{ github.event.inputs.branch }}
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/[email protected]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

CNAME

@@ -0,0 +1 @@
+pepr.databio.org

DESCRIPTION

@@ -1,11 +1,11 @@
 Package: pepr
 Type: Package
 Title: Reading Portable Encapsulated Projects
-Version: 0.4.0
-Date: 2020-10-15
+Version: 0.5.0
+Date: 2021-06-10
 Authors@R: c(person("Nathan", "Sheffield", email = "[email protected]",
     role = c("aut", "cph")),person("Michal","Stolarczyk",email="[email protected]",role=c("aut","cre")))
-Maintainer: Michal Stolarczyk <[email protected]>
+Maintainer: Nathan Sheffield <[email protected]>
 Description: A PEP, or Portable Encapsulated Project, is a dataset that 
     subscribes to the PEP structure for organizing metadata. It is written using
     a simple YAML + CSV format, it is your one-stop solution to metadata 
@@ -16,12 +16,15 @@ Imports:
     stringr,
     pryr,
     data.table,
-    methods
+    methods,
+    RCurl
 Suggests:
     knitr,
     testthat,
-    rmarkdown
+    rmarkdown,
+    curl
 VignetteBuilder: knitr
 License: BSD_2_clause + file LICENSE
 BugReports: https://github.com/pepkit/pepr
-RoxygenNote: 7.1.0
+RoxygenNote: 7.2.3
+Encoding: UTF-8

NAMESPACE

@@ -24,6 +24,7 @@ exportClasses(Project)
 exportMethods("$")
 exportMethods("[")
 exportMethods("[[")
+import(RCurl)
 import(pryr)
 import(stringr)
 import(yaml)

NEWS.md

@@ -1,3 +1,22 @@
+# pepr 0.5.0 - 2023-11-16
+
+## Fixed
+
+* result class of appended attributes; it's no longer wrapped in a `list`
+* various other fixes and improvements
+
+## Changed 
+
+* error message when nonexistent attribute is derived
+
+## Added
+
+* possibility to configure the sample and subsample table index attributes in the `Project` object constructor
+* possibility to initialize `Project` with no configuration file
+* ability to initialize a project from URL
+* auto initialization file detection: CSV (sample table) or YAML (project config)
+* duplicated sample auto-merging
+
 # pepr 0.4.0 - 2020-10-14
 
 ## Changed