fix notes from devtools::check() and add citation file format metadata

.Rbuildignore

@@ -1,2 +1,5 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
+^LICENSE\.md$
+^CITATION\.cff$
+^\.github$

.github/workflows/update-citation-cff.yaml

@@ -0,0 +1,58 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# The action runs when:
+# - A new release is published
+# - The DESCRIPTION or inst/CITATION are modified
+# - Can be run manually
+# For customizing the triggers, visit https://docs.github.com/en/actions/learn-github-actions/events-that-trigger-workflows
+on:
+  release:
+    types: [published]
+  push:
+    branches: [master, main]
+    paths:
+      - DESCRIPTION
+      - inst/CITATION
+  workflow_dispatch:
+
+name: Update CITATION.cff
+
+jobs:
+  update-citation-cff:
+    runs-on: macos-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v3
+      - uses: r-lib/actions/setup-r@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: |
+            any::cffr
+            any::V8
+
+      - name: Update CITATION.cff
+        run: |
+
+          library(cffr)
+
+          # Customize with your own code
+          # See https://docs.ropensci.org/cffr/articles/cffr.html
+
+          # Write your own keys
+          mykeys <- list()
+
+          # Create your CITATION.cff file
+          cff_write(keys = mykeys)
+
+        shell: Rscript {0}
+
+      - name: Commit results
+        run: |
+          git config --local user.name "github-actions[bot]"
+          git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com"
+          git add CITATION.cff
+          git commit -m 'Update CITATION.cff' || echo "No changes to commit"
+          git push origin || echo "No changes to commit"
+
+
+

CITATION.cff

@@ -0,0 +1,169 @@
+# -----------------------------------------------------------
+# CITATION file created with {cffr} R package, v0.5.0
+# See also: https://docs.ropensci.org/cffr/
+# -----------------------------------------------------------
+
+cff-version: 1.2.0
+message: 'To cite package "detectCilia" in publications use:'
+type: software
+license: GPL-3.0-or-later
+title: 'detectCilia: Detecting the lengths of primary cilia'
+version: 0.7.2
+doi: NN
+abstract: The package loads confocal fluorescence microscopy images and automatically
+  determines the positions and lengths of primary cilia of the cells and counts nuclei.
+authors:
+- family-names: Budde-Sagert
+  given-names: Kai
+  email: [email protected]
+- name: c
+- family-names: c)
+  given-names: comment =
+preferred-citation:
+  type: article
+  title: 'Studying the influence of cell culture medium composition on ciliary length
+    with detectCilia: An R package for automated detection and length measurement
+    of primary cilia'
+  authors:
+  - family-names: Budde-Sagert
+    given-names: Kai
+    email: [email protected]
+  - family-names: Krueger
+    given-names: Simone
+  - family-names: Sehlke
+    given-names: Clemens
+  - family-names: Jonitz-Heincke
+    given-names: Anika
+  - family-names: David
+    given-names: Robert
+  - family-names: Bader
+    given-names: Rainer
+  - family-names: Uhrmacher
+    given-names: Adelinde M.
+  doi: NN
+  year: '2023'
+  publisher:
+    name: NN
+  volume: '0'
+  issue: '0'
+  journal: NN
+  start: '0'
+repository-code: https://github.com/SFB-ELAINE/detectCilia
+url: https://github.com/SFB-ELAINE/detectCilia
+contact:
+- family-names: Budde-Sagert
+  given-names: Kai
+  email: [email protected]
+references:
+- type: software
+  title: 'R: A Language and Environment for Statistical Computing'
+  notes: Depends
+  url: https://www.R-project.org/
+  authors:
+  - name: R Core Team
+  location:
+    name: Vienna, Austria
+  year: '2023'
+  institution:
+    name: R Foundation for Statistical Computing
+  version: '>= 4.0.0'
+- type: software
+  title: dplyr
+  abstract: 'dplyr: A Grammar of Data Manipulation'
+  notes: Imports
+  url: https://dplyr.tidyverse.org
+  repository: https://CRAN.R-project.org/package=dplyr
+  authors:
+  - family-names: Wickham
+    given-names: Hadley
+    email: [email protected]
+    orcid: https://orcid.org/0000-0003-4757-117X
+  - family-names: François
+    given-names: Romain
+    orcid: https://orcid.org/0000-0002-2444-4226
+  - family-names: Henry
+    given-names: Lionel
+  - family-names: Müller
+    given-names: Kirill
+    orcid: https://orcid.org/0000-0002-1416-3412
+  year: '2023'
+  version: '>= 1.0.10'
+- type: software
+  title: EBImage
+  abstract: 'EBImage: Image processing and analysis toolbox for R'
+  notes: Imports
+  url: https://github.com/aoles/EBImage
+  repository: https://bioconductor.org/
+  authors:
+  - family-names: Oles
+    given-names: Andrzej
+  - family-names: Pau
+    given-names: Gregoire
+  - family-names: Smith
+    given-names: Mike
+  - family-names: Sklyar
+    given-names: Oleg
+  - family-names: Huber
+    given-names: Wolfgang
+  - family-names: Barry
+    given-names: with contributions from Joseph
+  - family-names: Marais
+    given-names: Philip A.
+  year: '2023'
+  version: '>= 4.40.0'
+- type: software
+  title: magrittr
+  abstract: 'magrittr: A Forward-Pipe Operator for R'
+  notes: Imports
+  url: https://magrittr.tidyverse.org
+  repository: https://CRAN.R-project.org/package=magrittr
+  authors:
+  - family-names: Bache
+    given-names: Stefan Milton
+    email: [email protected]
+  - family-names: Wickham
+    given-names: Hadley
+    email: [email protected]
+  year: '2023'
+  version: '>= 2.0.3'
+- type: software
+  title: readCzi
+  abstract: 'readCzi: Read czi image files, convert them to tifs, and save metadata'
+  notes: Imports
+  authors:
+  - name: c)
+  year: '2023'
+  version: '>= 0.2.3'
+- type: software
+  title: readr
+  abstract: 'readr: Read Rectangular Text Data'
+  notes: Imports
+  url: https://readr.tidyverse.org
+  repository: https://CRAN.R-project.org/package=readr
+  authors:
+  - family-names: Wickham
+    given-names: Hadley
+    email: [email protected]
+  - family-names: Hester
+    given-names: Jim
+  - family-names: Bryan
+    given-names: Jennifer
+    email: [email protected]
+    orcid: https://orcid.org/0000-0002-6983-2759
+  year: '2023'
+  version: '>= 2.1.3'
+- type: software
+  title: rlang
+  abstract: 'rlang: Functions for Base Types and Core R and ''Tidyverse'' Features'
+  notes: Imports
+  url: https://rlang.r-lib.org
+  repository: https://CRAN.R-project.org/package=rlang
+  authors:
+  - family-names: Henry
+    given-names: Lionel
+    email: [email protected]
+  - family-names: Wickham
+    given-names: Hadley
+    email: [email protected]
+  year: '2023'
+  version: '>= 1.0.6'

DESCRIPTION

@@ -1,17 +1,27 @@
 Package: detectCilia
 Type: Package
-Title: Detecting the total length of the primary cilium
-Version: 0.7.1
+Title: Detecting the lengths of primary cilia
+Version: 0.7.2
 Author: c(person("Kai", "Budde-Sagert", email = "[email protected]",
-    role = c("aut", "cre"))
+    role = c("aut", "cre"), comment = c(ORCID = "0000-0001-6836-9865"))
 Maintainer: Kai Budde-Sagert <[email protected]>
-Description: The package loads z-stack confocal fluorescence microscopy
-  images and automatically determines the positions and lengths of primary
+Description: The package loads confocal fluorescence microscopy images and
+  automatically determines the positions and lengths of primary
   cilia of the cells and counts nuclei.
-License: LICENSE
+URL: https://github.com/SFB-ELAINE/detectCilia
+BugReports: https://github.com/SFB-ELAINE/detectCilia/issues
+License: GPL (>= 3)
+Depends: 
+    R (>= 4.0.0)
+Imports:
+    dplyr (>= 1.0.10),
+    EBImage (>= 4.40.0),
+    magrittr (>= 2.0.3),
+    readCzi (>= 0.2.3),
+    readr (>= 2.1.3),
+    rlang (>= 1.0.6)
 Encoding: UTF-8
 LazyData: true
 ByteCompile: TRUE
 RoxygenNote: 7.2.3
 NeedsCompilation: no
-Imports: BiocManager, dplyr, devtools, reticulate