Improve project setup with workflows, licensing, and docs. (#9)

* Add github workflow actions.

* Add MIT license files.

* Update package metadata, authors, and CITATION.cff.

* Replace legacy journal metrics with JCR 2023 and Scimago 2025 data.

* Refactor R package code for ISSN helpers and journal sources.

* Add testthat coverage for ISSN helpers and pipeline.

* Update vignette for live Europe PMC tutorial workflow.

* Add NEWS.md changelog.

* Add contributing guidelines.

* Update CI workflow and R build configuration.

* Configure pkgdown with styling, navbar, and changelog.

* Rebuild pkgdown documentation site.

* Update DESCRIPTION and NAMESPACE to include rlang.

* Update example documentation.

* Update DESCRIPTION to suggest BiocManager and refactor ISSN handling in get_articles_with_journal_data function.

* Update .Rbuildignore to exclude CSV files.

* Add example_queries documentation and update pkgdown configuration.

Author: sdhutchins

.Rbuildignore

@@ -1,4 +1,7 @@
 ^docs$
+^data-raw$
 ^_pkgdown\.yml$
 ^.*\.Rproj$
 ^\.Rproj\.user$
+^LICENSE\.md$
+^data/.*\.csv$

.github/CONTRIBUTING.md

@@ -0,0 +1,92 @@
+# Contributing
+
+We welcome contributions! This document provides guidelines for contributing to JournalAnalysis.
+
+## Submitting Bugs
+
+### Before Submitting
+
+Before submitting a bug report, please do the following:
+
+- **Make sure you're on the latest version.** Your problem may have been solved already.
+- **Try older versions.** If you're on the latest release, try rolling back a few minor versions to help narrow down when the problem first arose.
+- **Search the project's issue tracker** to make sure it's not a known issue.
+
+### Bug Report Contents
+
+Make sure your report includes:
+
+- **Operating system:** Windows? macOS? Linux? Include version details.
+- **R version:** Output from `R.version.string` or `sessionInfo()`.
+- **Package version:** Output from `packageVersion("JournalAnalysis")`.
+- **RStudio version:** If the addin is involved, include your RStudio build.
+- **Installation method:** r-universe, GitHub (`devtools::install_github`), or source.
+- **Steps to reproduce:** Include a minimal example, the command or addin steps you used, and the full output or error message.
+
+## Contributing Changes
+
+### Licensing
+
+By contributing to this project, you agree that your contributions will be licensed under the same terms as the rest of the project (see the `LICENSE` file in the repository root).
+
+- Per-file copyright/license headers are typically not needed. Please don't add your own copyright headers to new files unless the project's license actually requires them.
+
+### Version Control
+
+- **Always make a new branch** for your work, no matter how small.
+- **Don't submit unrelated changes in the same branch/pull request.**
+- **Base your branch on `main`** for new features and most bug fixes.
+- If your PR has been sidelined for a while, **rebase or merge to latest `main`** before resubmitting.
+
+### Code Formatting
+
+- **Follow the style used in the repository.** Consistency with the rest of the project always trumps other considerations.
+- Use snake_case for functions and variables, `<-` for assignment, and 2-space indentation.
+
+### Documentation
+
+Documentation is required for all contributions:
+
+- **Roxygen2 comments** must be created or updated for exported functions.
+- **README or pkgdown docs** should be updated when user-facing behavior changes.
+- **Changelog entry** should credit the contributor when the change is user-visible.
+
+### Tests
+
+Tests are required for all contributions:
+
+- **Bug fixes** must include a test proving the existence of the bug being fixed.
+- **New features** must include tests proving they actually work.
+- Run `devtools::test()` locally before opening a pull request.
+
+## Workflow Example
+
+Here's an example workflow for contributing:
+
+### Preparing Your Fork
+
+1. Fork the repository on GitHub.
+2. Clone your fork: `git clone git@github.com:yourname/JournalAnalysis.git`
+3. `cd JournalAnalysis`
+4. Install development dependencies: `devtools::install_dev_deps()`
+5. Create a branch: `git checkout -b fix-description main`
+
+### Making Your Changes
+
+1. Write tests expecting the correct/fixed functionality; make sure they fail initially.
+2. Implement your changes.
+3. Run tests again: `devtools::test()`
+4. Run a full check: `devtools::check()`
+5. Update documentation as needed.
+6. Commit your changes: `git commit -m "Brief description of changes"`
+
+### Creating Pull Requests
+
+1. Push your branch: `git push origin HEAD`
+2. Visit GitHub and click the "Pull request" button.
+3. In the description field, reference the issue number (if fixing an existing issue) or describe the issue and your fix.
+4. Submit and be patient - maintainers will review when they can.
+
+## Questions?
+
+If you have questions about contributing, please [open an issue](https://github.com/vallenderlab/JournalAnalysis/issues) or contact the maintainers.

.github/workflows/pkgdown.yaml

@@ -0,0 +1,48 @@
+# 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]
+  pull_request:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown
+
+permissions: read-all
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - 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/github-pages-deploy-action@v4.5.0
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.github/workflows/r-cmd-check.yaml

@@ -0,0 +1,65 @@
+name: R-CMD-check
+
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+env:
+  R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+  GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+    env:
+      RSPM: ${{ matrix.config.rspm }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: windows-latest, r: "release"}
+          - {os: macOS-latest, r: "release"}
+          - {os: ubuntu-latest, r: "release", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
+          - {os: ubuntu-latest, r: "devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - name: Session info
+        run: |
+          options(width = 100)
+          sessioninfo::session_info()
+        shell: Rscript {0}
+
+      - name: Check
+        env:
+          _R_CHECK_CRAN_INCOMING_REMOTE_: false
+          _R_CHECK_FORCE_SUGGESTS_: false
+        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
+        shell: Rscript {0}
+
+      - name: Show testthat output
+        if: always()
+        run: find check -name 'testthat.Rout*' -exec cat '{}' \;
+        shell: bash
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          path: check

CITATION.cff

@@ -0,0 +1,19 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+type: software
+title: "JournalAnalysis: Explore and Identify Journals to Publish in."
+abstract: >-
+  A package for exploring and identifying the best journals in which to
+  publish a paper.
+authors:
+  - given-names: Robert
+    family-names: Gilmore
+    email: robgilmore127@gmail.com
+  - given-names: Shaurita
+    family-names: Hutchins
+    email: shaurita.d.hutchins@gmail.com
+version: 0.2.0
+date-released: 2026-06-10
+url: https://github.com/vallenderlab/JournalAnalysis
+repository-code: https://github.com/vallenderlab/JournalAnalysis
+license: MIT

DESCRIPTION

@@ -1,27 +1,29 @@
 Package: JournalAnalysis
 Title: Explore and Identify Journals to Publish in.
-Version: 0.0.1
+Version: 0.2.0
 Authors@R: c(
-    person("Robert", "Gilmore", email = "rgilmore@umc.edu", role = "cre"),
-    person("Shaurita", "Hutchins", email = "shutchins2@umc.edu", role = "aut"))
+    person("Robert", "Gilmore", email = "robgilmore127@gmail.com", role = c("aut", "cre")),
+    person("Shaurita", "Hutchins", email = "shaurita.d.hutchins@gmail.com", role = "aut"))
 Description: A package for exploring and identifying the best journals in which to publish a paper.
-Depends: R (>= 3.4.3)
-License: MIT
+Depends: 
+    R (>= 3.5)
+License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
 URL: https://github.com/vallenderlab/JournalAnalysis
 BugReports: https://github.com/vallenderlab/JournalAnalysis/issues
 Imports:
     dplyr,
     europepmc,
+    rlang,
     tibble,
-    magrittr,
     PubMedWordcloud,
-    ggplot2,
-    ggthemes,
-    stringr,
-    BiocParallel
-Suggests: knitr,
-    rmarkdown
+    stringr
+Suggests: 
+    knitr,
+    rmarkdown,
+    devtools,
+    testthat (>= 3.0.0)
 VignetteBuilder: knitr
-RoxygenNote: 6.1.0
+RoxygenNote: 7.3.3
+Config/testthat/edition: 3

LICENSE

@@ -0,0 +1,2 @@
+YEAR: 2026
+COPYRIGHT HOLDER: Vallender Lab

LICENSE.md

@@ -0,0 +1,21 @@
+# MIT License
+
+Copyright (c) 2018-2026 Vallender Lab
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

NAMESPACE

@@ -12,3 +12,9 @@ export(query1)
 export(query2)
 export(query3)
 export(save_as_csv)
+importFrom(grDevices,dev.off)
+importFrom(grDevices,png)
+importFrom(rlang,.data)
+importFrom(utils,install.packages)
+importFrom(utils,installed.packages)
+importFrom(utils,write.csv)

NEWS.md

@@ -0,0 +1,3 @@
+# JournalAnalysis 0.2.0
+
+* Initial package release on GitHub.