v0.12

.Rbuildignore

@@ -5,4 +5,17 @@
 ^pkgdown$
 ^\.github$
 ^vignettes/articles$
-^dev$
+^dev$
+^releases$
+(^|/)venv(/.*)?$
+LICENSE.md
+CITATION.cff
+^doc$
+^Meta$
+^scratch$
+cache
+(^|/)[^/]*cache[^/]*(/.*)?$
+^\.RDataTmp$
+^\.RData$
+^revdep$
+^cran-comments\.md$

.github/workflows/R-CMD-check.yaml

@@ -0,0 +1,75 @@
+# 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:
+
+name: R-CMD-check.yaml
+
+permissions: read-all
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - name: Install osmium-tool (Linux)
+        if: runner.os == 'Linux'
+        run: sudo apt-get install -y osmium-tool
+
+      - name: Install osmium-tool (macOS)
+        if: runner.os == 'macOS'
+        run: brew install osmium-tool
+
+      - name: Setup Conda (Windows)
+        if: runner.os == 'Windows'
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          channels: conda-forge
+          channel-priority: strict
+
+      - name: Install osmium-tool (Windows)
+        if: runner.os == 'Windows'
+        shell: bash -el {0}
+        run: |
+          conda install -y osmium-tool
+          echo "$CONDA_PREFIX/Library/bin" >> $GITHUB_PATH
+          echo "$CONDA_PREFIX/Scripts" >> $GITHUB_PATH
+          echo "$CONDA_PREFIX" >> $GITHUB_PATH
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/pkgdown.yaml

@@ -32,9 +32,21 @@ jobs:
         with:
           use-public-rspm: true
 
+      - name: Install osmium-tool (Linux)
+        run: sudo apt-get install -y osmium-tool
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+
+      - name: Install Python dependencies for neatnet (osm_centerlines)
+        run: |
+          python -m pip install --upgrade pip
+          pip install osmnx pandas geopandas shapely neatnet pyrosm
+
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::pkgdown, local::.
+          extra-packages: any::pkgdown, any::rosmium, any::reticulate, local::.
           needs: website
 
       - name: Build site

.github/workflows/test-coverage.yaml

@@ -0,0 +1,105 @@
+# 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:
+  pull_request:
+    branches: [main, master]
+
+name: test-coverage.yaml
+
+permissions: read-all
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      MOBILITY_DATABASE: ${{ secrets.MOBILITY_DATABASE }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          # testthat and rosmium are Suggests (optional) in DESCRIPTION so they
+          # are not guaranteed to be installed automatically — list them explicitly.
+          extra-packages: any::covr, any::xml2, any::testthat, any::rosmium, local::.
+          needs: coverage
+
+      - name: Run tests and compute coverage
+        run: |
+          install_path <- file.path(
+            normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package"
+          )
+
+          # Helper: print the .Rout.fail file so the actual test error is visible
+          # in the CI log instead of just a path reference.
+          dump_rout_fail <- function() {
+            fail_files <- list.files(install_path, pattern = "\\.Rout\\.fail$",
+                                     recursive = TRUE, full.names = TRUE)
+            if (length(fail_files) == 0) {
+              message("No .Rout.fail file found.")
+              return(invisible(NULL))
+            }
+            for (f in fail_files) {
+              message("\n========== ", basename(f), " ==========")
+              cat(readLines(f, warn = FALSE), sep = "\n")
+              message("============================================\n")
+            }
+          }
+
+          cov <- tryCatch(
+            covr::package_coverage(
+              quiet = FALSE,
+              clean = FALSE,
+              install_path = install_path
+            ),
+            error = function(e) {
+              message("\n--- Test suite failed. Dumping .Rout.fail for diagnosis ---\n")
+              dump_rout_fail()
+              stop(e)   # re-throw so the job still fails
+            }
+          )
+
+          # Print summary to the log
+          print(cov)
+
+          # Generate Cobertura XML report for Codecov upload
+          covr::to_cobertura(cov, filename = "coverage.xml")
+
+          # Compute total coverage percentage and write to GITHUB_ENV
+          pct <- covr::percent_coverage(cov)
+          message("Total coverage: ", round(pct, 2), "%")
+          writeLines(paste0("COVERAGE_PCT=", round(pct, 2)), Sys.getenv("GITHUB_ENV"))
+        shell: Rscript {0}
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v4
+        with:
+          files: coverage.xml
+          token: ${{ secrets.CODECOV_TOKEN }}
+          fail_ci_if_error: false   # don't fail the PR if Codecov is unreachable
+
+      - name: Upload Cobertura XML as workflow artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-report
+          path: coverage.xml
+
+      - name: Enforce minimum coverage threshold
+        run: |
+          pct <- as.numeric(Sys.getenv("COVERAGE_PCT"))
+          threshold <- 0   # Set your desired minimum coverage % here (e.g. 60)
+          if (!is.na(pct) && pct < threshold) {
+            stop(paste0(
+              "Coverage (", round(pct, 2), "%) is below the required threshold of ",
+              threshold, "%."
+            ))
+          } else {
+            message("Coverage check passed: ", round(pct, 2), "%")
+          }
+        shell: Rscript {0}

.gitignore

@@ -1,15 +1,16 @@
 .Rproj.user
 .Rhistory
 .RData
+.RDataTmp
 .Ruserdata
 inst/doc
 docs
 
-*.csv
-*.gpkg
-*.zip
-
 releases/
 vignettes/*_cache/*
 
-scratch/*
+scratch/*
+/doc/
+/Meta/
+*cache*
+revdep/

DESCRIPTION

@@ -1,47 +1,63 @@
-Package: GTFShift
 Type: Package
-Title: Explore and Analyse General Transit Feed Specification (GTFS) Files With a Focus on Urban Mobility 
-Version: 0.11.0
+Package: GTFShift
+Title: Explore and Analyse General Transit Feed Specification (GTFS) Files
+    with a Focus on Urban Mobility
+Version: 0.12.0
 Authors@R: c(
-  person(c("Gonçalo", "F."), "Matos", email = "goncaloafmatos@tecnico.pt", role = c("aut", "cre"), comment = c(ORCID = "0009-0001-3489-1732")),
-  person("Rosa", "Félix", email = "rosamfelix@tecnico.pt", role = c("aut"), comment = c(ORCID = "0000-0002-5642-6006")))
-Description: GTFShift emerged from the necessity to perform systematic analysis for academic research
-  over General Transit Feed Specification (GTFS) files that were not supported by any R library. It compiles 
-  the methods developed for this purpose, aiming to contribute to an open source culture.
-  Its functionality is built mostly on [tidytransit](https://r-transit.github.io/tidytransit/) package.
-License: GNU General Public License, Version 3 (GPL-3)
-Encoding: UTF-8
+    person(c("Gonçalo", "F."), "Matos", , "goncaloafmatos@tecnico.pt", role = c("aut", "cre"),
+           comment = c(ORCID = "0009-0001-3489-1732")),
+    person("Rosa", "Félix", , "rosamfelix@tecnico.pt", role = "aut",
+           comment = c(ORCID = "0000-0002-5642-6006")),
+    person("Miguel", "Relvas Pires", , "miguelpcrpires@tecnico.ulisboa.pt", role = "ctb")
+  )
+Description: This package encompasses a complete bundle of methods to
+    harmonize GTFS and OSM data, enabling the integration and exploration
+    of different layers of transit data, starting with the planned
+    operations (GTFS), but also the infrastructure topology (OSM) and
+    real-time information (GTFS-RT).
+License: GPL
+URL: https://github.com/U-Shift/GTFShift,
+    https://u-shift.github.io/GTFShift/
 Depends:
-  R (>= 4.1.0)
+    R (>= 4.1.0)
 Imports: 
   tidytransit,
   gtfstools,
-  zip,
   sf,
-  tidyverse,
+  tidyselect,
+  tidyr,
   lubridate,
-  gtfsrouter (>= 0.1.4),
   httr,
   jsonlite,
   dplyr,
   osmdata,
-  stplanr,
   stringr,
-  reticulate,
-  progress,
   callr,
-  stringi,
-  parallel
-URL: https://github.com/U-Shift/GTFShift, https://u-shift.github.io/GTFShift/
+  purrr,
+  rlang,
+  xml2,
+  withr
 Suggests: 
     knitr,
     rmarkdown,
     mapview,
-    xml2,
-    RProtoBuf,
     osmextract,
-    rosmium
-VignetteBuilder: knitr
+    rosmium,
+    testthat,
+    zip,
+    gtfsrouter (>= 0.1.4),
+    reticulate,
+    parallel,
+    RProtoBuf,
+    stplanr,
+    lwgeom,
+    progress,
+    stringi,
+    spelling
+VignetteBuilder: 
+    knitr
 Config/Needs/website: rmarkdown
 Config/roxygen2/version: 8.0.0
+Encoding: UTF-8
+Language: en-US
 RoxygenNote: 7.3.3