Merge pull request #473 from DOI-USGS/hydrogeofetch

Hydrogeofetch

Author: dblodgett-usgs

.Rbuildignore

@@ -29,5 +29,7 @@ CLAUDE.md
 dev
 .claude
 inst/build
-vignettes/drainage_area_figures
 PLAN.md
+^tests/testthat/fixtures$
+^vignettes/articles$
+^\.kiro$

.gitignore

@@ -23,3 +23,7 @@ CLAUDE.md
 dev
 vignettes/*.html
 vignettes/*_figures/
+vignettes/articles/*.html
+vignettes/articles/*_figures/
+vignettes/articles/*_files/
+.kiro/

.gitlab-ci.yml

@@ -2,28 +2,60 @@ variables:
   _R_CHECK_CRAN_INCOMING_: "false"
   _R_CHECK_FORCE_SUGGESTS_: "true"
   _R_CHECK_DONTTEST_EXAMPLES_: "false"
-  APT_PKGS: "p7zip-full"
+  _R_CHECK_RD_XREFS_: "false"
 
-before_script:
-  - wget --no-check-certificate -O /usr/local/share/ca-certificates/DOIRootCA2.crt https://raw.githubusercontent.com/dblodgett-usgs/hydrogeoenv/master/linux/DOIRootCA2.cer
-  - chmod 644 /usr/local/share/ca-certificates/DOIRootCA2.crt && update-ca-certificates
-  - apt-get update
-  - apt-get install -y --no-install-recommends ${APT_PKGS}
-  - apt-get install -y --no-install-recommends qpdf pandoc
-  - export PATH="/usr/local/lib/R/site-library/littler/examples/:${PATH}"
-  - echo "options(Ncpus = $(nproc --all))" >> /usr/local/lib/R/etc/Rprofile.site
-  - install2.r devtools
-  - r -e 'devtools::install_dev_deps()'
+stages:
+  - check
+  - build
+  - verify
 
-test:
-  stage: test
+workflow:
+  rules:
+    - if: $CI_COMMIT_BRANCH =~ /^rc\//
+
+.r-base:
   tags:
     - chs-shared
   image: ${CI_DEPENDENCY_PROXY_GROUP_IMAGE_PREFIX}/rocker/geospatial:latest
+  before_script:
+    - wget --no-check-certificate -O /usr/local/share/ca-certificates/DOIRootCA2.crt https://raw.githubusercontent.com/dblodgett-usgs/hydrogeoenv/master/linux/DOIRootCA2.cer
+    - chmod 644 /usr/local/share/ca-certificates/DOIRootCA2.crt && update-ca-certificates
+    - apt-get update
+    - apt-get install -y --no-install-recommends p7zip-full qpdf pandoc curl
+    - export PATH="/usr/local/lib/R/site-library/littler/examples/:${PATH}"
+    - echo "options(Ncpus = $(nproc --all))" >> /usr/local/lib/R/etc/Rprofile.site
+    - r -e 'pak::local_install_dev_deps()'
+
+check:
+  extends: .r-base
+  stage: check
+  script:
+    - R CMD build --no-build-vignettes --no-manual .
+    - R CMD check --no-tests --no-examples --no-vignettes --no-manual *.tar.gz
+  artifacts:
+    paths:
+      - "*.Rcheck"
+    when: always
+
+build:
+  extends: .r-base
+  stage: build
+  script:
+    - R CMD build .
+    - PKG_FILE=$(ls *.tar.gz)
+    - PKG_NAME=$(echo "$PKG_FILE" | sed 's/_.*//')
+    - PKG_VERSION=$(echo "$PKG_FILE" | sed 's/.*_\(.*\)\.tar\.gz/\1/')
+    - 'curl --silent --show-error --write-out "\nHTTP status: %{http_code}\n" --header "JOB-TOKEN: ${CI_JOB_TOKEN}" --upload-file "$PKG_FILE" "${CI_API_V4_URL}/projects/${CI_PROJECT_ID}/packages/generic/${PKG_NAME}/${PKG_VERSION}/${PKG_FILE}"'
+  artifacts:
+    paths:
+      - "*.tar.gz"
+
+verify:
+  extends: .r-base
+  stage: verify
   script:
-    - r -e 'devtools::check(check_dir = ".")'
-    - r -e 'capture.output(print(covr::coverage_to_list(covr::package_coverage(type = "all")), width = 20),  file = "covr.txt", split = TRUE)'
+    - R CMD check --as-cran --no-manual *.tar.gz
   artifacts:
     paths:
       - "*.Rcheck"
-      - "covr.txt"
+    when: always

DESCRIPTION

@@ -1,15 +1,15 @@
-Package: nhdplusTools
+Package: hydrogeofetch
 Type: Package
-Title: NHDPlus Tools
-Version: 1.5.0
+Title: Hydrologic Geospatial Fabric Extraction Tool Chain
+Version: 2.0.0
 Authors@R: c(person(given = "David", 
                     family = "Blodgett", 
                     role = c("aut", "cre"), 
                     email = "dblodgett@usgs.gov",
                     comment = c(ORCID = "0000-0001-9489-1710")),
              person(given = "Mike",
                     family = "Johnson",
-                    role = "aut",
+                    role = "ctb",
                     comment = c(ORCID = "0000-0002-5288-8350")),
              person(given = "Marc",
                     family = "Weber", 
@@ -23,18 +23,19 @@ Authors@R: c(person(given = "David",
                    family = "Koenig",
                    role = "ctb",
                    comment = c(ORCID = "0000-0002-7790-330X")))
-Description: Tools for traversing and working with National Hydrography Dataset Plus (NHDPlus) data. All methods implemented in 'nhdplusTools' are available in the NHDPlus documentation available from the US Environmental Protection Agency <https://www.epa.gov/waterdata/basic-information>.
+Description: Tools for traversing and working with National Hydrography Dataset Plus (NHDPlus) data. All methods implemented in 'hydrogeofetch' are available in the NHDPlus documentation available from the US Environmental Protection Agency <https://www.epa.gov/waterdata/basic-information>. Previously published as 'nhdplusTools'.
 URL: https://doi-usgs.github.io/nhdplusTools/ https://github.com/doi-usgs/nhdplusTools/
 BugReports: https://github.com/doi-usgs/nhdplusTools/issues/
 Depends:
     R (>= 4.1)
-Imports: hydroloom, dataRetrieval, dplyr, sf, units, magrittr, jsonlite, httr, xml2, R.utils, utils, tidyr, methods, maptiles, mapsf, fst, arrow, tools, zip, pbapply, memoise, digest
-Suggests: testthat, knitr, rmarkdown, ggmap, ggplot2, lwgeom, gifski, leaflet, httptest, future, future.apply, StreamCatTools, terra
+Imports: hydroloom, dataRetrieval, dplyr, sf, units, jsonlite, httr2, xml2, utils, data.table, methods, arrow, tools, zip, memoise, digest
+Suggests: testthat, knitr, rmarkdown, ggmap, ggplot2, lwgeom, gifski, leaflet, httptest2, StreamCatTools, terra, maptiles, mapsf
 License: CC0
 Encoding: UTF-8
-RoxygenNote: 7.3.3
 VignetteBuilder: knitr
 Config/testthat/parallel: true
 Config/testthat/edition: 3
 LazyData: true
+LazyDataCompression: xz
 Language: en-US
+Config/roxygen2/version: 8.0.0

NAMESPACE

@@ -1,10 +1,8 @@
 # Generated by roxygen2: do not edit by hand
 
-export(add_plus_network_attributes)
+export(add_mainstems)
 export(align_nhdplus_names)
-export(calculate_arbolate_sum)
-export(calculate_total_drainage_area)
-export(disambiguate_flowline_indexes)
+export(check_mainstems)
 export(discover_geoconnex_reference)
 export(discover_nhdplus_id)
 export(download_nhd)
@@ -13,72 +11,53 @@ export(download_nhdplusv2)
 export(download_rf1)
 export(download_vaa)
 export(download_wbd)
-export(fix_flowdir)
 export(get_3dhp)
-export(get_DD)
-export(get_DM)
-export(get_UM)
-export(get_UT)
 export(get_boundaries)
 export(get_catchment_characteristics)
 export(get_characteristics_metadata)
 export(get_drainage_area_estimates)
 export(get_elev_along_path)
-export(get_flowline_index)
 export(get_gagesII)
 export(get_geoconnex_reference)
 export(get_hr_data)
 export(get_huc)
-export(get_hydro_location)
-export(get_levelpaths)
 export(get_nhdarea)
 export(get_nhdphr)
 export(get_nhdplus)
 export(get_nhdplushr)
 export(get_nldi_basin)
 export(get_nldi_feature)
 export(get_nldi_index)
-export(get_node)
 export(get_nwis)
-export(get_partial_length)
-export(get_path_lengths)
-export(get_path_members)
-export(get_pathlength)
-export(get_pfaf)
 export(get_raindrop_trace)
-export(get_sorted)
 export(get_split_catchment)
-export(get_streamlevel)
-export(get_streamorder)
-export(get_terminal)
 export(get_tocomid)
 export(get_vaa)
 export(get_vaa_names)
 export(get_vaa_path)
 export(get_waterbodies)
-export(get_waterbody_index)
 export(get_wb_outlet)
 export(get_xs_point)
 export(get_xs_points)
-export(make_node_topology)
+export(hydrogeofetch_cache_settings)
+export(hydrogeofetch_data_dir)
 export(make_standalone)
 export(map_nhdplus)
-export(navigate_network)
 export(navigate_nldi)
-export(nhdplusTools_cache_settings)
-export(nhdplusTools_data_dir)
 export(nhdplus_path)
 export(plot_nhdplus)
 export(prepare_nhdplus)
-export(rename_geometry)
 export(rescale_catchment_characteristics)
-export(rescale_measures)
-export(st_compatibalize)
 export(subset_nhdplus)
 export(subset_rpu)
 export(subset_vpu)
+export(update_mainstems)
 importFrom(arrow,open_dataset)
+importFrom(arrow,read_csv_arrow)
 importFrom(arrow,s3_bucket)
+importFrom(arrow,write_parquet)
+importFrom(data.table,as.data.table)
+importFrom(data.table,dcast)
 importFrom(dataRetrieval,findNLDI)
 importFrom(digest,digest)
 importFrom(dplyr,across)
@@ -87,6 +66,7 @@ importFrom(dplyr,any_of)
 importFrom(dplyr,arrange)
 importFrom(dplyr,bind_rows)
 importFrom(dplyr,collect)
+importFrom(dplyr,contains)
 importFrom(dplyr,desc)
 importFrom(dplyr,distinct)
 importFrom(dplyr,everything)
@@ -102,48 +82,25 @@ importFrom(dplyr,select)
 importFrom(dplyr,starts_with)
 importFrom(dplyr,summarize)
 importFrom(dplyr,ungroup)
-importFrom(fst,metadata_fst)
-importFrom(fst,read.fst)
 importFrom(graphics,par)
-importFrom(httr,GET)
-importFrom(httr,RETRY)
-importFrom(httr,content)
-importFrom(httr,progress)
-importFrom(httr,write_disk)
-importFrom(hydroloom,accumulate_downstream)
-importFrom(hydroloom,add_levelpaths)
-importFrom(hydroloom,add_pathlength)
-importFrom(hydroloom,add_pfafstetter)
-importFrom(hydroloom,add_streamlevel)
-importFrom(hydroloom,add_streamorder)
+importFrom(httr2,req_perform)
+importFrom(httr2,request)
 importFrom(hydroloom,add_toids)
 importFrom(hydroloom,disambiguate_indexes)
-importFrom(hydroloom,fix_flowdir)
 importFrom(hydroloom,get_hydro_location)
 importFrom(hydroloom,get_node)
-importFrom(hydroloom,get_partial_length)
-importFrom(hydroloom,hy)
 importFrom(hydroloom,index_points_to_lines)
-importFrom(hydroloom,index_points_to_waterbodies)
-importFrom(hydroloom,make_fromids)
-importFrom(hydroloom,make_index_ids)
-importFrom(hydroloom,navigate_connected_paths)
 importFrom(hydroloom,navigate_hydro_network)
 importFrom(hydroloom,navigate_network_dfs)
 importFrom(hydroloom,rename_geometry)
 importFrom(hydroloom,rescale_measures)
 importFrom(hydroloom,sort_network)
-importFrom(hydroloom,st_compatibalize)
 importFrom(jsonlite,fromJSON)
-importFrom(magrittr,`%>%`)
 importFrom(memoise,cache_filesystem)
 importFrom(memoise,cache_memory)
 importFrom(memoise,memoise)
 importFrom(methods,as)
 importFrom(methods,is)
-importFrom(pbapply,pbapply)
-importFrom(pbapply,pblapply)
-importFrom(pbapply,pboptions)
 importFrom(sf,"st_geometry<-")
 importFrom(sf,read_sf)
 importFrom(sf,st_area)
@@ -171,12 +128,8 @@ importFrom(sf,st_union)
 importFrom(sf,st_zm)
 importFrom(sf,write_sf)
 importFrom(stats,weighted.mean)
-importFrom(tidyr,contains)
-importFrom(tidyr,pivot_wider)
-importFrom(tidyr,replace_na)
 importFrom(tools,R_user_dir)
 importFrom(units,set_units)
-importFrom(utils,combn)
 importFrom(utils,download.file)
 importFrom(utils,read.delim)
 importFrom(utils,tail)

NEWS.md

@@ -1,3 +1,47 @@
+hydrogeofetch 2.0.0
+==========
+
+`hydrogeofetch` is the renamed successor to `nhdplusTools`. The package scope has grown beyond NHDPlus, and the new name reflects its broader role as a hydrologic geospatial data access and network tool chain. `nhdplusTools` will remain on CRAN as a deprecation shim until October 2028.
+
+## New features
+
+- New `add_mainstems()` joins geoconnex mainstem identifiers onto a table containing NHDPlusV2 (comid/featureid) or NHDPlusHR (nhdplusid) identifiers, using a cached lookup table from the [ref_rivers](https://github.com/internetofwater/ref_rivers) release. #469
+- New `check_mainstems()` checks whether mainstem identifiers have been superseded by a newer reference release; new `update_mainstems()` re-indexes points with a known mainstem id onto its replacement using `hydroloom::index_points_to_lines()`. #470
+
+## Removed functions (moved to hydroloom)
+
+Network analysis and spatial indexing functions that duplicated [hydroloom](https://doi-usgs.github.io/hydroloom/) have been removed. Users should call hydroloom directly. See the [hydroloom reference](https://doi-usgs.github.io/hydroloom/reference/) for full documentation, especially the [indexing](https://doi-usgs.github.io/hydroloom/reference/index.html#indexing-and-linear-referencing) and [navigation](https://doi-usgs.github.io/hydroloom/reference/index.html#network-navigation-and-accumulation) sections.
+
+- `get_flowline_index()` → `hydroloom::index_points_to_lines()`
+- `get_waterbody_index()` → `hydroloom::index_points_to_waterbodies()`
+- `disambiguate_flowline_indexes()` → `hydroloom::disambiguate_indexes()`
+- `get_UT()`, `get_DD()` → `hydroloom::navigate_hydro_network(x, start, "UT")` / `"DD"`
+- `get_UM()`, `get_DM()` → `hydroloom::navigate_hydro_network(x, start, "UM")` / `"DM"` (note: the old wrappers also ran `align_nhdplus_names`, filtered, and supported `sort`/`include` arguments)
+- `navigate_network()` — workflow glue; use `navigate_nldi()` + `subset_nhdplus()` or hydroloom navigation directly
+- `get_sorted()` → `hydroloom::sort_network()`
+- `get_pathlength()` → `hydroloom::add_pathlength()`
+- `get_streamorder()` → `hydroloom::add_streamorder()`
+- `get_streamlevel()` → `hydroloom::add_streamlevel()`
+- `get_levelpaths()` → `hydroloom::add_levelpaths()`
+- `get_pfaf()` → `hydroloom::add_pfafstetter()`
+- `get_terminal()` → `hydroloom::sort_network(x, split = TRUE)`
+- `calculate_total_drainage_area()` → `hydroloom::accumulate_downstream(x, "area")`
+- `calculate_arbolate_sum()` → `hydroloom::accumulate_downstream(x, "length")`
+- `get_path_members()`, `get_path_lengths()` → `hydroloom::navigate_connected_paths()`
+- `make_node_topology()` → `hydroloom::make_node_topology()`
+- `add_plus_network_attributes()` → use hydroloom's `add_levelpaths()`, `add_pathlength()`, `accumulate_downstream()` etc. directly
+
+## Removed re-exports
+
+These hydroloom functions are no longer re-exported; call `hydroloom::fn()` directly:
+
+- `st_compatibalize()`, `rename_geometry()`, `get_node()`, `fix_flowdir()`, `rescale_measures()`, `get_hydro_location()`, `get_partial_length()`
+
+## Dependency changes
+
+- Removed `pbapply` from Imports (no longer needed)
+- Removed `future`, `future.apply` from Suggests (no longer needed)
+
 nhdplusTools 1.5.0
 ==========