dev to main, initial build

.Rbuildignore

@@ -0,0 +1,14 @@
+^fit_spatial_mask\.R$
+^demo_fit_spatial_mask\.R$
+^demo_holes_and_scale\.R$
+^vignette_fit_spatial_mask\.Rmd$
+^vignette_fit_spatial_mask\.html$
+^vignette_fit_spatial_mask_cache$
+^vignette_fit_spatial_mask_files$
+^_pkgdown\.yml$
+^pkgdown$
+^\.github$
+^.*\.Rproj$
+^\.Rproj\.user$
+^README\.Rmd$
+^LICENSE\.md$

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

@@ -0,0 +1,52 @@
+# R CMD check workflow
+# Runs on every push and pull request to main/master.
+# Tests on Ubuntu (release + devel), macOS (release), and Windows (release).
+
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: ubuntu-latest,  r: 'release'}
+          - {os: ubuntu-latest,  r: 'devel', http-user-agent: 'release'}
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+
+    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
+
+      - 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")'
+          args: 'c("--no-manual", "--as-cran")'

.github/workflows/pkgdown.yaml

@@ -0,0 +1,52 @@
+# pkgdown site deployment
+# Builds and deploys the pkgdown site to GitHub Pages on every push to main.
+# Requires GitHub Pages to be enabled with "Source: Deploy from a branch"
+# set to "gh-pages / (root)" in repository Settings > Pages.
+
+on:
+  push:
+    branches: [main, master]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown
+
+concurrency:
+  group: pkgdown-${{ github.event_name }}
+  cancel-in-progress: true
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+
+    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
+        uses: JamesIves/github-pages-deploy-action@v4
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.gitignore

@@ -40,7 +40,7 @@ vignettes/*.pdf
 .Renviron
 
 # pkgdown site
-docs/
+# docs/
 
 # translation temp files
 po/*~

DESCRIPTION

@@ -0,0 +1,37 @@
+Package: TissueMask
+Type: Package
+Title: Spatial Boundary Mask Fitting for Point Coordinate Data
+Version: 0.1.0
+Authors@R: person("Raredon Laboratory", role = c("aut", "cre"),
+    email = "raredonlab@yale.edu")
+Description: Fits polygon spatial masks to XY point coordinates such as
+    cell centroids or transcript locations from spatial transcriptomics
+    and spatial proteomics experiments. Supports four methods of
+    increasing topological complexity: convex hull, concave hull, kernel
+    density estimation (KDE), and a raster-based Gaussian smoothing
+    approach that naturally handles internal voids (vessel lumens,
+    necrotic cores, tissue tears) and disconnected tissue islands via
+    GEOS polygon dissolve.
+License: MIT + file LICENSE
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.3.3
+Depends:
+    R (>= 4.1.0)
+Imports:
+    sf (>= 1.0-0),
+    stats,
+    parallel
+Suggests:
+    concaveman,
+    MASS,
+    isoband,
+    ggplot2,
+    testthat (>= 3.0.0),
+    knitr,
+    rmarkdown,
+    patchwork
+VignetteBuilder: knitr
+URL: https://raredonlab.github.io/TissueMask/, https://github.com/RaredonLab/TissueMask
+BugReports: https://github.com/RaredonLab/TissueMask/issues
+Config/testthat/edition: 3

LICENSE

@@ -1,21 +1,2 @@
-MIT License
-
-Copyright (c) 2026 Raredon 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.
+YEAR: 2026
+COPYRIGHT HOLDER: Raredon Laboratory

LICENSE.md

@@ -0,0 +1,21 @@
+# MIT License
+
+Copyright (c) 2026 Raredon Laboratory
+
+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

@@ -0,0 +1,23 @@
+# Generated by roxygen2: do not edit by hand
+
+export(fit_spatial_mask)
+importFrom(parallel,mclapply)
+importFrom(sf,"st_crs<-")
+importFrom(sf,NA_crs_)
+importFrom(sf,st_area)
+importFrom(sf,st_as_sf)
+importFrom(sf,st_bbox)
+importFrom(sf,st_buffer)
+importFrom(sf,st_convex_hull)
+importFrom(sf,st_covered_by)
+importFrom(sf,st_difference)
+importFrom(sf,st_distance)
+importFrom(sf,st_geometry)
+importFrom(sf,st_make_valid)
+importFrom(sf,st_polygon)
+importFrom(sf,st_sf)
+importFrom(sf,st_sfc)
+importFrom(sf,st_simplify)
+importFrom(sf,st_union)
+importFrom(sf,st_within)
+importFrom(stats,filter)

R/TissueMask-package.R

@@ -0,0 +1,32 @@
+#' TissueMask: Spatial Boundary Mask Fitting for Point Coordinate Data
+#'
+#' @description
+#' TissueMask provides [`fit_spatial_mask()`], which fits polygon spatial masks
+#' to XY point coordinate data such as cell centroids or transcript locations
+#' from spatial transcriptomics and spatial proteomics experiments.
+#'
+#' Four masking methods are available, supporting geometries of increasing
+#' topological complexity — from simple convex hulls to multi-polygon masks
+#' with internal voids and disconnected islands:
+#'
+#' | Method | Holes/Islands | Speed | Recommended for |
+#' |---|---|---|---|
+#' | `"convex"` | No | Instant | Sanity checks |
+#' | `"concave"` | No | Fast | Simple non-convex shapes |
+#' | `"kde"` | Yes | Moderate | Dense, smooth datasets |
+#' | `"raster"` | Yes | Fast | Most use cases (default) |
+#'
+#' @section Part of TissueSuite:
+#' TissueMask is the first component of the **TissueSuite** package family
+#' developed at the Raredon Laboratory, Yale School of Medicine. The companion
+#' package **TissueField** uses TissueMask output to estimate steady-state
+#' molecular concentration fields via a diffusion–clearance PDE.
+#'
+#' @seealso [`fit_spatial_mask()`]
+#'
+#' @keywords internal
+"_PACKAGE"
+
+# Suppress R CMD check NOTE: "no visible binding for global variable 'x'/'y'"
+# These are ggplot2 aesthetic mappings in fit_spatial_mask(plot = TRUE).
+utils::globalVariables(c("x", "y"))