Dev/covar memberships

.Rbuildignore

@@ -5,4 +5,10 @@ HOWTO_WRITE_A_MODEL
 mkpkg$
 orig$
 LICENSE
+.vscode
+dev
 ^\.github$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
+^README\.Rmd$

.github/workflows/pkgdown.yaml

@@ -0,0 +1,49 @@
+# 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.yaml
+
+permissions: read-all
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v6
+
+      - 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/render-rmarkdown.yaml

@@ -0,0 +1,40 @@
+# 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:
+    paths: ["**.Rmd"]
+
+name: render-rmarkdown.yaml
+
+permissions: read-all
+
+jobs:
+  render-rmarkdown:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+
+      - uses: r-lib/actions/setup-r-dependencies@v1
+        with:
+          cache-version: 4
+          extra-packages: rmarkdown
+
+      - name: Render Rmarkdown files and Commit Results
+        run: |
+          RMD_PATH=($(git diff --name-only ${{ github.event.before }} ${{ github.sha }} | grep '[.]Rmd$'))
+          Rscript -e 'for (f in commandArgs(TRUE)) if (file.exists(f)) rmarkdown::render(f)' ${RMD_PATH[*]}
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
+          git commit ${RMD_PATH[*]/.Rmd/.md} -m 'Re-build Rmarkdown files' || echo "No changes to commit"
+          git push origin || echo "No changes to commit"

.github/workflows/test-coverage.yaml

@@ -0,0 +1,70 @@
+# 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: test-coverage.yaml
+
+permissions: read-all
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v6
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr, any::xml2
+          needs: coverage
+
+      - name: Test coverage
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+        run: |
+          cov <- covr::package_coverage(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )     
+          print(cov)
+          covr::to_cobertura(cov, filename = "cobertura.xml")
+          #covr::codecov(coverage=cov)
+        shell: Rscript {0}
+
+      - name: Debug files
+        run: |
+          pwd
+          ls -lah
+          find . -name "*.xml"
+
+      - uses: codecov/codecov-action@v5
+        with:
+          # Fail if error if not on PR, or if on PR and token is given
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }}
+          files: ./cobertura.xml
+          plugins: noop
+          token: ${{ secrets.CODECOV_TOKEN }}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

.gitignore

@@ -3,3 +3,5 @@
 .*.swp
 .*.swo
 .Rproj.user
+docs
+.vscode

DESCRIPTION

@@ -2,10 +2,8 @@ Package: blockmodels
 Type: Package
 Title: Latent and Stochastic Block Model Estimation by a 'V-EM'
         Algorithm
-Version: 1.1.5
-Date: 2021-12-01
-Author: Jean-Benoist Leger <jbleger@hds.utc.fr>, Pierre Barbillon <pierre.barbillon@agroparistech.fr>, Julien Chiquet <julien.chiquet@inrae.fr>
-Maintainer: Jean-Benoist Leger <jbleger@hds.utc.fr>
+Version: 1.2.1
+Date: 2026-03-05
 Description: Latent and Stochastic Block Model estimation by a Variational EM algorithm.
              Various probability distribution are provided (Bernoulli,
              Poisson...), with or without covariates.
@@ -18,6 +16,15 @@ Imports:
     parallel, 
     methods, 
     digest
+Suggests:
+    testthat (>= 3.0.0)
+Config/testthat/edition: 3
 Encoding: UTF-8
 URL: https://github.com/jb-leger/blockmodels
 BugReports: https://github.com/jb-leger/blockmodels/issues
+Authors@R: c(
+    person("Jean-Benoist", "Leger", , "jbleger@hds.utc.fr", role = c("aut", "cre")),
+    person("Pierre", "Barbillon", , "pierre.barbillon@agroparistech.fr", role = "aut"),
+    person("Julien", "Chiquet", , "julien.chiquet@inrae.fr", role = "aut"),
+    person("Louis", "Lacoste", , "louis.lacoste@inrae.fr", role = "aut")
+  )

NEWS.md

@@ -0,0 +1,4 @@
+# blockmodels 1.2.1
+
+* Beginning adding handling of `NA` values in the data. Only scalar (with or without covariates) bernoulli, poisson and gaussian emission distribution models are supported for now. The `NA` values are ignored in the likelihood calculations, and the corresponding entries in the data are not used to update the parameters of the model.
+* Added a `NEWS.md` file to track changes to the package.