AlertTools 1.2.0 release candidate

.Rbuildignore

@@ -1,2 +1,14 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
+^AlertTools$
+^AlertTools\.Rcheck$
+^AlertTools_[0-9.]+\.tar\.gz$
+^INSTRUCOES_AGENTE_REFATORACAO\.md$
+^plano_refatoracao_alerttools\.(qmd|html)$
+^docs/refactoring$
+^\.github$
+^_pkgdown\.yml$
+^\.lintr$
+^tools$
+^pkgdown-site$
+^data/(bairro2APS|locs|sinan)\.rda$

.github/PULL_REQUEST_TEMPLATE/consumer-migration.md

@@ -0,0 +1,23 @@
+## Consumidor migrado
+
+- ID no registro:
+- Repositório e arquivo:
+- Responsável:
+- API legada:
+- API nova:
+
+## Evidências
+
+- [ ] testes unitários do consumidor passaram;
+- [ ] execução com dados descartáveis passou;
+- [ ] schemas e cardinalidades foram comparados;
+- [ ] resultados epidemiológicos foram comparados e aprovados;
+- [ ] execução com `lifecycle_verbosity = "warning"` não registrou depreciações;
+- [ ] `consumer-registry.csv` foi atualizado com evidência e data.
+
+## Rollback
+
+- versão anterior do consumidor:
+- versão do AlertTools a fixar:
+- artefatos que precisam ser restaurados:
+- critério para acionar rollback:

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

@@ -0,0 +1,156 @@
+name: R-CMD-check
+
+on:
+  push:
+    branches: [master, main]
+  pull_request:
+
+permissions:
+  contents: read
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.os }} (R ${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest, r: release}
+          - {os: windows-latest, r: release}
+          - {os: ubuntu-latest, r: release}
+          - {os: ubuntu-latest, r: devel}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          use-public-rspm: true
+          extra-repositories: https://inla.r-inla-download.org/R/stable
+
+      - 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
+
+  postgres-integration:
+    runs-on: ubuntu-latest
+    name: PostgreSQL integration (R release)
+
+    services:
+      postgres:
+        image: postgres:16
+        env:
+          POSTGRES_USER: postgres
+          POSTGRES_PASSWORD: postgres
+          POSTGRES_DB: alerttools_test
+        ports:
+          - 5432:5432
+        options: >-
+          --health-cmd "pg_isready -U postgres -d alerttools_test"
+          --health-interval 10s
+          --health-timeout 5s
+          --health-retries 5
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+      ALERTTOOLS_TEST_POSTGRES: "true"
+      PGDATABASE: alerttools_test
+      PGHOST: 127.0.0.1
+      PGPORT: 5432
+      PGUSER: postgres
+      PGPASSWORD: postgres
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: release
+          use-public-rspm: true
+          extra-repositories: https://inla.r-inla-download.org/R/stable
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::devtools
+          needs: check
+
+      - name: Run the complete suite against ephemeral PostgreSQL
+        run: Rscript -e 'devtools::test(stop_on_failure = TRUE)'
+
+  coverage:
+    runs-on: ubuntu-latest
+    name: Coverage indicator (R release)
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: release
+          use-public-rspm: true
+          extra-repositories: https://inla.r-inla-download.org/R/stable
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr
+          needs: check
+
+      - name: Measure package coverage
+        run: Rscript -e 'coverage <- covr::package_coverage(); print(coverage); saveRDS(coverage, "coverage.rds")'
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: coverage-rds
+          path: coverage.rds
+
+  lint:
+    runs-on: ubuntu-latest
+    name: Static lint checks
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: release
+          use-public-rspm: true
+          extra-repositories: https://inla.r-inla-download.org/R/stable
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::lintr
+          needs: check
+
+      - name: Lint package sources
+        run: Rscript -e 'lintr::lint_package()'
+
+  migration-inventory:
+    runs-on: ubuntu-latest
+    name: Consumer migration inventory
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: release
+
+      - name: Validate migration registry and removal gate inputs
+        run: Rscript tools/check-migration-readiness.R

.github/workflows/pkgdown.yaml

@@ -0,0 +1,43 @@
+name: pkgdown
+
+on:
+  workflow_dispatch:
+    inputs:
+      confirmation:
+        description: Type publish after maintainer validation
+        required: true
+        type: string
+
+permissions:
+  contents: write
+
+jobs:
+  build-and-publish:
+    if: github.event.inputs.confirmation == 'publish'
+    runs-on: ubuntu-latest
+    environment: pkgdown-production
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: release
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown
+          needs: website
+
+      - name: Build the site
+        run: Rscript -e 'pkgdown::build_site_github_pages(new_process = FALSE, install = TRUE)'
+
+      - name: Publish the validated site
+        uses: JamesIves/github-pages-deploy-action@v4
+        with:
+          branch: gh-pages
+          folder: pkgdown-site
+          clean: true

.gitignore

@@ -31,5 +31,7 @@ vignettes/*.pdf
 # Temporary files created by R markdown
 *.utf8.md
 *.knit.md
+pkgdown-site/
+.DS_Store
 .Rproj.user
 .aider*

.lintr

@@ -0,0 +1,8 @@
+linters: list(
+    absolute_path_linter = absolute_path_linter(),
+    trailing_whitespace_linter = trailing_whitespace_linter(),
+    undesirable_function_linter = undesirable_function_linter(
+      fun = c("setwd" = "Do not change the caller's working directory.")
+    )
+  )
+encoding: "UTF-8"