preliminary merge alloc-params into main

Author: mmyrte

.Rbuildignore

@@ -9,3 +9,4 @@ air.toml
 ^_pkgdown\.yml$
 ^docs$
 ^pkgdown$
+^.devcontainer$

.devcontainer/Dockerfile

@@ -0,0 +1,19 @@
+FROM --platform=linux/amd64 ghcr.io/mmyrte/evoland:latest
+LABEL authors="Carlson Büth, Jan Hartman" \
+  version="8.3" \
+  description="Docker image for Dinamica EGO."
+
+# Vignettes are being built with quarto
+RUN /rocker_scripts/install_quarto.sh
+
+# Hand-knitted dependency discovery from DESCRIPTION avoids cache invalidation versus a
+# remotes::install_deps based solution.
+WORKDIR /builddir
+COPY DESCRIPTION /builddir/DESCRIPTION
+COPY .devcontainer/install_pkg_deps.r /builddir/install_pkg_deps.r
+RUN /builddir/install_pkg_deps.r && rm -r /builddir
+WORKDIR /
+
+# Install development dependencies for vscode-style development.
+COPY .devcontainer/install_vscode_devtools.sh /rocker_scripts/install_vscode_devtools.sh
+RUN /rocker_scripts/install_vscode_devtools.sh

.devcontainer/devcontainer.json

@@ -0,0 +1,40 @@
+// For format details, see https://aka.ms/devcontainer.json. For config options, see the README at:
+// https://github.com/microsoft/vscode-dev-containers/tree/v0.191.1/containers/debian
+{
+  "name": "evoland-devcontainer",
+  "build": {
+    "dockerfile": "Dockerfile",
+    "context": "..",
+    "args": {
+      "platform": "linux/amd64"
+    }
+  },
+  "mounts": [
+    {
+      "source": "${localEnv:EVOLAND_CACHEDIR}",
+      "target": "/mnt/evoland-cache",
+      "type": "bind"
+    }
+  ],
+  "containerEnv": {
+    "EVOLAND_CACHEDIR": "/mnt/evoland-cache"
+  },
+  "customizations": {
+    "vscode": {
+      "settings": {
+        "git.path": "/usr/bin/git",
+        "r.rterm.linux": "/usr/local/bin/radian",
+        "shellcheck.executablePath": "/usr/bin/shellcheck",
+        "r.plot.useHttpgd": true,
+        "r.bracketedPaste": true,
+        "rewrap.wrappingColumn": 88
+      },
+      "extensions": [
+        "RDebugger.r-debugger",
+        "REditorSupport.r",
+        "quarto.quarto",
+        "timonwong.shellcheck"
+      ]
+    }
+  }
+}

.devcontainer/install_pkg_deps.r

@@ -0,0 +1,19 @@
+#!/usr/bin/env Rscript
+
+# Reusing logic from remotes::local_package_deps
+# MIT licensed, source at https://github.com/r-lib/remotes/
+
+desc <- remotes:::read_dcf("DESCRIPTION")
+
+dependencies <- c("Depends", "Imports", "LinkingTo", "Suggests")
+dependencies <- intersect(dependencies, names(desc))
+pkg_deps <-
+  lapply(desc[dependencies], remotes:::parse_deps) |>
+  lapply(`[[`, "name") |>
+  unlist(use.names = FALSE)
+
+pkgs_to_install <- setdiff(pkg_deps, installed.packages()[, 1])
+install.packages(
+  pkgs_to_install,
+  Ncpus = max(1L, parallel::detectCores())
+)

.devcontainer/install_vscode_devtools.sh

@@ -0,0 +1,36 @@
+#!/usr/bin/env bash
+
+# Abort script if any command exits with non-zero status. Not foolproof.
+set -e 
+
+NCPUS=${NCPUS:-"-1"}
+
+apt-get update -qq
+apt-get -y --no-install-recommends install \
+  git \
+  htop \
+  libfontconfig1-dev \
+  libfribidi-dev \
+  libgit2-dev \
+  libharfbuzz-dev \
+  pipx \
+  shellcheck
+
+rm -rf /var/lib/apt/lists/*
+
+PIPX_BIN_DIR=/usr/local/bin pipx install radian
+
+install2.r --error --skipinstalled -n $NCPUS \
+    covr \
+    devtools \
+    languageserver \
+    lobstr \
+    microbenchmark \
+    profvis \
+    quarto \
+    rlang
+
+# httpgd is currently off of CRAN because of c++ compiler conflicts
+# https://github.com/nx10/httpgd/issues/218
+
+R -e "remotes::install_github('nx10/httpgd')"

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

@@ -0,0 +1,56 @@
+# 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]
+  workflow_dispatch:
+
+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-24.04-arm, 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 macOS system dependencies
+        if: runner.os == 'macos'
+        run: brew install gdal proj
+
+      - 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

@@ -3,7 +3,6 @@
 on:
   push:
     branches: [main, master]
-  pull_request:
   release:
     types: [published]
   workflow_dispatch:

.gitignore

@@ -56,3 +56,11 @@ docs
 
 # generally ignore databases, like .evolanddb, .duckdb, anything.db
 *db
+
+# IDE specific artefacts
+*compile_commands*
+*cobertura*
+.cache/
+
+# ignore drafts
+*suddel*

DESCRIPTION

@@ -10,28 +10,28 @@ URL: https://ethzplus.github.io/evoland-plus, https://github.com/ethzplus/evolan
 BugReports: https://github.com/ethzplus/evoland-plus/issues
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
 Depends:
     R (>= 4.2)
 Imports:
     curl,
     data.table,
     DBI,
-    duckdb,
+    duckdb (>= 1.4.3),
     glue,
-    purrr,
     qs2,
     R6,
     Rcpp,
-    rlang,
     stringi,
     terra
 Suggests:
+    base64enc,
     butcher,
     pROC,
-    tinytest,
+    processx,
     quarto,
-    ranger
+    ranger,
+    tinytest
 VignetteBuilder: quarto
 Config/testthat/edition: 3
 LinkingTo:
@@ -56,11 +56,13 @@ Collate:
     'periods_t.R'
     'pred_data_t.R'
     'pred_meta_t.R'
+    'reporting_t.R'
     'trans_meta_t.R'
     'trans_models_glm.R'
     'trans_models_rf.R'
     'trans_models_t.R'
     'trans_preds_t.R'
     'util.R'
+    'util_dinamica.r'
     'util_download.R'
     'util_terra.R'

NAMESPACE

@@ -30,6 +30,7 @@ S3method(validate,pred_data_t_bool)
 S3method(validate,pred_data_t_float)
 S3method(validate,pred_data_t_int)
 S3method(validate,pred_meta_t)
+S3method(validate,reporting_t)
 S3method(validate,trans_meta_t)
 S3method(validate,trans_models_t)
 S3method(validate,trans_preds_t)
@@ -43,6 +44,7 @@ export(as_neighbors_t)
 export(as_periods_t)
 export(as_pred_data_t)
 export(as_pred_meta_t)
+export(as_reporting_t)
 export(as_trans_meta_t)
 export(as_trans_models_t)
 export(as_trans_preds_t)
@@ -57,6 +59,7 @@ export(create_pred_meta_t)
 export(create_trans_meta_t)
 export(download_and_verify)
 export(evoland_db)
+export(exec_dinamica)
 export(extract_using_coords_t)
 export(fit_glm)
 export(fit_ranger)
@@ -65,6 +68,7 @@ export(gof_ranger)
 export(grrf_filter)
 export(parquet_duckdb)
 export(print_rowwise_yaml)
+export(run_evoland_dinamica_sim)
 export(validate)
 importFrom(Rcpp,sourceCpp)
 importFrom(data.table,":=")