R package fz wrapper — full implementation up to v1.1

.Rbuildignore

@@ -7,3 +7,6 @@
 ^LICENSE\.md$
 ^codecov\.yml$
 ^\.vscode$
+^\.claude$
+^cran-comments\.md$
+^tests/testthat/\.fz$

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

@@ -18,11 +18,8 @@ jobs:
       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-latest,   r: 'oldrel-1'}
+          - {os: ubuntu-latest, r: 'release'}
+          - {os: macos-latest,  r: 'release'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
@@ -44,16 +41,6 @@ jobs:
           extra-packages: any::rcmdcheck
           needs: check
 
-      - name: Set up Python
-        uses: actions/setup-python@v5
-        with:
-          python-version: '3.x'
-
-      - name: Install fz Python package
-        run: |
-          python -m pip install --upgrade pip
-          pip install fz || echo "fz package installation failed, continuing anyway"
-
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true

.github/workflows/test-with-python.yaml

@@ -0,0 +1,39 @@
+on:
+  push:
+    branches: [main, master, develop, 'claude/**']
+  pull_request:
+    branches: [main, master, develop]
+
+name: test-with-python
+
+jobs:
+  test-with-python:
+    runs-on: ubuntu-latest
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      NOT_CRAN: "true"
+      FZ_MAX_RETRIES: "1"
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - 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::testthat
+          needs: check
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.x'
+
+      - name: Install fz Python package
+        run: pip install funz-fz
+
+      - name: Run tests
+        run: Rscript -e "testthat::test_local()"

DESCRIPTION

@@ -1,16 +1,22 @@
 Package: fz
 Type: Package
-Title: R Wrapper for Fz Core Functions
-Version: 0.1.0
+Title: R Wrapper for the 'funz-fz' Parametric Simulation Framework
+Version: 1.1
 Authors@R: c(
-    person("Author", "Name", email = "author@example.com", role = c("aut", "cre"))
+    person("Yann", "Richet", email = "yann.richet@asnr.fr",
+           role = c("aut", "cre"), comment = c(ORCID = "0000-0002-5677-8458"))
     )
-Description: Provides R bindings to fz core functions using reticulate.
-    This package allows R users to access fz functionality directly from R.
-License: MIT + file LICENSE
+Description: Provides R bindings to the 'funz-fz' Python package using
+    'reticulate'. The 'fz' framework wraps arbitrary simulation codes to run
+    parameter sweeps, design-of-experiments studies, and iterative
+    algorithm-driven analyses by substituting variable placeholders in text
+    input files and collecting outputs into data frames. Calculators can run
+    locally (shell), over SSH, or on 'SLURM' clusters.
+License: BSD_3_clause + file LICENSE
 Encoding: UTF-8
-LazyData: true
-RoxygenNote: 7.2.3
+Language: en-US
+RoxygenNote: 7.3.3
+SystemRequirements: Python (>= 3.8), funz-fz Python package
 Imports:
     reticulate (>= 1.28)
 Suggests:
@@ -20,7 +26,7 @@ Suggests:
 Config/reticulate:
     list(
         packages = list(
-            list(package = "fz")
+            list(package = "funz-fz")
         )
     )
 VignetteBuilder: knitr

LICENSE

@@ -1,21 +1,3 @@
-MIT License
-
-Copyright (c) 2025 Funz
-
-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: 2025
+ORGANIZATION: Funz
+COPYRIGHT HOLDER: Funz

LICENSE.md

@@ -0,0 +1,28 @@
+# BSD 3-Clause License
+
+Copyright (c) 2025, Funz
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice,
+   this list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its contributors
+   may be used to endorse or promote products derived from this software
+   without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

NAMESPACE

@@ -2,6 +2,28 @@
 
 export(fz_available)
 export(fz_install)
+export(fzc)
+export(fzd)
+export(fzi)
+export(fzl)
+export(fzo)
+export(fzr)
+export(get_config)
+export(get_interpreter)
+export(get_log_level)
+export(install)
+export(install_algorithm)
+export(install_model)
+export(list_installed_algorithms)
+export(list_installed_models)
+export(list_models)
+export(print_config)
+export(reload_config)
+export(set_interpreter)
+export(set_log_level)
+export(uninstall)
+export(uninstall_algorithm)
+export(uninstall_model)
 importFrom(reticulate,import)
 importFrom(reticulate,py_install)
 importFrom(reticulate,py_module_available)

NEWS.md

@@ -1,10 +1,31 @@
-# fz 0.1.0
+# fz 1.1
 
-## Initial Release
+First release, aligned with funz-fz 1.1 on PyPI.
 
-* Initial release of fz R package
-* Provides R wrapper for fz Python package using reticulate
-* Functions for installing and checking fz availability
-* Comprehensive test suite with testthat
-* CI/CD setup with GitHub Actions for R CMD check and CRAN checks
-* Documentation and vignettes
+## Core functions
+
+* `fzi(input_path, model)` — parse variable names and defaults from a template file
+* `fzc(input_path, input_variables, model, output_dir)` — compile template by substituting variable values
+* `fzo(output_path, model)` — read and parse output files
+* `fzr(input_path, input_variables, model, ...)` — run full parametric study
+* `fzl(models, calculators, check)` — list installed models and calculators
+* `fzd(input_path, input_variables, model, output_expression, algorithm, ...)` — iterative algorithm-driven design of experiments
+
+## Model and algorithm management
+
+* `install_model(source, global)` / `install_algorithm(source, global)` — install from GitHub, URL, or local zip
+* `uninstall_model(model_name, global)` / `uninstall_algorithm(algorithm_name, global)` — remove installed items
+* `list_installed_models(global)` / `list_installed_algorithms(global)` — list what is installed
+* `list_models()` — alias for `list_installed_models()`
+* `install()` / `uninstall()` — generic aliases for model install/uninstall
+
+## Configuration
+
+* `get_interpreter()` / `set_interpreter(interpreter)` — get or set the formula interpreter (`"python"` or `"R"`)
+* `get_log_level()` / `set_log_level(level)` — control logging verbosity
+* `get_config()` / `print_config()` / `reload_config()` — inspect and reload `FZ_*` environment variable settings
+
+## Package helpers
+
+* `fz_install()` — install the `funz-fz` Python package via reticulate
+* `fz_available()` — check whether the Python package is importable

R/config.R

@@ -0,0 +1,139 @@
+#' Get the Current Interpreter
+#'
+#' Returns the global formula interpreter used when evaluating formula
+#' expressions inside template files (e.g. \code{"python"} or \code{"R"}).
+#'
+#' @return Character string naming the current interpreter.
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#' if (fz_available()) {
+#'   get_interpreter()  # e.g. "python"
+#' }
+#' }
+get_interpreter <- function() {
+  get_fz()$get_interpreter()
+}
+
+#' Set the Interpreter
+#'
+#' Sets the global formula interpreter for evaluating expressions inside
+#' template files.
+#'
+#' @param interpreter Character string: \code{"python"} or \code{"R"}.
+#'
+#' @return NULL (invisibly). Called for side effects.
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#' if (fz_available()) {
+#'   set_interpreter("R")      # evaluate formulas with R
+#'   set_interpreter("python") # evaluate formulas with Python (default)
+#' }
+#' }
+set_interpreter <- function(interpreter) {
+  get_fz()$set_interpreter(interpreter)
+}
+
+#' Get the Current Log Level
+#'
+#' Returns the current logging verbosity level.
+#'
+#' @return A log-level value (use \code{as.character()} to convert to a string
+#'   such as \code{"DEBUG"}, \code{"INFO"}, \code{"WARNING"}, \code{"ERROR"}).
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#' if (fz_available()) {
+#'   as.character(get_log_level())  # e.g. "WARNING"
+#' }
+#' }
+get_log_level <- function() {
+  get_fz()$get_log_level()
+}
+
+#' Set the Log Level
+#'
+#' Controls how much output fz emits during execution.
+#'
+#' @param level Character string or log-level object: one of \code{"DEBUG"},
+#'   \code{"INFO"}, \code{"WARNING"}, \code{"ERROR"}.
+#'
+#' @return NULL (invisibly). Called for side effects.
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#' if (fz_available()) {
+#'   set_log_level("DEBUG")    # maximum verbosity
+#'   set_log_level("WARNING")  # default
+#'   set_log_level("ERROR")    # errors only
+#' }
+#' }
+set_log_level <- function(level) {
+  get_fz()$set_log_level(level)
+}
+
+#' Get the Global Configuration
+#'
+#' Returns the fz configuration object. Values are controlled by environment
+#' variables such as \code{FZ_LOG_LEVEL}, \code{FZ_MAX_WORKERS},
+#' \code{FZ_MAX_RETRIES}, and \code{FZ_SHELL_PATH}.
+#'
+#' @return A Python \code{Config} object. Access fields with \code{$}, e.g.
+#'   \code{get_config()$max_workers}.
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#' if (fz_available()) {
+#'   cfg <- get_config()
+#'   cfg$max_workers
+#'   cfg$max_retries
+#' }
+#' }
+get_config <- function() {
+  get_fz()$get_config()
+}
+
+#' Print the Current Configuration
+#'
+#' Prints all fz configuration values in a human-readable format, including
+#' which settings come from environment variables.
+#'
+#' @return NULL (invisibly). Called for side effects.
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#' if (fz_available()) {
+#'   print_config()
+#' }
+#' }
+print_config <- function() {
+  get_fz()$print_config()
+}
+
+#' Reload Configuration from Environment Variables
+#'
+#' Re-reads all \code{FZ_*} environment variables and updates the live
+#' configuration. Useful after changing environment variables within the
+#' session.
+#'
+#' @return NULL (invisibly). Called for side effects.
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#' if (fz_available()) {
+#'   Sys.setenv(FZ_MAX_WORKERS = "8")
+#'   reload_config()
+#'   get_config()$max_workers  # now 8
+#' }
+#' }
+reload_config <- function() {
+  get_fz()$reload_config()
+}