Run Python-to-R file workflows from the project root

content/code/fmr.R

@@ -1,13 +1,16 @@
-# plots log(field metabolic rate) against log(body mass) for the Nagy et al 
-# 1999 dataset to a file fmr.pdf.
+# Plot log(field metabolic rate) against log(body mass) for the Nagy et al.
+# 1999 dataset. Run from the coursework project root with:
+# Rscript code/fmr.R
 
 cat("reading CSV\n")
 
-nagy <- read.csv('../data/nagy_et_al_1999.csv', stringsAsFactors = FALSE)
+nagy <- read.csv('data/nagy_et_al_1999.csv', stringsAsFactors = FALSE)
 
 cat("Creating graph\n")
-pdf('../results/fmr_plot.pdf', 11, 8.5)
+dir.create('results', showWarnings = FALSE)
+pdf('results/fmr_plot.pdf', 11, 8.5)
 col <- c(Aves='purple3', Mammalia='red3', Reptilia='green3')
+stopifnot(all(unique(nagy$Class) %in% names(col)))
 plot(log10(nagy$M.g), log10(nagy$FMR.kJ.day.1), pch=19, col=col[nagy$Class],
      xlab=~log[10](M), ylab=~log[10](FMR))
 for(class in unique(nagy$Class)){

content/code/test_r.py

@@ -1,5 +1,18 @@
+#!/usr/bin/env python3
+
+"""Run the small R example and save its output from the project root."""
+
 import subprocess
 
-subprocess.Popen("rscript --verbose test_r.r > \
-../results/test_r.rout 2> ../results/test_r_errFile.rout",\
- shell=True).wait()
+
+with open("results/test_r.rout", "w") as output_file, \
+     open("results/test_r_errFile.rout", "w") as error_file:
+    result = subprocess.run(
+        ["Rscript", "--verbose", "code/test_r.R"],
+        stdout=output_file,
+        stderr=error_file,
+        check=False,
+    )
+
+print("Return code:", result.returncode)
+raise SystemExit(result.returncode)

content/notebooks/python.ipynb

@@ -8964,16 +8964,16 @@
     "print(\"Hello, this is R!\")\n",
     "```\n",
     "\n",
-    "Then try running it from your bash terminal (*not* from the Python terminal) (e.g., using `Rscript test_r.R`). This should return in your terminal:\n",
+    "Then run it from your bash terminal (*not* from the Python terminal), starting at the coursework project root: `Rscript code/test_r.R`. This should return in your terminal:\n",
     "\n",
     "```bash\n",
     "[1] \"Hello, this is R!\"\n",
     "```\n",
     "\n",
-    "Then try `Rscript --verbose test_r.R`. This should return something like:\n",
+    "Then try `Rscript --verbose code/test_r.R`. This should return something like:\n",
     "\n",
     "```bash\n",
-    "  '/usr/lib/r/bin/r --no-echo --no-restore --file=test_r.R'\n",
+    "  '/usr/lib/r/bin/r --no-echo --no-restore --file=code/test_r.R'\n",
     "\n",
     "[1] \"Hello, this is R!\"\n",
     "```\n",
@@ -8987,10 +8987,10 @@
     "Now try:\n",
     "\n",
     "```bash\n",
-    "Rscript --verbose test_r.R > ../results/test_r.rout 2> ../results/test_r_errFile.rout\n",
+    "Rscript --verbose code/test_r.R > results/test_r.rout 2> results/test_r_errFile.rout\n",
     "```\n",
     "\n",
-    "Then check the contents of `test_r.rout` and `test_r_errFile.rout`. The former should contain the output of the R script, and the latter the additional information produced by the `--verbose` flag. \n",
+    "Then check `results/test_r.rout` and `results/test_r_errFile.rout`. The former should contain the output of the R script, and the latter the additional information produced by the `--verbose` flag. \n",
     "\n",
     "Now try running this using subprocess instead:"
    ]
@@ -9001,10 +9001,10 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "with open(\"../results/test_r.rout\", \"w\") as output_file, \\\n",
-    "     open(\"../results/test_r_errFile.rout\", \"w\") as error_file:\n",
+    "with open(\"results/test_r.rout\", \"w\") as output_file, \\\n",
+    "     open(\"results/test_r_errFile.rout\", \"w\") as error_file:\n",
     "    result = subprocess.run(\n",
-    "        [\"Rscript\", \"--verbose\", \"test_r.R\"],\n",
+    "        [\"Rscript\", \"--verbose\", \"code/test_r.R\"],\n",
     "        stdout=output_file,\n",
     "        stderr=error_file,\n",
     "        check=False,\n",
@@ -9034,24 +9034,25 @@
    "source": [
     "import subprocess\n",
     "\n",
-    "with open(\"../results/test_r.rout\", \"w\") as output_file, \\\n",
-    "     open(\"../results/test_r_errFile.rout\", \"w\") as error_file:\n",
+    "with open(\"results/test_r.rout\", \"w\") as output_file, \\\n",
+    "     open(\"results/test_r_errFile.rout\", \"w\") as error_file:\n",
     "    result = subprocess.run(\n",
-    "        [\"Rscript\", \"--verbose\", \"test_r.R\"],\n",
+    "        [\"Rscript\", \"--verbose\", \"code/test_r.R\"],\n",
     "        stdout=output_file,\n",
     "        stderr=error_file,\n",
     "        check=False,\n",
     "    )\n",
     "\n",
-    "print(\"Return code:\", result.returncode)"
+    "print(\"Return code:\", result.returncode)\n",
+    "raise SystemExit(result.returncode)"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
     "\n",
-    "Now run `test_r.py` (or `%run test_r.py` in IPython) and check `test_r.rout` and `test_r_errFile.rout`.\n",
+    "From the project root, run `python3 code/test_r.py` (or `%run code/test_r.py` in IPython) and check `results/test_r.rout` and `results/test_r_errFile.rout`.\n",
     "\n",
     "Also check what happens if you run (type directly in `ipython` or `python` console):"
    ]
@@ -9063,7 +9064,7 @@
    "outputs": [],
    "source": [
     "result = subprocess.run(\n",
-    "    [\"Rscript\", \"--verbose\", \"NonExistScript.R\"],\n",
+    "    [\"Rscript\", \"--verbose\", \"code/NonExistScript.R\"],\n",
     "    capture_output=True,\n",
     "    text=True,\n",
     ")\n",
@@ -9138,7 +9139,7 @@
     "\n",
     "#### Run an R analysis from Python\n",
     "\n",
-    "Download {download}`fmr.R <../code/fmr.R>` into `code/` and {download}`nagy_et_al_1999.csv <../data/nagy_et_al_1999.csv>` into `data/`. Read the R script, then write `run_fmr_r.py` that runs `Rscript fmr.R` from the coursework project's `code/` directory using `subprocess.run()` without `shell=True`.\n",
+    "Download {download}`fmr.R <../code/fmr.R>` into `code/` and {download}`nagy_et_al_1999.csv <../data/nagy_et_al_1999.csv>` into `data/`. Read the R script, then write `run_fmr_r.py` that runs `Rscript code/fmr.R` from the coursework project root using `subprocess.run()` without `shell=True`.\n",
     "\n",
     "Capture standard output and standard error as text, print both streams with labels, and print whether the command succeeded based on its return code. On success, verify that `results/fmr_plot.pdf` exists and is non-empty; on failure, exit with a non-zero status. Your wrapper is complete when a normal run reports success and deliberately using a nonexistent R script reports failure without a Python traceback.\n",
     "\n",

scripts/check_r_file_workflows.R

@@ -6,7 +6,11 @@ repository_root <- normalizePath(".")
 required_files <- c(
   "content/code/basic_io.R",
   "content/code/data_wrang.R",
+  "content/code/fmr.R",
+  "content/code/test_r.R",
+  "content/code/test_r.py",
   "content/data/trees.csv",
+  "content/data/nagy_et_al_1999.csv",
   "content/data/pound_hill_data.csv",
   "content/data/pound_hill_meta_data.csv"
 )
@@ -29,15 +33,24 @@ on.exit(unlink(project_root, recursive = TRUE), add = TRUE)
 
 stopifnot(
   all(file.copy(
-    file.path(repository_root, "content/code", c("basic_io.R", "data_wrang.R")),
+    file.path(
+      repository_root,
+      "content/code",
+      c("basic_io.R", "data_wrang.R", "fmr.R", "test_r.R", "test_r.py")
+    ),
     file.path(project_root, "code"),
     overwrite = TRUE
   )),
   all(file.copy(
     file.path(
       repository_root,
       "content/data",
-      c("trees.csv", "pound_hill_data.csv", "pound_hill_meta_data.csv")
+      c(
+        "trees.csv",
+        "nagy_et_al_1999.csv",
+        "pound_hill_data.csv",
+        "pound_hill_meta_data.csv"
+      )
     ),
     file.path(project_root, "data"),
     overwrite = TRUE
@@ -65,6 +78,31 @@ run_script("code/basic_io.R")
 basic_output <- file.path("results", "MyData.csv")
 stopifnot(file.exists(basic_output), file.info(basic_output)$size > 0)
 
+run_script("code/fmr.R")
+fmr_output <- file.path("results", "fmr_plot.pdf")
+stopifnot(file.exists(fmr_output), file.info(fmr_output)$size > 0)
+
+python_output <- system2(
+  Sys.which("python3"),
+  "code/test_r.py",
+  stdout = TRUE,
+  stderr = TRUE
+)
+python_status <- attr(python_output, "status")
+if (!is.null(python_status) && python_status != 0) {
+  stop(paste(python_output, collapse = "\n"), call. = FALSE)
+}
+stopifnot(
+  any(grepl("Return code: 0", python_output, fixed = TRUE)),
+  file.exists(file.path("results", "test_r.rout")),
+  file.exists(file.path("results", "test_r_errFile.rout")),
+  grepl(
+    "Hello, this is R!",
+    paste(readLines(file.path("results", "test_r.rout")), collapse = "\n"),
+    fixed = TRUE
+  )
+)
+
 run_script("code/data_wrang.R")
 wrangled_output <- read.csv(file.path("results", "pound_hill_long.csv"))
 stopifnot(

scripts/runtime_path_exceptions.yml

@@ -33,20 +33,6 @@ exceptions:
   reason: Known statistics workflow path awaiting dependency-aware chapter migration.
   owner: Statistics teaching owner
   target_phase: Phase 5
-- location: code/fmr.R
-  rule: parent_project_path
-  value: ../data/nagy_et_al_1999.csv
-  count: 1
-  reason: Known Python workflow path awaiting chapter and supplied-script migration.
-  owner: Python teaching owner
-  target_phase: Phase 4
-- location: code/fmr.R
-  rule: parent_project_path
-  value: ../results/fmr_plot.pdf
-  count: 1
-  reason: Known Python workflow path awaiting chapter and supplied-script migration.
-  owner: Python teaching owner
-  target_phase: Phase 4
 - location: code/glm.R
   rule: parent_project_path
   value: ../data/prac_data.csv
@@ -103,20 +89,6 @@ exceptions:
   reason: Known statistics workflow path awaiting dependency-aware chapter migration.
   owner: Statistics teaching owner
   target_phase: Phase 5
-- location: code/test_r.py
-  rule: parent_project_path
-  value: ../results/test_r.rout
-  count: 1
-  reason: Known Python workflow path awaiting chapter and supplied-script migration.
-  owner: Python teaching owner
-  target_phase: Phase 4
-- location: code/test_r.py
-  rule: parent_project_path
-  value: ../results/test_r_errFile.rout
-  count: 1
-  reason: Known Python workflow path awaiting chapter and supplied-script migration.
-  owner: Python teaching owner
-  target_phase: Phase 4
 - location: notebooks/anova.ipynb:cell 45
   rule: parent_project_path
   value: ../data/mammals.rdata
@@ -222,48 +194,6 @@ exceptions:
   reason: Known statistics workflow path awaiting dependency-aware chapter migration.
   owner: Statistics teaching owner
   target_phase: Phase 5
-- location: notebooks/python.ipynb:cell 587:fence 4
-  rule: parent_project_path
-  value: ../results/test_r.rout
-  count: 1
-  reason: Known Python workflow path awaiting chapter and supplied-script migration.
-  owner: Python teaching owner
-  target_phase: Phase 4
-- location: notebooks/python.ipynb:cell 587:fence 4
-  rule: parent_project_path
-  value: ../results/test_r_errFile.rout
-  count: 1
-  reason: Known Python workflow path awaiting chapter and supplied-script migration.
-  owner: Python teaching owner
-  target_phase: Phase 4
-- location: notebooks/python.ipynb:cell 588
-  rule: parent_project_path
-  value: ../results/test_r.rout
-  count: 1
-  reason: Known Python workflow path awaiting chapter and supplied-script migration.
-  owner: Python teaching owner
-  target_phase: Phase 4
-- location: notebooks/python.ipynb:cell 588
-  rule: parent_project_path
-  value: ../results/test_r_errFile.rout
-  count: 1
-  reason: Known Python workflow path awaiting chapter and supplied-script migration.
-  owner: Python teaching owner
-  target_phase: Phase 4
-- location: notebooks/python.ipynb:cell 591
-  rule: parent_project_path
-  value: ../results/test_r.rout
-  count: 1
-  reason: Known Python workflow path awaiting chapter and supplied-script migration.
-  owner: Python teaching owner
-  target_phase: Phase 4
-- location: notebooks/python.ipynb:cell 591
-  rule: parent_project_path
-  value: ../results/test_r_errFile.rout
-  count: 1
-  reason: Known Python workflow path awaiting chapter and supplied-script migration.
-  owner: Python teaching owner
-  target_phase: Phase 4
 - location: notebooks/regress.ipynb:cell 6
   rule: parent_project_path
   value: ../data/genome_size.csv