cleanup file tree function

rtenets

@@ -100,7 +100,7 @@ gitea() {
 
     local method="$1"
     local request="$2"
-    curl -X "${request}" -H "Content-Type: application/json" -H "Authorization: token ${TOKEN}" "${ENDPOINT}/${method}"
+    \curl -X "${request}" -H "Content-Type: application/json" -H "Authorization: token ${TOKEN}" "${ENDPOINT}/${method}"
 }
 
 # ----------------- Git commands -----------------------
@@ -145,8 +145,44 @@ init_repo() {
     \git init
 }
 
-# Create required files
-create_tenet_file_tree() {
+# Make bash script stub
+script_stub() {
+    local script_name="$1"
+    local start_phrase="$2"
+
+    if ! [ -f "${script_name}" ]; then
+        mkdir -p "$(dirname "${script_name}")"
+        cat << STUB > "${script_name}"
+#!/usr/bin/env bash
+set -euo pipefail
+
+main() {
+    printf "${start_phrase}\\n" 1>&2
+    # put code here
+}
+
+main "\$@"
+STUB
+        chmod +x "${script_name}"
+    fi
+}
+
+# Fetch licence
+fetch_licence() {
+    local licence="COPYING"
+
+    if ! [ -f "${licence}" ]; then
+        if has_command curl; then
+            info "setting licence to GPL by default, see https://www.gnu.org/licenses for more options"
+            \curl "https://www.gnu.org/licenses/gpl-3.0.txt" > "${licence}"
+        else
+            warning "please choose a free software licence, see https://www.gnu.org/licenses"
+        fi
+    fi
+}
+
+# Create README
+create_readme() {
     local readme="README.md~"
 
     if ! [ -f "${readme}" ]; then
@@ -169,7 +205,7 @@ Here are the dependencies to build and run the code:
 Here is how to run the code:
 
 \`\`\`
-<make_all_figures>
+./make_all_figures
 \`\`\`
 
 ## Tests
@@ -177,27 +213,27 @@ Here is how to run the code:
 Here is how to run the tests:
 
 \`\`\`
-<run_all_tests>
+./tests/run_all_tests
 \`\`\`
 READMEMSG
 
         info "wrote '${readme}'"
     fi
+}
 
+create_authors_file() {
     if ! [ -f AUTHORS ]; then
         printf "%s\\n" "${USER} <${EMAIL}> ${AFFILIATION}" > AUTHORS
     fi
+}
 
-    local licence="COPYING"
-
-    if ! [ -f "${licence}" ]; then
-        if has_command curl; then
-            info "setting licence to GPL by default, see https://www.gnu.org/licenses for more options"
-            curl "https://www.gnu.org/licenses/gpl-3.0.txt" > "${licence}"
-        else
-            warning "please choose a free software licence, see https://www.gnu.org/licenses"
-        fi
-    fi
+# Create required files
+create_tenet_file_tree() {
+    create_readme
+    create_authors_file
+    fetch_licence
+    script_stub tests/run_all_tests "Running all tests..."
+    script_stub make_all_figures "Generating figures..."
 }
 
 # Create git repository