Make generate_references.py configurable. (BlueBrain#1286)

Adds the ability to customize with which flags `nmodl` is run to
generate the references.

The default is `""` (for CoreNEURON) and `"--neuron"` (for NEURON).
These choices can be overridden by adding a file `references.json`
to the usecase directory.

Since the logic is slightly more involved, the Bash script is
reimplemented as a Python script.

.github/workflows/nmodl-ci.yml

@@ -206,12 +206,7 @@ jobs:
 
           for d in */
           do
-              if [[ "$d" == "references/" ]]
-              then
-                continue
-              fi
-
-              ./generate_references.sh nmodl "$d" "$OUTPUT_DIR/$d"
+              ./generate_references.py nmodl "$d" "$OUTPUT_DIR/$d"
           done
 
           cd $OUTPUT_DIR

test/usecases/generate_references.py

@@ -0,0 +1,68 @@
+#!/usr/bin/env python3
+import sys
+import glob
+import os
+import json
+import subprocess
+
+
+def substitute_line(lines, starts_with, replacement):
+    for k, line in enumerate(lines):
+        if line.startswith(starts_with):
+            lines[k] = replacement
+            break
+
+
+def generate_references(nmodl, usecase_dir, output_dir, nmodl_flags):
+    mod_files = glob.glob(os.path.join(usecase_dir, "*.mod"))
+    for mod_file in mod_files:
+        try:
+            subprocess.run(
+                ["nmodl", mod_file, *nmodl_flags, "-o", output_dir], check=True
+            )
+        except subprocess.CalledProcessError as e:
+            print(e.output)
+            raise e
+
+    cxx_files = glob.glob(os.path.join(output_dir, "*.cpp"))
+
+    for cxx_file in cxx_files:
+        with open(cxx_file, "r") as f:
+            cxx = f.readlines()
+
+        sub_date = "Created         : ", "Created         : DATE\n"
+        substitute_line(cxx, *sub_date)
+
+        sub_version = "NMODL Compiler  : ", "NMODL Compiler  : VERSION\n"
+        substitute_line(cxx, *sub_version)
+
+        with open(cxx_file, "w") as f:
+            f.writelines(cxx)
+
+
+def load_config(script_dir, usecase_dir):
+    config = os.path.join(usecase_dir, "references.json")
+    if os.path.exists(config):
+        with open(config, "r") as f:
+            return json.load(f)
+    else:
+        return [
+            {"output_reldir": "coreneuron", "nmodl_flags": []},
+            {"output_reldir": "neuron", "nmodl_flags": ["--neuron"]},
+        ]
+
+
+if __name__ == "__main__":
+    if len(sys.argv) != 4:
+        print(f"Usage: {sys.argv[0]} NMODL USECASE_DIR OUTPUT_DIR")
+        sys.exit(-1)
+
+    nmodl = sys.argv[1]
+    usecase_dir = sys.argv[2]
+    output_basedir = sys.argv[3]
+    script_dir = os.path.dirname(sys.argv[0])
+
+    config = load_config(script_dir=script_dir, usecase_dir=usecase_dir)
+    for c in config:
+        output_dir = os.path.join(output_basedir, c["output_reldir"])
+        generate_references(nmodl, usecase_dir, output_dir, c["nmodl_flags"])