#57 fix tutorial gen script paths

infra/CreateMarkdownTutorial.py

@@ -60,6 +60,7 @@
 import os
 import sys
 import re
+import subprocess
 
 # This had better match GenerateHowTo.py!
 HOWTO_TAG = "HOW_TO_TAG"
@@ -217,7 +218,12 @@ def ConvertTutorialToMarkdownText(test_file_path, test_file, other_files, revisi
     ugly_file_name = os.path.splitext(os.path.basename(test_file_path))[0] 
     nice_file_name = re.sub(regex, " ", ugly_file_name)
 
-    link_path = f"https://github.com/Chaste/PyChaste/blob/develop/test/tutorials/{ugly_file_name}.py"
+    root_dir = (
+        subprocess.check_output(["git", "rev-parse", "--show-toplevel"]).decode("ascii").strip()
+    )
+    link_path = os.path.relpath(os.path.abspath(test_file_path), root_dir)
+    link_path = f"https://github.com/Chaste/PyChaste/blob/develop/{link_path}"
+
     page_header = f"""
 ---
 title : "{nice_file_name}"

infra/GenerateWikiPages.py

@@ -37,6 +37,7 @@
 This script converts Python tutorials to markdown and jupyter notebook formats for use on the 
 PyChaste website.
 """
+
 import argparse
 import fnmatch
 import ntpath
@@ -56,43 +57,57 @@
     )
     args = parser.parse_args()
 
+    # Get the repository root directory
+    root_dir = (
+        subprocess.check_output(["git", "rev-parse", "--show-toplevel"])
+        .decode("ascii")
+        .strip()
+    )
+
     # Find all the tutorial files.
     tutorial_files = []
-    for root, dirs, files in os.walk("../test"):
+    for root, dirs, files in os.walk(os.path.join(root_dir, "test")):
         for file in files:
-            if fnmatch.fnmatch(file, "Test*LiteratePaper*") or fnmatch.fnmatch(
-                file, "Test*Tutorial*"
+            if fnmatch.fnmatch(file, "Test*LiteratePaper*.py") or fnmatch.fnmatch(
+                file, "Test*Tutorial*.py"
             ):
-                if not fnmatch.fnmatch(file, "*.pyc"):
-                    tutorial_files.append([root, file])
+                tutorial_files.append((root, file))
 
-    # Get git revision
-    revision = subprocess.check_output(['git', 'rev-parse', 'HEAD']).decode('ascii').strip()
+    # Get the git revision
+    revision = (
+        subprocess.check_output(["git", "rev-parse", "HEAD"]).decode("ascii").strip()
+    )
 
     if args.format == "markdown":
-        # Generate the markdown for each
-        for eachFile in tutorial_files:
-            outfile = (
-                "../doc/tutorials/"
-                + os.path.splitext(ntpath.basename(eachFile[1]))[0]
-                + ".md"
+        # Generate a markdown file for each tutorial
+        for tutorial_file in tutorial_files:
+            input_filepath = os.path.join(tutorial_file[0], tutorial_file[1])
+
+            output_filename = (
+                os.path.splitext(os.path.basename(tutorial_file[1]))[0] + ".md"
             )
-            inputfile = eachFile[0] + "/" + eachFile[1]
-            launch_string = f"../infra/CreateMarkdownTutorial.py {inputfile} {outfile} --revision {revision}"
+            output_filepath = os.path.join(
+                root_dir, "doc", "tutorials", output_filename
+            )
+
+            launch_string = f"{root_dir}/infra/CreateMarkdownTutorial.py {input_filepath} {output_filepath} --revision {revision}"
             os.system(launch_string)
 
     elif args.format == "jupyter":
-        # Generate the jupyter notebooks for each
-        for eachFile in tutorial_files:
-            outfile = (
-                "../doc/tutorials/"
-                + os.path.splitext(ntpath.basename(eachFile[1]))[0]
-                + ".ipynb"
+        # Generate a jupyter notebook for each tutorial
+        for tutorial_file in tutorial_files:
+            input_filepath = os.path.join(tutorial_file[0], tutorial_file[1])
+
+            output_filename = (
+                os.path.splitext(os.path.basename(tutorial_file[1]))[0] + ".ipynb"
             )
-            inputfile = eachFile[0] + "/" + eachFile[1]
-            launch_string = (
-                f"../infra/CreateJupyterNotebookTutorial.py {inputfile} {outfile}"
+            output_filepath = os.path.join(
+                root_dir, "doc", "tutorials", output_filename
             )
+
+            launch_string = f"{root_dir}/infra/CreateJupyterNotebookTutorial.py {input_filepath} {output_filepath}"
             os.system(launch_string)
 
-            subprocess.call(f"jupyter nbconvert --to notebook {outfile}", shell=True)
+            subprocess.call(
+                f"jupyter nbconvert --to notebook {output_filepath}", shell=True
+            )