Fixed PDF generation re %matplotlib magic

Fixed the scripts that comment out the matplotlib magic.
It was commenting out all of the magics - the first one, and
ones in markdown cells. It should only comment out the ones
in code cells, and leave the first one.

pdf/build_book.bat

@@ -1,5 +1,5 @@
-rem call run_notebooks
-rem cd ..
+call run_notebooks
+cd ..
 ipython merge_book.py
 
 jupyter nbconvert --to latex --template book book.ipynb

pdf/clean_book.bat

@@ -14,3 +14,4 @@ rm --f chapter.pdf
 
 rmdir  /S /Q book_files
 rmdir  /S /Q chapter_files
+rmdir  /S /Q tmp

pdf/rm_notebook.py

@@ -1,15 +1,29 @@
-import os, sys
+import os, sys, io
+
 print(sys.argv[1])
 infile = open(sys.argv[1], encoding="utf8")
 data = infile.read()
 infile.close()
 outfile = open(sys.argv[1], "w", encoding="utf8")
 
-data = data.replace("%matplotlib notebook", "#%matplotlib notebook")
-data = data.replace("%matplotlib inline #reset", "#%matplotlib inline #reset")
-data = data.replace("time.sleep", "#time.sleep")
-data = data.replace("fig.canvas.draw", "#fig.canvas.draw")
-data = data.replace("plt.gcf().canvas.draw", "#plt.gcf().canvas.draw")
+buf = io.StringIO(data)
+first_inline = False
+is_code_cell = False
+for line in buf:
+    # can't comment out first inline that is always in the first cell
+    if '"cell_type":' in line:
+        is_code_cell = '"code"' in line
+        
+    if is_code_cell:
+        if '%matplotlib inline' in line:
+            if first_inline:
+                line = line.replace("%matplotlib inline", "#%matplotlib inline")
+            first_inline = True
+        
+        line = line.replace("%matplotlib notebook", "#%matplotlib notebook")
+        line = line.replace("time.sleep", "#time.sleep")
+        line = line.replace("fig.canvas.draw", "#fig.canvas.draw")
+        line = line.replace("plt.gcf().canvas.draw", "#plt.gcf().canvas.draw")
+    outfile.write(line)
 
-outfile.write(data)
 outfile.close()

pdf/run_notebooks.bat

@@ -1,10 +1,10 @@
 mkdir tmp
-REM copy ..\*.ipynb .\tmp
-REM copy ..\*.py .\tmp
-REM cp -r ..\code\ .\tmp\code\
+copy ..\*.ipynb .\tmp
+copy ..\*.py .\tmp
+cp -r ..\code\ .\tmp\code\
 
 cd tmp
 
-REM forfiles /m *.ipynb /c "cmd /c ipython ..\rm_notebook.py @file"
-REM forfiles /m *.ipynb /c "cmd /c jupyter nbconvert --to notebook --execute @file --output @file"
+forfiles /m *.ipynb /c "cmd /c ipython ..\rm_notebook.py @file"
+forfiles /m *.ipynb /c "cmd /c jupyter nbconvert --to notebook --execute @file --output @file"