Bring in Bill Large's Stokes MOST updates

CVMix_tools/code_consistency.py

@@ -220,12 +220,14 @@ def check_r8_settings(self, file_and_line, line, comment_char="!"):
 
     fortran_files = [] # pylint: disable=C0103
     python_files = []  # pylint: disable=C0103
+    perl_files = []    # pylint: disable=C0103
     for root, dirs, files in os.walk(CVMIX_ROOT):
         for thisfile in files:
             if thisfile.endswith(".F90"):
                 fortran_files.append(os.path.join(root, thisfile))
             elif thisfile.endswith(".py"):
                 python_files.append(os.path.join(root, thisfile))
+    perl_files.append(os.path.join(CVMIX_ROOT, 'doc', 'protex'))
 
     # Use logging to write messages to stdout
     logging.basicConfig(format='%(message)s', level=logging.DEBUG)
@@ -267,7 +269,21 @@ def check_r8_settings(self, file_and_line, line, comment_char="!"):
     PYTHON_ERROR_COUNT = Tests.process()
     LOGGER.info("Python errors found: %d", PYTHON_ERROR_COUNT)
 
-    if FORTRAN_ERROR_COUNT + PYTHON_ERROR_COUNT > 0:
+    # Perl error checks
+    LOGGER.info("\nCheck perl files for coding standard violations:")
+    for thisfile in perl_files:
+        with open(thisfile, "r") as perl_file:
+            line_cnt = 0
+            for thisline in perl_file.readlines():
+                line_without_cr = thisline.rstrip("\n")
+                line_cnt = line_cnt + 1
+                file_and_line_number = "%s:%d" % (thisfile, line_cnt)
+                Tests.check_for_hard_tabs(file_and_line_number, line_without_cr)
+                Tests.check_for_trailing_whitespace(file_and_line_number, line_without_cr)
+    PERL_ERROR_COUNT = Tests.process()
+    LOGGER.info("Perl errors found: %d", PERL_ERROR_COUNT)
+
+    if FORTRAN_ERROR_COUNT + PYTHON_ERROR_COUNT + PERL_ERROR_COUNT > 0:
         LOGGER.info("\nTotal error count: %d", FORTRAN_ERROR_COUNT + PYTHON_ERROR_COUNT)
         sys.exit(1)
 

doc/.gitignore

@@ -0,0 +1 @@
+protex_out/*

doc/make_protex_file

@@ -1,9 +1,19 @@
-#!/bin/bash
+#!/bin/bash -e
 
 SRC=../src
 DRIVE=$SRC/drivers
 SHARE=$SRC/shared
-f90pdf                                       \
+
+mkdir -p protex_out
+rm -f protex_out/protex_documentation.*
+./protex -s -F -g +n                         \
+       $SRC/cvmix_driver.F90                 \
+       $DRIVE/cvmix_bgrnd_BL.F90             \
+       $DRIVE/cvmix_shear_drv.F90            \
+       $DRIVE/cvmix_tidal_Simmons.F90        \
+       $DRIVE/cvmix_ddiff_drv.F90            \
+       $DRIVE/cvmix_kpp_drv.F90              \
+       $SRC/cvmix_io.F90                     \
        $SHARE/cvmix_kinds_and_types.F90      \
        $SHARE/cvmix_background.F90           \
        $SHARE/cvmix_shear.F90                \
@@ -13,14 +23,10 @@ f90pdf                                       \
        $SHARE/cvmix_convection.F90           \
        $SHARE/cvmix_math.F90                 \
        $SHARE/cvmix_put_get.F90              \
-       $SHARE/cvmix_utils.F90                \
-       $SRC/cvmix_driver.F90                 \
-       $DRIVE/cvmix_bgrnd_BL.F90             \
-       $DRIVE/cvmix_shear_drv.F90            \
-       $DRIVE/cvmix_tidal_Simmons.F90        \
-       $DRIVE/cvmix_ddiff_drv.F90            \
-       $DRIVE/cvmix_kpp_drv.F90              \
-       $SRC/cvmix_io.F90
+       $SHARE/cvmix_utils.F90 >              \
+       protex_out/protex_documentation.tex
 
-rm -f output.tex
-mv -f output.pdf protex_documentation.pdf
+cd protex_out
+pdflatex protex_documentation.tex
+pdflatex protex_documentation.tex
+cp -f protex_documentation.pdf ../