eliminate tabs and trailing whitespace (#429)

+ setup a github action

.github/workflows/create_release.yml

@@ -2,8 +2,8 @@ on:
   push:
     # Sequence of patterns matched against refs/tags
     tags:
-      - '[0-9][0-9].[0-9][0-9]' 
-  
+      - '[0-9][0-9].[0-9][0-9]'
+
 name: Create Release
 
 jobs:

.github/workflows/style.yml

@@ -0,0 +1,22 @@
+name: Style
+
+on: [push, pull_request]
+
+concurrency:
+  group: ${{ github.ref }}-${{ github.head_ref }}-style
+  cancel-in-progress: true
+
+jobs:
+  tabs:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Tabs
+        run: .github/workflows/style/check_tabs.sh
+
+  trailing_whitespaces:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Trailing Whitespaces
+        run: .github/workflows/style/check_trailing_whitespaces.sh

.github/workflows/style/check_tabs.sh

@@ -0,0 +1,36 @@
+#!/usr/bin/env bash
+
+set -eu -o pipefail
+
+find . -type d \( -name .git \
+                  -o -path ./paper \
+                  -o -name build -o -name install \
+                  -o -name tmp_build_dir -o -name tmp_install_dir \
+               \) -prune -o \
+       -type f \( \( -name "*.H" -o -name "*.h" -o -name "*.hh" -o -name "*.hpp" \
+                  -o -name "*.c" -o -name "*.cc" -o -name "*.cpp" -o -name "*.cxx" \
+                  -o -name "*.f" -o -name "*.F" -o -name "*.f90" -o -name "*.F90" \
+                  -o -name "*.py" \
+                  -o -name "*.md" -o -name "*.rst" \
+                  -o -name "*.sh" \
+                  -o -name "*.tex" \
+                  -o -name "*.txt" \
+                  -o -name "*.yml" \) \
+                 -a \( ! -name "*.tab.h" -a ! -name "*.tab.nolint.H" \
+                    -a ! -name "*.lex.h" -a ! -name "*.lex.nolint.H" \) \
+               \) \
+    -exec grep -Iq . {} \; \
+    -exec sed -i 's/\t/\ \ \ \ /g' {} +
+
+gitdiff=`git diff`
+
+if [ -z "$gitdiff" ]
+then
+    exit 0
+else
+    echo -e "\nTabs are not allowed. Changes suggested by"
+    echo -e "  ${0}\n"
+    git --no-pager diff
+    echo ""
+    exit 1
+fi

.github/workflows/style/check_trailing_whitespaces.sh

@@ -0,0 +1,38 @@
+#!/usr/bin/env bash
+
+set -eu -o pipefail
+
+find . -type d \( -name .git \
+                  -o -path ./paper \
+                  -o -name build -o -name install \
+                  -o -name tmp_build_dir -o -name tmp_install_dir \
+                  -o -path ./util/gcem \
+               \) -prune -o \
+       -type f \( \( -name "*.H" -o -name "*.h" -o -name "*.hh" -o -name "*.hpp" \
+                  -o -name "*.c" -o -name "*.cc" -o -name "*.cpp" -o -name "*.cxx" \
+                  -o -name "*.f" -o -name "*.F" -o -name "*.f90" -o -name "*.F90" \
+                  -o -name "*.py" \
+                  -o -name "*.rst" \
+                  -o -name "*.sh" \
+                  -o -name "*.tex" \
+                  -o -name "*.txt" \
+                  -o -name "*.yml" \) \
+                 -a \( ! -name "*.tab.h" -a ! -name "*.tab.nolint.H" \
+                    -a ! -name "*.lex.h" -a ! -name "*.lex.nolint.H" \
+                    -a ! -path "./networks/*/reaclib_rates.H" \) \
+               \) \
+    -exec grep -Iq . {} \; \
+    -exec sed -i 's/[[:blank:]]\+$//g' {} +
+
+gitdiff=`git diff`
+
+if [ -z "$gitdiff" ]
+then
+    exit 0
+else
+    echo -e "\nTrailing whitespaces at the end of a line are not allowed. Changes suggested by"
+    echo -e "  ${0}\n"
+    git --no-pager diff
+    echo ""
+    exit 1
+fi

Exec/science/code_comp/analysis/image_animator.py

@@ -30,7 +30,7 @@ def image_animator(args):
 
     # Sort if necessary
     if args.sort is not None:
-        
+
         # Descending or ascending
         desc = args.sort < 0
         # Starting index
@@ -43,21 +43,21 @@ def image_animator(args):
         else:
             key = lambda filename: filename[start:start+nchars]
         images.sort(key=key, reverse=desc)
-        
+
     if args.out.endswith(".mp4"):
         args.out = args.out[:-4]
     if not args.out:
         sys.exit("Invalid output file!")
 
     with tf.TemporaryDirectory() as dir:
-        
+
         # The files are numbered
         # Padding with zeros preserves sort order
         ndigits = len(str(len(images)))
         baselink = "__fftemp_{:0%dd}.png" % ndigits
 
         for i, image in enumerate(map(os.path.abspath, images)):
-            
+
             # Create a symlink for each file
             linkname = baselink.format(i)
             linkname = os.path.join(dir, linkname)
@@ -75,4 +75,3 @@ def image_animator(args):
     args = parse_args()
 
     image_animator(args)
-

Exec/science/code_comp/analysis/plot_generator.py

@@ -100,14 +100,14 @@ def plot_generator(args):
     def get_width(ds, xlim=None, ylim=None, zlim=None):
         """ Get the width of the plot. """
 
-        if xlim is None: 
+        if xlim is None:
             xlim = ds.domain_left_edge[0], ds.domain_right_edge[0]
-        else: 
+        else:
             xlim = xlim[0] * cm, xlim[1] * cm
 
-        if ylim is None: 
+        if ylim is None:
             ylim = ds.domain_left_edge[1], ds.domain_right_edge[1]
-        else: 
+        else:
             ylim = ylim[0] * cm, ylim[1] * cm
 
         xwidth = (xlim[1] - xlim[0]).in_cgs()
@@ -116,9 +116,9 @@ def get_width(ds, xlim=None, ylim=None, zlim=None):
         if ds.domain_dimensions[2] == 1:
             zwidth = 0.0
         else:
-            if zlim is None: 
+            if zlim is None:
                 zlim = ds.domain_left_edge[2], ds.domain_right_edge[2]
-            else: 
+            else:
                 zlim = zlim[0] * cm, zlim[1] * cm
 
             zwidth = (zlim[1] - zlim[0]).in_cgs()
@@ -128,14 +128,14 @@ def get_width(ds, xlim=None, ylim=None, zlim=None):
     def get_center(ds, xlim=None, ylim=None, zlim=None):
         """ Get the coordinates of the center of the plot. """
 
-        if xlim is None: 
+        if xlim is None:
             xlim = ds.domain_left_edge[0], ds.domain_right_edge[0]
-        else: 
+        else:
             xlim = xlim[0] * cm, xlim[1] * cm
 
-        if ylim is None: 
+        if ylim is None:
             ylim = ds.domain_left_edge[1], ds.domain_right_edge[1]
-        else: 
+        else:
             ylim = ylim[0] * cm, ylim[1] * cm
 
         xctr = 0.5 * (xlim[0] + xlim[1])
@@ -144,9 +144,9 @@ def get_center(ds, xlim=None, ylim=None, zlim=None):
         if ds.domain_dimensions[2] == 1:
             zctr = 0.0
         else:
-            if zlim is None: 
+            if zlim is None:
                 zlim = ds.domain_left_edge[2], ds.domain_right_edge[2]
-            else: 
+            else:
                 zlim = zlim[0] * cm, zlim[1] * cm
 
             zctr = 0.5 * (zlim[0] + zlim[1])
@@ -157,14 +157,14 @@ def get_center(ds, xlim=None, ylim=None, zlim=None):
 
     # Loop and generate
     for ds in ts:
-        
+
         settings = {}
         settings['center'] = get_center(ds, args.xlim, args.ylim, args.zlim)
         settings['width'] = get_width(ds, args.xlim, args.ylim, args.zlim)
         settings['normal'] = args.normal
 
         plot = func(ds, fields=field, **settings)
-        if args.cmap: 
+        if args.cmap:
             plot.set_cmap(field=field, cmap=args.cmap)
 
         if args.linthresh:
@@ -180,9 +180,9 @@ def get_center(ds, xlim=None, ylim=None, zlim=None):
             plot.set_zlim(field, *args.bounds)
 
         if args.time:
-            
+
             time_format = f't = {{time:.{args.time}f}}{{units}}'
-            
+
             plot.annotate_timestamp(corner='upper_left', time_format=time_format,
                     time_unit='s', draw_inset_box=True, inset_box_args={'alpha': 0.0})
 

Exec/science/ecsn/analysis/vol-ecsn-enuc.py

@@ -21,7 +21,7 @@ def doit(plotfile):
 
     field = ('boxlib', 'Hnuc')
     ds._get_field_info(field).take_log = True
-        
+
     sc = Scene()
 
 
@@ -55,10 +55,10 @@ def doit(plotfile):
 
     sc.get_source(0).transfer_function = tf
 
-    cam = sc.add_camera(ds, lens_type="perspective")        
+    cam = sc.add_camera(ds, lens_type="perspective")
     cam.resolution = (1080, 1080)
     cam.position = 1.0*ds.domain_right_edge
-    
+
     # look toward the center -- we are dealing with an octant
     center = ds.domain_left_edge
     normal = (center - cam.position)
@@ -75,11 +75,11 @@ def doit(plotfile):
 
     sc.render()
     sc.save("{}_Hnuc".format(plotfile), sigma_clip=4.0)
-    sc.save_annotated("{}_Hnuc_annotated.png".format(plotfile), 
-                      text_annotate=[[(0.05, 0.05), 
+    sc.save_annotated("{}_Hnuc_annotated.png".format(plotfile),
+                      text_annotate=[[(0.05, 0.05),
                                       "t = {}".format(ds.current_time.d),
                                       dict(horizontalalignment="left")],
-                                     [(0.5,0.95), 
+                                     [(0.5,0.95),
                                       "MAESTROeX simulation of ECSN convection",
                                       dict(color="y", fontsize="24",
                                            horizontalalignment="center")]])
@@ -96,4 +96,4 @@ def doit(plotfile):
     doit(plotfile)
 
 
-        
+

Exec/science/ecsn/analysis/vol-ecsn-radvel.py

@@ -23,7 +23,7 @@ def doit(plotfile):
 
     field = ('boxlib', 'radial_velocity')
     ds._get_field_info(field).take_log = False
-        
+
     sc = Scene()
 
 
@@ -50,10 +50,10 @@ def doit(plotfile):
 
     sc.get_source(0).transfer_function = tf
 
-    cam = sc.add_camera(ds, lens_type="perspective")        
+    cam = sc.add_camera(ds, lens_type="perspective")
     cam.resolution = (1080, 1080)
     cam.position = 1.0*ds.domain_right_edge
-    
+
     # look toward the center -- we are dealing with an octant
     center = ds.domain_left_edge
     normal = (center - cam.position)
@@ -70,11 +70,11 @@ def doit(plotfile):
 
     sc.render()
     sc.save("{}_radvel".format(plotfile), sigma_clip=4.0)
-    # sc.save_annotated("{}_radvel_annotated.png".format(plotfile), 
-    #                   text_annotate=[[(0.05, 0.05), 
+    # sc.save_annotated("{}_radvel_annotated.png".format(plotfile),
+    #                   text_annotate=[[(0.05, 0.05),
     #                                   "t = {}".format(ds.current_time.d),
     #                                   dict(horizontalalignment="left")],
-    #                                  [(0.5,0.95), 
+    #                                  [(0.5,0.95),
     #                                   "Maestro simulation of He convection on a white dwarf",
     #                                   dict(color="y", fontsize="24",
     #                                        horizontalalignment="center")]])
@@ -91,4 +91,4 @@ def doit(plotfile):
     doit(plotfile)
 
 
-        
+

Exec/science/urca/MaestroInitData.cpp

@@ -59,7 +59,7 @@ void Maestro::InitLevelDataSphr(const int lev, const Real time, MultiFab& scal,
 
     Put1dArrayOnCart(lev, temp_vec, temp_mf, 0, 0, bcs_f, 0);
     MultiFab::Copy(scal, temp_mf, 0, Temp, 1, 0);
-    
+
     // initialize density
     for (auto l = 0; l <= base_geom.max_radial_level; ++l) {
         for (auto r = 0; r < base_geom.nr(l); ++r) {
@@ -166,7 +166,7 @@ void Maestro::InitLevelDataSphr(const int lev, const Real time, MultiFab& scal,
             scal_arr(i, j, k, Temp) = eos_state.T;
         });
 
-        
+
         const auto prob_lo = geom[lev].ProbLoArray();
         const auto prob_hi = geom[lev].ProbHiArray();
         const auto dx = geom[lev].CellSizeArray();

Exec/science/urca/analysis/UrcaAnalysis/yt_extensions/yt_extensions.py

@@ -9,7 +9,7 @@
 
 class PhysicalConstants:
     N_AVO = 6.02214129e23
-    
+
 class DatasetHelpers:
     @staticmethod
     def get_field(ds, field_name):
@@ -79,7 +79,7 @@ def setup(self, ds):
         except yt.utilities.exceptions.YTFieldNotFound:
             print('WARNING: enucdot_dqweak_urca23 could not be added because it relies on a field not in the dataset.')
             pass
-        
+
         try:
             ds.add_field(('boxlib','enucloss_sneut'), sampling_type='cell', units='g',
                          function=UrcaShellFields._enucloss_sneut)
@@ -128,7 +128,7 @@ def setup(self, ds):
         except yt.utilities.exceptions.YTFieldNotFound:
             print('WARNING: xc12_complement could not be added because it relies on a field not in the dataset.')
             pass
-        
+
     @staticmethod
     def _urca23_shell_unscaled(field, data):
         return data['boxlib','ecap23']*data['boxlib','beta23']*data['boxlib','X(na23)']*data['boxlib','X(ne23)']