Merge pull request #680 from gonuke/660_uwuw_tally

Addressing a number of miscellaneous changes from #660

Author: pshriwise

.gitignore

@@ -5,6 +5,7 @@
 #*
 # vscode settings
 .vscode
+*.code-workspace
 
 # Ignore built documentation
 gh-build

misc/tests/test_uwuw_preproc_model.py

@@ -28,9 +28,8 @@ def test_model_material():
     # group_list is the final list of group names found on the CAD h5m file
     for k in pseudo_list:
         if ("mat:" in k):
-            index = k.index('\n')
-            k = k[0:index]
-            group_list.append(k.rstrip("\n"))
+            idx = k.index('\n')
+            group_list.append(k[0:idx].rstrip("\n"))
     # tag_list is the list of group names obtained by running get_tag_values
     # function
     tag_list = gtag.get_tag_values(filename, output_filename)

news/PR-0680.rst

@@ -0,0 +1,18 @@
+**Added:** None
+
+**Changed:** 
+* a few small fixes prompted by PullRequest review #660
+* only changed files in 
+    * `uwuw`
+    * `tally`
+    * `overlap_check`
+    * `build_obb`
+    * `misc/tests`
+
+**Deprecated:** None
+
+**Removed:** None
+
+**Fixed:** None
+
+**Security:** None

src/build_obb/build_obb.cpp

@@ -25,7 +25,12 @@ int main(int argc, char* argv[]) {
   // sets the output filename if none specified
   if (out_file == "") {
     int pos = dag_file.find(".h5m");
-    out_file = dag_file.substr(0, pos) + "_obb.h5m";
+    if (pos != std::string::npos) {
+      out_file = dag_file.substr(0, pos);
+    } else {
+      out_file = dag_file;
+    }
+    out_file = out_file + "_obb.h5m";
     std::cout << "Setting default outfile to be " << out_file << std::endl;
   }
 

src/overlap_check/ProgressBar.cpp

@@ -2,6 +2,7 @@
 
 #include "ProgressBar.hpp"
 
+#include <string>
 #include <sstream>
 #include <iostream>
 #include <iomanip>
@@ -12,13 +13,10 @@
 
 #define BAR_WIDTH 72
 
-ProgressBar::ProgressBar() {
-  // initialize bar
-  set_value(0.0);
-}
-
 ProgressBar::~ProgressBar() {
-  std::cout << "\n";
+  if (need_final_newline) {
+    std::cout << std::endl;
+  }
 }
 
 bool ProgressBar::is_terminal() {
@@ -62,7 +60,9 @@ void ProgressBar::set_value(double val) {
 
   // write the bar to screen
   std::cout << '\r' << bar.str() << std::flush;
+
   if (val >= 100.0) {
     std::cout << "\n";
+    need_final_newline = false;
   }
 }

src/overlap_check/ProgressBar.hpp

@@ -2,13 +2,14 @@
 #ifndef DAGMC_PROGRESSBAR_H
 #define DAGMC_PROGRESSBAR_H
 
-#include <string>
-
 class ProgressBar {
 
  public:
   // constructor
-  ProgressBar();
+  ProgressBar() {
+    // initialize bar
+    set_value(0.0);
+  };
 
   // destructor
   ~ProgressBar();
@@ -19,6 +20,7 @@ class ProgressBar {
 
  private:
   int current {0};
+  bool need_final_newline {true};
 };
 
 #endif // HEADER GUARD

src/overlap_check/app/overlap_check.cpp

@@ -19,7 +19,9 @@ int main(int argc, char* argv[]) {
 
   std::string filename;
   int points_per_tri_edge {0};
+#ifdef _OPENMP
   int n_threads {0};
+#endif
 
   po.addRequiredArg<std::string>("dag_file", "Path to DAGMC file to check", &filename);
 

src/overlap_check/overlap.cpp

@@ -104,11 +104,11 @@ check_instance_for_overlaps(std::shared_ptr<Interface> MBI,
   #pragma omp parallel shared(overlap_map, num_checked)
   {
     #pragma omp for schedule(auto)
-    for (int i = 0; i < all_verts.size(); i++) {
+    for (size_t i = 0; i < all_verts.size(); i++) {
 
       EntityHandle vert = all_verts[i];
       CartVect loc;
-      rval = MBI->get_coords(&vert, 1, loc.array());
+      MBI->get_coords(&vert, 1, loc.array());
 
       rval = check_location_for_overlap(GQT, all_vols, loc, dir, overlap_map);
       MB_CHK_SET_ERR_CONT(rval, "Failed to check location " << loc << " for an overlap");
@@ -129,7 +129,7 @@ check_instance_for_overlaps(std::shared_ptr<Interface> MBI,
     // (curve edges are likely in here too,
     //  but it isn't hurting anything to check more locations)
     #pragma omp for schedule(auto)
-    for (int i = 0; i < all_edges.size() ; i++) {
+    for (size_t i = 0; i < all_edges.size() ; i++) {
 
       EntityHandle edge = all_edges[i];
       Range edge_verts;

src/overlap_check/test/overlap_check_test.cpp

@@ -27,7 +27,7 @@ void OverlapTest::TearDown() {
 };
 
 class OverlappingVolumesTest : public OverlapTest {
-  virtual void SetFilename() { filename = "overlap.h5m"; }
+  virtual void SetFilename() override { filename = "overlap.h5m"; }
 };
 
 TEST_F(OverlappingVolumesTest, test1) {
@@ -43,7 +43,7 @@ TEST_F(OverlappingVolumesTest, test1) {
 }
 
 class NonOverlappingVolumesTest : public OverlapTest {
-  virtual void SetFilename() { filename = "no_overlap.h5m"; }
+  virtual void SetFilename() override { filename = "no_overlap.h5m"; }
 };
 
 TEST_F(NonOverlappingVolumesTest, test2) {
@@ -62,7 +62,7 @@ TEST_F(NonOverlappingVolumesTest, test2) {
 }
 
 class NonOverlappingImprintedVolumesTest : public OverlapTest {
-  virtual void SetFilename() { filename = "no_overlap_imp.h5m"; }
+  virtual void SetFilename() override { filename = "no_overlap_imp.h5m"; }
 };
 
 TEST_F(NonOverlappingImprintedVolumesTest, test3) {
@@ -81,7 +81,7 @@ TEST_F(NonOverlappingImprintedVolumesTest, test3) {
 }
 
 class EnclosedVolumeTest : public OverlapTest {
-  virtual void SetFilename() { filename = "enclosed.h5m"; }
+  virtual void SetFilename() override { filename = "enclosed.h5m"; }
 };
 
 TEST_F(EnclosedVolumeTest, test1) {

src/overlap_check/test/overlap_check_test.hpp

@@ -5,8 +5,8 @@ using namespace moab;
 
 class OverlapTest : public::testing::Test {
  protected:
-  virtual void SetUp();
-  virtual void TearDown();
+  virtual void SetUp() override;
+  virtual void TearDown() override;
   virtual void SetFilename() {};
 
   std::string filename;