From d1248032328b6a02973c0843fb45d16d2ec5ccae Mon Sep 17 00:00:00 2001
From: Berkeley <berkeley@mrwhite>
Date: Wed, 17 Sep 2014 16:18:24 -0700
Subject: [PATCH 01/23] Added feature for folder arguments

---
 include/command_line/command_line.h |   1 +
 include/command_line/folder_arg.h   | 178 ++++++++++++++++++++++++++++
 2 files changed, 179 insertions(+)
 create mode 100644 include/command_line/folder_arg.h

diff --git a/include/command_line/command_line.h b/include/command_line/command_line.h
index 8ce724f..12aba1c 100644
--- a/include/command_line/command_line.h
+++ b/include/command_line/command_line.h
@@ -20,6 +20,7 @@
 #include "include/command_line/command_line_config.h"
 #include "include/command_line/file_arg.h"
 #include "include/command_line/flag_arg.h"
+#include "include/command_line/folder_arg.h"
 #include "include/command_line/heading.h"
 #include "include/command_line/value_arg.h"
 
diff --git a/include/command_line/folder_arg.h b/include/command_line/folder_arg.h
new file mode 100644
index 0000000..16d2c7d
--- /dev/null
+++ b/include/command_line/folder_arg.h
@@ -0,0 +1,178 @@
+// Copyright 2014 eric schkufza
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+//     http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+#ifndef CPPUTIL_INCLUDE_COMMAND_LINE_FOLDER_ARG_H
+#define CPPUTIL_INCLUDE_COMMAND_LINE_FOLDER_ARG_H
+
+#include <string>
+#include <vector>
+
+#include <dirent.h>
+#include <unistd.h>
+#include <sys/stat.h>
+#include <sys/types.h>
+
+#include <cstdio>
+
+#include "include/command_line/arg.h"
+#include "include/serialize/text_reader.h"
+#include "include/serialize/text_writer.h"
+
+namespace cpputil {
+
+template <typename T, typename R = TextReader<T>, typename W = TextWriter<T>>
+class FolderArg : public Arg {
+ public:
+  virtual ~FolderArg() = default;
+
+  /** Creates and registers a new flag */
+  static FolderArg& create(const std::string& opt) {
+    return *(new FolderArg(opt));
+  }
+
+  /** Consumes indices from first alias to next - */
+  virtual std::pair<size_t, size_t> read(int argc, char** argv) {
+    for (const auto i : get_appearances(argc, argv)) {
+      if (i == (argc - 1) || argv[i + 1][0] == '-') {
+        error(parse_error_);
+        return std::make_pair(i, i);
+      }
+
+      // some code borrowed from 
+      // http://www.cplusplus.com/forum/beginner/10292/
+      DIR *dp = opendir(argv[i+1]);
+      if(dp == NULL) {
+        perror("could not open directory");
+        error(folder_error_);        
+      }
+
+      struct dirent *dirp;
+      while((dirp = readdir(dp))) {
+        std::string filepath = std::string(argv[i+1]) + "/" + dirp->d_name;
+
+        struct stat filestat;
+        if (stat(filepath.c_str(), &filestat)) continue;
+        if (S_ISDIR(filestat.st_mode)) continue;
+
+        std::ifstream ifs(filepath);
+        if (!ifs.is_open()) {
+          error(file_error_);
+        } else {
+          T temp = T();
+          R()(ifs, temp);
+
+          if (ifs.fail()) {
+            continue;
+            // This could be a parse error; but for now I'm opting to
+            // silently ignore files that can't be parsed.  FIXME.
+          } else {
+            val_.push_back(temp);
+          }
+        }
+      }
+      closedir(dp);
+
+      return std::make_pair(i, i + 1);
+    }
+
+    return std::make_pair(0, 0);
+  }
+
+  /** Create a new arg alias (hashes implicit; chars get 1, strings 2) */
+  FolderArg& alternate(const std::string& a) {
+    Arg::alternate(a);
+    return *this;
+  }
+
+  /** Reset arg usage */
+  FolderArg& usage(const std::string& u) {
+    Arg::usage(u);
+    return *this;
+  }
+
+  /** Reset arg description */
+  FolderArg& description(const std::string& d) {
+    Arg::description(d);
+    return *this;
+  }
+
+  /** Resets arg default value */
+  FolderArg& default_val(const std::vector<T>& t) {
+    val_ = t;
+    return *this;
+  }
+
+  /** Resets parse error message */
+  FolderArg& parse_error(const std::string& pe) {
+    parse_error_ = pe;
+    return *this;
+  }
+
+  /** Resets file error message */
+  FolderArg& file_error(const std::string& fe) {
+    file_error_ = fe;
+    return *this;
+  }
+
+  /** Resets folder error message */
+  FolderArg & folder_error(const std::string& fe) {
+    folder_error_ = fe;
+    return *this;
+  }
+
+  /** Implicit conversion to underlying type */
+  operator std::vector<T>& () {
+    return val_;
+  }
+
+  /** Explicit conversion to underlying type */
+  std::vector<T>& value() {
+    return val_;
+  }
+
+  /** Prints underlying value using writer */
+  virtual void debug(std::ostream& os) const {
+    os << "[" << std::endl;
+    for (auto& it : val_) {
+      W()(os, it);
+      os << std::endl;
+    }
+    os << "]";
+  }
+
+ private:
+  /** Underlying value, optionally specified on command line */
+  std::vector<T> val_;
+  /** String to emit if an error occurs during read() */
+  std::string parse_error_;
+  /** String to emit if unable to open source file during read() */
+  std::string file_error_;
+  /** String to emit if unable to open directory */
+  std::string folder_error_;
+
+  /** FolderArgs are assigned default constructor values by default */
+  FolderArg(const std::string& opt) :
+    Arg {opt} {
+    usage("<value>");
+    parse_error("Unable to parse value!");
+    file_error("Unable to open one of the files!");
+    folder_error("Unable to open drectory!");
+  }
+};
+
+} // namespace cpputil
+
+#endif
+
+

From a10f3bcd5b2ebf6bebe8ad4a2ebf3afa5db7e528 Mon Sep 17 00:00:00 2001
From: eric <eric.schkufza@gmail.com>
Date: Fri, 17 Oct 2014 18:52:21 -0700
Subject: [PATCH 02/23] Added const void* data() member to bit string.

---
 include/container/bit_string.h | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/include/container/bit_string.h b/include/container/bit_string.h
index 9afd391..ceaf5e7 100644
--- a/include/container/bit_string.h
+++ b/include/container/bit_string.h
@@ -593,6 +593,10 @@ class BitString {
   void* data() {
     return contents_.data();
   }
+	/** Underlying data. */
+	const void* data() const {
+		return contents_.data();
+	}
 
   /** Subscript operator. */
   bit_type operator[](size_t i) {

From 99a6ca74047e5e0f3135c57be78c3453d77af74d Mon Sep 17 00:00:00 2001
From: "Berkeley Churchill (on mrwhite)" <berkeley@berkeleychurchill.com>
Date: Sat, 8 Nov 2014 23:52:42 -0800
Subject: [PATCH 03/23] Fix for #6.

---
 include/container/bit_string.h | 47 ++++++++++++++++++++++++++++++----
 1 file changed, 42 insertions(+), 5 deletions(-)

diff --git a/include/container/bit_string.h b/include/container/bit_string.h
index 9afd391..1d8ca57 100644
--- a/include/container/bit_string.h
+++ b/include/container/bit_string.h
@@ -30,6 +30,9 @@ namespace cpputil {
 template <typename T>
 class BitString {
  public:
+
+  /* This class iterates through the indexes of the set bits in a bit string.
+   * This is the epitomy of stuff you'll find in hacker's delight. */
   class const_set_bit_index_iterator {
     friend class BitString;
 
@@ -40,15 +43,34 @@ class BitString {
     }
     /** Increment. */
     const_set_bit_index_iterator& operator++() {
+
+      /* Round-down the current bit to the next lowest 64 bits.  This means
+         the index contains the starting bit of the current 64-bit chunk. */
       BitManip<uint64_t>::unset_rightmost(index_, 6);
+
+      /* The unset_rightmost clears the lowest bit in the whole bitstring;
+         if it returns 0, this means we need to move up to the next 64-bit
+         chunk; otherwise, we stay in the same chunk */
       if (BitManip<uint64_t>::unset_rightmost(current_) == 0) {
+
+        /* Iterate through the 64-bit chunks to find the next non-zero one */
         const auto old_itr = itr_;
         for (++itr_; itr_ != end_ && *itr_ == 0; ++itr_);
-        index_ += 64 * (itr_ - old_itr);
         current_ = *itr_;
+        if(itr_ != end_) {
+          /* found it; recompute the index */
+          index_ += 64 * (itr_ - old_itr) + BitManip<uint64_t>::ntz(current_);
+          assert(index_ < num_bits_);
+        } else {
+          /* we're at the end */
+          index_ = num_bits_;
+        }
+      } else {
+        /* Compute the index of the next bit, using the starting index of the
+         * chunk computed earlier. */
+        index_ += BitManip<uint64_t>::ntz(current_);
+        assert(index_ < num_bits_);
       }
-      index_ += BitManip<uint64_t>::ntz(current_);
-      index_ = std::min(num_bits_, index_);
       return *this;
     }
     /** Equality. */
@@ -65,16 +87,31 @@ class BitString {
     const_set_bit_index_iterator(typename T::const_iterator i, typename T::const_iterator begin,
                                  typename T::const_iterator end, size_t num_bits) :
       end_(end), num_bits_(num_bits) {
+      /* Iterate through 64-bit chunks to find the next lowest index */
       for (itr_ = i; itr_ != end_ && *itr_ == 0; ++itr_);
       current_ = *itr_;
-      index_ = 64 * (itr_ - begin) + BitManip<uint64_t>::ntz(current_);
-      index_ = std::min(num_bits_, index_);
+      if(itr_ != end_) {
+        /* found it; find the index of the lowest bit in the 64-bit chunk */
+        index_ = 64 * (itr_ - begin) + BitManip<uint64_t>::ntz(current_);
+        assert(index_ < num_bits_);
+      } else {
+        /* there are no set bits at all */
+        index_ = num_bits_;
+      }
     }
 
+    /* This is the index of the currently set bit */
     size_t index_;
+
+    /* These iterate over the 64-bit chunks in the bitstring */
     typename T::const_iterator itr_;
     typename T::const_iterator end_;
+
+    /* The total number of bits available */
     size_t num_bits_;
+
+    /* This is the index of the object of type T (generally a uint64_t) the
+     * current bit is stored in. */
     uint64_t current_;
   };
 

From 61580a27927e93a287ad4338bb90047ddad7006e Mon Sep 17 00:00:00 2001
From: "Berkeley Churchill (on mrwhite)" <berkeley@berkeleychurchill.com>
Date: Sun, 9 Nov 2014 00:06:48 -0800
Subject: [PATCH 04/23] accidentally made fix for #6 off of master instead of
 develop.  Should be ok now.

---
 include/container/bit_string.h | 51 ++++++++++++++++++++++++++++------
 1 file changed, 42 insertions(+), 9 deletions(-)

diff --git a/include/container/bit_string.h b/include/container/bit_string.h
index ceaf5e7..1d8ca57 100644
--- a/include/container/bit_string.h
+++ b/include/container/bit_string.h
@@ -30,6 +30,9 @@ namespace cpputil {
 template <typename T>
 class BitString {
  public:
+
+  /* This class iterates through the indexes of the set bits in a bit string.
+   * This is the epitomy of stuff you'll find in hacker's delight. */
   class const_set_bit_index_iterator {
     friend class BitString;
 
@@ -40,15 +43,34 @@ class BitString {
     }
     /** Increment. */
     const_set_bit_index_iterator& operator++() {
+
+      /* Round-down the current bit to the next lowest 64 bits.  This means
+         the index contains the starting bit of the current 64-bit chunk. */
       BitManip<uint64_t>::unset_rightmost(index_, 6);
+
+      /* The unset_rightmost clears the lowest bit in the whole bitstring;
+         if it returns 0, this means we need to move up to the next 64-bit
+         chunk; otherwise, we stay in the same chunk */
       if (BitManip<uint64_t>::unset_rightmost(current_) == 0) {
+
+        /* Iterate through the 64-bit chunks to find the next non-zero one */
         const auto old_itr = itr_;
         for (++itr_; itr_ != end_ && *itr_ == 0; ++itr_);
-        index_ += 64 * (itr_ - old_itr);
         current_ = *itr_;
+        if(itr_ != end_) {
+          /* found it; recompute the index */
+          index_ += 64 * (itr_ - old_itr) + BitManip<uint64_t>::ntz(current_);
+          assert(index_ < num_bits_);
+        } else {
+          /* we're at the end */
+          index_ = num_bits_;
+        }
+      } else {
+        /* Compute the index of the next bit, using the starting index of the
+         * chunk computed earlier. */
+        index_ += BitManip<uint64_t>::ntz(current_);
+        assert(index_ < num_bits_);
       }
-      index_ += BitManip<uint64_t>::ntz(current_);
-      index_ = std::min(num_bits_, index_);
       return *this;
     }
     /** Equality. */
@@ -65,16 +87,31 @@ class BitString {
     const_set_bit_index_iterator(typename T::const_iterator i, typename T::const_iterator begin,
                                  typename T::const_iterator end, size_t num_bits) :
       end_(end), num_bits_(num_bits) {
+      /* Iterate through 64-bit chunks to find the next lowest index */
       for (itr_ = i; itr_ != end_ && *itr_ == 0; ++itr_);
       current_ = *itr_;
-      index_ = 64 * (itr_ - begin) + BitManip<uint64_t>::ntz(current_);
-      index_ = std::min(num_bits_, index_);
+      if(itr_ != end_) {
+        /* found it; find the index of the lowest bit in the 64-bit chunk */
+        index_ = 64 * (itr_ - begin) + BitManip<uint64_t>::ntz(current_);
+        assert(index_ < num_bits_);
+      } else {
+        /* there are no set bits at all */
+        index_ = num_bits_;
+      }
     }
 
+    /* This is the index of the currently set bit */
     size_t index_;
+
+    /* These iterate over the 64-bit chunks in the bitstring */
     typename T::const_iterator itr_;
     typename T::const_iterator end_;
+
+    /* The total number of bits available */
     size_t num_bits_;
+
+    /* This is the index of the object of type T (generally a uint64_t) the
+     * current bit is stored in. */
     uint64_t current_;
   };
 
@@ -593,10 +630,6 @@ class BitString {
   void* data() {
     return contents_.data();
   }
-	/** Underlying data. */
-	const void* data() const {
-		return contents_.data();
-	}
 
   /** Subscript operator. */
   bit_type operator[](size_t i) {

From 87f9973f64a8e571bc09f6ddb98637467f44b3b7 Mon Sep 17 00:00:00 2001
From: "Berkeley Churchill (on mrwhite)" <berkeley@berkeleychurchill.com>
Date: Sun, 9 Nov 2014 00:20:20 -0800
Subject: [PATCH 05/23] Still cleaning up from the bad branch.  Fixed
 indentation too.

---
 include/container/bit_string.h | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/include/container/bit_string.h b/include/container/bit_string.h
index 1d8ca57..21a6713 100644
--- a/include/container/bit_string.h
+++ b/include/container/bit_string.h
@@ -630,6 +630,10 @@ class BitString {
   void* data() {
     return contents_.data();
   }
+  /** Underlying data. */
+  void* data() const {
+    return contents_.data();
+  }
 
   /** Subscript operator. */
   bit_type operator[](size_t i) {

From e0651828e64ed8c5d592b7b0a3d5b14e8eeb9f82 Mon Sep 17 00:00:00 2001
From: "Berkeley Churchill (on mrwhite)" <berkeley@berkeleychurchill.com>
Date: Sun, 9 Nov 2014 00:23:21 -0800
Subject: [PATCH 06/23] Another iteration of testing against stoke foe #6...

---
 include/container/bit_string.h | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/include/container/bit_string.h b/include/container/bit_string.h
index 21a6713..d576f1b 100644
--- a/include/container/bit_string.h
+++ b/include/container/bit_string.h
@@ -631,7 +631,7 @@ class BitString {
     return contents_.data();
   }
   /** Underlying data. */
-  void* data() const {
+  const void* data() const {
     return contents_.data();
   }
 

From 0c4413d58c3d92ba2dbd653b4c6b8d148dd0434f Mon Sep 17 00:00:00 2001
From: "Berkeley Churchill (on mrwhite)" <berkeley@berkeleychurchill.com>
Date: Sun, 9 Nov 2014 00:31:35 -0800
Subject: [PATCH 07/23] Found another undefined read in #6

---
 include/container/bit_string.h | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/include/container/bit_string.h b/include/container/bit_string.h
index d576f1b..804c620 100644
--- a/include/container/bit_string.h
+++ b/include/container/bit_string.h
@@ -56,9 +56,9 @@ class BitString {
         /* Iterate through the 64-bit chunks to find the next non-zero one */
         const auto old_itr = itr_;
         for (++itr_; itr_ != end_ && *itr_ == 0; ++itr_);
-        current_ = *itr_;
         if(itr_ != end_) {
           /* found it; recompute the index */
+          current_ = *itr_;
           index_ += 64 * (itr_ - old_itr) + BitManip<uint64_t>::ntz(current_);
           assert(index_ < num_bits_);
         } else {
@@ -89,9 +89,9 @@ class BitString {
       end_(end), num_bits_(num_bits) {
       /* Iterate through 64-bit chunks to find the next lowest index */
       for (itr_ = i; itr_ != end_ && *itr_ == 0; ++itr_);
-      current_ = *itr_;
       if(itr_ != end_) {
         /* found it; find the index of the lowest bit in the 64-bit chunk */
+        current_ = *itr_;
         index_ = 64 * (itr_ - begin) + BitManip<uint64_t>::ntz(current_);
         assert(index_ < num_bits_);
       } else {

From 7f7964ed64d38356f61ba7b2ec51417ff1996ac0 Mon Sep 17 00:00:00 2001
From: Stefan Heule <stefanheule@gmail.com>
Date: Fri, 21 Nov 2014 01:08:00 -0800
Subject: [PATCH 08/23] Fixes #9.

---
 include/command_line/folder_arg.h | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/include/command_line/folder_arg.h b/include/command_line/folder_arg.h
index 16d2c7d..10694e4 100644
--- a/include/command_line/folder_arg.h
+++ b/include/command_line/folder_arg.h
@@ -73,9 +73,11 @@ class FolderArg : public Arg {
           R()(ifs, temp);
 
           if (ifs.fail()) {
-            continue;
-            // This could be a parse error; but for now I'm opting to
-            // silently ignore files that can't be parsed.  FIXME.
+            std::string err = "Unable to parse the file '";
+            err += dirp->d_name;
+            err += "'!";
+            error(err);
+            return std::make_pair(i, i);
           } else {
             val_.push_back(temp);
           }

From 16242b23d3f0ad64c915e7d4fcacc02c9c974607 Mon Sep 17 00:00:00 2001
From: Stefan Heule <stefanheule@gmail.com>
Date: Mon, 1 Dec 2014 19:20:40 -0800
Subject: [PATCH 09/23] Fixes #10.

---
 include/command_line/command_line_config.h | 1 +
 1 file changed, 1 insertion(+)

diff --git a/include/command_line/command_line_config.h b/include/command_line/command_line_config.h
index 2467709..1f4cbc9 100644
--- a/include/command_line/command_line_config.h
+++ b/include/command_line/command_line_config.h
@@ -96,6 +96,7 @@ class CommandLineConfig {
         exit(1);
       }
       write_config_file(ofs, argv[0]);
+      exit(0);
     }
   }
 

From f71b2186bbe5908eba21989754037aa28e2c700a Mon Sep 17 00:00:00 2001
From: Stefan Heule <stefanheule@gmail.com>
Date: Tue, 2 Dec 2014 14:35:32 -0800
Subject: [PATCH 10/23] Allow arguments to be required.  Fixes #11.

---
 examples/command_line/command_line.cc      |  2 +-
 include/command_line/arg.h                 | 27 +++++++++++++++++++++-
 include/command_line/command_line_config.h | 15 ++++++++++++
 include/command_line/file_arg.h            |  8 +++++++
 include/command_line/folder_arg.h          |  7 ++++++
 include/command_line/value_arg.h           |  7 ++++++
 6 files changed, 64 insertions(+), 2 deletions(-)

diff --git a/examples/command_line/command_line.cc b/examples/command_line/command_line.cc
index efb6ae6..6098755 100644
--- a/examples/command_line/command_line.cc
+++ b/examples/command_line/command_line.cc
@@ -31,7 +31,7 @@ auto& i = ValueArg<int, RangeReader<int, Range<int, 1, 10>>>::create("i")
           .alternate("int")
           .usage("<int>")
           .description("i | 1 <= i <= 10")
-          .default_val(5);
+          .required();
 
 auto& h = ValueArg<uint64_t, HexReader<uint64_t>, HexWriter<uint64_t>>::create("j")
           .alternate("hex")
diff --git a/include/command_line/arg.h b/include/command_line/arg.h
index 4582914..72a962b 100644
--- a/include/command_line/arg.h
+++ b/include/command_line/arg.h
@@ -86,6 +86,16 @@ class Arg {
     os << error_;
   }
 
+  /** Is this argument required? */
+  bool is_required() const {
+    return required_;
+  }
+
+  /** Has this argument been set (or does it have a default value)? */
+  bool has_been_provided() const {
+    return is_provided_;
+  }
+
   /** Prints the value of an arg */
   virtual void debug(std::ostream& os) const = 0;
 
@@ -100,11 +110,12 @@ class Arg {
   };
 
   /** An arg must be assigned at least one alias */
-  Arg(const std::string& opt) {
+  Arg(const std::string& opt) : is_provided_(false) {
     alternate(opt);
     usage("");
     description("(no description provided)");
     error("");
+    required(false);
 
     auto& ar = Singleton<ArgRegistry>::get();
     ar.insert(this);
@@ -166,6 +177,16 @@ class Arg {
     error_ = error;
   }
 
+  /** Reset the required argument. */
+  void required(const bool val = true) {
+    required_ = val;
+  }
+
+  /** Indicate that this argument has been set now. */
+  void set_provided() {
+    is_provided_ = true;
+  }
+
  private:
   /** Aliases for this arg ,ie: "-h --help" */
   std::set<std::string> opts_;
@@ -178,6 +199,10 @@ class Arg {
   std::string description_;
   /** A non-empty value here indicates that a survivable error occurred */
   std::string error_;
+  /** Is this argument mandatory? */
+  bool required_;
+  /** Has this argument been provided in some way? */
+  bool is_provided_;
 };
 
 } // namespace cpputil
diff --git a/include/command_line/command_line_config.h b/include/command_line/command_line_config.h
index 1f4cbc9..d667a79 100644
--- a/include/command_line/command_line_config.h
+++ b/include/command_line/command_line_config.h
@@ -89,6 +89,21 @@ class CommandLineConfig {
       exit(0);
     }
 
+    auto missing_arg = false;
+    for (auto it = Args::arg_begin(); it != Args::arg_end(); ++it) {
+      auto arg = *it;
+      if (arg->is_required() && !arg->has_been_provided()) {
+        if (!missing_arg) {
+          std::cerr << "Errors:" << std::endl;
+        }
+        missing_arg = true;
+        std::cerr << "  Argument '" << *arg->alias_begin() << "' is required!" << std::endl;
+      }
+    }
+    if (missing_arg) {
+      exit(1);
+    }
+
     if (write_config.value() != "") {
       std::ofstream ofs(write_config.value());
       if (!ofs.is_open()) {
diff --git a/include/command_line/file_arg.h b/include/command_line/file_arg.h
index 3d0cf09..d204bfb 100644
--- a/include/command_line/file_arg.h
+++ b/include/command_line/file_arg.h
@@ -54,6 +54,8 @@ class FileArg : public Arg {
           val_ = temp;
         }
       }
+
+      set_provided();
       return std::make_pair(i, i + 1);
     }
 
@@ -84,6 +86,12 @@ class FileArg : public Arg {
     return *this;
   }
 
+  /** Resets the required value. */
+  FileArg& required(const bool val = true) {
+    Arg::required(val);
+    return *this;
+  }
+
   /** Resets parse error message */
   FileArg& parse_error(const std::string& pe) {
     parse_error_ = pe;
diff --git a/include/command_line/folder_arg.h b/include/command_line/folder_arg.h
index 10694e4..d1377a4 100644
--- a/include/command_line/folder_arg.h
+++ b/include/command_line/folder_arg.h
@@ -85,6 +85,7 @@ class FolderArg : public Arg {
       }
       closedir(dp);
 
+      set_provided();
       return std::make_pair(i, i + 1);
     }
 
@@ -115,6 +116,12 @@ class FolderArg : public Arg {
     return *this;
   }
 
+  /** Resets the required value. */
+  FolderArg& required(const bool val = true) {
+    Arg::required(val);
+    return *this;
+  }
+
   /** Resets parse error message */
   FolderArg& parse_error(const std::string& pe) {
     parse_error_ = pe;
diff --git a/include/command_line/value_arg.h b/include/command_line/value_arg.h
index 7b99d8e..d42ef13 100644
--- a/include/command_line/value_arg.h
+++ b/include/command_line/value_arg.h
@@ -50,6 +50,7 @@ class ValueArg : public Arg {
       } else {
         val_ = temp;
       }
+      set_provided();
       return std::make_pair(i, i + 1);
     }
 
@@ -86,6 +87,12 @@ class ValueArg : public Arg {
     return *this;
   }
 
+  /** Resets the required value. */
+  ValueArg& required(const bool val = true) {
+    Arg::required(val);
+    return *this;
+  }
+
   /** Implicit conversion to underlying type */
   operator T& () {
     return val_;

From 2fba3395d31182370ba970623e13bc229d20edfd Mon Sep 17 00:00:00 2001
From: Stefan Heule <stefanheule@gmail.com>
Date: Tue, 2 Dec 2014 14:41:50 -0800
Subject: [PATCH 11/23] Fixes #13.

---
 include/command_line/command_line_config.h | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/include/command_line/command_line_config.h b/include/command_line/command_line_config.h
index d667a79..a790027 100644
--- a/include/command_line/command_line_config.h
+++ b/include/command_line/command_line_config.h
@@ -32,7 +32,7 @@ namespace cpputil {
 class CommandLineConfig {
  public:
   /** Strict parse with help, config, and debug support */
-  static void strict_with_convenience(int argc, char** argv) {
+  static void strict_with_convenience(int argc, char** argv, bool sort_args = false) {
     Heading::create("Help and argument utilities:");
     auto& help = FlagArg::create("h")
                  .alternate("help")
@@ -48,9 +48,11 @@ class CommandLineConfig {
                          .default_val("")
                          .description("Print an example configuration file");
 
-    Args::sort_args([](Arg * a1, Arg * a2) {
-      return *(a1->alias_begin()) < *(a2->alias_begin());
-    });
+    if (sort_args) {
+      Args::sort_args([](Arg * a1, Arg * a2) {
+        return *(a1->alias_begin()) < *(a2->alias_begin());
+      });
+    }
     Args::read(argc, argv);
 
     if (help) {

From dc25c9b0e7da08fac822360ef5ed6a0dea654746 Mon Sep 17 00:00:00 2001
From: Stefan Heule <stefanheule@gmail.com>
Date: Tue, 2 Dec 2014 15:26:13 -0800
Subject: [PATCH 12/23] Better help, especially showing defaults.  Fixes #12.

---
 include/command_line/arg.h                 | 14 +++++++++++++-
 include/command_line/command_line_config.h | 16 ++++++++++++++--
 include/command_line/file_arg.h            |  1 +
 include/command_line/folder_arg.h          |  1 +
 include/command_line/value_arg.h           |  1 +
 5 files changed, 30 insertions(+), 3 deletions(-)

diff --git a/include/command_line/arg.h b/include/command_line/arg.h
index 72a962b..2797cf8 100644
--- a/include/command_line/arg.h
+++ b/include/command_line/arg.h
@@ -96,6 +96,11 @@ class Arg {
     return is_provided_;
   }
 
+  /** Does this argument have a default? */
+  bool has_default() const {
+    return has_default_;
+  }
+
   /** Prints the value of an arg */
   virtual void debug(std::ostream& os) const = 0;
 
@@ -110,7 +115,7 @@ class Arg {
   };
 
   /** An arg must be assigned at least one alias */
-  Arg(const std::string& opt) : is_provided_(false) {
+  Arg(const std::string& opt) : is_provided_(false), has_default_(false) {
     alternate(opt);
     usage("");
     description("(no description provided)");
@@ -182,6 +187,11 @@ class Arg {
     required_ = val;
   }
 
+  /** Reset whether this argument has a default. */
+  void set_has_default(const bool val = true) {
+    has_default_ = val;
+  }
+
   /** Indicate that this argument has been set now. */
   void set_provided() {
     is_provided_ = true;
@@ -203,6 +213,8 @@ class Arg {
   bool required_;
   /** Has this argument been provided in some way? */
   bool is_provided_;
+  /** Does this argument have a default? */
+  bool has_default_;
 };
 
 } // namespace cpputil
diff --git a/include/command_line/command_line_config.h b/include/command_line/command_line_config.h
index a790027..6e705d2 100644
--- a/include/command_line/command_line_config.h
+++ b/include/command_line/command_line_config.h
@@ -41,11 +41,9 @@ class CommandLineConfig {
                   .description("Print program arguments and quit");
     auto& read_config = ValueArg<std::string>::create("config")
                         .usage("<path/to/file.conf>")
-                        .default_val("")
                         .description("Read program args from a configuration file");
     auto& write_config = ValueArg<std::string>::create("example_config")
                          .usage("<path/to/file.conf>")
-                         .default_val("")
                          .description("Print an example configuration file");
 
     if (sort_args) {
@@ -94,6 +92,7 @@ class CommandLineConfig {
     auto missing_arg = false;
     for (auto it = Args::arg_begin(); it != Args::arg_end(); ++it) {
       auto arg = *it;
+      assert(!(arg->is_required() && arg->has_default()) && "Arguments cannot be both required and have a default.");
       if (arg->is_required() && !arg->has_been_provided()) {
         if (!missing_arg) {
           std::cerr << "Errors:" << std::endl;
@@ -209,6 +208,19 @@ class CommandLineConfig {
         (*a)->description(wrap);
         wrap << std::endl;
 
+        // try to print the default value
+        if ((*a)->has_default()) {
+          std::ostringstream ss;
+          (*a)->debug(ss);
+          auto default_val = ss.str();
+          if (default_val.find("\n") == std::string::npos) {
+            // only show default argument if the default does not take more than one line
+            wrap << "Default: " << default_val << std::endl;
+          }
+        } else if ((*a)->is_required()) {
+          wrap << "Required argument" << std::endl;
+        }
+
         ofs.filter().unindent(2);
       }
       ofs << std::endl;
diff --git a/include/command_line/file_arg.h b/include/command_line/file_arg.h
index d204bfb..7eebd75 100644
--- a/include/command_line/file_arg.h
+++ b/include/command_line/file_arg.h
@@ -82,6 +82,7 @@ class FileArg : public Arg {
 
   /** Resets arg default value */
   FileArg& default_val(const T& t) {
+    set_has_default();
     val_ = t;
     return *this;
   }
diff --git a/include/command_line/folder_arg.h b/include/command_line/folder_arg.h
index d1377a4..9b50b6d 100644
--- a/include/command_line/folder_arg.h
+++ b/include/command_line/folder_arg.h
@@ -112,6 +112,7 @@ class FolderArg : public Arg {
 
   /** Resets arg default value */
   FolderArg& default_val(const std::vector<T>& t) {
+    set_has_default();
     val_ = t;
     return *this;
   }
diff --git a/include/command_line/value_arg.h b/include/command_line/value_arg.h
index d42ef13..1a50cad 100644
--- a/include/command_line/value_arg.h
+++ b/include/command_line/value_arg.h
@@ -77,6 +77,7 @@ class ValueArg : public Arg {
 
   /** Resets arg default value */
   ValueArg& default_val(const T& t) {
+    set_has_default();
     val_ = t;
     return *this;
   }

From d13efddd1ac19d6e7aea8d87d061c3bd58f2bfd0 Mon Sep 17 00:00:00 2001
From: eric <eric.schkufza@gmail.com>
Date: Tue, 2 Dec 2014 17:06:41 -0800
Subject: [PATCH 13/23] Prefix io filter.

---
 examples/Makefile     |  1 +
 examples/io/prefix.cc | 31 ++++++++++++++++++++++++++
 include/io/prefix.h   | 51 +++++++++++++++++++++++++++++++++++++++++++
 3 files changed, 83 insertions(+)
 create mode 100644 examples/io/prefix.cc
 create mode 100644 include/io/prefix.h

diff --git a/examples/Makefile b/examples/Makefile
index d62d413..b47f664 100644
--- a/examples/Makefile
+++ b/examples/Makefile
@@ -30,6 +30,7 @@ EX  = command_line/command_line \
 			io/indent \
 			io/line_comment \
 			io/multistream \
+			io/prefix \
 			io/redact \
 			io/redirectstream \
 			io/shunt \
diff --git a/examples/io/prefix.cc b/examples/io/prefix.cc
new file mode 100644
index 0000000..07ffa19
--- /dev/null
+++ b/examples/io/prefix.cc
@@ -0,0 +1,31 @@
+// Copyright 2014 eric schkufza
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+//     http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+#include <iostream>
+#include <string>
+
+#include "include/io/filterstream.h"
+#include "include/io/prefix.h"
+
+using namespace cpputil;
+using namespace std;
+
+int main() {
+  ofilterstream<Prefix> os(cout);
+  os.filter().prefix("Hello world: ");
+
+	os << "This is" << endl << "a " << endl << "multi-line message" << endl;
+
+  return 0;
+}
diff --git a/include/io/prefix.h b/include/io/prefix.h
new file mode 100644
index 0000000..19081d9
--- /dev/null
+++ b/include/io/prefix.h
@@ -0,0 +1,51 @@
+// Copyright 2014 eric schkufza
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+//     http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+#ifndef CPPUTIL_INCLUDE_IO_PREFIX_H
+#define CPPUTIL_INCLUDE_IO_PREFIX_H
+
+#include <string>
+
+namespace cpputil {
+
+class Prefix {
+ public:
+  Prefix() : prefix_(""), pending_(true) { }
+
+	Prefix& prefix(const std::string& p) {
+		prefix_ = p;
+		return *this;
+	}
+
+  void operator()(std::streambuf* sb, char c) {
+		if (pending_) {
+			for (auto p : prefix_) {
+				sb->sputc(p);
+			}
+			pending_ = false;
+		}
+		if (c == '\n') {
+			pending_ = true;
+		}
+		sb->sputc(c);
+	}
+
+ private:
+	std::string prefix_;
+	bool pending_;
+};
+
+} // namespace cpputil
+
+#endif

From c6e707982646ec57c093d1e2cc397952177d3726 Mon Sep 17 00:00:00 2001
From: eric <eric.schkufza@gmail.com>
Date: Tue, 2 Dec 2014 17:36:55 -0800
Subject: [PATCH 14/23] Added abort filter.

---
 examples/Makefile    |  1 +
 examples/io/abort.cc | 31 +++++++++++++++++++++++++++++++
 include/io/abort.h   | 44 ++++++++++++++++++++++++++++++++++++++++++++
 3 files changed, 76 insertions(+)
 create mode 100644 examples/io/abort.cc
 create mode 100644 include/io/abort.h

diff --git a/examples/Makefile b/examples/Makefile
index b47f664..817dc2b 100644
--- a/examples/Makefile
+++ b/examples/Makefile
@@ -25,6 +25,7 @@ EX  = command_line/command_line \
 			container/maputil \
 			container/tokenizer \
 			debug/stl_print \
+			io/abort \
 			io/column \
 			io/filterstream \
 			io/indent \
diff --git a/examples/io/abort.cc b/examples/io/abort.cc
new file mode 100644
index 0000000..60a30fd
--- /dev/null
+++ b/examples/io/abort.cc
@@ -0,0 +1,31 @@
+// Copyright 2014 eric schkufza
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+//     http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+#include <iostream>
+#include <string>
+
+#include "include/io/filterstream.h"
+#include "include/io/abort.h"
+
+using namespace cpputil;
+using namespace std;
+
+int main() {
+  ofilterstream<Abort> os(cout);
+  os.filter().code(1);
+
+	os << "You should see this..." << endl << "... but not this" << endl;
+
+  return 0;
+}
diff --git a/include/io/abort.h b/include/io/abort.h
new file mode 100644
index 0000000..12163c6
--- /dev/null
+++ b/include/io/abort.h
@@ -0,0 +1,44 @@
+// Copyright 2014 eric schkufza
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+//     http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+#ifndef CPPUTIL_INCLUDE_IO_ABORT_H
+#define CPPUTIL_INCLUDE_IO_ABORT_H
+
+#include <cstdlib>
+
+namespace cpputil {
+
+class Abort {
+ public:
+  Abort() : code_(0) { }
+
+	Abort& code(int c) {
+		code_ = c;
+		return *this;
+	}
+
+  void operator()(std::streambuf* sb, char c) {
+		sb->sputc(c);
+		if (c == '\n') {
+			exit(code_);
+		}
+	}
+
+ private:
+	int code_;
+};
+
+} // namespace cpputil
+
+#endif

From edaa3e66c5ab2f7791d206c05d66c6d1a545c494 Mon Sep 17 00:00:00 2001
From: eric <eric.schkufza@gmail.com>
Date: Tue, 2 Dec 2014 21:12:14 -0800
Subject: [PATCH 15/23] Added LineReader class.

---
 examples/Makefile               |  2 ++
 examples/serialize/line.cc      | 36 +++++++++++++++++++++++++++++++++
 include/serialize/line_reader.h | 34 +++++++++++++++++++++++++++++++
 include/serialize/text_style.h  |  7 ++++++-
 4 files changed, 78 insertions(+), 1 deletion(-)
 create mode 100644 examples/serialize/line.cc
 create mode 100644 include/serialize/line_reader.h

diff --git a/examples/Makefile b/examples/Makefile
index d62d413..75adfef 100644
--- a/examples/Makefile
+++ b/examples/Makefile
@@ -25,6 +25,7 @@ EX  = command_line/command_line \
 			container/maputil \
 			container/tokenizer \
 			debug/stl_print \
+			io/abort \
 			io/column \
 			io/filterstream \
 			io/indent \
@@ -41,6 +42,7 @@ EX  = command_line/command_line \
 			meta/indices \
 			patterns/singleton \
 			serialize/hex \
+			serialize/line \
 			serialize/text \
 			signal/debug_handler \
 			system/terminal
diff --git a/examples/serialize/line.cc b/examples/serialize/line.cc
new file mode 100644
index 0000000..52304c7
--- /dev/null
+++ b/examples/serialize/line.cc
@@ -0,0 +1,36 @@
+// Copyright 2014 eric schkufza
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+//     http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+#include <iostream>
+#include <sstream>
+#include <string>
+
+#include "include/serialize/line_reader.h"
+
+using namespace cpputil;
+using namespace std;
+
+int main() {
+	stringstream ss;
+	ss << "Line 1: You should see this." << endl;
+	ss << "Line 2: You shouldn't see this." << endl;
+
+	string s;
+	LineReader<> lr;
+	lr(ss, s);
+
+	cout << s << endl;
+
+  return 0;
+}
diff --git a/include/serialize/line_reader.h b/include/serialize/line_reader.h
new file mode 100644
index 0000000..f431cb5
--- /dev/null
+++ b/include/serialize/line_reader.h
@@ -0,0 +1,34 @@
+// Copyright 2014 eric schkufza
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+//     http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+#ifndef CPPUTIL_INCLUDE_SERIALIZE_LINE_READER_H
+#define CPPUTIL_INCLUDE_SERIALIZE_LINE_READER_H
+
+#include <iostream>
+#include <string>
+
+#include "include/serialize/text_style.h"
+
+namespace cpputil {
+
+template <typename Style = TextStyle<>>
+struct LineReader {
+	void operator()(std::istream& is, std::string& s) const {
+		getline(is, s, Style::eol());
+	}
+};
+
+} // namespace cpputil
+
+#endif
diff --git a/include/serialize/text_style.h b/include/serialize/text_style.h
index 5eca748..69c787a 100644
--- a/include/serialize/text_style.h
+++ b/include/serialize/text_style.h
@@ -18,7 +18,8 @@
 namespace cpputil {
 
 template <char Dec = true, size_t HexGroup = 8,
-          char Open = '{', char Close = '}', char Quote = '"', char Etc = '.'>
+          char Open = '{', char Close = '}', char Quote = '"', char Etc = '.',
+					char Eol = '\n'>
 struct TextStyle {
   static constexpr bool dec() {
     return Dec;
@@ -43,6 +44,10 @@ struct TextStyle {
   static constexpr char etc() {
     return Etc;
   }
+
+	static constexpr char eol() {
+		return Eol;
+	}
 };
 
 } // namespace cpputil

From 609f948eb0c713e2bd2b65d3f03bc2580641f6b7 Mon Sep 17 00:00:00 2001
From: Stefan Heule <stefanheule@gmail.com>
Date: Wed, 3 Dec 2014 01:35:05 -0800
Subject: [PATCH 16/23] Improve default printing in --help, and add an option
 to Args to not print defaults.

---
 include/command_line/args.h                | 15 ++++++++++++
 include/command_line/command_line_config.h | 27 +++++++++++++++++-----
 2 files changed, 36 insertions(+), 6 deletions(-)

diff --git a/include/command_line/args.h b/include/command_line/args.h
index 3b1f822..71202bf 100644
--- a/include/command_line/args.h
+++ b/include/command_line/args.h
@@ -46,6 +46,9 @@ class Args {
     std::vector<std::string> anonymous;
   };
 
+  /** Are defaults shown in the help? */
+  static bool show_defaults_;
+
  public:
   /** Iterator over registered args */
   typedef ArgRegistry::arg_iterator arg_iterator;
@@ -145,6 +148,16 @@ class Args {
     return Singleton<Parse>::get().anonymous.end();
   }
 
+  /** Set whether defaults are shown in the help. */
+  static void set_show_defaults(bool val) {
+    show_defaults_ = val;
+  }
+
+  /** Should defaults be shown in the help? */
+  static bool show_defaults() {
+    return show_defaults_;
+  }
+
   /** Sort arg groups */
   template <typename Comp>
   static void sort_groups(Comp c) {
@@ -238,6 +251,8 @@ class Args {
   }
 };
 
+bool Args::show_defaults_ = true;
+
 } // namespace cpputil
 
 #endif
diff --git a/include/command_line/command_line_config.h b/include/command_line/command_line_config.h
index 6e705d2..a50a878 100644
--- a/include/command_line/command_line_config.h
+++ b/include/command_line/command_line_config.h
@@ -194,13 +194,28 @@ class CommandLineConfig {
     ofilterstream<Indent> ofs(os);
     ofs.filter().indent();
 
+    auto show_defaults = Args::show_defaults();
+
     for (auto g = Args::group_begin(); g != Args::group_end(); ++g) {
       ofs << g->heading() << std::endl;
       ofs << std::endl;
       for (auto a = g->arg_begin(); a != g->arg_end(); ++a) {
+        std::string default_val;
+        bool short_default = false;
+
         write_arg(ofs, *a);
-        ofs << std::endl;
 
+        if (show_defaults && (*a)->has_default()) {
+          std::ostringstream ss;
+          (*a)->debug(ss);
+          default_val = ss.str();
+          if (default_val.length() < 20) {
+            short_default = true;
+            ofs << " (default: " << default_val << ")";
+          }
+        }
+
+        ofs << std::endl;
         ofs.filter().indent(2);
 
         ofilterstream<Wrap> wrap(ofs);
@@ -209,15 +224,15 @@ class CommandLineConfig {
         wrap << std::endl;
 
         // try to print the default value
-        if ((*a)->has_default()) {
-          std::ostringstream ss;
-          (*a)->debug(ss);
-          auto default_val = ss.str();
+        if (show_defaults && !short_default && (*a)->has_default()) {
           if (default_val.find("\n") == std::string::npos) {
             // only show default argument if the default does not take more than one line
             wrap << "Default: " << default_val << std::endl;
+          } else {
+            wrap << "Default: use --debug_args to see this default" << std::endl;
           }
-        } else if ((*a)->is_required()) {
+        }
+        if ((*a)->is_required()) {
           wrap << "Required argument" << std::endl;
         }
 

From 9dc6cc44baf7e0dd63a34f54f8fa344786968bb0 Mon Sep 17 00:00:00 2001
From: Stefan Heule <stefanheule@gmail.com>
Date: Wed, 3 Dec 2014 01:41:28 -0800
Subject: [PATCH 17/23] Fix compilation issue.

---
 include/command_line/args.h                | 15 ---------------
 include/command_line/command_line_config.h |  8 ++++----
 2 files changed, 4 insertions(+), 19 deletions(-)

diff --git a/include/command_line/args.h b/include/command_line/args.h
index 71202bf..3b1f822 100644
--- a/include/command_line/args.h
+++ b/include/command_line/args.h
@@ -46,9 +46,6 @@ class Args {
     std::vector<std::string> anonymous;
   };
 
-  /** Are defaults shown in the help? */
-  static bool show_defaults_;
-
  public:
   /** Iterator over registered args */
   typedef ArgRegistry::arg_iterator arg_iterator;
@@ -148,16 +145,6 @@ class Args {
     return Singleton<Parse>::get().anonymous.end();
   }
 
-  /** Set whether defaults are shown in the help. */
-  static void set_show_defaults(bool val) {
-    show_defaults_ = val;
-  }
-
-  /** Should defaults be shown in the help? */
-  static bool show_defaults() {
-    return show_defaults_;
-  }
-
   /** Sort arg groups */
   template <typename Comp>
   static void sort_groups(Comp c) {
@@ -251,8 +238,6 @@ class Args {
   }
 };
 
-bool Args::show_defaults_ = true;
-
 } // namespace cpputil
 
 #endif
diff --git a/include/command_line/command_line_config.h b/include/command_line/command_line_config.h
index a50a878..2fef79c 100644
--- a/include/command_line/command_line_config.h
+++ b/include/command_line/command_line_config.h
@@ -32,7 +32,7 @@ namespace cpputil {
 class CommandLineConfig {
  public:
   /** Strict parse with help, config, and debug support */
-  static void strict_with_convenience(int argc, char** argv, bool sort_args = false) {
+  static void strict_with_convenience(int argc, char** argv, bool sort_args = false, bool show_defaults_in_Help = true) {
     Heading::create("Help and argument utilities:");
     auto& help = FlagArg::create("h")
                  .alternate("help")
@@ -57,7 +57,7 @@ class CommandLineConfig {
       std::cout << std::endl;
       std::cout << "Usage: " << argv[0] << " [options]" << std::endl;
       std::cout << std::endl;
-      write_help(std::cout);
+      write_help(std::cout, show_defaults_in_Help);
       exit(0);
     }
 
@@ -190,11 +190,11 @@ class CommandLineConfig {
   }
 
   /** Prints arg aliases, usages, and descriptions */
-  static void write_help(std::ostream& os) {
+  static void write_help(std::ostream& os, bool show_defaults_in_Help) {
     ofilterstream<Indent> ofs(os);
     ofs.filter().indent();
 
-    auto show_defaults = Args::show_defaults();
+    auto show_defaults = show_defaults_in_Help;
 
     for (auto g = Args::group_begin(); g != Args::group_end(); ++g) {
       ofs << g->heading() << std::endl;

From 6a30f2e55769a9360c33e37902143e4248fb8615 Mon Sep 17 00:00:00 2001
From: Stefan Heule <stefanheule@gmail.com>
Date: Wed, 3 Dec 2014 02:08:04 -0800
Subject: [PATCH 18/23] minor fix

---
 include/command_line/command_line_config.h | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/include/command_line/command_line_config.h b/include/command_line/command_line_config.h
index 2fef79c..5ffb2ed 100644
--- a/include/command_line/command_line_config.h
+++ b/include/command_line/command_line_config.h
@@ -202,6 +202,7 @@ class CommandLineConfig {
       for (auto a = g->arg_begin(); a != g->arg_end(); ++a) {
         std::string default_val;
         bool short_default = false;
+        bool default_has_newline = false;
 
         write_arg(ofs, *a);
 
@@ -209,7 +210,9 @@ class CommandLineConfig {
           std::ostringstream ss;
           (*a)->debug(ss);
           default_val = ss.str();
-          if (default_val.length() < 20) {
+          if (default_val.find("\n") != std::string::npos) {
+            default_has_newline = true;
+          } else if (default_val.length() < 20) {
             short_default = true;
             ofs << " (default: " << default_val << ")";
           }
@@ -225,7 +228,7 @@ class CommandLineConfig {
 
         // try to print the default value
         if (show_defaults && !short_default && (*a)->has_default()) {
-          if (default_val.find("\n") == std::string::npos) {
+          if (!default_has_newline) {
             // only show default argument if the default does not take more than one line
             wrap << "Default: " << default_val << std::endl;
           } else {

From 6c7ad1a063014f87c2055bf4dbda91df6825836e Mon Sep 17 00:00:00 2001
From: Stefan Heule <stefanheule@gmail.com>
Date: Wed, 3 Dec 2014 12:07:05 -0800
Subject: [PATCH 19/23] don't show overly long defaults

---
 include/command_line/command_line_config.h | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/include/command_line/command_line_config.h b/include/command_line/command_line_config.h
index 5ffb2ed..25f83c0 100644
--- a/include/command_line/command_line_config.h
+++ b/include/command_line/command_line_config.h
@@ -228,7 +228,7 @@ class CommandLineConfig {
 
         // try to print the default value
         if (show_defaults && !short_default && (*a)->has_default()) {
-          if (!default_has_newline) {
+          if (!default_has_newline && default_val.length() < 150) {
             // only show default argument if the default does not take more than one line
             wrap << "Default: " << default_val << std::endl;
           } else {

From dd1da45f8d240a3f445cd5c4fe2762e4355c213a Mon Sep 17 00:00:00 2001
From: eric <eric.schkufza@gmail.com>
Date: Thu, 4 Dec 2014 14:05:28 -0800
Subject: [PATCH 20/23] Bit-twiddling hack where we don't have intrinsics.

---
 include/bits/bit_manip.h | 25 +++++++++++++++++++------
 1 file changed, 19 insertions(+), 6 deletions(-)

diff --git a/include/bits/bit_manip.h b/include/bits/bit_manip.h
index 084b687..77a1826 100644
--- a/include/bits/bit_manip.h
+++ b/include/bits/bit_manip.h
@@ -16,9 +16,8 @@
 #define CPPUTIL_INCLUDE_BITS_BIT_MANIP_H
 
 #include <cassert>
-#include <stdint.h>
-
 #include <immintrin.h>
+#include <stdint.h>
 
 namespace cpputil {
 
@@ -32,8 +31,16 @@ class BitManip<uint64_t> {
 #ifdef __BMI__
     return _tzcnt_u64(x);
 #else
-    assert(false);
-    return 0;
+	// See https://graphics.stanford.edu/~seander/bithacks.html
+	uint64_t res = 64; 
+	x &= -((int64_t)x);
+	if (x) res--;
+	if (x & 0x0000ffff0000ffff) res -= 16;
+	if (x & 0x00ff00ff00ff00ff) res -= 8;
+	if (x & 0x0f0f0f0f0f0f0f0f) res -= 4;
+	if (x & 0x3333333333333333) res -= 2;
+	if (x & 0x5555555555555555) res -= 1;
+	return res;
 #endif
   }
 
@@ -41,8 +48,14 @@ class BitManip<uint64_t> {
 #ifdef __POPCNT__
 		return _popcnt64(x);
 #else
-		assert(false);
-		return 0;
+	// See https://graphics.stanford.edu/~seander/bithacks.html
+	uint64_t res = x - ((x >> 1) & 0x5555555555555555);
+	res = ((res >> 2) & 0x3333333333333333) + (res & 0x3333333333333333);
+	res = ((res >> 4) + res) & 0x0f0f0f0f0f0f0f0f;
+	res = ((res >> 8) + res) & 0x00ff00ff00ff00ff;
+	res = ((res >> 16) + res) & 0x0000ffff0000ffff;
+	res = ((res >> 32) + res) & 0x00000000ffffffff;
+	return res;
 #endif
 	}
 

From 68b65edf7388cc595534985be2dc94a5f2f537e1 Mon Sep 17 00:00:00 2001
From: eric <eric.schkufza@gmail.com>
Date: Thu, 4 Dec 2014 16:54:00 -0800
Subject: [PATCH 21/23] Think that should fix the ntz bugs.

---
 include/bits/bit_manip.h | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/include/bits/bit_manip.h b/include/bits/bit_manip.h
index 77a1826..63968c0 100644
--- a/include/bits/bit_manip.h
+++ b/include/bits/bit_manip.h
@@ -29,12 +29,13 @@ class BitManip<uint64_t> {
  public:
   static size_t ntz(uint64_t x) {
 #ifdef __BMI__
-    return _tzcnt_u64(x);
+    return __builtin_ctzll(x);
 #else
 	// See https://graphics.stanford.edu/~seander/bithacks.html
 	uint64_t res = 64; 
 	x &= -((int64_t)x);
 	if (x) res--;
+	if (x & 0x00000000ffffffff) res -= 32;
 	if (x & 0x0000ffff0000ffff) res -= 16;
 	if (x & 0x00ff00ff00ff00ff) res -= 8;
 	if (x & 0x0f0f0f0f0f0f0f0f) res -= 4;
@@ -46,7 +47,7 @@ class BitManip<uint64_t> {
 
 	static size_t pop_count(uint64_t x) {
 #ifdef __POPCNT__
-		return _popcnt64(x);
+		return __builtin_popcountll(x);
 #else
 	// See https://graphics.stanford.edu/~seander/bithacks.html
 	uint64_t res = x - ((x >> 1) & 0x5555555555555555);

From 154a5cd5699f212f7e925367c81f87218d08741b Mon Sep 17 00:00:00 2001
From: "Berkeley Churchill (on mrwhite)" <berkeley@berkeleychurchill.com>
Date: Sun, 7 Dec 2014 20:24:32 -0800
Subject: [PATCH 22/23] Potential fix for #20, needs testing

---
 include/command_line/file_arg.h   | 2 +-
 include/command_line/folder_arg.h | 2 +-
 include/command_line/value_arg.h  | 2 +-
 include/container/bit_string.h    | 6 +++---
 4 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/include/command_line/file_arg.h b/include/command_line/file_arg.h
index 3d0cf09..1147c3a 100644
--- a/include/command_line/file_arg.h
+++ b/include/command_line/file_arg.h
@@ -35,7 +35,7 @@ class FileArg : public Arg {
 
   /** Consumes indices from first alias to next - */
   virtual std::pair<size_t, size_t> read(int argc, char** argv) {
-    for (const auto i : get_appearances(argc, argv)) {
+    for (const int i : get_appearances(argc, argv)) {
       if (i == (argc - 1) || argv[i + 1][0] == '-') {
         error(parse_error_);
         return std::make_pair(i, i);
diff --git a/include/command_line/folder_arg.h b/include/command_line/folder_arg.h
index 16d2c7d..306beae 100644
--- a/include/command_line/folder_arg.h
+++ b/include/command_line/folder_arg.h
@@ -43,7 +43,7 @@ class FolderArg : public Arg {
 
   /** Consumes indices from first alias to next - */
   virtual std::pair<size_t, size_t> read(int argc, char** argv) {
-    for (const auto i : get_appearances(argc, argv)) {
+    for (const int i : get_appearances(argc, argv)) {
       if (i == (argc - 1) || argv[i + 1][0] == '-') {
         error(parse_error_);
         return std::make_pair(i, i);
diff --git a/include/command_line/value_arg.h b/include/command_line/value_arg.h
index 7b99d8e..4456f19 100644
--- a/include/command_line/value_arg.h
+++ b/include/command_line/value_arg.h
@@ -35,7 +35,7 @@ class ValueArg : public Arg {
 
   /** Consumes indices from first alias to next - */
   virtual std::pair<size_t, size_t> read(int argc, char** argv) {
-    for (const auto i : get_appearances(argc, argv)) {
+    for (const int i : get_appearances(argc, argv)) {
       if (i == (argc - 1) || argv[i + 1][0] == '-') {
         error(parse_error_);
         return std::make_pair(i, i);
diff --git a/include/container/bit_string.h b/include/container/bit_string.h
index 804c620..f6b76e7 100644
--- a/include/container/bit_string.h
+++ b/include/container/bit_string.h
@@ -510,7 +510,7 @@ class BitString {
 
   /** Bit-wise and. */
   BitString& operator&=(const BitString& rhs) {
-    auto i = 0;
+    size_t i = 0;
 
 #if defined(__AVX2__) && defined(__AVX__)
     for (; i + 4 <= contents_.size(); i += 4) {
@@ -546,7 +546,7 @@ class BitString {
 
   /** Bit-wise or. */
   BitString& operator|=(const BitString& rhs) {
-    auto i = 0;
+    size_t i = 0;
 
 #if defined(__AVX2__) && defined(__AVX__)
     for (; i + 4 <= contents_.size() ; i += 4) {
@@ -582,7 +582,7 @@ class BitString {
 
   /** Bit-wise xor. */
   BitString& operator^=(const BitString& rhs) {
-    auto i = 0;
+    size_t i = 0;
 
 #if defined(__AVX2__) && defined(__AVX__)
     for (; i + 4 <= contents_.size() ; i += 4) {

From 20c8d05d8afd586180e6a88a3f11ed286d949ba3 Mon Sep 17 00:00:00 2001
From: Stefan Heule <stefanheule@gmail.com>
Date: Mon, 5 Jan 2015 14:27:35 -0800
Subject: [PATCH 23/23] Fix --example_config when there are required arguments.

---
 include/command_line/command_line_config.h | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/include/command_line/command_line_config.h b/include/command_line/command_line_config.h
index 25f83c0..0bb0c0b 100644
--- a/include/command_line/command_line_config.h
+++ b/include/command_line/command_line_config.h
@@ -89,6 +89,16 @@ class CommandLineConfig {
       exit(0);
     }
 
+    if (write_config.value() != "") {
+      std::ofstream ofs(write_config.value());
+      if (!ofs.is_open()) {
+        std::cerr << "Unable to write config file!" << std::endl;
+        exit(1);
+      }
+      write_config_file(ofs, argv[0]);
+      exit(0);
+    }
+
     auto missing_arg = false;
     for (auto it = Args::arg_begin(); it != Args::arg_end(); ++it) {
       auto arg = *it;
@@ -104,16 +114,6 @@ class CommandLineConfig {
     if (missing_arg) {
       exit(1);
     }
-
-    if (write_config.value() != "") {
-      std::ofstream ofs(write_config.value());
-      if (!ofs.is_open()) {
-        std::cerr << "Unable to write config file!" << std::endl;
-        exit(1);
-      }
-      write_config_file(ofs, argv[0]);
-      exit(0);
-    }
   }
 
  private: