Merge pull request #409 from devosoft/bits_overhaul

Bits overhaul

.github/workflows/CI.yml

@@ -12,6 +12,7 @@ jobs:
     name: Tests
     runs-on: ubuntu-18.04
     strategy:
+      fail-fast: false
       matrix:
         cxx: [clang++, g++]
         test-set:

.gitignore

@@ -13,6 +13,7 @@
 *.wasm
 *.wast
 *-bak.cc
+*-bak.cpp
 *.dat
 *.exe
 *tmp.*
@@ -45,7 +46,7 @@ demos/Avida/Avida
 demos/Avida/web/Avida.js
 demos/Emphatic/Emphatic
 demos/Emphatic/examples/ConceptTest
-demos/Emphatic/examples/ConceptTest.cc
+demos/Emphatic/examples/ConceptTest.cpp
 demos/MABE/examples/NK
 demos/NK.bak/
 demos/NK/NK
@@ -69,6 +70,7 @@ demos/NK/Makefile
 demos/NK/source
 demos/NK/source/native
 demos/NK/source/NKWorld.h
+demos/NK/source/NKWorld.hpp
 demos/NK/source/web
 demos/NK/web/jquery-1.11.2.min.js
 demos/NK/web/NK.asm.js
@@ -77,12 +79,14 @@ demos/NK/web/NK.js.mem
 
 doc/doxygen/
 examples/*/*
+!examples/*/*.cc
 !examples/*/*.cpp
+!examples/*/*.h
 !examples/*/*.hpp
 !examples/*/*.html
 !examples/*/images
 !examples/*/Makefile
-examples/timing/short_strings.html
+!examples/timing/BENCHMARKS
 
 tests/*.csv
 tests/StatsConfig.cfg

Dockerfile

@@ -1,5 +1,5 @@
 # Pull base image.
-FROM ubuntu:18.04
+FROM ubuntu:bionic-20210416
 
 COPY . /opt/Empirical
 
@@ -21,7 +21,16 @@ RUN \
 # Install apt packages
 # xvfb nonsense adapted from https://github.com/samgiles/docker-xvfb
 # remove -backports, -updates, -proposed, -security repositories
+# looks like we have to grab libxxhash0 from -updates now
 RUN \
+  apt-get update -y \
+    && \
+  apt-get install --no-install-recommends libxxhash0 \
+    && \
+  apt-get clean \
+    && \
+  rm -rf /var/lib/apt/lists/* \
+    && \
   find /etc/apt -type f -name '*.list' -exec sed -i 's/\(^deb.*-backports.*\)/#\1/; s/\(^deb.*-updates.*\)/#\1/; s/\(^deb.*-proposed.*\)/#\1/; s/\(^deb.*-security.*\)/#\1/' {} + \
     && \
   apt-get update -y \

demos/EasyChair/ProcessReviews.cpp

@@ -0,0 +1,324 @@
+#include <iostream>
+#include <sstream>
+#include <string>
+
+#include "../../include/emp/base/vector.hpp"
+#include "../../include/emp/io/File.hpp"
+#include "../../include/emp/tools/string_utils.hpp"
+
+
+///////////////////////
+//  ReviewInfo
+///////////////////////
+
+struct ReviewInfo
+{
+  bool is_meta = false;
+  std::string reviewer_name = "";
+
+  // scores (only overall used for meta-reviews)
+  int overall = 0;
+  int novelty = 0;
+  int writing = 0;
+  int lit_review = 0;
+  int methods = 0;
+  int relevance = 0;
+  int quality = 0;
+  int confidence = 0;
+
+  void Write(std::ostream & os=std::cout) const {
+    if (is_meta) {
+      os << "METAREVIEW by " << reviewer_name << ": ";
+      if (overall == -1) os << "reject\n";
+      if (overall == 0) os << "UNDECIDED\n";
+      else os << "accept!\n";
+    }
+    else {
+      os << "REVIEW by " << reviewer_name << ":\n";
+      os << " Overall evaluation: " << overall << std::endl;
+      os << " Novelty/Originality: " << novelty << std::endl;
+      os << " Writing Clarity: " << writing << std::endl;
+      os << " Thoroughness of Literature Review: " << lit_review << std::endl;
+      os << " Thoroughness of Methods: " << methods << std::endl;
+      os << " Relevance to Artificial Life Conference: " << relevance << std::endl;
+      os << " Overall Quality of Work: " << quality << std::endl;
+      os << " Reviewer's confidence: " << confidence << std::endl;
+    }
+  }
+
+  void WriteCSV(std::ostream & os=std::cout) const {
+    os << "\"" << reviewer_name << "\"," << overall;
+    if (!is_meta) {
+      os << "," << novelty
+         << "," << writing
+         << "," << lit_review
+         << "," << methods
+         << "," << relevance
+         << "," << quality
+         << "," << confidence;
+    }
+  }
+
+  static void WriteCSVMetaHeaders(std::ostream & os=std::cout) {
+    os << "Metareviewer,Recommendation";
+  }
+
+  static void WriteCSVHeaders(std::ostream & os=std::cout) {
+    os << "Reviewer,Overall"
+        << ",Novelty"
+        << ",Writing"
+        << ",Lit Review"
+        << ",Methods"
+        << ",Eelevance"
+        << ",Quality"
+        << ",Confidence";
+  }
+};
+
+
+///////////////////////
+//  PaperInfo
+///////////////////////
+
+struct PaperInfo
+{
+  int id = -1;
+  std::string title = "";
+  emp::vector<std::string> authors;
+  ReviewInfo meta_review;
+  emp::vector<ReviewInfo> reviews;
+  std::string session = "";
+  std::string presentation = "";   // Type of presentation requested.
+  size_t length = 0;
+
+  void SetAuthors(std::string in_authors) {
+    authors = emp::slice(in_authors, ',');
+
+    // Check to see if we need to split the last one.
+    size_t split_pos = authors.back().find(" and ");
+    if (split_pos != std::string::npos) {
+      std::string last_author = authors.back().substr(split_pos+5);
+      authors.back().resize(split_pos);
+      authors.push_back(last_author);
+    }
+
+    // Remove all spaces at the beginning and end of author's names.
+    for (std::string & author : authors) emp::justify(author);
+  }
+
+  std::string GetAuthors() const {
+    std::stringstream ss;
+    ss << authors[0];
+    for (size_t i = 1; i < authors.size(); i++) {
+      ss << ", " << authors[i];
+    }
+    return ss.str();
+  }
+
+  void Write(std::ostream & os=std::cout) const {
+    os << "PAPER ID: " << id << std::endl
+       << "AUTHORS:  " << GetAuthors() << std::endl
+       << "TITLE:    " << title << std::endl;
+    meta_review.Write(os);
+    for (const ReviewInfo & review : reviews) {
+      review.Write(os);
+    }
+    os << std::endl;
+  }
+
+  void WriteCSV(std::ostream & os=std::cout) const {
+    // One line for each review.
+    for (const ReviewInfo & review : reviews) {
+      os << id << ",\""
+         << GetAuthors() << "\",\""
+         << title << "\","
+         << length << ",\""
+         << presentation << "\",\""
+         << session << "\",";
+      meta_review.WriteCSV(os);
+      os << ",";
+      review.WriteCSV(os);
+      os << "\n";
+    }
+  }
+
+  void WriteCSVHeaders(std::ostream & os=std::cout) const {
+    os << "Paper ID,Authors,Title,Length,Presentation,Session,";
+    ReviewInfo::WriteCSVMetaHeaders(os);
+    os << ",";
+    ReviewInfo::WriteCSVHeaders(os);
+    os << std::endl;
+  }
+};
+
+
+///////////////////////
+//  PaperSet
+///////////////////////
+
+struct PaperSet {
+  emp::vector<PaperInfo> papers;
+  size_t cur_line = 0;             // File line being processed.
+  int cur_id = -1;                 // Current paper being setup.
+
+  PaperSet(const std::string & review_filename, const std::string & catagory_filename)
+  {
+    ProcessReviewFile(review_filename);
+    ProcessCatagoryFile(catagory_filename);
+  }
+
+  // For the moment, summaries are not used - just fast-forward.
+  void ProcessSummary(const emp::File & file) {
+    // Summary mode ends with an empty line.
+    while (file[cur_line] != "") cur_line++;
+  }
+
+  // Process details about a meta-review
+  void ProcessMeta(const emp::File & file) {
+    const std::string & line = file[cur_line++];
+    ReviewInfo & info = papers[cur_id].meta_review;
+    info.is_meta = true;
+    info.reviewer_name = line.substr(23,line.size()-34);
+
+    // Collect recommendation result (-1 = decline, 0 = undecided, 1 = accept)
+    const std::string & result = file[cur_line++].substr(16);
+    if (result == "accept") info.overall = 1;
+    else if (result == "reject") info.overall = -1;
+    else info.overall = 0;
+
+    // Meta mode ends with an empty line.
+    while (file[cur_line] != "") cur_line++;
+  }
+
+  bool CheckRating(const std::string & line, const std::string & name, int & value) {
+    if (emp::has_prefix(line, name)) {
+      size_t pos = name.size() + 1;
+      value = emp::from_string<int>(emp::string_get_word(line, pos));
+      return true;
+    }
+    return false;
+  }
+
+  // Process details about a meta-review
+  void ProcessReview(const emp::File & file) {
+    const std::string & line = file[cur_line++];
+    papers[cur_id].reviews.push_back(ReviewInfo{});
+    ReviewInfo & info = papers[cur_id].reviews.back();
+    info.is_meta = false;
+    info.reviewer_name = line.substr(21,line.size()-32);
+
+    // Reviews end with an empty line.
+    while (file[cur_line] != "") {
+      CheckRating(file[cur_line], "Overall evaluation:", info.overall);
+      CheckRating(file[cur_line], "Novelty/Originality:", info.novelty);
+      CheckRating(file[cur_line], "Writing Clarity:", info.writing);
+      CheckRating(file[cur_line], "Thoroughness of Literature Review:", info.lit_review);
+      CheckRating(file[cur_line], "Thoroughness of Methods:", info.methods);
+      CheckRating(file[cur_line], "Relevance to Artificial Life Conference:", info.relevance);
+      CheckRating(file[cur_line], "Overall Quality of Work:", info.quality);
+      CheckRating(file[cur_line], "Reviewer's confidence:", info.confidence);
+
+      cur_line++;
+    }
+  }
+
+  void ProcessReviewFile(const std::string & filename) {
+    emp::File file(filename);
+
+    // Scan through the file, loading each review.
+    for (cur_line = 0; cur_line < file.size(); ++cur_line) {
+      std::string line = file[cur_line];
+
+      // New paper?
+      if (emp::has_prefix(line, "*********************** PAPER")) {
+        std::string id_string = emp::string_get_word(line, 30);
+        cur_id = emp::from_string<int>(id_string);
+        if (papers.size() <= (size_t) cur_id) papers.resize(cur_id+1);
+        papers[cur_id].id = cur_id;
+        continue;
+      }
+
+      // If we made it this far, we need to have an id.
+      emp_assert(cur_id >= 0);
+
+      if (emp::has_prefix(line, "AUTHORS:")) {
+        emp::string_pop_word(line);
+        papers[cur_id].SetAuthors(line);
+        continue;
+      }
+
+      if (emp::has_prefix(line, "TITLE:")) {
+        emp::string_pop_word(line);
+        papers[cur_id].title = line;
+        emp::justify(papers[cur_id].title);
+        continue;
+      }
+
+      // Is this a summary?
+      if (line == "================== SUMMARY OF REVIEWS =================") {
+        ProcessSummary(file);
+        continue;
+      }
+
+      // Is this a metareview?
+      if (emp::has_prefix(line, "++++++++++ METAREVIEW")) {
+        ProcessMeta(file);
+        continue;
+      }
+
+      // Is this a regular review?
+      if (emp::has_prefix(line, "++++++++++ REVIEW")) {
+        ProcessReview(file);
+        continue;
+      }
+    }
+  }
+
+  void ProcessCatagoryFile(const std::string & filename) {
+    emp::File file(filename);
+
+    // Skip the first line; process the rest.
+    for (size_t i=1; i < file.size(); i++) {
+      auto row = file.ViewRowSlices(i);
+      size_t id = emp::from_string<size_t>(row[0]);
+      if (row.size() > 4) papers[id].length = emp::from_string<size_t>(row[3]);
+      if (row.size() > 4) papers[id].presentation = row[4];
+      if (row.size() > 5) papers[id].session = row[5];
+    }
+  }
+
+  void Print() {
+    // Print the results...
+    for (const auto & paper : papers) {
+      if (paper.id < 0) continue;
+      paper.Write();
+    }
+  }
+
+  void PrintCVS() {
+    // Find the first review and use it to print the headers.
+    size_t first = 0;
+    while (papers[first].id < 0) first++;
+    papers[first].WriteCSVHeaders();
+
+    // Now print all of the actual reviews.
+    for (const auto & paper : papers) {
+      if (paper.id < 0) continue;
+      paper.WriteCSV();
+    }
+  }
+
+};
+
+int main(int argc, char * argv[])
+{
+  if (argc != 3) {
+    std::cerr << "Format: " << argv[0] << " [review filename] [catagory filename]\n";
+    exit(1);
+  }
+
+  std::string review_filename(argv[1]);
+  std::string catagory_filename(argv[2]);
+  PaperSet ps(review_filename, catagory_filename);
+  ps.PrintCVS();
+}