sync with upstream (#1)

* Add actual map size reporting. * Parse width and heights as ints. Fix test. * add verst to organizationWhitelist.txt * Update the description of quiet mode output. * Update organizationWhitelist.txt * Count number of workers down * Take apostrophe out of website * Limited # of characters accepted by getString() Limit presently set at 24000 * Put a random bot replay on intro halite * Update basics_intro_halite * Fixes to ErrorFilterCompiler * Fixed some networking bugs * Fixed env such that "boom.py" no longer breaks it * Fix to updateOrgs * Take out "Final map size:" * Require equality in worker tests * Update organizationWhitelists.txt Added my company name qure.ai to the whitelist. * Include xss script in electron visualizer. * Use a colorblind safe palatte for the visualizer. * Closes HaliteChallenge#347 * Add interview waiving note * Initial pull-mu-sigma with some related refactoring * Update README.md * Store the last 500,000 games * Update color palette after more feedback. * parsereplay.js indentation * Revert "Merge branch 'colorblind'" This reverts commit ca2b332, reversing changes made to f8aa93f. * One more visualizer color change. * Switch to lighter cyan. * Reinstate debugging disabled code. * Fix formatting. * Possible runaway crash bot fix. * Update advanced_third_party.php * Add in fix to sametine problem * Add num users * Add in num submissions * Revert "Add in num submissions" This reverts commit 8433141. * Revert "Add num users" This reverts commit 4ef3011. * Update organizationWhitelist.txt * Update INSTALL.md * Update third party list * Update titles * Small latency fix to tier picking * Update advanced_third_party.php * Replay file dumps and third party edits * Adding association window and capabilities * Add @nmalaguti's visualizer * Change numRows back practice * Add KalraA's new tutorial * Update organizationWhitelist.txt * Update advanced_third_party.php * Add number of coders on the homepage * try out an increase in memory * added -r for no replay, added -i for replay directory * added -r for no replay, added -i for replay directory * typo * Indentation * JS run fix * Make dummy data easier to deal with * Performance improvement for Java Starter Package: Got rid of object churn The current implementation of the java starter package has the disadvantage that it produces a lot of object churn mainly because the game map is re-created upon each turn. This commit prevents the object churn by creating the game map, locations, and sites once and updating them later on. * Changed replay to a new favorite * Changed default speed for homepage vis * Trying another color scheme * Colors (hopefully) fixed * popped out 1&4 * Dropped HaliteChallenge#11 * -i no longer requires lagging / and supports " * Killed light green * Center initial player positions in the visualizer. * Revert "Performance improvement for Java Starter Package: Got rid of object churn" * Update downloads.php * Initial inclusion of nmalaguti's extra visualizer graphs. * Adding Edinburgh to orgs * Fix vis fps bug Now limits to 20 when idle to decrease lag using <> and mouse when paused. * Make sponsor images smaller * Clear graphics before toggling extra graphs. * Force a render after clearing graphics before changing graphs. * Improve speed of game parsing. * Fix parsereplay.js's indentation * Scala starter package bug: Fix size parsing for unequal width/height Added utilities in Grid that I've found useful so far. * Performance improvement for Java Starter Package: Got rid of object churn The current implementation of the java starter package has the disadvantage that it produces a lot of object churn mainly because the game map is re-created upon each turn. This commit prevents the object churn by creating the game map, locations, and sites once and updating them later on. * Changed visibility of var production in Site from private to to public * Stop indirect mutation of gameMap. * Allow loading another replay after starting one in the local visualizers. * Update about.php * Update about.php * Typo * Make the cumulative graphs, cumulative on the final frame. * Make trueskill updates dependant on numSubmissions not changing. This should solve a race condition when a new submission comes in after a game has already been accepted but not yet had trueskill updated. * Fix visualizer maxHeight calculation when not using minimal display. * Leave space for the file select button. * Take scrimmage out of UI * Fully remove scrimmages from the UI * Take out unnecesary associate.php code * Force associate on sign up * Bump up worker limit * Add levels to leaderboard * Take out currently unneeded scrimmage and high school code * Revert "Take out currently unneeded scrimmage and high school code" This reverts commit 6c43d76. * Remove currently unneeded scrimmage code * Fully remove scrimmages from the db * Remove unnecessary level logic * Take out bold associate styling * Add back j-clap's proper organization reporting * wait message * Fixes * Bump user to server ratio * Put level before org * Update associate.js * Adding University of Bordeaux * Added University of Bordeaux (student addresses) * Fix symlinks in visualizer/lib * add wargaming.net organization * Change Horace Mann name * Fix to updateOrgs.py * Adding UoE students forgot to include them before >.> * Fix extended graph off by one error. * Refining association page and adding an email request button * Revert "Revert "Add num users"" This reverts commit 515152a. * Default user value to prevent caching problems * Update end date * Bumped Init time to 30 sec * Add ./ to julia runGame.sh * Archive starter package julia fix * Fix * Hopefully fixes CI * Janzert CI fix * Make CI patch nicer * On the user page, always show if a bot errored in a game. * Add dash to error column * Eliminate error column in user page gamelist. * Show mark if any opponents error out of a game. * Add number of others that also errored out in tooltip. * Changed make.bat to @nmalaguti's * Moved back but modified... hoping for appveyor * added appveyor.yml * Perhaps fixed spacing? * Update appveyor.yml * Update appveyor.yml * Update appveyor.yml * Update appveyor.yml * Update appveyor.yml * Update appveyor.yml * Update make.bat * Update appveyor.yml * build * Changed Windows download to link to Appveyor * switched to static build * Updated version number [build] * Add Grand Valley State University to whitelist * add aqr to the whitelist * Return GameUser.versionNumber in api/web/game results. * Force ssh host key accept * Added derivco * Added Nerdery * Added URochester * End date clarification * Add another harvard email * Script to reset all user ranks and scores. * Add median mu and sigma to status page. * Stick with old stable phpunit that will work with php 5.6. * Use versioned filenamefor phpunit. * Changes to manager task api for finals. Add setting to stop game tasks being handed out. Add setting to change to uniform seeding for the finals. * Script to check for tasks completion. * Print out last gameID after all tasks completed. * Add option to close submissions in the web api. * Only display bot submit button when bot submissions are open. Also fixes config section name in WebsiteAPI.php for closing submissions. * Add alfred's suggestions * Add 'tentative' * More games allowed * Try bumped timeouts * Revert "Try bumped timeouts" This reverts commit f09e12c. * Add Erdman's Halite Lint to third party tools * Seed Players above 1000 * Add workerID to Game * Top 500 seed * We are now at 200 games; Limit finals to silver and above * Halite end note * Added Citi from email request
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diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -0,0 +1,46 @@
+# Halite Contributing Guide
+
+If you find a bug or have a feature request, please [open an issue](https://github.com/HaliteChallenge/Halite/issues/new).
+
+Want to help out? Have you implemented a patch or a new feature? Send us a pull request! If you are looking for things to do, check out [our open issues](https://github.com/HaliteChallenge/Halite/issues).
+
+## Common Contributions 
+
+### Writing a Starter Package
+
+If you'd like to write a starter package for a new language, see this [guide](https://halite.io/advanced_writing_sp.php).
+
+### Adding Your Company or University
+
+Edit [this whitelist](https://github.com/HaliteChallenge/Halite/edit/master/website/organizationWhitelist.txt) and send us a pull request. If you need to change your email, head [here](https://halite.io/email.php). We'll make sure to tag all members of your organization who have already signed up.
+
+## Folder Contents
+
+- `admin/` - A collection of administrative resources (ex. a technical specification)
+- `airesources/` - The language-specific starter kits for writing bots
+- `environment/` - The halite game engine 
+- `tests/` - All of the project's unit and integration tests
+- `website/` - The website that hosts the competition. Includes the API that manages the game servers.
+- `worker/` - The source for the worker servers that compile bots and run games safely
+
+## Installing the website on Ubuntu
+
+Clone the repo:
+
+    git clone https://github.com/HaliteChallenge/Halite.git
+
+Run the website install script with root user permissions. This will install php, apache, python (and some python modules), and composer (and some composer packages):
+
+    cd website; sudo ./install.sh
+
+Run the database install script with root user permissions. This will install mysql and insert our schema into a database titled Halite.
+
+    cd sql; sudo ./install.sh
+
+Create a `halite.ini` file using your favorite text editor in the root project directory. Place information about your local database setup in there. Your `halite.ini` file should look like this;
+
+    [database]
+    hostname = 127.0.0.1 
+    username = YOUR_LOCAL_MYSQL_USERNAME
+    password = YOUR_LOCAL_MYSQL_PASSWORD
+    name = Halite
diff --git a/README.md b/README.md
@@ -5,23 +5,16 @@
 
 Halite is a programming competition. Contestants write bots to play an original multi-player turn-based strategy game played on a rectangular grid. For more information about the game, visit [our website](http://halite.io).
 
-## Folder Contents
-
-- `admin/` - A collection of administrative resources (ex. a technical specification)
-- `airesources/` - The language-specific starter kits for writing bots
-- `environment/` - The halite game engine 
-- `tests/` - All of the project's unit and integration tests
-- `website/` - The website that hosts the competition. Includes the API that manages the game servers.
-- `worker/` - The source for the worker servers that compile bots and run games safely
-
 ## Contributing
 
-If you find a bug or have a feature request, please [open an issue](https://github.com/HaliteChallenge/Halite/issues/new).
+See [the Contributing Guide](CONTRIBUTING.md).
+
+## Questions
 
-Want to help out? Have you implemented a patch or a new feature? Send us a pull request! If you are looking for things to do, check out [our open issues](https://github.com/HaliteChallenge/Halite/issues).
+See [the Forums](http://forums.halite.io) and [our Discord chat](https://discordapp.com/invite/rbVDB4n).
 
-If you'd like to write a starter package for a new language, see this [guide](https://halite.io/advanced_writing_sp.php).
+## Authors
 
-### Authors
+Halite was primarily created by [Ben Spector](https://github.com/Sydriax) and [Michael Truell](https://github.com/truell20) for Two Sigma during their summer 2016 internship. 
 
-Halite was primarily created by [Ben Spector](https://github.com/Sydriax) and [Michael Truell](https://github.com/truell20) for Two Sigma during their summer 2016 internship. However, many others contributed to Halite's developement, including [Matt Adereth](https://github.com/adereth) and [Trammell Hudson](https://github.com/osresearch) from Two Sigma and [Arnaud Sahuguet](https://github.com/sahuguet) and [Scot Spinner](https://github.com/awesomescot) from Cornell Tech.
+Many others contributed to Halite's developement, including [Matt Adereth](https://github.com/adereth), [Trammell Hudson](https://github.com/osresearch), and Jaques Clapauch from Two Sigma and [Arnaud Sahuguet](https://github.com/sahuguet) and [Scot Spinner](https://github.com/awesomescot) from Cornell Tech. Halite's participants, including [Nick Malaguti](https://github.com/nmalaguti), [Travis Erdman](https://github.com/erdman), and [Janzert](https://github.com/janzert), have also been instrumental to the project.
diff --git a/admin/checkTaskCompletion.py b/admin/checkTaskCompletion.py
@@ -0,0 +1,62 @@
+#!/usr/bin/env python3
+
+import configparser
+import time
+from datetime import datetime
+
+import pymysql
+
+parser = configparser.ConfigParser()
+parser.read("../halite.ini")
+
+DB_CONFIG = parser["database"]
+
+def check_compiles(db):
+    db.begin()
+    with db.cursor() as cursor:
+        cursor.execute("SELECT COUNT(*) FROM User WHERE compileStatus != 0")
+        return cursor.fetchone()['COUNT(*)']
+
+def check_workers(db, start_time):
+    db.begin()
+    with db.cursor() as cursor:
+        cursor.execute("SELECT workerID, lastRequestTime FROM Worker ORDER BY workerID")
+        workers = cursor.fetchall()
+    waiting = list()
+    for w in workers:
+        if w["lastRequestTime"] < start_time:
+            waiting.append(w)
+    return waiting
+
+def main():
+    if ("compState" not in parser or "noGameTasks" not in parser["compState"] or
+            not parser["compState"]["noGameTasks"]):
+        print(parser["compState"]["noGameTasks"])
+        print("Game tasks still activated. Disable in halite.ini [compState] noGameTasks")
+        return
+    start_time = datetime.now()
+    db = pymysql.connect(host=DB_CONFIG['hostname'], user=DB_CONFIG['username'], passwd=DB_CONFIG['password'], db=DB_CONFIG['name'], cursorclass=pymysql.cursors.DictCursor)
+
+    compiles = 1
+    workers = [1]
+    while compiles or workers:
+        compiles = check_compiles(db)
+        workers = check_workers(db, start_time)
+        if compiles:
+            print("Waiting for %d more compiles to complete." % (compiles,))
+        if workers:
+            print("Waiting for workers: ", end="")
+            print(", ".join(str(w["workerID"]) for w in workers[:5]), end="")
+            if len(workers) > 5:
+                print(" and %d more" % (len(workers) - 5,))
+            else:
+                print()
+        time.sleep(5)
+    db.begin()
+    with db.cursor() as cursor:
+        cursor.execute("SELECT MAX(gameID) FROM Game")
+        max_game = cursor.fetchone()["MAX(gameID)"]
+    print("All tasks completed, last gameID %d." % (max_game,))
+
+if __name__ == "__main__":
+    main()
diff --git a/admin/commandRunner.py b/admin/commandRunner.py
@@ -7,7 +7,7 @@
 
 def runOnWorker(worker, keyPath, command):
     print("########"+worker['ipAddress']+"########")
-    os.system("ssh -i \""+keyPath+"\" ubuntu@"+worker['ipAddress']+" '"+command+"'")
+    os.system("ssh -oStrictHostKeyChecking=no -i \""+keyPath+"\" ubuntu@"+worker['ipAddress']+" '"+command+"'")
     print("########"+worker['ipAddress']+"########")
 
 parser = configparser.ConfigParser()

diff --git a/admin/cron/workerChecker.py b/admin/cron/workerChecker.py
@@ -21,6 +21,4 @@
     print("All good!")
 else:
     message = "Some workers haven't communicated with the manager in a while!<br><br>"
-    for res in results:
-        message += "Worker with an id of "+str(res[0])+" and an api key "+str(res[1])+" hasn't contacted the manager for over 30 minutes.<br>"
-    haliteEmailer.sendEmail(HALITE_EMAIL, HALITE_EMAIL_PASSWORD, "WORKER ALERT", message, HALITE_EMAIL)
+    haliteEmailer.sendEmail(HALITE_EMAIL, HALITE_EMAIL_PASSWORD, str(len(results))+" workers down", message, HALITE_EMAIL)
diff --git a/admin/md/INSTALL.md b/admin/md/INSTALL.md
@@ -23,7 +23,6 @@ Finish Apache setup:
  * [Allow the following of symlinks by apache](http://superuser.com/questions/244245/how-do-i-get-apache-to-follow-symlinks)
  * [Allow .htaccess override](http://stackoverflow.com/a/22526144)
  * [Redirect root directory to website directory](http://serverfault.com/questions/9992/how-to-get-apache2-to-redirect-to-a-subdirectory)
- * Tell apache to forbid access to the storage/errors and storage/bots folders and to the halite.ini file
  * [Increase your max file upload size (worker's posting large replays, users posting big bot archives)](http://stackoverflow.com/questions/2184513/php-change-the-maximum-upload-file-size)
 
 To setup automatic backups on the website server, copy the `backupWebsite` file in the `Halite/website/cron` folder into the server's `/etc/cron.hourly` folder, change the IP address in the file to that of the backup server, and make sure that the ssh key of the website server is in the `~/.ssh/authorized_keys` file on the backup server. Once copied, mark the `backupWebsite` file as executable and give cron permission to execute it like so:

diff --git a/admin/rankReset.py b/admin/rankReset.py
@@ -0,0 +1,26 @@
+#!/usr/bin/env python3
+
+import configparser
+import pymysql
+
+parser = configparser.ConfigParser()
+parser.read("../halite.ini")
+
+DB_CONFIG = parser["database"]
+
+def main():
+    confirm = input("This will clear all current ranks, are you sure? [y/N] ")
+    if confirm != "y":
+        return
+    db = pymysql.connect(host=DB_CONFIG["hostname"], user=DB_CONFIG['username'], passwd=DB_CONFIG['password'], db=DB_CONFIG['name'], cursorclass=pymysql.cursors.DictCursor)
+    cursor = db.cursor()
+    cursor.execute("SELECT COUNT(*) FROM User WHERE isRunning=1")
+    num_active = cursor.fetchone()['COUNT(*)']
+    cursor.execute("INSERT INTO UserHistory (userID, versionNumber, lastRank, lastNumPlayers, lastNumGames) SELECT userID, numSubmissions, rank, %d, numGames FROM User WHERE isRunning=1" % (num_active,))
+    cursor.execute("UPDATE User SET numSubmissions=numSubmissions+1, numGames=0, mu=25.0, sigma=8.333 WHERE isRunning=1")
+    db.commit()
+    db.close()
+    print("All ranks successfully reset.")
+
+if __name__ == "__main__":
+    main()
diff --git a/admin/updateOrgs.py b/admin/updateOrgs.py
@@ -20,12 +20,15 @@
         continue
 
     realUserOrg = "Other"
-    emailDomain = user["email"].split("@")[1]
+    try:
+        emailDomain = user["email"].split("@")[1]
+    except:
+        pass
     for org in orgs:
         if emailDomain == org[1]:
             realUserOrg = org[0]
             break
-    if realUserOrg != "Other" and realUserOrg != user["organization"]:
-        print(user["organization"] + " " + realUserOrg)
+    if (realUserOrg != "Other" or user["organization"] == "") and realUserOrg != user["organization"]:
+        print("%s, %s, %s" % (realUserOrg, user["organization"], user["email"]))
         cursor.execute("update User set organization = '"+realUserOrg+"' where userID="+str(user["userID"]))
         db.commit()
diff --git a/airesources/C/MyBot.c b/airesources/C/MyBot.c
@@ -0,0 +1,36 @@
+#include <stdio.h>
+#include <stdlib.h>
+#include <time.h>
+
+#include "hlt.h"
+
+#define BOT_NAME "MyCBot"
+
+int main(void) {
+
+    GAME game;
+    int x, y, direction;
+
+    srand(time(NULL));
+
+    game = GetInit();
+    SendInit(BOT_NAME);
+
+    while (1) {
+
+        GetFrame(game);
+
+        for (x = 0 ; x < game.width ; x++) {
+            for (y = 0 ; y < game.height ; y++) {
+                if (game.owner[x][y] == game.playertag) {
+                    direction = rand() % 5;
+                    SetMove(game, x, y, direction);
+                }
+            }
+        }
+
+        SendFrame(game);
+    }
+
+    return 0;
+}
diff --git a/airesources/C/RandomBot.c b/airesources/C/RandomBot.c
@@ -0,0 +1,36 @@
+#include <stdio.h>
+#include <stdlib.h>
+#include <time.h>
+
+#include "hlt.h"
+
+#define BOT_NAME "RandomCBot"
+
+int main(void) {
+
+    GAME game;
+    int x, y, direction;
+
+    srand(time(NULL));
+
+    game = GetInit();
+    SendInit(BOT_NAME);
+
+    while (1) {
+
+        GetFrame(game);
+
+        for (x = 0 ; x < game.width ; x++) {
+            for (y = 0 ; y < game.height ; y++) {
+                if (game.owner[x][y] == game.playertag) {
+                    direction = rand() % 5;
+                    SetMove(game, x, y, direction);
+                }
+            }
+        }
+
+        SendFrame(game);
+    }
+
+    return 0;
+}