Merge pull request Revolutionary-Games#735 from Revolutionary-Games/675

675

README.md

@@ -30,7 +30,7 @@ both for guidelines on code formatting and git usage.
 And [AngelScript primer][asprimer] for scripting help.
 
 ### C++ Programmers 
-To compile Thrive yourself, you will not only need to follow the [setup instructions][setupguide].
+To compile Thrive yourself, you will need to follow the [setup instructions][setupguide].
 
 Be sure to have a look at the [styleguide][styleguide],
 both for guidelines on code formatting and git usage.

SetupThrive.rb

@@ -78,7 +78,7 @@ def parseExtraArgs
 leviathan = Leviathan.new(
   # Use this if you always want the latest commit
   # version: "develop",
-  version: "55f85074961175d8ffecfca2e318eb093b2d9c68",
+  version: "28cd2c52dd583e9537f1df32cac91d9b4ed2da2d",
   # Doesn't actually work, but leviathan doesn't install with sudo by
   # default, or install at all for that matter
   noInstallSudo: true

doc/setup_instructions.md

@@ -1,7 +1,7 @@
 What's this?
 ============
 
-This is the setup instructions for compiling Thrive.
+These are the setup instructions for compiling Thrive.
 
 Important Note: If you run into any trouble with the setup scripts, please 
 bring them up on the development discord or open a github issue. 
@@ -174,7 +174,8 @@ graphical tool for reviewing the exact lines you have changed, but you
 can also commit on the command line) you can publish them to your fork
 with (assuming you used the master branch, when working with the main
 thrive repository you MUST create a different branch but when working
-with a fork that isn't required):
+with a fork that isn't required, but still strongly recommended as
+making multiple pull requests with one branch is messy):
 
 ```
 git push fork master

doc/style_guide.md

@@ -1,14 +1,14 @@
 Code Style Guide
 ================
 
-To maintain a consistent coding style, contributors should follow the rules 
-outlined on this page. This style guide is separated into four parts: common 
+To maintain a consistent coding style, contributors should follow the rules
+outlined on this page. This style guide is separated into four parts: common
 rules, rules specific for C++, rules specific for AngelScript and guidelines for
 using git.
 
-The style rules are intended to increase readability of the source code. The 
-most important rule of all is: **Use common sense**. If you have to break 
-some rules to make the code more readable (and not just for you, but for 
+The style rules are intended to increase readability of the source code. The
+most important rule of all is: **Use common sense**. If you have to break
+some rules to make the code more readable (and not just for you, but for
 everyone who has to read your code), break it.
 
 Common (Both C++ and AngelScript)
@@ -17,11 +17,11 @@ Common (Both C++ and AngelScript)
 - Indentation is 4 spaces
 
 - Names (that includes variables, functions and classes) should be descriptive.
-  Avoid abbreviations. Do not shorten variable names just to save key strokes, 
+  Avoid abbreviations. Do not shorten variable names just to save key strokes,
   it will be read far more often than it will be written.
 
-- Variables and functions are camelCase with leading lower case. Classes are 
-  CamelCase with leading upper case. Constants are CONSTANT_CASE with 
+- Variables and functions are camelCase with leading lower case. Classes are
+  CamelCase with leading upper case. Constants are CONSTANT_CASE with
   underscores.
 
 - Filenames are lower_case with underscores. The reason for this is
@@ -34,46 +34,47 @@ Common (Both C++ and AngelScript)
 C++
 ---
 
+- Format your code with [clang-format](clang_format.md) this is the
+  official formatting and most important thing to consider. If you
+  don't automatic checks on your code will fail.
+
 - Macros are CONSTANT_CASE
 
 - Header files end in .h, source files in .cpp
 
-- Header files should begin with `#pragma once`. Old-style header 
+- Header files should begin with `#pragma once`. Old-style header
   guards (with `ifdef`) are discouraged because they are very verbose and
   the pragma is understood by all relevant compilers.
-
-- Format your code with [clang-format](clang_format.md)
-
-- Opening braces go in the same line as the control statement, closing braces
-  are aligned below the first character of the opening control statement
 
 - Keep header files minimal. Ideally, they show only functions / classes that
   are useful to other code. All internal helper functions / classes should be
   declared and defined in the source file.
 
 - All classes and their public and protected members should be documented by
-  doxygen comments in the header file. If the function's purpose is clear 
-  from the name and its parameters (which should be the usual case), the 
+  doxygen comments in the header file. If the function's purpose is clear
+  from the name and its parameters (which should be the usual case), the
   comment can be very basic and only serves to shut up doxygen warnings about
   undocumented stuff.
 
 - Inline comments inside functions can and should be used to describe why
   you wrote the function like this (and, sometimes more importantly, why you
   didn't go another way).
 
-- Member variables of classes are prefixed with \p m_. This is to 
-  differentiate them from local or global variables when using their 
+- Empty lines are encouraged between blocks of code to improve readability.
+
+- Member variables of classes are prefixed with \p m_. This is to
+  differentiate them from local or global variables when using their
   unqualified name (without `this->`) inside member functions. The prefix can
   be omitted for very simple structs if they don't have member functions and
   serve only as data container.
 
-(- When calling member functions from another member function, their names are
-  qualified with `this->` to differentiate them from global non-member 
-  functions.)
+- When calling member functions from another member function, their names may be
+  qualified with `this->` to differentiate them from global non-member
+  functions. This rule is not enforced.
 
-- Function signatures are formatted like the clang-format options file makes them to be formatted
-
-- For non-trivial classes that would pull in a lot of other headers, use the pimpl idiom to hide implem  entation details and only include the ton of headers in the .cpp file.
+- For non-trivial classes that would pull in a lot of other headers,
+  use the pimpl idiom to hide implementation details and only include
+  the ton of headers in the .cpp file.
 
   ```cpp
     // In the header:
@@ -92,12 +93,12 @@ C++
         ~MyClass();
 
     private:
-      
+
         struct Implementation;
         std::unique_ptr<Implementation> m_impl;
     };
   ```
-  
+
   ```cpp
     // In the source file:
 
@@ -112,24 +113,24 @@ C++
 
     MyClass::~MyClass() {} // Define destructor
   ```
-
-- Try to avoid include statements inside header files unless
-  absolutely necessary. Prefer forward declarations and put the
-  include inside the source file instead. And use the pimpl idiom if
-  this cannot be avoided and the headers are large.
 
-- Prefer C++11's `using` over `typedef`. With the `using` keyword, type 
+- Try to avoid include statements inside header files. Prefer forward
+  declarations and put the include inside the source file instead. And
+  use the pimpl idiom if this cannot be avoided and the headers are
+  large.
+
+- Use C++11's `using` over `typedef`. With the `using` keyword, type
   aliases look more like familiar variable assignment, with no ambiguity as
   to which is the newly defined type name.
 
-- Virtual member functions overridden in derived classes are marked with the 
-  C++11 `override` keyword. This will (correctly) cause a compile time error 
-  when the function signature in the base class changes and the programmer 
+- Virtual member functions overridden in derived classes are marked with the
+  C++11 `override` keyword. This will (correctly) cause a compile time error
+  when the function signature in the base class changes and the programmer
   forgot to update the derived class.
 
 - Classes not intended as base classes are marked with the `final` keyword
   like this:
-  
+
   ```cpp
     class MyClass final {
         // ...
@@ -147,7 +148,7 @@ C++
 
       #include <Entities/Component.h>
       #include <Entities/System.h>
-      
+
       #include <OgreMatrix4.h>
 
       #include <vector>
@@ -160,18 +161,16 @@ C++
 AngelScript
 -----------
 
-- A class's public data members are *not* prefixed by `m_`, unlike C++. 
-
-(This is because in AngelScript, all member variables are accessed with their qualified
-  names (like `this.memberVariable`), so there is no need to mark them.)
+- A class's public data members don't need to be prefixed by `m_`, unlike C++.
 
 - A class's private data members and functions are declared `private`
   (everything is public by default) and optionally prefixed with an
   underscore. This is a convention adopted from Python's PEP8 style
-  guide.
+  guide. This same rule may also be used in C++.
 
-- Doxygen does not support AngelScript natively, but for consistency's sake, AngelScript 
-  classes and functions are still documented with doxygen style comments.
+- Doxygen does not support AngelScript natively, but for consistency's
+  sake, AngelScript classes and functions are still documented with
+  doxygen style comments.
 
 - For consistency with C++ adding semicolons after class declarations
   is recommended, but not an error if omitted. This is one of the
@@ -181,9 +180,11 @@ AngelScript
 Git
 ---
 
-- Do not work in the master branch, always create a private feature branch
-  if you want to edit something
-
+- Do not work in the master branch, always create a private feature
+  branch if you want to edit something. Even when working with a fork
+  this is recommended to reduce problems with subsequent pull
+  requests.
+
 - If you don't have access to the main repository yet (you will be
   granted access after your first accepted pull request) fork the
   Thrive repository and work in your fork and once done open a pull
@@ -204,7 +205,10 @@ Git
 - When the master branch is updated, you should usually keep your
   feature branch as-is. If you really need the new features from
   master, do a merge. Or if there is a merge conflict preventing your
-  pull request from being merged.
+  pull request from being merged. Quite often the master branch needs
+  to be merged in before merging a pull request. For this it is
+  cleaner if the pull request is rebased onto master, but this is not
+  required.
 
 - When a feature branch is done, open a pull request on GitHub so that others
   can review it. Chances are that during this review, there will still be
@@ -215,13 +219,16 @@ Git
   done (take note people accepting pull requests) from the Github
   accept pull request button, hit the arrow to the right side and
   select "merge and squash". Bigger feature branches that are dozens
-  of commits from multiple people will be merged normally to attribute
-  all of the authors on Github feeds.
-
-- For maintainers: When manually squashing GitHub (which is something
-  you should avoid) requires a merge commit to recognize the merging
-  of a pull request. A "git merge --squash" does not create a merge
-  commit and will leave the pull request's branch "dangling". To make
-  GitHub properly reflect the merge, follow the procedure outlined in
-  the previous bullet point, then click the "Merge Pull Request"
-  button on GitHub (or do a normal "git merge".
+  of commits or from multiple people need to be manually squashed into
+  a few commits while keeping commits from different authors separate
+  in order to attribute all of the authors on Github feeds. These kind
+  of pull requests can be merged normally **if** all the commits in them
+  are "clean" to not dirty up master.
+
+- For maintainers: When manually merging (which is something you
+  should avoid) GitHub requires a merge commit to recognize the
+  merging of a pull request. A "git merge --squash" does not create a
+  merge commit and will leave the pull request's branch "dangling". To
+  make GitHub properly reflect the merge, follow the procedure
+  outlined in the previous bullet point, then click the "Merge Pull
+  Request" button on GitHub (or do a normal "git merge").

scripts/SimulationParameters/MicrobeStage/BioProcesses.json

@@ -79,11 +79,12 @@
         "name": "Nitrogen Fixing",
 
         "inputs": {
-            "atp": 0.5
+            "oxygen": 1.0,
+            "atp": 5
         },
 
         "outputs": {
-            "ammonia": 0.1
+            "ammonia": 0.5
         }
     },
 
@@ -110,5 +111,18 @@
         "outputs": {
             "glucose": 0.33
         }
+    },
+
+    "iron_chemolithoautotrophy": {
+        "name": "Iron Chemolithoautotrophy",
+
+        "inputs": {
+            "carbondioxide": 0.09,
+            "iron": 0.175
+        },
+
+        "outputs": {
+            "atp": 10.0
+        }
     }
 }

scripts/SimulationParameters/MicrobeStage/Biomes.json

@@ -154,7 +154,7 @@
                 "density": 0.00002,
                 "dissolved": 0.0
             },
-            
+
             "oxygen": {
                 "amount": 0,
                 "density": 0.0,
@@ -208,7 +208,7 @@
                 "density": 0.00002,
                 "dissolved": 0.0
             },
-            
+
             "oxygen": {
                 "amount": 0,
                 "density": 0.0,
@@ -430,7 +430,7 @@
                 "density": 0.00002,
                 "dissolved": 0.0
             },
-            
+
             "oxygen": {
                 "amount": 0,
                 "density": 0.0,

scripts/SimulationParameters/MicrobeStage/Compounds.json

@@ -19,9 +19,9 @@
         "isUseful": true,
         "isEnvironmental": false,
         "colour": {
-            "r": 0.6,
-            "g": 0.7,
-            "b": 0.2
+            "r": 1.0,
+            "g": 0.4,
+            "b": 0.1
         }
     },
 
@@ -45,9 +45,9 @@
         "isUseful": false,
         "isEnvironmental": false,
         "colour": {
-            "r": 1.0,
-            "g": 0.4,
-            "b": 0.1
+            "r": 0.6,
+            "g": 0.7,
+            "b": 0.2
         }
     },
 
@@ -77,6 +77,19 @@
         }
     },
 
+    "iron": {
+        "name": "Iron",
+        "volume": 1,
+        "isCloud": true,
+        "isUseful": false,
+        "isEnvironmental": false,
+        "colour": {
+            "r": 0.28,
+            "g": 0.098,
+            "b": 0.02
+        }
+    },
+
     "oxygen": {
         "name": "Oxygen",
         "volume": 1,

scripts/gui/microbe_editor.mjs

@@ -52,6 +52,10 @@ const organelleSelectionElements = [
         element: document.getElementById("addChemoSynthisizingProteins"),
         organelle: "chemoSynthisizingProteins"
     },
+    {
+        element: document.getElementById("addRusticyanin"),
+        organelle: "rusticyanin"
+    },
     {
         element: document.getElementById("addFlagellum"),
         organelle: "flagellum"