Auto evo exploration species flagging

.appveyor.yml

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+version: 1.0.{build}-{branch}
+
+environment:
+  BOOST_ROOT: C:/Libraries/boost_1_69_0
+  PATH: C:\Ruby25-x64\bin;$(PATH);C:\cygwin64\bin
+  VULKAN_SDK: C:/VulkanSDK/1.1.114.0
+  GIT_LFS_SKIP_SMUDGE: 1
+
+image:
+  - Visual Studio 2017
+
+platform: x64
+
+cache:
+  - ThirdParty
+  - assets
+  - VulkanSDK.exe
+  - .git/lfs/objects  
+
+install:
+  - gem install os colorize rubyzip json sha3
+  - if not exist VulkanSDK.exe curl -L --silent --show-error --output VulkanSDK.exe https://vulkan.lunarg.com/sdk/download/1.1.114.0/windows/VulkanSDK-1.1.114.0-Installer.exe?Human=true
+  - VulkanSDK.exe /S
+
+build_script:
+  - git lfs pull  
+#   - ruby SetupThrive.rb --precompiled
+
+# test_script:
+#   - cd build\bin
+#   - .\ThriveTest ~[xrequired]
+
+# This takes too much space to work
+# artifacts:
+#   - path: build/bin
+#     name: bin folder
+#     type: zip

.circleci/config.yml

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+version: 2.1
+jobs:
+   jetbrains:
+     working_directory: ~/Thrive
+     docker:
+       - image: hhyyrylainen/godot-ci:v9
+     environment:
+       GIT_LFS_SKIP_SMUDGE: 1
+       CIRCLE_COMPARE_URL: << pipeline.project.git_url >>/compare/<< pipeline.git.base_revision >>..<<pipeline.git.revision>>
+     steps:
+       - checkout
+       - restore_cache:
+           keys:
+             - v7-lfs-{{ .Branch }}
+             - v7-lfs-master
+       - run:
+           name: Pull Git LFS files, retry up to 5 times
+           command: |
+             for i in {1..5}; do git reset --hard HEAD && git clean -fd && git lfs pull && exit 0; done; exit 1
+       - save_cache:
+          key: v7-lfs-{{ .Branch }}
+          paths:
+            - .git/lfs
+       - run:
+           name: Detect changed files (since last commit and against master)
+           command: |
+             git fetch origin master
+             git diff-tree --no-commit-id --name-only -r HEAD..origin/master > files_to_check.txt
+             git diff-tree --no-commit-id --name-only -r `echo ${CIRCLE_COMPARE_URL} | cut -d/ -f 7` >> files_to_check.txt || true
+       - restore_cache:
+           keys:
+             - v8-import-{{ .Branch }}
+             - v8-import-master
+       - run: mkdir -p builds
+       # Don't care if this fails, it's enough that the C# build works
+       - run:
+           name: Just make C# project valid; don't care if asset import fails
+           command: |
+             godot --export "Linux/X11" "builds/a.x86_64" || true
+       - save_cache:
+           key: v8-import-{{ .Branch }}
+           paths:
+             - .import
+       - restore_cache:
+           keys:
+             - v3-nuget-{{ .Branch }}
+       - run: dotnet restore Thrive.sln
+       - save_cache:
+          key: v3-nuget-{{ .Branch }}
+          paths:
+            - ~/.nuget/packages
+       # Makes sure that there aren't any changes at this point to not make the CI trip up on them
+       - run:
+           name: Make sure no changes to git tracked files at this point
+           command: git reset --hard HEAD
+       # Inspect code (this only takes like 40 seconds for all files)
+       - run: ./check_formatting.rb -c inspectcode
+       - run: ./check_formatting.rb -c duplicatecode
+       # Cleanup, this takes a *long* time when checking a lot of files
+       - run: ./check_formatting.rb -c cleanupcode
+       - run:
+           when: always
+           command: |
+             git diff > cleanup_diff.patch
+             if grep -q '[^[:space:]]' < cleanup_diff.patch; then
+                 echo "Code cleanup found things to be fixed:"
+                 cat cleanup_diff.patch
+                 exit 1
+             else
+                 echo "No changes made"
+                 rm -f cleanup_diff.patch
+             fi
+       - store_artifacts:
+          path: files_to_check.txt
+       - store_artifacts:
+          path: inspect_results.xml
+       - store_artifacts:
+          path: duplicate_results.xml
+       - store_artifacts:
+          path: cleanup_diff.patch
+   format_script:
+     working_directory: ~/Thrive
+     docker:
+       - image: hhyyrylainen/thrive-lint:v9
+     environment:
+       GIT_LFS_SKIP_SMUDGE: 1
+     steps:
+       - checkout
+       - run: ./check_formatting.rb -c files,localization
+       - run:
+           when: always
+           command: |
+             git diff > format_diff.patch
+             if grep -q '[^[:space:]]' < format_diff.patch; then
+                 echo "Formatter found things to be fixed:"
+                 cat format_diff.patch
+                 exit 1
+             else
+                 echo "No changes made"
+                 rm -f format_diff.patch
+             fi
+       - store_artifacts:
+          path: format_diff.patch
+
+workflows:
+  version: 2
+  format:
+    # Unfortunately godot is setup so that a build can't happen without having all the assets processed
+    # so the format script can't check C# files
+    jobs:
+      - format_script
+      - jetbrains

.clang-format

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+---
+Language: Cpp
+AccessModifierOffset: '-4'
+AlignAfterOpenBracket: DontAlign
+AlignConsecutiveAssignments: 'false'
+AlignConsecutiveDeclarations: 'false'
+AlignEscapedNewlinesLeft: Left
+AlignTrailingComments: 'false'
+AllowAllParametersOfDeclarationOnNextLine: 'false'
+AllowShortBlocksOnASingleLine: 'false'
+AllowShortCaseLabelsOnASingleLine: 'true'
+AllowShortFunctionsOnASingleLine: Empty
+AllowShortIfStatementsOnASingleLine: 'false'
+AllowShortLoopsOnASingleLine: 'false'
+AlwaysBreakAfterReturnType: All
+AlwaysBreakBeforeMultilineStrings: 'false'
+AlwaysBreakTemplateDeclarations: 'false'
+BinPackArguments: 'true'
+BinPackParameters: 'false'
+BreakBeforeBinaryOperators: None
+# BreakBeforeBraces: Attach
+BreakBeforeBraces: Custom
+BraceWrapping:
+    AfterClass: false
+    AfterControlStatement: false
+    AfterEnum: false
+    AfterFunction: true
+    AfterNamespace: false
+    AfterStruct: false
+    AfterUnion: false
+    # AfterExternBlock: false
+    BeforeCatch: false
+    BeforeElse: false
+    IndentBraces: false
+    SplitEmptyFunction: true
+    SplitEmptyRecord: false
+    SplitEmptyNamespace: true
+BreakBeforeInheritanceComma: 'false'
+BreakBeforeTernaryOperators: 'false'
+BreakConstructorInitializers: AfterColon
+# Works fine even without this
+# CommentPragmas: '^! \\'
+CompactNamespaces: 'true'
+ConstructorInitializerAllOnOneLineOrOnePerLine: 'false'
+Cpp11BracedListStyle: 'true'
+DerivePointerAlignment: 'false'
+IndentCaseLabels: 'false'
+IndentWidth: '4'
+IndentWrappedFunctionNames: 'true'
+KeepEmptyLinesAtTheStartOfBlocks: 'true'
+MaxEmptyLinesToKeep: '3'
+NamespaceIndentation: None
+PointerAlignment: Left
+ReflowComments: 'true'
+SortIncludes: 'true'
+SortUsingDeclarations: 'true'
+SpaceAfterCStyleCast: 'false'
+SpaceAfterTemplateKeyword: 'false'
+SpaceBeforeAssignmentOperators: 'true'
+SpaceBeforeParens: Never
+# This is also a new setting not yet available
+# SpaceBeforeRangeBasedForLoopColon: 'true'
+SpaceInEmptyParentheses: 'false'
+SpacesBeforeTrailingComments: '1'
+SpacesInAngles: 'false'
+SpacesInCStyleCastParentheses: 'false'
+SpacesInParentheses: 'false'
+SpacesInContainerLiterals: 'false'
+SpacesInParentheses: 'false'
+SpacesInSquareBrackets: 'false'
+Standard: Cpp11
+TabWidth: '4'
+UseTab: Never
+
+...

.config/dotnet-tools.json

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+{
+  "version": 1,
+  "isRoot": true,
+  "tools": {
+    "jetbrains.resharper.globaltools": {
+      "version": "2022.2.1",
+      "commands": [
+        "jb"
+      ]
+    }
+  }
+}

.gitattributes

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+* text=auto
+*.po text linguist-generated=true
+en.po text linguist-generated=false
+*.pot text
+*.rb text
+*.sln text
+*.csproj text
+*.json text
+*.md text
+*.txt text
+*.cs text
+*.yml text
+*.tscn text
+*.tres text
+*.shader text
+*.xml text
+*.*.import text
+*.asset filter=lfs diff=lfs merge=lfs -text
+*.png filter=lfs diff=lfs merge=lfs -text
+*.mkv filter=lfs diff=lfs merge=lfs -text
+*.ogg filter=lfs diff=lfs merge=lfs -text
+*.ico filter=lfs diff=lfs merge=lfs -text
+*.ttf filter=lfs diff=lfs merge=lfs -text
+*.jpg filter=lfs diff=lfs merge=lfs -text
+*.zip filter=lfs diff=lfs merge=lfs -text
+*.dae filter=lfs diff=lfs merge=lfs -text
+*.blend filter=lfs diff=lfs merge=lfs -text
+*.gltf filter=lfs diff=lfs merge=lfs -text
+*.glb filter=lfs diff=lfs merge=lfs -text
+*.bin filter=lfs diff=lfs merge=lfs -text
+*.fbx filter=lfs diff=lfs merge=lfs -text
+*.material filter=lfs diff=lfs merge=lfs -text
+*.webm filter=lfs diff=lfs merge=lfs -text
+*.mesh filter=lfs diff=lfs merge=lfs -text
+*.anim filter=lfs diff=lfs merge=lfs -text
+*.otf filter=lfs diff=lfs merge=lfs -text
+*.shape filter=lfs diff=lfs merge=lfs -text
+*.jpeg filter=lfs diff=lfs merge=lfs -text
+*.ogv filter=lfs diff=lfs merge=lfs -text

.github/FUNDING.yml

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+patreon: thrivegame
+custom: https://revolutionarygamesstudio.com/donate/

.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: Bug report
+about: Report technical issues (bugs)
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Important**
+Please only submit technical bug reports here. This is not a place to make feature requests
+or suggestions. For that please visit our suggestions site:
+https://suggestions.revolutionarygamesstudio.com/
+
+Or our community forums for longer discussions
+https://community.revolutionarygamesstudio.com/
+
+**Describe the bug**
+
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behaviour:
+1. Go to '...'
+2. Click on new game / something else '....'
+3. Play and do '....'
+4. See error
+
+**Expected behaviour**
+A clear and concise description of what you expected to happen, instead of what actually
+happened.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**System info (please complete the following information):**
+- OS: [e.g. Windows 10]
+- Graphics card (you can find this in the game logs) [e.g. OpenGL ES 3.0 Renderer:
+    GeForce GTX 1080 Ti/PCIe/SSE2]
+- Thrive version [e.g. 0.4.0.2]
+
+**Logs**
+
+Please use a text hosting service (for example https://pastebin.com/) to submit your logs.
+You can copy the launcher output or the contents of the following files: `log.txt` and mono
+log file. You can find these log files by reading the game log to see their location.
+For example:
+```
+Mono: Logfile is: /home/hhyyrylainen/.local/share/godot/mono/mono_logs/2020_07_21 23.10.26 (265121).txt
+Game logs are written to: /home/hhyyrylainen/.local/share/Thrive/logs latest log is 'log.txt'
+```
+
+**Additional context**
+Add any other context about the problem here.

.github/dependabot.yml

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+version: 2
+updates:
+  - package-ecosystem: "nuget"
+    directory: "/"
+    schedule:
+      interval: "daily"
+    labels:
+      - "review"
+      - "dependencies"
+    open-pull-requests-limit: 3
+    reviewers:
+      - "Revolutionary-Games/programming"

.github/pull_request_template.md

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+**Brief Description of What This PR Does**
+
+This PR does some stuff...
+
+**Related Issues**
+
+<!-- List all issues this PR closes here with the closes syntax: 
+https://docs.github.com/en/github/managing-your-work-on-github/linking-a-pull-request-to-an-issue#linking-a-pull-request-to-an-issue-using-a-keyword
+If this is not related to an issue, it should be described in more detail why this PR is needed here instead.
+-->
+
+**Progress Checklist**
+
+Note: before starting this checklist the PR should be marked as non-draft.
+
+- [ ] PR author has checked that this PR works as intended and doesn't
+      break existing features:
+      https://wiki.revolutionarygamesstudio.com/wiki/Testing_Checklist
+      (this is important as to not waste the time of Thrive team
+      members reviewing this PR)
+- [ ] Initial code review passed (this and further items should not be checked by the PR author)
+- [ ] Functionality is confirmed working by another person (see above checklist link)
+- [ ] Final code review is passed and code conforms to the 
+      [styleguide](https://github.com/Revolutionary-Games/Thrive/blob/master/doc/style_guide.md).
+
+Before merging all CI jobs should finish on this PR without errors, if
+there are automatically detected style issues they should be fixed by
+the PR author. Merging must follow our
+[styleguide](https://github.com/Revolutionary-Games/Thrive/blob/master/doc/style_guide.md#git).