[CLOSED PR] Pathology to Microbiology

[github_bot]

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[WIP][input wanted][help wanted][tgui][experimental][feature][rework][add to wiki]
About the PR

Forum users: I hear you! I am unable to respond because I lost the password to the email linked to my forum account. I'll try to resolve this ASAP and keep conversations there.

6/27/2022: Take everything you read below this message with a grain of salt. Almost all of the previous writing has been made obsolete through development. I will likely write up reports when I seek admin/developer input (within the next few weeks).

Progress:

Part 0: Back-End Developments
- [ ] Clean, modernize, and standardize code to meet code guidelines
- [ ] Pitch the PR to admins/devs after sufficient progress (mind that the sentiments on 'pathology' are still controversial)
- [ ] Find adequate admin/developer oversight and sponsorship
- [x] Rebuild microbio's admin tools and panels
- [ ] Write documentation for building new effects and explaining code structure
- [ ] Resolve any remaining runtimes
- [ ] Perform isolated trials to check code stability and to find possible exploits
- [ ] Update changelog to include all contributors and proper detail
- [ ] Vouch for the opportunity to playtest
- [ ] Resolve issues from playtesting
- [ ] Repeat previous until developers, admins, and players are satisfied
- [ ] Merge!

---

Part I: Basic Microbiology as Biochemistry

- [x] Design datumized reagents
- [x] Identify relevant reagents that are not implemented
- [x] Integrate enhancement mechanisms into related code
- [x] Develop necessary machines
- [ ] Test reagent effects for stability and bugs
---

Part II: Advanced Microbiology and Customizable Germs

- [X] Slash and comment block old patho code to reusable components
- [X] Refactor peripheral vars to ensure functional continuity
- [X] Comment, reorganize, and salvage patho code
- [X] Readd/redefine foundational microbe vars
- [x] Redesign infection duration and effect probabilities (no stages, big switch cases, or massive if-nests, just mathematical curves)
- [x] Refactor old effects
- [x] Rework the curing system (One and Done, not Suppressed until Regressed)
- [x] Add new curing possibilities
- [x] Define 'Tells' and address transmissions
- [x] Review effect probability handling and refactor if necessary
- [ ] Rehabilitate machines
- [ ] Build rudimentary UI in html (disgusting, I apologize) OR find help to build TGUI
- [x] Review, triage, and readd tools
- [x] Build the microbe_controller global datum from the old pathogen_controller


Patho Rework Design Docs (feel free to add comments there, these are living documents):
General Ideas and UI Mockups: https://hackmd.io/@XyzzyThePretender/B10Kp-DP5
Organization of main pathology code: https://hackmd.io/@XyzzyThePretender/SJv6BtTP5
Dev Diary 1: [pathology.dm](https://hackmd.io/@XyzzyThePretender/ryK0d2kdq)
Dev Diary 2: [microbodies.dm](https://hackmd.io/@XyzzyThePretender/rJNuGgbOc)
Dev Diary 3: [Transience and Chronic Illnesses](https://hackmd.io/@XyzzyThePretender/H1GJwb-u5)
Dev Diary 4: [Feedback on the forums: p.I](https://hackmd.io/@XyzzyThePretender/HyNFJiWO5)
Pitch Document: [Pathology to Microbiology](https://hackmd.io/@XyzzyThePretender/SJgU-wf_c)
Effect Guidelines: [Design Guidelines for Microbiology Effects](https://hackmd.io/@XyzzyThePretender/HksxP7K_9)

I will be referring to comments made from the last pathology playtest to justify my rework, organized in a living HackMD document with all of the quotes: https://hackmd.io/@XyzzyThePretender/BkKFc11Oq

Pathology is now an investigative/bounty-oriented system, where pathologists write up reports for the CDC to earn money and research points (like genetics) to buy or discover good and bad symptoms and to create novel pathogens for the benefit (or detriment) of the crew.

The primary inspiration for the rework is from Plague Inc., because that game drove initial development for pathology. Symptoms are organized into severity techtrees and are unlocked sequentially through purchase or through accurate report identification.

All aspects of this redesign focus on enabling and rewarding player interaction outside of the pathology bay. **Interaction with other crewmembers is a key design principle throughout this PR.** (thanks for the wording Flourish) [26]

The DNA clue system is dropped entirely in favor of reagent testing, visual inspection, and IC testimony/"controlled" monkey testing. Most symptoms are obvious and clear to discern between other mechanics. Communication is the fastest way to learn about and stop diseases. [27]

Transmission is simplified to contact, fluid, and aerobic infections. Pathogen puddles and clouds are removed. Clear, distinct text messages tell potentally infected players when they have been exposed. Transmission is dependent on if a pathogen has symptoms that would allow for it (i.e. coughing and sneezing allows aerobic, vomiting and sweating allows for fluid, etc.) [1] [13] [14] [25] [28]

Pathogens will always have a cure. On meeting the requirements for the cure, the player is completely cured within a short period of time (10-30 seconds). Remission is no longer a problem. [2]

Pathogens no longer mutate. Leave mutation as a game mechanic to the geneticists. [4]

Random event outbreaks replace low-hygiene infections on RP. Being filthy only increases your risk of being a patient zero and will not be a guaranteed instant illness. Low hygiene diseases will seldom be contagious and even then will infect very few people. [9] [10] [11]

Game-ending symptoms are removed. [5]

More neutral symptoms are introduced to dilute the effect of natural outbreaks. [22]

RNG will be negligible by giving the player many CDC test samples for reports (3 different pathogens per crate). This allows an experienced player to earn money and points quickly to buy up the desired symptoms for a designer pathogen, while giving a new player plenty to experience without creating much risk. [3]

Pathologists are encouraged (NOT required) to work with cargo to make money and to progress the symptom trees. The bounties provided by the CDC are enormous (think 100k+ for high-risk!), but the upfront 10% deposit based on the expected pathogens' worth will be hefty enough to avoid QM spam. [17] [33]

Pathologists are also incentivized to work closely with other crew like ranchers for eggs, engineers for constructing different atmospheric rooms (implying N2o/plasma breathability symptoms), the HoP/MD for access permits, and even botanists/bartenders for specialized chems. Cooperation is not necessary to progress since research can be bought, but interacting outside of the system enabling disease outbreaks allows pathologists to create high-quality, lifesaving diseases at a much faster pace than by themselves. [19] [26]

Pathologists will be able to create simple pathogens roundstart. Whenever a pathogen is created, a report on the pathogen is stored and printed and health scanners will always identify the pathogen. The cost to create a pathogen depends on the microbody type, symptoms, and cure. Beneficial symptoms reduce the cost, so even if a person wants to make a bad virus, they will likely have to include some positive symptoms to get a reasonable price.

The old UI has been revamped in TGUI. Symptoms are organized in techtrees, and one main panel is used in analysis and creation. (gee this isn't very helpful...) [33]

All created and CDC-reported pathogens are added automatically to MedTrak and show up on health scanners with descriptive information on curing, transmission, and stage. Additionally, reports can be printed for distribution so that people can learn how to help themselves. [16] [18]

Even without a report, health scanners are still able to give a round diagnosis for infected individuals, showing the cure type and hints about the pathogen's characteristics. With enough experience, this info may sometimes be enough to figure out the right cure. [23] [24]

The Pathology areas are reorganized to allow for multiple pathologists to work in tandem. [12]

A toggle for non-antagging pathologists is implemented. Detailed adminlogs are implemented to precisely track pathogen creation and outbreak propogation. [15][29]

The scope of this PR is limited to reconstructing the foundations of Pathology, leaving additional features to smaller subsequent PRs.

Why's this needed?
Why is Pathology worth remaking?
1. Offers the medical department a proactive interdepartmental role with almost every job.
2. Clears technical debt.
3. Gives medbay a way to make money outside of genetics taking from payroll.
4. As far as I am aware, a viable replacement (Mycology) is not coming anytime soon.
5. Some players liked some aspects of pathology and want to see a rework happen.
6. Provides job substance for Test Subjects and other flavor roles.
7. Addresses RP hygiene.
8. Creating a frenemy for genetics.

Changelog

Code:

changelog
(u)XyzzyThePretender
(*)Introducing Microbiology! No, those microbes can't cause outbreaks (yet).

PULL REQUEST DETAILS

[Kotlol]

We can still have game-ending symptons but only from ANTAGONISTS. Aka emagged devices and such...

But other wise this is me thinking abit.. I am a newb to pathology but I would love to see it back. When it was around .... people kept spreading viruses from pathology each shift. It was turned off, since it was a pandemic and every shift having people quarantined and wearing masks ... wasn't a great form of escapism...

But now it should be fine with abit of rework. Can't wait for all mechanics to work in harmony again!

[TheMaskedMan2]

I’m going to play devils advocate and say that while Patho did grow out of control on older rounds - a lot of that was simply due to players not adjusting or knowing how to cure things. Once you figured it out it wasn’t too hard.

But I am a pathology apologist, anyways I am glad someone is working on it again. I hope there is still disease creation and mutation, I also realize part of some of it is saying to make diseases simpler to cure, but I hope it isn’t so simple that any half competent player can cure themselves in 30 seconds of a disease some antag took an hour to make.

A little bit of discovery to find the proper chem cure for more advanced diseases. (Not all diseases.)

Though I suppose it should start small codewise and balance considered later, either way I expect when it’s re-added even as a test, a ton of people will claim its broken and OP cause they didn’t learn the counters yet.

Rambling aside, I am not sure how well they all fit into goon, but Virology is a thing on a lot of codebases still, I wonder how they have changed over the years and if there’s any good ideas.

/ramble

[Frank_Stein]

Thought about pathology

Something we seem to get stuck on is balancing "good" and "bad" pathogens. TBH, I think that's a niche genetics already fills. I think it would be worth reconsidering the entire concept and think about what role pathology could serve in relation to existing mechanics and departments, the way botany does with kitchen or chemistry.

Pathology could be more like a biological aspect of science. Maybe they could serve a roll in medical production in making medicine. Maybe they produce advanced yeasts for the chef for baking and alcohol brewing. Create microbial energy cells to add Engineering with Power Production. Analyze forensic samples to aid with Security investigations.

[Kotlol]

Thought about pathology

Something we seem to get stuck on is balancing "good" and "bad" pathogens. TBH, I think that's a niche genetics already fills. I think it would be worth reconsidering the entire concept and think about what role pathology could serve in relation to existing mechanics and departments, the way botany does with kitchen or chemistry.

Pathology could be more like a biological aspect of science. Maybe they could serve a roll in medical production in making medicine. Maybe they produce advanced yeasts for the chef for baking and alcohol brewing. Create microbial energy cells to add Engineering with Power Production. Analyze forensic samples to aid with Security investigations.

I would love them to do a mirco level atopsy that gives hints of how the person died and maybe a hint to a player like:
"A scrap of yellow fabric was found" Thus implicating the killer wore yellow clothing (or engineer clothing) at the time of killing.

Maybe rework pathology into Micro-biology... thus you can check samples of diseases, grow stuff to help, forensics, but also checking DNA of several things.
We could also put in a "xenobiology" part to it in checking alien samples? Wich could unlock more mutations and such? Where do you find these? You order them or find them somehow.
Anyhow... I am overspeculating... but making it MICRO-BIOLOGY insted of pathology makes more sense the way Frank is suggesting it.

[Rilor]

Thought about pathology

Something we seem to get stuck on is balancing "good" and "bad" pathogens. TBH, I think that's a niche genetics already fills. I think it would be worth reconsidering the entire concept and think about what role pathology could serve in relation to existing mechanics and departments, the way botany does with kitchen or chemistry.

Pathology could be more like a biological aspect of science. Maybe they could serve a roll in medical production in making medicine. Maybe they produce advanced yeasts for the chef for baking and alcohol brewing. Create microbial energy cells to add Engineering with Power Production. Analyze forensic samples to aid with Security investigations.

I do like the idea of pathology having more ways to help everyone on the station than just rushing a beneficial plague every round. Also this could open up more options for gimmicks for pathology than "make everyone Shakespeare" or "sell the vaccine for a harmless but annoying plague you unleash to become rich."

[TheMaskedMan2]

I do like my plagues though and still want them to be a part of it, but maybe not the only part of it? Perhaps weirdness with biological micro-organisms in general would be cool. Though anyways it's easy to throw out ideas, maybe should focus more on getting the basics working again at least?

[babayetu83]

parasitology might be an interesting direction to consider in pathology