GeoDUDE!

The good thing about funding being a sensitive topic is that everyone feels this way, not just you. We would all love to pretend funding doesn't matter and that we just want to do great research, but everyone knows that we don't live in a pretend world. So, even if it comes out a little awkwardly, your professors will understand because they have been and are currently in similar situations too.
 
If you read blogs online by professors, you'll see that they also encounter similar uncomfortable-ness when discussing things like salary, promotions, lab space negotiation, making arrangements on how to split the pay of a group/lab member etc.
 
I feel very comfortable talking to my supervisor about things but it is still a tiny bit awkward to ask about getting money to attend a conference for example. In many cases, I know the money is there and I know they will agree to pay for it, but I still need to ask because I don't want to develop an attitude where I just assume I'll get all the money I need. But talking about money is a critical part of this job as well as many other jobs outside of academia.
 
Also, it might be a touchy topic or make you a little uncomfortable to talk about, but the way I see it, the consequences of not talking about it and then missing an opportunity or getting screwed is way too high. I'd much rather endure a slightly awkward conversation than suddenly find myself with way less funding than I expected.

I would not pay for a graduate degree, especially one that involves a thesis. 

Yeah! I don't have a car (I bike everywhere) so all the money spent towards a car is savings, or nice clohtes... or new pots and pans (oh god, I'm trying my best to resist). 

During my masters, I was shocked at how easy it was to live off 13k a year, and actually save money.  How much stuff my parents and people who make a ton of money have is somewhat gratuitous, though I imagine once my 7 year grad school stint is over  ill have that kinda stuff. 

I'm sorry you feel that wasn't advice. There are other options besides going to graduate school and paying. Going into a program where you must research and take out loans is a type of stress you should not consider. You are destined to fail. Some people come through ok, but many don't. Research is a fickle thing, sometimes it works out, sometimes it doesn't. Do you really want to wrack up debt on something that variable?
 
I'll let you know that I also switched fields, got into a single funded masters program and used that to leverage myself into the PhD program of my choosing. you can do this too, I had terrible grades in undergrad. Luck plays a role, figure out a way to get lucky.

Learning new software is not a good reason to do a PhD in Earth Sciences. The requirement for a PhD is much greater than learning new software: you are better served just learning it on your own (even if you have to pay out of hand). 
 
 
 If the job you want requires you to get a PhD, then get the PhD. 

I have a master's in bioinformatics so I know about the comp bio field. You don't need a good background in CS to get into a funded program and you definitely don't need a CS masters. You will be able to take programming classes your first year in a PhD program. Comp bio is an interdisciplinary area so you are expected to come into the program weak in some areas. Plenty of the PhD students at the school I did my MS had no programming experience at all when they came into the program. I would look for a research position. Youll gain research and programming skills through this method, just like you would during a masters. You'll get paid instead of paying though! If your uGPA is reasonable and do you well on GRE quant then you should be able to apply straight into computation bio PhD programs after gaining some research experience.

I would not pay for a graduate degree, especially one that involves a thesis. 

I would not pay for a graduate degree, especially one that involves a thesis. 

I would not pay for a graduate degree, especially one that involves a thesis. 

PhD positions in other countries are treated and regulated like industry jobs - thats the way it should be in the US, that is all I am arguing for. People should get paid parental leave (yes, male and female, raising a child dual responsibility), and vacations. While its a choice to go to graduate school, it is also somewhat ridiculous that the opportunity cost is so much. 

I don't think its good to think that just because one situation is shitty another place should also be shitty. That is essentially your argument, in case you want to revise. 

I think if you think graduate school isn't 100% analogous to a job you are in a rude awakening.... you would never tell a grade school teacher never to have a child because she/he only makes 30k a year.
 
The thought that anyone is special for going to graduate school is special, or that graduate school is special just because its graduate school is really arrogant and misinformed. Its up to the individuals to make that time special, just like anything else. There is a reason why graduate students don't walk around in black and white robes like nuns. 

Fellowships, RAs, TAs ect.  The summer is the same for graduate students as the rest of the year just not taking classes. 
 
You should talk to your advisor about summer funding. One of the conditions of me attending a school was summer funding for the duration of my program, through one way or another. Even if you have guaranteed funding, you should be applying for summer money (so that previous money can be used else where). 

Assume you will pay, let him pay for you if he offers.

TLDR (from thread): She has money. She wants to pay someone to do something a certain way. You are not doing it that way. If you do not do it that way, you will get fired. Figure out what that way is or you will be fired.  
 
You have the chance to learn a life lesson without having many negative consequences, I suggest you take it. 

TLDR (from thread): She has money. She wants to pay someone to do something a certain way. You are not doing it that way. If you do not do it that way, you will get fired. Figure out what that way is or you will be fired.  
 
You have the chance to learn a life lesson without having many negative consequences, I suggest you take it. 

TLDR (from thread): She has money. She wants to pay someone to do something a certain way. You are not doing it that way. If you do not do it that way, you will get fired. Figure out what that way is or you will be fired.  
 
You have the chance to learn a life lesson without having many negative consequences, I suggest you take it. 

TLDR (from thread): She has money. She wants to pay someone to do something a certain way. You are not doing it that way. If you do not do it that way, you will get fired. Figure out what that way is or you will be fired.  
 
You have the chance to learn a life lesson without having many negative consequences, I suggest you take it. 

TLDR (from thread): She has money. She wants to pay someone to do something a certain way. You are not doing it that way. If you do not do it that way, you will get fired. Figure out what that way is or you will be fired.  
 
You have the chance to learn a life lesson without having many negative consequences, I suggest you take it. 

TLDR (from thread): She has money. She wants to pay someone to do something a certain way. You are not doing it that way. If you do not do it that way, you will get fired. Figure out what that way is or you will be fired.  
 
You have the chance to learn a life lesson without having many negative consequences, I suggest you take it. 

Are you going to be able to find a job that pays more than 15 dollars an hour for 20 hours a week?
 
You will also have to pay tuition. 
 
You are not better off.
 
going into debt for graduate school is a terrible financial investment. 

I hope you all get into Rice.

While I sympathize with the frustration that you must be feeling thinking that you are doing well and then suddenly finding out that you are close to being fired, I agree with everyone else above that you need to make a few big changes and have some important and direct conversations with your supervisor.
 
I agree with the others that you need to change your perspective on these conflicts. While I usually argue that students and supervisors should be more collegial, I usually mean it in terms of scientific opinions (i.e. a professor should not simply dismiss a student's scientific argument because they are a student instead of on the academic merits). In this case, when it comes to work expectations, your supervisor should set the standard and you should strive to meet it. They are the boss and you are the employee. As others said, you don't get to judge their own schedule and you don't get to question their motivations or decisions because you likely don't know all of the details.
 
Just to provide a few examples. It's just as easy for us to rationalize your supervisor's actions as for you to rationalize your own.
 
1. The professor's schedule: As others said, they might be working late. One professor I worked for usually comes in around 11am, leaves at 4pm, cooks dinner, spends time with his kids at home, puts them to bed, and then works again from 9pm to 2am (I can tell from the timing of his emails). In any case, it's not up to you to judge them, and they are perfectly right to insist that you work from X am to Y pm while they follow a different schedule.
 
2. Not including you on that email: She could have forgotten, or she might not have known you did not submit the form when she first wrote that email. Or, perhaps all of your colleagues, when they realised they had forgotten the form, they informed the professor. It sounds like you only realised you forgot this form when she confronted you about it in her office. I think it is very irresponsible of you to forget it so much that your supervisor had to remind you. I also think it is irresponsible for you to call it a problem "which she could have solved". No. It is a problem that is your responsibility to solve, not hers (she might have solved it for others because they asked her for help, and how do you know that she didn't get upset at them too). You failed to do this task, and these are the consequences.
 
3. Being upset at you for not showing up on that Monday: This is 100% your fault and it is a serious infraction, in my opinion. During all those delays, it would have taken you 10 minutes to send an email to your professor letting her know that your flight had been delayed, including the time it would have taken to figure out whatever crappy WiFi the airport you were stuck in were using. As someone else mentioned, in most jobs, you will lose your job for failing to show up without notice.
 
4. Lack of communication: This is also on you. Communication is definitely a two-way street and I do think that perhaps you are both at fault here. But, it is certainly your responsibility to ensure you meet with your supervisor at timely intervals. You should not always be waiting for her to schedule a meeting. You should take the initiative sometimes too! 
 
5. The "surprise" ultimatum: I don't think she is doing this to get back at you or because she hates you. It is really hard to fire someone or even have the tough conversation to tell them to get their act together! It might help to read this: https://tenureshewrote.wordpress.com/2013/11/21/can-we-measure-a-lab-members-productivity/. The reason it might have taken so long to have this conversation with you was because it is a hard thing to do and because she might have had to get the right documentation together so that she can protect herself in case she does need to fire you and the split doesn't go well.
 
--> There is no reason to purposely plan a meeting just to upset you. Even if she just wanted to make your life miserable, she would have upset you and then fired you right there. Why would she give you 3 months to get your act together if she didn't actually want you to do so? This is why in most jobs, when you are fired with two weeks notice, you actually are asked to leave right away and they'll just pay you 2 weeks after your termination date. No point having you stick around if they want to get rid of you. 
 
Okay, I am sorry to sound like I am piling on and blaming a lot of things on you. I just wanted to show that just as you have tried to rationalize your actions, you can easily rationalize hers as well. I also want to echo St Andrews Lynx's final statement about the "most recent/tangible symptom".
 
Here's what I think the main problems are (from the point of view of a neutral third party) and how you can address them:
 
There are misunderstanding of expectations. Specifically, the whole lateness thing. You need to come back to her office, tell her you have thought about what she said over the weekend and let her know that you are ready to fix this issue. Come up with a solution and a way to keep yourself accountable. For example, you might suggest that you will now be in the lab from 9:30am to 6pm (or whatever is appropriate) and suggest that you keep a logsheet. Maybe even buy a notebook and start on Monday June 15. You don't have to show it to her every week, but just keep it in the lab so that 1) you keep yourself on track and 2) you show that you are taking responsibility for this. I think it is very important that you come up with the solution and you keep yourself accountable. Sincerely show that you are taking this advice to heart and are taking efforts to fix it. 
 
There is a lack of communication. I think you need to take the initiative and talk to your supervisor more often. I am surprised to hear that once you did not show up for work that Monday and that the admin assistant had to personally call/email you to ask what was wrong, you did not immediately check in with the professor first thing Tuesday morning. When you meet with her this week to discuss your tardiness, perhaps you can ask to have a regular meeting time scheduled as well? Maybe once every 2 weeks if weekly does not work out for your busy lab. If this is not possible, then take the initiative and knock on her door or send her more than one email to schedule a meeting when you need to see her.
 
(Sorry to be blunt but) Your actions have been irresponsible and unreliable. Not just the actions that you told us about, but the way you portray them here seems like you aren't really taking responsibility for your actions. You say that you accept you've made the series of mistakes, but you aren't accepting the consequence. I do not think it is unreasonable to fire you for the mistakes you've mentioned here. I think giving you a warning and a deadline to get things together is a fair result. I strongly encourage you to stop making excuses, stop rationalizing, accept that this warning to be fired is the correct consequence for your actions and move on from there.
 
As to your medical condition, I agree that you are not obligated to say details. But you do have to say that such a condition exist if you want it to be factored into their evaluation of you. Again, as you and others said, check with the laws that govern you. At my school, we have sick leave. We do need to disclose that we have to take leave for a medical reason but we do not have to prove it or disclose any of the details (i.e. the type of illness etc.) It is not unreasonable to expect you to say that you need medical leave though.
 
Good luck!

Oh, good, you'll be fine then.