Merge pull request #451 from katyhuff/2025-updates

2025 updates

Author: katyhuff

manual/guides/guides.md

@@ -16,7 +16,9 @@ that can be captured in one.
 # <a name="gettingstarted"></a>Getting Started
 
 You're new to the research group. There are a lot of tasks to get done before
-you can really fly.
+you can really fly. When you start in the group, work with Prof. Huff to set up 
+a GitHub Project with the following tasks designed as issues to get you 
+started. 
 
 - Handle HR stuff.
 - Get a [GitHub](https://git-scm.com/book/en/v2/GitHub-Account-Setup-and-Configuration) account

manual/guides/katy/codereq.md

@@ -5,23 +5,23 @@ subtitle: "You have a bug. I am not your only hope."
 permalink: /manual/guides/katy/codereq
 ---
 
-![Googling the Error Message](https://pbs.twimg.com/media/CfFPuvoWwAALmcC.jpg "The most important fake book of our time."){:width="270px"}
+![Googling the Error Message](https://raw.githubusercontent.com/denitdao/o-rly-collection/refs/heads/main/public/book_covers/google-error-message.jpg "The most important fake book of our time."){:width="270px"}
 ![Trying Stuff Until It Works](https://pbs.twimg.com/media/CfSQdwUW8AErog1.jpg:large "Another important fake book on persistence."){:width="270px"}
 
+
 # Google it
 
 Please don't come to me with a question that can be solved by a Google search 
-of the error. Especially if you are a Millenial from the U.S., Google really 
-should be in your blood by now. For better google skills, consider 
-[powering up your search tactics](http://www.powersearchingwithgoogle.com/course/aps/skills).
+of the error. In these modern times, Google really 
+should be in your blood by now.
 
-Once you google it, of course, try the things you found on google. 
+Once you google it, of course, try the things you found on google, take notes, 
+and read the errors for clues. 
 
 # Stack Overflow
 
 If Google isn't sufficiently refined, or if your code issue isn't extremely 
-urgent, consider asking your question on the largest programming bug forum in  
-the solar system... [Stack Overflow](http://stackoverflow.com/). Be forewarned: the SO community 
+urgent, consider asking your question on the largest programming bug forum in the solar system... [Stack Overflow](http://stackoverflow.com/). Be forewarned: the SO community 
 is not always friendly or well-moderated for snark. That said, you can definitely improve your odds of kind 
 answers by following [these tips on asking a question 
 well.](http://stackoverflow.com/help/how-to-ask).
@@ -58,14 +58,29 @@ you will need to formulate a [Minimal Working
 Example.](http://stackoverflow.com/help/mcve)
 
 Yes, sometimes a minimal working example is hard to create. If that's the case, 
-I understand. However, you should still do what you can to document what you 
-are trying to do, how you got where you are, how you tried to fix it. I will 
-need this information to help you.
+I understand. However, simply the act of creating one is often enough to 
+provide clues about the source of the error. As you proceed, please do what you 
+can to document what you are trying to do, how you got where you are, how you 
+tried to fix it. I will need this information to help you.
+
+# Collaborate
+
+You're probably in the office as you're doing your research, so you have an 
+excellent resource very nearby! Your colleagues! You might just show them the 
+error you're dealing with, or share your minimal working example on GitHub.  
+Either way, try discussing it in person or on Slack with the other students, 
+and maybe they can help.
 
 # Contact me
 
-If you have tried _everything_ above and nothing has been clarified, then 
-should you email me.  The email should include your minimal working example or 
+There should be ample opportunities to ask me quick questions about what you 
+can try to solve your bug -- try to drop by Coffee Chat or pop by my office if 
+you think it'll only take a few minutes. 
+
+If you have tried _everything_ above and nothing has been clarified,  and you 
+think it might take a while to debut, then 
+should you email me or Slack message me.  If possible, it should point to details somewhere (ideally 
+GitHub or a Gist) about your minimal working example or 
 your detailed documentation of the problem (above). I may need a few days to 
 look it over (so you may as well also add it to Stack Overflow in case they're 
 faster than me.) If I can't help you fix it by email, I'll let you know we 

manual/guides/katy/commreq.md

@@ -8,19 +8,19 @@ permalink: /manual/guides/katy/commreq
 # Conditions
 
 - Your research should be something I can substantively comment on. 
-- Please schedule all committee meetings well in advance (at least two months).
+- Please schedule all committee meetings well in advance (at least a few weeks)..
 - You must have a reproducibility plan for your research that describes how a 
   scientist could reproduce your work. This may involve pointing to data, 
   scripting analysis, version controlling all scripts you use in your work, and 
   recording any details of software that you rely on.
 - You should provide me with yearly updates on your progress.
 - I will need at least two weeks to review any document under 100 pages. For 
-  documents over 100 pages, I will need one month. 
+  documents over 100 pages, I may need longer. 
 - All documents should be provided in PDF format. If you happen to be version 
   controlling the documents you are writing, I am happy to make line comments 
   via GitHub.
-- If I don't know you well, I may ask to set up a meeting before agreeing to be 
-  on your committee.
+- If I don't know you or your research well, I may ask to set up a meeting 
+  before agreeing to be on your committee.
 
 # Asking
 
@@ -29,7 +29,7 @@ information. I'll need to know:
 
 - Where I know you from.
 - Your advisor's name
-- Your topic
+- Your thesis topic
 - Your year in school
 - Your general timeline
 - Your expected graduation date

manual/guides/katy/meeting.md

@@ -7,26 +7,35 @@ permalink: /manual/guides/katy/meeting
 
 I look forward to speaking with you virtually or in person.
 
+# How
+
+I am always open to discuss new ideas with
+colleagues, group members, students, and potential collaborators. My office
+door is often open for this reason. Feel free to pop by. However, if you'd like 
+to schedule a meeting either virtually or in person, you're welcome to use the 
+form described below. 
+
+
 # When
 
-If you are a student in my class, you should meet with me during my stated
-office hours for that course.
+Here's a url where you can pick a time and place that works for you: 
+[katyhuff.youcanbook.me](http://katyhuff.youcanbook.me).  This form works best 
+for scheduling meetings that I've already agreed to (including office hours or 
+student advising meetings). Please email to request a meeting if you think this 
+booking might be a surprise to me. 
 
-For everyone else: here's a url where you can pick a time and place that works for you:
-[katyhuff.youcanbook.me](http://katyhuff.youcanbook.me). It syncs with my
-calendar. Once you've filled it out, we'll both receive an email that confirms
-the details.
+This web app syncs with my calendars. The default duration is 30 minutes. If 
+you need to meet for longer, please change the duration at the top left hand 
+side of the form. Once you've filled it out, we'll both receive an email that 
+confirms the details.
 
 - If it's 5 minutes, try dropping by my office. 
 - If it's 15 minutes, schedule me for a 15 minute meeting. 
 - If it's 30 minutes, schedule me for a 30 minute meeting and come prepared.
 - If it's longer than 30 minutes, are you sure?
 
-# How
 
-I look forward to meeting with you. I am always open to discuss new ideas with
-colleagues, group members, students, and potential collaborators. My office
-door is often open for this reason.  However, please be aware that I
+However, please be aware that I
 think my office hours work most effectively if I arrive prepared. To get the
 most out of your time with me:
 

manual/guides/katy/recreq.md

@@ -14,10 +14,11 @@ first whether I would be willing to support your application.
 
 I am very happy to write a letter of reference for most people who:
 
-- took at least one course from me
-- worked in my research group
-- collaborated with me or my research group
-- or interacted with me in some other way relevant to the application
+- took at least one course from me,
+- worked in my research group,
+- collaborated with me or my research group,
+- served on the UIUC ANS executive committee,
+- or interacted with me in some other way relevant to the application.
 
 In all cases, I consider letter writing an exercise in integrity. I seek to be
 simultaneously as honest and generous as possible. Given this, please use your
@@ -33,8 +34,7 @@ information:
 - Please make your request well in advance (at least a few weeks) before it will be due.
 - Please don't forget to [write a professional email](http://chrisblattman.com/2010/11/08/students-how-to-email-to-your-professor-employer-and-professional-peers/).
 
-I'm going to need some information. 
-Most importantly, if I don't see you on a 
+I'm going to need some information.  Most importantly, if I don't see you on a 
 daily basis, please remind me how we know one another and when we met (what 
 year). 
 

manual/guides/software_templates.md

@@ -17,7 +17,12 @@ that can be useful in software development. If your project falls under the
 range of capabilities they have you can save a lot of time by using them or 
 adapting them to start your project.
 
-## Shablona
+## Scientific Python Development Tools
+[learnscientificpython.org](https://learn.scientific-python.org/development/guides/packaging-simple/) 
+has templates and tutorials guiding development of python packages using the 
+most updated standards and norms in the scientific python community. 
+
+## Shablona 
 [Shablona](https://github.com/uwescience/shablona) is a template repository that 
 is designed for scientific python projects. The template comes with everything a 
 small-scale project might need, and can be easily adapted for python projects.

manual/guides/writing/dissertation.md

@@ -10,7 +10,7 @@ permalink: /manual/guides/writing/dissertation
 - The preliminary examination must be successful before dissertation writing 
   can begin.
 - Create a repository to hold your dissertation during the writing process.
-- A UIUC template is available at: 
+- A UIUC template is available in the ARFC GitHub organization. 
 - Review an outline with your advisor.
 - Collect figures and tables. Arrange them to tell a story.
 - Determine a timeline for each chapter draft to be completed. 

manual/guides/writing/ms-thesis.md

@@ -99,10 +99,10 @@ In Prof. Huff's experience, it is best to enable chapter-by-chapter review of yo
 A great way to do this with Prof. Huff is the following workflow:
 
 - Note the [ms-thesis-template](https://github.com/arfc/ms-thesis-template) in the arfc github org.
-- Create a GitHub respository in your own GitHub user space (ideally, usetemplate).
+- Create a GitHub respository in the ARFC GitHub space (ideally, using the template).
 - Work on this document in your repository. Feel free to use feature branches 
   and merge into master, or just commit directly to master as you go.
-- You need to give Prof. Huff collaborator permission on this repository to allow issue assignment.
+- If your MS repository is in your own GitHub user pace, then give Prof. Huff collaborator permission on this repository to allow issue assignment.
 - At some point, you decide that a part of your masters thesis is ready for 
   Prof. Huff's review (e.g. the literature review chapter) 
 - (optional) Tag the repository at that state. (e.g. ch1-draft-1)
@@ -125,6 +125,7 @@ Both the thesis advisor and the second reader should be given at least two weeks
 
 ## After Writing
 
+- Check the NPRE and UIUC grad college websites for the most recent requirements.
 - Add yourself to the degree list.
 - Get the TDA form from Kristie. 
 - Get Prof. Huff, the 2nd reader, and the NPRE department head to sign the 

manual/guides/writing/prelim.md

@@ -9,8 +9,12 @@ permalink: /manual/guides/writing/prelim
 
 Review the graduate handbook.
 
-- fill ou the PhD Preliminary and Final Exam Proposal form available in the Student Services Office.
-- the students advisor and the department head must approve the thesis committee.
+
+- Work out a plan, scope, and schedule, with Prof. Huff.
+- Fill out the PhD Preliminary and Final Exam Proposal form available in the Student Services Office.
+- Ensure that your advisor and the department head approve the thesis committee.
+- Set up a repository based on the UIUC dissertation template in the ARFC 
+  GitHub org. 
 
 ## Rules of the Prelim