Expand the expectations and better format for manual

manual/communication.md

@@ -2,6 +2,15 @@
 title: Communication
 ---
 
+{% import "macros.html" as macros %}
+
+<div class="lead">
+
+How we communicate in the lab and policies for external engagement when
+representing the lab.
+
+</div>
+
 ## Within the lab
 
 * **Chat:** We have a lab chat room on the [Software Underground's Mattermost server](https://mattermost.softwareunderground.org/).
@@ -39,4 +48,5 @@ title: Communication
 ## Social media
 
 * Lab members are encouraged to be respectful and kind while participating in
-  social media if they are representing themselves as lab members.
+  social media. **If you are representing yourself as a lab member, the lab
+  {{ macros.page_link("manual/coc", page, site) }} applies!**

manual/expectations.md

@@ -2,20 +2,69 @@
 title: Expectations
 ---
 
-We intend to foster a collegial lab atmosphere, with opportunities for
-spontaneous discussions and creative opportunities.
-A large part of that is taking care of our mental well-being:
+{% import "macros.html" as macros %}
 
-* Lab members are **not** expected to sacrifice personal or leisure time in
+<div class="lead">
+
+We intend to foster a **healthy and collegial lab atmosphere**, with
+opportunities for spontaneous discussions, creativity, close collaboration, and
+career progression.
+
+</div>
+
+## Expectations of lab members
+
+A large part of fostering a healthy work environment is taking care of our
+mental well-being:
+
+* Lab members are **not expected to sacrifice personal or leisure time** in
   service of projects.
 * Working long hours without interruption can lead to burnout, exhaustion, and
   overall **impedes** the type of atmosphere we are trying to develop.
+* Lab members are encouraged to **take anual breaks and vacation** time. This
+  is particularly important after periods of high stress (exams, thesis
+  defense, qualifying exams, workshops, etc). Please **let Leo know** when you
+  will be away.
+
+<div class="callout">
+
+Time as a graduate students and as a postdoc is [known to cause undue
+stress](https://www.theatlantic.com/education/archive/2018/11/anxiety-depression-mental-health-graduate-school/576769/),
+resulting in consequences ranging from mild to extremely severe. **Please reach
+out and use the resources in {{ macros.page_link("manual/health", page, site)
+}} if you ever need help.**
+
+</div>
 
 We strive to be a part of the intellectual community at our host universities.
-As such, lab members should endeavor to be good university "citizens",
+As such, lab members should endeavor to be **good university "citizens"**,
 including:
 
-* Participating in department seminars and all-hands meetings.
-* Contributing to department projects (research, teaching, and outreach).
-* Collaborating with individuals from other groups around campus.
+* Participating in **department seminars**, meetings, and other academic activities.
+* Collaborating with individuals from other groups/departments around campus.
 * Fostering new collaborations, both internally and externally.
+
+As lab members, Leo expects you to:
+
+* Be proactive in communicating your needs and desires (guidance, equipment, personal time, career plans, chance of project/mentorship, etc).
+* Be present and working regularly during term time. Please let Leo know if you are busy with other commitments (personal or academic) and won't be working on your project for a time.
+* Follow the lab {{ macros.page_link("manual/coc", page, site) }} and general
+  {{ macros.page_link("manual/open-science", page, site) }} guidelines.
+* Keep on top of your own deadlines (assignments, reports, conferences, etc). Remember to give Leo **at least 1 week** (but preferably more) to give feedback on any piece of work. 
+* Care for the physical environment of the lab, including lab computers.
+
+## What you can expect from Leo
+
+* Lead and set directions for the group's research efforts.
+* Prioritize and support your career progression and well-being, providing the
+  required training and resources for your praticular needs.
+* Be willing to listen to critism and suggestions for improvement.
+* Adjust the style of mentorship to what works best for you (please let me know
+  if something isn't working well).
+* Respond to your messages and requests within a reasonable time, which is
+  around 1 day to 1 week depending on urgency and Leo's schedule.
+* Respect your personal time and not ask for things to be done during evenings,
+  weekends, holidays, and vacation time. You may get a message at these times
+  due to Leo's own working hours but you have no obligation to respond.
+* Seek funding to support lab activities, purchase equipment, scholarships, and
+  conference attendance.

manual/health.md

@@ -2,24 +2,28 @@
 title: Health and well-being
 ---
 
+<div class="lead">
+
 **Your first priority should always be your own health, safety, and
 well-being.**
-No project, paper, grant or collaboration is more important than that.
-In particular, time as a graduate students and as a postdoc is
-[known to cause undue stress](https://www.theatlantic.com/education/archive/2018/11/anxiety-depression-mental-health-graduate-school/576769/),
-resulting in consequences ranging from mild to extremely severe.
+No project, paper, grant, or collaboration is more important than that.
+
+</div>
 
 ## At Universidade de São Paulo
 
 * [Hospital Universitário](https://www.hu.usp.br/): The campus hospital is
   excellent, has a walk-in service and provides free medical for the university
   community.
+* [CEPE USP](https://cepe.usp.br/): The university sports center is full of
+  free activities that you can sign up for and has a large range of pools and
+  fields that also be used.
 * [Clinica Odontológica](https://sau.usp.br/clinica-odontologica/): The São
   Paulo campus also has a free dental health service for the community.
 * [Ministério da Saúde - Suicídio (Prevenção)](https://www.gov.br/saude/pt-br/assuntos/saude-de-a-a-z/s/suicidio-prevencao):
   The ministry of health website has resources for suicide prevention and how
   to get help with mental health issues.
-
+* [Centro de Valorização da Vida](https://cvv.org.br/): Offers a 24h help line by phone, chat, email, and in-person (the closest center to campus is in [Pinheiros](https://www.google.com/maps/place/R.+Cerro+Cor%C3%A1,+792+-+21+-+Vila+Romana,+S%C3%A3o+Paulo+-+SP,+05061-100/@-23.5401302,-46.7049922,19.29z/data=!4m5!3m4!1s0x94ce57d3e451c08b:0x28663176a7d2cad5!8m2!3d-23.5397673!4d-46.7047116?entry=ttu)). 
 
 ## At University of Liverpool
 

manual/index.md

@@ -2,13 +2,12 @@
 title: Lab manual
 toc_table:
   - manual/coc
-  - manual/authorship
-  - manual/open-science
   - manual/induction
+  - manual/open-science
   - manual/expectations
-  - manual/communication
-  - manual/ethics
   - manual/health
+  - manual/authorship
+  - manual/communication
   - manual/software
   - manual/computing
   - manual/resources

manual/induction.md

@@ -4,12 +4,15 @@ title: Getting started
 
 {% import "macros.html" as macros %}
 
+<div class="lead">
+
 When you first join the lab (ideally within the first few weeks), you will have
 a meeting with Leo to introduce lab protocols, set expectations, add you to
-communication channels, etc. **If you don't hear from Leo within a week of
-starting, please remind him by email.**
+communication channels, etc. 
+
+</div>
 
-Things to do after joining:
+## Things to do after joining the lab
 
 1. Create an account on the chat room (see {{ macros.page_link("manual/communication", page, site) }}) and send Leo a message (`@leouieda`) so he can add you to the `CompGeoLab` channel.
 1. Install the [Mattermost app][mattermost]. You don't need to have it on your phone if you prefer not to, but at least install it on your comuter.
@@ -23,7 +26,7 @@ Things to do after joining:
 1. Read the main references for your project (if Leo doesn't send them to you, please remind him).
 1. Go and start making something brilliant!
 
-Leo's To Do list:
+## Leo's To Do list
 
 1. Introduce the [lab website][website] and [GitHub organization][gh] where all
    our research projects live.

manual/open-science.md

@@ -32,6 +32,30 @@ or other restrictions).
   kept confidential at the external collaborators discretion, although our
   preference is for them to be open.
 
+## Research ethics
+
+Our actions should be guided by the ethics of participating in the global
+scientific community.
+This means:
+
+* When other researchers request assistance with software developed in the lab,
+  we should attempt to make a best effort to assist them. It is not
+  unreasonable to ask for authorship, particularly if the collaboration is
+  extensive.
+* Provide citations to all software that assisted in the development of the
+  scholarly work. In general it is acceptable to cite the layers of software in
+  the analysis stack (e.g., NumPy, Matplotlib, IPython/Jupyter, Fatiando, etc.)
+* Provide citations to data sources (DOIs and publications) wherever possible,
+  and where not possible, should be included as footnotes.
+* Plagiarism is unacceptable in any form. This includes "first pass" text
+  included in papers or proposals. If including text from an external source,
+  it must be clearly marked as such to ensure it is not accidentally included
+  in the final product.
+* Prioritizing our professional obligations over fear of being "scooped." For
+  instance, it is unacceptable to interfere with the peer-review process for a
+  paper out of concern of protecting one's own work (i.e., "sitting" on a
+  review for it, making unreasonable requests to delay publication, and so on.)
+
 ## Data and code availability
 
 * All data and models generated by the lab will be made available in both raw