Merge branch 'main' into instrument-refactor

Author: j-atkins

docs/conf.py

@@ -75,6 +75,10 @@
     "user-guide/assignments/Research_Proposal_only": "user-guide/_images/MFP.jpg",
     "user-guide/assignments/Virtualship_research_proposal": "user-guide/_images/AnnaWeber.jpeg",
     "user-guide/assignments/sciencecommunication_assignment": "user-guide/_images/marine_ss.jpg",
-    "user-guide/assignments/Sail_the_ship": "user-guide/_images/vessel.jpg",
+    "user-guide/assignments/Sail_the_ship": "user-guide/_images/freepik_research_vessel.jpg",
+    "user-guide/assignments/Code_of_conduct": "user-guide/_images/freepik_code_of_conduct.jpg",
 }
+
+sphinx_gallery_conf = {"default_thumb_file": "_static/virtual_ship_logo.png"}
+
 nbsphinx_execute = "never"

docs/user-guide/_images/ILOs.jpg

@@ -0,0 +1,104 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Code of conduct\n",
+    "_As used during the Dynamical Oceanography 2024/25 course at Utrecht University_"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "_Please read this code of conduct, fill out the [parts between brackets] after consultation with your group, remove these italic sections, and then all individually upload a copy._ \n",
+    "\n",
+    "_Note that the Code of Conduct applies to the actual collaboration within your group in the Virtual Ship Assignment; so is not about how you would work on the ship._"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "This code of conduct has been decided by [NAMES] for their group project during the Virtual Ship Classroom and is enacted from [DD-MM-YYYY]. The procedure is based on [this exercise by Aurelia Moser](http://aureliamoser.com/aaas-guides/conduct/index.html)\n",
+    "\n",
+    "Everyone taking part in the course and group discussions (mentors, helpers, coordinators, and learners) is required to conform to the following Code of Conduct. Coordinators will oversee adherence to this code throughout the course.\n",
+    "\n",
+    "Characteristics we value: [FILL IN]\n",
+    "\n",
+    "Behaviors we encourage: [FILL IN]\n",
+    "\n",
+    "Behaviors we discourage: [FILL IN]\n",
+    "\n",
+    "The way we redistribute the grade: [FILL IN]\n",
+    "\n",
+    "Choose for example “Everyone in the team gets the same grade”, “Everyone can propose a bonus point to one other person, which is then subtracted from other team member’s grades”, “We decide as a group who gets up to x bonus/penalty points”, or any other way to redistribute the grade, as long as the average of the group is not affected. \n",
+    "\n",
+    "We make each others feel safe and supported by: [FILL IN]\n",
+    "\n",
+    "How to report an issue, should someone violate the code?\n",
+    "1.\tContact the course instructor by private message, or in person. All communication will be treated as confidential.\n",
+    "2.\tIf for any reason you don’t want to do 1, you can contact the university Academic Integrity Counsellor."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Community Participation Guidelines"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Apart from the code of conduct, all participants in this course must follow these general guidelines.\n",
+    "Participation \n",
+    "\n",
+    "When participating in Dynamical Oceanography, respect the Utrecht University guideline for academic and scientific integrity and code of conduct. These guidelines cover our behaviour as participants, mentors, experts, staff, volunteers, and anyone else involved in making this course possible.\n",
+    "\n",
+    "How to treat each other\n",
+    "\n",
+    "To create a collaborative and inviting learning environment, we also emphasise certain values in how we treat each other:\n",
+    "*\tBe respectful and value each other’s ideas, styles and viewpoints.\n",
+    "*\tBe direct but professional; we cannot withhold hard truths.\n",
+    "*\tBe inclusive and help new perspectives be heard.\n",
+    "*\tAppreciate and accommodate our many cultural practices, attitudes and beliefs.\n",
+    "*\tBe open to learning from others.\n",
+    "*\tLead by example and match your actions with your words.\n",
+    "\n",
+    "The following will not be tolerated during the activities related to this course:\n",
+    "*\tviolence and threats of violence.\n",
+    "*\tpersonal attacks; derogatory language.\n",
+    "*\tunwelcome sexual attention or physical contact.\n",
+    "*\tdisruptive behavior.\n",
+    "*\tinfluencing unacceptable behavior.\n",
+    "\n",
+    "### Inclusion and Diversity\n",
+    "\n",
+    "We welcome contributions from everyone as long as they interact constructively with our community, including, but not limited to people of varied age, culture, ethnicity, gender, gender-identity, language, race, sexual orientation, geographical location and religious views.\n",
+    "\n",
+    "Raising Issues\n",
+    "\n",
+    "If you believe you‘re experiencing practices which don‘t meet the above policies, or if you feel you are being harassed in any way, please immediately contact the course coordinator, or the university Academic Integrity Counsellor.\n",
+    "\n",
+    "The course coordinator reserves the right to refuse admission to anyone violating these policies, and/or take further action including reporting to the responsible figure for academic integrity at the department.\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "[Thumbnail image](_images/freepik_code_of_conduct.jpg)"
+   ]
+  }
+ ],
+ "metadata": {
+  "language_info": {
+   "name": "python"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

docs/user-guide/_images/freepik_code_of_conduct.jpg

@@ -177,6 +177,13 @@
     "![Our ocean provides](https://seewhatgrows.org/wp-content/uploads/2019/06/our-ocean.jpg)\n",
     "![10 ways to help our ocean](https://oceanservice.noaa.gov/ocean/help-ocean.jpg)"
    ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "[Thumbnail image](_images/freepik_research_vessel.jpg)"
+   ]
   }
  ],
  "metadata": {

docs/user-guide/_images/freepik_research_vessel.jpg

@@ -5,9 +5,9 @@
 maxdepth: 1
 caption: Assignments
 ---
+Virtualship_research_proposal.ipynb
 Research_proposal_intro.ipynb
 Research_Proposal_only.ipynb
-Virtualship_research_proposal.ipynb
 sciencecommunication_assignment.ipynb
 <!-- Sail_the_ship.ipynb -->
 ```

docs/user-guide/_images/vessel.jpg

@@ -4,6 +4,7 @@
 :maxdepth: 1
 
 quickstart
+teacher-content/index
 tutorials/index
 assignments/index
 ```

docs/user-guide/assignments/Code_of_conduct.ipynb

@@ -0,0 +1,69 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "84d1c60b",
+   "metadata": {},
+   "source": [
+    "# Aligned learning outcomes\n",
+    "\n",
+    "_Aligned using the revised version of Blooms taxonomy (Anderson et al. 2001)_\n",
+    "\n",
+    "1. Identify practical challenges of planning sea-based research, such as:\n",
+    "\n",
+    "- Availability and capabilities of research vessels and equipment, e.g. ice breaker vessel needed, infrastructure for equipment available\n",
+    "- General logistics, e.g. transportation of container labs and other equipment\n",
+    "- Requesting permits\n",
+    "  - Travel permits for staff\n",
+    "  - Diplomatic clearance (EEZ)\n",
+    "  - Customs documents\n",
+    "- Safety trainings (beforehand and onboard)\n",
+    "- Preparing, testing and transporting equipment\n",
+    "\n",
+    "2. Be aware of (describe) matters during sea-based research, such as:\n",
+    "\n",
+    "- Contingency due to weather conditions and other unforeseen circumstances\n",
+    "- The need to be flexible and patient\n",
+    "- Taking notes, recording coordinates, stations, casts\n",
+    "- Measurement protocols\n",
+    "- Communication with crew, e.g. captain, winch driver\n",
+    "- Living at sea, e.g. sea legs, seasickness, relaxation, water/energy/waste footprint\n",
+    "\n",
+    "3. Give examples of uncertainty and variability of sea-based observations, such as:\n",
+    "\n",
+    "- Likely errors or wrong values, and seeing the data through the noise\n",
+    "- Time and date coordinates, e.g. UTC, local time, ship time\n",
+    "- Variability and limitations of measurements\n",
+    "- Different scales of variability, e.g. tidal, seasonal\n",
+    "- ‘Synopticity’ of measurements (i.e. not possible to measure with one ship at multiple locations at the same time; therefore mixing time and space variability)\n",
+    "- Instrument specific qualities, e.g. ADCP reflection\n",
+    "\n",
+    "4. Learn how to analyse and interpret sea-based observations. Be able to:\n",
+    "\n",
+    "- Read in different data formats, e.g. nc, csv, zarr\n",
+    "- Manipulate arrays and other data structures in python\n",
+    "- Create and interpret density/TS profiles\n",
+    "- Create spatial temperature/salinity/velocity maps, do GIS things\n",
+    "- Interpret plots and deduce ocean circulation\n",
+    "- Report findings\n",
+    "- Contribute to a cruise report with pictures or plots\n",
+    "\n",
+    "5. Plan a research cruise. Be able to:\n",
+    "\n",
+    "- Formulate research questions\n",
+    "- Select sampling sites\n",
+    "- Consider the duration of deployments, e.g. time a CTD station takes\n",
+    "- Decide on on-site measurement order\n",
+    "- Plan rest/working shifts for scientific personnel\n",
+    "- Deal with contingency, e.g. consider what sites/measurements are essential, which are ok to skip"
+   ]
+  }
+ ],
+ "metadata": {
+  "language_info": {
+   "name": "python"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}