Updated assignment docs for DyOc 2025/26

README.md

@@ -34,7 +34,7 @@
 
 <!-- Insert catchy summary -->
 
-VirtualShipParcels is a command line simulator allowing students to plan and conduct a virtual research expedition, receiving measurements as if they were coming from actual oceanographic instruments including:
+VirtualShip is a command line simulator allowing students to plan and conduct a virtual research expedition, receiving measurements as if they were coming from actual oceanographic instruments including:
 
 - ADCP (currents)
 - CTD (conductivity and temperature + biogeochemical variables)

docs/conf.py

@@ -2,7 +2,7 @@
 
 import importlib.metadata
 
-project = "Virtual Ship Parcels"
+project = "VirtualShip Parcels"
 copyright = "2024, Emma Daniëls"
 author = "Emma Daniëls"
 version = release = importlib.metadata.version("virtualship")

docs/index.md

@@ -1,4 +1,4 @@
-# Virtual Ship Parcels
+# VirtualShip
 
 ```{toctree}
 :maxdepth: 1

docs/user-guide/assignments/Code_of_conduct.ipynb

@@ -5,39 +5,41 @@
    "metadata": {},
    "source": [
     "## Code of conduct\n",
-    "_As used during the Dynamical Oceanography 2024/25 course at Utrecht University_"
+    "_As used during the Dynamical Oceanography 2025/26 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",
+    "_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 to Brightspace before Wednesday 18 February 13:00._ \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._"
+    "**Note that the Code of Conduct applies to the actual collaboration within your group in the VirtualShip Assignment; so is not about how you would work on the ship.**\n",
+    "\n",
+    "---"
    ]
   },
   {
    "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 an exercise by Aurelia Moser.\n",
+    "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",
+    "**Characteristics we value**: [FILL IN]\n",
     "\n",
-    "Behaviors we discourage: [FILL IN]\n",
+    "**Behaviours we encourage**: [FILL IN]\n",
+    "    \n",
+    "**Behaviours we discourage**: [FILL IN]\n",
     "\n",
-    "The way we redistribute the grade: [FILL IN]\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",
+    "_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",
+    "**We make each others feel safe and supported by**: [FILL IN]\n",
     "\n",
-    "How to report an issue, should someone violate the code?\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."
    ]
@@ -54,11 +56,12 @@
    "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",
+    "**Participation Guidelines**\n",
+    "\n",
+    "When participating in Dynamical Oceanography, respect the Utrecht University guideline for [academic and scientific integrity](https://www.uu.nl/sites/default/files/code_of_conduct_for_scrupulous_academic_conduct_and_integrity_-_en_def_0.pdf) and [code of conduct](https://www.universiteitenvannederland.nl/files/publications/Netherlands%20Code%20of%20Conduct%20for%20Research%20Integrity%202018.pdf). 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",
+    "**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",
@@ -77,13 +80,13 @@
     "\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",
+    "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",
+    "**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"
+    "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."
    ]
   }
  ],

docs/user-guide/assignments/Sail_the_ship.ipynb

@@ -113,10 +113,10 @@
     "### Upload the coordinates to your virtual machine\n",
     "\n",
     "<div class=\"alert alert-block alert-warning\"> \n",
-    "**IMPORTANT**: _If you have not done so already_, make sure you create a folder for your group's expedition data in the persistent storage on SURF RC (i.e. the `data/storage-osl/` folder). You can do so by running `mkdir /data/storage-osl/{your-group-name}` in Terminal, replacing `{your-group-name}` with your actual group name, or by using the \"New Folder\" button in the JupyterLab file explorer panel.\n",
+    "**IMPORTANT**: _If you have not done so already_, make sure you create a folder for your group's expedition data in the persistent storage on SURF RC (i.e. the `data/storage/` folder). You can do so by running `mkdir /data/storage/{your-group-name}` in Terminal, replacing `{your-group-name}` with your actual group name, or by using the \"New Folder\" button in the JupyterLab file explorer panel.\n",
     "</div>\n",
     "\n",
-    "Back in the SURF RC JupyterLab interface, use the **file explorer** on the left hand side to navigate to the directory where your group will be running your expedition (i.e. `data/storage-osl/{your-group-name}`). \n",
+    "Back in the SURF RC JupyterLab interface, use the **file explorer** on the left hand side to navigate to the directory where your group will be running your expedition (i.e. `data/storage/{your-group-name}`). \n",
     "\n",
     "Then upload the exported .xlsx file (it will be called something like \"Coordinates-20251125T1403.xlsx\") by either dragging and dropping it from your laptop's Downloads into the file explorer, or by using the \"Upload Files\" button (the icon with an upward arrow) at the top of the file explorer panel."
    ]
@@ -130,7 +130,7 @@
     "Open a Terminal window if you do not already have one open. Remember, this can be done from the Launcher tab by clicking on \"Terminal\" button under the \"Other\" section, or by going to the \"File\" menu --> \"New\" --> \"Terminal\".\n",
     "\n",
     "<div class=\"alert alert-block alert-warning\"> \n",
-    "**IMPORTANT**: Once in Terminal, navigate to where you would like your expedition to be run on your (virtual) machine. You can do so by `cd /data/storage-osl/{your-group-name}`, replacing `{your-group-name}` with your actual group name. This is where you will be working from for the rest of the session.\n",
+    "**IMPORTANT**: Once in Terminal, navigate to where you would like your expedition to be run on your (virtual) machine. You can do so by `cd /data/storage/{your-group-name}`, replacing `{your-group-name}` with your actual group name. This is where you will be working from for the rest of the session.\n",
     "</div>\n",
     "\n",
     "Now enter the following command in the Terminal (changing `EXPEDITION_NAME` to something more meaningful for your group's expedition):\n",
@@ -246,9 +246,9 @@
     "\n",
     "From here you can carry on your analysis. In general, we encourage you to explore and analyse these data using [Xarray](https://docs.xarray.dev/en/stable/). We also provide various further [VirtualShip tutorials](https://virtualship.readthedocs.io/en/latest/user-guide/tutorials/index.html) which provide examples of how to visualise data recorded by the VirtualShip instruments. Use these to help you get started!\n",
     "\n",
-    "If you are using VirtualShip in class, the same tutorial notebooks will be uploaded in your SURF RC environment for you to use and interact directly with the code. These should be available in e.g. the `data/storage-osl/tutorials/` directory. You will notice that there is a notebook file dedicated to visualising each of the different instruments available in VirtualShip. \n",
+    "If you are using VirtualShip in class, the same tutorial notebooks will be uploaded in your SURF RC environment for you to use and interact directly with the code. These should be available in e.g. the `data/storage/tutorials/` directory. You will notice that there is a notebook file dedicated to visualising each of the different instruments available in VirtualShip. \n",
     "\n",
-    "To run these notebooks with your own data, you will need to copy the them over to your expedition working directory (i.e. `data/storage-osl/{your-group-name}`). This can be done by either 1) using the file explorer panel in JupyterLab to copy the relevant files or the via the command line in Terminal. In the terminal, running `cp -r /data/storage-osl/tutorials/* /data/storage-osl/{your-group-name}/` would copy __all__ the tutorial notebooks to your group's directory, so if you only want to copy specific ones, make sure to adjust the command accordingly."
+    "To run these notebooks with your own data, you will need to copy the them over to your expedition working directory (i.e. `data/storage/{your-group-name}`). This can be done by either 1) using the file explorer panel in JupyterLab to copy the relevant files or the via the command line in Terminal. In the terminal, running `cp -r /data/storage/tutorials/* /data/storage/{your-group-name}/` would copy __all__ the tutorial notebooks to your group's directory, so if you only want to copy specific ones, make sure to adjust the command accordingly."
    ]
   },
   {

docs/user-guide/assignments/index.md

@@ -5,9 +5,8 @@
 maxdepth: 1
 caption: Assignments
 ---
-Virtualship_research_proposal.ipynb
 Research_proposal_intro.ipynb
-Research_Proposal_only.ipynb
+Virtualship_research_proposal.ipynb
 sciencecommunication_assignment.ipynb
 Code_of_conduct.ipynb
 case_studies_virtualship.ipynb