diff --git a/installation/index.html b/installation/index.html
index a6c9183..b770390 100755
--- a/installation/index.html
+++ b/installation/index.html
@@ -735,17 +735,29 @@ Note: WiFi access for Cefas staff
Laptop Installation
For this course you will need to have Python installed on your laptop, including some extra packages. Follow the instructions below to set up your Python environment. Make sure you do this do this before the course, including running the test as below. There will be a troubleshooting session on the first day at 8:30 as advertised in the invite email.
As an alternative you can use cloud hosting by 
to run all the lessons with the data here contained (it is not possible to load your own data), but any changes made won't be saved.
-Feel free to contact Jenny at Cefas or Eliza at UEA if you have any problems with the installation (but better do an internet search first!)
+
Feel free to contact Claire at Cefas or Eliza at UEA if you have any problems with the installation (but better do an internet search first!)
Note: The course is designed in Python 3.9 but even if you have a different version installed, 3.9 will be installed when creating a conda environment in step 3 below.
1. Install Python distribution
1.1. Cefas Users
You will neet to request in advance a temporary administrator password to make the installation.
As a government organisation we do not have free access to Anaconda, so please use the free alternative mambaforge. For those in academia, we also recommend this as a more lightweight (and often faster) python installation option!
+
1.2. Students or UEA Staff
-1.2.1. Download Anaconda with Python 3 for your OS.
-1.2.2. Install it following these instructions. Be sure to select install "just me" when prompted.
+
1.3 UEA HPC (Ada)
If you already have an account on Ada, then it would be possible to run the Jupyter notebooks of the lessons by starting a session on Ada OnDemand. You can try to follow the instructions for laptops for copying and running the lessons, but we won't be able to provide specific support, and so the preferred method is to use your laptop or MyBinder.
2. Download course materials
diff --git a/search/search_index.json b/search/search_index.json
index 67fa8d5..d0e823a 100755
--- a/search/search_index.json
+++ b/search/search_index.json
@@ -1 +1 @@
-{"config":{"indexing":"full","lang":["en"],"min_search_length":3,"prebuild_index":false,"separator":"[\\s\\-]+"},"docs":[{"location":"","text":"Introduction to Python in Environmental Sciences Delivered by ARIES Doctoral Training Programme & the Centre for Environment, Fisheries and Acquaculture Studies General information The 3-day course organised by ARIES DTP and Cefas giving a hands-on introduction to Python programming language. You will learn Python programming, starting from the basics, and evolving into data analysis and visualisation using data formats commonly used in environmental sciences. If you have no programming experience in any language, it is recommended that beforehand you take a 1-2 hour online course, such as Python Basics on datacamp , to get confortable with basic concepts such as variables. Suitable for both python novices and intermediate users. In person course at the UEA ( Zicer Building , room 0.02). Lunch and refreshments will be provided. We will offer a limited number of places online for ARIES studends that are not registered with the UEA and CEFAS staff based in Weymouth. When and where Day Time (BST) Topics covered 1st of July 2024 8:30 - 17:00 Python basics 2nd of July 2024 9:00 - 17:00 Functions, simple programs and arrays 3rd of July 2024 9:00 - 17:00 Plotting and data analysis Topics covered by the course Python basics and programming environment Core scientific libraries: numpy, scipy, pandas Simple visualisation in matplotlib Plotting data on maps Working with environmental sciences data formats Ahead of the course If you have no programming experience in any language, it is recommended that beforehand you take a 1-2 hour online course beforehand to get yourself familiarised with basic concepts such as variables. e.g. Python Basics on datacamp . Install course environment and materials in the week before. Bring your own laptop. Registration and enquiries The course is free for Aries DTP students Cefas staff and CASE students The course is open to all UEA students and staff but there is a fee of 50 GBP. See contact below for enquiries. Register at Eventbrite . If you have queries please contact: Claire (Cefas) Eliza (UEA, Aries) Support after the course? Cefas The PyFAS group meets regularly, to present work, discuss python problems and provide general support. Contact Claire Beraud to join the group and receive future invites. The Turn up & Code code group meets regularly to support personal development in programming in any language. Contact Lianne Harrison if you want to receive calendar invites. UEA The UEA Python group meets occasionally. Check the archives of previous sessions here: https://ueapy.github.io . Or join our Slack workspace to ask questions and take part in weekly coding drop ins.","title":"Home"},{"location":"#introduction-to-python-in-environmental-sciences","text":"Delivered by ARIES Doctoral Training Programme & the Centre for Environment, Fisheries and Acquaculture Studies","title":"Introduction to Python in Environmental Sciences"},{"location":"#general-information","text":"The 3-day course organised by ARIES DTP and Cefas giving a hands-on introduction to Python programming language. You will learn Python programming, starting from the basics, and evolving into data analysis and visualisation using data formats commonly used in environmental sciences. If you have no programming experience in any language, it is recommended that beforehand you take a 1-2 hour online course, such as Python Basics on datacamp , to get confortable with basic concepts such as variables. Suitable for both python novices and intermediate users. In person course at the UEA ( Zicer Building , room 0.02). Lunch and refreshments will be provided. We will offer a limited number of places online for ARIES studends that are not registered with the UEA and CEFAS staff based in Weymouth.","title":"General information"},{"location":"#when-and-where","text":"Day Time (BST) Topics covered 1st of July 2024 8:30 - 17:00 Python basics 2nd of July 2024 9:00 - 17:00 Functions, simple programs and arrays 3rd of July 2024 9:00 - 17:00 Plotting and data analysis","title":"When and where"},{"location":"#topics-covered-by-the-course","text":"Python basics and programming environment Core scientific libraries: numpy, scipy, pandas Simple visualisation in matplotlib Plotting data on maps Working with environmental sciences data formats","title":"Topics covered by the course"},{"location":"#ahead-of-the-course","text":"If you have no programming experience in any language, it is recommended that beforehand you take a 1-2 hour online course beforehand to get yourself familiarised with basic concepts such as variables. e.g. Python Basics on datacamp . Install course environment and materials in the week before. Bring your own laptop.","title":"Ahead of the course"},{"location":"#registration-and-enquiries","text":"The course is free for Aries DTP students Cefas staff and CASE students The course is open to all UEA students and staff but there is a fee of 50 GBP. See contact below for enquiries. Register at Eventbrite . If you have queries please contact: Claire (Cefas) Eliza (UEA, Aries)","title":"Registration and enquiries"},{"location":"#support-after-the-course","text":"","title":"Support after the course?"},{"location":"#cefas","text":"The PyFAS group meets regularly, to present work, discuss python problems and provide general support. Contact Claire Beraud to join the group and receive future invites. The Turn up & Code code group meets regularly to support personal development in programming in any language. Contact Lianne Harrison if you want to receive calendar invites.","title":"Cefas"},{"location":"#uea","text":"The UEA Python group meets occasionally. Check the archives of previous sessions here: https://ueapy.github.io . Or join our Slack workspace to ask questions and take part in weekly coding drop ins.","title":"UEA"},{"location":"content/","text":"Course content You can view the course content on nbviewer . If you want to go through the course material on your own PC, see the installation instructions for information on how to set up a Python environment with the appropriate packages. You can also run Python exercises using a cloud session: . It will let you run interactively the Python code without downloading anything to your local machine. Documentation Below is the documentation for packages used in the course: python jupyter numpy matplotlib seaborn pandas cartopy xarray","title":"Content"},{"location":"content/#course-content","text":"You can view the course content on nbviewer . If you want to go through the course material on your own PC, see the installation instructions for information on how to set up a Python environment with the appropriate packages. You can also run Python exercises using a cloud session: . It will let you run interactively the Python code without downloading anything to your local machine.","title":"Course content"},{"location":"content/#documentation","text":"Below is the documentation for packages used in the course: python jupyter numpy matplotlib seaborn pandas cartopy xarray","title":"Documentation"},{"location":"installation/","text":"Installation instructions Note: WiFi access for Cefas staff If your laptop is configured to use the eduroam academic network this will be available across campus. Alternatively register to Sky's free WiFi The Cloud . Laptop Installation For this course you will need to have Python installed on your laptop, including some extra packages. Follow the instructions below to set up your Python environment. Make sure you do this do this before the course, including running the test as below. There will be a troubleshooting session on the first day at 8:30 as advertised in the invite email. As an alternative you can use cloud hosting by to run all the lessons with the data here contained (it is not possible to load your own data), but any changes made won't be saved. Feel free to contact Jenny at Cefas or Eliza at UEA if you have any problems with the installation (but better do an internet search first!) Note: The course is designed in Python 3.9 but even if you have a different version installed, 3.9 will be installed when creating a conda environment in step 3 below. 1. Install Python distribution 1.1. Cefas Users You will neet to request in advance a temporary administrator password to make the installation. As a government organisation we do not have free access to Anaconda, so please use the free alternative mambaforge. For those in academia, we also recommend this as a more lightweight (and often faster) python installation option! Download Mambaforge for your OS After downloading, follow the instructions as suggested here 1.2. Students or UEA Staff 1.2.1. Download Anaconda with Python 3 for your OS . 1.2.2. Install it following these instructions . Be sure to select install \"just me\" when prompted. 1.3 UEA HPC (Ada) If you already have an account on Ada, then it would be possible to run the Jupyter notebooks of the lessons by starting a session on Ada OnDemand . You can try to follow the instructions for laptops for copying and running the lessons, but we won't be able to provide specific support, and so the preferred method is to use your laptop or MyBinder. 2. Download course materials From the Friday before the course (28th of June) the material for the workshop can be downloaded as a zip file or can be cloned from our GitHub repository . 2.1. Option 1: Download ZIP file (easier) Download the materials as a zip file and unpack it in a suitable directory, for example, in Downloads folder. Jump to 3. Create the environment . 2.2. Option 2: Using Git (allows restoring originals after modifications) 2.2.1. Install Git If you don't have git version control system installed, you can install it following these instructions: Linux Use your package manager. For example, using aptitude you would run the following terminal command: sudo apt-get install git Mac The XCode command line tools need to be installed. Install XCode if it isn\u2019t already. XCode is available in the Mac App Store for free. Launch XCode and accept the license agreement. Quit XCode. Open a new terminal and run the command xcode-select --install Select install on the pop-up menu. Windows Download and install Git for Windows . 2.2.2. Clone the repository Open the command line (Git bash, terminal or cmd.exe) (Linux or Mac, optional) Change to a suitable directory (e.g. cd /home/yourname/Documents ) Clone the repo by typing git clone https://github.com/ueapy/pythoncourse2024-materials.git This should create a local copy of the course materials in the current directory. Windows-users, double check that it has been cloned in the directory you wanted. 3. Create the environment 3.1. Make sure Anaconda or Mambaforge is installed and the course materials are downloaded 3.2. Open the command line or python prompt (i.e., search \"Terminal\" on Mac Spotlight Seach; search \"Anaconda prompt\" or \"mamba\" on Windows start menu) 3.3. Navigate to folder containing the cloned / downloaded course materials. Use the cd command, for example: cd C:\\Users\\myname\\Downloads\\pythoncourse2024-materials\\ 3.4. Create the environment using conda package manager: conda env create -f environment.yml or if you installed mamba mamba env create -f environment.yml This will take some time depending on your Internet speed (<15 minutes). If you get stuck try typing return or, failing this, creating the environment again. 4. Activate the environment Linux / Mac If your default shell is NOT bash, first type bash . Activate the relevant environment by typing: conda activate course2024 Windows Still in the command line (Anaconda/mamba prompt), type: conda activate course2024 5. Test the installation (essential!) From the terminal type: python -c \"import seaborn\" If you don't get any errors then your installation was sucessful. 6. Launch Jupyter Once the environment is activated, type jupyter notebook in the command line. This should open Jupyter Notebook in your browser. We will also demonstrate using Jupyterlab, which is ery similar but offer a more flexible interface. For this type jupyter lab Still having trouble? If you are unable to install Anaconda Python on your PC, contact the course organisers . Another option: launch the course in the cloud! This requires no installation but progress and modifications won't be saved.","title":"Installation"},{"location":"installation/#installation-instructions","text":"","title":"Installation instructions"},{"location":"installation/#note-wifi-access-for-cefas-staff","text":"If your laptop is configured to use the eduroam academic network this will be available across campus. Alternatively register to Sky's free WiFi The Cloud .","title":"Note: WiFi access for Cefas staff"},{"location":"installation/#laptop-installation","text":"For this course you will need to have Python installed on your laptop, including some extra packages. Follow the instructions below to set up your Python environment. Make sure you do this do this before the course, including running the test as below. There will be a troubleshooting session on the first day at 8:30 as advertised in the invite email. As an alternative you can use cloud hosting by to run all the lessons with the data here contained (it is not possible to load your own data), but any changes made won't be saved. Feel free to contact Jenny at Cefas or Eliza at UEA if you have any problems with the installation (but better do an internet search first!) Note: The course is designed in Python 3.9 but even if you have a different version installed, 3.9 will be installed when creating a conda environment in step 3 below.","title":"Laptop Installation"},{"location":"installation/#1-install-python-distribution","text":"","title":"1. Install Python distribution"},{"location":"installation/#11-cefas-users","text":"You will neet to request in advance a temporary administrator password to make the installation. As a government organisation we do not have free access to Anaconda, so please use the free alternative mambaforge. For those in academia, we also recommend this as a more lightweight (and often faster) python installation option! Download Mambaforge for your OS After downloading, follow the instructions as suggested here","title":"1.1. Cefas Users"},{"location":"installation/#12-students-or-uea-staff","text":"1.2.1. Download Anaconda with Python 3 for your OS . 1.2.2. Install it following these instructions . Be sure to select install \"just me\" when prompted.","title":"1.2. Students or UEA Staff"},{"location":"installation/#13-uea-hpc-ada","text":"If you already have an account on Ada, then it would be possible to run the Jupyter notebooks of the lessons by starting a session on Ada OnDemand . You can try to follow the instructions for laptops for copying and running the lessons, but we won't be able to provide specific support, and so the preferred method is to use your laptop or MyBinder.","title":"1.3 UEA HPC (Ada)"},{"location":"installation/#2-download-course-materials","text":"From the Friday before the course (28th of June) the material for the workshop can be downloaded as a zip file or can be cloned from our GitHub repository .","title":"2. Download course materials"},{"location":"installation/#21-option-1-download-zip-file-easier","text":"Download the materials as a zip file and unpack it in a suitable directory, for example, in Downloads folder. Jump to 3. Create the environment .","title":"2.1. Option 1: Download ZIP file (easier)"},{"location":"installation/#22-option-2-using-git-allows-restoring-originals-after-modifications","text":"","title":"2.2. Option 2: Using Git (allows restoring originals after modifications)"},{"location":"installation/#221-install-git","text":"If you don't have git version control system installed, you can install it following these instructions:","title":"2.2.1. Install Git"},{"location":"installation/#linux","text":"Use your package manager. For example, using aptitude you would run the following terminal command: sudo apt-get install git","title":"Linux"},{"location":"installation/#mac","text":"The XCode command line tools need to be installed. Install XCode if it isn\u2019t already. XCode is available in the Mac App Store for free. Launch XCode and accept the license agreement. Quit XCode. Open a new terminal and run the command xcode-select --install Select install on the pop-up menu.","title":"Mac"},{"location":"installation/#windows","text":"Download and install Git for Windows .","title":"Windows"},{"location":"installation/#222-clone-the-repository","text":"Open the command line (Git bash, terminal or cmd.exe) (Linux or Mac, optional) Change to a suitable directory (e.g. cd /home/yourname/Documents ) Clone the repo by typing git clone https://github.com/ueapy/pythoncourse2024-materials.git This should create a local copy of the course materials in the current directory. Windows-users, double check that it has been cloned in the directory you wanted.","title":"2.2.2. Clone the repository"},{"location":"installation/#3-create-the-environment","text":"3.1. Make sure Anaconda or Mambaforge is installed and the course materials are downloaded 3.2. Open the command line or python prompt (i.e., search \"Terminal\" on Mac Spotlight Seach; search \"Anaconda prompt\" or \"mamba\" on Windows start menu) 3.3. Navigate to folder containing the cloned / downloaded course materials. Use the cd command, for example: cd C:\\Users\\myname\\Downloads\\pythoncourse2024-materials\\ 3.4. Create the environment using conda package manager: conda env create -f environment.yml or if you installed mamba mamba env create -f environment.yml This will take some time depending on your Internet speed (<15 minutes). If you get stuck try typing return or, failing this, creating the environment again.","title":"3. Create the environment"},{"location":"installation/#4-activate-the-environment","text":"","title":"4. Activate the environment"},{"location":"installation/#linux-mac","text":"If your default shell is NOT bash, first type bash . Activate the relevant environment by typing: conda activate course2024","title":"Linux / Mac"},{"location":"installation/#windows_1","text":"Still in the command line (Anaconda/mamba prompt), type: conda activate course2024","title":"Windows"},{"location":"installation/#5-test-the-installation-essential","text":"From the terminal type: python -c \"import seaborn\" If you don't get any errors then your installation was sucessful.","title":"5. Test the installation (essential!)"},{"location":"installation/#6-launch-jupyter","text":"Once the environment is activated, type jupyter notebook in the command line. This should open Jupyter Notebook in your browser. We will also demonstrate using Jupyterlab, which is ery similar but offer a more flexible interface. For this type jupyter lab","title":"6. Launch Jupyter"},{"location":"installation/#still-having-trouble","text":"If you are unable to install Anaconda Python on your PC, contact the course organisers . Another option: launch the course in the cloud! This requires no installation but progress and modifications won't be saved.","title":"Still having trouble?"},{"location":"programme/","text":"Programme Before the course, follow the installation instructions and make sure to run the tests . Day 1 - Python basics Monday 1st of July 2024, 8:30 - 17:00 BST Location: UEA BDS 0.21 Notebook # Topic Type Time Duration Troubleshoot installation Support 8:30 0:30 Welcome Lecture 9:00 0:15 0 Introduction to Python Lecture 9:15 0:30 1 How to run Python scripts Lecture 9:45 0:15 2 Jupyter Notebooks Lecture 10:00 0:30 Break 10:30 0:15 3 Python syntax Lecture 10:45 0:35 Mini break 11:20 0:05 4 Python semantics Lecture 11:25 0:35 Lunch break (BDS 0.35) 12:00 1:00 5 Scalar types Lecture 13:00 0:45 Mini break 13:45 0:05 6 Data structures Lecture 13:50 1:00 6 Data structures Exercises 14:50 0:30 Break 15:20 0:15 7 Control flow statements Lectures 15:35 1:00 Day 2 - Functions, simple programs and arrays Tuesday 2nd of July 2024, 9:00 - 17:00 BST Location: UEA BDS 0.21 Notebook # Topic Type Time Duration 7 Control flow statements Lecture 9:00 0:55 Mini break 9:55 0:05 GP 1 Guided practice 1 Exercise 10:00 0:55 Break 10:55 0:15 8 Defining functions Lecture 11:10 0:50 Lunch break (BDS 0.35) 12:00 1:00 9 Build a simple program Exercise 13:00 0:45 10 Errors and exceptions Lecture 13:45 0:20 Mini break 14:05 0:05 11 Modularity and packages Lecture 14:10 0:30 12 Create Module Exercise 14:40 0:30 Break 15:10 0:15 13 NumPy: basics Lecture 15:25 1:00 Mini break 16:25 0:05 13 NumPy: explore arrays Lecture 16:30 0:30 Day 3 - Plotting and data analysis Friday 3rd of July 2024, 9:00 - 17:00 BST Location: UEA BDS 0.21 Notebook # Topic Type Time Duration 13 NumPy: advanced Lecture 9:00 0:55 Mini break 9:55 0:05 14 Intro to matplotlib Lecture 10:00 1:00 Break 11:00 0:15 GP 2 Guided practice 2 Exercise 11:15 0:30 15 Datetime Lecture 11:45 0:15 Lunch break (BDS 0.35) 12:00 1:00 14 More matplotlib Exercise 13:00 0:55 Mini break 13:55 0:05 16 Intro to cartopy Lecture 14:00 0:35 17 Intro to pandas Lecture 14:35 0:45 Break 15:20 0:15 17 More pandas Lecture 15:35 0:30 18,19 xarray and Seaborn Lecture 16:05 0:30","title":"Programme"},{"location":"programme/#programme","text":"Before the course, follow the installation instructions and make sure to run the tests .","title":"Programme"},{"location":"programme/#day-1-python-basics","text":"Monday 1st of July 2024, 8:30 - 17:00 BST Location: UEA BDS 0.21 Notebook # Topic Type Time Duration Troubleshoot installation Support 8:30 0:30 Welcome Lecture 9:00 0:15 0 Introduction to Python Lecture 9:15 0:30 1 How to run Python scripts Lecture 9:45 0:15 2 Jupyter Notebooks Lecture 10:00 0:30 Break 10:30 0:15 3 Python syntax Lecture 10:45 0:35 Mini break 11:20 0:05 4 Python semantics Lecture 11:25 0:35 Lunch break (BDS 0.35) 12:00 1:00 5 Scalar types Lecture 13:00 0:45 Mini break 13:45 0:05 6 Data structures Lecture 13:50 1:00 6 Data structures Exercises 14:50 0:30 Break 15:20 0:15 7 Control flow statements Lectures 15:35 1:00","title":"Day 1 - Python basics"},{"location":"programme/#day-2-functions-simple-programs-and-arrays","text":"Tuesday 2nd of July 2024, 9:00 - 17:00 BST Location: UEA BDS 0.21 Notebook # Topic Type Time Duration 7 Control flow statements Lecture 9:00 0:55 Mini break 9:55 0:05 GP 1 Guided practice 1 Exercise 10:00 0:55 Break 10:55 0:15 8 Defining functions Lecture 11:10 0:50 Lunch break (BDS 0.35) 12:00 1:00 9 Build a simple program Exercise 13:00 0:45 10 Errors and exceptions Lecture 13:45 0:20 Mini break 14:05 0:05 11 Modularity and packages Lecture 14:10 0:30 12 Create Module Exercise 14:40 0:30 Break 15:10 0:15 13 NumPy: basics Lecture 15:25 1:00 Mini break 16:25 0:05 13 NumPy: explore arrays Lecture 16:30 0:30","title":"Day 2 - Functions, simple programs and arrays"},{"location":"programme/#day-3-plotting-and-data-analysis","text":"Friday 3rd of July 2024, 9:00 - 17:00 BST Location: UEA BDS 0.21 Notebook # Topic Type Time Duration 13 NumPy: advanced Lecture 9:00 0:55 Mini break 9:55 0:05 14 Intro to matplotlib Lecture 10:00 1:00 Break 11:00 0:15 GP 2 Guided practice 2 Exercise 11:15 0:30 15 Datetime Lecture 11:45 0:15 Lunch break (BDS 0.35) 12:00 1:00 14 More matplotlib Exercise 13:00 0:55 Mini break 13:55 0:05 16 Intro to cartopy Lecture 14:00 0:35 17 Intro to pandas Lecture 14:35 0:45 Break 15:20 0:15 17 More pandas Lecture 15:35 0:30 18,19 xarray and Seaborn Lecture 16:05 0:30","title":"Day 3 - Plotting and data analysis"}]}
\ No newline at end of file
+{"config":{"indexing":"full","lang":["en"],"min_search_length":3,"prebuild_index":false,"separator":"[\\s\\-]+"},"docs":[{"location":"","text":"Introduction to Python in Environmental Sciences Delivered by ARIES Doctoral Training Programme & the Centre for Environment, Fisheries and Acquaculture Studies General information The 3-day course organised by ARIES DTP and Cefas giving a hands-on introduction to Python programming language. You will learn Python programming, starting from the basics, and evolving into data analysis and visualisation using data formats commonly used in environmental sciences. If you have no programming experience in any language, it is recommended that beforehand you take a 1-2 hour online course, such as Python Basics on datacamp , to get confortable with basic concepts such as variables. Suitable for both python novices and intermediate users. In person course at the UEA ( Zicer Building , room 0.02). Lunch and refreshments will be provided. We will offer a limited number of places online for ARIES studends that are not registered with the UEA and CEFAS staff based in Weymouth. When and where Day Time (BST) Topics covered 1st of July 2024 8:30 - 17:00 Python basics 2nd of July 2024 9:00 - 17:00 Functions, simple programs and arrays 3rd of July 2024 9:00 - 17:00 Plotting and data analysis Topics covered by the course Python basics and programming environment Core scientific libraries: numpy, scipy, pandas Simple visualisation in matplotlib Plotting data on maps Working with environmental sciences data formats Ahead of the course If you have no programming experience in any language, it is recommended that beforehand you take a 1-2 hour online course beforehand to get yourself familiarised with basic concepts such as variables. e.g. Python Basics on datacamp . Install course environment and materials in the week before. Bring your own laptop. Registration and enquiries The course is free for Aries DTP students Cefas staff and CASE students The course is open to all UEA students and staff but there is a fee of 50 GBP. See contact below for enquiries. Register at Eventbrite . If you have queries please contact: Claire (Cefas) Eliza (UEA, Aries) Support after the course? Cefas The PyFAS group meets regularly, to present work, discuss python problems and provide general support. Contact Claire Beraud to join the group and receive future invites. The Turn up & Code code group meets regularly to support personal development in programming in any language. Contact Lianne Harrison if you want to receive calendar invites. UEA The UEA Python group meets occasionally. Check the archives of previous sessions here: https://ueapy.github.io . Or join our Slack workspace to ask questions and take part in weekly coding drop ins.","title":"Home"},{"location":"#introduction-to-python-in-environmental-sciences","text":"Delivered by ARIES Doctoral Training Programme & the Centre for Environment, Fisheries and Acquaculture Studies","title":"Introduction to Python in Environmental Sciences"},{"location":"#general-information","text":"The 3-day course organised by ARIES DTP and Cefas giving a hands-on introduction to Python programming language. You will learn Python programming, starting from the basics, and evolving into data analysis and visualisation using data formats commonly used in environmental sciences. If you have no programming experience in any language, it is recommended that beforehand you take a 1-2 hour online course, such as Python Basics on datacamp , to get confortable with basic concepts such as variables. Suitable for both python novices and intermediate users. In person course at the UEA ( Zicer Building , room 0.02). Lunch and refreshments will be provided. We will offer a limited number of places online for ARIES studends that are not registered with the UEA and CEFAS staff based in Weymouth.","title":"General information"},{"location":"#when-and-where","text":"Day Time (BST) Topics covered 1st of July 2024 8:30 - 17:00 Python basics 2nd of July 2024 9:00 - 17:00 Functions, simple programs and arrays 3rd of July 2024 9:00 - 17:00 Plotting and data analysis","title":"When and where"},{"location":"#topics-covered-by-the-course","text":"Python basics and programming environment Core scientific libraries: numpy, scipy, pandas Simple visualisation in matplotlib Plotting data on maps Working with environmental sciences data formats","title":"Topics covered by the course"},{"location":"#ahead-of-the-course","text":"If you have no programming experience in any language, it is recommended that beforehand you take a 1-2 hour online course beforehand to get yourself familiarised with basic concepts such as variables. e.g. Python Basics on datacamp . Install course environment and materials in the week before. Bring your own laptop.","title":"Ahead of the course"},{"location":"#registration-and-enquiries","text":"The course is free for Aries DTP students Cefas staff and CASE students The course is open to all UEA students and staff but there is a fee of 50 GBP. See contact below for enquiries. Register at Eventbrite . If you have queries please contact: Claire (Cefas) Eliza (UEA, Aries)","title":"Registration and enquiries"},{"location":"#support-after-the-course","text":"","title":"Support after the course?"},{"location":"#cefas","text":"The PyFAS group meets regularly, to present work, discuss python problems and provide general support. Contact Claire Beraud to join the group and receive future invites. The Turn up & Code code group meets regularly to support personal development in programming in any language. Contact Lianne Harrison if you want to receive calendar invites.","title":"Cefas"},{"location":"#uea","text":"The UEA Python group meets occasionally. Check the archives of previous sessions here: https://ueapy.github.io . Or join our Slack workspace to ask questions and take part in weekly coding drop ins.","title":"UEA"},{"location":"content/","text":"Course content You can view the course content on nbviewer . If you want to go through the course material on your own PC, see the installation instructions for information on how to set up a Python environment with the appropriate packages. You can also run Python exercises using a cloud session: . It will let you run interactively the Python code without downloading anything to your local machine. Documentation Below is the documentation for packages used in the course: python jupyter numpy matplotlib seaborn pandas cartopy xarray","title":"Content"},{"location":"content/#course-content","text":"You can view the course content on nbviewer . If you want to go through the course material on your own PC, see the installation instructions for information on how to set up a Python environment with the appropriate packages. You can also run Python exercises using a cloud session: . It will let you run interactively the Python code without downloading anything to your local machine.","title":"Course content"},{"location":"content/#documentation","text":"Below is the documentation for packages used in the course: python jupyter numpy matplotlib seaborn pandas cartopy xarray","title":"Documentation"},{"location":"installation/","text":"Installation instructions Note: WiFi access for Cefas staff If your laptop is configured to use the eduroam academic network this will be available across campus. Alternatively register to Sky's free WiFi The Cloud . Laptop Installation For this course you will need to have Python installed on your laptop, including some extra packages. Follow the instructions below to set up your Python environment. Make sure you do this do this before the course, including running the test as below. There will be a troubleshooting session on the first day at 8:30 as advertised in the invite email. As an alternative you can use cloud hosting by to run all the lessons with the data here contained (it is not possible to load your own data), but any changes made won't be saved. Feel free to contact Claire at Cefas or Eliza at UEA if you have any problems with the installation (but better do an internet search first!) Note: The course is designed in Python 3.9 but even if you have a different version installed, 3.9 will be installed when creating a conda environment in step 3 below. 1. Install Python distribution 1.1. Cefas Users You will neet to request in advance a temporary administrator password to make the installation. As a government organisation we do not have free access to Anaconda, so please use the free alternative mambaforge. For those in academia, we also recommend this as a more lightweight (and often faster) python installation option! Download Mambaforge for your OS After downloading, follow the instructions as suggested here 1.2. Students or UEA Staff Download Anaconda with Python 3 for your OS . Install it following these instructions . Be sure to select install \"just me\" when prompted. 1.3 UEA HPC (Ada) If you already have an account on Ada, then it would be possible to run the Jupyter notebooks of the lessons by starting a session on Ada OnDemand . You can try to follow the instructions for laptops for copying and running the lessons, but we won't be able to provide specific support, and so the preferred method is to use your laptop or MyBinder. 2. Download course materials From the Friday before the course (28th of June) the material for the workshop can be downloaded as a zip file or can be cloned from our GitHub repository . 2.1. Option 1: Download ZIP file (easier) Download the materials as a zip file and unpack it in a suitable directory, for example, in Downloads folder. Jump to 3. Create the environment . 2.2. Option 2: Using Git (allows restoring originals after modifications) 2.2.1. Install Git If you don't have git version control system installed, you can install it following these instructions: Linux Use your package manager. For example, using aptitude you would run the following terminal command: sudo apt-get install git Mac The XCode command line tools need to be installed. Install XCode if it isn\u2019t already. XCode is available in the Mac App Store for free. Launch XCode and accept the license agreement. Quit XCode. Open a new terminal and run the command xcode-select --install Select install on the pop-up menu. Windows Download and install Git for Windows . 2.2.2. Clone the repository Open the command line (Git bash, terminal or cmd.exe) (Linux or Mac, optional) Change to a suitable directory (e.g. cd /home/yourname/Documents ) Clone the repo by typing git clone https://github.com/ueapy/pythoncourse2024-materials.git This should create a local copy of the course materials in the current directory. Windows-users, double check that it has been cloned in the directory you wanted. 3. Create the environment 3.1. Make sure Anaconda or Mambaforge is installed and the course materials are downloaded 3.2. Open the command line or python prompt (i.e., search \"Terminal\" on Mac Spotlight Seach; search \"Anaconda prompt\" or \"mamba\" on Windows start menu) 3.3. Navigate to folder containing the cloned / downloaded course materials. Use the cd command, for example: cd C:\\Users\\myname\\Downloads\\pythoncourse2024-materials\\ 3.4. Create the environment using conda package manager: conda env create -f environment.yml or if you installed mamba mamba env create -f environment.yml This will take some time depending on your Internet speed (<15 minutes). If you get stuck try typing return or, failing this, creating the environment again. 4. Activate the environment Linux / Mac If your default shell is NOT bash, first type bash . Activate the relevant environment by typing: conda activate course2024 Windows Still in the command line (Anaconda/mamba prompt), type: conda activate course2024 5. Test the installation (essential!) From the terminal type: python -c \"import seaborn\" If you don't get any errors then your installation was sucessful. 6. Launch Jupyter Once the environment is activated, type jupyter notebook in the command line. This should open Jupyter Notebook in your browser. We will also demonstrate using Jupyterlab, which is ery similar but offer a more flexible interface. For this type jupyter lab Still having trouble? If you are unable to install Anaconda Python on your PC, contact the course organisers . Another option: launch the course in the cloud! This requires no installation but progress and modifications won't be saved.","title":"Installation"},{"location":"installation/#installation-instructions","text":"","title":"Installation instructions"},{"location":"installation/#note-wifi-access-for-cefas-staff","text":"If your laptop is configured to use the eduroam academic network this will be available across campus. Alternatively register to Sky's free WiFi The Cloud .","title":"Note: WiFi access for Cefas staff"},{"location":"installation/#laptop-installation","text":"For this course you will need to have Python installed on your laptop, including some extra packages. Follow the instructions below to set up your Python environment. Make sure you do this do this before the course, including running the test as below. There will be a troubleshooting session on the first day at 8:30 as advertised in the invite email. As an alternative you can use cloud hosting by to run all the lessons with the data here contained (it is not possible to load your own data), but any changes made won't be saved. Feel free to contact Claire at Cefas or Eliza at UEA if you have any problems with the installation (but better do an internet search first!) Note: The course is designed in Python 3.9 but even if you have a different version installed, 3.9 will be installed when creating a conda environment in step 3 below.","title":"Laptop Installation"},{"location":"installation/#1-install-python-distribution","text":"","title":"1. Install Python distribution"},{"location":"installation/#11-cefas-users","text":"You will neet to request in advance a temporary administrator password to make the installation. As a government organisation we do not have free access to Anaconda, so please use the free alternative mambaforge. For those in academia, we also recommend this as a more lightweight (and often faster) python installation option! Download Mambaforge for your OS After downloading, follow the instructions as suggested here","title":"1.1. Cefas Users"},{"location":"installation/#12-students-or-uea-staff","text":"Download Anaconda with Python 3 for your OS . Install it following these instructions . Be sure to select install \"just me\" when prompted.","title":"1.2. Students or UEA Staff"},{"location":"installation/#13-uea-hpc-ada","text":"If you already have an account on Ada, then it would be possible to run the Jupyter notebooks of the lessons by starting a session on Ada OnDemand . You can try to follow the instructions for laptops for copying and running the lessons, but we won't be able to provide specific support, and so the preferred method is to use your laptop or MyBinder.","title":"1.3 UEA HPC (Ada)"},{"location":"installation/#2-download-course-materials","text":"From the Friday before the course (28th of June) the material for the workshop can be downloaded as a zip file or can be cloned from our GitHub repository .","title":"2. Download course materials"},{"location":"installation/#21-option-1-download-zip-file-easier","text":"Download the materials as a zip file and unpack it in a suitable directory, for example, in Downloads folder. Jump to 3. Create the environment .","title":"2.1. Option 1: Download ZIP file (easier)"},{"location":"installation/#22-option-2-using-git-allows-restoring-originals-after-modifications","text":"","title":"2.2. Option 2: Using Git (allows restoring originals after modifications)"},{"location":"installation/#221-install-git","text":"If you don't have git version control system installed, you can install it following these instructions:","title":"2.2.1. Install Git"},{"location":"installation/#linux","text":"Use your package manager. For example, using aptitude you would run the following terminal command: sudo apt-get install git","title":"Linux"},{"location":"installation/#mac","text":"The XCode command line tools need to be installed. Install XCode if it isn\u2019t already. XCode is available in the Mac App Store for free. Launch XCode and accept the license agreement. Quit XCode. Open a new terminal and run the command xcode-select --install Select install on the pop-up menu.","title":"Mac"},{"location":"installation/#windows","text":"Download and install Git for Windows .","title":"Windows"},{"location":"installation/#222-clone-the-repository","text":"Open the command line (Git bash, terminal or cmd.exe) (Linux or Mac, optional) Change to a suitable directory (e.g. cd /home/yourname/Documents ) Clone the repo by typing git clone https://github.com/ueapy/pythoncourse2024-materials.git This should create a local copy of the course materials in the current directory. Windows-users, double check that it has been cloned in the directory you wanted.","title":"2.2.2. Clone the repository"},{"location":"installation/#3-create-the-environment","text":"3.1. Make sure Anaconda or Mambaforge is installed and the course materials are downloaded 3.2. Open the command line or python prompt (i.e., search \"Terminal\" on Mac Spotlight Seach; search \"Anaconda prompt\" or \"mamba\" on Windows start menu) 3.3. Navigate to folder containing the cloned / downloaded course materials. Use the cd command, for example: cd C:\\Users\\myname\\Downloads\\pythoncourse2024-materials\\ 3.4. Create the environment using conda package manager: conda env create -f environment.yml or if you installed mamba mamba env create -f environment.yml This will take some time depending on your Internet speed (<15 minutes). If you get stuck try typing return or, failing this, creating the environment again.","title":"3. Create the environment"},{"location":"installation/#4-activate-the-environment","text":"","title":"4. Activate the environment"},{"location":"installation/#linux-mac","text":"If your default shell is NOT bash, first type bash . Activate the relevant environment by typing: conda activate course2024","title":"Linux / Mac"},{"location":"installation/#windows_1","text":"Still in the command line (Anaconda/mamba prompt), type: conda activate course2024","title":"Windows"},{"location":"installation/#5-test-the-installation-essential","text":"From the terminal type: python -c \"import seaborn\" If you don't get any errors then your installation was sucessful.","title":"5. Test the installation (essential!)"},{"location":"installation/#6-launch-jupyter","text":"Once the environment is activated, type jupyter notebook in the command line. This should open Jupyter Notebook in your browser. We will also demonstrate using Jupyterlab, which is ery similar but offer a more flexible interface. For this type jupyter lab","title":"6. Launch Jupyter"},{"location":"installation/#still-having-trouble","text":"If you are unable to install Anaconda Python on your PC, contact the course organisers . Another option: launch the course in the cloud! This requires no installation but progress and modifications won't be saved.","title":"Still having trouble?"},{"location":"programme/","text":"Programme Before the course, follow the installation instructions and make sure to run the tests . Day 1 - Python basics Monday 1st of July 2024, 8:30 - 17:00 BST Location: UEA BDS 0.21 Notebook # Topic Type Time Duration Troubleshoot installation Support 8:30 0:30 Welcome Lecture 9:00 0:15 0 Introduction to Python Lecture 9:15 0:30 1 How to run Python scripts Lecture 9:45 0:15 2 Jupyter Notebooks Lecture 10:00 0:30 Break 10:30 0:15 3 Python syntax Lecture 10:45 0:35 Mini break 11:20 0:05 4 Python semantics Lecture 11:25 0:35 Lunch break (BDS 0.35) 12:00 1:00 5 Scalar types Lecture 13:00 0:45 Mini break 13:45 0:05 6 Data structures Lecture 13:50 1:00 6 Data structures Exercises 14:50 0:30 Break 15:20 0:15 7 Control flow statements Lectures 15:35 1:00 Day 2 - Functions, simple programs and arrays Tuesday 2nd of July 2024, 9:00 - 17:00 BST Location: UEA BDS 0.21 Notebook # Topic Type Time Duration 7 Control flow statements Lecture 9:00 0:55 Mini break 9:55 0:05 GP 1 Guided practice 1 Exercise 10:00 0:55 Break 10:55 0:15 8 Defining functions Lecture 11:10 0:50 Lunch break (BDS 0.35) 12:00 1:00 9 Build a simple program Exercise 13:00 0:45 10 Errors and exceptions Lecture 13:45 0:20 Mini break 14:05 0:05 11 Modularity and packages Lecture 14:10 0:30 12 Create Module Exercise 14:40 0:30 Break 15:10 0:15 13 NumPy: basics Lecture 15:25 1:00 Mini break 16:25 0:05 13 NumPy: explore arrays Lecture 16:30 0:30 Day 3 - Plotting and data analysis Friday 3rd of July 2024, 9:00 - 17:00 BST Location: UEA BDS 0.21 Notebook # Topic Type Time Duration 13 NumPy: advanced Lecture 9:00 0:55 Mini break 9:55 0:05 14 Intro to matplotlib Lecture 10:00 1:00 Break 11:00 0:15 GP 2 Guided practice 2 Exercise 11:15 0:30 15 Datetime Lecture 11:45 0:15 Lunch break (BDS 0.35) 12:00 1:00 14 More matplotlib Exercise 13:00 0:55 Mini break 13:55 0:05 16 Intro to cartopy Lecture 14:00 0:35 17 Intro to pandas Lecture 14:35 0:45 Break 15:20 0:15 17 More pandas Lecture 15:35 0:30 18,19 xarray and Seaborn Lecture 16:05 0:30","title":"Programme"},{"location":"programme/#programme","text":"Before the course, follow the installation instructions and make sure to run the tests .","title":"Programme"},{"location":"programme/#day-1-python-basics","text":"Monday 1st of July 2024, 8:30 - 17:00 BST Location: UEA BDS 0.21 Notebook # Topic Type Time Duration Troubleshoot installation Support 8:30 0:30 Welcome Lecture 9:00 0:15 0 Introduction to Python Lecture 9:15 0:30 1 How to run Python scripts Lecture 9:45 0:15 2 Jupyter Notebooks Lecture 10:00 0:30 Break 10:30 0:15 3 Python syntax Lecture 10:45 0:35 Mini break 11:20 0:05 4 Python semantics Lecture 11:25 0:35 Lunch break (BDS 0.35) 12:00 1:00 5 Scalar types Lecture 13:00 0:45 Mini break 13:45 0:05 6 Data structures Lecture 13:50 1:00 6 Data structures Exercises 14:50 0:30 Break 15:20 0:15 7 Control flow statements Lectures 15:35 1:00","title":"Day 1 - Python basics"},{"location":"programme/#day-2-functions-simple-programs-and-arrays","text":"Tuesday 2nd of July 2024, 9:00 - 17:00 BST Location: UEA BDS 0.21 Notebook # Topic Type Time Duration 7 Control flow statements Lecture 9:00 0:55 Mini break 9:55 0:05 GP 1 Guided practice 1 Exercise 10:00 0:55 Break 10:55 0:15 8 Defining functions Lecture 11:10 0:50 Lunch break (BDS 0.35) 12:00 1:00 9 Build a simple program Exercise 13:00 0:45 10 Errors and exceptions Lecture 13:45 0:20 Mini break 14:05 0:05 11 Modularity and packages Lecture 14:10 0:30 12 Create Module Exercise 14:40 0:30 Break 15:10 0:15 13 NumPy: basics Lecture 15:25 1:00 Mini break 16:25 0:05 13 NumPy: explore arrays Lecture 16:30 0:30","title":"Day 2 - Functions, simple programs and arrays"},{"location":"programme/#day-3-plotting-and-data-analysis","text":"Friday 3rd of July 2024, 9:00 - 17:00 BST Location: UEA BDS 0.21 Notebook # Topic Type Time Duration 13 NumPy: advanced Lecture 9:00 0:55 Mini break 9:55 0:05 14 Intro to matplotlib Lecture 10:00 1:00 Break 11:00 0:15 GP 2 Guided practice 2 Exercise 11:15 0:30 15 Datetime Lecture 11:45 0:15 Lunch break (BDS 0.35) 12:00 1:00 14 More matplotlib Exercise 13:00 0:55 Mini break 13:55 0:05 16 Intro to cartopy Lecture 14:00 0:35 17 Intro to pandas Lecture 14:35 0:45 Break 15:20 0:15 17 More pandas Lecture 15:35 0:30 18,19 xarray and Seaborn Lecture 16:05 0:30","title":"Day 3 - Plotting and data analysis"}]}
\ No newline at end of file
diff --git a/sitemap.xml.gz b/sitemap.xml.gz
index e5184fc..e7ed30c 100755
Binary files a/sitemap.xml.gz and b/sitemap.xml.gz differ