diff --git a/.codespellrc b/.codespellrc index 93489c8..0e48280 100644 --- a/.codespellrc +++ b/.codespellrc @@ -1,4 +1,4 @@ [codespell] skip = '.git' check-hidden = true -ignore-words-list = portugues \ No newline at end of file +ignore-words-list = portugues,fo \ No newline at end of file diff --git a/docs/source/_static/osw_images/animals-in-motion-card.png b/docs/source/_static/osw_images/animals-in-motion-card.png index 1cead8e..f25688a 100644 Binary files a/docs/source/_static/osw_images/animals-in-motion-card.png and b/docs/source/_static/osw_images/animals-in-motion-card.png differ diff --git a/docs/source/conf.py b/docs/source/conf.py index 1598f0e..65d31e6 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -71,6 +71,7 @@ # https://github.com/neuroinformatics-unit/actions/pull/24#issue-1978966182 linkcheck_anchors_ignore_for_url = ["https://neuroinformatics.zulipchat.com/"] linkcheck_ignore = [ + "https://www.dropbox.com", "https://opensource.org", "https://www.incf.org/recommendations-gsoc-contributors", "https://www.incf.org/sites/default/files/files/INCF_GSoC_2022_Application_template.pdf", diff --git a/docs/source/open-software-week/animals-in-motion.md b/docs/source/open-software-week/animals-in-motion.md index 53f4a1e..490c45f 100644 --- a/docs/source/open-software-week/animals-in-motion.md +++ b/docs/source/open-software-week/animals-in-motion.md @@ -30,28 +30,78 @@ __Wednesday:__ The second day will be dedicated to a practical tutorial on [movement](https://movement.neuroinformatics.dev)—a Python toolbox for analysing animal body movements across space and time. You'll learn how to load, clean, visualise, and quantify motion tracks, and apply this knowledge to specific use cases through computational exercises. +::: {admonition} Course materials +:class: note + +All course materials will be made available at during the workshop and will remain accessible afterwards. + +The source code for the course materials is publicly hosted at . +::: + ## Instructors - [Niko Sirmpilatze](https://github.com/niksirbi) - [Sofía Miñano](https://github.com/sfmig) - [Chang Huan Lo](https://github.com/lochhh) -## Pre-requisites +(target-animals-in-motion-prerequisites)= +## Prerequisites ### Hardware -As this is a hands-on workshop, we recommend bringing your own laptop. -A mouse is also recommended for tasks like image annotation. -A dedicated GPU is __not__ required +This is a hands-on course, so please bring your own **laptop** and **charger**. +A **mouse** is strongly recommended, especially for tasks like image annotation. +A dedicated **GPU is not required**, though it may speed up some computations. ### Software -Please ensure you have the following installed: -- A Python IDE such as: - - [Visual Studio Code](https://code.visualstudio.com/) with the [Python extension](https://marketplace.visualstudio.com/items?itemName=ms-python.python) - - [PyCharm](https://www.jetbrains.com/pycharm/) - - [JupyterLab](https://jupyter.org/install) -- A working `conda` (or `mamba`) installation. If you don't have it, install via [Miniforge](https://github.com/conda-forge/miniforge). -- A working [Git](https://git-scm.com/) installation. +For general software requirements, please see the [prerequisites](target-general-prerequisites) on the main event page and make sure you have these installed and properly configured. + +In addition to the general tools, you will need to install +the following specialised software: + +::::{tab-set} + +:::{tab-item} SLEAP + +Please install [SLEAP](https://sleap.ai/) following the [official installation instructions](https://sleap.ai/installation.html). + +For this workshop, use **SLEAP version 1.3.4**. Be sure to replace the default version number (e.g. 1.4.1) in the instructions with 1.3.4. + +This should create a `conda` environment named `sleap` with the necessary dependencies. You can verify the installation by running: + +```bash +conda activate sleap +sleap-label +``` +This should launch the SLEAP graphical user interface (GUI). + +::: -We will email you at least a week before the event with instructions on installing any additional required software. +:::{tab-item} movement + +You will also need a separate `conda` environment to use for interactive coding exercises. +This environment will include the [movement](https://movement.neuroinformatics.dev/) and [jupyter](https://jupyter.org/) packages. + +We recommend cloning the workshop's GitHub repository and creating the environment using the provided `environment.yaml` file: + +```bash +git clone https://github.com/neuroinformatics-unit/animals-in-motion.git +cd animals-in-motion +conda env create -n animals-in-motion-env -f environment.yaml +``` + +To test your setup, run: +```bash +conda activate animals-in-motion-env +movement launch +``` + +This should open the [movement GUI](https://movement.neuroinformatics.dev/user_guide/gui.html), i.e. the [napari](https://napari.org/) image viewer with the `movement` plugin docked on the right. + +There are other ways to [install the movement package](https://movement.neuroinformatics.dev/user_guide/installation.html). +However, for this workshop, we recommend using the `environment.yaml` file to ensure that all necessary dependencies, including those beyond `movement`, are included. + +::: + +:::: ### Python knowledge If you're new to Python, we recommend attending our __Intro to Python__ workshop on Monday, or completing an equivalent course beforehand. @@ -61,6 +111,13 @@ This hands-on session will cover the basics, including data types, control flow, Bringing your own data is encouraged but not required. This could include video recordings of animal behaviour and/or motion tracks you've already generated. It's a great chance to get feedback on your data and learn from others. -If you don't have your own data, we will provide example datasets for you to work with. + +::: {admonition} Download example datasets +:class: note + +We also provide some example datasets for you to use during the workshop. +Please download these from [Dropbox](https://www.dropbox.com/scl/fo/81ug5hoy9msc7v7bteqa0/AH32RLdbZqWZJstIeR4YHZY?rlkey=blgagtaizw8aac5areja6h7q1&st=w1zueyi9&dl=0) before the workshop starts (they are a few GB in size). + +::: We expect that participant-led ideas emerging from this track may inspire collaborative projects during the __Hackday__ on Friday. diff --git a/docs/source/open-software-week/big-imaging-data.md b/docs/source/open-software-week/big-imaging-data.md index c3b1110..e470b02 100644 --- a/docs/source/open-software-week/big-imaging-data.md +++ b/docs/source/open-software-week/big-imaging-data.md @@ -33,20 +33,16 @@ The discussions will then be fed back to the wider group, and result in the publ - [Igor Tatarnikov](https://github.com/IgorTatarnikov) - [Adam Tyson](https://github.com/adamltyson) -## Pre-requisites +(target-imaging-prerequisites)= +## Prerequisites ### Hardware As this is a hands-on workshop, you will need to bring your own laptop. Any fairly recent laptop will be suitable, you don't need a GPU etc. ### Software -Please ensure you have the following installed: -- A Python IDE such as: - - [Visual Studio Code](https://code.visualstudio.com/) with the [Python extension](https://marketplace.visualstudio.com/items?itemName=ms-python.python) - - [PyCharm](https://www.jetbrains.com/pycharm/) -- A working `conda` (or `mamba`) installation. If you don't have it, install via [Miniforge](https://github.com/conda-forge/miniforge). -- A working [Git](https://git-scm.com/) installation. - -We will email you at least a week before the event with instructions on installing any additional required software. +For general software requirements, please see the [prerequisites](target-general-prerequisites) on the main event page and make sure you have these installed and properly configured. + +Specialised software beyond the above general requirements will be installed during the course. ### Python knowledge If you're new to Python, we recommend attending our __Intro to Python__ workshop on Monday, or completing an equivalent course beforehand. diff --git a/docs/source/open-software-week/brainglobe.md b/docs/source/open-software-week/brainglobe.md index 3b8ff50..f263f30 100644 --- a/docs/source/open-software-week/brainglobe.md +++ b/docs/source/open-software-week/brainglobe.md @@ -38,20 +38,16 @@ Participants are encouraged to run BrainGlobe on their own data, discuss use cas - [Igor Tatarnikov](https://github.com/IgorTatarnikov) - [Adam Tyson](https://github.com/adamltyson) -## Pre-requisites +(target-brainglobe-prerequisites)= +## Prerequisites ### Hardware As this is a hands-on workshop, you will need to bring your own laptop. Any fairly recent laptop will be suitable, you don't need a GPU etc. ### Software -Please ensure you have the following installed: -- A Python IDE such as: - - [Visual Studio Code](https://code.visualstudio.com/) with the [Python extension](https://marketplace.visualstudio.com/items?itemName=ms-python.python) - - [PyCharm](https://www.jetbrains.com/pycharm/) -- A working `conda` (or `mamba`) installation. If you don't have it, install via [Miniforge](https://github.com/conda-forge/miniforge). -- A working [Git](https://git-scm.com/) installation. - -We will email you at least a week before the event with instructions on installing any additional required software. +For general software requirements, please see the [prerequisites](target-general-prerequisites) on the main event page and make sure you have these installed and properly configured. + +Specialised software beyond the above general requirements, including BrainGlobe itself, will be installed during the course. ### Python knowledge If you're new to Python, we recommend attending our __Intro to Python__ workshop on Monday, or completing an equivalent course beforehand. diff --git a/docs/source/open-software-week/index.md b/docs/source/open-software-week/index.md index c943688..0a42010 100644 --- a/docs/source/open-software-week/index.md +++ b/docs/source/open-software-week/index.md @@ -3,18 +3,16 @@ We are excited to announce our inaugural **NIU Open Software Week**, taking place in **August 2025** in **London, UK**. This event will bring together researchers, developers, and users of open-source software for some hands-on training, community-building and hacking. -:::{admonition} Application Period Closed. We will notify applicants of acceptance as soon as possible. +:::{admonition} Application period has ended and selected applicants have been notified. :class: info **August 11-15 2025**, [Sainsbury Wellcome Centre](https://maps.app.goo.gl/CzWFFjXJZwX87aMj6) - ~~**April 16th 2025**: Applications open~~ - ~~**June 6th 2025**: Applications close~~ -- **End of June/Early July 2025**: Applicants are notified of acceptance +- ~~**End of June/Early July 2025**: Applicants are notified of acceptance~~ ::: -To maximise our impact, we aim to select participants that would benefit the most from the event, and that can bring the experience back to a diverse set of fields. Please be specific in your application and tailor it to the main track(s) that you are planning to attend. Attendance is free of charge (coffee and lunch are provided) and we expect to be able to offer 10-15 travel stipends of between £300 and £1500 for those that make a strong case for attendance and lack alternative funding sources. - ## Schedule Sessions will run daily between **10:00** and **17:00**. @@ -77,7 +75,21 @@ A beginner-friendly workshop for those who are new to programming and want to le :color: primary :icon: briefcase -A discussion for those interested in exploring non-traditional career paths in research, such as Research Software Engineer, Image Analyst, or Data Scientist. +The Careers Clinic will consist of a panel discussion from diverse Research Technology Professionals with a background in life sciences. +We hope for the discussion to benefit those interested in exploring non-traditional career paths in research. +The audience is encouraged to prepare questions for the panellists, and reflect on their own careers. + +Panelists include: + +- **Mayo Faulkner**, Senior User Experience Engineer at the International Brain Lab +- **Vicki Yorke-Edwards**, Senior Research Data Steward at UCL Advanced Research Computing Centre +- **Batool Almarzouq**, Manager of Imago (Imagery Smart Data Service), part of the Smart Data Research UK programme +- **Laura Porta**, Senior Research Software Engineer in the Neuroinformatics Unit +- **Jonas Hartmann**, Postdoctoral Researcher at UCL Cell + Developmental Biology + +If you've signed up for the Careers Clinic, please arrive at the Sainsbury Wellcome Centre +by **11:30** on **Thursday**. This will give you a chance to grab a coffee from the Ground Floor Lecture Theatre before being guided to the 3rd Floor Seminar Room for +the panel discussion, which will start at **11:45**. ::: :::{dropdown} Collaborative coding with git @@ -93,7 +105,59 @@ Learn how to version control your code and collaborate with others using `git` a :color: primary :icon: people -Put into practice what you have learned during the week and collaborate with others to tackle a real-world problem using open-source tools. The goal will be to end the day with several pull requests to open-source projects. +If you've signed up for the Hackday on **Friday, 15 August**, we encourage you to start thinking about potential project ideas. +You can propose an idea by visiting this [GitHub repository](https://github.com/neuroinformatics-unit/osw25-hackday) and clicking **"New Issue" > "Hackday project idea"**. + +You can browse existing proposals on this [board](https://github.com/orgs/neuroinformatics-unit/projects/19/views/1). +If something catches your eye, feel free to leave a comment under the relevant issue to express your interest or ask questions. +We hope that this will get the ball rolling on team formation, which will be finalised on Friday morning. +Don't worry if you don't have a concrete idea just yet — we expect plenty of Hackday ideas to emerge organically throughout Open Software Week. + +**Projects don't need to involve coding.** As long as it's something that would benefit from collaboration with other Open Software Week participants, it's fair game! +Here are a few examples of the kinds of projects that could be a great fit: + +- **Apply a tool**: Use any software you learned about during the week to analyse an interesting dataset (your own or a public one). +- **Give feedback**: Raise issues on relevant open-source tools. Suggest missing features, report bugs, or flag unclear documentation. +- **Make a contribution**: Submit a pull request to an open-source repository. If it's your first time, don't worry; there'll be plenty of people around to support you. +- **Collaborative writing**: Draft something together, like a blog post, white paper, or improved documentation. +- **Prototype an idea**: Try out a cool new analysis or method on real-world data and share your findings. + +We're looking forward to seeing what you come up with! You will get the chance to present your progress at the end of the Hackday. + +::: + +(target-general-prerequisites)= +## Prerequisites + +As this is a hands-on event, you will need to bring your own **laptop** and **charger**. Any fairly recent laptop will be suitable, you don't need a dedicated GPU. + +:::{note} +If you already have a working Anaconda or Miniconda installation and have used it to run Python scripts or Jupyter notebooks, you can likely skip ahead to the [additional track-specific prerequisites](target-track-specific-prerequisites). +::: + +To prepare your computer for Python development, we recommend following the [Software Carpentries installation instructions](https://carpentries.github.io/workshop-template/install_instructions), in particular: + +- [Bash Shell](https://carpentries.github.io/workshop-template/install_instructions/#shell), to run terminal commands +- [Git](https://carpentries.github.io/workshop-template/install_instructions/#git), including a GitHub account +- [Python](https://carpentries.github.io/workshop-template/install_instructions/#python), via the [conda-forge installer](https://conda-forge.org/download/). Please make sure you install a __Python version >= 3.12__ (e.g. 3.12 is fine, 3.10 is not). + +You'll also need a code editor (IDE) configured for Python. +If you already have one you're comfortable with, feel free to use it. Otherwise, we recommend: + +- [Visual Studio Code](https://code.visualstudio.com/) with the [Python extension](https://marketplace.visualstudio.com/items?itemName=ms-python.python) +- [PyCharm](https://www.jetbrains.com/pycharm/) +- [JupyterLab](https://jupyterlab.readthedocs.io/en/stable/) + +(target-track-specific-prerequisites)= +:::{admonition} Additional track-specific prerequisites +:class: warning + +Apart from the general development tools mentioned above, each track may have additional prerequisites. The following links will take you there: +- [Animals in Motion](target-animals-in-motion-prerequisites) +- [BrainGlobe](target-brainglobe-prerequisites) +- [Big Imaging Data](target-imaging-prerequisites) + +Please arrive 30 minutes early if you are facing problems installing course prerequisites. ::: ## Funding