From aab23859f0cd8d6c3dd4483ab4c5f0e71538958f Mon Sep 17 00:00:00 2001 From: Huw Day <85741581+HuwWDay@users.noreply.github.com> Date: Thu, 20 Feb 2025 09:50:03 +0000 Subject: [PATCH 1/4] Update other-services.md Adding info about the research data service --- pages/resources/other-services.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/pages/resources/other-services.md b/pages/resources/other-services.md index a61aaf1..fbb6f1c 100644 --- a/pages/resources/other-services.md +++ b/pages/resources/other-services.md @@ -21,6 +21,9 @@ The other important type of Ask-JGI query are costing related. The Ask-JGI email - [High performance computing](https://www.bristol.ac.uk/acrc/high-performance-computing/) (HPC) support. Email contact: hpc-help@bristol.ac.uk
The University's HPC systems can be used to accelerate your computational research. High-performance computing (HPC) is the ability to process data and perform complex calculations at high speeds. Today, HPC is essential for many types of workloads, including AI/ML, physical simulations, and big data analysis. +- [The Research Data Service](https://www.bristol.ac.uk/staff/researchers/data/​) +The Research Data Service can help review data management plans for funding applications, review consent forms and participant information sheets, advise on RDSF (see below) and support with Data publication. +Relevant links include: [data.bris repository​](https://data.bris.ac.uk/data/​) and [Support services](https://data.bris.ac.uk/​​). Can also email: "data-bris@bristol.ac.uk".​ - [Research Data Storage Facility](https://www.bristol.ac.uk/acrc/research-data-storage-facility/) (RDSF) support. Email contact: rdsf-help@bristol.ac.uk
The RDSF (Research Data Storage Facility) is designed for the secure storage of your University Research data in the medium to long-term. Each Principal Investigator / academic data steward at the University of Bristol currently receives 5 Terabytes (TB) of allocated storage on the RDSF to use across your multiple RDSF research projects. From 915524fd715cd6438dab9ccad72e7a8dde082913 Mon Sep 17 00:00:00 2001 From: James Thomas Date: Thu, 20 Feb 2025 16:38:52 +0000 Subject: [PATCH 2/4] Remove invisible characters --- pages/resources/other-services.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pages/resources/other-services.md b/pages/resources/other-services.md index fbb6f1c..265a9a4 100644 --- a/pages/resources/other-services.md +++ b/pages/resources/other-services.md @@ -21,9 +21,9 @@ The other important type of Ask-JGI query are costing related. The Ask-JGI email - [High performance computing](https://www.bristol.ac.uk/acrc/high-performance-computing/) (HPC) support. Email contact: hpc-help@bristol.ac.uk
The University's HPC systems can be used to accelerate your computational research. High-performance computing (HPC) is the ability to process data and perform complex calculations at high speeds. Today, HPC is essential for many types of workloads, including AI/ML, physical simulations, and big data analysis. -- [The Research Data Service](https://www.bristol.ac.uk/staff/researchers/data/​) +- [The Research Data Service](https://www.bristol.ac.uk/staff/researchers/data/) The Research Data Service can help review data management plans for funding applications, review consent forms and participant information sheets, advise on RDSF (see below) and support with Data publication. -Relevant links include: [data.bris repository​](https://data.bris.ac.uk/data/​) and [Support services](https://data.bris.ac.uk/​​). Can also email: "data-bris@bristol.ac.uk".​ +Relevant links include: [data.bris repository](https://data.bris.ac.uk/data/) and [Support services](https://data.bris.ac.uk/). Can also email: "data-bris@bristol.ac.uk". - [Research Data Storage Facility](https://www.bristol.ac.uk/acrc/research-data-storage-facility/) (RDSF) support. Email contact: rdsf-help@bristol.ac.uk
The RDSF (Research Data Storage Facility) is designed for the secure storage of your University Research data in the medium to long-term. Each Principal Investigator / academic data steward at the University of Bristol currently receives 5 Terabytes (TB) of allocated storage on the RDSF to use across your multiple RDSF research projects. From 0eb75fd1ff05a9a86d84a9485791ee7aeffa62cd Mon Sep 17 00:00:00 2001 From: James Thomas Date: Thu, 20 Feb 2025 16:45:57 +0000 Subject: [PATCH 3/4] Tidy up and one sentence per line: https://sive.rs/1s --- pages/resources/other-services.md | 86 +++++++++++++++---------------- 1 file changed, 41 insertions(+), 45 deletions(-) diff --git a/pages/resources/other-services.md b/pages/resources/other-services.md index 265a9a4..c260203 100644 --- a/pages/resources/other-services.md +++ b/pages/resources/other-services.md @@ -1,66 +1,62 @@ # Signposting and other services ```{note} -Sign-posting is an important part of Ask-JGI. Some queries may be -better addressed by other university services, some of which are listed below. +Sign-posting is an important part of Ask-JGI. +Some queries may be better addressed by other university services, some of which are listed below. ``` ## Ask-RSE -We also get emails from the currently dormant Ask-RSE mailbox. These queries are Research Software Engineering related and whilst this does have an overlap with the remit of the Ask-JGI helpdesk, we are not expected to be able to help with all of the queries and the researchers contacting us through this route should be made aware of this. If we’re able to directly support then we should. +We also get emails from the currently dormant Ask-RSE mailbox. +These queries are Research Software Engineering related and whilst this does have an overlap with the remit of the Ask-JGI helpdesk, we are not expected to be able to help with all of the queries and the researchers contacting us through this route should be made aware of this. +If we're able to directly support then we should. ## Getting JGI Data Scientists Involved -Occasionally, some queries will fall out of the remit of Ask-JGI PhD students but might be appropriate for the full time JGI Data Science/Research Software Engineering team. These will usually be more specialised data science tasks and ideally these will be approached with a buddy system approach, where the JGI Data Scientist/RSE attends with an Ask-JGI PhD student. Sometimes, these activities might just be signposting exercises, where the query requires specialist expertise from a researcher at the university. +Occasionally, some queries will fall out of the remit of Ask-JGI PhD students but might be appropriate for the full time JGI Data Science/Research Software Engineering team. +These will usually be more specialised data science tasks and ideally these will be approached with a buddy system approach, where the JGI Data Scientist/RSE attends with an Ask-JGI PhD student. +Sometimes, these activities might just be signposting exercises, where the query requires specialist expertise from a researcher at the university. ## Costing -The other important type of Ask-JGI query are costing related. The Ask-JGI email is the one we encourage researchers to use when enquiring about costing out JGI Data Scientists, so any queries of this nature should be handled by the Data Science team (you could just post on the teams channel and tag the Ask-JGI Lead). The Ask-RSE mailbox also frequently receives emails of this type and those emails should also be passed on to the Data Science team. +The other important type of Ask-JGI query are costing related. +The Ask-JGI email is the one we encourage researchers to use when enquiring about costing out JGI Data Scientists, so any queries of this nature should be handled by the Data Science team (you could just post on the teams channel and tag the Ask-JGI Lead). +The Ask-RSE mailbox also frequently receives emails of this type and those emails should also be passed on to the Data Science team. ## Other services -- [High performance computing](https://www.bristol.ac.uk/acrc/high-performance-computing/) (HPC) support. Email contact: hpc-help@bristol.ac.uk
-The University's HPC systems can be used to accelerate your computational research. High-performance computing (HPC) is the ability to process data and perform complex calculations at high speeds. Today, HPC is essential for many types of workloads, including AI/ML, physical simulations, and big data analysis. -- [The Research Data Service](https://www.bristol.ac.uk/staff/researchers/data/) -The Research Data Service can help review data management plans for funding applications, review consent forms and participant information sheets, advise on RDSF (see below) and support with Data publication. -Relevant links include: [data.bris repository](https://data.bris.ac.uk/data/) and [Support services](https://data.bris.ac.uk/). Can also email: "data-bris@bristol.ac.uk". -- [Research Data Storage Facility](https://www.bristol.ac.uk/acrc/research-data-storage-facility/) (RDSF) support. Email contact: rdsf-help@bristol.ac.uk
-The RDSF (Research Data Storage Facility) is designed for the secure storage of your University Research data in the medium to long-term. -Each Principal Investigator / academic data steward at the University of Bristol currently receives 5 Terabytes (TB) of allocated storage on the RDSF to use across your multiple RDSF research projects. -- Data science, coding/programming and other training. Researchers sometimes contact us asking about the training we offer in programming and coding. All the information about courses offered can be found on the University of Bristol [Data Science and Research Software Engineering Training website](https://bristol-training.github.io/). They can also email contact: jgi-training@bristol.ac.uk to enquire for more details. -- [Research IT](https://www.bristol.ac.uk/research-it/about) provide - support to UoB researchers in the writing of the technical aspects - of bid applications and identifying ways software can realise their - research goals. Can provide help with software or programming to - support research on a consultancy basis. Research IT can be - contracted to consult on projects for shorter durations than data scientists or RSEs (i.e. at a day rate). - Email contact: research-it@bristol.ac.uk
-- [Library Research Support](http://www.bristol.ac.uk/library/research-support/): - Support services in research data management, copyright enquiries, - literature review. Email contact: lib-research-support@bristol.ac.uk

- +- [High performance computing](https://www.bristol.ac.uk/acrc/high-performance-computing/) (HPC) support. + The University's HPC systems can be used to accelerate your computational research. + HPC is the ability to process data and perform complex calculations at high speeds. + Today, HPC is essential for many types of workloads, including AI/ML, physical simulations, and big data analysis. + Email contact: hpc-help@bristol.ac.uk +- [The Research Data Service](https://www.bristol.ac.uk/staff/researchers/data) can help review data management plans for funding applications, review consent forms and participant information sheets, advise on RDSF (see below) and support with data publication. + Relevant links include: [data.bris repository](https://data.bris.ac.uk/data/) and [Support services](https://data.bris.ac.uk). + Can also email: data-bris@bristol.ac.uk +- [Research Data Storage Facility](https://www.bristol.ac.uk/acrc/research-data-storage-facility/) (RDSF) support. + The RDSF (Research Data Storage Facility) is designed for the secure storage of your University Research data in the medium to long-term. + Each Principal Investigator / academic data steward at the University of Bristol currently receives 5 Terabytes (TB) of allocated storage on the RDSF to use across your multiple RDSF research projects. + Email contact: rdsf-help@bristol.ac.uk +- Data science, coding/programming and other training. + Researchers sometimes contact us asking about the training we offer in programming and coding. + All the information about courses offered can be found on the University of Bristol [Data Science and Research Software Engineering Training website](https://bristol-training.github.io/). + They can also email contact: jgi-training@bristol.ac.uk to enquire for more details. +- [Research IT](https://www.bristol.ac.uk/research-it/about) provide support to UoB researchers in the writing of the technical aspects of bid applications and identifying ways software can realise their research goals. + Can provide help with software or programming to support research on a consultancy basis. + Research IT can be contracted to consult on projects for shorter durations than data scientists or RSEs (i.e. at a day rate). + Email contact: research-it@bristol.ac.uk +- [Library Research Support](http://www.bristol.ac.uk/library/research-support/) provide support services in research data management, copyright enquiries, literature review. + Email contact: lib-research-support@bristol.ac.uk ## Signposting email text You can use the following to explain the available services to university staff: -```Text -Other resources are available for help with data science related queries at the -Univeristy of Bristol. -- For help with coding or data intensive projects that may need advanced computational - or storage resources the [Advanced Computing Research - Centre](http://www.bris.ac.uk/acrc/contact/) deliver training courses in coding, - high performance computing and data storage. They can also be contracted to help - with longer term projects. -- For help writing the more technical aspects of grant proposals, as well as - ongoing help with short-term projects, [Research IT](https://www.bristol.ac.uk/research-it/about) - are a useful resource. -- For help with research data management, literature search and literature reviews - using advanced search tools, [Library Research - Support](http://www.bristol.ac.uk/library/research-support/) is also available. -- If you have an idea for an interdisciplinary research project and would like - funding to support a pilot, the JGI is happy to accept applications for seedcorn funding. - -If you are not sure which service will be most helpful to you, Ask-JGI can speak -with you about your needs. -``` +> Other resources are available for help with data science related queries at the University of Bristol. +> - For help with coding or data intensive projects that may need advanced computational or storage resources the [Advanced Computing Research Centre](http://www.bris.ac.uk/acrc/contact/) deliver training courses in coding, high performance computing and data storage. +> They can also be contracted to help with longer term projects. +> - For help writing the more technical aspects of grant proposals, as well as ongoing help with short-term projects, [Research IT](https://www.bristol.ac.uk/research-it/about) are a useful resource. +> - For help with research data management, literature search and literature reviews using advanced search tools, [Library Research Support](http://www.bristol.ac.uk/library/research-support/) is also available. +> - If you have an idea for an interdisciplinary research project and would like funding to support a pilot, the JGI is happy to accept applications for seedcorn funding. +> +> If you are not sure which service will be most helpful to you, Ask-JGI can speak with you about your needs. From b437fdbc4fc16610c1e7304c8f5b1ca295c6218f Mon Sep 17 00:00:00 2001 From: James Thomas Date: Thu, 20 Feb 2025 16:55:42 +0000 Subject: [PATCH 4/4] Update GitHub Actions to Python 3.12 and use newer actions --- .github/workflows/build-site.yml | 58 +++++++++++-------------- .github/workflows/deploy-site.yml | 72 +++++++++++++++---------------- 2 files changed, 58 insertions(+), 72 deletions(-) diff --git a/.github/workflows/build-site.yml b/.github/workflows/build-site.yml index 95293c6..2ddf06d 100644 --- a/.github/workflows/build-site.yml +++ b/.github/workflows/build-site.yml @@ -1,42 +1,32 @@ -# This workflow builds the Jupyter Book, and is triggered when a push is made to the main branch of this repo - name: build-site -# Controls when the action will run. +# Run this when there is a pull request on the main branch on: - # Triggers the workflow on push or pull request events but only for the main branch for the book content directory. - push: - branches: [ main ] - pull_request: - branches: [ main ] + branches: + - main - # Allows you to run this workflow manually from the Actions tab - workflow_dispatch: - -# A workflow run is made up of one or more jobs that can run sequentially or in parallel +# This job installs dependencies and builds the book, to see if there are any errors jobs: - # This workflow contains a single job called "deploy-book" - build-book: - # The type of runner that the job will run on + build-site: runs-on: ubuntu-latest - - # Steps represent a sequence of tasks that will be executed as part of the job + permissions: + pages: write + id-token: write steps: - # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it - - uses: actions/checkout@v2 - - # Install dependencies - - name: Set up Python 3.7 - uses: actions/setup-python@v1 - with: - python-version: 3.7 - - - name: Install dependencies - run: | - pip install -r requirements.txt - - # Build the book - - name: Build the book - run: | - jupyter-book build . + - uses: actions/checkout@v3 + + # Install dependencies + - name: Set up Python 3.12 + uses: actions/setup-python@v4 + with: + python-version: 3.12 + + - name: Install dependencies + run: | + pip install -r requirements.txt + + # Build the book + - name: Build the book + run: | + jupyter-book build . diff --git a/.github/workflows/deploy-site.yml b/.github/workflows/deploy-site.yml index 8fa2d93..63f853a 100644 --- a/.github/workflows/deploy-site.yml +++ b/.github/workflows/deploy-site.yml @@ -1,47 +1,43 @@ -# This is a basic workflow to help you get started with Actions - name: deploy-book -# Controls when the action will run. +# Run this when the main branch changes on: - # Triggers the workflow on push or pull request events but only for the main branch for the book content directory. push: - branches: [ main ] - - - # Allows you to run this workflow manually from the Actions tab - workflow_dispatch: + branches: + - main -# A workflow run is made up of one or more jobs that can run sequentially or in parallel +# This job installs dependencies, builds the book, and pushes it to `gh-pages` jobs: - # This workflow contains a single job called "deploy-book" deploy-book: - # The type of runner that the job will run on runs-on: ubuntu-latest - - # Steps represent a sequence of tasks that will be executed as part of the job + permissions: + pages: write + id-token: write steps: - # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it - - uses: actions/checkout@v2 - - # Install dependencies - - name: Set up Python 3.7 - uses: actions/setup-python@v1 - with: - python-version: 3.7 - - - name: Install dependencies - run: | - pip install -r requirements.txt - - # Build the book - - name: Build the book - run: | - jupyter-book build . - - # Push the book's HTML to github-pages - - name: GitHub Pages action - uses: peaceiris/actions-gh-pages@v3.6.1 - with: - github_token: ${{ secrets.GITHUB_TOKEN }} - publish_dir: _build/html + - uses: actions/checkout@v3 + + # Install dependencies + - name: Set up Python 3.12 + uses: actions/setup-python@v4 + with: + python-version: 3.12 + + - name: Install dependencies + run: | + pip install -r requirements.txt + + # Build the book + - name: Build the book + run: | + jupyter-book build . + + # Upload the book's HTML as an artifact + - name: Upload artifact + uses: actions/upload-pages-artifact@v2 + with: + path: "_build/html" + + # Deploy the book's HTML to GitHub Pages + - name: Deploy to GitHub Pages + id: deployment + uses: actions/deploy-pages@v2