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_quarto.yml
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project:
type: website
output-dir: _site
render:
- "*.qmd"
- "!*.py"
- "!*.R"
- "!*.jl"
- "!*.org"
- "!*.csv"
- "!*_old.qmd"
- "!*_bk.qmd"
- "!/git/intro_intro_old.qmd"
- "!/git/intro_revisiting_old_commits_alternate.qmd"
- "!/python/ws_webscraping_old.qmd"
- "!/tools/quarto/"
- "!/tools/wb_quarto_slides_first_more_wordy_version.qmd"
- "!/tools/wb_quarto_staff2staff_slides.qmd"
- "!/talks/2024_sfu_bdh_bccai_outline.pdf"
- "!/talks/2024_sfu_bdh_bccai_contract.pdf"
website:
title: Research Computing
image: /img/favicon_sfudrac.png
favicon: /img/favicon_sfu.png
site-url: https://mint.westdri.ca/
repo-url: https://github.com/WestDRI/arc-training
page-navigation: true
bread-crumbs: false
page-footer:
left:
- text: About
href: about.qmd
- text: Talks
href: talks/index.qmd
# center:
right:
- icon: github
href: https://github.com/WestDRI
target: _blank
aria-label: GitHub organization
- icon: wikipedia
href: https://docs.alliancecan.ca/wiki/Technical_documentation
target: _blank
aria-label: Alliance wikipedia
- icon: youtube
href: https://www.youtube.com/channel/UCfgds4Qf7VFOv4ORRvFFmhw
target: _blank
aria-label: YouTube channel
- icon: calendar-week
href: https://mint.westdri.ca/calendar
aria-label: Training calendar
- icon: envelope-fill
href: https://mint.westdri.ca/newsletter
aria-label: Newsletter
- icon: mailbox2
href: https://mint.westdri.ca/contact
aria-label: Contact us
navbar:
background: light
logo: /img/favicon_sfudrac.png
logo-alt: "SFU & DRAC logos"
title: false
left:
- text: AI
href: ai/index.qmd
- text: R
href: r/index.qmd
- text: Python
href: python/index.qmd
- text: Julia
href: julia/index.qmd
- text: Git
href: git/index.qmd
- text: Bash/Zsh
href: bash/index.qmd
- text: Emacs
href: emacs/index.qmd
- text: Tools
href: tools/index.qmd
tools:
- icon: github
href: https://github.com/WestDRI
target: _blank
aria-label: GitHub organization
- icon: wikipedia
href: https://docs.alliancecan.ca/wiki/Technical_documentation
target: _blank
aria-label: Alliance wikipedia
- icon: youtube
href: https://www.youtube.com/channel/UCfgds4Qf7VFOv4ORRvFFmhw
target: _blank
aria-label: YouTube channel
- icon: calendar-week
href: calendar.qmd
aria-label: Training calendar
- icon: envelope-fill
href: newsletter.qmd
aria-label: Newsletter
- icon: mailbox2
href: contact.qmd
aria-label: Contact us
sidebar:
- id: ai
collapse-level: 1
contents:
- text: "<br> <em><b>AI</b></em><br><br>"
href: ai/index.qmd
- section: <b><em>PyTorch</em></b>
href: ai/top_pt.qmd
contents:
- text: Introduction
href: ai/pt/pt_intro.qmd
- text: Which framework to choose?
href: ai/pt/pt_choosing_frameworks.qmd
- text: High-level frameworks
href: ai/pt/pt_high_level_frameworks.qmd
- text: Introduction to NN
href: ai/pt/pt_nn.qmd
- text: The PyTorch API
href: ai/pt/pt_pytorch.qmd
- text: PyTorch tensors
href: ai/pt/pt_tensors.qmd
# - text: Loading data
# href: ai/pt/pt_data.qmd
# - text: Building models
# href: ai/pt/pt_model.qmd
- text: Automatic differentiation
href: ai/pt/pt_autograd.qmd
- text: Workflow
href: ai/pt/pt_workflow.qmd
# - text: Training
# href: ai/pt/pt_training.qmd
- text: Creating checkpoints
href: ai/pt/pt_checkpoints.qmd
- text: "Example: the MNIST"
href: ai/pt/pt_mnist.qmd
- text: DL on production clusters
href: ai/pt/pt_hpc.qmd
- text: Resources
href: ai/pt/pt_resources.qmd
- "---"
- section: <b><em>JAX</em></b>
href: ai/top_jx.qmd
contents:
- text: Why JAX?
href: ai/jx/jx_why.qmd
- text: How does it work?
href: ai/jx/jx_map.qmd
- text: Installation
href: ai/jx/jx_install.qmd
- text: Running jobs
href: ai/jx/jx_jobs.qmd
- text: Relation to NumPy
href: ai/jx/jx_numpy.qmd
- text: JIT compilation
href: ai/jx/jx_jit.qmd
- text: Benchmarking JAX code
href: ai/jx/jx_benchmark.qmd
- text: Accelerators
href: ai/jx/jx_accelerator.qmd
- text: Pytrees
href: ai/jx/jx_pytree.qmd
- text: Automatic differentiation
href: ai/jx/jx_ad.qmd
- text: Parallel computing
href: ai/jx/jx_parallel.qmd
- text: Pushing optimizations further
href: ai/jx/jx_optimizations.qmd
- text: Libraries on top of JAX
href: ai/jx/jx_libraries.qmd
- text: Resources
href: ai/jx/jx_resources.qmd
- "---"
- section: <b><em>Flax</em></b>
href: ai/top_fl.qmd
contents:
- text: Deep learning with JAX
href: ai/jx/fl_jaxdl.qmd
- text: Installation & setup
href: ai/jx/fl_install.qmd
- text: "Flax's handling of model states"
href: ai/jx/fl_state.qmd
- text: Loading datasets
href: ai/jx/fl_data.qmd
- text: Model architecture
href: ai/jx/fl_model.qmd
- text: Training on Alliance clusters
href: ai/jx/fl_training.qmd
# - text: Checkpointing
# href: ai/jx/fl_checkpoint.qmd
# - text: Regularization
# href: ai/jx/fl_regularization.qmd
# - text: Optimizations
# href: ai/jx/fl_optimization.qmd
# - text: Transfer learning
# href: ai/jx/fl_tl.qmd
- text: Resources
href: ai/jx/fl_resources.qmd
- "---"
- section: <b><em>Scikit-learn</em></b>
href: ai/sk_intro.qmd
contents:
- text: What is scikit-learn?
href: ai/sk_intro.qmd
- text: Sklearn workflow
href: ai/sk_workflow.qmd
- "---"
- section: <b><em>Workshops</em></b>
href: ai/top_ws.qmd
contents:
# - text: AI in agrotech
# href: ai/agrotech.qmd
- text: Audio DataLoader with PyTorch
href: ai/pt/ws_audio_dataloader.qmd
- text: Finding pre-trained models
href: ai/pt/ws_pretrained_models.qmd
- text: Intro ML for the humanities
href: ai/ws_hss_intro.qmd
- text: Quick intro to DL, NLP, and LLMs
href: ai/ws_dl_nlp_llm.qmd
- "---"
# - section: <b><em>DL readings</em></b>
# href: ai/concepts.qmd
# contents:
# - text: "Concepts: AI, ML, DL, NN"
# href: ai/concepts.qmd
# - text: Supervised learning
# href: ai/supervised_learning.qmd
# - "---"
- section: <b><em>Webinars</em></b>
href: ai/top_wb.qmd
contents:
- text: Map of current ML frameworks
href: ai/wb_frameworks.qmd
- text: Data & model version control
href: ai/wb_dvc.qmd
- text: Accelerated array & AD with JAX
href: ai/jx/wb_jax.qmd
- text: Image upscaling
href: ai/pt/wb_upscaling.qmd
- text: AI-powered coding with Copilot
href: ai/wb_copilot.qmd
- text: Easier PyTorch with fastai
href: ai/pt/wb_fastai.qmd
- text: DL in Julia with Flux
href: ai/wb_flux.qmd
- text: PyTorch tensors in depth
href: ai/pt/wb_torchtensors.qmd
- text: Bayesian inference in JAX
href: ai/jx/wb_bayesian.qmd
- id: r
collapse-level: 1
contents:
- text: "<br> <img src=\"img/logo_r.png\" class=\"img-fluid\" style=\"width:1.5em\" alt=\"noshadow\"><br><br>"
href: r/index.qmd
- section: <em><b>Getting started</b></em>
href: r/top_intro.qmd
contents:
- text: "R: why and for whom?"
href: r/intro_why.qmd
- text: Running R
href: r/intro_run.qmd
- text: First steps in R
href: r/intro_basics.qmd
- text: Packages
href: r/intro_packages.qmd
- text: Data types and structures
href: r/intro_data_structure.qmd
- text: Indexing
href: r/intro_indexing.qmd
- text: Function definition
href: r/intro_functions.qmd
- text: Control flow
href: r/intro_control_flow.qmd
- text: The tidyverse
href: r/intro_tidyverse.qmd
- text: Data exploration
href: r/intro_explore.qmd
- text: Data extraction
href: r/intro_manipulate.qmd
- text: Data import and export
href: r/intro_import.qmd
- text: Automation
href: r/intro_automation.qmd
- text: Plotting
href: r/intro_plotting.qmd
- text: Publishing
href: r/intro_publishing.qmd
- text: Resources
href: r/intro_resources.qmd
- "---"
- section: <em><b>R for the humanities</b></em>
href: r/top_hss.qmd
contents:
- text: "R: why and for whom?"
href: r/hss_why.qmd
- text: Running R
href: r/hss_run.qmd
- text: Help and documentation
href: r/hss_help.qmd
- text: Packages
href: r/hss_packages.qmd
- text: The tidyverse
href: r/hss_tidyverse.qmd
- text: Data exploration
href: r/hss_explore.qmd
- text: Data extraction
href: r/hss_manipulate.qmd
- text: Data visualization
href: r/hss_vis.qmd
- text: Data types and structures
href: r/hss_data_types.qmd
- text: Data import and export
href: r/hss_import.qmd
- text: Automation
href: r/hss_automation.qmd
- text: Function definition
href: r/hss_functions.qmd
# - text: Writing scripts
# href: r/hss_vis.qmd
# - text: Data analysis
# href: r/hss_analyze.qmd
- text: Publishing
href: r/hss_publish.qmd
- text: Resources
href: r/hss_resources.qmd
- "---"
- section: <b><em>High-performance R</em></b>
href: r/top_hpc.qmd
contents:
- text: SSH login
href: r/hpc_run.qmd
- text: R on HPC clusters
href: r/hpc_clusters.qmd
- text: Measuring performance
href: r/hpc_performance.qmd
- text: Optimizations
href: r/hpc_optimizations.qmd
- text: Memory management
href: r/hpc_memory.qmd
- text: "Parallelism: concepts"
href: r/hpc_parallelism.qmd
# - text: Running R code in parallel
# href: r/hpc_parallel_r.qmd
- text: The future package
href: r/hpc_future.qmd
- text: foreach and doFuture
href: r/hpc_foreach.qmd
# - text: Data on HPC clusters
# href: r/hpc_data.qmd
- text: Partitioning data
href: r/hpc_partition.qmd
- text: Writing C++ in R with Rcpp
href: r/hpc_rcpp.qmd
- text: Resources for HPC in R
href: r/hpc_resources.qmd
- "---"
- section: <b><em>Workshops</em></b>
href: r/top_ws.qmd
contents:
- text: Web scraping with rvest
href: r/ws_webscraping.qmd
- text: Intro to GIS mapping with R
href: r/ws_gis_intro.qmd
- text: Intro R for the humanities
href: r/ws_hss_intro.qmd
- text: A little demo of R programming
href: r/ws_r_demo.qmd
- "---"
- section: <em><b>Webinars</b></em>
href: r/top_wb.qmd
contents:
- text: Intro to GIS mapping in R
href: r/wb_gis_mapping.qmd
- text: High-performance computing
href: r/wb_hpc.qmd
# - text: Creating packages
# href: r/wb_package.qmd
- id: python
collapse-level: 1
contents:
- text: "<br> <img src=\"img/logo_python.svg\" class=\"img-fluid\" style=\"width:1.55em\" alt=\"noshadow\"><br><br>"
href: python/index.qmd
- section: <b><em>Getting started</em></b>
href: python/top_intro.qmd
contents:
- text: Running Python
href: python/intro_run.qmd
- text: "Python: the basics"
href: python/intro_basics.qmd
- text: Collections
href: python/intro_collections.qmd
- text: Playing with text
href: python/intro_text.qmd
- text: Control flow
href: python/intro_control_flow.qmd
- text: Functions
href: python/intro_functions.qmd
- text: Modules and libraries
href: python/intro_packages.qmd
- text: Intro HPC in Python
href: python/intro_hpc.qmd
- text: Resources
href: python/intro_resources.qmd
- "---"
- section: <b><em>Faster Python</em></b>
href: python/top_hpc.qmd
contents:
- text: "JAX: accelerated arrays & AD"
href: python/hpc_jax.qmd
- section: "Polars: faster data frames"
href: python/hpc_polars.qmd
contents:
- text: The world of data frames
href: python/polars_dataframes.qmd
- text: Installation
href: python/polars_install.qmd
- text: Data types
href: python/polars_types.qmd
- text: Data structures
href: python/polars_structures.qmd
- text: Data frame inspection
href: python/polars_inspection.qmd
- text: Subsetting data
href: python/polars_subset.qmd
- text: Lazy evaluation
href: python/polars_lazy.qmd
- text: Comparison with pandas
href: python/polars_pandas.qmd
- text: Resources
href: python/polars_resources.qmd
- "---"
- section: <b><em>Text analysis</em></b>
href: python/top_nlp.qmd
contents:
- text: Package installation
href: python/nlp_install.qmd
- text: Getting the data
href: python/nlp_data.qmd
- text: Text processing
href: python/nlp_processing.qmd
- text: Text normalization
href: python/nlp_normalization.qmd
- text: Sentiment analysis
href: python/nlp_analysis.qmd
- section: <em><b>Workshops</b></em>
href: python/top_ws.qmd
contents:
- text: Web scraping with bs4
href: python/ws_webscraping.qmd
- text: Data frames with pandas
href: python/ws_pandas.qmd
- "---"
- section: <em><b>Webinars</b></em>
href: python/top_wb.qmd
contents:
- text: Faster data frames with Polars
href: python/wb_polars.qmd
- text: Accelerated arrays & AD with JAX
href: python/wb_jax.qmd
- text: Intro programming for HSS
href: python/wb_hss_prog.qmd
- id: julia
collapse-level: 1
contents:
- text: "<br> <img src=\"img/logo_julia.png\" class=\"img-fluid\" style=\"width:1.65em\" alt=\"noshadow\"><br><br>"
href: julia/index.qmd
- section: <b><em>Getting started</em></b>
href: julia/top_intro.qmd
contents:
- text: Introduction to Julia
href: julia/intro_intro.qmd
- text: Basics of the Julia language
href: julia/intro_basics.qmd
- text: Collections
href: julia/intro_collections.qmd
- text: Types
href: julia/intro_types.qmd
- text: Functions
href: julia/intro_functions.qmd
- text: Control flow
href: julia/intro_control_flow.qmd
- text: Macros
href: julia/intro_macros.qmd
- text: Packages
href: julia/intro_packages.qmd
- text: Plotting
href: julia/intro_plotting.qmd
- text: Working with tabular data
href: julia/intro_tabular.qmd
- text: Non interactive execution
href: julia/intro_non_interactive.qmd
- text: Resources
href: julia/intro_resources.qmd
- "---"
- section: <b><em>High-performance Julia</em></b>
href: julia/top_hpc.qmd
contents:
- text: Intro to HPC in Julia
href: julia/hpc_intro.qmd
- text: Performance
href: julia/hpc_performance.qmd
- text: Multi-threading
href: julia/hpc_multithreading.qmd
- text: Distributed computing
href: julia/hpc_distributed.qmd
- "---"
- section: <b><em>Webinars</em></b>
href: julia/top_wb.qmd
contents:
- text: Data visualization with Makie
href: julia/wb_makie.qmd
- text: First gentle dab at Julia
href: julia/wb_firstdab.qmd
- text: Deep learning with Flux
href: julia/wb_flux.qmd
- id: git
collapse-level: 1
contents:
- text: "<br> <img src=\"img/logo_git.png\" class=\"img-fluid\" style=\"width:1.5em\" alt=\"noshadow\"><br><br>"
href: git/index.qmd
- section: <b><em>Getting started</em></b>
href: git/top_intro.qmd
contents:
- text: What is Git?
href: git/intro_intro.qmd
- text: Installation and setup
href: git/intro_install.qmd
- text: Documentation
href: git/intro_documentation.qmd
- text: First steps
href: git/intro_first_steps.qmd
- text: Excluding from version control
href: git/intro_ignore.qmd
- text: Inspecting changes
href: git/intro_changes.qmd
- text: Getting information on commits
href: git/intro_logs.qmd
# - text: The three trees of Git
# href: git/intro_three_trees.qmd
- text: Stashing
href: git/intro_stash.qmd
- text: Revisiting old commits
href: git/intro_time_travel.qmd
- text: Tags
href: git/intro_tags.qmd
- text: Aliases
href: git/intro_aliases.qmd
- text: Branches
href: git/intro_branches.qmd
- text: Remotes
href: git/intro_remotes.qmd
- text: Undoing
href: git/intro_undo.qmd
- text: Tools for a friendlier Git
href: git/intro_tools.qmd
- text: Resources
href: git/intro_resources.qmd
- "---"
- section: <b><em>Workshops</em></b>
href: git/top_ws.qmd
contents:
- text: Searching a Git project
href: git/practice_repo/ws_search.qmd
- text: Collaborating through Git
href: git/ws_collab.qmd
- text: Contributing to projects
href: git/ws_contrib.qmd
- "---"
- section: <b><em>Webinars</em></b>
href: git/top_wb.qmd
contents:
- text: Data version control with DVC
href: git/wb_dvc.qmd
- text: "A great Git UI: lazygit"
href: git/wb_lazygit.qmd
- id: bash
collapse-level: 1
contents:
- text: "<br> <img src=\"img/logo_bash.png\" class=\"img-fluid\" style=\"width:1.6em\" alt=\"noshadow\"> / <img src=\"img/logo_zsh.svg\" class=\"img-fluid\" style=\"width:1.3em\" alt=\"noshadow\"><br><br>"
href: bash/index.qmd
- section: <b><em>Getting started</em></b>
href: bash/top_intro.qmd
contents:
- text: Introduction
href: bash/intro_intro.qmd
- text: Shell basics
href: bash/intro_basics.qmd
- text: The Unix filesystem
href: bash/intro_filesystem.qmd
- text: Variables
href: bash/intro_variables.qmd
- text: Wildcards
href: bash/molecules/intro_wildcards.qmd
- text: Regular expressions
href: bash/intro_regexp.qmd
- text: Redirections & pipes
href: bash/molecules/intro_redirections.qmd
- text: Control flow
href: bash/molecules/intro_control_flow.qmd
- text: Functions
href: bash/intro_functions.qmd
- text: Special parameters
href: bash/intro_special_parameters.qmd
- text: Aliases
href: bash/intro_aliases.qmd
- text: Writing scripts
href: bash/molecules/intro_script.qmd
# - text: Finding files
# href: bash/molecules/intro_find.qmd
# - text: Archives
# href: bash/intro_archives.qmd
- text: Transferring files
href: bash/intro_transfer.qmd
- text: Modern utilities
href: bash/intro_modern.qmd
- text: Z shell
href: bash/intro_zsh.qmd
- text: Resources
href: bash/intro_resources.qmd
- "---"
- section: <b><em>Workshops</em></b>
href: bash/top_ws.qmd
contents:
- text: Scripting for beginners
href: bash/ws_scripting.qmd
- text: Searching & manipulating text
href: bash/ws_text.qmd
- "---"
- section: <b><em>Webinars</em></b>
href: bash/top_wb.qmd
contents:
- text: Fun tools for the command line
href: bash/wb_tools1.qmd
- text: More fun tools for the CLI
href: bash/wb_tools2.qmd
- text: Modern shell utilities
href: bash/wb_tools3.qmd
- id: emacs
collapse-level: 1
contents:
- text: "<br> <img src=\"img/logo_emacs.png\" class=\"img-fluid\" style=\"width:1.75em\" alt=\"noshadow\"><br><br>"
href: emacs/index.qmd
- section: <em><b>Getting started</b></em>
href: emacs/top_intro.qmd
contents:
- text: Why Emacs?
href: emacs/intro_why.qmd
- text: Installation and access
href: emacs/intro_install.qmd
- text: Running Emacs
href: emacs/intro_run.qmd
- text: User interface
href: emacs/intro_ui.qmd
- text: Key bindings
href: emacs/intro_kbd.qmd
- text: Emacs modes
href: emacs/intro_modes.qmd
- text: Automation
href: emacs/intro_automation.qmd
- text: Directory editor
href: emacs/intro_dired.qmd
- text: Other functionalities
href: emacs/intro_shells.qmd
- text: Backups and auto-saving
href: emacs/intro_backup.qmd
- text: Customizing Emacs
href: emacs/intro_customize.qmd
- text: Packages
href: emacs/intro_packages.qmd
- text: Undoing and redoing
href: emacs/intro_undo.qmd
- text: Completion frameworks
href: emacs/intro_completion.qmd
- text: Editing remote files
href: emacs/intro_remote.qmd
- text: Resources
href: emacs/intro_resources.qmd
- "---"
- section: <b><em>Webinars</em></b>
href: emacs/top_wb.qmd
contents:
- text: Emacs as a programming IDE
href: emacs/wb_emacs_ide.qmd
- text: Modern, faster & better Emacs
href: emacs/wb_emacs_new_tools.qmd
- text: Understanding Emacs modes
href: emacs/wb_emacs_modes.qmd
- id: tools
collapse-level: 1
contents:
- text: "<br> <em><b>Tools</b></em><br><br>"
href: tools/index.qmd
- section: <em><b>Workshops</b></em>
href: tools/ws_quarto.qmd
contents:
- text: Authoring with Quarto
href: tools/ws_quarto.qmd
- "---"
- section: <b><em>Webinars</em></b>
href: tools/top_wb.qmd
contents:
- text: "Quarto: the new R Markdown"
href: tools/wb_quarto.qmd
- text: "A great Git UI: lazygit"
href: tools/wb_lazygit.qmd
- text: Data version control with DVC
href: tools/wb_dvc.qmd
- text: Fun tools for the command line
href: tools/wb_tools1.qmd
- text: More command line tools
href: tools/wb_tools2.qmd
- text: Getting help online
href: tools/wb_help.qmd
- id: talks
collapse-level: 1
contents:
- section: "<br> <em><b>Conference talks</b></em><br><br>"
href: talks/index.qmd
contents:
- text: Advanced research instruments
href: talks/2023_driconnect.qmd
- text: Big data in the agrotech industry
href: talks/2024_bccai.qmd
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