diff --git a/_static/theme.css b/_static/theme.css index 00c65dda..6de46d06 100644 --- a/_static/theme.css +++ b/_static/theme.css @@ -163,3 +163,18 @@ div.pdf-container > div > object[type="application/pdf"] { width: 100%; height: 100%; } + +.sidebar-drawer { + justify-content: center; + min-width: 15em; + max-width: 18rem; + color: #fcfcfc; +} + +.main { + display: flex; +} + +.content { + flex: 1; +} diff --git a/bibliography/mri.md b/bibliography/mri.md index cb86e407..6ff7d77a 100644 --- a/bibliography/mri.md +++ b/bibliography/mri.md @@ -30,7 +30,7 @@ * [Jupyter book](https://shimming-toolbox.github.io/B1-shimming/) covering the basics of static B1+ shimming * [Gaspard Cereza's MSc thesis](https://www.dropbox.com/s/4cv8s4t0ioll32q/Master_thesis_Gaspard_Cereza_corrected_2.pdf?dl=0) -* [🔒 🎥 Universal Pulse]() TODO +* 🔒 🎥 Universal Pulse TODO * [🔒 VOP creation (internal documentation)](https://docs.google.com/document/d/1uqr4UX4VY8H8cZ_DB9zaj12o0xrswRj44AxE3FZauHM/edit#heading=h.uf4xboevl4xa) @Gaspard todo: (notably list talks from UHF meeting) diff --git a/computing-resources/data/duke.md b/computing-resources/data/duke.md index c2ec66c7..53e5cb55 100644 --- a/computing-resources/data/duke.md +++ b/computing-resources/data/duke.md @@ -20,7 +20,7 @@ The shared folders are: ## Access from stations -When [connecting with `ssh`](../../#ssh-command-line), `duke` is available at `/mnt/duke/`, e.g.: +When [connecting with `ssh`](../neuropoly/README.md#ssh-command-line), `duke` is available at `/mnt/duke/`, e.g.: ``` u932945@joplin:~$ ls -l /mnt/duke @@ -36,7 +36,7 @@ drwxr-xr-x 2 u108545 domain users 4096 Jun 8 16:44 temp ## Mount with GUI -When working on campus or [over the VPN](../../#vpn), you can connect your computer to `duke`: +When working on campus or [over the VPN](../neuropoly/README.md#vpn), you can connect your computer to `duke`: ````{tabbed} macOS 1. Open Finder diff --git a/computing-resources/data/git-datasets.md b/computing-resources/data/git-datasets.md index 07125517..21da27d8 100644 --- a/computing-resources/data/git-datasets.md +++ b/computing-resources/data/git-datasets.md @@ -4,8 +4,8 @@ This server includes private MRI and microscopy datasets, which have been curate `git+ssh://data.neuro.polymtl.ca` has a max size of ~1TB. -It hosts [BIDS](https://bids-specification.readthedocs.io) datasets, version-controlled using [`git-annex`](git-annex.branchable.com/). -It is locked behind a [VPN](../../#vpn) because much of our data is under medical ethics protections, and needs to be kept off the general internet. +It hosts [BIDS](https://bids-specification.readthedocs.io) datasets, version-controlled using [`git-annex`](https://git-annex.branchable.com/). +It is locked behind a [VPN](../neuropoly/README.md#vpn) because much of our data is under medical ethics protections, and needs to be kept off the general internet. Initial setup @@ -13,7 +13,7 @@ Initial setup ### Prerequisites -0. You must have a \*nix OS with `git-annex>=8` installed. See [`git-annex` installation](./git-annex.md#installation). +0. You must have a \*nix OS with `git-annex>=8` installed. See [`git-annex` installation](../../geek-tips/git-annex.md#installation). 2. Make sure you have an ssh key. * If not, run `ssh-keygen -t ed25519 -C your.name@polymtl.ca`. Your keys will be in the hidden folder `~/.ssh/`. @@ -50,7 +50,7 @@ Because this server contains private medical data, you need to be on campus, con *If connecting from off-campus*, connect to [polyvpn](http://www.polymtl.ca/si/reseaux/acces-securise-rvp-ou-vpn). -> 🏚️ Verify connectivity by `ping data.neuro.polymtl.ca`. If **you cannot ping** then you need to double-check your VPN connection; make sure it is connected, make sure you can reach `joplin`, and if it still isn't working *ask the [Poly network admins](dge.informatique@polymtl.ca)* to unblock your account from this server. +> 🏚️ Verify connectivity by `ping data.neuro.polymtl.ca`. If **you cannot ping** then you need to double-check your VPN connection; make sure it is connected, make sure you can reach `joplin`, and if it still isn't working *ask the [Poly network admins](mailto:dge.informatique@polymtl.ca)* to unblock your account from this server. Verify you can use the server by `ssh git@data.neuro.polymtl.ca help`. If it hangs, triple-check again your VPN. If it rejects you, your account is not created yet, or you have switched machines. A successful connection looks like: @@ -78,7 +78,7 @@ Usage During daily usage, you will need to be [*on the polyvpn network*](#connection). -You should also make sure to [configure git annex](./git-annex.md#global-git-config) for the best performance. +You should also make sure to [configure git annex](../../geek-tips/git-annex.md#global-git-config) for the best performance. ### List @@ -159,7 +159,7 @@ git annex sync --no-content --only-annex git push ``` -Finally, ask one of that dataset's reviewers to [look at your pull request](#Reviewing-Pull-Requests) by opening an issue on [neuropoly/data-management](https://github.com/neuropoly/data-management). +Finally, ask one of that dataset's reviewers to [look at your pull request](#reviewing-pull-requests) by opening an issue on [neuropoly/data-management](https://github.com/neuropoly/data-management). ### Reviewing Pull Requests @@ -232,7 +232,7 @@ git push origin :synced/xy/branchname ### New repository -To make a new repo, follow this [recipe](./git-annex.md#new-repo). +To make a new repo, follow this [recipe](../../geek-tips/git-annex.md#new-repo). Then, to upload it, pick a name under `datasets/`, e.g. "my-new-repo", and do diff --git a/computing-resources/neuropoly/README.md b/computing-resources/neuropoly/README.md index 647f99ae..21cf49f8 100644 --- a/computing-resources/neuropoly/README.md +++ b/computing-resources/neuropoly/README.md @@ -25,7 +25,7 @@ getent passwd ### Home folder -Every [GRAMES](../#poly-grames) account has a school-wide personal home folder. It is backed-up nightly. +Every GRAMES account has a school-wide personal home folder. It is backed-up nightly. ````{tabbed} macOS 1. Open Finder @@ -252,7 +252,7 @@ will attach the remote `/tmp/` to the local `./cluster_folder` ```{note} -If you are experiencing mounting issues on macOs, [this]([url](https://github.com/neuropoly/intranet.neuro.polymtl.ca/issues/57)) might help. +If you are experiencing mounting issues on macOs, [this](https://github.com/neuropoly/intranet.neuro.polymtl.ca/issues/57) might help. ``` diff --git a/computing-resources/neuropoly/cpus.md b/computing-resources/neuropoly/cpus.md index 51d33c94..376d854d 100644 --- a/computing-resources/neuropoly/cpus.md +++ b/computing-resources/neuropoly/cpus.md @@ -4,7 +4,7 @@ description: How to use CPU clusters at Neuropoly # CPU Clusters -Unless otherwise stated, use your [connect with your polygrames credentials](./computing-resources-neuropoly.md#TODO) +Unless otherwise stated, use your [connect with your polygrames credentials](README.md) ## `joplin` diff --git a/computing-resources/neuropoly/gpus.md b/computing-resources/neuropoly/gpus.md index 452b219e..d21a4041 100644 --- a/computing-resources/neuropoly/gpus.md +++ b/computing-resources/neuropoly/gpus.md @@ -1035,7 +1035,7 @@ You can also see all this information plotted over time for each machine at * [https://monitor.neuro.polymtl.ca/host/rosenberg.neuro.polymtl.ca/](https://monitor.neuro.polymtl.ca/host/rosenberg.neuro.polymtl.ca/) * [https://monitor.neuro.polymtl.ca/host/romane.neuro.polymtl.ca/](https://monitor.neuro.polymtl.ca/host/romane.neuro.polymtl.ca/) -#### Monitoring GPUs +### Monitoring GPUs As above, you can see the computation amount, allocated RAM, temperature, fan speed of the GPUs on the command line with diff --git a/computing-resources/printer.md b/computing-resources/printer.md index 59a92e96..ad51d138 100644 --- a/computing-resources/printer.md +++ b/computing-resources/printer.md @@ -7,7 +7,7 @@ IP address: See [NeuroPoly Internal Document: Printer](https://docs.google.com/d ## Troubleshooting -#### Brother HL-3170CDW - Error: "low toner" +### Brother HL-3170CDW - Error: "low toner" If it doesn't print and it says “low toner” on the printer, do the following: diff --git a/conf.py b/conf.py index 88139f43..f2f03af7 100644 --- a/conf.py +++ b/conf.py @@ -34,6 +34,7 @@ extensions = [ 'myst_parser', # there's also myst_nb, which supports embedding Jupyter notebooks, but is heavier. 'sphinx_panels', + 'sphinx_inline_tabs', ] myst_heading_anchors = 4 # enable #section links: https://myst-parser.readthedocs.io/en/latest/syntax/optional.html#syntax-header-anchors @@ -52,7 +53,7 @@ # The theme to use for HTML and HTML Help pages. See the documentation for # a list of builtin themes. # -html_theme = 'sphinx_book_theme' +html_theme = 'furo' # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, @@ -68,15 +69,31 @@ html_sourcelink_suffix = ".md" # our sources are in markdown; but this only has an effect if "use_download_button": True html_theme_options = { - "toc_title": "Page Contents", - "search_bar_text": "Search...", - - "repository_url": "https://github.com/neuropoly/intranet.neuro.polymtl.ca", - "use_fullscreen_button": False, - "use_edit_page_button": True, - "use_download_button": False, - - #"logo_only": True, # hides html_title and just shows html_logo + "sidebar_hide_name": False, + "source_repository": "https://github.com/neuropoly/intranet.neuro.polymtl.ca", + "source_branch": "master", + "light_css_variables": { + "color-background-primary": "#fcfcfc", + "color-sidebar-background": "#d0d0d0", + "color-sidebar-item-background--hover": "#5a5a58", + "color-sidebar-link-text": "#fcfcfc", + "color-sidebar-link-text--top-level": "#000000", + "color-content-foreground": "#000000", + "color-foreground-primary": "#000000", + "color-sidebar-search-foreground": "#000000", + }, + "dark_css_variables": { + "color-sidebar-brand-text": "#FFFFFF", + "color-sidebar-background": "#3d3d3c", + "color-sidebar-search-foreground": "#FFFFFF", + "color-sidebar-item-background--hover": "#5a5a58", + "color-sidebar-link-text": "#fcfcfc", + "color-sidebar-link-text--top-level": "#FFFFFF", + "color-foreground-primary": "#FFFFFF", + "color-content-foreground": "#FFFFFF", + "color-admonition-title--note": "#0054af", + "color-admonition-title-background--note": "#0054af5c", + } } diff --git a/courses.md b/courses.md index ef745c04..bf32a096 100644 --- a/courses.md +++ b/courses.md @@ -2,7 +2,7 @@ ## Requirements for Polytechnique -````{tabbed} MSc +```{tab} MSc * Details of the program on the [Polymtl website](https://www.polymtl.ca/programmes/programmes/maitrise-professionnelle-ou-recherche-en-genie-biomedical-programme-conjoint). * The rules say that "At most 6 credits can be undergraduate courses and at least 8 credits must be courses in the field of biomedical engineering or other and approved by the CPÉS", but this is a relaxed rules. Courses in computer science, deep learning, etc. are accepted. * For [exemption of additional fees as foreign student](https://www.polymtl.ca/etudiants-internationaux/en/financial-questions/exemption-differential-fees), you need at least 6 credits completed, of grad courses at Polytechnique Montréal. @@ -15,15 +15,14 @@ See [this link](https://etudiant.polymtl.ca/etudes/en/graduate-studies/thesis-an Please refer to the [Règlements généraux des études supérieures ](https://www.polymtl.ca/renseignements-generaux/documents-officiels/5-affaires-academiques-et-vie-etudiante) (53.4 COMPOSITION ET NOMINATION DU JURY). -```` +``` -````{tabbed} PhD +```{tab} PhD * Details of the program on the [Polymtl website](https://www.polymtl.ca/programmes/programmes/doctorat-en-genie-biomedical-programme-conjoint#). * Candidates who already hold a graduate degree may obtain an exemption from all or part of their graduate course credits according to the procedures specified in article 73.1.1 of the specific regulations for graduate studies. -```{important} -There exist an agreement between universities across Quebec, called [CREPUQ](https://www.bci-qc.ca/en/aehe/agreement/), that allow students to transfer academic credits between institutions. So for example, you could attend a course at UdeM or McGill and receive the credits at Polytechnique Montreal as part of your gradutate program. -``` +> **Important**: There exist an agreement between universities across Quebec, called [CREPUQ](https://www.bci-qc.ca/en/aehe/agreement/), that allow students to transfer academic credits between institutions. So for example, you could attend a course at UdeM or McGill and receive the credits at Polytechnique Montreal as part of your gradutate program. + ### Writing your thesis @@ -32,7 +31,7 @@ See [this link](https://etudiant.polymtl.ca/etudes/en/graduate-studies/thesis-an ### Jury Please refer to the [Règlements généraux des études supérieures ](https://www.polymtl.ca/renseignements-generaux/documents-officiels/5-affaires-academiques-et-vie-etudiante) (76.4 COMPOSITION ET NOMINATION DU JURY). -```` +``` ## Medical imaging diff --git a/geek-tips/contributing.md b/geek-tips/contributing.md index 02c22bc8..49303188 100644 --- a/geek-tips/contributing.md +++ b/geek-tips/contributing.md @@ -7,7 +7,7 @@ First off, thanks for taking the time to contribute to one of **NeuroPoly**'s pr This set of guidelines provides general instruction on how to make any one of the following contributions: * Submitting a bug report or feature request (See: [Opening an Issue](#opening-an-issue-on-github)) -* Fixing a bug or developing a feature (See: [Developing](#developing) and [Submitting a Pull Request](#submitting-a-pull-request)) +* Fixing a bug or developing a feature (See: [Developing](#developing-code) and [Submitting a Pull Request](#submitting-a-pull-request)) ## Project-Specific Guidance diff --git a/geek-tips/deep-learning/README.md b/geek-tips/deep-learning/README.md index 1e41ba01..d3bf336e 100644 --- a/geek-tips/deep-learning/README.md +++ b/geek-tips/deep-learning/README.md @@ -19,7 +19,7 @@ misc -### Frameworks/Libraries +## Frameworks/Libraries [https://github.com/kjw0612/awesome-deep-vision](https://github.com/kjw0612/awesome-deep-vision) diff --git a/geek-tips/deep-learning/tensorflow.md b/geek-tips/deep-learning/tensorflow.md index a4d03f1a..7aeec4d3 100644 --- a/geek-tips/deep-learning/tensorflow.md +++ b/geek-tips/deep-learning/tensorflow.md @@ -12,7 +12,7 @@ export LD_LIBRARY_PATH=/usr/local/cuda-8.0/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY export CUDA_HOME=/usr/local/cuda ``` -### Install tensorflow +## Install tensorflow ```bash # This is for install tensorflow with GTX1080 drvier. @@ -72,7 +72,7 @@ python test_tensorflow.py echo ------------------- End script ------------------- ``` -### Fix CUDA driver version +## Fix CUDA driver version ```bash sudo add-apt-repository ppa:graphics-drivers/ppa @@ -80,14 +80,14 @@ sudo apt-get update sudo apt-get install nvidia-367 ``` -### Fix module tensorflow import error +## Fix module tensorflow import error ```bash sudo pip uninstall six sudo pip install six --upgrade --target="/usr/lib/python2.7/dist-packages" ``` -### Reference +## Reference [Install with GPU support](https://github.com/uher/InstallGpuEnableTensorflow) diff --git a/geek-tips/git-annex.md b/geek-tips/git-annex.md index e8673b23..ac6a68a2 100644 --- a/geek-tips/git-annex.md +++ b/geek-tips/git-annex.md @@ -1,6 +1,6 @@ # git-annex -[`git annex`](git-annex.branchable.com/) is an extension to git that lets it handle large repos spread in pieces across multiple servers/disks/accounts. +[`git annex`](https://git-annex.branchable.com/) is an extension to git that lets it handle large repos spread in pieces across multiple servers/disks/accounts. We are using it because @@ -73,7 +73,7 @@ git config --global annex.thin true # save disk space by de-duplicating checked git config --global annex.private true # prevent attempting to share your local copy of the annex, which is impossible when working in a team ``` -See [below](#hardlinks) to understand what this setting offers. +See [below](#annexthin-hardlinks) to understand what this setting offers. ## New repo diff --git a/geek-tips/image-processing-software/diffusion-simulator.md b/geek-tips/image-processing-software/diffusion-simulator.md index ec137bee..9e527de9 100644 --- a/geek-tips/image-processing-software/diffusion-simulator.md +++ b/geek-tips/image-processing-software/diffusion-simulator.md @@ -14,7 +14,7 @@ You can choose the permeability of the barriers via p but not the thickness. However, you can also build any kind of shape using a PLY file \(3D object file\). Here is a tutorial for this option: [Monte-Carlo Mesh Simulation](http://cmic.cs.ucl.ac.uk/camino/index.php?n=Tutorials.MCMeshSimulation). -### Recommendations +## Recommendations * `cylindersep` must be at least twice as big as `cylinderrad` \(cylinders mustn't overlap\) * Be very careful at high q-values \(>0.14 um-1\). You need lots of walkers \(200 000\), and time steps \(-tmax 3000\) diff --git a/geek-tips/image-processing-software/itk-snap.md b/geek-tips/image-processing-software/itk-snap.md index 7c3132a4..4634e9a0 100644 --- a/geek-tips/image-processing-software/itk-snap.md +++ b/geek-tips/image-processing-software/itk-snap.md @@ -2,7 +2,7 @@ [ITK-SNAP](http://www.itksnap.org/pmwiki/pmwiki.php) is a software package used to segment structures in 3D medical images. -### Create a mesh out of a binary file +## Create a mesh out of a binary file ITK-SNAP allows you to construct a mesh \(`.vtk`\) with a binary mask. diff --git a/geek-tips/misc/docker/README.md b/geek-tips/misc/docker/README.md index 6ed723cd..c8522309 100644 --- a/geek-tips/misc/docker/README.md +++ b/geek-tips/misc/docker/README.md @@ -17,7 +17,7 @@ docker-for-deep-learning ## Using Docker -#### Search for remote image +### Search for remote image ```text docker search ubuntu # will search for ubuntu distrib @@ -25,7 +25,7 @@ docker search ubuntu # will search for ubuntu distrib [List of Ubuntu images](https://hub.docker.com/_/ubuntu) -#### Install & Run Linux distribution +### Install & Run Linux distribution ```text docker pull debian # will install debian @@ -33,13 +33,13 @@ docker pull ubuntu:16.04 docker pull centos ``` -#### List local Docker images +### List local Docker images ```text docker images ``` -#### Run Docker image +### Run Docker image To run in interactive mode, use flag `-i` @@ -49,7 +49,7 @@ docker run -it ubuntu:trusty /bin/bash docker run -it ubuntu:16.04 ``` -#### Remove Docker image or containers \(force deletion\) +### Remove Docker image or containers \(force deletion\) ```text docker rmi -f IMAGE_ID @@ -57,7 +57,7 @@ docker rmi $(docker images -a -q) # WARNING!!! This will remove all images docker rm $(docker ps -a -f status=exited -q) # WARNING!!! This will remove all containers ``` -#### Save a Docker image +### Save a Docker image The example below shows how to install useful items on a standard ubuntu image, and then save the image locally. @@ -75,7 +75,7 @@ docker ps -a docker commit your_name/ubuntu:16.04 ``` -#### Build Docker container from Dockerfile +### Build Docker container from Dockerfile 1. Create a Dockerfile by running \`touch Dockerfile\` 2. Inside the Dockerfile write the following \(items below are just given as an example\): @@ -105,7 +105,7 @@ ENV PATH "/sct/bin:${PATH}" 1. Build docker image: \`docker build -t <container\_id> .\` 2. Run it: \`docker run -it <container\_id>\` -#### Run with DISPLAY redirection +### Run with DISPLAY redirection In order to run scripts with GUI you need to allow X11 redirection: @@ -117,7 +117,7 @@ In order to run scripts with GUI you need to allow X11 redirection: 1. On OSX: \`docker run -e DISPLAY=host.docker.internal:0 -it <CONTAINER\_ID>\` 2. On Linux: \`docker run -ti –rm -e DISPLAY=$DISPLAY -v /tmp/.X11-unix:/tmp/.X11-unix <CONTAINER\_ID>\` -#### Copy file into container +### Copy file into container ```bash # list container diff --git a/geek-tips/misc/git-and-github.md b/geek-tips/misc/git-and-github.md index e6fd79ad..7dae3563 100644 --- a/geek-tips/misc/git-and-github.md +++ b/geek-tips/misc/git-and-github.md @@ -374,7 +374,7 @@ git push -f ## HOW TO -#### Configure git +### Configure git Before starting: configure git to identify you for each commit @@ -392,7 +392,7 @@ git config --global alias. more info: [http://www.atlassian.com/git/tutorial/git-basics#!config](http://www.atlassian.com/git/tutorial/git-basics#!config)Edit -#### Show changed files between two commits +### Show changed files between two commits ``` git diff --name-only SHA1 SHA2 @@ -501,7 +501,7 @@ Removed tracked files git rm "file name" ``` -#### Download +### Download Download (server → local station) a repository for the first time @@ -511,7 +511,7 @@ get address of repos, and type git clone git@bitbucket.org:neuropoly/spinalcordtoolbox_dev.git ``` -#### Reset your branch (revert your local commits) +### Reset your branch (revert your local commits) Using the Terminal: @@ -532,7 +532,7 @@ Using Sourcetree: assume you are on the branch `example-fix`. Find the commit with `origin/example-fix`, and right click on it. Select in the menu `Reset example-fix to this commit` and a dialog will appear. If don't want to keep the changes, you can select `Hard`, else select `Soft` -#### Upload +### Upload Upload (local –> server) a repository for the first time @@ -552,7 +552,7 @@ git commit -m "First commit" git push -u origin master ``` -#### Discard local changes (if pull doesn't work) +### Discard local changes (if pull doesn't work) For a specific file use: @@ -568,7 +568,7 @@ git checkout -- . ## TODO -#### Ignore file mode +### Ignore file mode If you cannot do a pull due to a change of file mode, you can ignore it: @@ -576,7 +576,7 @@ If you cannot do a pull due to a change of file mode, you can ignore it: git config core.fileMode false ``` -#### +### ## Rebase @@ -663,7 +663,7 @@ filename:my_file ## Tags -#### Checkout specific tag or commit +### Checkout specific tag or commit List all tags @@ -727,11 +727,11 @@ alias gb="git branch" ## Git Software -#### Pycharm +### Pycharm Interactive squash, rebase: [https://www.jetbrains.com/help/pycharm/edit-project-history.html](https://www.jetbrains.com/help/pycharm/edit-project-history.html) -#### SourceTree +### SourceTree **Select default branches for pushing** diff --git a/geek-tips/misc/microsoft-word.md b/geek-tips/misc/microsoft-word.md index 5e736142..97bd339b 100644 --- a/geek-tips/misc/microsoft-word.md +++ b/geek-tips/misc/microsoft-word.md @@ -1,13 +1,13 @@ # Microsoft Word -#### Useful shortcuts for OSX +## Useful shortcuts for OSX | Action | Keyboard shortcut | | :--- | :--- | | Turn track changes on or off | COMMAND + Shift + E | | Add comment | COMMMAND + ALT + A | -#### How to always open a page with "page width" view +## How to always open a page with "page width" view Create a new macro in Normal.dot template: diff --git a/geek-tips/misc/virtual-machines/vagrant.md b/geek-tips/misc/virtual-machines/vagrant.md index 26ca6ab2..a103b0db 100644 --- a/geek-tips/misc/virtual-machines/vagrant.md +++ b/geek-tips/misc/virtual-machines/vagrant.md @@ -4,12 +4,12 @@ Tutorial: [https://www.youtube.com/watch?v=vBreXjkizgo](https://www.youtube.com/watch?v=vBreXjkizgo)​ -### Installing +## Installing 1. To use **Vagrant**, you will first need to install **VirtualBox**: [https://www.virtualbox.org/wiki/Downloads](https://www.virtualbox.org/wiki/Downloads)​ 2. Install Vagrant from here: [https://learn.hashicorp.com/tutorials/vagrant/getting-started-index?in=vagrant/getting-started](https://learn.hashicorp.com/tutorials/vagrant/getting-started-index?in=vagrant/getting-started)​ -### Getting Started & Basic Commands +## Getting Started & Basic Commands To create a box: diff --git a/geek-tips/misc/virtual-machines/virtualbox.md b/geek-tips/misc/virtual-machines/virtualbox.md index 04b12a1c..c2d9447f 100644 --- a/geek-tips/misc/virtual-machines/virtualbox.md +++ b/geek-tips/misc/virtual-machines/virtualbox.md @@ -1,6 +1,6 @@ # VirtualBox -### Import a .ova file +## Import a .ova file If you have a Virtual Machine (VM) that has a .ova extension here's what to do to use it with Virtualbox @@ -10,15 +10,15 @@ If you have a Virtual Machine (VM) that has a .ova extension here's what to do t * It may take several minutes to import * Once it's done just select your machine and click on Show to run it -### Shared folder +## Shared folder -#### Using Guest Additions (recommended) +### Using Guest Additions (recommended) [https://www.virtualbox.org/manual/ch04.html#idp91444064](https://www.virtualbox.org/manual/ch04.html#idp91444064) On Linux: once you ran all the instructions here, a CD-ROM will be mounted on the guest. Then, go to /mnt/ and run the file ./VBoxLinuxAdditions.run in a terminal. -#### Manual method +### Manual method [https://www.virtualbox.org/manual/ch04.html#idp91444064](https://www.virtualbox.org/manual/ch04.html#idp91444064) If you want to transfer files between your computer (host) and your Virtual Machine (guest) you'll need a shared folder. diff --git a/geek-tips/os-guides/macosx.md b/geek-tips/os-guides/macosx.md index 44ca21ba..9693b1f8 100644 --- a/geek-tips/os-guides/macosx.md +++ b/geek-tips/os-guides/macosx.md @@ -94,7 +94,7 @@ Full list of QuickLook modules [here](https://www.quicklookplugins.com/page/2/)\ ## General -#### Global default config +### Global default config [https://gist.github.com/brandonb927/3195465](https://gist.github.com/brandonb927/3195465) diff --git a/mri-scanning/unf-3t-prisma.md b/mri-scanning/unf-3t-prisma.md index c4450010..29f077fb 100644 --- a/mri-scanning/unf-3t-prisma.md +++ b/mri-scanning/unf-3t-prisma.md @@ -8,10 +8,10 @@ More details on the UNF website: [https://unf-montreal.ca/en/documentation/facil ## Booking the scanner -Details about the booking system [here]([url](https://unf-montreal.ca/en/documentation/facility/reservation/)). +Details about the booking system [here](https://unf-montreal.ca/en/documentation/facility/reservation/). ```{note} -Under the `session name` you will need to enter a study suffix that is listed in this [JSON file]([url](https://github.com/UNFmontreal/bids_configs/blob/master/studies.json)). Look for the fields that start with `neuropoly`. +Under the `session name` you will need to enter a study suffix that is listed in this [JSON file](https://github.com/UNFmontreal/bids_configs/blob/master/studies.json). Look for the fields that start with `neuropoly`. ``` diff --git a/onboarding/campus-access.md b/onboarding/campus-access.md index 3d453dc5..724a312d 100644 --- a/onboarding/campus-access.md +++ b/onboarding/campus-access.md @@ -6,13 +6,13 @@ description: >- # Campus Access -### Please advise one of the PIs before arriving for the first time on campus in order to organize the logistics together. +## Please advise one of the PIs before arriving for the first time on campus in order to organize the logistics together. -### Campus Map +## Campus Map [http://www.polymtl.ca/rensgen/en/coordonnees/campus.php](http://www.polymtl.ca/rensgen/en/coordonnees/campus.php) -### Lab rooms at Polytechnique +## Lab rooms at Polytechnique As a NeuroPoly lab member, the majority of your time at Polytechnique will be spent in one of two main rooms, depending on the focus of your work: @@ -21,17 +21,17 @@ As a NeuroPoly lab member, the majority of your time at Polytechnique will be sp There are also separate rooms for servers (L-7944.A) and printers (L-5619). Some of these doors require codes to access, these can be found in the [Internal Document](https://docs.google.com/document/d/13iNhiBKYZWT9ytsvYeeYV4FJn6Wn00q9Ctka7toMV08/edit#heading=h.o24dt0r1154g). -### Desk/computer access +## Desk/computer access Desk access is given on a first-come-first-serve basis. Once you find a seat that you like, please put your name somewhere (e.g. on a sheet of paper) so we know that a desk has been claimed. If you work on a personal laptop and need desktop equipment (a monitor, mouse, keyboard, etc.) please contact your supervisor. If instead you need to be provided a workstation (e.g. iMac), please consult the [List of Computing Resources](https://intranet.neuro.polymtl.ca/computing-resources/neuropoly/README.html) document, then pick a workstation that is not being used by another lab member. -### Requirements for room access +## Requirements for room access To be able to access the lab rooms, you will need a Polytechnique card and to activate it for the specific rooms you wish to access. To activate it, please follow the onboarding procedure. -### COVID-19 Protocol +## COVID-19 Protocol In addition to the above requirement, please also complete the following steps specific to COVID-19: diff --git a/onboarding/infrastructure.md b/onboarding/infrastructure.md index 42310169..9cfe61d1 100644 --- a/onboarding/infrastructure.md +++ b/onboarding/infrastructure.md @@ -1,11 +1,11 @@ # Infrastructure -### Computers +## Computers * [Computer facilities - Neuropoly](https://intranet.neuro.polymtl.ca/computing-resources/neuropoly/README.html#cpu-gpu-clusters) * [Computer facilities - Compute Canada](https://intranet.neuro.polymtl.ca/computing-resources/compute-canada.html) -### Data +## Data Internal database managed with git-annex. @@ -13,7 +13,7 @@ Contact persons: Nick & Mathieu. 👉 [How to get data?](https://intranet.neuro.polymtl.ca/computing-resources/data/git-datasets.html) -### MRI +## MRI [MRI scanning procedures](https://intranet.neuro.polymtl.ca/mri-scanning/README.html) diff --git a/setup.py b/setup.py index d44bbde4..13fc6cc9 100644 --- a/setup.py +++ b/setup.py @@ -19,8 +19,9 @@ extras_require={ "sphinx": [ "myst-parser", - "sphinx-book-theme", + "furo", "sphinx-panels", + "sphinx-inline-tabs", # pinned because of this bug https://github.com/pydata/pydata-sphinx-theme/pull/509 # and that the patched sphinx-book-theme isn't out yet: https://github.com/executablebooks/sphinx-book-theme/issues/428#issuecomment-966021270 "sphinx~=4.2.0", # TODO: unpin when the next sphinx-book-theme is released