Lint and update Markdown files

benz0li · benz0li · commit b9040c03f141 · 2023-11-10T15:29:19.000+01:00
diff --git a/.gitignore b/.gitignore
@@ -9,7 +9,10 @@
 !/.gitattributes
 !/.gitignore
 !/.hadolint.yml
+!/.markdownlint.yml
 !/CODE_OF_CONDUCT.md
+!/CUDA_NOTES.md
+!/DEVTOOLS_NOTES.md
 !/LICENSE
 !/NOTES.md
 !/README.md
diff --git a/.markdownlint.yml b/.markdownlint.yml
@@ -0,0 +1,3 @@
+MD033: false
+MD036: false
+MD041: false
diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md
@@ -45,16 +45,16 @@ or harmful.
 
 Community leaders have the right and responsibility to remove, edit, or reject
 comments, commits, code, wiki edits, issues, and other contributions that are
-not aligned to this Code of Conduct, and will communicate reasons for
-moderation decisions when appropriate.
+not aligned to this Code of Conduct, and will communicate reasons formoderation
+decisions when appropriate.
 
 ## Scope
 
 This Code of Conduct applies within all community spaces, and also applies when
 an individual is officially representing the community in public spaces.
-Examples of representing our community include using an official e-mail
-address, posting via an official social media account, or acting as an
-appointed representative at an online or offline event.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
 
 ## Enforcement
 
@@ -116,13 +116,17 @@ the community.
 
 This Code of Conduct is adapted from the [Contributor Covenant][homepage],
 version 2.0, available at
-https://www.contributor-covenant.org/version/2/0/code_of_conduct.html.
+[https://www.contributor-covenant.org/version/2/0/code_of_conduct.html][v2.0].
 
-Community Impact Guidelines were inspired by [Mozilla's code of conduct
-enforcement ladder](https://github.com/mozilla/diversity).
-
-[homepage]: https://www.contributor-covenant.org
+Community Impact Guidelines were inspired by
+[Mozilla's code of conduct enforcement ladder][Mozilla CoC].
 
 For answers to common questions about this code of conduct, see the FAQ at
-https://www.contributor-covenant.org/faq. Translations are available at
-https://www.contributor-covenant.org/translations.
+[https://www.contributor-covenant.org/faq][FAQ]. Translations are available
+at [https://www.contributor-covenant.org/translations][translations].
+
+[homepage]: https://www.contributor-covenant.org
+[v2.0]: https://www.contributor-covenant.org/version/2/0/code_of_conduct.html
+[Mozilla CoC]: https://github.com/mozilla/diversity
+[FAQ]: https://www.contributor-covenant.org/faq
+[translations]: https://www.contributor-covenant.org/translations
diff --git a/CUDA_NOTES.md b/CUDA_NOTES.md
@@ -0,0 +1,62 @@
+# Notes on CUDA
+
+The CUDA and OS versions are selected as follows:
+
+* CUDA: The lastest version that has image flavour `devel` including cuDNN
+  available.
+* OS: The latest version that has TensortRT libraries for `amd64` available.  
+  :information_source: It is taking quite a long time for these to be available
+  for `arm64`.
+
+## Tweaks
+
+**R images**
+
+* R: Provide NVBLAS-enabled `R_` and `Rscript_`.
+  * Enabled at runtime and only if `nvidia-smi` and at least one GPU are
+    present.
+
+### Environment variables
+
+**Versions**
+
+* `CUDA_VERSION`
+
+**Miscellaneous**
+
+* `CUDA_IMAGE`: The CUDA image it is derived from.
+* `CUDA_VISIBLE_DEVICES`: If unset (default), CUDA will use all available
+  CUDA-capable devices.  
+  :point_right: User-settable at runtime.
+
+## Settings
+
+### Default
+
+**R images**
+
+* VS Code
+  * Extensions > R > Rterm: Linux: `/usr/local/bin/R`
+
+## Basic Linear Algebra Subprograms (BLAS)
+
+The **R images** use OpenBLAS by default.
+
+To have `R` and `Rscript` use NVBLAS instead,
+
+1. copy the NVBLAS-enabled executables to `~/.local/bin`  
+
+       for file in $(which {R,Rscript}); do
+         cp "$file"_ "~/.local/bin/$(basename "$file")";
+       done
+
+1. set Extensions > R > Rterm > Linux: `/home/USER/.local/bin/R` in VS Code
+   settings  
+   :point_right: Substitute `USER` with your user name.
+
+and restart the R terminal.
+
+:information_source: The
+[xgboost](https://cran.r-project.org/package=xgboost) package benefits greatly
+from NVBLAS, if it is
+[installed correctly](https://xgboost.readthedocs.io/en/stable/build.html).
diff --git a/DEVTOOLS_NOTES.md b/DEVTOOLS_NOTES.md
@@ -0,0 +1,28 @@
+# Notes on `INSTALL_DEVTOOLS`
+
+If `INSTALL_DEVTOOLS` is set, the required tools according to [microsoft/vscode > Wiki > How to Contribute](https://github.com/Microsoft/vscode/wiki/How-to-Contribute)
+and [coder/code-server > Docs > Contributing](https://github.com/coder/code-server/blob/main/docs/CONTRIBUTING.md)
+are installed.
+
+Node.js is installed with corepack enabled by default. Use it to manage Yarn
+and/or pnpm:
+
+* [Installation | Yarn - Package Manager > Updating the global Yarn version](https://yarnpkg.com/getting-started/install#updating-the-global-yarn-version)
+* [Installation | pnpm > Using Corepack](https://pnpm.io/installation#using-corepack)
+
+## Environment variables
+
+**Versions**
+
+* `NODE_VERSION`
+
+## System Python
+
+Package `libsecret-1-dev` depends on `python3` from the system's package
+repository.
+
+The system's Python version is installed at `/usr/bin`.  
+
+:information_source: Because a [more recent Python version](NOTES.md#python) is
+installed at `/usr/local/bin`, it takes precedence over the system's Python
+version.
diff --git a/NOTES.md b/NOTES.md
@@ -9,10 +9,11 @@ variables and incorporate most tweaks and default settings of the
 [docker](https://github.com/b-data/jupyterlab-python-docker-stack)
 [stacks](https://github.com/b-data/jupyterlab-r-docker-stack).
 
-They depend on very few 
+They depend on very few
 [Dev Container Features](https://containers.dev/features) and add some extra
 customisation through build argument (`build.args`) and environment variables
-(`remoteEnv`).
+(`remoteEnv`).  
+:information_source: See [Notes on `INSTALL_DEVTOOLS`](DEVTOOLS_NOTES.md).
 
 ## Tweaks
 
@@ -55,8 +56,8 @@ The following startup scripts are put in place:
   miniconda.
 * `QT_QPA_PLATFORM` (R qgisprocess image): Qt Platform Plugin to use.  
   :point_right: User-settable at runtime.
-    * `offscreen`: Renders to an offscreen buffer. (default)
-    * unset: Auto-detect Qt Platform Plugin.
+  * `offscreen`: Renders to an offscreen buffer. (default)
+  * unset: Auto-detect Qt Platform Plugin.
 * `LIBGL_ALWAYS_SOFTWARE=1` (R qgisprocess image): Always use software
   rendering.  
   :point_right: User-settable at runtime.
@@ -82,8 +83,8 @@ The following startup scripts are put in place:
   :point_right: User-settable at build time with `SET_TZ`.
 * `PIP_USER`: The Python package install directory.  
   :point_right: User-settable at runtime.
-    * `1`: user directory (`~/.local`, persistent (default))
-    * `0`: system directory (`/usr/local`, not persistent)
+  * `1`: user directory (`~/.local`, persistent (default))
+  * `0`: system directory (`/usr/local`, not persistent)
 * `CTAN_REPO`: The CTAN mirror URL. (Julia pubtools, Python scipy, R verse+
   images)
 * `OMP_NUM_THREADS`: If unset (default), BLAS/OpenMP will use as many
@@ -108,59 +109,59 @@ are installed.
 ### Default
 
 * [IPython](.devcontainer/conf/ipython/usr/local/etc/ipython/ipython_config.py):
-    * Only enable figure formats `svg` and `pdf` for IPython.
+  * Only enable figure formats `svg` and `pdf` for IPython.
 * [JupyterLab](.devcontainer/conf/jupyterlab/usr/local/share/jupyter/lab/settings/overrides.json):
-    * Theme > Selected Theme: JupyterLab Dark
-    * Python LSP Server: Example settings according to [jupyter-lsp/jupyterlab-lsp > Installation > Configuring the servers](https://github.com/jupyter-lsp/jupyterlab-lsp#configuring-the-servers)
+  * Theme > Selected Theme: JupyterLab Dark
+  * Python LSP Server: Example settings according to [jupyter-lsp/jupyterlab-lsp > Installation > Configuring the servers](https://github.com/jupyter-lsp/jupyterlab-lsp#configuring-the-servers)
 * VS Code
-    * Extensions > GitLab Workflow
-        * Ai Assisted Code Suggestions: Enabled: false
-    * Extensions > GitLens — Git supercharged
-        * General > Show Welcome On Install: false
-        * General > Show Whats New After Upgrade: false
-    * Extensions > Resource Monitor Configuration
-        * Show: Battery: false
-        * Show: Cpufreq: false
+  * Extensions > GitLab Workflow
+    * Ai Assisted Code Suggestions: Enabled: false
+  * Extensions > GitLens — Git supercharged
+    * General > Show Welcome On Install: false
+    * General > Show Whats New After Upgrade: false
+  * Extensions > Resource Monitor Configuration
+    * Show: Battery: false
+    * Show: Cpufreq: false
 * Zsh
-    * Oh My Zsh: `~/.zshrc`
-        * Set PATH so it includes user's private bin if it exists
+  * Oh My Zsh: `~/.zshrc`
+    * Set PATH so it includes user's private bin if it exists
 
 **Julia images**
 
 * VS Code
-    * Extensions > Julia
-        * Enable Crash Reporter: false
-        * Enable Telemetry: false
+  * Extensions > Julia
+    * Enable Crash Reporter: false
+    * Enable Telemetry: false
 
 **R images**
 
 * R: `$(R RHOME)/etc/Rprofile.site`
-    * IRkernel: Only enable `image/svg+xml` and `application/pdf` for plot
+  * IRkernel: Only enable `image/svg+xml` and `application/pdf` for plot
     display.
-    * R Extension (VS Code): Disable help panel and revert to old behaviour.
+  * R Extension (VS Code): Disable help panel and revert to old behaviour.
 * [JupyterLab](.devcontainer/r-base/conf/jupyterlab/usr/local/share/jupyter/lab/settings/overrides.json):
-    * R LSP Server: Example settings according to [jupyter-lsp/jupyterlab-lsp > Installation > Configuring the servers](https://github.com/jupyter-lsp/jupyterlab-lsp#configuring-the-servers)
+  * R LSP Server: Example settings according to [jupyter-lsp/jupyterlab-lsp > Installation > Configuring the servers](https://github.com/jupyter-lsp/jupyterlab-lsp#configuring-the-servers)
 * VS Code
-    * Extensions > R
-        * Bracketed Paste: true
-        * Plot: Use Httpgd: true
-        * Rterm: Linux: `/usr/local/bin/radian`
-        * Rterm: Option: `["--no-save", "--no-restore"]`
-        * Workspace Viewer: Show Object Size: true
+  * Extensions > R
+    * Bracketed Paste: true
+    * Plot: Use Httpgd: true
+    * Rterm: Linux: `/usr/local/bin/radian`
+    * Rterm: Option: `["--no-save", "--no-restore"]`
+    * Workspace Viewer: Show Object Size: true
 
 ### Customise
 
 * IPython: Create file `~/.ipython/profile_default/ipython_config.py`
-    * Valid figure formats: `png`, `retina`, `jpeg`, `svg`, `pdf`.
+  * Valid figure formats: `png`, `retina`, `jpeg`, `svg`, `pdf`.
 * JupyterLab: Settings > Advanced Settings Editor
 * VS Code Server: Manage > Settings
 * Zsh
-    * Oh My Zsh: Edit `~/.zshrc`.
+  * Oh My Zsh: Edit `~/.zshrc`.
 
 **R images**
 
 * R: Create file `~/.Rprofile`
-    * Valid plot mimetypes: `image/png`, `image/jpeg`, `image/svg+xml`,
+  * Valid plot mimetypes: `image/png`, `image/jpeg`, `image/svg+xml`,
     `application/pdf`.  
     :information_source: MIME type `text/plain` must always be specified.
 
@@ -173,95 +174,3 @@ The Python version is selected as follows:
   such as numba, tensorflow, etc. – are already compatible with it.
 
 This Python version is installed at `/usr/local/bin`.
-
-# Additional notes on CUDA
-
-The CUDA and OS versions are selected as follows:
-
-* CUDA: The lastest version that has image flavour `devel` including cuDNN
-  available.
-* OS: The latest version that has TensortRT libraries for `amd64` available.  
-  :information_source: It is taking quite a long time for these to be available
-  for `arm64`.
-
-## Tweaks
-
-**R images**
-
-* R: Provide NVBLAS-enabled `R_` and `Rscript_`.
-    * Enabled at runtime and only if `nvidia-smi` and at least one GPU are
-    present.
-
-### Environment variables
-
-**Versions**
-
-* `CUDA_VERSION`
-
-**Miscellaneous**
-
-* `CUDA_IMAGE`: The CUDA image it is derived from.
-* `CUDA_VISIBLE_DEVICES`: If unset (default), CUDA will use all available
-  CUDA-capable devices.  
-  :point_right: User-settable at runtime.
-
-## Settings
-
-### Default
-
-**R images**
-
-* VS Code
-    * Extensions > R > Rterm: Linux: `/usr/local/bin/R`
-
-## Basic Linear Algebra Subprograms (BLAS)
-
-The **R images** use OpenBLAS by default.
-
-To have `R` and `Rscript` use NVBLAS instead,
-
-1. copy the NVBLAS-enabled executables to `~/.local/bin`  
-   ```bash
-   for file in $(which {R,Rscript}); do
-     cp "$file"_ "~/.local/bin/$(basename "$file")";
-   done
-   ```
-1. set Extensions > R > Rterm > Linux: `/home/USER/.local/bin/R` in VS Code
-   settings  
-   :point_right: Substitute `USER` with your user name.
-
-and restart the R terminal.
-
-:information_source: The
-[xgboost](https://cran.r-project.org/package=xgboost) package benefits greatly
-from NVBLAS, if it is
-[installed correctly](https://xgboost.readthedocs.io/en/stable/build.html).
-
-# Additional notes on `INSTALL_DEVTOOLS`
-
-If `INSTALL_DEVTOOLS` is set, the required tools according to [microsoft/vscode > Wiki > How to Contribute](https://github.com/Microsoft/vscode/wiki/How-to-Contribute)
-and [coder/code-server > Docs > Contributing](https://github.com/coder/code-server/blob/main/docs/CONTRIBUTING.md)
-are installed.
-
-Node.js is installed with corepack enabled by default. Use it to manage Yarn
-and/or pnpm:
-
-* [Installation | Yarn - Package Manager > Updating the global Yarn version](https://yarnpkg.com/getting-started/install#updating-the-global-yarn-version)
-* [Installation | pnpm > Using Corepack](https://pnpm.io/installation#using-corepack)
-
-## Environment variables
-
-**Versions**
-
-* `NODE_VERSION`
-
-## System Python
-
-Package `libsecret-1-dev` depends on `python3` from the system's package
-repository.
-
-The system's Python version is installed at `/usr/bin`.  
-
-:information_source: Because [a more recent Python version](#python) is
-installed at `/usr/local/bin`, it takes precedence over the system's Python
-version.
diff --git a/README.md b/README.md
diff --git a/SECURITY.md b/SECURITY.md

Original file line number	Diff line number	Diff line change
`@@ -0,0 +1,3 @@`
	`1`	`+MD033: false`
	`2`	`+MD036: false`
	`3`	`+MD041: false`