misc updates formatting

.devcontainer/Dockerfile.math-api

@@ -1,11 +1,11 @@
-# syntax=docker/dockerfile:1.5-labs
-FROM node:18-alpine AS deps
+# syntax=docker/dockerfile:1
+FROM node:20-alpine AS deps
 
 WORKDIR /usr/src/app
 ADD https://github.com/bryanwweber/math-api.git .
 RUN yarn install --frozen-lockfile
 
-FROM node:18-alpine AS builder
+FROM node:20-alpine AS builder
 WORKDIR /usr/src/app
 COPY --from=deps /usr/src/app/server.ts .
 COPY --from=deps /usr/src/app/index.ts .
@@ -15,7 +15,7 @@ COPY --from=deps /usr/src/app/package.json .
 COPY --from=deps /usr/src/app/node_modules ./node_modules
 RUN npm run build
 
-FROM node:18-alpine as runner
+FROM node:20-alpine as runner
 
 WORKDIR /usr/src/app
 ENV NODE_ENV=production

.devcontainer/Dockerfile.workspace

@@ -1,71 +1,51 @@
-FROM python:3.10-alpine as pdm
+FROM julia:1.10-bookworm as julia-builder
 
-RUN mkdir -p /tmp/pdm
-COPY pyproject.toml pdm.lock /tmp/pdm/
+COPY Project.toml Manifest.toml /root/.julia/environments/v1.10/
 
-WORKDIR /tmp/pdm
+RUN julia -e "using Pkg; Pkg.instantiate(); Pkg.precompile();"
+
+FROM python:3.12-slim-bookworm as python-builder
+
+ENV PIP_ROOT_USER_ACTION=ignore
 
 RUN --mount=type=cache,target=/root/.cache \
- pip3 --disable-pip-version-check install pdm \
- && pdm export -f requirements > /tmp/pdm/requirements.txt
-
-FROM alpine:3 as julia
-ARG JULIA_VERSION=1.9.0-rc1
-ARG JULIA_ARCH="x86_64"
-
-RUN mkdir -p /tmp/julia
-WORKDIR /tmp
-
-RUN set -x && \
- if [ "$JULIA_ARCH" == "aarm64" ]; then \
- JULIA_ARCH="aarch64"; \
- S3_ARCH="aarch64"; \
- elif [ "$JULIA_ARCH" == "aarch64" ]; then \
- S3_ARCH="aarch64"; \
- elif [ "$JULIA_ARCH" == "x86_64" ]; then \
- S3_ARCH="x64"; \
- fi; \
- JULIA_INSTALLER="julia-${JULIA_VERSION}-linux-${JULIA_ARCH}.tar.gz" \
- && wget --quiet "https://julialang-s3.julialang.org/bin/checksums/julia-${JULIA_VERSION}.sha256" \
- && wget --quiet "https://julialang-s3.julialang.org/bin/linux/${S3_ARCH}/${JULIA_VERSION:0:3}/${JULIA_INSTALLER}" \
- && grep ${JULIA_INSTALLER} "julia-${JULIA_VERSION}.sha256" | sha256sum -cs \
- && tar -xf "${JULIA_INSTALLER}" -C /tmp/julia --strip-components=1 \
- && rm "${JULIA_INSTALLER}"
-
-FROM python:3.10-bullseye as workspace
+ python -m pip install pdm
+
+COPY pyproject.toml pdm.lock /project/
+WORKDIR /project
+RUN --mount=type=cache,target=/root/.cache \
+ mkdir __pypackages__ \
+ && pdm sync
+
+FROM python:3.12-bookworm as workspace
 
 ARG USERNAME=vscode
 ARG USER_UID=1000
 ARG USER_GID=$USER_UID
-ARG JULIA_DIR=/opt/julia
 
-ENV PATH="${JULIA_DIR}/bin:${PATH}" \
- HOME="/home/${USERNAME}"
+ENV HOME="/home/${USERNAME}" \
+ PYTHONPATH=/project/pkgs \
+ JULIA_PATH=/usr/local/julia \
+ JULIA_HOME=/home/${USERNAME}/.julia
+
+# Has to be a separate instruction to get the JULIA_PATH variable
+ENV PATH="${JULIA_PATH}/bin:${PATH}"
+
 COPY .devcontainer/fix-permissions /usr/local/bin/fix-permissions
 RUN chmod a+rx /usr/local/bin/fix-permissions
 
-# Create USERNAME with name vscode user with UID=1000 and in the 'users' group
-# and make sure these dirs are writable by the `users` group.
+# Create USERNAME with name vscode with UID=1000 and in the 'users' group
 RUN groupadd --gid ${USER_GID} ${USERNAME} \
- && useradd --uid $USER_UID --gid ${USERNAME} --shell /bin/bash --create-home ${USERNAME} \
- && mkdir -p "${JULIA_DIR}" \
- && chown "${USER_UID}:${USER_GID}" "${JULIA_DIR}" \
- && chmod g+w /etc/passwd \
- && fix-permissions "${HOME}" \
- && fix-permissions "${JULIA_DIR}"
-
-COPY --from=pdm /tmp/pdm/requirements.txt /tmp/pip-tmp/
-RUN --mount=type=cache,target=/root/.cache \
- pip3 --disable-pip-version-check install -r /tmp/pip-tmp/requirements.txt \
- && rm -rf /tmp/pip-tmp
+ && useradd --uid ${USER_UID} --gid ${USER_GID} --shell /bin/bash --create-home ${USERNAME}
 
-USER ${USERNAME}
+COPY --from=python-builder /project/__pypackages__/3.12/lib /project/pkgs
+COPY --from=python-builder /project/__pypackages__/3.12/bin/* /bin/
+COPY --from=julia-builder /usr/local/julia ${JULIA_PATH}
+COPY --from=julia-builder /root/.julia ${HOME}/.julia
 
-COPY --from=julia /tmp/julia/ "${JULIA_DIR}/"
-COPY .devcontainer/packages.jl /tmp/packages.jl
+RUN chown -R "${USER_UID}:${USER_GID}" "${JULIA_HOME}" \
+ && fix-permissions "${JULIA_HOME}"
 
-RUN fix-permissions "${JULIA_DIR}"
-RUN julia "/tmp/packages.jl" \
- && fix-permissions "${HOME}/.julia"
+USER ${USERNAME}
 
 WORKDIR /workspaces/orbital-mechanics-notes

.devcontainer/devcontainer.json

@@ -2,48 +2,44 @@
 // README at: https://github.com/devcontainers/templates/tree/main/src/docker-existing-docker-compose
 {
  "name": "Orbital Mechanics Notes",
-
  // Update the 'dockerComposeFile' list if you have more compose files or use different names.
  // The .devcontainer/docker-compose.yml file contains any overrides you need/want to make.
- "dockerComposeFile": ["docker-compose.yml"],
-
+ "dockerComposeFile": [
+ "docker-compose.yml"
+ ],
  // The 'service' property is the name of the service for the container that VS Code should
  // use. Update this value and .devcontainer/docker-compose.yml to the real service name.
  "service": "workspace",
-
  // The optional 'workspaceFolder' property is the path VS Code should open by default when
  // connected. This is typically a file mount in .devcontainer/docker-compose.yml
  "workspaceFolder": "/workspaces/${localWorkspaceFolderBasename}",
-
  // Use 'forwardPorts' to make a list of ports inside the container available locally.
- "forwardPorts": [8080],
-
+ "forwardPorts": [
+ 8080
+ ],
  // Uncomment the next line if you want start specific services in your Docker Compose config.
- "runServices": ["http-server", "math-api"],
-
+ "runServices": [
+ "http-server",
+ "math-api"
+ ],
  // Uncomment the next line if you want to keep your containers running after VS Code shuts down.
  "shutdownAction": "stopCompose",
-
  // Configure tool-specific properties.
  "customizations": {
  "vscode": {
  "extensions": [
  "DavidAnson.vscode-markdownlint",
  "ms-python.python",
  "ms-toolsai.jupyter",
- "redhat.vscode-yaml",
  "streetsidesoftware.code-spell-checker",
  "tamasfe.even-better-toml",
  "VisualStudioExptTeam.vscodeintellicode"
  ],
- "settings": {
- }
+ "settings": {}
  }
  },
-
  // Uncomment to connect as an existing user other than the container default. More info: https://aka.ms/dev-containers-non-root.
  "containerUser": "vscode",
  "remoteUser": "vscode",
  "updateRemoteUserUID": true
-
 }

.devcontainer/docker-compose.yml

@@ -41,7 +41,7 @@ services:
  - ..:/workspaces/orbital-mechanics-notes:cached
  command: /bin/sh -c "while sleep 1000; do :; done"
  http-server:
- image: python:3.10-alpine
+ image: python:3.12-alpine
  ports: ["8080:8080"]
  command: python3 -m http.server 8080 -d /html
  volumes:

.github/workflows/deploy-book.yml

@@ -20,7 +20,7 @@ jobs:
  uses: pdm-project/setup-pdm@v4
  with:
  cache: true
- python-version: "3.11"
+ python-version: "3.12"
  - name: Install dependencies
  run: pdm sync --prod
  # Build the book

.markdownlint-cli2.jsonc

@@ -1,7 +1,18 @@
 {
- "globs": ["**/*.md", "!.venv"],
+ "globs": [
+ "**/*.md",
+ "!.venv",
+ "!_build",
+ "!_static"
+ ],
  "config": {
+ "MD003": false,
  "MD013": false,
- "MD037": false
+ "MD024": false,
+ "MD033": false,
+ "MD037": false,
+ "MD041": false,
+ "MD055": false,
+ "MD056": false
  }
 }

.mise.toml

@@ -1,8 +1,28 @@
 [tools]
-python = { version = "3.11", virtualenv = ".venv" }
+python = { version = "3.12", virtualenv = ".venv" }
 markdownlint-cli2 = "latest"
 pdm = "latest"
+julia = "latest"
 
 [plugins]
 pdm = "https://github.com/1oglop1/asdf-pdm"
 markdownlint-cli2 = "https://github.com/paulo-ferraz-oliveira/asdf-markdownlint-cli2"
+julia = "https://github.com/rkyleg/asdf-julia.git"
+
+[tasks]
+lint = { depends = [
+ "ruff_check_lint",
+ "ruff_format_lint",
+ "markdownlint_lint",
+], description = "Run all the linter tools", env = { MISE_JOBS = "1" } }
+ruff_check_lint = { description = "Run the ruff linter", run = "ruff check ." }
+ruff_format_lint = { run = "ruff format --check .", description = "Run the ruff formatter in check mode" }
+markdownlint_lint = { run = "markdownlint-cli2", description = "Run markdownlint" }
+ruff_check_format = { run = "ruff check --fix .", description = "Run the ruff linter in fix mode" }
+ruff_format_format = { run = "ruff format .", description = "Run the ruff formatter" }
+markdownlint_format = { run = "markdownlint-cli2 --fix", description = "Run markdownlint in fix mode" }
+format = { depends = [
+ "ruff_check_format",
+ "ruff_format_format",
+ "markdownlint_format",
+], description = "Run all the formatting tools", env = { MISE_JOBS = "1" } }

.mise/tasks/build

@@ -0,0 +1,6 @@
+#!/usr/bin/env bash
+# mise description="Build the book"
+# mise env={PYDEVD_DISABLE_FILE_VALIDATION = "1"}
+# mise source=["**/*.md", "**/*.ipynb", "**/*.svg"]
+# mise outputs=["_build/html/**/*.html"]
+jupyter-book build -W .

.vscode/settings.json

@@ -25,6 +25,7 @@
  // "---([\\n\\(\\)]|[^(\\$\\$)])*---"
  // ]
  }
- ]
+ ],
+ "editor.formatOnSave": true
 
 }

INSTALL.md

@@ -1,5 +1,7 @@
 # Install/Build the Book
 
-The repo is set up to use [mise](https://mise.jdx.dev) to install required tools. Once `mise` is installed, changing into this directory should install the correct tools with the right versions.
+The repo is set up to use [mise](https://mise.jdx.dev) to install required tools. Once `mise` is installed, changing into this directory should install the correct tools with the right versions. If not, run `mise install` to install everything.
 
 After that, running `pdm install` should install the dependencies. Then `doit build_jb` will build the book.
+
+If you want to work on the book, you may also need to install Julia dependencies. `mise` should install Julia. Running `julia --project=. -e 'using Pkg; Pkg.instantiate(); Pkg.precompile();'` should install dependencies in a local project.