Cos

.JuliaFormatter.toml

@@ -0,0 +1,3 @@
+style = "sciml"
+format_markdown = true
+format_docstrings = true

.buildkite/.gitignore

@@ -0,0 +1 @@
+ssh_deploy.key

.buildkite/0_webui.yml

@@ -0,0 +1,28 @@
+agents:
+  queue: "juliaecosystem"
+  sandbox.jl: true
+
+steps:
+  - label: ":unlock: Launch tutorials build if hash check successful"
+    branches: "!gh-pages"
+    plugins:
+      - staticfloat/cryptic#v2:
+          signed_pipelines:
+            - pipeline: .buildkite/launch_tutorials.yml
+              signature_file: .buildkite/launch_tutorials.yml.signature
+              inputs:
+                - .buildkite/run_tutorial.yml
+                - .buildkite/publish_tutorials_output.sh
+              allow_hash_override: true
+    command: "true"
+
+  - label: ":runner: Dynamically launch test suite"
+    plugins:
+      - staticfloat/forerunner:
+          # This will create one job overall, throwing all path information away
+          watch:
+            - "src/**/*.jl"
+            - "src/*.jl"
+            - "**/*.toml"
+          target: .buildkite/test_sciml.yml
+          target_type: simple

.buildkite/cryptic_repo_keys/.gitignore

@@ -0,0 +1,7 @@
+
+# Ignore the unencrypted repo_key
+repo_key
+
+# Ignore any agent keys (public or private) we have stored
+agent_key*
+

.buildkite/launch_test_sciml.yml

@@ -0,0 +1,16 @@
+agents:
+  queue: "juliaecosystem"
+  sandbox.jl: true
+
+steps:
+  - label: ":runner: Dynamically launch test_sciml"
+    branches: "!gh-pages"
+    plugins:
+      - staticfloat/forerunner:
+          # This will create one job overall, throwing all path information away
+          watch:
+            - "src/**/*.jl"
+            - "src/*.jl"
+            - "**/*.toml"
+          target: .buildkite/test_sciml.yml
+          target_type: simple

.buildkite/launch_tutorials.yml

@@ -0,0 +1,19 @@
+agents:
+  queue: "juliaecosystem"
+  sandbox.jl: true
+
+steps:
+  - label: ":runner: Dynamically launch run_tutorial.yml"
+    branches: "!gh-pages"
+    env:
+      BUILDKITE_PLUGIN_CRYPTIC_BASE64_SIGNED_JOB_ID_SECRET: ${BUILDKITE_PLUGIN_CRYPTIC_BASE64_SIGNED_JOB_ID_SECRET?}
+    depends_on:
+    plugins:
+      - staticfloat/forerunner:
+          # This will create one job per project
+          watch:
+            - tutorials/**/*.jmd
+            - tutorials/**/*.toml
+          path_processor: .buildkite/path_processors/project-coalescing
+          target: .buildkite/run_tutorial.yml
+          target_type: template

.buildkite/launch_tutorials.yml.signature

@@ -0,0 +1,2 @@
+Salted__�
+�HX�+��D�;�H�N2qhb=�c�����$J��0~0~d��х3�A܉����Y�r����B{��?��󒟭����zP

.buildkite/path_processors/project-coalescing

@@ -0,0 +1,62 @@
+#!/bin/bash
+
+# When a `.jmd` file is modified, it gets rewritten by itself; but when a `.toml` file
+# (such as a `Project.toml` or a `Manifest.toml`) gets modified, we rebuild the entire
+# directory.  To avoid double-building, we coalesce all changes here, by converting
+# changed files that end in `.toml` to their directory, then dropping all other files
+# within that folder.
+
+# This will hold all files that need to be rebuilt, keyed by path and pointing to their
+# containing project
+declare -A FILES
+
+# This will hold all projects that need to be rebuilt, and will allow us to suppress
+# values from FILES_TO_RUN
+declare -A PROJECTS
+
+# Helper function to find the directory that contains the `Project.toml` for this file
+function find_project() {
+    d="${1}"
+    # We define a basecase, that the path must begin with `tutorials` and is not allowed
+    # to move outside of that subtree.
+    while [[ "${d}" =~ tutorials/.* ]]; do
+        if [[ -f "${d}/Project.toml" ]]; then
+            echo "${d}"
+            return
+        fi
+        d="$(dirname "${d}")"
+    done
+}
+
+# For each file, find its project, then if its a `.jmd` file, we add it to `FILES`
+# If it's a `.toml` file, we add it to `PROJECTS`.
+for f in "$@"; do
+    proj=$(find_project "${f}")
+    if [[ -z "${proj}" ]]; then
+        buildkite-agent annotate "Unable to find project for ${f}" --style "error"
+        continue
+    fi
+
+    if [[ "${f}" == *.jmd ]]; then
+        FILES["${f}"]="${proj}"
+    elif [[ "${f}" == *.toml ]]; then
+        PROJECTS["${proj}"]=1
+    else
+        buildkite-agent annotate "Unknown weave type for file ${f}" --style "error"
+    fi
+done
+
+# We're going to emit the project directories first:
+BUILD_TARGETS="${!PROJECTS[@]}"
+
+# But we're also going to emit any single files whose projects are _not_ contained
+# in the projects we're already building
+for f in "${!FILES[@]}"; do
+    proj=${FILES[$f]}
+    if ! [ ${PROJECTS[$proj]+x} ]; then
+        BUILD_TARGETS="${BUILD_TARGETS} ${f}"
+    fi
+done
+
+# Output the build targets
+echo "${BUILD_TARGETS}"

.buildkite/publish_tutorials_output.sh

@@ -0,0 +1,25 @@
+#!/bin/bash
+
+# Ensure that our git wants to talk to github without prompting
+mkdir -p ~/.ssh
+ssh-keyscan github.com >> ~/.ssh/known_hosts
+git config --global user.email "buildkite@julialang.org"
+git config --global user.name "SciML Tutorials CI"
+
+# Clone SciMLTutorialsOutput to temporary directory
+temp_dir=$(mktemp -d)
+git -C "${temp_dir}" clone git@github.com:SciML/SciMLTutorialsOutput .
+
+# Copy our output artifacts into it:
+for d in docs html notebook pdf script markdown; do
+    cp -vRa "${d}/" "${temp_dir}"
+done
+cp -va *.md *.bib "${temp_dir}"
+
+# Commit the result up to output
+set -e
+git -C "${temp_dir}" add .
+git -C "${temp_dir}" commit -m "Automatic build\nPublished by build of: ${BUILDKITE_REPO%.git}/commit/${BUILDKITE_COMMIT}"
+git -C "${temp_dir}" push
+
+rm -rf "${temp_dir}"

.buildkite/run_tutorial.yml

@@ -0,0 +1,94 @@
+agents:
+  queue: "juliaecosystem"
+  sandbox.jl: true
+  arch: "x86_64"
+
+# This is a pipeline that weaves a tutorial, then uploads the resultant
+# .PDF and other reports as (buildkite, not Julia) artifacts.  The `coppermind`
+# configuration memoizes the result, so that identical inputs don't get
+# weaved multiple times.
+steps:
+  - label: ":hammer: {PATH}"
+    key: "tutorial-{SANITIZED_PATH}"
+    env:
+      BUILDKITE_PLUGIN_CRYPTIC_BASE64_SIGNED_JOB_ID_SECRET: ${BUILDKITE_PLUGIN_CRYPTIC_BASE64_SIGNED_JOB_ID_SECRET?}
+    plugins:
+      - staticfloat/cryptic#v2:
+          variables:
+            - BUILDKITE_S3_ACCESS_KEY_ID="U2FsdGVkX1/ckce1vUF8A17rHLxcAlAou4aokaeS8YL6omsA1Vq1IDZko5cL1Z+t"
+            - BUILDKITE_S3_SECRET_ACCESS_KEY="U2FsdGVkX1+SPF81nkK7KQ64DsafSl0qq2iG7BsQs1xlTYEtZV3MqQl3l/NWaiocaEywZZFbAB5zpnKPD0xHTQ=="
+            - BUILDKITE_S3_DEFAULT_REGION="U2FsdGVkX1/cORlxhXcxhja2JkqC0f8RmaGYxvGBbEg="
+      - JuliaCI/julia#v1:
+          version: 1.8
+      - staticfloat/sandbox:
+          rootfs_url: "https://jc-rootfs-images.s3.amazonaws.com/aws_uploader-2021-11-12.x86_64.tar.gz"
+          rootfs_treehash: "986217e5b36efd3b3b91ed90df8e36d628cf543f"
+          workspaces:
+            # Include the julia we just downloaded
+            - "/cache/julia-buildkite-plugin:/cache/julia-buildkite-plugin"
+      - staticfloat/coppermind#v1:
+          inputs:
+            # We are sensitive to the actual tutorial changing
+            - {PATH}
+            # We are sensitive to the source code of this package changing
+            - src/**/*.jl
+            # We are sensitive to our overall dependencies changing
+            - ./*.toml
+          outputs:
+            #- html/**/*.html
+            - markdown/**/figures/*.png
+            - markdown/**/*.md
+            - notebook/**/*.ipynb
+            - pdf/**/*.pdf
+            - script/**/*.jl
+          s3_prefix: s3://julialang-buildkite-artifacts/scimltutorials
+    timeout_in_minutes: 1000
+    commands: |
+      # Instantiate, to install the overall project dependencies
+      echo "--- Instantiate"
+      julia --project=. -e 'using Pkg; Pkg.instantiate(); Pkg.build()'
+
+      # Run tutorial
+      echo "+++ Run tutorial for {PATH}"
+      julia --project=. weave_tutorials.jl "{PATH}"
+
+  - label: ":rocket: Publish {PATH}"
+    env:
+      BUILDKITE_PLUGIN_CRYPTIC_BASE64_SIGNED_JOB_ID_SECRET: ${BUILDKITE_PLUGIN_CRYPTIC_BASE64_SIGNED_JOB_ID_SECRET?}
+    plugins:
+      - staticfloat/cryptic#v2:
+          variables:
+            - BUILDKITE_S3_ACCESS_KEY_ID="U2FsdGVkX1/ckce1vUF8A17rHLxcAlAou4aokaeS8YL6omsA1Vq1IDZko5cL1Z+t"
+            - BUILDKITE_S3_SECRET_ACCESS_KEY="U2FsdGVkX1+SPF81nkK7KQ64DsafSl0qq2iG7BsQs1xlTYEtZV3MqQl3l/NWaiocaEywZZFbAB5zpnKPD0xHTQ=="
+            - BUILDKITE_S3_DEFAULT_REGION="U2FsdGVkX1/cORlxhXcxhja2JkqC0f8RmaGYxvGBbEg="
+          files:
+            - .buildkite/ssh_deploy.key
+      - JuliaCI/julia#v1:
+          version: 1.8
+      - staticfloat/sandbox:
+          rootfs_url: "https://jc-rootfs-images.s3.amazonaws.com/aws_uploader-2021-11-12.x86_64.tar.gz"
+          rootfs_treehash: "986217e5b36efd3b3b91ed90df8e36d628cf543f"
+          workspaces:
+            # Include the julia we just downloaded
+            - "/cache/julia-buildkite-plugin:/cache/julia-buildkite-plugin"
+      # Use coppermind to download the tutorial results that were calculated in the
+      # weaving job above.  Note we still list `outputs` here, since we have the
+      # option to extract only a subset of them here.
+      - staticfloat/coppermind#v1:
+          input_from: "tutorial-{SANITIZED_PATH}"
+          outputs:
+            #- html/**/*.html
+            - markdown/**/figures/*.png
+            - markdown/**/*.md
+            - notebook/**/*.ipynb
+            - pdf/**/*.pdf
+            - script/**/*.jl
+          s3_prefix: s3://julialang-buildkite-artifacts/scimltutorials
+      - staticfloat/ssh-agent:
+          keyfiles:
+            - .buildkite/ssh_deploy.key
+    commands: .buildkite/publish_tutorials_output.sh
+    # Don't run this unless we're on the master branch, and not until the actual weave
+    # command has had a chance to run.
+    depends_on: "tutorial-{SANITIZED_PATH}"
+    branches: "master"

.buildkite/test_sciml.yml

@@ -0,0 +1,24 @@
+agents:
+  queue: "juliaecosystem"
+  arch: "x86_64"
+
+steps:
+  - label: ":julia: Run tests on 1.8"
+    plugins:
+      - JuliaCI/julia#v1:
+          version: 1.8
+      - JuliaCI/julia-test#v1:
+    timeout_in_minutes: 20
+    artifact_paths:
+       # Upload .html
+      - "html/Testing/*.html"
+      # Upload markdown
+      - "markdown/Testing/*.md"
+      # Upload notebook
+      - "notebook/Testing/*.ipynb"
+      # Upload .pdf files
+      - "pdf/Testing/*.pdf"
+      # Upload Julia script
+      - "script/Testing/*.jl"
+    agents:
+      queue: "juliaecosystem"

.github/dependabot.yml

@@ -0,0 +1,7 @@
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "weekly"

.github/workflows/CompatHelper.yml

@@ -0,0 +1,26 @@
+name: CompatHelper
+
+on:
+  schedule:
+    - cron: '00 00 * * *'
+  issues:
+    types: [opened, reopened]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v5
+      - name: Pkg.add("CompatHelper")
+        run: julia -e 'using Pkg; Pkg.add("CompatHelper")'
+      - name: CompatHelper.main()
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          julia -e '
+            using CompatHelper
+            dirs = filter(
+                d -> isdir(d) && isfile(joinpath(d, "Project.toml")),
+                readdir("tutorials"; join=true),
+            )
+            CompatHelper.main(; subdirs=["", dirs...])'

.github/workflows/TagBot.yml

@@ -0,0 +1,15 @@
+name: TagBot
+on:
+  issue_comment:
+    types:
+      - created
+  workflow_dispatch:
+jobs:
+  TagBot:
+    if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'
+    runs-on: ubuntu-latest
+    steps:
+      - uses: JuliaRegistries/TagBot@v1
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          ssh: ${{ secrets.DOCUMENTER_KEY }}

.gitignore

@@ -1,9 +1,18 @@
-*.jl.cov
-*.jl.*.cov
-*.jl.mem
 .ipynb_checkpoints
+*/.ipynb_checkpoints/*
 *.tmp
 *.aux
 *.log
 *.out
 *.tex
+tmp*/
+gks.svg
+/*/*/jl_*/
+/Manifest.toml
+
+# We're going to store these in a separate repository now
+html/
+script/
+pdf/
+notebook/
+markdown/

.gitlab-ci.yml

@@ -0,0 +1,8 @@
+include: https://raw.githubusercontent.com/SciML/RebuildAction/master/rebuild.yml
+variables:
+  CONTENT_DIR: tutorials
+  EXCLUDE: exercises/02-workshop_solutions, models/06-pendulum_bayesian_inference
+  GITHUB_REPOSITORY: SciML/SciMLTutorials.jl
+  GPU_TAG: nvidia-benchmark
+  NEEDS_GPU: advanced/01-beeler_reuter
+  TAGS: nvidia-benchmark

CITATION.bib

@@ -0,0 +1,13 @@
+@article{DifferentialEquations.jl-2017,
+ author = {Rackauckas, Christopher and Nie, Qing},
+ doi = {10.5334/jors.151},
+ journal = {The Journal of Open Research Software},
+ keywords = {Applied Mathematics},
+ note = {Exported from https://app.dimensions.ai on 2019/05/05},
+ number = {1},
+ pages = {},
+ title = {DifferentialEquations.jl – A Performant and Feature-Rich Ecosystem for Solving Differential Equations in Julia},
+ url = {https://app.dimensions.ai/details/publication/pub.1085583166 and http://openresearchsoftware.metajnl.com/articles/10.5334/jors.151/galley/245/download/},
+ volume = {5},
+ year = {2017}
+}