From c0dc95b1c39564f1753dfc0f30bcba631a7b0533 Mon Sep 17 00:00:00 2001 From: Penelope Yong Date: Wed, 14 Aug 2024 14:11:51 +0100 Subject: [PATCH] Improvements to docs infrastructure (#497) * Gitignore Python venv and other temporary files * Fix typo in versions.sh script * Use single Project.toml for entire repo * Include Manifest hashes in GHA cache key Closes #496 * Fix caching in PR preview workflow as well * Generate Manifest.toml before hashing it * Add temp workflow to regenerate docs for #497 * Revert "Add temp workflow to regenerate docs for #497" This reverts commit d34c7452ba2cb0b329472d8a3d5b1855ea9e042d. * Expand version check script The action now: - runs on all PRs to main / backport branches - runs on pushes to main / backport branches It always checks that the version of Turing in Project.toml matches that in _quarto.yml. Additionally, if the PR is targeted at main / the push is to the main branch, it also checks that the version of Turing matches the latest release on GitHub. * Don't ignore Manifest, update deps * Check Manifest file in GHA as well * Instantiate project environment in publish workflow * Modify version check action to also suggest updates as a PR * Add comment at the top of version check workflow * Separate version check script into its own file * Don't need --project as the script sets it up --- .github/workflows/preview.yml | 13 +- .github/workflows/publish.yml | 13 +- .github/workflows/vcheck.yml | 43 - .github/workflows/version_check.jl | 139 + .github/workflows/version_check.yml | 74 + .gitignore | 7 +- .../Manifest.toml => Manifest.toml | 1290 ++++++--- Project.toml | 55 + assets/scripts/versions.sh | 20 +- tutorials/00-introduction/Manifest.toml | 2207 --------------- tutorials/00-introduction/Project.toml | 6 - .../01-gaussian-mixture-model/Manifest.toml | 2207 --------------- .../01-gaussian-mixture-model/Project.toml | 8 - .../02-logistic-regression/Manifest.toml | 2330 ---------------- tutorials/02-logistic-regression/Project.toml | 10 - .../03-bayesian-neural-network/Manifest.toml | 2388 ---------------- .../03-bayesian-neural-network/Project.toml | 9 - .../04-hidden-markov-model/Manifest.toml | 2207 --------------- tutorials/04-hidden-markov-model/Project.toml | 4 - tutorials/05-linear-regression/Manifest.toml | 2364 ---------------- tutorials/05-linear-regression/Project.toml | 10 - .../06-infinite-mixture-model/Manifest.toml | 2137 -------------- .../06-infinite-mixture-model/Project.toml | 4 - tutorials/07-poisson-regression/Manifest.toml | 2225 --------------- tutorials/07-poisson-regression/Project.toml | 9 - .../Manifest.toml | 2330 ---------------- .../Project.toml | 9 - .../09-variational-inference/Manifest.toml | 2475 ----------------- .../09-variational-inference/Project.toml | 13 - .../Project.toml | 8 - tutorials/11-probabilistic-pca/Manifest.toml | 2231 --------------- tutorials/11-probabilistic-pca/Project.toml | 9 - tutorials/12-gplvm/Manifest.toml | 2271 --------------- tutorials/12-gplvm/Project.toml | 11 - .../13-seasonal-time-series/Manifest.toml | 2207 --------------- .../13-seasonal-time-series/Project.toml | 7 - tutorials/14-minituring/Manifest.toml | 1421 ---------- tutorials/14-minituring/Project.toml | 8 - tutorials/15-gaussian-processes/Manifest.toml | 2219 --------------- tutorials/15-gaussian-processes/Project.toml | 10 - tutorials/16-contexts/Manifest.toml | 1421 ---------- tutorials/16-contexts/Project.toml | 6 - .../docs-00-getting-started/Manifest.toml | 2207 --------------- .../docs-00-getting-started/Project.toml | 3 - .../Manifest.toml | 1421 ---------- .../Project.toml | 2 - .../Manifest.toml | 643 ----- .../Project.toml | 4 - .../Manifest.toml | 1421 ---------- .../Project.toml | 6 - .../Manifest.toml | 1427 ---------- .../Project.toml | 3 - .../Manifest.toml | 1474 ---------- .../Project.toml | 3 - .../docs-12-using-turing-guide/Manifest.toml | 2264 --------------- .../docs-12-using-turing-guide/Project.toml | 5 - .../Manifest.toml | 1427 ---------- .../Project.toml | 5 - .../Manifest.toml | 2207 --------------- .../Project.toml | 4 - .../Manifest.toml | 2207 --------------- .../Project.toml | 6 - .../Manifest.toml | 1653 ----------- .../Project.toml | 8 - .../Manifest.toml | 2213 --------------- .../Project.toml | 12 - .../docs-17-mode-estimation/Manifest.toml | 1559 ----------- .../docs-17-mode-estimation/Project.toml | 8 - 68 files changed, 1210 insertions(+), 57417 deletions(-) delete mode 100644 .github/workflows/vcheck.yml create mode 100644 .github/workflows/version_check.jl create mode 100644 .github/workflows/version_check.yml rename tutorials/10-bayesian-differential-equations/Manifest.toml => Manifest.toml (70%) mode change 100755 => 100644 create mode 100644 Project.toml delete mode 100755 tutorials/00-introduction/Manifest.toml delete mode 100755 tutorials/00-introduction/Project.toml delete mode 100755 tutorials/01-gaussian-mixture-model/Manifest.toml delete mode 100755 tutorials/01-gaussian-mixture-model/Project.toml delete mode 100755 tutorials/02-logistic-regression/Manifest.toml delete mode 100755 tutorials/02-logistic-regression/Project.toml delete mode 100755 tutorials/03-bayesian-neural-network/Manifest.toml delete mode 100755 tutorials/03-bayesian-neural-network/Project.toml delete mode 100755 tutorials/04-hidden-markov-model/Manifest.toml delete mode 100755 tutorials/04-hidden-markov-model/Project.toml delete mode 100755 tutorials/05-linear-regression/Manifest.toml delete mode 100755 tutorials/05-linear-regression/Project.toml delete mode 100755 tutorials/06-infinite-mixture-model/Manifest.toml delete mode 100755 tutorials/06-infinite-mixture-model/Project.toml delete mode 100755 tutorials/07-poisson-regression/Manifest.toml delete mode 100755 tutorials/07-poisson-regression/Project.toml delete mode 100755 tutorials/08-multinomial-logistic-regression/Manifest.toml delete mode 100755 tutorials/08-multinomial-logistic-regression/Project.toml delete mode 100755 tutorials/09-variational-inference/Manifest.toml delete mode 100755 tutorials/09-variational-inference/Project.toml delete mode 100755 tutorials/10-bayesian-differential-equations/Project.toml delete mode 100755 tutorials/11-probabilistic-pca/Manifest.toml delete mode 100755 tutorials/11-probabilistic-pca/Project.toml delete mode 100755 tutorials/12-gplvm/Manifest.toml delete mode 100755 tutorials/12-gplvm/Project.toml delete mode 100755 tutorials/13-seasonal-time-series/Manifest.toml delete mode 100755 tutorials/13-seasonal-time-series/Project.toml delete mode 100755 tutorials/14-minituring/Manifest.toml delete mode 100755 tutorials/14-minituring/Project.toml delete mode 100755 tutorials/15-gaussian-processes/Manifest.toml delete mode 100755 tutorials/15-gaussian-processes/Project.toml delete mode 100755 tutorials/16-contexts/Manifest.toml delete mode 100755 tutorials/16-contexts/Project.toml delete mode 100644 tutorials/docs-00-getting-started/Manifest.toml delete mode 100644 tutorials/docs-00-getting-started/Project.toml delete mode 100755 tutorials/docs-04-for-developers-abstractmcmc-turing/Manifest.toml delete mode 100755 tutorials/docs-04-for-developers-abstractmcmc-turing/Project.toml delete mode 100755 tutorials/docs-06-for-developers-interface/Manifest.toml delete mode 100755 tutorials/docs-06-for-developers-interface/Project.toml delete mode 100755 tutorials/docs-09-using-turing-advanced/Manifest.toml delete mode 100755 tutorials/docs-09-using-turing-advanced/Project.toml delete mode 100755 tutorials/docs-10-using-turing-autodiff/Manifest.toml delete mode 100755 tutorials/docs-10-using-turing-autodiff/Project.toml delete mode 100755 tutorials/docs-11-using-turing-dynamichmc/Manifest.toml delete mode 100755 tutorials/docs-11-using-turing-dynamichmc/Project.toml delete mode 100755 tutorials/docs-12-using-turing-guide/Manifest.toml delete mode 100755 tutorials/docs-12-using-turing-guide/Project.toml delete mode 100755 tutorials/docs-13-using-turing-performance-tips/Manifest.toml delete mode 100755 tutorials/docs-13-using-turing-performance-tips/Project.toml delete mode 100755 tutorials/docs-14-using-turing-quick-start/Manifest.toml delete mode 100755 tutorials/docs-14-using-turing-quick-start/Project.toml delete mode 100755 tutorials/docs-15-using-turing-sampler-viz/Manifest.toml delete mode 100755 tutorials/docs-15-using-turing-sampler-viz/Project.toml delete mode 100755 tutorials/docs-16-using-turing-external-samplers/Manifest.toml delete mode 100755 tutorials/docs-16-using-turing-external-samplers/Project.toml delete mode 100644 tutorials/docs-17-implementing-samplers/Manifest.toml delete mode 100644 tutorials/docs-17-implementing-samplers/Project.toml delete mode 100644 tutorials/docs-17-mode-estimation/Manifest.toml delete mode 100755 tutorials/docs-17-mode-estimation/Project.toml diff --git a/.github/workflows/preview.yml b/.github/workflows/preview.yml index 6e3ca18f5..31e1e543c 100644 --- a/.github/workflows/preview.yml +++ b/.github/workflows/preview.yml @@ -22,29 +22,30 @@ jobs: with: version: '1.10' + - name: Instantiate Julia environment + run: julia --project=. -e 'using Pkg; Pkg.instantiate()' + - name: Set up Quarto uses: quarto-dev/quarto-actions/setup@v2 - name: Restore cached _freeze folder - id: cache-primes-restore + id: cache-restore uses: actions/cache/restore@v4 with: path: | _freeze/ - key: ${{ runner.os }}-primes-${{ github.run_id }} - restore-keys: | - ${{ runner.os }}-primes + key: ${{ runner.os }}-${{ hashFiles('**/Manifest.toml') }} - name: Render Quarto site run: quarto render - name: Save _freeze folder - id: cache-primes-save + id: cache-save uses: actions/cache/save@v4 with: path: | _freeze/ - key: ${{ runner.os }}-primes-${{ github.run_id }} + key: ${{ runner.os }}-${{ hashFiles('**/Manifest.toml') }} - name: Deploy to GitHub Pages uses: JamesIves/github-pages-deploy-action@v4 diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml index d7260d1fb..7a3790bf4 100644 --- a/.github/workflows/publish.yml +++ b/.github/workflows/publish.yml @@ -20,6 +20,9 @@ jobs: with: version: '1.10' + - name: Instantiate Julia environment + run: julia --project=. -e 'using Pkg; Pkg.instantiate()' + - name: Set up Quarto uses: quarto-dev/quarto-actions/setup@v2 @@ -27,14 +30,12 @@ jobs: run: sudo apt-get install jq - name: Restore cached _freeze folder - id: cache-primes-restore + id: cache-restore uses: actions/cache/restore@v4 with: path: | _freeze/ - key: ${{ runner.os }}-primes-${{ github.run_id }} - restore-keys: | - ${{ runner.os }}-primes + key: ${{ runner.os }}-${{ hashFiles('**/Manifest.toml') }} - name: Extract version from _quarto.yml id: extract_version @@ -70,12 +71,12 @@ jobs: run: mv _site/search.json _site/search_original.json - name: Save _freeze folder - id: cache-primes-save + id: cache-save uses: actions/cache/save@v4 with: path: | _freeze/ - key: ${{ runner.os }}-primes-${{ github.run_id }} + key: ${{ runner.os }}-${{ hashFiles('**/Manifest.toml') }} - name: Fetch search_original.json from main site run: curl -O https://raw.githubusercontent.com/TuringLang/turinglang.github.io/gh-pages/search_original.json diff --git a/.github/workflows/vcheck.yml b/.github/workflows/vcheck.yml deleted file mode 100644 index 99ab0a156..000000000 --- a/.github/workflows/vcheck.yml +++ /dev/null @@ -1,43 +0,0 @@ -name: Check Turing.jl Version -on: - pull_request: - paths: ['_quarto.yml'] - workflow_dispatch: - -jobs: - check-version: - runs-on: ubuntu-latest - steps: - - name: Checkout - uses: actions/checkout@v4 - - - name: Extract current minor version - id: extract_minor_version - run: | - minor_version=$(grep -oP 'text:\s+"v\K\d+\.\d+' _quarto.yml) - echo "MINOR_VERSION=$minor_version" >> $GITHUB_OUTPUT - - - name: Fetch latest minor version - id: fetch_latest_minor - run: | - repo_url="https://api.github.com/repos/TuringLang/Turing.jl/releases/latest" - latest=$(curl -s $repo_url | jq -r .tag_name) - actual_latest_minor=${latest%.*} - echo "LATEST_MINOR=$actual_latest_minor" >> $GITHUB_OUTPUT - echo "LATEST=$latest" >> $GITHUB_OUTPUT - - - name: Update _quarto.yml if outdated - run: | - minor_version=${{ steps.extract_minor_version.outputs.MINOR_VERSION }} - latest_minor=${{ steps.fetch_latest_minor.outputs.LATEST_MINOR }} - if [ "$minor_version" != "$latest_minor" ]; then - awk -v old="v$minor_version" -v new="$latest_minor" '{gsub(old, new); print}' _quarto.yml > temp.yml && mv temp.yml _quarto.yml - echo "Updated _quarto.yml to latest minor version: $latest_minor" - fi - - - name: Suggest Changes - uses: getsentry/action-git-diff-suggestions@main - with: - message: 'The version in _quarto.yml is outdated. Please update to the latest version.' - github-token: ${{ secrets.GITHUB_TOKEN }} - continue-on-error: true diff --git a/.github/workflows/version_check.jl b/.github/workflows/version_check.jl new file mode 100644 index 000000000..f3ae7381d --- /dev/null +++ b/.github/workflows/version_check.jl @@ -0,0 +1,139 @@ +# Set up a temporary environment just to run this script +using Pkg +Pkg.activate(temp=true) +Pkg.add(["YAML", "TOML", "JSON", "HTTP"]) +import YAML +import TOML +import JSON +import HTTP + +PROJECT_TOML_PATH = "Project.toml" +QUARTO_YML_PATH = "_quarto.yml" +MANIFEST_TOML_PATH = "Manifest.toml" + +function major_minor_match(vs...) + first = vs[1] + all(v.:major == first.:major && v.:minor == first.:minor for v in vs) +end + +function major_minor_patch_match(vs...) + first = vs[1] + all(v.:major == first.:major && v.:minor == first.:minor && v.:patch == first.:patch for v in vs) +end + +""" +Update the version number in Project.toml to match `target_version`. + +This uses a naive regex replacement on lines, i.e. sed-like behaviour. Parsing +the file, editing the TOML and then re-serialising also works and would be more +correct, but the entries in the output file can end up being scrambled, which +would lead to unnecessarily large diffs in the PR. +""" +function update_project_toml(filename, target_version::VersionNumber) + lines = readlines(filename) + open(filename, "w") do io + for line in lines + if occursin(r"^Turing\s*=\s*\"\d+\.\d+\"\s*$", line) + println(io, "Turing = \"$(target_version.:major).$(target_version.:minor)\"") + else + println(io, line) + end + end + end +end + +""" +Update the version number in _quarto.yml to match `target_version`. + +See `update_project_toml` for implementation rationale. +""" +function update_quarto_yml(filename, target_version::VersionNumber) + # Don't deserialise/serialise as this will scramble lines + lines = readlines(filename) + open(filename, "w") do io + for line in lines + m = match(r"^(\s+)- text:\s*\"v\d+\.\d+\"\s*$", line) + if m !== nothing + println(io, "$(m[1])- text: \"v$(target_version.:major).$(target_version.:minor)\"") + else + println(io, line) + end + end + end +end + +# Retain the original version number string for error messages, as +# VersionNumber() will tack on a patch version of 0 +quarto_yaml = YAML.load_file(QUARTO_YML_PATH) +quarto_version_str = quarto_yaml["website"]["navbar"]["right"][1]["text"] +quarto_version = VersionNumber(quarto_version_str) +println("_quarto.yml version: ", quarto_version_str) + +project_toml = TOML.parsefile(PROJECT_TOML_PATH) +project_version_str = project_toml["compat"]["Turing"] +project_version = VersionNumber(project_version_str) +println("Project.toml version: ", project_version_str) + +manifest_toml = TOML.parsefile(MANIFEST_TOML_PATH) +manifest_version = VersionNumber(manifest_toml["deps"]["Turing"][1]["version"]) +println("Manifest.toml version: ", manifest_version) + +errors = [] + +if ENV["TARGET_IS_MASTER"] == "true" + # This environment variable is set by the GitHub Actions workflow. If it is + # true, fetch the latest version from GitHub and update files to match this + # version if necessary. + + resp = HTTP.get("https://api.github.com/repos/TuringLang/Turing.jl/releases/latest") + latest_version = VersionNumber(JSON.parse(String(resp.body))["tag_name"]) + println("Latest Turing.jl version: ", latest_version) + + if !major_minor_match(latest_version, project_version) + push!(errors, "$(PROJECT_TOML_PATH) out of date") + println("$(PROJECT_TOML_PATH) is out of date; updating") + update_project_toml(PROJECT_TOML_PATH, latest_version) + end + + if !major_minor_match(latest_version, quarto_version) + push!(errors, "$(QUARTO_YML_PATH) out of date") + println("$(QUARTO_YML_PATH) is out of date; updating") + update_quarto_yml(QUARTO_YML_PATH, latest_version) + end + + if !major_minor_patch_match(latest_version, manifest_version) + push!(errors, "$(MANIFEST_TOML_PATH) out of date") + # Attempt to automatically update Manifest + println("$(MANIFEST_TOML_PATH) is out of date; updating") + old_env = Pkg.project().path + Pkg.activate(".") + Pkg.update() + # Check if versions match now, error if not + Pkg.activate(old_env) + manifest_toml = TOML.parsefile(MANIFEST_TOML_PATH) + manifest_version = VersionNumber(manifest_toml["deps"]["Turing"][1]["version"]) + if !major_minor_patch_match(latest_version, manifest_version) + push!(errors, "Failed to update $(MANIFEST_TOML_PATH) to match latest Turing.jl version") + end + end + + if isempty(errors) + println("All good") + else + error("The following errors occurred during version checking: \n", join(errors, "\n")) + end + +else + # If this is not true, then we are running on a backport-v* branch, i.e. docs + # for a non-latest version. In this case we don't attempt to fetch the latest + # patch version from GitHub to check the Manifest (we could, but it is more + # work as it would involve paging through the list of releases). Instead, + # we just check that the minor versions match. + if !major_minor_match(quarto_version, project_version, manifest_version) + error("The minor versions of Turing.jl in _quarto.yml, Project.toml, and Manifest.toml are inconsistent: + - _quarto.yml: $quarto_version_str + - Project.toml: $project_version_str + - Manifest.toml: $manifest_version + ") + end +end diff --git a/.github/workflows/version_check.yml b/.github/workflows/version_check.yml new file mode 100644 index 000000000..fae0bff61 --- /dev/null +++ b/.github/workflows/version_check.yml @@ -0,0 +1,74 @@ +# This action checks that the minor versions of Turing.jl specified in the +# Project.toml, _quarto.yml, and Manifest.toml files are consistent. +# +# For pushes to master or PRs to master, it additionally also checks that the +# version specified in Manifest.toml matches the latest release on GitHub. +# +# If any discrepancies are observed, it will open a PR to fix them. + +name: Check Turing.jl version consistency +on: + push: + branches: + - master + - backport-* + pull_request: + branches: + - master + - backport-* + workflow_dispatch: + +jobs: + check-version: + runs-on: ubuntu-latest + + permissions: + contents: write + pull-requests: write + + env: + # Determine whether the target branch is master (i.e. this is a push to + # master or a PR to master). + TARGET_IS_MASTER: ${{ (github.event_name == 'push' && github.ref_name == 'master') || (github.event_name == 'pull_request' && github.base_ref == 'master') }} + # Disable precompilation as it takes a long time and is not needed for this workflow + JULIA_PKG_PRECOMPILE_AUTO: 0 + + steps: + - name: Checkout + uses: actions/checkout@v4 + + - name: Setup Julia + uses: julia-actions/setup-julia@v2 + + - name: Log GitHub context variables + run: | + echo github.event_name: ${{ github.event_name }} + echo github.ref_name: ${{ github.ref_name }} + echo github.base_ref: ${{ github.base_ref }} + echo TARGET_IS_MASTER: ${{ env.TARGET_IS_MASTER }} + + - name: Check version consistency + continue-on-error: true + run: julia --color=yes .github/workflows/version_check.jl + + - name: Create a PR with suggested changes + id: create_pr + if: env.TARGET_IS_MASTER + uses: peter-evans/create-pull-request@v6 + with: + base: ${{ github.event_name == 'pull_request' && github.head_ref || github.ref_name }} + branch: update-turing-version/${{ github.event_name == 'pull_request' && github.head_ref || github.ref_name }} + commit-message: "Update Turing.jl version to match latest release" + body: "This PR is automatically generated by the `version_check.yml` GitHub Action." + title: "Update Turing.jl version to match latest release" + + - name: Comment on PR about suggested changes + if: ${{ github.event_name == 'pull_request' && steps.create_pr.outputs.pull-request-operation == 'created' }} + uses: thollander/actions-comment-pull-request@v2 + with: + message: | + Hello! The versions of Turing.jl in your `Project.toml`, `_quarto.yml`, and/or `Manifest.toml` did not match the latest release version found on GitHub (https://github.com/TuringLang/Turing.jl/releases/latest). + + I've made a PR to update these files to match the latest release: ${{ steps.create_pr.outputs.pull-request-url }} + + Please review the changes and merge the PR if they look good. diff --git a/.gitignore b/.gitignore index f22e3834d..efe4be87b 100644 --- a/.gitignore +++ b/.gitignore @@ -13,12 +13,13 @@ /tutorials/**/index_files/* Testing/ /*/*/jl_*/ -/Manifest.toml -/test/Manifest.toml .vscode _freeze _site .quarto /.quarto/ changelog.qmd -versions.qmd \ No newline at end of file +versions.qmd +tmp.gif +.venv +venv diff --git a/tutorials/10-bayesian-differential-equations/Manifest.toml b/Manifest.toml old mode 100755 new mode 100644 similarity index 70% rename from tutorials/10-bayesian-differential-equations/Manifest.toml rename to Manifest.toml index d90cd243d..6f8f1feae --- a/tutorials/10-bayesian-differential-equations/Manifest.toml +++ b/Manifest.toml @@ -1,8 +1,8 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.10.0" +julia_version = "1.10.4" manifest_format = "2.0" -project_hash = "1cf8b95959ac0235940751347a1e8ff1481cfa25" +project_hash = "4dbb593d041b187abd261fc4e92a2df5baf55b80" [[deps.ADTypes]] git-tree-sha1 = "016833eb52ba2d6bea9fcb50ca295980e728ee24" @@ -20,6 +20,12 @@ weakdeps = ["ChainRulesCore", "Test"] AbstractFFTsChainRulesCoreExt = "ChainRulesCore" AbstractFFTsTestExt = "Test" +[[deps.AbstractGPs]] +deps = ["ChainRulesCore", "Distributions", "FillArrays", "IrrationalConstants", "KernelFunctions", "LinearAlgebra", "PDMats", "Random", "RecipesBase", "Reexport", "Statistics", "StatsBase", "Test"] +git-tree-sha1 = "010e6b5e06a9a6b1be6b146a7f29d5848490cc64" +uuid = "99985d1d-32ba-4be9-9821-2ec096f28918" +version = "0.5.21" + [[deps.AbstractMCMC]] deps = ["BangBang", "ConsoleProgressMonitor", "Distributed", "FillArrays", "LogDensityProblems", "Logging", "LoggingExtras", "ProgressLogging", "Random", "StatsBase", "TerminalLoggers", "Transducers"] git-tree-sha1 = "b0489adc45a7c8cf0d8e2ddf764f89c1c3decebd" @@ -39,9 +45,9 @@ version = "0.4.5" [[deps.Accessors]] deps = ["CompositionsBase", "ConstructionBase", "Dates", "InverseFunctions", "LinearAlgebra", "MacroTools", "Markdown", "Test"] -git-tree-sha1 = "c0d491ef0b135fd7d63cbc6404286bc633329425" +git-tree-sha1 = "f61b15be1d76846c0ce31d3fcfac5380ae53db6a" uuid = "7d9f7c33-5ae7-4f3b-8dc6-eff91059b697" -version = "0.1.36" +version = "0.1.37" [deps.Accessors.extensions] AccessorsAxisKeysExt = "AxisKeys" @@ -60,9 +66,9 @@ version = "0.1.36" [[deps.Adapt]] deps = ["LinearAlgebra", "Requires"] -git-tree-sha1 = "6a55b747d1812e699320963ffde36f1ebdda4099" +git-tree-sha1 = "cde29ddf7e5726c9fb511f340244ea3481267608" uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" -version = "4.0.4" +version = "3.7.2" weakdeps = ["StaticArrays"] [deps.Adapt.extensions] @@ -86,9 +92,9 @@ version = "0.6.1" [[deps.AdvancedMH]] deps = ["AbstractMCMC", "Distributions", "FillArrays", "LinearAlgebra", "LogDensityProblems", "Random", "Requires"] -git-tree-sha1 = "16589dbdd36c782ff01700908e962b303474f641" +git-tree-sha1 = "fa4e8d6f9bae913aaa40224cf9407163e693d829" uuid = "5b7e9947-ddc0-4b3f-9b55-0d8042f74170" -version = "0.8.1" +version = "0.8.2" weakdeps = ["DiffResults", "ForwardDiff", "MCMCChains", "StructArrays"] [deps.AdvancedMH.extensions] @@ -108,9 +114,10 @@ weakdeps = ["Libtask"] [[deps.AdvancedVI]] deps = ["ADTypes", "Bijectors", "DiffResults", "Distributions", "DistributionsAD", "DocStringExtensions", "ForwardDiff", "LinearAlgebra", "ProgressMeter", "Random", "Requires", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "187f67ab998f25208651262fee9539d845016b26" +git-tree-sha1 = "3e97de1a2ccce08978cd80570d8cbb9ff3f08bd3" uuid = "b5ca4192-6429-45e5-a2d9-87aec30a685c" -version = "0.2.5" +version = "0.2.6" +weakdeps = ["Enzyme", "Flux", "ReverseDiff", "Zygote"] [deps.AdvancedVI.extensions] AdvancedVIEnzymeExt = ["Enzyme"] @@ -118,12 +125,6 @@ version = "0.2.5" AdvancedVIReverseDiffExt = ["ReverseDiff"] AdvancedVIZygoteExt = ["Zygote"] - [deps.AdvancedVI.weakdeps] - Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" - Flux = "587475ba-b771-5e3f-ad9e-33799f191a9c" - ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" - Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" - [[deps.AliasTables]] deps = ["PtrArrays", "Random"] git-tree-sha1 = "9876e1e164b144ca45e9e3198d0b689cadfed9ff" @@ -158,19 +159,16 @@ uuid = "68821587-b530-5797-8361-c406ea357684" version = "3.5.1+1" [[deps.ArrayInterface]] -deps = ["Adapt", "LinearAlgebra", "SparseArrays", "SuiteSparse"] -git-tree-sha1 = "133a240faec6e074e07c31ee75619c90544179cf" +deps = ["Adapt", "LinearAlgebra", "Requires", "SparseArrays", "SuiteSparse"] +git-tree-sha1 = "c5aeb516a84459e0318a02507d2261edad97eb75" uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" -version = "7.10.0" +version = "7.7.1" [deps.ArrayInterface.extensions] ArrayInterfaceBandedMatricesExt = "BandedMatrices" ArrayInterfaceBlockBandedMatricesExt = "BlockBandedMatrices" ArrayInterfaceCUDAExt = "CUDA" - ArrayInterfaceCUDSSExt = "CUDSS" - ArrayInterfaceChainRulesExt = "ChainRules" ArrayInterfaceGPUArraysCoreExt = "GPUArraysCore" - ArrayInterfaceReverseDiffExt = "ReverseDiff" ArrayInterfaceStaticArraysCoreExt = "StaticArraysCore" ArrayInterfaceTrackerExt = "Tracker" @@ -178,18 +176,15 @@ version = "7.10.0" BandedMatrices = "aae01518-5342-5314-be14-df237901396f" BlockBandedMatrices = "ffab5731-97b5-5995-9138-79e8c1846df0" CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" - CUDSS = "45b445bb-4962-46a0-9369-b4df9d0f772e" - ChainRules = "082447d4-558c-5d27-93f4-14fc19e9eca2" GPUArraysCore = "46192b85-c4d5-4398-a991-12ede77f4527" - ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" StaticArraysCore = "1e83bf80-4336-4d27-bf5d-d5a4f845583c" Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" [[deps.ArrayLayouts]] deps = ["FillArrays", "LinearAlgebra"] -git-tree-sha1 = "33207a8be6267bc389d0701e97a9bce6a4de68eb" +git-tree-sha1 = "ce2ca959f932f5dad70697dd93133d1167cf1e4e" uuid = "4c555306-a7a7-4459-81d9-ec55ddd5c99a" -version = "1.9.2" +version = "1.10.2" weakdeps = ["SparseArrays"] [deps.ArrayLayouts.extensions] @@ -218,19 +213,19 @@ version = "0.4.7" [[deps.BandedMatrices]] deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra", "PrecompileTools"] -git-tree-sha1 = "30b7ea34abc4fe816eb1a5f434a43da804836163" +git-tree-sha1 = "0b816941273b5b162be122a6c94d706e3b3125ca" uuid = "aae01518-5342-5314-be14-df237901396f" -version = "1.7.0" +version = "0.17.38" weakdeps = ["SparseArrays"] [deps.BandedMatrices.extensions] BandedMatricesSparseArraysExt = "SparseArrays" [[deps.BangBang]] -deps = ["Accessors", "Compat", "ConstructionBase", "InitialValues", "LinearAlgebra", "Requires"] -git-tree-sha1 = "08e5fc6620a8d83534bf6149795054f1b1e8370a" +deps = ["Accessors", "ConstructionBase", "InitialValues", "LinearAlgebra", "Requires"] +git-tree-sha1 = "e2144b631226d9eeab2d746ca8880b7ccff504ae" uuid = "198e06fe-97b7-11e9-32a5-e1d131e6ad66" -version = "0.4.2" +version = "0.4.3" [deps.BangBang.extensions] BangBangChainRulesCoreExt = "ChainRulesCore" @@ -256,43 +251,52 @@ git-tree-sha1 = "aebf55e6d7795e02ca500a689d326ac979aaf89e" uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" +[[deps.BenchmarkTools]] +deps = ["JSON", "Logging", "Printf", "Profile", "Statistics", "UUIDs"] +git-tree-sha1 = "f1dff6729bc61f4d49e140da1af55dcd1ac97b2f" +uuid = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf" +version = "1.5.0" + [[deps.Bijectors]] -deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "49491db48b1c70eefa5115e626100dbd6c0ff4c0" +deps = ["ArgCheck", "ChainRules", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "DocStringExtensions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] +git-tree-sha1 = "6e686c360af8375162531708acb824ae1182b1d5" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.13.12" -weakdeps = ["DistributionsAD", "ForwardDiff", "LazyArrays", "ReverseDiff", "Tracker", "Zygote"] +version = "0.13.16" [deps.Bijectors.extensions] BijectorsDistributionsADExt = "DistributionsAD" BijectorsForwardDiffExt = "ForwardDiff" BijectorsLazyArraysExt = "LazyArrays" BijectorsReverseDiffExt = "ReverseDiff" + BijectorsTapirExt = "Tapir" BijectorsTrackerExt = "Tracker" BijectorsZygoteExt = "Zygote" + [deps.Bijectors.weakdeps] + DistributionsAD = "ced4e74d-a319-5a8a-b0ac-84af2272839c" + ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" + LazyArrays = "5078a376-72f3-5289-bfd5-ec5146d43c02" + ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" + Tapir = "07d77754-e150-4737-8c94-cd238a1fb45b" + Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" + Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" + [[deps.BitFlags]] -git-tree-sha1 = "2dc09997850d68179b69dafb58ae806167a32b1b" +git-tree-sha1 = "0691e34b3bb8be9307330f88d1a3c3f25466c24d" uuid = "d1d4a3ce-64b1-5f1a-9ba4-7e7e69966f35" -version = "0.1.8" +version = "0.1.9" [[deps.BitTwiddlingConvenienceFunctions]] deps = ["Static"] -git-tree-sha1 = "0c5f81f47bbbcf4aea7b2959135713459170798b" +git-tree-sha1 = "f21cfd4950cb9f0587d5067e69405ad2acd27b87" uuid = "62783981-4cbd-42fc-bca8-16325de8dc4b" -version = "0.1.5" +version = "0.1.6" [[deps.BoundaryValueDiffEq]] -deps = ["ADTypes", "Adapt", "ArrayInterface", "BandedMatrices", "ConcreteStructs", "DiffEqBase", "FastAlmostBandedMatrices", "FastClosures", "ForwardDiff", "LinearAlgebra", "LinearSolve", "Logging", "NonlinearSolve", "OrdinaryDiffEq", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "SparseArrays", "SparseDiffTools"] -git-tree-sha1 = "005b55fa2eebaa4d7bf3cfb8097807f47116175f" +deps = ["ArrayInterface", "BandedMatrices", "DiffEqBase", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "NonlinearSolve", "Reexport", "SciMLBase", "Setfield", "SparseArrays", "TruncatedStacktraces", "UnPack"] +git-tree-sha1 = "f7392ce20e6dafa8fee406142b1764de7d7cd911" uuid = "764a87c0-6b3e-53db-9096-fe964310641d" -version = "5.7.1" - - [deps.BoundaryValueDiffEq.extensions] - BoundaryValueDiffEqODEInterfaceExt = "ODEInterface" - - [deps.BoundaryValueDiffEq.weakdeps] - ODEInterface = "54ca160b-1b9f-5127-a996-1867f4bc2a2c" +version = "4.0.1" [[deps.Bzip2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -307,9 +311,15 @@ version = "0.5.0" [[deps.CPUSummary]] deps = ["CpuId", "IfElse", "PrecompileTools", "Static"] -git-tree-sha1 = "585a387a490f1c4bd88be67eea15b93da5e85db7" +git-tree-sha1 = "5a97e67919535d6841172016c9530fd69494e5ec" uuid = "2a0fbf3d-bb9c-48f3-b0a9-814d99fd7ab9" -version = "0.2.5" +version = "0.2.6" + +[[deps.CSV]] +deps = ["CodecZlib", "Dates", "FilePathsBase", "InlineStrings", "Mmap", "Parsers", "PooledArrays", "PrecompileTools", "SentinelArrays", "Tables", "Unicode", "WeakRefStrings", "WorkerUtilities"] +git-tree-sha1 = "6c834533dc1fabd820c1db03c839bf97e45a3fab" +uuid = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b" +version = "0.10.14" [[deps.Cairo_jll]] deps = ["Artifacts", "Bzip2_jll", "CompilerSupportLibraries_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "JLLWrappers", "LZO_jll", "Libdl", "Pixman_jll", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Zlib_jll", "libpng_jll"] @@ -328,17 +338,35 @@ git-tree-sha1 = "0970356c3bb9113309c74c27c87083cf9c73880a" uuid = "7057c7e9-c182-5462-911a-8362d720325c" version = "0.3.13" +[[deps.CategoricalArrays]] +deps = ["DataAPI", "Future", "Missings", "Printf", "Requires", "Statistics", "Unicode"] +git-tree-sha1 = "1568b28f91293458345dabba6a5ea3f183250a61" +uuid = "324d7699-5711-5eae-9e2f-1d82baa6b597" +version = "0.10.8" + + [deps.CategoricalArrays.extensions] + CategoricalArraysJSONExt = "JSON" + CategoricalArraysRecipesBaseExt = "RecipesBase" + CategoricalArraysSentinelArraysExt = "SentinelArrays" + CategoricalArraysStructTypesExt = "StructTypes" + + [deps.CategoricalArrays.weakdeps] + JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6" + RecipesBase = "3cdcf5f2-1ef4-517c-9805-6587b60abb01" + SentinelArrays = "91c51154-3ec4-41a3-a24f-3f23e20d615c" + StructTypes = "856f2bd8-1eba-4b0a-8007-ebc267875bd4" + [[deps.ChainRules]] deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "SparseInverseSubset", "Statistics", "StructArrays", "SuiteSparse"] -git-tree-sha1 = "291821c1251486504f6bae435227907d734e94d2" +git-tree-sha1 = "227985d885b4dbce5e18a96f9326ea1e836e5a03" uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2" -version = "1.66.0" +version = "1.69.0" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra"] -git-tree-sha1 = "575cd02e080939a33b6df6c5853d14924c08e35b" +git-tree-sha1 = "71acdbf594aab5bbb2cec89b208c41b4c411e49f" uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" -version = "1.23.0" +version = "1.24.0" weakdeps = ["SparseArrays"] [deps.ChainRulesCore.extensions] @@ -356,9 +384,9 @@ weakdeps = ["InverseFunctions"] [[deps.CloseOpenIntervals]] deps = ["Static", "StaticArrayInterface"] -git-tree-sha1 = "70232f82ffaab9dc52585e0dd043b5e0c6b714f1" +git-tree-sha1 = "05ba0d07cd4fd8b7a39541e31a7b0254704ea581" uuid = "fb6a15b2-703c-40df-9091-08a04967cfa9" -version = "0.1.12" +version = "0.1.13" [[deps.Clustering]] deps = ["Distances", "LinearAlgebra", "NearestNeighbors", "Printf", "Random", "SparseArrays", "Statistics", "StatsBase"] @@ -366,17 +394,23 @@ git-tree-sha1 = "9ebb045901e9bbf58767a9f34ff89831ed711aae" uuid = "aaaa29a8-35af-508c-8bc3-b662a17a0fe5" version = "0.15.7" +[[deps.CodecBzip2]] +deps = ["Bzip2_jll", "Libdl", "TranscodingStreams"] +git-tree-sha1 = "f8889d1770addf59d0a015c49a473fa2bdb9f809" +uuid = "523fee87-0ab8-5b00-afb7-3ecf72e48cfd" +version = "0.8.3" + [[deps.CodecZlib]] deps = ["TranscodingStreams", "Zlib_jll"] -git-tree-sha1 = "59939d8a997469ee05c4b4944560a820f9ba0d73" +git-tree-sha1 = "b8fe8546d52ca154ac556809e10c75e6e7430ac8" uuid = "944b1d66-785c-5afd-91f1-9de20f533193" -version = "0.7.4" +version = "0.7.5" [[deps.ColorSchemes]] deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "PrecompileTools", "Random"] -git-tree-sha1 = "4b270d6465eb21ae89b732182c20dc165f8bf9f2" +git-tree-sha1 = "b5278586822443594ff615963b0c09755771b3e0" uuid = "35d6a980-a343-548e-a6ea-1d62b119f2f4" -version = "3.25.0" +version = "3.26.0" [[deps.ColorTypes]] deps = ["FixedPointNumbers", "Random"] @@ -418,9 +452,9 @@ version = "0.3.0" [[deps.Compat]] deps = ["TOML", "UUIDs"] -git-tree-sha1 = "b1c55339b7c6c350ee89f2c1604299660525b248" +git-tree-sha1 = "8ae8d32e09f0dcf42a36b90d4e17f5dd2e4c4215" uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" -version = "4.15.0" +version = "4.16.0" weakdeps = ["Dates", "LinearAlgebra"] [deps.Compat.extensions] @@ -429,7 +463,26 @@ weakdeps = ["Dates", "LinearAlgebra"] [[deps.CompilerSupportLibraries_jll]] deps = ["Artifacts", "Libdl"] uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae" -version = "1.0.5+1" +version = "1.1.1+0" + +[[deps.ComponentArrays]] +deps = ["ArrayInterface", "ChainRulesCore", "ForwardDiff", "Functors", "LinearAlgebra", "PackageExtensionCompat", "StaticArrayInterface", "StaticArraysCore"] +git-tree-sha1 = "cf30651e65a87b20b12601b91169a18838eab2df" +uuid = "b0b7db55-cfe3-40fc-9ded-d10e2dbeff66" +version = "0.15.16" +weakdeps = ["Adapt", "ConstructionBase", "GPUArrays", "Optimisers", "RecursiveArrayTools", "ReverseDiff", "SciMLBase", "Tracker", "TruncatedStacktraces", "Zygote"] + + [deps.ComponentArrays.extensions] + ComponentArraysAdaptExt = "Adapt" + ComponentArraysConstructionBaseExt = "ConstructionBase" + ComponentArraysGPUArraysExt = "GPUArrays" + ComponentArraysOptimisersExt = "Optimisers" + ComponentArraysRecursiveArrayToolsExt = "RecursiveArrayTools" + ComponentArraysReverseDiffExt = "ReverseDiff" + ComponentArraysSciMLBaseExt = "SciMLBase" + ComponentArraysTrackerExt = "Tracker" + ComponentArraysTruncatedStacktracesExt = "TruncatedStacktraces" + ComponentArraysZygoteExt = "Zygote" [[deps.CompositionsBase]] git-tree-sha1 = "802bb88cd69dfd1509f6670416bd4434015693ad" @@ -447,9 +500,9 @@ version = "0.2.3" [[deps.ConcurrentUtilities]] deps = ["Serialization", "Sockets"] -git-tree-sha1 = "6cbbd4d241d7e6579ab354737f4dd95ca43946e1" +git-tree-sha1 = "ea32b83ca4fefa1768dc84e504cc0a94fb1ab8d1" uuid = "f0e56b4a-5159-44fe-b623-3e5288b988bb" -version = "2.4.1" +version = "2.4.2" [[deps.ConsoleProgressMonitor]] deps = ["Logging", "ProgressMeter"] @@ -459,15 +512,21 @@ version = "0.1.2" [[deps.ConstructionBase]] deps = ["LinearAlgebra"] -git-tree-sha1 = "260fd2400ed2dab602a7c15cf10c1933c59930a2" +git-tree-sha1 = "d8a9c0b6ac2d9081bf76324b39c78ca3ce4f0c98" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.5.5" +version = "1.5.6" weakdeps = ["IntervalSets", "StaticArrays"] [deps.ConstructionBase.extensions] ConstructionBaseIntervalSetsExt = "IntervalSets" ConstructionBaseStaticArraysExt = "StaticArrays" +[[deps.ContextVariablesX]] +deps = ["Compat", "Logging", "UUIDs"] +git-tree-sha1 = "25cc3803f1030ab855e383129dcd3dc294e322cc" +uuid = "6add18c4-b38d-439d-96f6-d6bc489c04c5" +version = "0.1.3" + [[deps.Contour]] git-tree-sha1 = "439e35b0b36e2e5881738abc8857bd92ad6ff9a8" uuid = "d38c429a-6771-53c6-b99e-75d170b6e991" @@ -489,6 +548,18 @@ git-tree-sha1 = "abe83f3a2f1b857aac70ef8b269080af17764bbe" uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a" version = "1.16.0" +[[deps.DataDeps]] +deps = ["HTTP", "Libdl", "Reexport", "SHA", "Scratch", "p7zip_jll"] +git-tree-sha1 = "8ae085b71c462c2cb1cfedcb10c3c877ec6cf03f" +uuid = "124859b0-ceae-595e-8997-d05f6a7a8dfe" +version = "0.7.13" + +[[deps.DataFrames]] +deps = ["Compat", "DataAPI", "DataStructures", "Future", "InlineStrings", "InvertedIndices", "IteratorInterfaceExtensions", "LinearAlgebra", "Markdown", "Missings", "PooledArrays", "PrecompileTools", "PrettyTables", "Printf", "REPL", "Random", "Reexport", "SentinelArrays", "SortingAlgorithms", "Statistics", "TableTraits", "Tables", "Unicode"] +git-tree-sha1 = "04c738083f29f86e62c8afc341f0967d8717bdb8" +uuid = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" +version = "1.6.1" + [[deps.DataStructures]] deps = ["Compat", "InteractiveUtils", "OrderedCollections"] git-tree-sha1 = "1d0a14036acb104d9e89698bd408f63ab58cdc82" @@ -504,6 +575,12 @@ version = "1.0.0" deps = ["Printf"] uuid = "ade2ca70-3891-5945-98fb-dc099432e06a" +[[deps.Dbus_jll]] +deps = ["Artifacts", "Expat_jll", "JLLWrappers", "Libdl"] +git-tree-sha1 = "fc173b380865f70627d7dd1190dc2fce6cc105af" +uuid = "ee1fde0b-3d02-5ea6-8484-8dfef6360eab" +version = "1.14.10+0" + [[deps.DefineSingletons]] git-tree-sha1 = "0fba8b706d0178b4dc7fd44a96a92382c9065c2c" uuid = "244e2a9f-e319-4986-a169-4d1fe445cd52" @@ -511,9 +588,9 @@ version = "0.1.2" [[deps.DelayDiffEq]] deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "LinearAlgebra", "Logging", "OrdinaryDiffEq", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SimpleNonlinearSolve", "SimpleUnPack"] -git-tree-sha1 = "5959ae76ebd198f70e9af81153644543da0cfaf2" +git-tree-sha1 = "e40378efd2af7658d0a0579aa9e15b17137368f4" uuid = "bcd4f6db-9728-5f36-b5f7-82caef46ccdb" -version = "5.47.3" +version = "5.44.0" [[deps.DelimitedFiles]] deps = ["Mmap"] @@ -528,16 +605,13 @@ uuid = "b429d917-457f-4dbc-8f4c-0cc954292b1d" version = "0.4.0" [[deps.DiffEqBase]] -deps = ["ArrayInterface", "ConcreteStructs", "DataStructures", "DocStringExtensions", "EnumX", "EnzymeCore", "FastBroadcast", "FastClosures", "ForwardDiff", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "Parameters", "PreallocationTools", "PrecompileTools", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "Setfield", "SparseArrays", "Static", "StaticArraysCore", "Statistics", "Tricks", "TruncatedStacktraces"] -git-tree-sha1 = "50382fbd95a4b7120df58d87b6038479be14d767" +deps = ["ArrayInterface", "ChainRulesCore", "DataStructures", "DocStringExtensions", "EnumX", "FastBroadcast", "ForwardDiff", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "Parameters", "PreallocationTools", "PrecompileTools", "Printf", "RecursiveArrayTools", "Reexport", "Requires", "SciMLBase", "SciMLOperators", "Setfield", "SparseArrays", "Static", "StaticArraysCore", "Statistics", "Tricks", "TruncatedStacktraces", "ZygoteRules"] +git-tree-sha1 = "0d9982e8dee851d519145857e79a17ee33ede154" uuid = "2b5f629d-d688-5b77-993f-72d75c75574e" -version = "6.151.0" +version = "6.130.0" [deps.DiffEqBase.extensions] - DiffEqBaseCUDAExt = "CUDA" - DiffEqBaseChainRulesCoreExt = "ChainRulesCore" DiffEqBaseDistributionsExt = "Distributions" - DiffEqBaseEnzymeExt = ["ChainRulesCore", "Enzyme"] DiffEqBaseGeneralizedGeneratedExt = "GeneralizedGenerated" DiffEqBaseMPIExt = "MPI" DiffEqBaseMeasurementsExt = "Measurements" @@ -545,12 +619,10 @@ version = "6.151.0" DiffEqBaseReverseDiffExt = "ReverseDiff" DiffEqBaseTrackerExt = "Tracker" DiffEqBaseUnitfulExt = "Unitful" + DiffEqBaseZygoteExt = "Zygote" [deps.DiffEqBase.weakdeps] - CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" - ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f" - Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" GeneralizedGenerated = "6b9d7cbe-bcb9-11e9-073f-15a7a543e2eb" MPI = "da04e1cc-30fd-572f-bb4f-1f8673147195" Measurements = "eff96d63-e80a-5855-80a2-b1b0885c5ab7" @@ -558,19 +630,20 @@ version = "6.151.0" ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d" + Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.DiffEqCallbacks]] -deps = ["DataStructures", "DiffEqBase", "ForwardDiff", "Functors", "LinearAlgebra", "Markdown", "NonlinearSolve", "Parameters", "RecipesBase", "RecursiveArrayTools", "SciMLBase", "StaticArraysCore"] -git-tree-sha1 = "c959cfd2657d16beada157a74d52269e8556500e" +deps = ["DataStructures", "DiffEqBase", "ForwardDiff", "Functors", "LinearAlgebra", "Markdown", "NLsolve", "Parameters", "RecipesBase", "RecursiveArrayTools", "SciMLBase", "StaticArraysCore"] +git-tree-sha1 = "d0b94b3694d55e7eedeee918e7daee9e3b873399" uuid = "459566f4-90b8-5000-8ac3-15dfb0a30def" -version = "3.6.2" +version = "2.35.0" weakdeps = ["OrdinaryDiffEq", "Sundials"] [[deps.DiffEqNoiseProcess]] deps = ["DiffEqBase", "Distributions", "GPUArraysCore", "LinearAlgebra", "Markdown", "Optim", "PoissonRandom", "QuadGK", "Random", "Random123", "RandomNumbers", "RecipesBase", "RecursiveArrayTools", "Requires", "ResettableStacks", "SciMLBase", "StaticArraysCore", "Statistics"] -git-tree-sha1 = "65cbbe1450ced323b4b17228ccd96349d96795a7" +git-tree-sha1 = "ed0158e758723b4d429afbbb5d98c5afd3458dc1" uuid = "77a26b50-5914-5dd7-bc55-306e6241c503" -version = "5.21.0" +version = "5.22.0" weakdeps = ["ReverseDiff"] [deps.DiffEqNoiseProcess.extensions] @@ -590,9 +663,20 @@ version = "1.15.1" [[deps.DifferentialEquations]] deps = ["BoundaryValueDiffEq", "DelayDiffEq", "DiffEqBase", "DiffEqCallbacks", "DiffEqNoiseProcess", "JumpProcesses", "LinearAlgebra", "LinearSolve", "NonlinearSolve", "OrdinaryDiffEq", "Random", "RecursiveArrayTools", "Reexport", "SciMLBase", "SteadyStateDiffEq", "StochasticDiffEq", "Sundials"] -git-tree-sha1 = "81042254a307980b8ab5b67033aca26c2e157ebb" +git-tree-sha1 = "96a19f498504e4a3b39524196b73eb60ccef30e9" uuid = "0c46a032-eb83-5123-abaf-570d42b7fbaa" -version = "7.13.0" +version = "7.10.0" + +[[deps.DispatchDoctor]] +deps = ["MacroTools", "Preferences"] +git-tree-sha1 = "114474c54e14f9ae53b8a5088507560278db15c3" +uuid = "8d63f2c5-f18a-4cf2-ba9d-b3f60fc568c8" +version = "0.4.13" +weakdeps = ["ChainRulesCore", "EnzymeCore"] + + [deps.DispatchDoctor.extensions] + DispatchDoctorChainRulesCoreExt = "ChainRulesCore" + DispatchDoctorEnzymeCoreExt = "EnzymeCore" [[deps.Distances]] deps = ["LinearAlgebra", "Statistics", "StatsAPI"] @@ -611,9 +695,9 @@ uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" [[deps.Distributions]] deps = ["AliasTables", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] -git-tree-sha1 = "22c595ca4146c07b16bcf9c8bea86f731f7109d2" +git-tree-sha1 = "0e0a1264b0942f1f3abb2b30891f2a590cc652ac" uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" -version = "0.25.108" +version = "0.25.110" weakdeps = ["ChainRulesCore", "DensityInterface", "Test"] [deps.Distributions.extensions] @@ -626,7 +710,6 @@ deps = ["Adapt", "ChainRules", "ChainRulesCore", "Compat", "Distributions", "Fil git-tree-sha1 = "f4dd7727b07b4b7fff5ff4149118ee06e83dfab7" uuid = "ced4e74d-a319-5a8a-b0ac-84af2272839c" version = "0.6.55" -weakdeps = ["ForwardDiff", "LazyArrays", "ReverseDiff", "Tracker"] [deps.DistributionsAD.extensions] DistributionsADForwardDiffExt = "ForwardDiff" @@ -634,6 +717,12 @@ weakdeps = ["ForwardDiff", "LazyArrays", "ReverseDiff", "Tracker"] DistributionsADReverseDiffExt = "ReverseDiff" DistributionsADTrackerExt = "Tracker" + [deps.DistributionsAD.weakdeps] + ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" + LazyArrays = "5078a376-72f3-5289-bfd5-ec5146d43c02" + ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" + Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" + [[deps.DocStringExtensions]] deps = ["LibGit2"] git-tree-sha1 = "2fb1e02f2b635d0845df5d7c167fec4dd739b00d" @@ -651,11 +740,17 @@ git-tree-sha1 = "5837a837389fccf076445fce071c8ddaea35a566" uuid = "fa6b7ba4-c1ee-5f82-b5fc-ecf0adba8f74" version = "0.6.8" +[[deps.DynamicHMC]] +deps = ["ArgCheck", "DocStringExtensions", "FillArrays", "LinearAlgebra", "LogDensityProblems", "LogExpFunctions", "ProgressMeter", "Random", "SimpleUnPack", "Statistics", "TensorCast"] +git-tree-sha1 = "9285af003a31272b4105c8e80d90b99eaf4b8c05" +uuid = "bbc10e6e-7c05-544b-b16e-64fede858acb" +version = "3.4.7" + [[deps.DynamicPPL]] deps = ["ADTypes", "AbstractMCMC", "AbstractPPL", "Accessors", "BangBang", "Bijectors", "Compat", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MacroTools", "OrderedCollections", "Random", "Requires", "Test"] -git-tree-sha1 = "882510df0da64bae763a65240b07fb4b1c462317" +git-tree-sha1 = "f017bc2020220697b795ff636dc595537b9d271f" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.27.1" +version = "0.28.2" weakdeps = ["ChainRulesCore", "EnzymeCore", "ForwardDiff", "MCMCChains", "ReverseDiff", "ZygoteRules"] [deps.DynamicPPL.extensions] @@ -685,20 +780,18 @@ version = "1.0.4" [[deps.Enzyme]] deps = ["CEnum", "EnzymeCore", "Enzyme_jll", "GPUCompiler", "LLVM", "Libdl", "LinearAlgebra", "ObjectFile", "Preferences", "Printf", "Random"] -git-tree-sha1 = "259fc20bdf3f48d16cdc673806877c631c883dd3" +git-tree-sha1 = "3fb48f9c18de1993c477457265b85130756746ae" uuid = "7da242da-08ed-463a-9acd-ee780be4f1d9" -version = "0.12.7" -weakdeps = ["ChainRulesCore", "SpecialFunctions", "StaticArrays"] +version = "0.11.20" +weakdeps = ["SpecialFunctions"] [deps.Enzyme.extensions] - EnzymeChainRulesCoreExt = "ChainRulesCore" EnzymeSpecialFunctionsExt = "SpecialFunctions" - EnzymeStaticArraysExt = "StaticArrays" [[deps.EnzymeCore]] -git-tree-sha1 = "18394bc78ac2814ff38fe5e0c9dc2cd171e2810c" +git-tree-sha1 = "1bc328eec34ffd80357f84a84bb30e4374e9bd60" uuid = "f151be2c-9106-41f4-ab19-57ee4f262869" -version = "0.7.2" +version = "0.6.6" weakdeps = ["Adapt"] [deps.EnzymeCore.extensions] @@ -706,9 +799,9 @@ weakdeps = ["Adapt"] [[deps.Enzyme_jll]] deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] -git-tree-sha1 = "b28ef691d1cc6425ee63c59e3f62e81a3ec072d4" +git-tree-sha1 = "32d418c804279c60dd38ac7868126696f3205a4f" uuid = "7cc45869-7501-5eee-bdea-0790c847d4ef" -version = "0.0.111+0" +version = "0.0.102+0" [[deps.EpollShim_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -739,6 +832,11 @@ git-tree-sha1 = "27415f162e6028e81c72b82ef756bf321213b6ec" uuid = "e2ba6199-217a-4e67-a87a-7c52f15ade04" version = "0.1.10" +[[deps.ExternalDocstrings]] +git-tree-sha1 = "1224740fc4d07c989949e1c1b508ebd49a65a5f6" +uuid = "e189563c-0753-4f5e-ad5c-be4293c83fb4" +version = "0.1.1" + [[deps.FFMPEG]] deps = ["FFMPEG_jll"] git-tree-sha1 = "b57e3acbe22f8484b4b5ff66a7499717fe1a9cc8" @@ -763,10 +861,16 @@ git-tree-sha1 = "c6033cc3892d0ef5bb9cd29b7f2f0331ea5184ea" uuid = "f5851436-0d7a-5f13-b9de-f02708fd171a" version = "3.3.10+0" -[[deps.FastAlmostBandedMatrices]] -deps = ["ArrayInterface", "ArrayLayouts", "BandedMatrices", "ConcreteStructs", "LazyArrays", "LinearAlgebra", "MatrixFactorizations", "PrecompileTools", "Reexport"] -git-tree-sha1 = "9dc913faf8552fd09b92a0d7fcc25f1d5609d795" -uuid = "9d29842c-ecb8-4973-b1e9-a27b1157504e" +[[deps.FLoops]] +deps = ["BangBang", "Compat", "FLoopsBase", "InitialValues", "JuliaVariables", "MLStyle", "Serialization", "Setfield", "Transducers"] +git-tree-sha1 = "0a2e5873e9a5f54abb06418d57a8df689336a660" +uuid = "cc61a311-1640-44b5-9fba-1b764f453329" +version = "0.2.2" + +[[deps.FLoopsBase]] +deps = ["ContextVariablesX"] +git-tree-sha1 = "656f7a6859be8673bf1f35da5670246b923964f7" +uuid = "b9860ae5-e623-471e-878b-f6a53c775ea6" version = "0.1.1" [[deps.FastBroadcast]] @@ -782,9 +886,21 @@ version = "0.3.2" [[deps.FastLapackInterface]] deps = ["LinearAlgebra"] -git-tree-sha1 = "f4102aab9c7df8691ed09f9c42e34f5ab5458ab9" +git-tree-sha1 = "cbf5edddb61a43669710cbc2241bc08b36d9e660" uuid = "29a986be-02c6-4525-aec4-84b980013641" -version = "2.0.3" +version = "2.0.4" + +[[deps.FileIO]] +deps = ["Pkg", "Requires", "UUIDs"] +git-tree-sha1 = "82d8afa92ecf4b52d78d869f038ebfb881267322" +uuid = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549" +version = "1.16.3" + +[[deps.FilePathsBase]] +deps = ["Compat", "Dates", "Mmap", "Printf", "Test", "UUIDs"] +git-tree-sha1 = "9f00e42f8d99fdde64d40c8ea5d14269a2e2c1aa" +uuid = "48062228-2e41-5def-b9a4-89aafe57970f" +version = "0.9.21" [[deps.FileWatching]] uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" @@ -823,6 +939,36 @@ git-tree-sha1 = "05882d6995ae5c12bb5f36dd2ed3f61c98cbb172" uuid = "53c48c17-4a7d-5ca2-90c5-79b7896eea93" version = "0.8.5" +[[deps.Flux]] +deps = ["Adapt", "ChainRulesCore", "Compat", "Functors", "LinearAlgebra", "MLUtils", "MacroTools", "NNlib", "OneHotArrays", "Optimisers", "Preferences", "ProgressLogging", "Random", "Reexport", "SparseArrays", "SpecialFunctions", "Statistics", "Zygote"] +git-tree-sha1 = "edacf029ed6276301e455e34d7ceeba8cc34078a" +uuid = "587475ba-b771-5e3f-ad9e-33799f191a9c" +version = "0.14.16" + + [deps.Flux.extensions] + FluxAMDGPUExt = "AMDGPU" + FluxCUDAExt = "CUDA" + FluxCUDAcuDNNExt = ["CUDA", "cuDNN"] + FluxMetalExt = "Metal" + + [deps.Flux.weakdeps] + AMDGPU = "21141c5a-9bdb-4563-92ae-f87d6854732e" + CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" + Metal = "dde4c033-4e86-420c-a63e-0dd931031962" + cuDNN = "02a925ec-e4fe-4b08-9a7e-0d78e3d38ccd" + +[[deps.Folds]] +deps = ["Accessors", "BangBang", "Baselet", "DefineSingletons", "Distributed", "ExternalDocstrings", "InitialValues", "MicroCollections", "Referenceables", "Requires", "Test", "ThreadedScans", "Transducers"] +git-tree-sha1 = "7eb4bc88d8295e387a667fd43d67c157ddee76cf" +uuid = "41a02a25-b8f0-4f67-bc48-60067656b558" +version = "0.2.10" + + [deps.Folds.extensions] + FoldsOnlineStatsBaseExt = "OnlineStatsBase" + + [deps.Folds.weakdeps] + OnlineStatsBase = "925886fa-5bf2-5e8e-b522-a9147a512338" + [[deps.Fontconfig_jll]] deps = ["Artifacts", "Bzip2_jll", "Expat_jll", "FreeType2_jll", "JLLWrappers", "Libdl", "Libuuid_jll", "Zlib_jll"] git-tree-sha1 = "db16beca600632c95fc8aca29890d83788dd8b23" @@ -875,49 +1021,55 @@ version = "0.1.3" [[deps.Functors]] deps = ["LinearAlgebra"] -git-tree-sha1 = "d3e63d9fa13f8eaa2f06f64949e2afc593ff52c2" +git-tree-sha1 = "64d8e93700c7a3f28f717d265382d52fac9fa1c1" uuid = "d9f16b24-f501-4c13-a1f2-28368ffc5196" -version = "0.4.10" +version = "0.4.12" [[deps.Future]] deps = ["Random"] uuid = "9fa8497b-333b-5362-9e8d-4d0656e87820" [[deps.GLFW_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Libglvnd_jll", "Xorg_libXcursor_jll", "Xorg_libXi_jll", "Xorg_libXinerama_jll", "Xorg_libXrandr_jll"] -git-tree-sha1 = "ff38ba61beff76b8f4acad8ab0c97ef73bb670cb" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Libglvnd_jll", "Xorg_libXcursor_jll", "Xorg_libXi_jll", "Xorg_libXinerama_jll", "Xorg_libXrandr_jll", "libdecor_jll", "xkbcommon_jll"] +git-tree-sha1 = "532f9126ad901533af1d4f5c198867227a7bb077" uuid = "0656b61e-2033-5cc2-a64a-77c0f6c09b89" -version = "3.3.9+0" +version = "3.4.0+1" + +[[deps.GLM]] +deps = ["Distributions", "LinearAlgebra", "Printf", "Reexport", "SparseArrays", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "StatsModels"] +git-tree-sha1 = "273bd1cd30768a2fddfa3fd63bbc746ed7249e5f" +uuid = "38e38edf-8417-5370-95a0-9cbb8c7f171a" +version = "1.9.0" [[deps.GPUArrays]] deps = ["Adapt", "GPUArraysCore", "LLVM", "LinearAlgebra", "Printf", "Random", "Reexport", "Serialization", "Statistics"] -git-tree-sha1 = "68e8ff56a4a355a85d2784b94614491f8c900cde" +git-tree-sha1 = "85d7fb51afb3def5dcb85ad31c3707795c8bccc1" uuid = "0c68f7d7-f131-5f86-a1c3-88cf8149b2d7" -version = "10.1.0" +version = "9.1.0" [[deps.GPUArraysCore]] deps = ["Adapt"] -git-tree-sha1 = "ec632f177c0d990e64d955ccc1b8c04c485a0950" +git-tree-sha1 = "2d6ca471a6c7b536127afccfa7564b5b39227fe0" uuid = "46192b85-c4d5-4398-a991-12ede77f4527" -version = "0.1.6" +version = "0.1.5" [[deps.GPUCompiler]] deps = ["ExprTools", "InteractiveUtils", "LLVM", "Libdl", "Logging", "Scratch", "TimerOutputs", "UUIDs"] -git-tree-sha1 = "1600477fba37c9fc067b9be21f5e8101f24a8865" +git-tree-sha1 = "a846f297ce9d09ccba02ead0cae70690e072a119" uuid = "61eb1bfa-7361-4325-ad38-22787b887f55" -version = "0.26.4" +version = "0.25.0" [[deps.GR]] -deps = ["Artifacts", "Base64", "DelimitedFiles", "Downloads", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Preferences", "Printf", "Random", "Serialization", "Sockets", "TOML", "Tar", "Test", "p7zip_jll"] -git-tree-sha1 = "ddda044ca260ee324c5fc07edb6d7cf3f0b9c350" +deps = ["Artifacts", "Base64", "DelimitedFiles", "Downloads", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Preferences", "Printf", "Qt6Wayland_jll", "Random", "Serialization", "Sockets", "TOML", "Tar", "Test", "p7zip_jll"] +git-tree-sha1 = "629693584cef594c3f6f99e76e7a7ad17e60e8d5" uuid = "28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71" -version = "0.73.5" +version = "0.73.7" [[deps.GR_jll]] deps = ["Artifacts", "Bzip2_jll", "Cairo_jll", "FFMPEG_jll", "Fontconfig_jll", "FreeType2_jll", "GLFW_jll", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libtiff_jll", "Pixman_jll", "Qt6Base_jll", "Zlib_jll", "libpng_jll"] -git-tree-sha1 = "278e5e0f820178e8a26df3184fcb2280717c79b1" +git-tree-sha1 = "a8863b69c2a0859f2c2c87ebdc4c6712e88bdf0d" uuid = "d2c73de3-f751-5644-a686-071e5b155ba9" -version = "0.73.5+0" +version = "0.73.7+0" [[deps.GenericSchur]] deps = ["LinearAlgebra", "Printf"] @@ -945,15 +1097,33 @@ version = "1.3.14+0" [[deps.Graphs]] deps = ["ArnoldiMethod", "Compat", "DataStructures", "Distributed", "Inflate", "LinearAlgebra", "Random", "SharedArrays", "SimpleTraits", "SparseArrays", "Statistics"] -git-tree-sha1 = "4f2b57488ac7ee16124396de4f2bbdd51b2602ad" +git-tree-sha1 = "ebd18c326fa6cee1efb7da9a3b45cf69da2ed4d9" uuid = "86223c79-3864-5bf0-83f7-82e725a168b6" -version = "1.11.0" +version = "1.11.2" [[deps.Grisu]] git-tree-sha1 = "53bb909d1151e57e2484c3d1b53e19552b887fb2" uuid = "42e2da0e-8278-4e71-bc24-59509adca0fe" version = "1.0.2" +[[deps.HDF5]] +deps = ["Compat", "HDF5_jll", "Libdl", "MPIPreferences", "Mmap", "Preferences", "Printf", "Random", "Requires", "UUIDs"] +git-tree-sha1 = "e856eef26cf5bf2b0f95f8f4fc37553c72c8641c" +uuid = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f" +version = "0.17.2" + + [deps.HDF5.extensions] + MPIExt = "MPI" + + [deps.HDF5.weakdeps] + MPI = "da04e1cc-30fd-572f-bb4f-1f8673147195" + +[[deps.HDF5_jll]] +deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LLVMOpenMP_jll", "LazyArtifacts", "LibCURL_jll", "Libdl", "MPICH_jll", "MPIPreferences", "MPItrampoline_jll", "MicrosoftMPI_jll", "OpenMPI_jll", "OpenSSL_jll", "TOML", "Zlib_jll", "libaec_jll"] +git-tree-sha1 = "38c8874692d48d5440d5752d6c74b0c6b0b60739" +uuid = "0234f1f7-429e-5d53-9886-15a909be8d59" +version = "1.14.2+1" + [[deps.HTTP]] deps = ["Base64", "CodecZlib", "ConcurrentUtilities", "Dates", "ExceptionUnwrapping", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"] git-tree-sha1 = "d1d712be3164d61d1fb98e7ce9bcbc6cc06b45ed" @@ -968,9 +1138,15 @@ version = "2.8.1+1" [[deps.HostCPUFeatures]] deps = ["BitTwiddlingConvenienceFunctions", "IfElse", "Libdl", "Static"] -git-tree-sha1 = "eb8fed28f4994600e29beef49744639d985a04b2" +git-tree-sha1 = "8e070b599339d622e9a081d17230d74a5c473293" uuid = "3e5b6fbb-0976-4d2c-9146-d79de83f2fb0" -version = "0.1.16" +version = "0.1.17" + +[[deps.Hwloc_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "5e19e1e4fa3e71b774ce746274364aef0234634e" +uuid = "e33a78d0-f292-5ffc-b300-72abe9b543c8" +version = "2.11.1+0" [[deps.HypergeometricFunctions]] deps = ["DualNumbers", "LinearAlgebra", "OpenLibm_jll", "SpecialFunctions"] @@ -990,15 +1166,28 @@ uuid = "615f187c-cbe4-4ef1-ba3b-2fcf58d6d173" version = "0.1.1" [[deps.Inflate]] -git-tree-sha1 = "ea8031dea4aff6bd41f1df8f2fdfb25b33626381" +git-tree-sha1 = "d1b1b796e47d94588b3757fe84fbf65a5ec4a80d" uuid = "d25df0c9-e2be-5dd7-82c8-3ad0b3e990b9" -version = "0.1.4" +version = "0.1.5" [[deps.InitialValues]] git-tree-sha1 = "4da0f88e9a39111c2fa3add390ab15f3a44f3ca3" uuid = "22cec73e-a1b8-11e9-2c92-598750a2cf9c" version = "0.3.1" +[[deps.InlineStrings]] +git-tree-sha1 = "45521d31238e87ee9f9732561bfee12d4eebd52d" +uuid = "842dd82b-1e85-43dc-bf29-5d0ee9dffc48" +version = "1.4.2" + + [deps.InlineStrings.extensions] + ArrowTypesExt = "ArrowTypes" + ParsersExt = "Parsers" + + [deps.InlineStrings.weakdeps] + ArrowTypes = "31f734f8-188a-4ce0-8406-c8a06bd891cd" + Parsers = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" + [[deps.InplaceOps]] deps = ["LinearAlgebra", "Test"] git-tree-sha1 = "50b41d59e7164ab6fda65e71049fee9d890731ff" @@ -1007,9 +1196,9 @@ version = "0.3.0" [[deps.IntelOpenMP_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "be50fe8df3acbffa0274a744f1a99d29c45a57f4" +git-tree-sha1 = "14eb2b542e748570b56446f4c50fbfb2306ebc45" uuid = "1d5cc7b8-4909-519e-a0f8-d0f5ad9712d0" -version = "2024.1.0+0" +version = "2024.2.0+0" [[deps.InteractiveUtils]] deps = ["Markdown"] @@ -1038,9 +1227,9 @@ weakdeps = ["Random", "RecipesBase", "Statistics"] [[deps.InverseFunctions]] deps = ["Test"] -git-tree-sha1 = "e7cbed5032c4c397a6ac23d1493f3289e01231c4" +git-tree-sha1 = "18c59411ece4838b18cd7f537e56cf5e41ce5bfd" uuid = "3587e190-3f89-42d0-90ee-14403ec27112" -version = "0.1.14" +version = "0.1.15" weakdeps = ["Dates"] [deps.InverseFunctions.extensions] @@ -1052,9 +1241,9 @@ uuid = "41ab1584-1d38-5bbf-9106-f11c6c58b48f" version = "1.3.0" [[deps.IrrationalConstants]] -git-tree-sha1 = "630b497eafcc20001bba38a4651b327dcfc491d2" +git-tree-sha1 = "7fd44fd4ff43fc60815f8e764c0f352b83c49151" uuid = "92d709cd-6900-40b7-9082-c6be49f344b6" -version = "0.2.2" +version = "0.1.1" [[deps.IterTools]] git-tree-sha1 = "42d5f897009e7ff2cf88db414a389e5ed1bdd023" @@ -1090,11 +1279,17 @@ git-tree-sha1 = "c84a835e1a09b289ffcd2271bf2a337bbdda6637" uuid = "aacddb02-875f-59d6-b918-886e6ef4fbf8" version = "3.0.3+0" +[[deps.JuliaVariables]] +deps = ["MLStyle", "NameResolution"] +git-tree-sha1 = "49fb3cb53362ddadb4415e9b73926d6b40709e70" +uuid = "b14d175d-62b4-44ba-8fb7-3064adc8c3ec" +version = "0.2.4" + [[deps.JumpProcesses]] -deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "FunctionWrappers", "Graphs", "LinearAlgebra", "Markdown", "PoissonRandom", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "StaticArrays", "SymbolicIndexingInterface", "UnPack"] -git-tree-sha1 = "ed08d89318be7d625613f3c435d1f6678fba4850" +deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "FunctionWrappers", "Graphs", "LinearAlgebra", "Markdown", "PoissonRandom", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "StaticArrays", "UnPack"] +git-tree-sha1 = "c451feb97251965a9fe40bacd62551a72cc5902c" uuid = "ccbc3e58-028d-4f4c-8cd5-9ae44345cda5" -version = "9.11.1" +version = "9.10.1" weakdeps = ["FastBroadcast"] [deps.JumpProcesses.extensions] @@ -1102,15 +1297,15 @@ weakdeps = ["FastBroadcast"] [[deps.KLU]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse_jll"] -git-tree-sha1 = "07649c499349dad9f08dde4243a4c597064663e9" +git-tree-sha1 = "884c2968c2e8e7e6bf5956af88cb46aa745c854b" uuid = "ef3ab10e-7fda-4108-b977-705223b18434" -version = "0.6.0" +version = "0.4.1" [[deps.KernelAbstractions]] deps = ["Adapt", "Atomix", "InteractiveUtils", "LinearAlgebra", "MacroTools", "PrecompileTools", "Requires", "SparseArrays", "StaticArrays", "UUIDs", "UnsafeAtomics", "UnsafeAtomicsLLVM"] -git-tree-sha1 = "db02395e4c374030c53dc28f3c1d33dec35f7272" +git-tree-sha1 = "ed7167240f40e62d97c1f5f7735dea6de3cc5c49" uuid = "63c18a36-062a-441e-b654-da1e3ab1ce7c" -version = "0.9.19" +version = "0.9.18" weakdeps = ["EnzymeCore"] [deps.KernelAbstractions.extensions] @@ -1122,6 +1317,12 @@ git-tree-sha1 = "7d703202e65efa1369de1279c162b915e245eed1" uuid = "5ab0869b-81aa-558d-bb23-cbf5423bbe9b" version = "0.6.9" +[[deps.KernelFunctions]] +deps = ["ChainRulesCore", "Compat", "CompositionsBase", "Distances", "FillArrays", "Functors", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "Random", "Requires", "SpecialFunctions", "Statistics", "StatsBase", "TensorCore", "Test", "ZygoteRules"] +git-tree-sha1 = "4a38fbd48503f2839b1d6033e0f7ffaec90dda33" +uuid = "ec8451be-7e33-11e9-00cf-bbf324bd1392" +version = "0.10.64" + [[deps.Krylov]] deps = ["LinearAlgebra", "Printf", "SparseArrays"] git-tree-sha1 = "267dad6b4b7b5d529c76d40ff48d33f7e94cb834" @@ -1186,38 +1387,42 @@ version = "1.3.1" [[deps.Latexify]] deps = ["Format", "InteractiveUtils", "LaTeXStrings", "MacroTools", "Markdown", "OrderedCollections", "Requires"] -git-tree-sha1 = "e0b5cd21dc1b44ec6e64f351976f961e6f31d6c4" +git-tree-sha1 = "ce5f5621cac23a86011836badfedf664a612cee4" uuid = "23fbe1c1-3f47-55db-b15f-69d7ec21a316" -version = "0.16.3" +version = "0.16.5" [deps.Latexify.extensions] DataFramesExt = "DataFrames" + SparseArraysExt = "SparseArrays" SymEngineExt = "SymEngine" [deps.Latexify.weakdeps] DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" + SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" SymEngine = "123dc426-2d89-5057-bbad-38513e3affd8" [[deps.LayoutPointers]] deps = ["ArrayInterface", "LinearAlgebra", "ManualMemory", "SIMDTypes", "Static", "StaticArrayInterface"] -git-tree-sha1 = "62edfee3211981241b57ff1cedf4d74d79519277" +git-tree-sha1 = "a9eaadb366f5493a5654e843864c13d8b107548c" uuid = "10f19ff3-798f-405d-979b-55457f8fc047" -version = "0.1.15" - -[[deps.LazyArrays]] -deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra", "MacroTools", "MatrixFactorizations", "SparseArrays"] -git-tree-sha1 = "35079a6a869eecace778bcda8641f9a54ca3a828" -uuid = "5078a376-72f3-5289-bfd5-ec5146d43c02" -version = "1.10.0" -weakdeps = ["StaticArrays"] - - [deps.LazyArrays.extensions] - LazyArraysStaticArraysExt = "StaticArrays" +version = "0.1.17" [[deps.LazyArtifacts]] deps = ["Artifacts", "Pkg"] uuid = "4af54fe1-eca0-43a8-85a7-787d91b784e3" +[[deps.LazyStack]] +deps = ["ChainRulesCore", "Compat", "LinearAlgebra"] +git-tree-sha1 = "aff621f1f49e9262a34aaf0d57d02ea3b35aec60" +uuid = "1fad7336-0346-5a1a-a56f-a06ba010965b" +version = "0.1.3" + +[[deps.LearnBase]] +deps = ["LinearAlgebra", "StatsBase"] +git-tree-sha1 = "47e6f4623c1db88570c7a7fa66c6528b92ba4725" +uuid = "7f8f8fb0-2700-5f03-b4bd-41f8cfc144b6" +version = "0.3.0" + [[deps.LeftChildRightSiblingTrees]] deps = ["AbstractTrees"] git-tree-sha1 = "fb6803dafae4a5d62ea5cab204b1e657d9737e7f" @@ -1313,50 +1518,41 @@ version = "2.40.1+0" [[deps.LineSearches]] deps = ["LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "Printf"] -git-tree-sha1 = "7bbea35cec17305fc70a0e5b4641477dc0789d9d" +git-tree-sha1 = "e4c3be53733db1051cc15ecf573b1042b3a712a1" uuid = "d3d80556-e9d4-5f37-9878-2ab0fcc64255" -version = "7.2.0" +version = "7.3.0" [[deps.LinearAlgebra]] deps = ["Libdl", "OpenBLAS_jll", "libblastrampoline_jll"] uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" [[deps.LinearSolve]] -deps = ["ArrayInterface", "ChainRulesCore", "ConcreteStructs", "DocStringExtensions", "EnumX", "FastLapackInterface", "GPUArraysCore", "InteractiveUtils", "KLU", "Krylov", "LazyArrays", "Libdl", "LinearAlgebra", "MKL_jll", "Markdown", "PrecompileTools", "Preferences", "RecursiveFactorization", "Reexport", "SciMLBase", "SciMLOperators", "Setfield", "SparseArrays", "Sparspak", "StaticArraysCore", "UnPack"] -git-tree-sha1 = "efd815eaa56c0ffdf86581df5aaefb7e901323a0" +deps = ["ArrayInterface", "ConcreteStructs", "DocStringExtensions", "EnumX", "EnzymeCore", "FastLapackInterface", "GPUArraysCore", "InteractiveUtils", "KLU", "Krylov", "Libdl", "LinearAlgebra", "MKL_jll", "PrecompileTools", "Preferences", "RecursiveFactorization", "Reexport", "Requires", "SciMLBase", "SciMLOperators", "Setfield", "SparseArrays", "Sparspak", "SuiteSparse", "UnPack"] +git-tree-sha1 = "9f27ba34f5821a0495efb09ea3a465c31326495a" uuid = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae" -version = "2.30.0" +version = "2.10.0" [deps.LinearSolve.extensions] - LinearSolveBandedMatricesExt = "BandedMatrices" LinearSolveBlockDiagonalsExt = "BlockDiagonals" LinearSolveCUDAExt = "CUDA" - LinearSolveCUDSSExt = "CUDSS" - LinearSolveEnzymeExt = ["Enzyme", "EnzymeCore"] - LinearSolveFastAlmostBandedMatricesExt = ["FastAlmostBandedMatrices"] + LinearSolveEnzymeExt = "Enzyme" LinearSolveHYPREExt = "HYPRE" LinearSolveIterativeSolversExt = "IterativeSolvers" LinearSolveKernelAbstractionsExt = "KernelAbstractions" LinearSolveKrylovKitExt = "KrylovKit" LinearSolveMetalExt = "Metal" LinearSolvePardisoExt = "Pardiso" - LinearSolveRecursiveArrayToolsExt = "RecursiveArrayTools" [deps.LinearSolve.weakdeps] - BandedMatrices = "aae01518-5342-5314-be14-df237901396f" BlockDiagonals = "0a1fb500-61f7-11e9-3c65-f5ef3456f9f0" CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" - CUDSS = "45b445bb-4962-46a0-9369-b4df9d0f772e" Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" - EnzymeCore = "f151be2c-9106-41f4-ab19-57ee4f262869" - FastAlmostBandedMatrices = "9d29842c-ecb8-4973-b1e9-a27b1157504e" HYPRE = "b5ffcf37-a2bd-41ab-a3da-4bd9bc8ad771" IterativeSolvers = "42fd0dbc-a981-5370-80f2-aaf504508153" KernelAbstractions = "63c18a36-062a-441e-b654-da1e3ab1ce7c" KrylovKit = "0b1a1467-8014-51b9-945f-bf0ae24f4b77" Metal = "dde4c033-4e86-420c-a63e-0dd931031962" Pardiso = "46dd5b70-b6fb-5a00-ae2d-e8fea33afaf2" - RecursiveArrayTools = "731186ca-8d62-57ce-b412-fbd966d074cd" [[deps.LogDensityProblems]] deps = ["ArgCheck", "DocStringExtensions", "Random"] @@ -1392,9 +1588,9 @@ version = "1.9.0" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "18144f3e9cbe9b15b070288eef858f71b291ce37" +git-tree-sha1 = "a2d09619db4e765091ee5c6ffe8872849de0feea" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.27" +version = "0.3.28" weakdeps = ["ChainRulesCore", "ChangesOfVariables", "InverseFunctions"] [deps.LogExpFunctions.extensions] @@ -1413,15 +1609,89 @@ version = "1.0.3" [[deps.LoopVectorization]] deps = ["ArrayInterface", "CPUSummary", "CloseOpenIntervals", "DocStringExtensions", "HostCPUFeatures", "IfElse", "LayoutPointers", "LinearAlgebra", "OffsetArrays", "PolyesterWeave", "PrecompileTools", "SIMDTypes", "SLEEFPirates", "Static", "StaticArrayInterface", "ThreadingUtilities", "UnPack", "VectorizationBase"] -git-tree-sha1 = "8f6786d8b2b3248d79db3ad359ce95382d5a6df8" +git-tree-sha1 = "8084c25a250e00ae427a379a5b607e7aed96a2dd" uuid = "bdcacae8-1622-11e9-2a5c-532679323890" -version = "0.12.170" +version = "0.12.171" weakdeps = ["ChainRulesCore", "ForwardDiff", "SpecialFunctions"] [deps.LoopVectorization.extensions] ForwardDiffExt = ["ChainRulesCore", "ForwardDiff"] SpecialFunctionsExt = "SpecialFunctions" +[[deps.Lux]] +deps = ["ADTypes", "Adapt", "ArrayInterface", "ChainRulesCore", "ConcreteStructs", "ConstructionBase", "Functors", "GPUArraysCore", "LinearAlgebra", "LuxCore", "LuxDeviceUtils", "LuxLib", "MacroTools", "Markdown", "Optimisers", "PrecompileTools", "Random", "Reexport", "Setfield", "SparseArrays", "Statistics", "TruncatedStacktraces", "WeightInitializers"] +git-tree-sha1 = "979b0437f42453b65175c6390314b2fd76eefbd4" +uuid = "b2108857-7c20-44ae-9111-449ecde12c47" +version = "0.5.16" + + [deps.Lux.extensions] + LuxChainRulesExt = "ChainRules" + LuxComponentArraysExt = "ComponentArrays" + LuxComponentArraysReverseDiffExt = ["ComponentArrays", "ReverseDiff"] + LuxFluxTransformExt = "Flux" + LuxLuxAMDGPUExt = "LuxAMDGPU" + LuxReverseDiffExt = "ReverseDiff" + LuxTrackerExt = "Tracker" + LuxZygoteExt = "Zygote" + + [deps.Lux.weakdeps] + ChainRules = "082447d4-558c-5d27-93f4-14fc19e9eca2" + ComponentArrays = "b0b7db55-cfe3-40fc-9ded-d10e2dbeff66" + FillArrays = "1a297f60-69ca-5386-bcde-b61e274b549b" + Flux = "587475ba-b771-5e3f-ad9e-33799f191a9c" + LuxAMDGPU = "83120cb1-ca15-4f04-bf3b-6967d2e6b60b" + ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" + Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" + Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" + +[[deps.LuxCore]] +deps = ["Compat", "DispatchDoctor", "Functors", "Random", "Setfield"] +git-tree-sha1 = "c3aeb50a8b894f9975e6b89c0ee67ccc6f256bb3" +uuid = "bb33d45b-7691-41d6-9220-0943567d0623" +version = "0.1.19" + +[[deps.LuxDeviceUtils]] +deps = ["Adapt", "ChainRulesCore", "Functors", "LuxCore", "Preferences", "Random", "SparseArrays"] +git-tree-sha1 = "cffc2222bf9dc01730f6fc904266f8056abb8e83" +uuid = "34f89e08-e1d5-43b4-8944-0b49ac560553" +version = "0.1.11" + + [deps.LuxDeviceUtils.extensions] + LuxDeviceUtilsFillArraysExt = "FillArrays" + LuxDeviceUtilsLuxAMDGPUExt = "LuxAMDGPU" + LuxDeviceUtilsLuxCUDAExt = "LuxCUDA" + LuxDeviceUtilsMetalExt = "Metal" + LuxDeviceUtilsZygoteExt = "Zygote" + + [deps.LuxDeviceUtils.weakdeps] + FillArrays = "1a297f60-69ca-5386-bcde-b61e274b549b" + LuxAMDGPU = "83120cb1-ca15-4f04-bf3b-6967d2e6b60b" + LuxCUDA = "d0bbae9a-e099-4d5b-a835-1c6931763bda" + Metal = "dde4c033-4e86-420c-a63e-0dd931031962" + Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" + +[[deps.LuxLib]] +deps = ["ChainRulesCore", "FastClosures", "KernelAbstractions", "LuxCore", "Markdown", "NNlib", "PrecompileTools", "Random", "Reexport", "Statistics"] +git-tree-sha1 = "b1f81a8aa8313c1f1b4cbfb18733db17c023427e" +uuid = "82251201-b29d-42c6-8e01-566dec8acb11" +version = "0.3.14" + + [deps.LuxLib.extensions] + LuxLibForwardDiffExt = "ForwardDiff" + LuxLibReverseDiffExt = "ReverseDiff" + LuxLibTrackerAMDGPUExt = ["AMDGPU", "Tracker"] + LuxLibTrackerExt = "Tracker" + LuxLibTrackercuDNNExt = ["CUDA", "Tracker", "cuDNN"] + LuxLibcuDNNExt = ["CUDA", "cuDNN"] + + [deps.LuxLib.weakdeps] + AMDGPU = "21141c5a-9bdb-4563-92ae-f87d6854732e" + CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" + ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" + ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" + Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" + cuDNN = "02a925ec-e4fe-4b08-9a7e-0d78e3d38ccd" + [[deps.MCMCChains]] deps = ["AbstractMCMC", "AxisArrays", "Dates", "Distributions", "IteratorInterfaceExtensions", "KernelDensity", "LinearAlgebra", "MCMCDiagnosticTools", "MLJModelInterface", "NaturalSort", "OrderedCollections", "PrettyTables", "Random", "RecipesBase", "Statistics", "StatsBase", "StatsFuns", "TableTraits", "Tables"] git-tree-sha1 = "d28056379864318172ff4b7958710cfddd709339" @@ -1436,15 +1706,62 @@ version = "0.3.10" [[deps.MKL_jll]] deps = ["Artifacts", "IntelOpenMP_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "oneTBB_jll"] -git-tree-sha1 = "80b2833b56d466b3858d565adcd16a4a05f2089b" +git-tree-sha1 = "f046ccd0c6db2832a9f639e2c669c6fe867e5f4f" uuid = 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"3da0fdf6-3ccc-4f1b-acd9-58baa6c99267" +version = "0.1.11" + +[[deps.MPItrampoline_jll]] +deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML"] +git-tree-sha1 = "8c35d5420193841b2f367e658540e8d9e0601ed0" +uuid = "f1f71cc9-e9ae-5b93-9b94-4fe0e1ad3748" +version = "5.4.0+0" [[deps.MacroTools]] deps = ["Markdown", "Random"] @@ -1466,17 +1783,17 @@ version = "0.4.2" deps = ["Base64"] uuid = "d6f4376e-aef5-505a-96c1-9c027394607a" -[[deps.MatrixFactorizations]] -deps = ["ArrayLayouts", "LinearAlgebra", "Printf", "Random"] -git-tree-sha1 = "6731e0574fa5ee21c02733e397beb133df90de35" -uuid = "a3b82374-2e81-5b9e-98ce-41277c0e4c87" -version = "2.2.0" +[[deps.MathOptInterface]] +deps = ["BenchmarkTools", "CodecBzip2", "CodecZlib", "DataStructures", "ForwardDiff", "JSON", "LinearAlgebra", "MutableArithmetics", "NaNMath", "OrderedCollections", "PrecompileTools", "Printf", "SparseArrays", "SpecialFunctions", "Test", "Unicode"] +git-tree-sha1 = "c0fe113e9c72aa0c9a185fd3c5ca1daa51de1486" +uuid = "b8f27783-ece8-5eb3-8dc8-9495eed66fee" +version = "1.31.1" -[[deps.MaybeInplace]] -deps = ["ArrayInterface", "LinearAlgebra", "MacroTools", "SparseArrays"] -git-tree-sha1 = "b1f2f92feb0bc201e91c155ef575bcc7d9cc3526" -uuid = "bb5d69b7-63fc-4a16-80bd-7e42200c7bdb" -version = "0.1.2" +[[deps.MathProgBase]] +deps = ["LinearAlgebra", "SparseArrays"] +git-tree-sha1 = "9abbe463a1e9fc507f12a69e7f29346c2cdc472c" +uuid = "fdba3010-5040-5b88-9595-932c9decdf73" +version = "0.7.8" [[deps.MbedTLS]] deps = ["Dates", "MbedTLS_jll", "MozillaCACerts_jll", "NetworkOptions", "Random", "Sockets"] @@ -1494,12 +1811,30 @@ git-tree-sha1 = "c13304c81eec1ed3af7fc20e75fb6b26092a1102" uuid = "442fdcdd-2543-5da2-b0f3-8c86c306513e" version = "0.3.2" +[[deps.Memoization]] +deps = ["MacroTools"] +git-tree-sha1 = "073f080e733bc6697411901224ed4fd15fefaffa" +uuid = "6fafb56a-5788-4b4e-91ca-c0cea6611c73" +version = "0.2.1" + +[[deps.MicroCanonicalHMC]] +deps = ["AbstractMCMC", "Adapt", "Distributions", "ForwardDiff", "HDF5", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "MCMCDiagnosticTools", "Markdown", "ProgressMeter", "Random", "Statistics"] +git-tree-sha1 = "99fd367f8b8fc9d479420d33e8f16f3dab3162f4" +uuid = "234d2aa0-2291-45f7-9047-6fa6f316b0a8" +version = "0.1.6" + [[deps.MicroCollections]] deps = ["Accessors", "BangBang", "InitialValues"] git-tree-sha1 = "44d32db644e84c75dab479f1bc15ee76a1a3618f" uuid = "128add7d-3638-4c79-886c-908ea0c25c34" version = "0.2.0" +[[deps.MicrosoftMPI_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "f12a29c4400ba812841c6ace3f4efbb6dbb3ba01" +uuid = "9237b28f-5490-5468-be7b-bb81f5f5e6cf" +version = "10.1.4+2" + [[deps.Missings]] deps = ["DataAPI"] git-tree-sha1 = "ec4f7fbeab05d7747bdf98eb74d130a2a2ed298d" @@ -1509,6 +1844,12 @@ version = "1.2.0" [[deps.Mmap]] uuid = "a63ad114-7e13-5084-954f-fe012c677804" +[[deps.Mocking]] +deps = ["Compat", "ExprTools"] +git-tree-sha1 = "ead0dbb33b6808578c385ffaab20d9b57053661b" +uuid = "78c3b35d-d492-501b-9361-3d52fe80e533" +version = "0.8.0" + [[deps.MozillaCACerts_jll]] uuid = "14a3606d-f60d-562e-9121-12d972cd8159" version = "2023.1.10" @@ -1519,10 +1860,16 @@ uuid = "46d2c3a1-f734-5fdb-9937-b9b9aeba4221" version = "0.2.4" [[deps.MultivariateStats]] -deps = ["Arpack", "LinearAlgebra", "SparseArrays", "Statistics", "StatsAPI", "StatsBase"] -git-tree-sha1 = "68bf5103e002c44adfd71fea6bd770b3f0586843" +deps = ["Arpack", "Distributions", "LinearAlgebra", "SparseArrays", "Statistics", "StatsAPI", "StatsBase"] +git-tree-sha1 = "816620e3aac93e5b5359e4fdaf23ca4525b00ddf" uuid = "6f286f6a-111f-5878-ab1e-185364afe411" -version = "0.10.2" +version = "0.10.3" + +[[deps.MutableArithmetics]] +deps = ["LinearAlgebra", "SparseArrays", "Test"] +git-tree-sha1 = "d0a6b1096b584a2b88efb70a92f8cb8c881eb38a" +uuid = "d8a4904e-b15c-11e9-3269-09a3773c0cb0" +version = "1.4.6" [[deps.NLSolversBase]] deps = ["DiffResults", "Distributed", "FiniteDiff", "ForwardDiff"] @@ -1530,6 +1877,18 @@ git-tree-sha1 = "a0b464d183da839699f4c79e7606d9d186ec172c" uuid = "d41bc354-129a-5804-8e4c-c37616107c6c" version = "7.8.3" +[[deps.NLopt]] +deps = ["MathOptInterface", "MathProgBase", "NLopt_jll"] +git-tree-sha1 = "5a7e32c569200a8a03c3d55d286254b0321cd262" +uuid = "76087f3c-5699-56af-9a33-bf431cd00edd" +version = "0.6.5" + +[[deps.NLopt_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "9b1f15a08f9d00cdb2761dcfa6f453f5d0d6f973" +uuid = "079eb43e-fd8e-5478-9966-2cf3e3edb778" +version = "2.7.1+0" + [[deps.NLsolve]] deps = ["Distances", "LineSearches", "LinearAlgebra", "NLSolversBase", "Printf", "Reexport"] git-tree-sha1 = "019f12e9a1a7880459d0173c182e6a99365d7ac1" @@ -1538,20 +1897,22 @@ version = "4.5.1" [[deps.NNlib]] deps = ["Adapt", "Atomix", "ChainRulesCore", "GPUArraysCore", "KernelAbstractions", "LinearAlgebra", "Pkg", "Random", "Requires", "Statistics"] -git-tree-sha1 = "e0cea7ec219ada9ac80ec2e82e374ab2f154ae05" +git-tree-sha1 = "190dcada8cf9520198058c4544862b1f88c6c577" uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" -version = "0.9.16" +version = "0.9.21" [deps.NNlib.extensions] NNlibAMDGPUExt = "AMDGPU" NNlibCUDACUDNNExt = ["CUDA", "cuDNN"] NNlibCUDAExt = "CUDA" NNlibEnzymeCoreExt = "EnzymeCore" + NNlibFFTWExt = "FFTW" [deps.NNlib.weakdeps] AMDGPU = "21141c5a-9bdb-4563-92ae-f87d6854732e" CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" EnzymeCore = "f151be2c-9106-41f4-ab19-57ee4f262869" + FFTW = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341" cuDNN = "02a925ec-e4fe-4b08-9a7e-0d78e3d38ccd" [[deps.NaNMath]] @@ -1560,11 +1921,17 @@ git-tree-sha1 = "0877504529a3e5c3343c6f8b4c0381e57e4387e4" uuid = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3" version = "1.0.2" +[[deps.NameResolution]] +deps = ["PrettyPrint"] +git-tree-sha1 = "1a0fa0e9613f46c9b8c11eee38ebb4f590013c5e" +uuid = "71a1bf82-56d0-4bbc-8a3c-48b961074391" +version = "0.1.5" + [[deps.NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] -git-tree-sha1 = "0ae91efac93c3859f5c812a24c9468bb9e50b028" +git-tree-sha1 = "58e317b3b956b8aaddfd33ff4c3e33199cd8efce" uuid = "86f7a689-2022-50b4-a561-43c23ac3c673" -version = "0.10.1" +version = "0.10.3" [[deps.NaturalSort]] git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21" @@ -1573,51 +1940,25 @@ version = "1.0.0" [[deps.NearestNeighbors]] deps = ["Distances", "StaticArrays"] -git-tree-sha1 = "ded64ff6d4fdd1cb68dfcbb818c69e144a5b2e4c" +git-tree-sha1 = "91a67b4d73842da90b526011fa85c5c4c9343fe0" uuid = "b8a86587-4115-5ab1-83bc-aa920d37bbce" -version = "0.4.16" +version = "0.4.18" [[deps.NetworkOptions]] uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908" version = "1.2.0" [[deps.NonlinearSolve]] -deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "DiffEqBase", "FastBroadcast", "FastClosures", "FiniteDiff", "ForwardDiff", "LazyArrays", "LineSearches", "LinearAlgebra", "LinearSolve", "MaybeInplace", "PrecompileTools", "Preferences", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SimpleNonlinearSolve", "SparseArrays", "SparseDiffTools", "StaticArraysCore", "SymbolicIndexingInterface", "TimerOutputs"] -git-tree-sha1 = "dc0d78eeed89323526203b8a11a4fa6cdbe25cd6" +deps = ["ArrayInterface", "DiffEqBase", "EnumX", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "LinearSolve", "PrecompileTools", "RecursiveArrayTools", "Reexport", "SciMLBase", "SimpleNonlinearSolve", "SparseArrays", "SparseDiffTools", "StaticArraysCore", "UnPack"] +git-tree-sha1 = "e10debcea868cd6e51249e8eeaf191c25f68a640" uuid = "8913a72c-1f9b-4ce2-8d82-65094dcecaec" -version = "3.11.0" - - [deps.NonlinearSolve.extensions] - NonlinearSolveBandedMatricesExt = "BandedMatrices" - NonlinearSolveFastLevenbergMarquardtExt = "FastLevenbergMarquardt" - NonlinearSolveFixedPointAccelerationExt = "FixedPointAcceleration" - NonlinearSolveLeastSquaresOptimExt = "LeastSquaresOptim" - NonlinearSolveMINPACKExt = "MINPACK" - NonlinearSolveNLSolversExt = "NLSolvers" - NonlinearSolveNLsolveExt = "NLsolve" - NonlinearSolveSIAMFANLEquationsExt = "SIAMFANLEquations" - NonlinearSolveSpeedMappingExt = "SpeedMapping" - NonlinearSolveSymbolicsExt = "Symbolics" - NonlinearSolveZygoteExt = "Zygote" - - [deps.NonlinearSolve.weakdeps] - BandedMatrices = "aae01518-5342-5314-be14-df237901396f" - FastLevenbergMarquardt = "7a0df574-e128-4d35-8cbd-3d84502bf7ce" - FixedPointAcceleration = "817d07cb-a79a-5c30-9a31-890123675176" - LeastSquaresOptim = "0fc2ff8b-aaa3-5acd-a817-1944a5e08891" - MINPACK = "4854310b-de5a-5eb6-a2a5-c1dee2bd17f9" - NLSolvers = "337daf1e-9722-11e9-073e-8b9effe078ba" - NLsolve = "2774e3e8-f4cf-5e23-947b-6d7e65073b56" - SIAMFANLEquations = "084e46ad-d928-497d-ad5e-07fa361a48c4" - SpeedMapping = "f1835b91-879b-4a3f-a438-e4baacf14412" - Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7" - Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" +version = "1.10.1" [[deps.ObjectFile]] deps = ["Reexport", "StructIO"] -git-tree-sha1 = "195e0a19842f678dd3473ceafbe9d82dfacc583c" +git-tree-sha1 = "7249afa1c4dfd86bfbcc9b28939ab6ef844f4e11" uuid = "d8793406-e978-5875-9003-1fc021f44a92" -version = "0.4.1" +version = "0.4.2" [[deps.Observables]] git-tree-sha1 = "7438a59546cf62428fc9d1bc94729146d37a7225" @@ -1625,9 +1966,9 @@ uuid = "510215fc-4207-5dde-b226-833fc4488ee2" version = "0.5.5" [[deps.OffsetArrays]] -git-tree-sha1 = "e64b4f5ea6b7389f6f046d13d4896a8f9c1ba71e" +git-tree-sha1 = "1a27764e945a152f7ca7efa04de513d473e9542e" uuid = "6fe1bfb0-de20-5000-8ca7-80f57d26f881" -version = "1.14.0" +version = "1.14.1" weakdeps = ["Adapt"] [deps.OffsetArrays.extensions] @@ -1639,16 +1980,28 @@ git-tree-sha1 = "887579a3eb005446d514ab7aeac5d1d027658b8f" uuid = "e7412a2a-1a6e-54c0-be00-318e2571c051" version = "1.3.5+1" +[[deps.OneHotArrays]] +deps = ["Adapt", "ChainRulesCore", "Compat", "GPUArraysCore", "LinearAlgebra", "NNlib"] +git-tree-sha1 = "963a3f28a2e65bb87a68033ea4a616002406037d" +uuid = "0b1bfda6-eb8a-41d2-88d8-f5af5cad476f" +version = "0.2.5" + [[deps.OpenBLAS_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"] uuid = "4536629a-c528-5b80-bd46-f80d51c5b363" -version = "0.3.23+2" +version = "0.3.23+4" [[deps.OpenLibm_jll]] deps = ["Artifacts", "Libdl"] uuid = "05823500-19ac-5b8b-9628-191a04bc5112" version = "0.8.1+2" +[[deps.OpenMPI_jll]] +deps = ["Artifacts", "CompilerSupportLibraries_jll", "Hwloc_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML", "Zlib_jll"] +git-tree-sha1 = "bfce6d523861a6c562721b262c0d1aaeead2647f" +uuid = "fe0851c0-eecd-5654-98d4-656369965a5c" +version = "5.0.5+0" + [[deps.OpenSSL]] deps = ["BitFlags", "Dates", "MozillaCACerts_jll", "OpenSSL_jll", "Sockets"] git-tree-sha1 = "38cb508d080d21dc1128f7fb04f20387ed4c0af4" @@ -1657,9 +2010,9 @@ version = "1.4.3" [[deps.OpenSSL_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "3da7367955dcc5c54c1ba4d402ccdc09a1a3e046" +git-tree-sha1 = "a028ee3cb5641cccc4c24e90c36b0a4f7707bdf5" uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95" -version = "3.0.13+1" +version = "3.0.14+0" [[deps.OpenSpecFun_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"] @@ -1672,19 +2025,56 @@ deps = ["Compat", "FillArrays", "ForwardDiff", "LineSearches", "LinearAlgebra", git-tree-sha1 = "d9b79c4eed437421ac4285148fcadf42e0700e89" uuid = "429524aa-4258-5aef-a3af-852621145aeb" version = "1.9.4" +weakdeps = ["MathOptInterface"] [deps.Optim.extensions] OptimMOIExt = "MathOptInterface" - [deps.Optim.weakdeps] - MathOptInterface = "b8f27783-ece8-5eb3-8dc8-9495eed66fee" - [[deps.Optimisers]] deps = ["ChainRulesCore", "Functors", "LinearAlgebra", "Random", "Statistics"] git-tree-sha1 = "6572fe0c5b74431aaeb0b18a4aa5ef03c84678be" uuid = "3bd65402-5787-11e9-1adc-39752487f4e2" version = "0.3.3" +[[deps.Optimization]] +deps = ["ADTypes", "ArrayInterface", "ConsoleProgressMonitor", "DocStringExtensions", "LinearAlgebra", "Logging", "LoggingExtras", "Pkg", "Printf", "ProgressLogging", "Reexport", "Requires", "SciMLBase", "SparseArrays", "TerminalLoggers"] +git-tree-sha1 = "1aa7ffea6e171167e9cae620d749e16d5874414a" +uuid = "7f7a1694-90dd-40f0-9382-eb1efda571ba" +version = "3.19.3" + + [deps.Optimization.extensions] + OptimizationEnzymeExt = "Enzyme" + OptimizationFiniteDiffExt = "FiniteDiff" + OptimizationForwardDiffExt = "ForwardDiff" + OptimizationMTKExt = "ModelingToolkit" + OptimizationReverseDiffExt = "ReverseDiff" + OptimizationSparseDiffExt = ["SparseDiffTools", "Symbolics", "ReverseDiff"] + OptimizationTrackerExt = "Tracker" + OptimizationZygoteExt = "Zygote" + + [deps.Optimization.weakdeps] + Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" + FiniteDiff = "6a86dc24-6348-571c-b903-95158fe2bd41" + ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" + ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78" + ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" + SparseDiffTools = "47a9eef4-7e08-11e9-0b38-333d64bd3804" + Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7" + Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" + Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" + +[[deps.OptimizationNLopt]] +deps = ["NLopt", "Optimization", "Reexport"] +git-tree-sha1 = "dc1b76eae7c47ae77560803587911d4d219af531" +uuid = "4e6fcdb7-1186-4e1f-a706-475e75c168bb" +version = "0.1.8" + +[[deps.OptimizationOptimJL]] +deps = ["Optim", "Optimization", "Reexport", "SparseArrays"] +git-tree-sha1 = "bea24fb320d58cb639e3cbc63f8eedde6c667bd3" +uuid = "36348300-93cb-4f02-beb5-3c3902f8871e" +version = "0.1.14" + [[deps.Opus_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] git-tree-sha1 = "51a08fb14ec28da2ec7a927c4337e4332c2a4720" @@ -1697,10 +2087,10 @@ uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" version = "1.6.3" [[deps.OrdinaryDiffEq]] -deps = ["ADTypes", "Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "ExponentialUtilities", "FastBroadcast", "FastClosures", "FillArrays", "FiniteDiff", "ForwardDiff", "FunctionWrappersWrappers", "IfElse", "InteractiveUtils", "LineSearches", "LinearAlgebra", "LinearSolve", "Logging", "MacroTools", "MuladdMacro", "NonlinearSolve", "Polyester", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SciMLStructures", "SimpleNonlinearSolve", "SimpleUnPack", "SparseArrays", "SparseDiffTools", "StaticArrayInterface", "StaticArrays", "TruncatedStacktraces"] -git-tree-sha1 = "a6ef55f6ce8a64e2d3c804d1c56fdafdd1528f86" +deps = ["ADTypes", "Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "ExponentialUtilities", "FastBroadcast", "FastClosures", "FiniteDiff", "ForwardDiff", "FunctionWrappersWrappers", "IfElse", "InteractiveUtils", "LineSearches", "LinearAlgebra", "LinearSolve", "Logging", "LoopVectorization", "MacroTools", "MuladdMacro", "NLsolve", "NonlinearSolve", "Polyester", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLNLSolve", "SciMLOperators", "SimpleNonlinearSolve", "SimpleUnPack", "SparseArrays", "SparseDiffTools", "StaticArrayInterface", "StaticArrays", "TruncatedStacktraces"] +git-tree-sha1 = "f0f43037c0ba045e96f32d65858eb825a211b817" uuid = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" -version = "6.77.1" +version = "6.58.2" [[deps.PCRE2_jll]] deps = ["Artifacts", "Libdl"] @@ -1713,12 +2103,24 @@ git-tree-sha1 = "949347156c25054de2db3b166c52ac4728cbad65" uuid = "90014a1f-27ba-587c-ab20-58faa44d9150" version = "0.11.31" +[[deps.PSIS]] +deps = ["LinearAlgebra", "LogExpFunctions", "Printf", "RecipesBase", "Statistics"] +git-tree-sha1 = "72a16ef4d76e0cb071d704ff50dc086b6715d2f9" +uuid = "ce719bf2-d5d0-4fb9-925d-10a81b42ad04" +version = "0.7.2" + [[deps.PackageExtensionCompat]] git-tree-sha1 = "fb28e33b8a95c4cee25ce296c817d89cc2e53518" uuid = "65ce6f38-6b18-4e1d-a461-8949797d7930" version = "1.0.2" weakdeps = ["Requires", "TOML"] +[[deps.Pango_jll]] +deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "FriBidi_jll", "Glib_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl"] +git-tree-sha1 = "cb5a2ab6763464ae0f19c86c56c63d4a2b0f5bda" +uuid = "36c8627f-9965-5494-a995-c6b170f724f3" +version = "1.52.2+0" + [[deps.Parameters]] deps = ["OrderedCollections", "UnPack"] git-tree-sha1 = "34c0e9ad262e5f7fc75b10a9952ca7692cfc5fbe" @@ -1731,6 +2133,18 @@ git-tree-sha1 = "8489905bcdbcfac64d1daa51ca07c0d8f0283821" uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" version = "2.8.1" +[[deps.PartialFunctions]] +deps = ["MacroTools"] +git-tree-sha1 = "47b49a4dbc23b76682205c646252c0f9e1eb75af" +uuid = "570af359-4316-4cb7-8c74-252c00c2016b" +version = "1.2.0" + +[[deps.Pathfinder]] +deps = ["Accessors", "Distributions", "Folds", "ForwardDiff", "IrrationalConstants", "LinearAlgebra", "LogDensityProblems", "Optim", "Optimization", "OptimizationOptimJL", "PDMats", "PSIS", "ProgressLogging", "Random", "Requires", "SciMLBase", "Statistics", "StatsBase", "Transducers", "UnPack"] +git-tree-sha1 = "9276ab48cb3a900e0bca214912c756d52625dadb" +uuid = "b1d3bc72-d0e7-4279-b92f-7fa5d6d2d454" +version = "0.7.0" + [[deps.Pipe]] git-tree-sha1 = "6842804e7867b115ca9de748a0cf6b364523c16d" uuid = "b98c9c47-44ae-5843-9183-064241ee97a0" @@ -1749,9 +2163,9 @@ version = "1.10.0" [[deps.PlotThemes]] deps = ["PlotUtils", "Statistics"] -git-tree-sha1 = "1f03a2d339f42dca4a4da149c7e15e9b896ad899" +git-tree-sha1 = "6e55c6841ce3411ccb3457ee52fc48cb698d6fb0" uuid = "ccf2f8ad-2431-5c83-bf29-c5338b663b6a" -version = "3.1.0" +version = "3.2.0" [[deps.PlotUtils]] deps = ["ColorSchemes", "Colors", "Dates", "PrecompileTools", "Printf", "Random", "Reexport", "Statistics"] @@ -1760,10 +2174,10 @@ uuid = "995b91a9-d308-5afd-9ec6-746e21dbc043" version = "1.4.1" [[deps.Plots]] -deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "PrecompileTools", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "UnitfulLatexify", "Unzip"] -git-tree-sha1 = "442e1e7ac27dd5ff8825c3fa62fbd1e86397974b" +deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "PrecompileTools", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "TOML", "UUIDs", "UnicodeFun", "UnitfulLatexify", "Unzip"] +git-tree-sha1 = "082f0c4b70c202c37784ce4bfbc33c9f437685bf" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.40.4" +version = "1.40.5" [deps.Plots.extensions] FileIOExt = "FileIO" @@ -1787,15 +2201,21 @@ version = "0.4.4" [[deps.Polyester]] deps = ["ArrayInterface", "BitTwiddlingConvenienceFunctions", "CPUSummary", "IfElse", "ManualMemory", "PolyesterWeave", "Requires", "Static", "StaticArrayInterface", "StrideArraysCore", "ThreadingUtilities"] -git-tree-sha1 = "b3e2bae88cf07baf0a051fe09666b8ef97aefe93" +git-tree-sha1 = "9ff799e8fb8ed6717710feee3be3bc20645daa97" uuid = "f517fe37-dbe3-4b94-8317-1923a5111588" -version = "0.7.14" +version = "0.7.15" [[deps.PolyesterWeave]] deps = ["BitTwiddlingConvenienceFunctions", "CPUSummary", "IfElse", "Static", "ThreadingUtilities"] -git-tree-sha1 = "240d7170f5ffdb285f9427b92333c3463bf65bf6" +git-tree-sha1 = "645bed98cd47f72f67316fd42fc47dee771aefcd" uuid = "1d0040c9-8b98-4ee7-8388-3f51789ca0ad" -version = "0.2.1" +version = "0.2.2" + +[[deps.PooledArrays]] +deps = ["DataAPI", "Future"] +git-tree-sha1 = "36d8b4b899628fb92c2749eb488d884a926614d3" +uuid = "2dfb63ee-cc39-5dd5-95bd-886bf059d720" +version = "1.4.3" [[deps.PositiveFactorizations]] deps = ["LinearAlgebra"] @@ -1805,9 +2225,9 @@ version = "0.2.4" [[deps.PreallocationTools]] deps = ["Adapt", "ArrayInterface", "ForwardDiff"] -git-tree-sha1 = "a660e9daab5db07adf3dedfe09b435cc530d855e" +git-tree-sha1 = "d7f3f63331c7c8c81245b4ee2815b7d496365833" uuid = "d236fae5-4411-538c-8e31-a6e3d9e00b46" -version = "0.4.21" +version = "0.4.23" weakdeps = ["ReverseDiff"] [deps.PreallocationTools.extensions] @@ -1825,16 +2245,25 @@ git-tree-sha1 = "9306f6085165d270f7e3db02af26a400d580f5c6" uuid = "21216c6a-2e73-6563-6e65-726566657250" version = "1.4.3" +[[deps.PrettyPrint]] +git-tree-sha1 = "632eb4abab3449ab30c5e1afaa874f0b98b586e4" +uuid = "8162dcfd-2161-5ef2-ae6c-7681170c5f98" +version = "0.2.0" + [[deps.PrettyTables]] deps = ["Crayons", "LaTeXStrings", "Markdown", "PrecompileTools", "Printf", "Reexport", "StringManipulation", "Tables"] -git-tree-sha1 = "88b895d13d53b5577fd53379d913b9ab9ac82660" +git-tree-sha1 = "66b20dd35966a748321d3b2537c4584cf40387c7" uuid = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d" -version = "2.3.1" +version = "2.3.2" [[deps.Printf]] deps = ["Unicode"] uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7" +[[deps.Profile]] +deps = ["Printf"] +uuid = "9abbd945-dff8-562f-b5e8-e1ebf5ef1b79" + [[deps.ProgressLogging]] deps = ["Logging", "SHA", "UUIDs"] git-tree-sha1 = "80d919dee55b9c50e8d9e2da5eeafff3fe58b539" @@ -1843,26 +2272,56 @@ version = "0.1.4" [[deps.ProgressMeter]] deps = ["Distributed", "Printf"] -git-tree-sha1 = "763a8ceb07833dd51bb9e3bbca372de32c0605ad" +git-tree-sha1 = "8f6bc219586aef8baf0ff9a5fe16ee9c70cb65e4" uuid = "92933f4c-e287-5a05-a399-4b506db050ca" -version = "1.10.0" +version = "1.10.2" [[deps.PtrArrays]] -git-tree-sha1 = "077664975d750757f30e739c870fbbdc01db7913" +git-tree-sha1 = "f011fbb92c4d401059b2212c05c0601b70f8b759" uuid = "43287f4e-b6f4-7ad1-bb20-aadabca52c3d" -version = "1.1.0" +version = "1.2.0" [[deps.Qt6Base_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Fontconfig_jll", "Glib_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "OpenSSL_jll", "Vulkan_Loader_jll", "Xorg_libSM_jll", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Xorg_libxcb_jll", "Xorg_xcb_util_cursor_jll", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_keysyms_jll", "Xorg_xcb_util_renderutil_jll", "Xorg_xcb_util_wm_jll", "Zlib_jll", "libinput_jll", "xkbcommon_jll"] -git-tree-sha1 = "37b7bb7aabf9a085e0044307e1717436117f2b3b" +git-tree-sha1 = "492601870742dcd38f233b23c3ec629628c1d724" uuid = "c0090381-4147-56d7-9ebc-da0b1113ec56" -version = "6.5.3+1" +version = "6.7.1+1" + +[[deps.Qt6Declarative_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Qt6Base_jll", "Qt6ShaderTools_jll"] +git-tree-sha1 = "e5dd466bf2569fe08c91a2cc29c1003f4797ac3b" +uuid = "629bc702-f1f5-5709-abd5-49b8460ea067" +version = "6.7.1+2" + +[[deps.Qt6ShaderTools_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Qt6Base_jll"] +git-tree-sha1 = "1a180aeced866700d4bebc3120ea1451201f16bc" +uuid = "ce943373-25bb-56aa-8eca-768745ed7b5a" +version = "6.7.1+1" + +[[deps.Qt6Wayland_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Qt6Base_jll", "Qt6Declarative_jll"] +git-tree-sha1 = "729927532d48cf79f49070341e1d918a65aba6b0" +uuid = "e99dba38-086e-5de3-a5b1-6e4c66e897c3" +version = "6.7.1+1" [[deps.QuadGK]] deps = ["DataStructures", "LinearAlgebra"] -git-tree-sha1 = "9b23c31e76e333e6fb4c1595ae6afa74966a729e" +git-tree-sha1 = "e237232771fdafbae3db5c31275303e056afaa9f" uuid = "1fd47b50-473d-5c70-9696-f719f8f3bcdc" -version = "2.9.4" +version = "2.10.1" + +[[deps.RData]] +deps = ["CategoricalArrays", "CodecZlib", "DataFrames", "Dates", "FileIO", "Requires", "TimeZones", "Unicode"] +git-tree-sha1 = "19e47a495dfb7240eb44dc6971d660f7e4244a72" +uuid = "df47a6cb-8c03-5eed-afd8-b6050d6c41da" +version = "0.8.3" + +[[deps.RDatasets]] +deps = ["CSV", "CodecZlib", "DataFrames", "FileIO", "Printf", "RData", "Reexport"] +git-tree-sha1 = "2720e6f6afb3e562ccb70a6b62f8f308ff810333" +uuid = "ce6b1742-4840-55fa-b093-852dadbb1d8b" +version = "0.7.7" [[deps.REPL]] deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"] @@ -1918,26 +2377,20 @@ uuid = "01d81517-befc-4cb6-b9ec-a95719d0359c" version = "0.6.12" [[deps.RecursiveArrayTools]] -deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "SparseArrays", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] -git-tree-sha1 = "758bc86b90e9fee2edc4af2a750b0d3f2d5c02c5" +deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "Requires", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] +git-tree-sha1 = "d7087c013e8a496ff396bae843b1e16d9a30ede8" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "3.19.0" +version = "2.38.10" [deps.RecursiveArrayTools.extensions] - RecursiveArrayToolsFastBroadcastExt = "FastBroadcast" - RecursiveArrayToolsForwardDiffExt = "ForwardDiff" RecursiveArrayToolsMeasurementsExt = "Measurements" RecursiveArrayToolsMonteCarloMeasurementsExt = "MonteCarloMeasurements" - RecursiveArrayToolsReverseDiffExt = ["ReverseDiff", "Zygote"] RecursiveArrayToolsTrackerExt = "Tracker" RecursiveArrayToolsZygoteExt = "Zygote" [deps.RecursiveArrayTools.weakdeps] - FastBroadcast = "7034ab61-46d4-4ed7-9d0f-46aef9175898" - ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" Measurements = "eff96d63-e80a-5855-80a2-b1b0885c5ab7" MonteCarloMeasurements = "0987c9cc-fe09-11e8-30f0-b96dd679fdca" - ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" @@ -1952,6 +2405,12 @@ git-tree-sha1 = "45e428421666073eab6f2da5c9d310d99bb12f9b" uuid = "189a3867-3050-52da-a836-e630ba90ab69" version = "1.2.2" +[[deps.Referenceables]] +deps = ["Adapt"] +git-tree-sha1 = "02d31ad62838181c1a3a5fd23a1ce5914a643601" +uuid = "42d2dcc6-99eb-4e98-b66c-637b7d73030e" +version = "0.1.3" + [[deps.RelocatableFolders]] deps = ["SHA", "Scratch"] git-tree-sha1 = "ffdaf70d81cf6ff22c2b6e733c900c3321cab864" @@ -1990,9 +2449,9 @@ version = "0.4.2+0" [[deps.Roots]] deps = ["Accessors", "ChainRulesCore", "CommonSolve", "Printf"] -git-tree-sha1 = "1ab580704784260ee5f45bffac810b152922747b" +git-tree-sha1 = "3484138c9fa4296a0cf46a74ca3f97b59d12b1d0" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.1.5" +version = "2.1.6" [deps.Roots.extensions] RootsForwardDiffExt = "ForwardDiff" @@ -2023,9 +2482,9 @@ version = "0.1.0" [[deps.SLEEFPirates]] deps = ["IfElse", "Static", "VectorizationBase"] -git-tree-sha1 = "3aac6d68c5e57449f5b9b865c9ba50ac2970c4cf" +git-tree-sha1 = "456f610ca2fbd1c14f5fcf31c6bfadc55e7d66e0" uuid = "476501e8-09a2-5ece-8869-fb82de89a1fa" -version = "0.6.42" +version = "0.6.43" [[deps.SSMProblems]] deps = ["AbstractMCMC"] @@ -2034,29 +2493,20 @@ uuid = "26aad666-b158-4e64-9d35-0e672562fa48" version = "0.1.1" [[deps.SciMLBase]] -deps = ["ADTypes", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "Printf", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "SciMLStructures", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] -git-tree-sha1 = "265f1a7a804d8093fa0b17e33e45373a77e56ca5" +deps = ["ADTypes", "ArrayInterface", "ChainRulesCore", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FillArrays", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces", "ZygoteRules"] +git-tree-sha1 = "916b8a94c0d61fa5f7c5295649d3746afb866aff" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "2.38.0" +version = "1.98.1" +weakdeps = ["Zygote"] [deps.SciMLBase.extensions] - SciMLBaseChainRulesCoreExt = "ChainRulesCore" - SciMLBaseMakieExt = "Makie" - SciMLBasePartialFunctionsExt = "PartialFunctions" - SciMLBasePyCallExt = "PyCall" - SciMLBasePythonCallExt = "PythonCall" - SciMLBaseRCallExt = "RCall" - SciMLBaseZygoteExt = "Zygote" - - [deps.SciMLBase.weakdeps] - ChainRules = "082447d4-558c-5d27-93f4-14fc19e9eca2" - ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" - Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a" - PartialFunctions = "570af359-4316-4cb7-8c74-252c00c2016b" - PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0" - PythonCall = "6099a3de-0909-46bc-b1f4-468b9a2dfc0d" - RCall = "6f49c342-dc21-5d91-9882-a32aef131414" - Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" + ZygoteExt = "Zygote" + +[[deps.SciMLNLSolve]] +deps = ["DiffEqBase", "LineSearches", "NLsolve", "Reexport", "SciMLBase"] +git-tree-sha1 = "765b788339abd7d983618c09cfc0192e2b6b15fd" +uuid = "e9a6253c-8580-4d32-9898-8661bb511710" +version = "0.1.9" [[deps.SciMLOperators]] deps = ["ArrayInterface", "DocStringExtensions", "LinearAlgebra", "MacroTools", "Setfield", "SparseArrays", "StaticArraysCore"] @@ -2066,14 +2516,9 @@ version = "0.3.8" [[deps.SciMLSensitivity]] deps = ["ADTypes", "Adapt", "ArrayInterface", "ChainRulesCore", "DiffEqBase", "DiffEqCallbacks", "DiffEqNoiseProcess", "Distributions", "EllipsisNotation", "Enzyme", "FiniteDiff", "ForwardDiff", "FunctionProperties", "FunctionWrappersWrappers", "Functors", "GPUArraysCore", "LinearAlgebra", "LinearSolve", "Markdown", "OrdinaryDiffEq", "Parameters", "PreallocationTools", "QuadGK", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "ReverseDiff", "SciMLBase", "SciMLOperators", "SparseDiffTools", "StaticArrays", "StaticArraysCore", "Statistics", "StochasticDiffEq", "Tracker", "TruncatedStacktraces", "Zygote"] -git-tree-sha1 = "d3a211a19c01187a2818d581fd24593bd6469255" +git-tree-sha1 = "3b0fde1944502bd736bcdc3d0df577dddb54d189" uuid = "1ed8b502-d754-442c-8d5d-10ac956f44a1" -version = "7.58.0" - -[[deps.SciMLStructures]] -git-tree-sha1 = "d778a74df2f64059c38453b34abad1953b2b8722" -uuid = "53ae85a6-f571-4167-b2af-e1d143709226" -version = "1.2.0" +version = "7.51.0" [[deps.ScientificTypesBase]] git-tree-sha1 = "a8e18eb383b5ecf1b5e6fc237eb39255044fd92b" @@ -2088,9 +2533,9 @@ version = "1.2.1" [[deps.SentinelArrays]] deps = ["Dates", "Random"] -git-tree-sha1 = "363c4e82b66be7b9f7c7c7da7478fdae07de44b9" +git-tree-sha1 = "ff11acffdb082493657550959d4feb4b6149e73a" uuid = "91c51154-3ec4-41a3-a24f-3f23e20d615c" -version = "1.4.2" +version = "1.4.5" [[deps.Serialization]] uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b" @@ -2105,6 +2550,16 @@ version = "1.1.1" deps = ["Distributed", "Mmap", "Random", "Serialization"] uuid = "1a1011a3-84de-559e-8e89-a11a2f7dc383" +[[deps.ShiftedArrays]] +git-tree-sha1 = "503688b59397b3307443af35cd953a13e8005c16" +uuid = "1277b4bf-5013-50f5-be3d-901d8477a67a" +version = "2.0.0" + +[[deps.ShowCases]] +git-tree-sha1 = "7f534ad62ab2bd48591bdeac81994ea8c445e4a5" +uuid = "605ecd9f-84a6-4c9e-81e2-4798472b76a3" +version = "0.1.0" + [[deps.Showoff]] deps = ["Dates", "Grisu"] git-tree-sha1 = "91eddf657aca81df9ae6ceb20b959ae5653ad1de" @@ -2117,26 +2572,14 @@ uuid = "777ac1f9-54b0-4bf8-805c-2214025038e7" version = "1.1.0" [[deps.SimpleNonlinearSolve]] -deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "DiffEqBase", "DiffResults", "FastClosures", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "MaybeInplace", "PrecompileTools", "Reexport", "SciMLBase", "StaticArraysCore"] -git-tree-sha1 = "c020028bb22a2f23cbd88cb92cf47cbb8c98513f" +deps = ["ArrayInterface", "DiffEqBase", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "PackageExtensionCompat", "PrecompileTools", "Reexport", "SciMLBase", "StaticArraysCore"] +git-tree-sha1 = "15ff97fa4881133caa324dacafe28b5ac47ad8a2" uuid = "727e6d20-b764-4bd8-a329-72de5adea6c7" -version = "1.8.0" +version = "0.1.23" +weakdeps = ["NNlib"] [deps.SimpleNonlinearSolve.extensions] - SimpleNonlinearSolveChainRulesCoreExt = "ChainRulesCore" - SimpleNonlinearSolvePolyesterForwardDiffExt = "PolyesterForwardDiff" - SimpleNonlinearSolveReverseDiffExt = "ReverseDiff" - SimpleNonlinearSolveStaticArraysExt = "StaticArrays" - SimpleNonlinearSolveTrackerExt = "Tracker" - SimpleNonlinearSolveZygoteExt = "Zygote" - - [deps.SimpleNonlinearSolve.weakdeps] - ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" - PolyesterForwardDiff = "98d1487c-24ca-40b6-b7ab-df2af84e126b" - ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" - StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" - Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" - Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" + SimpleNonlinearSolveNNlibExt = "NNlib" [[deps.SimpleTraits]] deps = ["InteractiveUtils", "MacroTools"] @@ -2218,10 +2661,10 @@ uuid = "aedffcd0-7271-4cad-89d0-dc628f76c6d3" version = "0.8.10" [[deps.StaticArrayInterface]] -deps = ["ArrayInterface", "Compat", "IfElse", "LinearAlgebra", "PrecompileTools", "Requires", "SparseArrays", "Static", "SuiteSparse"] -git-tree-sha1 = "5d66818a39bb04bf328e92bc933ec5b4ee88e436" +deps = ["ArrayInterface", "Compat", "IfElse", "LinearAlgebra", "PrecompileTools", "Requires", "Static"] +git-tree-sha1 = "c3668ff1a3e4ddf374fc4f8c25539ce7194dcc39" uuid = "0d7ed370-da01-4f52-bd93-41d350b8b718" -version = "1.5.0" +version = "1.6.0" weakdeps = ["OffsetArrays", "StaticArrays"] [deps.StaticArrayInterface.extensions] @@ -2230,9 +2673,9 @@ weakdeps = ["OffsetArrays", "StaticArrays"] [[deps.StaticArrays]] deps = ["LinearAlgebra", "PrecompileTools", "Random", "StaticArraysCore"] -git-tree-sha1 = "9ae599cd7529cfce7fea36cf00a62cfc56f0f37c" +git-tree-sha1 = "eeafab08ae20c62c44c8399ccb9354a04b80db50" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.9.4" +version = "1.9.7" weakdeps = ["ChainRulesCore", "Statistics"] [deps.StaticArrays.extensions] @@ -2240,15 +2683,15 @@ weakdeps = ["ChainRulesCore", "Statistics"] StaticArraysStatisticsExt = "Statistics" [[deps.StaticArraysCore]] -git-tree-sha1 = "36b3d696ce6366023a0ea192b4cd442268995a0d" +git-tree-sha1 = "192954ef1208c7019899fbf8049e717f92959682" uuid = "1e83bf80-4336-4d27-bf5d-d5a4f845583c" -version = "1.4.2" +version = "1.4.3" [[deps.StatisticalTraits]] deps = ["ScientificTypesBase"] -git-tree-sha1 = "30b9236691858e13f167ce829490a68e1a597782" +git-tree-sha1 = "542d979f6e756f13f862aa00b224f04f9e445f11" uuid = "64bff920-2084-43da-a3e6-9bb72801c0c9" -version = "3.2.0" +version = "3.4.0" [[deps.Statistics]] deps = ["LinearAlgebra", "SparseArrays"] @@ -2263,9 +2706,9 @@ version = "1.7.0" [[deps.StatsBase]] deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] -git-tree-sha1 = "5cf7606d6cef84b543b483848d4ae08ad9832b21" +git-tree-sha1 = "d1bf48bfcc554a3761a133fe3a9bb01488e06916" uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" -version = "0.34.3" +version = "0.33.21" [[deps.StatsFuns]] deps = ["HypergeometricFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] @@ -2278,6 +2721,12 @@ weakdeps = ["ChainRulesCore", "InverseFunctions"] StatsFunsChainRulesCoreExt = "ChainRulesCore" StatsFunsInverseFunctionsExt = "InverseFunctions" +[[deps.StatsModels]] +deps = ["DataAPI", "DataStructures", "LinearAlgebra", "Printf", "REPL", "ShiftedArrays", "SparseArrays", "StatsAPI", "StatsBase", "StatsFuns", "Tables"] +git-tree-sha1 = "5cf6c4583533ee38639f73b880f35fc85f2941e0" +uuid = "3eaba693-59b7-5ba5-a881-562e759f1c8d" +version = "0.7.3" + [[deps.StatsPlots]] deps = ["AbstractFFTs", "Clustering", "DataStructures", "Distributions", "Interpolations", "KernelDensity", "LinearAlgebra", "MultivariateStats", "NaNMath", "Observables", "Plots", "RecipesBase", "RecipesPipeline", "Reexport", "StatsBase", "TableOperations", "Tables", "Widgets"] git-tree-sha1 = "3b1dcbf62e469a67f6733ae493401e53d92ff543" @@ -2285,22 +2734,40 @@ uuid = "f3b207a7-027a-5e70-b257-86293d7955fd" version = "0.15.7" [[deps.SteadyStateDiffEq]] -deps = ["ConcreteStructs", "DiffEqBase", "DiffEqCallbacks", "LinearAlgebra", "Reexport", "SciMLBase"] -git-tree-sha1 = "1158cfdf0da5b0eacdfcfba7c16b174a37bdf6c7" +deps = ["DiffEqBase", "DiffEqCallbacks", "LinearAlgebra", "NLsolve", "Reexport", "SciMLBase"] +git-tree-sha1 = "2ca69f4be3294e4cd987d83d6019037d420d9fc1" uuid = "9672c7b4-1e72-59bd-8a11-6ac3964bc41f" -version = "2.2.0" +version = "1.16.1" [[deps.StochasticDiffEq]] -deps = ["Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DiffEqNoiseProcess", "DocStringExtensions", "FiniteDiff", "ForwardDiff", "JumpProcesses", "LevyArea", "LinearAlgebra", "Logging", "MuladdMacro", "NLsolve", "OrdinaryDiffEq", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SparseArrays", "SparseDiffTools", "StaticArrays", "UnPack"] -git-tree-sha1 = "97e5d0b7e5ec2e68eec6626af97c59e9f6b6c3d0" +deps = ["Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DiffEqNoiseProcess", "DocStringExtensions", "FillArrays", "FiniteDiff", "ForwardDiff", "JumpProcesses", "LevyArea", "LinearAlgebra", "Logging", "MuladdMacro", "NLsolve", "OrdinaryDiffEq", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SparseArrays", "SparseDiffTools", "StaticArrays", "UnPack"] +git-tree-sha1 = "b341540a647b39728b6d64eaeda82178e848f76e" uuid = "789caeaf-c7a9-5a7d-9973-96adeb23e2a0" -version = "6.65.1" +version = "6.62.0" [[deps.StrideArraysCore]] deps = ["ArrayInterface", "CloseOpenIntervals", "IfElse", "LayoutPointers", "LinearAlgebra", "ManualMemory", "SIMDTypes", "Static", "StaticArrayInterface", "ThreadingUtilities"] -git-tree-sha1 = "25349bf8f63aa36acbff5e3550a86e9f5b0ef682" +git-tree-sha1 = "f35f6ab602df8413a50c4a25ca14de821e8605fb" uuid = "7792a7ef-975c-4747-a70f-980b88e8d1da" -version = "0.5.6" +version = "0.5.7" + +[[deps.Strided]] +deps = ["LinearAlgebra", "StridedViews", "TupleTools"] +git-tree-sha1 = "d85461cb47420b6dcecf51de8142fc60484dd0b3" +uuid = "5e0ebb24-38b0-5f93-81fe-25c709ecae67" +version = "2.1.1" + +[[deps.StridedViews]] +deps = ["LinearAlgebra", "PackageExtensionCompat"] +git-tree-sha1 = "2917996ce0fa6b8a3a85240a5e9ff930e2aeaa43" +uuid = "4db3bf67-4bd7-4b4e-b153-31dc3fb37143" +version = "0.3.1" + + [deps.StridedViews.extensions] + StridedViewsCUDAExt = "CUDA" + + [deps.StridedViews.weakdeps] + CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" [[deps.StringManipulation]] deps = ["PrecompileTools"] @@ -2338,9 +2805,9 @@ version = "7.2.1+1" [[deps.Sundials]] deps = ["CEnum", "DataStructures", "DiffEqBase", "Libdl", "LinearAlgebra", "Logging", "PrecompileTools", "Reexport", "SciMLBase", "SparseArrays", "Sundials_jll"] -git-tree-sha1 = "e15f5a73f0d14b9079b807a9d1dac13e4302e997" +git-tree-sha1 = "71dc65a2d7decdde5500299c9b04309e0138d1b4" uuid = "c3572dad-4567-51f8-b174-8c6c989267f4" -version = "4.24.0" +version = "4.20.1" [[deps.Sundials_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "SuiteSparse_jll", "libblastrampoline_jll"] @@ -2349,16 +2816,22 @@ uuid = "fb77eaff-e24c-56d4-86b1-d163f2edb164" version = "5.2.2+0" [[deps.SymbolicIndexingInterface]] -deps = ["Accessors", "ArrayInterface", "RuntimeGeneratedFunctions", "StaticArraysCore"] -git-tree-sha1 = "b479c7a16803f08779ac5b7f9844a42621baeeda" +deps = ["DocStringExtensions"] +git-tree-sha1 = "f8ab052bfcbdb9b48fad2c80c873aa0d0344dfe5" uuid = "2efcf032-c050-4f8e-a9bb-153293bab1f5" -version = "0.3.21" +version = "0.2.2" [[deps.TOML]] deps = ["Dates"] uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76" version = "1.0.3" +[[deps.TZJData]] +deps = ["Artifacts"] +git-tree-sha1 = "1607ad46cf8d642aa779a1d45af1c8620dbf6915" +uuid = "dc5dba14-91b3-4cab-a142-028a31da12f7" +version = "1.2.0+2024a" + [[deps.TableOperations]] deps = ["SentinelArrays", "Tables", "Test"] git-tree-sha1 = "e383c87cf2a1dc41fa30c093b2a19877c83e1bc1" @@ -2372,16 +2845,22 @@ uuid = "3783bdb8-4a98-5b6b-af9a-565f29a5fe9c" version = "1.0.1" [[deps.Tables]] -deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "OrderedCollections", "TableTraits"] -git-tree-sha1 = "cb76cf677714c095e535e3501ac7954732aeea2d" +deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "OrderedCollections", "TableTraits"] +git-tree-sha1 = "598cd7c1f68d1e205689b1c2fe65a9f85846f297" uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" -version = "1.11.1" +version = "1.12.0" [[deps.Tar]] deps = ["ArgTools", "SHA"] uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e" version = "1.10.0" +[[deps.TensorCast]] +deps = ["ChainRulesCore", "Compat", "LazyStack", "LinearAlgebra", "MacroTools", "Random", "StaticArrays", "TransmuteDims"] +git-tree-sha1 = "82a477d3afe53673393dd387806e34cd682a5ac4" +uuid = "02d47bb6-7ce6-556a-be16-bb1710789e2b" +version = "0.4.8" + [[deps.TensorCore]] deps = ["LinearAlgebra"] git-tree-sha1 = "1feb45f88d133a655e001435632f019a9a1bcdb6" @@ -2398,12 +2877,28 @@ version = "0.1.7" deps = ["InteractiveUtils", "Logging", "Random", "Serialization"] uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40" +[[deps.ThreadedScans]] +deps = ["ArgCheck"] +git-tree-sha1 = "ca1ba3000289eacba571aaa4efcefb642e7a1de6" +uuid = "24d252fe-5d94-4a69-83ea-56a14333d47a" +version = "0.1.0" + [[deps.ThreadingUtilities]] deps = ["ManualMemory"] git-tree-sha1 = "eda08f7e9818eb53661b3deb74e3159460dfbc27" uuid = "8290d209-cae3-49c0-8002-c8c24d57dab5" version = "0.5.2" +[[deps.TimeZones]] +deps = ["Dates", "Downloads", "InlineStrings", "Mocking", "Printf", "Scratch", "TZJData", "Unicode", "p7zip_jll"] +git-tree-sha1 = "b92aebdd3555f3a7e3267cf17702033c2814ef48" +uuid = "f269a46b-ccf7-5d73-abea-4c690281aa53" +version = "1.18.0" +weakdeps = ["RecipesBase"] + + [deps.TimeZones.extensions] + TimeZonesRecipesBaseExt = "RecipesBase" + [[deps.TimerOutputs]] deps = ["ExprTools", "Printf"] git-tree-sha1 = "5a13ae8a41237cff5ecf34f73eb1b8f42fff6531" @@ -2421,9 +2916,9 @@ weakdeps = ["PDMats"] TrackerPDMatsExt = "PDMats" [[deps.TranscodingStreams]] -git-tree-sha1 = "5d54d076465da49d6746c647022f3b3674e64156" +git-tree-sha1 = "96612ac5365777520c3c5396314c8cf7408f436a" uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" -version = "0.10.8" +version = "0.11.1" weakdeps = ["Random", "Test"] [deps.TranscodingStreams.extensions] @@ -2449,16 +2944,22 @@ version = "0.4.82" OnlineStatsBase = "925886fa-5bf2-5e8e-b522-a9147a512338" Referenceables = "42d2dcc6-99eb-4e98-b66c-637b7d73030e" +[[deps.TransmuteDims]] +deps = ["Adapt", "ChainRulesCore", "GPUArraysCore", "LinearAlgebra", "Requires", "Strided"] +git-tree-sha1 = "5b6f1f2ba5e91983eabc47cb362f92d9a96b579f" +uuid = "24ddb15e-299a-5cc3-8414-dbddc482d9ca" +version = "0.1.16" + [[deps.TriangularSolve]] deps = ["CloseOpenIntervals", "IfElse", "LayoutPointers", "LinearAlgebra", "LoopVectorization", "Polyester", "Static", "VectorizationBase"] -git-tree-sha1 = "66c68a20907800c0b7c04ff8a6164115e8747de2" +git-tree-sha1 = "be986ad9dac14888ba338c2554dcfec6939e1393" uuid = "d5829a12-d9aa-46ab-831f-fb7c9ab06edf" -version = "0.2.0" +version = "0.2.1" [[deps.Tricks]] -git-tree-sha1 = "eae1bb484cd63b36999ee58be2de6c178105112f" +git-tree-sha1 = "7822b97e99a1672bfb1b49b668a6d46d58d8cbcb" uuid = "410a4b4d-49e4-4fbc-ab6d-cb71b17b3775" -version = "0.1.8" +version = "0.1.9" [[deps.TruncatedStacktraces]] deps = ["InteractiveUtils", "MacroTools", "Preferences"] @@ -2466,20 +2967,22 @@ git-tree-sha1 = "ea3e54c2bdde39062abf5a9758a23735558705e1" uuid = "781d530d-4396-4725-bb49-402e4bee1e77" version = "1.4.0" +[[deps.TupleTools]] +git-tree-sha1 = "41d61b1c545b06279871ef1a4b5fcb2cac2191cd" +uuid = "9d95972d-f1c8-5527-a6e0-b4b365fa01f6" +version = "1.5.0" + [[deps.Turing]] -deps = ["ADTypes", "AbstractMCMC", "Accessors", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] -git-tree-sha1 = "cfb3b446a5e52e1da4cc71b77a9350c309c581f0" +deps = ["ADTypes", "AbstractMCMC", "Accessors", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "Compat", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Optimization", "OptimizationOptimJL", "OrderedCollections", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] +git-tree-sha1 = "a11ea6fcba56924d2dd151b3ec5a6dd553a3b65c" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.32.0" +version = "0.33.3" +weakdeps = ["DynamicHMC", "Optim"] [deps.Turing.extensions] TuringDynamicHMCExt = "DynamicHMC" TuringOptimExt = "Optim" - [deps.Turing.weakdeps] - DynamicHMC = "bbc10e6e-7c05-544b-b16e-64fede858acb" - Optim = "429524aa-4258-5aef-a3af-852621145aeb" - [[deps.URIs]] git-tree-sha1 = "67db6cc7b3821e19ebe75791a9dd19c9b1188f2b" uuid = "5c2747f8-b7ea-4ff2-ba2e-563bfd36b1d4" @@ -2505,9 +3008,9 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "dd260903fdabea27d9b6021689b3cd5401a57748" +git-tree-sha1 = "d95fe458f26209c66a187b1114df96fd70839efd" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.20.0" +version = "1.21.0" weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] @@ -2516,9 +3019,9 @@ weakdeps = ["ConstructionBase", "InverseFunctions"] [[deps.UnitfulLatexify]] deps = ["LaTeXStrings", "Latexify", "Unitful"] -git-tree-sha1 = "e2d817cc500e960fdbafcf988ac8436ba3208bfd" +git-tree-sha1 = "975c354fcd5f7e1ddcc1f1a23e6e091d99e99bc8" uuid = "45397f5d-5981-4c77-b2b3-fc36d6e9b728" -version = "1.6.3" +version = "1.6.4" [[deps.UnsafeAtomics]] git-tree-sha1 = "6331ac3440856ea1988316b46045303bef658278" @@ -2527,9 +3030,9 @@ version = "0.2.1" [[deps.UnsafeAtomicsLLVM]] deps = ["LLVM", "UnsafeAtomics"] -git-tree-sha1 = "323e3d0acf5e78a56dfae7bd8928c989b4f3083e" +git-tree-sha1 = "bf2c553f25e954a9b38c9c0593a59bb13113f9e5" uuid = "d80eeb9a-aca5-4d75-85e5-170c8b632249" -version = "0.1.3" +version = "0.1.5" [[deps.Unzip]] git-tree-sha1 = "ca0969166a028236229f63514992fc073799bb78" @@ -2538,9 +3041,9 @@ version = "0.2.0" [[deps.VectorizationBase]] deps = ["ArrayInterface", "CPUSummary", "HostCPUFeatures", "IfElse", "LayoutPointers", "Libdl", "LinearAlgebra", "SIMDTypes", "Static", "StaticArrayInterface"] -git-tree-sha1 = "6129a4faf6242e7c3581116fbe3270f3ab17c90d" +git-tree-sha1 = "e7f5b81c65eb858bed630fe006837b935518aca5" uuid = "3d5dd08c-fd9d-11e8-17fa-ed2836048c2f" -version = "0.21.67" +version = "0.21.70" [[deps.VertexSafeGraphs]] deps = ["Graphs"] @@ -2566,6 +3069,24 @@ git-tree-sha1 = "93f43ab61b16ddfb2fd3bb13b3ce241cafb0e6c9" uuid = "2381bf8a-dfd0-557d-9999-79630e7b1b91" version = "1.31.0+0" +[[deps.WeakRefStrings]] +deps = ["DataAPI", "InlineStrings", "Parsers"] +git-tree-sha1 = "b1be2855ed9ed8eac54e5caff2afcdb442d52c23" +uuid = "ea10d353-3f73-51f8-a26c-33c1cb351aa5" +version = "1.4.2" + +[[deps.WeightInitializers]] +deps = ["ChainRulesCore", "LinearAlgebra", "PartialFunctions", "PrecompileTools", "Random", "SpecialFunctions", "Statistics"] +git-tree-sha1 = "f0e6760ef9d22f043710289ddf29e4a4048c4822" +uuid = "d49dbf32-c5c2-4618-8acc-27bb2598ef2d" +version = "0.1.7" + + [deps.WeightInitializers.extensions] + WeightInitializersCUDAExt = "CUDA" + + [deps.WeightInitializers.weakdeps] + CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" + [[deps.Widgets]] deps = ["Colors", "Dates", "Observables", "OrderedCollections"] git-tree-sha1 = "fcdae142c1cfc7d89de2d11e08721d0f2f86c98a" @@ -2578,17 +3099,22 @@ git-tree-sha1 = "c1a7aa6219628fcd757dede0ca95e245c5cd9511" uuid = "efce3f68-66dc-5838-9240-27a6d6f5f9b6" version = "1.0.0" +[[deps.WorkerUtilities]] +git-tree-sha1 = "cd1659ba0d57b71a464a29e64dbc67cfe83d54e7" +uuid = "76eceee3-57b5-4d4a-8e66-0e911cebbf60" +version = "1.6.1" + [[deps.XML2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"] -git-tree-sha1 = "52ff2af32e591541550bd753c0da8b9bc92bb9d9" +git-tree-sha1 = "d9717ce3518dc68a99e6b96300813760d887a01d" uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" -version = "2.12.7+0" +version = "2.13.1+0" [[deps.XSLT_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "Pkg", "XML2_jll", "Zlib_jll"] -git-tree-sha1 = "91844873c4085240b95e795f692c4cec4d805f8a" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "XML2_jll", "Zlib_jll"] +git-tree-sha1 = "a54ee957f4c86b526460a720dbc882fa5edcbefc" uuid = "aed1982a-8fda-507f-9586-7b0439959a61" -version = "1.1.34+0" +version = "1.1.41+0" [[deps.XZ_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -2676,9 +3202,9 @@ version = "0.1.1+0" [[deps.Xorg_libxcb_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "XSLT_jll", "Xorg_libXau_jll", "Xorg_libXdmcp_jll", "Xorg_libpthread_stubs_jll"] -git-tree-sha1 = "b4bfde5d5b652e22b9c790ad00af08b6d042b97d" +git-tree-sha1 = "bcd466676fef0878338c61e655629fa7bbc69d8e" uuid = "c7cfdc94-dc32-55de-ac96-5a1b8d977c5b" -version = "1.15.0+0" +version = "1.17.0+0" [[deps.Xorg_libxkbfile_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libX11_jll"] @@ -2787,6 +3313,12 @@ git-tree-sha1 = "3516a5630f741c9eecb3720b1ec9d8edc3ecc033" uuid = "1a1c6b14-54f6-533d-8383-74cd7377aa70" version = "3.1.1+0" +[[deps.libaec_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "46bf7be2917b59b761247be3f317ddf75e50e997" +uuid = "477f73a3-ac25-53e9-8cc3-50b2fa2566f0" +version = "1.1.2+0" + [[deps.libaom_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] git-tree-sha1 = "1827acba325fdcdf1d2647fc8d5301dd9ba43a9d" @@ -2804,6 +3336,12 @@ deps = ["Artifacts", "Libdl"] uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" version = "5.8.0+1" +[[deps.libdecor_jll]] +deps = ["Artifacts", "Dbus_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "Pango_jll", "Wayland_jll", "xkbcommon_jll"] +git-tree-sha1 = "9bf7903af251d2050b467f76bdbe57ce541f7f4f" +uuid = "1183f4f0-6f2a-5f1a-908b-139f9cdfea6f" +version = "0.2.2+0" + [[deps.libevdev_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] git-tree-sha1 = "141fe65dc3efabb0b1d5ba74e91f6ad26f84cc22" @@ -2830,9 +3368,9 @@ version = "1.6.43+1" [[deps.libvorbis_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Ogg_jll", "Pkg"] -git-tree-sha1 = "b910cb81ef3fe6e78bf6acee440bda86fd6ae00c" +git-tree-sha1 = "490376214c4721cdaca654041f635213c6165cb3" uuid = "f27f6e37-5d2b-51aa-960f-b287f2bc3b7a" -version = "1.3.7+1" +version = "1.3.7+2" [[deps.mtdev_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] diff --git a/Project.toml b/Project.toml new file mode 100644 index 000000000..cdfa84dd5 --- /dev/null +++ b/Project.toml @@ -0,0 +1,55 @@ +[deps] +ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b" +AbstractGPs = "99985d1d-32ba-4be9-9821-2ec096f28918" +AbstractMCMC = "80f14c24-f653-4e6a-9b94-39d6b0f70001" +AdvancedHMC = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" +AdvancedMH = "5b7e9947-ddc0-4b3f-9b55-0d8042f74170" +Bijectors = "76274a88-744f-5084-9051-94815aaf08c4" +CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b" +ComponentArrays = "b0b7db55-cfe3-40fc-9ded-d10e2dbeff66" +DataDeps = "124859b0-ceae-595e-8997-d05f6a7a8dfe" +DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" +DifferentialEquations = "0c46a032-eb83-5123-abaf-570d42b7fbaa" +Distributed = "8ba89e20-285c-5b6f-9357-94700520ee1b" +Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f" +DynamicHMC = "bbc10e6e-7c05-544b-b16e-64fede858acb" +FillArrays = "1a297f60-69ca-5386-bcde-b61e274b549b" +Flux = "587475ba-b771-5e3f-ad9e-33799f191a9c" +ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" +Functors = "d9f16b24-f501-4c13-a1f2-28368ffc5196" +GLM = "38e38edf-8417-5370-95a0-9cbb8c7f171a" +LaTeXStrings = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f" +LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" +LogDensityProblems = "6fdf6af0-433a-55f7-b3ed-c6c6e0b8df7c" +LogDensityProblemsAD = "996a588d-648d-4e1f-a8f0-a84b347e47b1" +LogExpFunctions = "2ab3a3ac-af41-5b50-aa03-7779005ae688" +Lux = "b2108857-7c20-44ae-9111-449ecde12c47" +MCMCChains = "c7f686f2-ff18-58e9-bc7b-31028e88f75d" +MLDataUtils = "cc2ba9b6-d476-5e6d-8eaf-a92d5412d41d" +MLUtils = "f1d291b0-491e-4a28-83b9-f70985020b54" +MacroTools = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" +Measures = "442fdcdd-2543-5da2-b0f3-8c86c306513e" +Memoization = "6fafb56a-5788-4b4e-91ca-c0cea6611c73" +MicroCanonicalHMC = "234d2aa0-2291-45f7-9047-6fa6f316b0a8" +NNlib = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" +Optimization = "7f7a1694-90dd-40f0-9382-eb1efda571ba" +OptimizationNLopt = "4e6fcdb7-1186-4e1f-a706-475e75c168bb" +OptimizationOptimJL = "36348300-93cb-4f02-beb5-3c3902f8871e" +PDMats = "90014a1f-27ba-587c-ab20-58faa44d9150" +Pathfinder = "b1d3bc72-d0e7-4279-b92f-7fa5d6d2d454" +Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" +RDatasets = "ce6b1742-4840-55fa-b093-852dadbb1d8b" +Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" +ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" +SciMLSensitivity = "1ed8b502-d754-442c-8d5d-10ac956f44a1" +Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" +StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" +StatsFuns = "4c63d2b9-4356-54db-8cca-17b64c39e42c" +StatsPlots = "f3b207a7-027a-5e70-b257-86293d7955fd" +Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" +Turing = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" +UnPack = "3a884ed6-31ef-47d7-9d2a-63182c4928ed" +Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" + +[compat] +Turing = "0.33" diff --git a/assets/scripts/versions.sh b/assets/scripts/versions.sh index 53c9ca1d7..1542873dd 100644 --- a/assets/scripts/versions.sh +++ b/assets/scripts/versions.sh @@ -44,7 +44,7 @@ include-in-header: # Latest Version | | | | | --- | --- | --- | -| $(remove_bugfix "$LATEST_VERSION") | [Documention](versions/${LATEST_VERSION}/) | [Changelog](changelog.qmd) | +| $(remove_bugfix "$LATEST_VERSION") | [Documentation](versions/${LATEST_VERSION}/) | [Changelog](changelog.qmd) | # Previous Versions | | | @@ -57,7 +57,7 @@ for MINOR_TAG in $MINOR_TAGS; do LATEST_BUG_FIX=$(echo "$STABLE_TAGS" | grep "^${MINOR_TAG%.*}" | sort -r | head -n 1) # Remove trailing .0 from display version DISPLAY_MINOR_TAG=$(remove_bugfix "$MINOR_TAG") - VERSIONS_CONTENT="${VERSIONS_CONTENT}| ${DISPLAY_MINOR_TAG} | [Documention](versions/${LATEST_BUG_FIX}/) | + VERSIONS_CONTENT="${VERSIONS_CONTENT}| ${DISPLAY_MINOR_TAG} | [Documentation](versions/${LATEST_BUG_FIX}/) | " fi done @@ -69,14 +69,14 @@ Documentation for archived versions is available on our deprecated documentation | | | | --- | --- | -| v0.31 | [Documention](../v0.31.4/) | -| v0.30 | [Documention](../v0.30.9/) | -| v0.29 | [Documention](../v0.29.3/) | -| v0.28 | [Documention](../v0.28.3/) | -| v0.27 | [Documention](../v0.27.0/) | -| v0.26 | [Documention](../v0.26.6/) | -| v0.25 | [Documention](../v0.25.3/) | -| v0.24 | [Documention](../v0.24.4/) | +| v0.31 | [Documentation](../v0.31.4/) | +| v0.30 | [Documentation](../v0.30.9/) | +| v0.29 | [Documentation](../v0.29.3/) | +| v0.28 | [Documentation](../v0.28.3/) | +| v0.27 | [Documentation](../v0.27.0/) | +| v0.26 | [Documentation](../v0.26.6/) | +| v0.25 | [Documentation](../v0.25.3/) | +| v0.24 | [Documentation](../v0.24.4/) | " # Write the content to the versions.qmd file diff --git a/tutorials/00-introduction/Manifest.toml b/tutorials/00-introduction/Manifest.toml deleted file mode 100755 index 5e2a4ac55..000000000 --- a/tutorials/00-introduction/Manifest.toml +++ /dev/null @@ -1,2207 +0,0 @@ -# This file is machine-generated - editing it directly is not advised - -julia_version = "1.10.0" -manifest_format = "2.0" -project_hash = "b45878f3df6dffef908d7ec87e98124988d559f6" - -[[deps.ADTypes]] -git-tree-sha1 = "daf26bbdec60d9ca1c0003b70f389d821ddb4224" -uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" -version = "1.2.1" - - [deps.ADTypes.extensions] - ADTypesChainRulesCoreExt = "ChainRulesCore" - ADTypesEnzymeCoreExt = "EnzymeCore" - - [deps.ADTypes.weakdeps] - 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"c7f686f2-ff18-58e9-bc7b-31028e88f75d" -Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" -StatsPlots = "f3b207a7-027a-5e70-b257-86293d7955fd" -Turing = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" diff --git a/tutorials/01-gaussian-mixture-model/Manifest.toml b/tutorials/01-gaussian-mixture-model/Manifest.toml deleted file mode 100755 index fcef503b8..000000000 --- a/tutorials/01-gaussian-mixture-model/Manifest.toml +++ /dev/null @@ -1,2207 +0,0 @@ -# This file is machine-generated - editing it directly is not advised - -julia_version = "1.10.3" -manifest_format = "2.0" -project_hash = "eaea37cdde9f1d06a5695c8ca16ab89aa3a9a2b4" - -[[deps.ADTypes]] -git-tree-sha1 = "daf26bbdec60d9ca1c0003b70f389d821ddb4224" -uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" -version = "1.2.1" - - [deps.ADTypes.extensions] - ADTypesChainRulesCoreExt = "ChainRulesCore" - ADTypesEnzymeCoreExt = "EnzymeCore" - - [deps.ADTypes.weakdeps] - ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" - EnzymeCore = 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-UnPack = "3a884ed6-31ef-47d7-9d2a-63182c4928ed" diff --git a/tutorials/10-bayesian-differential-equations/Project.toml b/tutorials/10-bayesian-differential-equations/Project.toml deleted file mode 100755 index 689c2b205..000000000 --- a/tutorials/10-bayesian-differential-equations/Project.toml +++ /dev/null @@ -1,8 +0,0 @@ -[deps] -DifferentialEquations = "0c46a032-eb83-5123-abaf-570d42b7fbaa" -LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" -Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" -SciMLSensitivity = "1ed8b502-d754-442c-8d5d-10ac956f44a1" -StatsPlots = "f3b207a7-027a-5e70-b257-86293d7955fd" -Turing = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" diff --git a/tutorials/11-probabilistic-pca/Manifest.toml b/tutorials/11-probabilistic-pca/Manifest.toml deleted file mode 100755 index 9db395250..000000000 --- a/tutorials/11-probabilistic-pca/Manifest.toml +++ /dev/null @@ -1,2231 +0,0 @@ -# This file is machine-generated - editing it 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"Xorg_xkeyboard_config_jll"] -git-tree-sha1 = "9c304562909ab2bab0262639bd4f444d7bc2be37" -uuid = "d8fb68d0-12a3-5cfd-a85a-d49703b185fd" -version = "1.4.1+1" diff --git a/tutorials/11-probabilistic-pca/Project.toml b/tutorials/11-probabilistic-pca/Project.toml deleted file mode 100755 index a9a44d433..000000000 --- a/tutorials/11-probabilistic-pca/Project.toml +++ /dev/null @@ -1,9 +0,0 @@ -[deps] -DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" -FillArrays = "1a297f60-69ca-5386-bcde-b61e274b549b" -LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" -Measures = "442fdcdd-2543-5da2-b0f3-8c86c306513e" -Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" -ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" -StatsPlots = "f3b207a7-027a-5e70-b257-86293d7955fd" -Turing = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" diff --git a/tutorials/12-gplvm/Manifest.toml b/tutorials/12-gplvm/Manifest.toml deleted file mode 100755 index 61130dc57..000000000 --- a/tutorials/12-gplvm/Manifest.toml +++ 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"7d0ea0f4895ef2f5cb83645fa689e52cb55cf493" -uuid = "1317d2d5-d96f-522e-a858-c73665f53c3e" -version = "2021.12.0+0" - -[[deps.p7zip_jll]] -deps = ["Artifacts", "Libdl"] -uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" -version = "17.4.0+2" - -[[deps.x264_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "4fea590b89e6ec504593146bf8b988b2c00922b2" -uuid = "1270edf5-f2f9-52d2-97e9-ab00b5d0237a" -version = "2021.5.5+0" - -[[deps.x265_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "ee567a171cce03570d77ad3a43e90218e38937a9" -uuid = "dfaa095f-4041-5dcd-9319-2fabd8486b76" -version = "3.5.0+0" - -[[deps.xkbcommon_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Wayland_jll", "Wayland_protocols_jll", "Xorg_libxcb_jll", "Xorg_xkeyboard_config_jll"] -git-tree-sha1 = "9c304562909ab2bab0262639bd4f444d7bc2be37" -uuid = "d8fb68d0-12a3-5cfd-a85a-d49703b185fd" -version = "1.4.1+1" diff --git a/tutorials/12-gplvm/Project.toml b/tutorials/12-gplvm/Project.toml deleted file mode 100755 index 56443e0e9..000000000 --- a/tutorials/12-gplvm/Project.toml +++ /dev/null @@ -1,11 +0,0 @@ -[deps] -AbstractGPs = "99985d1d-32ba-4be9-9821-2ec096f28918" -FillArrays = "1a297f60-69ca-5386-bcde-b61e274b549b" -LaTeXStrings = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f" -LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" -Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -RDatasets = "ce6b1742-4840-55fa-b093-852dadbb1d8b" -Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" -ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" -StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" -Turing = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" diff --git a/tutorials/13-seasonal-time-series/Manifest.toml b/tutorials/13-seasonal-time-series/Manifest.toml deleted file mode 100755 index a826828c1..000000000 --- a/tutorials/13-seasonal-time-series/Manifest.toml +++ /dev/null @@ -1,2207 +0,0 @@ -# This file is machine-generated - editing it directly is not 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b/tutorials/13-seasonal-time-series/Project.toml deleted file mode 100755 index 48cc4e418..000000000 --- a/tutorials/13-seasonal-time-series/Project.toml +++ /dev/null @@ -1,7 +0,0 @@ -[deps] -FillArrays = "1a297f60-69ca-5386-bcde-b61e274b549b" -LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" -Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" -Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" -StatsPlots = "f3b207a7-027a-5e70-b257-86293d7955fd" -Turing = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" diff --git a/tutorials/14-minituring/Manifest.toml b/tutorials/14-minituring/Manifest.toml deleted file mode 100755 index 075fbc090..000000000 --- a/tutorials/14-minituring/Manifest.toml +++ /dev/null @@ -1,1421 +0,0 @@ -# This file is machine-generated - editing it directly is not advised - -julia_version = "1.10.0" -manifest_format = "2.0" -project_hash = "31266805170f7b1d6aa8609e6114be070df1b249" - -[[deps.ADTypes]] -git-tree-sha1 = "daf26bbdec60d9ca1c0003b70f389d821ddb4224" -uuid = 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["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Wayland_jll", "Wayland_protocols_jll", "Xorg_libxcb_jll", "Xorg_xkeyboard_config_jll"] -git-tree-sha1 = "9c304562909ab2bab0262639bd4f444d7bc2be37" -uuid = "d8fb68d0-12a3-5cfd-a85a-d49703b185fd" -version = "1.4.1+1" diff --git a/tutorials/15-gaussian-processes/Project.toml b/tutorials/15-gaussian-processes/Project.toml deleted file mode 100755 index 61c6c8a5c..000000000 --- a/tutorials/15-gaussian-processes/Project.toml +++ /dev/null @@ -1,10 +0,0 @@ -[deps] -AbstractGPs = "99985d1d-32ba-4be9-9821-2ec096f28918" -CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b" -DataDeps = "124859b0-ceae-595e-8997-d05f6a7a8dfe" -DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" -LogExpFunctions = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" -ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" -Turing = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" diff --git a/tutorials/16-contexts/Manifest.toml b/tutorials/16-contexts/Manifest.toml deleted file mode 100755 index 075fbc090..000000000 --- a/tutorials/16-contexts/Manifest.toml +++ /dev/null @@ -1,1421 +0,0 @@ -# This file is machine-generated - editing it directly is not advised - -julia_version = "1.10.0" -manifest_format = "2.0" -project_hash = "31266805170f7b1d6aa8609e6114be070df1b249" - -[[deps.ADTypes]] -git-tree-sha1 = "daf26bbdec60d9ca1c0003b70f389d821ddb4224" -uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" -version = "1.2.1" - - [deps.ADTypes.extensions] - ADTypesChainRulesCoreExt = "ChainRulesCore" - ADTypesEnzymeCoreExt = "EnzymeCore" - - [deps.ADTypes.weakdeps] - ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" - EnzymeCore = "f151be2c-9106-41f4-ab19-57ee4f262869" - -[[deps.AbstractFFTs]] -deps = ["LinearAlgebra"] -git-tree-sha1 = "d92ad398961a3ed262d8bf04a1a2b8340f915fef" -uuid = "621f4979-c628-5d54-868e-fcf4e3e8185c" -version = "1.5.0" -weakdeps = ["ChainRulesCore", 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b/tutorials/16-contexts/Project.toml deleted file mode 100755 index 63514f5bd..000000000 --- a/tutorials/16-contexts/Project.toml +++ /dev/null @@ -1,6 +0,0 @@ -[deps] -AbstractMCMC = "80f14c24-f653-4e6a-9b94-39d6b0f70001" -Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f" -MCMCChains = "c7f686f2-ff18-58e9-bc7b-31028e88f75d" -MacroTools = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" -Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" diff --git a/tutorials/docs-00-getting-started/Manifest.toml b/tutorials/docs-00-getting-started/Manifest.toml deleted file mode 100644 index 4039e97d5..000000000 --- a/tutorials/docs-00-getting-started/Manifest.toml +++ /dev/null @@ -1,2207 +0,0 @@ -# This file is machine-generated - editing it directly is not advised - -julia_version = "1.10.3" -manifest_format = "2.0" -project_hash = "102d486b18af7951cac72d56aec7c8e37b50a316" - -[[deps.ADTypes]] -git-tree-sha1 = "daf26bbdec60d9ca1c0003b70f389d821ddb4224" -uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" 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a/tutorials/docs-12-using-turing-guide/Project.toml b/tutorials/docs-12-using-turing-guide/Project.toml deleted file mode 100755 index ac63fc48c..000000000 --- a/tutorials/docs-12-using-turing-guide/Project.toml +++ /dev/null @@ -1,5 +0,0 @@ -[deps] -Distributed = "8ba89e20-285c-5b6f-9357-94700520ee1b" -StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" -StatsPlots = "f3b207a7-027a-5e70-b257-86293d7955fd" -Turing = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" diff --git a/tutorials/docs-13-using-turing-performance-tips/Manifest.toml b/tutorials/docs-13-using-turing-performance-tips/Manifest.toml deleted file mode 100755 index 3df92c96b..000000000 --- a/tutorials/docs-13-using-turing-performance-tips/Manifest.toml +++ /dev/null @@ -1,1427 +0,0 @@ -# This file is machine-generated - editing it directly is not advised - -julia_version = "1.10.0" -manifest_format = "2.0" -project_hash = "f00de2f83fe88b91151dd081220b759ce23173e6" - -[[deps.ADTypes]] -git-tree-sha1 = 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a/tutorials/docs-13-using-turing-performance-tips/Project.toml +++ /dev/null @@ -1,5 +0,0 @@ -[deps] -FillArrays = "1a297f60-69ca-5386-bcde-b61e274b549b" -Memoization = "6fafb56a-5788-4b4e-91ca-c0cea6611c73" -Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" -Turing = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" diff --git a/tutorials/docs-14-using-turing-quick-start/Manifest.toml b/tutorials/docs-14-using-turing-quick-start/Manifest.toml deleted file mode 100755 index 75598ea94..000000000 --- a/tutorials/docs-14-using-turing-quick-start/Manifest.toml +++ /dev/null @@ -1,2207 +0,0 @@ -# This file is machine-generated - editing it directly is not advised - -julia_version = "1.10.0" -manifest_format = "2.0" -project_hash = "98395e891759166da437a82de77230ae2de18e0f" - -[[deps.ADTypes]] -git-tree-sha1 = "daf26bbdec60d9ca1c0003b70f389d821ddb4224" -uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" -version = "1.2.1" - - [deps.ADTypes.extensions] - ADTypesChainRulesCoreExt = "ChainRulesCore" - 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"9a3f8284-a2c9-5f02-9a11-845980a1fd5c" -StatsPlots = "f3b207a7-027a-5e70-b257-86293d7955fd" -Turing = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" diff --git a/tutorials/docs-15-using-turing-sampler-viz/Manifest.toml b/tutorials/docs-15-using-turing-sampler-viz/Manifest.toml deleted file mode 100755 index d0c891e56..000000000 --- a/tutorials/docs-15-using-turing-sampler-viz/Manifest.toml +++ /dev/null @@ -1,2207 +0,0 @@ -# This file is machine-generated - editing it directly is not advised - -julia_version = "1.10.0" -manifest_format = "2.0" -project_hash = "d42320247f27a85a88c7c5de8259eefe9da423db" - -[[deps.ADTypes]] -git-tree-sha1 = "daf26bbdec60d9ca1c0003b70f389d821ddb4224" -uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" -version = "1.2.1" - - [deps.ADTypes.extensions] - ADTypesChainRulesCoreExt = "ChainRulesCore" - ADTypesEnzymeCoreExt = "EnzymeCore" - - [deps.ADTypes.weakdeps] - ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" - EnzymeCore = "f151be2c-9106-41f4-ab19-57ee4f262869" 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a/tutorials/docs-16-using-turing-external-samplers/Manifest.toml b/tutorials/docs-16-using-turing-external-samplers/Manifest.toml deleted file mode 100755 index 89e3a1b98..000000000 --- a/tutorials/docs-16-using-turing-external-samplers/Manifest.toml +++ /dev/null @@ -1,1653 +0,0 @@ -# This file is machine-generated - editing it directly is not advised - -julia_version = "1.10.0" -manifest_format = "2.0" -project_hash = "6559f27b923d65d4f9f21538db968bd03760e383" - -[[deps.ADTypes]] -git-tree-sha1 = "daf26bbdec60d9ca1c0003b70f389d821ddb4224" -uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" -version = "1.2.1" - - [deps.ADTypes.extensions] - ADTypesChainRulesCoreExt = "ChainRulesCore" - ADTypesEnzymeCoreExt = "EnzymeCore" - - [deps.ADTypes.weakdeps] - ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" - EnzymeCore = "f151be2c-9106-41f4-ab19-57ee4f262869" - -[[deps.AbstractFFTs]] -deps = ["LinearAlgebra"] -git-tree-sha1 = "d92ad398961a3ed262d8bf04a1a2b8340f915fef" -uuid = 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a/tutorials/docs-16-using-turing-external-samplers/Project.toml +++ /dev/null @@ -1,8 +0,0 @@ -[deps] -AdvancedHMC = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -AdvancedMH = "5b7e9947-ddc0-4b3f-9b55-0d8042f74170" -LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" -MicroCanonicalHMC = "234d2aa0-2291-45f7-9047-6fa6f316b0a8" -Pathfinder = "b1d3bc72-d0e7-4279-b92f-7fa5d6d2d454" -Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" -Turing = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" diff --git a/tutorials/docs-17-implementing-samplers/Manifest.toml b/tutorials/docs-17-implementing-samplers/Manifest.toml deleted file mode 100644 index 896578584..000000000 --- a/tutorials/docs-17-implementing-samplers/Manifest.toml +++ /dev/null @@ -1,2213 +0,0 @@ -# This file is machine-generated - editing it directly is not advised - -julia_version = "1.10.3" -manifest_format = "2.0" -project_hash = "e7abaa44e953afb86f736a79878a3856db9f77a8" - -[[deps.ADTypes]] -git-tree-sha1 = 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"37e2e3b7-166d-5795-8a7a-e32c996b4267" -StatsPlots = "f3b207a7-027a-5e70-b257-86293d7955fd" -Turing = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" diff --git a/tutorials/docs-17-mode-estimation/Manifest.toml b/tutorials/docs-17-mode-estimation/Manifest.toml deleted file mode 100644 index c07a7f9cc..000000000 --- a/tutorials/docs-17-mode-estimation/Manifest.toml +++ /dev/null @@ -1,1559 +0,0 @@ -# This file is machine-generated - editing it directly is not advised - -julia_version = "1.10.3" -manifest_format = "2.0" -project_hash = "83d22eae75c51307701765c5fbe616f2da4efa69" - -[[deps.ADTypes]] -git-tree-sha1 = "daf26bbdec60d9ca1c0003b70f389d821ddb4224" -uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" -version = "1.2.1" - - [deps.ADTypes.extensions] - ADTypesChainRulesCoreExt = "ChainRulesCore" - ADTypesEnzymeCoreExt = "EnzymeCore" - - [deps.ADTypes.weakdeps] - ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" - EnzymeCore = "f151be2c-9106-41f4-ab19-57ee4f262869" - -[[deps.AbstractFFTs]] 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