From fed7a800267c006efe7971150d366c42e988a1e3 Mon Sep 17 00:00:00 2001 From: rob-p Date: Fri, 6 Dec 2024 17:35:38 -0500 Subject: [PATCH] update cargo dist --- .github/workflows/release.yml | 123 +++++++++++++++++++--------------- Cargo.lock | 14 ++-- Cargo.toml | 37 ++++++---- 3 files changed, 102 insertions(+), 72 deletions(-) diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index d271dfd..0e9bca8 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -1,20 +1,21 @@ -# Copyright 2022-2023, axodotdev +# This file was autogenerated by dist: https://opensource.axo.dev/cargo-dist/ +# +# Copyright 2022-2024, axodotdev # SPDX-License-Identifier: MIT or Apache-2.0 # # CI that: # # * checks for a Git Tag that looks like a release -# * builds artifacts with cargo-dist (archives, installers, hashes) +# * builds artifacts with dist (archives, installers, hashes) # * uploads those artifacts to temporary workflow zip -# * on success, uploads the artifacts to a Github Release +# * on success, uploads the artifacts to a GitHub Release # -# Note that the Github Release will be created with a generated +# Note that the GitHub Release will be created with a generated # title/body based on your changelogs. name: Release - permissions: - contents: write + "contents": "write" # This task will run whenever you push a git tag that looks like a version # like "1.0.0", "v0.1.0-prerelease.1", "my-app/0.1.0", "releases/v1.0.0", etc. @@ -23,30 +24,30 @@ permissions: # must be a Cargo-style SemVer Version (must have at least major.minor.patch). # # If PACKAGE_NAME is specified, then the announcement will be for that -# package (erroring out if it doesn't have the given version or isn't cargo-dist-able). +# package (erroring out if it doesn't have the given version or isn't dist-able). # # If PACKAGE_NAME isn't specified, then the announcement will be for all -# (cargo-dist-able) packages in the workspace with that version (this mode is +# (dist-able) packages in the workspace with that version (this mode is # intended for workspaces with only one dist-able package, or with all dist-able # packages versioned/released in lockstep). # # If you push multiple tags at once, separate instances of this workflow will -# spin up, creating an independent announcement for each one. However Github +# spin up, creating an independent announcement for each one. However, GitHub # will hard limit this to 3 tags per commit, as it will assume more tags is a # mistake. # # If there's a prerelease-style suffix to the version, then the release(s) # will be marked as a prerelease. on: + pull_request: push: tags: - '**[0-9]+.[0-9]+.[0-9]+*' - pull_request: jobs: - # Run 'cargo dist plan' (or host) to determine what tasks we need to do + # Run 'dist plan' (or host) to determine what tasks we need to do plan: - runs-on: ubuntu-latest + runs-on: "ubuntu-20.04" outputs: val: ${{ steps.plan.outputs.manifest }} tag: ${{ !github.event.pull_request && github.ref_name || '' }} @@ -58,11 +59,16 @@ jobs: - uses: actions/checkout@v4 with: submodules: recursive - - name: Install cargo-dist + - name: Install dist # we specify bash to get pipefail; it guards against the `curl` command # failing. otherwise `sh` won't catch that `curl` returned non-0 shell: bash - run: "curl --proto '=https' --tlsv1.2 -LsSf https://github.com/axodotdev/cargo-dist/releases/download/v0.11.1/cargo-dist-installer.sh | sh" + run: "curl --proto '=https' --tlsv1.2 -LsSf https://github.com/axodotdev/cargo-dist/releases/download/v0.25.1/cargo-dist-installer.sh | sh" + - name: Cache dist + uses: actions/upload-artifact@v4 + with: + name: cargo-dist-cache + path: ~/.cargo/bin/dist # sure would be cool if github gave us proper conditionals... # so here's a doubly-nested ternary-via-truthiness to try to provide the best possible # functionality based on whether this is a pull_request, and whether it's from a fork. @@ -70,8 +76,8 @@ jobs: # but also really annoying to build CI around when it needs secrets to work right.) - id: plan run: | - cargo dist ${{ (!github.event.pull_request && format('host --steps=create --tag={0}', github.ref_name)) || 'plan' }} --output-format=json > plan-dist-manifest.json - echo "cargo dist ran successfully" + dist ${{ (!github.event.pull_request && format('host --steps=create --tag={0}', github.ref_name)) || 'plan' }} --output-format=json > plan-dist-manifest.json + echo "dist ran successfully" cat plan-dist-manifest.json echo "manifest=$(jq -c "." plan-dist-manifest.json)" >> "$GITHUB_OUTPUT" - name: "Upload dist-manifest.json" @@ -89,12 +95,12 @@ jobs: if: ${{ fromJson(needs.plan.outputs.val).ci.github.artifacts_matrix.include != null && (needs.plan.outputs.publishing == 'true' || fromJson(needs.plan.outputs.val).ci.github.pr_run_mode == 'upload') }} strategy: fail-fast: false - # Target platforms/runners are computed by cargo-dist in create-release. + # Target platforms/runners are computed by dist in create-release. # Each member of the matrix has the following arguments: # # - runner: the github runner - # - dist-args: cli flags to pass to cargo dist - # - install-dist: expression to run to install cargo-dist on the runner + # - dist-args: cli flags to pass to dist + # - install-dist: expression to run to install dist on the runner # # Typically there will be: # - 1 "global" task that builds universal installers @@ -105,11 +111,13 @@ jobs: GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} BUILD_MANIFEST_NAME: target/distrib/${{ join(matrix.targets, '-') }}-dist-manifest.json steps: + - name: enable windows longpaths + run: | + git config --global core.longpaths true - uses: actions/checkout@v4 with: submodules: recursive - - uses: swatinem/rust-cache@v2 - - name: Install cargo-dist + - name: Install dist run: ${{ matrix.install_dist }} # Get the dist-manifest - name: Fetch local artifacts @@ -124,8 +132,8 @@ jobs: - name: Build artifacts run: | # Actually do builds and make zips and whatnot - cargo dist build ${{ needs.plan.outputs.tag-flag }} --print=linkage --output-format=json ${{ matrix.dist_args }} > dist-manifest.json - echo "cargo dist ran successfully" + dist build ${{ needs.plan.outputs.tag-flag }} --print=linkage --output-format=json ${{ matrix.dist_args }} > dist-manifest.json + echo "dist ran successfully" - id: cargo-dist name: Post-build # We force bash here just because github makes it really hard to get values up @@ -135,7 +143,7 @@ jobs: run: | # Parse out what we just built and upload it to scratch storage echo "paths<> "$GITHUB_OUTPUT" - jq --raw-output ".artifacts[]?.path | select( . != null )" dist-manifest.json >> "$GITHUB_OUTPUT" + jq --raw-output ".upload_files[]" dist-manifest.json >> "$GITHUB_OUTPUT" echo "EOF" >> "$GITHUB_OUTPUT" cp dist-manifest.json "$BUILD_MANIFEST_NAME" @@ -160,9 +168,12 @@ jobs: - uses: actions/checkout@v4 with: submodules: recursive - - name: Install cargo-dist - shell: bash - run: "curl --proto '=https' --tlsv1.2 -LsSf https://github.com/axodotdev/cargo-dist/releases/download/v0.11.1/cargo-dist-installer.sh | sh" + - name: Install cached dist + uses: actions/download-artifact@v4 + with: + name: cargo-dist-cache + path: ~/.cargo/bin/ + - run: chmod +x ~/.cargo/bin/dist # Get all the local artifacts for the global tasks to use (for e.g. checksums) - name: Fetch local artifacts uses: actions/download-artifact@v4 @@ -173,12 +184,12 @@ jobs: - id: cargo-dist shell: bash run: | - cargo dist build ${{ needs.plan.outputs.tag-flag }} --output-format=json "--artifacts=global" > dist-manifest.json - echo "cargo dist ran successfully" + dist build ${{ needs.plan.outputs.tag-flag }} --output-format=json "--artifacts=global" > dist-manifest.json + echo "dist ran successfully" # Parse out what we just built and upload it to scratch storage echo "paths<> "$GITHUB_OUTPUT" - jq --raw-output ".artifacts[]?.path | select( . != null )" dist-manifest.json >> "$GITHUB_OUTPUT" + jq --raw-output ".upload_files[]" dist-manifest.json >> "$GITHUB_OUTPUT" echo "EOF" >> "$GITHUB_OUTPUT" cp dist-manifest.json "$BUILD_MANIFEST_NAME" @@ -206,8 +217,12 @@ jobs: - uses: actions/checkout@v4 with: submodules: recursive - - name: Install cargo-dist - run: "curl --proto '=https' --tlsv1.2 -LsSf https://github.com/axodotdev/cargo-dist/releases/download/v0.11.1/cargo-dist-installer.sh | sh" + - name: Install cached dist + uses: actions/download-artifact@v4 + with: + name: cargo-dist-cache + path: ~/.cargo/bin/ + - run: chmod +x ~/.cargo/bin/dist # Fetch artifacts from scratch-storage - name: Fetch artifacts uses: actions/download-artifact@v4 @@ -215,11 +230,10 @@ jobs: pattern: artifacts-* path: target/distrib/ merge-multiple: true - # This is a harmless no-op for Github Releases, hosting for that happens in "announce" - id: host shell: bash run: | - cargo dist host ${{ needs.plan.outputs.tag-flag }} --steps=upload --steps=release --output-format=json > dist-manifest.json + dist host ${{ needs.plan.outputs.tag-flag }} --steps=upload --steps=release --output-format=json > dist-manifest.json echo "artifacts uploaded and released successfully" cat dist-manifest.json echo "manifest=$(jq -c "." dist-manifest.json)" >> "$GITHUB_OUTPUT" @@ -229,8 +243,29 @@ jobs: # Overwrite the previous copy name: artifacts-dist-manifest path: dist-manifest.json + # Create a GitHub Release while uploading all files to it + - name: "Download GitHub Artifacts" + uses: actions/download-artifact@v4 + with: + pattern: artifacts-* + path: artifacts + merge-multiple: true + - name: Cleanup + run: | + # Remove the granular manifests + rm -f artifacts/*-dist-manifest.json + - name: Create GitHub Release + env: + PRERELEASE_FLAG: "${{ fromJson(steps.host.outputs.manifest).announcement_is_prerelease && '--prerelease' || '' }}" + ANNOUNCEMENT_TITLE: "${{ fromJson(steps.host.outputs.manifest).announcement_title }}" + ANNOUNCEMENT_BODY: "${{ fromJson(steps.host.outputs.manifest).announcement_github_body }}" + RELEASE_COMMIT: "${{ github.sha }}" + run: | + # Write and read notes from a file to avoid quoting breaking things + echo "$ANNOUNCEMENT_BODY" > $RUNNER_TEMP/notes.txt + + gh release create "${{ needs.plan.outputs.tag }}" --target "$RELEASE_COMMIT" $PRERELEASE_FLAG --title "$ANNOUNCEMENT_TITLE" --notes-file "$RUNNER_TEMP/notes.txt" artifacts/* - # Create a Github Release while uploading all files to it announce: needs: - plan @@ -246,21 +281,3 @@ jobs: - uses: actions/checkout@v4 with: submodules: recursive - - name: "Download Github Artifacts" - uses: actions/download-artifact@v4 - with: - pattern: artifacts-* - path: artifacts - merge-multiple: true - - name: Cleanup - run: | - # Remove the granular manifests - rm -f artifacts/*-dist-manifest.json - - name: Create Github Release - uses: ncipollo/release-action@v1 - with: - tag: ${{ needs.plan.outputs.tag }} - name: ${{ fromJson(needs.host.outputs.val).announcement_title }} - body: ${{ fromJson(needs.host.outputs.val).announcement_github_body }} - prerelease: ${{ fromJson(needs.host.outputs.val).announcement_is_prerelease }} - artifacts: "artifacts/*" diff --git a/Cargo.lock b/Cargo.lock index 84cf4c0..72edcfa 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -32,7 +32,7 @@ dependencies = [ [[package]] name = "alevin-fry" -version = "0.10.0" +version = "0.11.0" dependencies = [ "ahash", "anyhow", @@ -323,9 +323,9 @@ dependencies = [ [[package]] name = "clap" -version = "4.5.21" +version = "4.5.23" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "fb3b4b9e5a7c7514dfa52869339ee98b3156b0bfb4e8a77c4ff4babb64b1604f" +checksum = "3135e7ec2ef7b10c6ed8950f0f792ed96ee093fa088608f1c76e569722700c84" dependencies = [ "clap_builder", "clap_derive", @@ -333,9 +333,9 @@ dependencies = [ [[package]] name = "clap_builder" -version = "4.5.21" +version = "4.5.23" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "b17a95aa67cc7b5ebd32aa5370189aa0d79069ef1c64ce893bd30fb24bff20ec" +checksum = "30582fc632330df2bd26877bde0c1f4470d57c582bbc070376afcd04d8cb4838" dependencies = [ "anstream", "anstyle", @@ -358,9 +358,9 @@ dependencies = [ [[package]] name = "clap_lex" -version = "0.7.3" +version = "0.7.4" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "afb84c814227b90d6895e01398aee0d8033c00e7466aca416fb6a8e0eb19d8a7" +checksum = "f46ad14479a25103f283c0f10005961cf086d8dc42205bb44c46ac563475dca6" [[package]] name = "colorchoice" diff --git a/Cargo.toml b/Cargo.toml index 80b2d0e..0319f12 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -1,13 +1,13 @@ [package] -name = "alevin-fry" -version = "0.10.0" authors = [ - "Avi Srivastava ", - "Hirak Sarkar ", - "Dongze He ", - "Mohsen Zakeri ", + "Avi Srivastava ", + "Hirak Sarkar ", + "Dongze He .zakeri@gmail.com>", + "Noor Pratap Singh ", "Rob Patro ", ] +name = "alevin-fry" +version = "0.11.0" edition = "2021" description = "A suite of tools for the rapid, accurate and memory-frugal processing single-cell and single-nucleus sequencing data." license-file = "LICENSE" @@ -27,6 +27,7 @@ keywords = [ "single-cell", "preprocessing", "RNA-seq", + "ATAC-seq", "single-nucleus", "RNA-velocity", ] @@ -71,7 +72,15 @@ sce = { git = "https://github.com/parazodiac/SingleCellExperiment", branch = "de # no shenanigans; clap makes breaking "fixes" too often to allow variability # in the version different from what we tested with -clap = { version = "4.5.9", features = ["derive", "wrap_help", "cargo", "help", "usage", "string", "error-context"] } +clap = { version = "4.5.23", features = [ + "derive", + "wrap_help", + "cargo", + "help", + "usage", + "string", + "error-context", +] } noodles = { version = "0.85.0", features = ["bam", "bgzf", "sam"] } dashmap = { version = "6.1.0", features = ["serde", "inline"] } @@ -88,18 +97,22 @@ opt-level = 3 inherits = "release" lto = "thin" -# Config for 'cargo dist' +# Config for 'dist' [workspace.metadata.dist] -# The preferred cargo-dist version to use in CI (Cargo.toml SemVer syntax) -cargo-dist-version = "0.11.1" +# The preferred dist version to use in CI (Cargo.toml SemVer syntax) +cargo-dist-version = "0.25.1" # CI backends to support -ci = ["github"] +ci = "github" # The installers to generate for each app installers = ["shell"] # Target platforms to build apps for (Rust target-triple syntax) targets = ["aarch64-apple-darwin", "x86_64-apple-darwin", "x86_64-unknown-linux-gnu"] -# Publish jobs to run in CI +# Which actions to run on pull requests pr-run-mode = "plan" +# Path that installers should place binaries in +install-path = "CARGO_HOME" +# Whether to install an updater program +install-updater = true [workspace.metadata.dist.github-custom-runners] aarch64-apple-darwin = "macos-14"