Merge pull request #186 from COMBINE-lab/refactor

Refactor

Author: rob-p

.github/workflows/release.yml

@@ -1,12 +1,12 @@
-# This file was autogenerated by cargo-dist: https://opensource.axo.dev/cargo-dist/
+# This file was autogenerated by dist: https://axodotdev.github.io/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
 #
@@ -24,10 +24,10 @@ 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).
 #
@@ -45,9 +45,9 @@ on:
       - '**[0-9]+.[0-9]+.[0-9]+*'
 
 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-20.04"
+    runs-on: "ubuntu-22.04"
     outputs:
       val: ${{ steps.plan.outputs.manifest }}
       tag: ${{ !github.event.pull_request && github.ref_name || '' }}
@@ -56,32 +56,33 @@ jobs:
     env:
       GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
         with:
+          persist-credentials: false
           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/v0.21.1/cargo-dist-installer.sh | sh"
-      - name: Cache cargo-dist
-        uses: actions/upload-artifact@v4
+        run: "curl --proto '=https' --tlsv1.2 -LsSf https://github.com/axodotdev/cargo-dist/releases/download/v0.31.0/cargo-dist-installer.sh | sh"
+      - name: Cache dist
+        uses: actions/upload-artifact@v6
         with:
           name: cargo-dist-cache
-          path: ~/.cargo/bin/cargo-dist
+          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.
       # (PRs run on the *source* but secrets are usually on the *target* -- that's *good*
       # 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"
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v6
         with:
           name: artifacts-plan-dist-manifest
           path: plan-dist-manifest.json
@@ -95,33 +96,42 @@ 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
       # - N "local" tasks that build each platform's binaries and platform-specific installers
       matrix: ${{ fromJson(needs.plan.outputs.val).ci.github.artifacts_matrix }}
     runs-on: ${{ matrix.runner }}
+    container: ${{ matrix.container && matrix.container.image || null }}
     env:
       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
+      - uses: actions/checkout@v6
         with:
+          persist-credentials: false
           submodules: recursive
-      - name: Install cargo-dist
-        run: ${{ matrix.install_dist }}
+      - name: Install Rust non-interactively if not already installed
+        if: ${{ matrix.container }}
+        run: |
+          if ! command -v cargo > /dev/null 2>&1; then
+            curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y
+            echo "$HOME/.cargo/bin" >> $GITHUB_PATH
+          fi
+      - name: Install dist
+        run: ${{ matrix.install_dist.run }}
       # Get the dist-manifest
       - name: Fetch local artifacts
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v7
         with:
           pattern: artifacts-*
           path: target/distrib/
@@ -132,8 +142,8 @@ 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 ${{ matrix.dist_args }} > dist-manifest.json
+          echo "dist ran successfully"
       - id: cargo-dist
         name: Post-build
         # We force bash here just because github makes it really hard to get values up
@@ -143,12 +153,12 @@ jobs:
         run: |
           # Parse out what we just built and upload it to scratch storage
           echo "paths<<EOF" >> "$GITHUB_OUTPUT"
-          jq --raw-output ".upload_files[]" dist-manifest.json >> "$GITHUB_OUTPUT"
+          dist print-upload-files-from-manifest --manifest dist-manifest.json >> "$GITHUB_OUTPUT"
           echo "EOF" >> "$GITHUB_OUTPUT"
 
           cp dist-manifest.json "$BUILD_MANIFEST_NAME"
       - name: "Upload artifacts"
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v6
         with:
           name: artifacts-build-local-${{ join(matrix.targets, '_') }}
           path: |
@@ -160,32 +170,33 @@ jobs:
     needs:
       - plan
       - build-local-artifacts
-    runs-on: "ubuntu-20.04"
+    runs-on: "ubuntu-22.04"
     env:
       GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
       BUILD_MANIFEST_NAME: target/distrib/global-dist-manifest.json
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
         with:
+          persist-credentials: false
           submodules: recursive
-      - name: Install cached cargo-dist
-        uses: actions/download-artifact@v4
+      - name: Install cached dist
+        uses: actions/download-artifact@v7
         with:
           name: cargo-dist-cache
           path: ~/.cargo/bin/
-      - run: chmod +x ~/.cargo/bin/cargo-dist
+      - 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
+        uses: actions/download-artifact@v7
         with:
           pattern: artifacts-*
           path: target/distrib/
           merge-multiple: true
       - 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<<EOF" >> "$GITHUB_OUTPUT"
@@ -194,7 +205,7 @@ jobs:
 
           cp dist-manifest.json "$BUILD_MANIFEST_NAME"
       - name: "Upload artifacts"
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v6
         with:
           name: artifacts-build-global
           path: |
@@ -206,46 +217,47 @@ jobs:
       - plan
       - build-local-artifacts
       - build-global-artifacts
-    # Only run if we're "publishing", and only if local and global didn't fail (skipped is fine)
-    if: ${{ always() && needs.plan.outputs.publishing == 'true' && (needs.build-global-artifacts.result == 'skipped' || needs.build-global-artifacts.result == 'success') && (needs.build-local-artifacts.result == 'skipped' || needs.build-local-artifacts.result == 'success') }}
+    # Only run if we're "publishing", and only if plan, local and global didn't fail (skipped is fine)
+    if: ${{ always() && needs.plan.result == 'success' && needs.plan.outputs.publishing == 'true' && (needs.build-global-artifacts.result == 'skipped' || needs.build-global-artifacts.result == 'success') && (needs.build-local-artifacts.result == 'skipped' || needs.build-local-artifacts.result == 'success') }}
     env:
       GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-    runs-on: "ubuntu-20.04"
+    runs-on: "ubuntu-22.04"
     outputs:
       val: ${{ steps.host.outputs.manifest }}
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
         with:
+          persist-credentials: false
           submodules: recursive
-      - name: Install cached cargo-dist
-        uses: actions/download-artifact@v4
+      - name: Install cached dist
+        uses: actions/download-artifact@v7
         with:
           name: cargo-dist-cache
           path: ~/.cargo/bin/
-      - run: chmod +x ~/.cargo/bin/cargo-dist
+      - run: chmod +x ~/.cargo/bin/dist
       # Fetch artifacts from scratch-storage
       - name: Fetch artifacts
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v7
         with:
           pattern: artifacts-*
           path: target/distrib/
           merge-multiple: true
       - 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"
       - name: "Upload dist-manifest.json"
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v6
         with:
           # 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
+        uses: actions/download-artifact@v7
         with:
           pattern: artifacts-*
           path: artifacts
@@ -274,10 +286,11 @@ jobs:
     # still allowing individual publish jobs to skip themselves (for prereleases).
     # "host" however must run to completion, no skipping allowed!
     if: ${{ always() && needs.host.result == 'success' }}
-    runs-on: "ubuntu-20.04"
+    runs-on: "ubuntu-22.04"
     env:
       GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
         with:
+          persist-credentials: false
           submodules: recursive

.gitignore

@@ -22,3 +22,6 @@ TEST_REF
 TEST_REF_CLAPV4
 TEST_REF_ROERS
 blarg
+
+# macOS Finder metadata
+**/.DS_Store

Cargo.lock

@@ -1,7 +1,7 @@
 [package]
 name = "simpleaf"
 version = "0.19.5"
-edition = "2021"
+edition = "2024"
 authors = [
   "Rob Patro <rob@cs.umd.edu>",
   "Dongze He <dhe17@umd.edu>",
@@ -15,6 +15,7 @@ homepage = "https://simpleaf.readthedocs.io"
 #documentation = "https://fry.readthedocs.io/en/latest/"
 include = [
   "/src/*.rs",
+  "/src/core/*.rs",
   "/src/utils/*.rs",
   "/src/utils/af_utils/*.rs",
   "/src/atac/*.rs",
@@ -85,6 +86,7 @@ regex = { version = "1.11.1", default-features = false, features = [
 tempfile = "3.19.1"
 ureq = { version = "3.0.11", features = ["json"] }
 af-anndata = { version = "0.3.3", git = "https://github.com/COMBINE-lab/af-anndata" }
+file-requirements = "0.1.0"
 
 [profile.release]
 lto = "thin"
@@ -94,27 +96,3 @@ opt-level = 3
 [profile.dist]
 inherits = "release"
 lto = "thin"
-
-# Config for 'cargo dist'
-[workspace.metadata.dist]
-# The preferred cargo-dist version to use in CI (Cargo.toml SemVer syntax)
-cargo-dist-version = "0.21.1"
-# CI backends to support
-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",
-]
-# Which actions to run on pull requests
-pr-run-mode = "plan"
-# Whether to install an updater program
-install-updater = true
-# Path that installers should place binaries in
-install-path = "CARGO_HOME"
-
-[workspace.metadata.dist.github-custom-runners]
-aarch64-apple-darwin = "macos-14"

Cargo.toml

@@ -0,0 +1,22 @@
+[workspace]
+members = ["cargo:."]
+
+# Config for 'dist'
+[dist]
+# The preferred dist version to use in CI (Cargo.toml SemVer syntax)
+cargo-dist-version = "0.31.0"
+# CI backends to support
+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", "aarch64-unknown-linux-gnu", "x86_64-apple-darwin", "x86_64-unknown-linux-gnu"]
+# Which actions to run on pull requests
+pr-run-mode = "plan"
+# Whether to install an updater program
+install-updater = true
+# Path that installers should place binaries in
+install-path = "CARGO_HOME"
+
+[dist.github-custom-runners]
+aarch64-apple-darwin = "macos-14"