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Merge branch 'latest' of https://github.com/sourmash-bio/sourmash int…
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…o fix_multigather_output
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ctb committed Oct 19, 2023
2 parents 3d0467e + 246e3cd commit 5905e18
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Showing 53 changed files with 2,519 additions and 2,381 deletions.
2 changes: 1 addition & 1 deletion .github/workflows/asv.yml
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Expand Up @@ -13,7 +13,7 @@ jobs:
runs-on: ubuntu-latest

steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4
with:
fetch-depth: 0

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6 changes: 3 additions & 3 deletions .github/workflows/build_wheel.yml
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Expand Up @@ -35,7 +35,7 @@ jobs:
fail-fast: false

steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4
with:
fetch-depth: 0

Expand All @@ -45,7 +45,7 @@ jobs:
python-version: '3.9'

- name: Build wheels
uses: pypa/cibuildwheel@v2.15.0
uses: pypa/cibuildwheel@v2.16.2
env:
CIBW_ENVIRONMENT_MACOS: ${{ matrix.macos_target }}
CIBW_ARCHS_LINUX: ${{ matrix.arch }}
Expand All @@ -60,7 +60,7 @@ jobs:
env:
PYODIDE_VERSION: "0.23.0"
steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4
- uses: actions/setup-python@v4
with:
python-version: "3.11.2"
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6 changes: 3 additions & 3 deletions .github/workflows/build_wheel_all_archs.yml
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Expand Up @@ -35,7 +35,7 @@ jobs:
fail-fast: false

steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4
with:
fetch-depth: 0

Expand All @@ -61,12 +61,12 @@ jobs:
- name: Set up QEMU
if: runner.os == 'Linux'
uses: docker/setup-qemu-action@v2
uses: docker/setup-qemu-action@v3
with:
platforms: all

- name: Build wheels
uses: pypa/cibuildwheel@v2.15.0
uses: pypa/cibuildwheel@v2.16.2
env:
CIBW_ENVIRONMENT_MACOS: ${{ matrix.macos_target }}
CIBW_ARCHS_LINUX: ${{ matrix.arch }}
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6 changes: 3 additions & 3 deletions .github/workflows/dev_envs.yml
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Expand Up @@ -7,11 +7,11 @@ jobs:
nix:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4
with:
fetch-depth: 0

- uses: cachix/install-nix-action@v22
- uses: cachix/install-nix-action@v23
with:
extra_nix_config: |
access-tokens = github.com=${{ secrets.GITHUB_TOKEN }}
Expand All @@ -28,7 +28,7 @@ jobs:
mamba:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4
with:
fetch-depth: 0

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4 changes: 2 additions & 2 deletions .github/workflows/draft-pdf.yml
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Expand Up @@ -6,15 +6,15 @@ jobs:
name: Paper Draft
steps:
- name: Checkout
uses: actions/checkout@v2
uses: actions/checkout@v4
- name: Build draft PDF
uses: openjournals/openjournals-draft-action@master
with:
journal: joss
# This should be the path to the paper within your repo.
paper-path: paper.md
- name: Upload
uses: actions/upload-artifact@v1
uses: actions/upload-artifact@v3
with:
name: paper
# This is the output path where Pandoc will write the compiled
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2 changes: 1 addition & 1 deletion .github/workflows/hypothesis.yml
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Expand Up @@ -11,7 +11,7 @@ jobs:
test:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4
with:
fetch-depth: 0

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2 changes: 1 addition & 1 deletion .github/workflows/metadata.yml
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Expand Up @@ -12,7 +12,7 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Checkout sources
uses: actions/checkout@v3
uses: actions/checkout@v4

- name: Trigger new archival in software heritage on new tags
if: startsWith(github.ref, 'refs/tags/')
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4 changes: 2 additions & 2 deletions .github/workflows/python.yml
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Expand Up @@ -18,7 +18,7 @@ jobs:
fail-fast: false

steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4
with:
fetch-depth: 0

Expand Down Expand Up @@ -57,7 +57,7 @@ jobs:

- name: Start Redis
if: startsWith(runner.os, 'Linux') && (matrix.py == '3.9')
uses: supercharge/redis-github-action@1.6.0
uses: supercharge/redis-github-action@1.7.0
with:
redis-version: 6

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27 changes: 11 additions & 16 deletions .github/workflows/rust.yml
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Expand Up @@ -4,11 +4,6 @@ on:
push:
branches: [latest]
pull_request:
paths:
- 'Cargo.lock'
- 'src/core/**'
- 'tests/test-data/**'
- '.github/workflows/rust.yml'
schedule:
- cron: "0 0 * * *" # daily

Expand All @@ -18,7 +13,7 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Checkout sources
uses: actions/checkout@v3
uses: actions/checkout@v4

- name: Install stable toolchain
uses: actions-rs/toolchain@v1
Expand Down Expand Up @@ -56,7 +51,7 @@ jobs:
rust: stable
continue: false
steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4

- uses: actions-rs/toolchain@v1
with:
Expand All @@ -72,7 +67,7 @@ jobs:
test_all_features:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4

- uses: actions-rs/toolchain@v1
with:
Expand All @@ -91,7 +86,7 @@ jobs:
coverage:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4

- uses: actions-rs/toolchain@v1
with:
Expand All @@ -109,7 +104,7 @@ jobs:
run: cargo binstall --no-confirm cargo-tarpaulin

- name: Coverage with tarpaulin
run: cargo tarpaulin --all --all-features --timeout 600 --out Xml -- --test-threads 1
run: cargo tarpaulin --all --all-features --timeout 600 --out xml -- --test-threads 1

- name: Upload Rust coverage to codecov
uses: codecov/codecov-action@v3
Expand All @@ -131,7 +126,7 @@ jobs:
rust: stable
steps:
- name: Checkout sources
uses: actions/checkout@v3
uses: actions/checkout@v4

- name: Install Rust toolchain
uses: actions-rs/toolchain@v1
Expand All @@ -157,7 +152,7 @@ jobs:
name: Check if wasm-pack builds a valid package for the sourmash crate
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4

- uses: actions-rs/toolchain@v1
with:
Expand Down Expand Up @@ -192,7 +187,7 @@ jobs:
name: Run tests under wasm32-wasi
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4
- name: Install wasm32-wasi target
uses: actions-rs/toolchain@v1
with:
Expand Down Expand Up @@ -225,7 +220,7 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Checkout sources
uses: actions/checkout@v3
uses: actions/checkout@v4

- name: Install stable toolchain
uses: actions-rs/toolchain@v1
Expand All @@ -243,7 +238,7 @@ jobs:
minimum_rust_version:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4

- uses: actions-rs/toolchain@v1
with:
Expand All @@ -263,7 +258,7 @@ jobs:
name: "Check if cbindgen runs cleanly for generating the C headers"
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4

- uses: actions-rs/toolchain@v1
with:
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4 changes: 2 additions & 2 deletions .github/workflows/rust_publish.yml
Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@ jobs:
name: Check if wasm-pack builds a valid package for the sourmash crate
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4
- uses: actions-rs/toolchain@v1
with:
toolchain: stable
Expand Down Expand Up @@ -40,7 +40,7 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Checkout sources
uses: actions/checkout@v3
uses: actions/checkout@v4

- name: Install stable toolchain
uses: actions-rs/toolchain@v1
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1 change: 0 additions & 1 deletion .readthedocs.yml
Original file line number Diff line number Diff line change
Expand Up @@ -20,4 +20,3 @@ python:
path: .
extra_requirements:
- doc
system_packages: true
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