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Version 1.5.0 release PR - "Able adenine" #14

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merged 36 commits into from
Jun 28, 2024
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3cdae04
Run Tarpaulin job outside a container, because without cmake building…
MatthiasZepper May 6, 2024
ba81651
Update dependencies.
MatthiasZepper Apr 9, 2024
833fad5
Add gzp library for parallel compression.
MatthiasZepper Apr 10, 2024
3da0567
Drop custom types, due to name collisions those just complicated matt…
MatthiasZepper Apr 10, 2024
5ecda09
Doesn't work like this...dyn ZWriter cannot be sent between threads s…
MatthiasZepper Apr 10, 2024
3f94806
Intermediate commit, refactor file for clarity.
MatthiasZepper Apr 11, 2024
b585b22
Refactor functions and disentagle editing the FastQ records from writ…
MatthiasZepper Apr 11, 2024
7ed7483
Reimplement new writer logic for plain and compressed output.
MatthiasZepper Apr 12, 2024
532ac89
Finish the output writers: Integrate with bio::io::fastq::Writer
MatthiasZepper Apr 13, 2024
771c52f
Integrate new multi-threaded writer into the main program.
MatthiasZepper Apr 13, 2024
2c5d250
Directly map output writing error to RuntimeErrors::ReadWriteError
MatthiasZepper Apr 13, 2024
6d3c414
Lint code
MatthiasZepper Apr 25, 2024
6786745
Update Tarpaulin command to include the integration tests as well.
MatthiasZepper Apr 25, 2024
2a25c00
Attempt fixing issues detected by Clippy.
MatthiasZepper Apr 29, 2024
64152ea
Update dependencies to latest.
MatthiasZepper Apr 29, 2024
6e116e2
After the update, dialoguer doesn't show the prompt anymore, so can't…
MatthiasZepper Apr 29, 2024
1a0df50
Fixed the integration text that relies on an interactive prompt with …
MatthiasZepper May 2, 2024
4d7814e
Add Codecov upload.
MatthiasZepper May 6, 2024
075d487
Add shield.io badges to README.
MatthiasZepper May 6, 2024
0ca36af
Implement multi-threaded FastQ compression for umi-transfer
MatthiasZepper May 6, 2024
56442e4
If multiple output files need to be written, I obviously can't use th…
MatthiasZepper May 7, 2024
764fe38
Alias bio::io::fastq::Reader as FastqReader analogous to FastqWriter.
MatthiasZepper May 22, 2024
8bffbce
Prepare the addition of binary test files to tests.
MatthiasZepper May 22, 2024
8d00d87
Test for compressed output files as well.
MatthiasZepper May 22, 2024
f774bf1
Create test for compression level setting.
MatthiasZepper May 22, 2024
ec8852c
Readme updates to accomodate the new multi-threaded output compression.
MatthiasZepper May 22, 2024
690e31f
Code formatting.
MatthiasZepper May 22, 2024
e058ec6
Bump version in main.
MatthiasZepper May 22, 2024
2e575a7
Bump Docker build action.
MatthiasZepper May 23, 2024
d568f01
Update Debian disto in Docker image from bullseye to bookworm (stable).
MatthiasZepper May 24, 2024
caaaf2b
Push dev container image also when workflow is manually dispatched.
MatthiasZepper May 24, 2024
152c1b4
Added benchmark results to readme.
MatthiasZepper May 27, 2024
bf57a71
Update CLI help text for maximum thread number.
MatthiasZepper May 28, 2024
3585661
Small fixes in the Readme.
MatthiasZepper Jun 3, 2024
4af3d9b
Update README.md
MatthiasZepper Jun 17, 2024
babdb13
Merge pull request #13 from MatthiasZepper/Improved_thread_setting
MatthiasZepper Jun 17, 2024
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10 changes: 5 additions & 5 deletions .github/workflows/container.yml
Original file line number Diff line number Diff line change
Expand Up @@ -27,29 +27,29 @@ jobs:
echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> ${GITHUB_ENV}

- name: Log in to Docker Hub
uses: docker/login-action@v2
uses: docker/login-action@v3
with:
username: ${{ secrets.DOCKERHUB_USERNAME }}
password: ${{ secrets.DOCKERHUB_TOKEN }}

- name: Login to GitHub Container Registry
uses: docker/login-action@v2
uses: docker/login-action@v3
with:
registry: ghcr.io
username: ${{ github.repository_owner }}
password: ${{ secrets.GITHUB_TOKEN }}

- name: Push dev image
uses: docker/build-push-action@v3
if: github.event_name == 'push'
uses: docker/build-push-action@v5
if: github.event_name == 'push' || github.event_name == 'workflow_dispatch'
with:
push: true
tags: |
${{ secrets.DOCKERHUB_USERNAME }}/${{ env.REPOTITLE_LOWERCASE }}:dev
ghcr.io/${{ env.REPO_LOWERCASE }}:dev

- name: Push release image
uses: docker/build-push-action@v3
uses: docker/build-push-action@v5
if: github.event_name == 'release'
with:
push: true
Expand Down
26 changes: 21 additions & 5 deletions .github/workflows/testing.yml
Original file line number Diff line number Diff line change
Expand Up @@ -88,7 +88,7 @@ jobs:
continue-on-error: true

- name: Create an artifact from clippy results
uses: actions/upload-artifact@v3
uses: actions/upload-artifact@v4
with:
name: ClippyResults
path: rust-clippy-results.sarif
Expand All @@ -102,16 +102,32 @@ jobs:
tarpaulin:
name: Determine test coverage with Tarpaulin
runs-on: ubuntu-latest
container:
image: xd009642/tarpaulin:develop-nightly
options: --security-opt seccomp=unconfined
steps:
- name: Checkout repository
uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4

- name: Setup Rust
uses: dtolnay/rust-toolchain@stable

- name: Install tarpaulin
run: cargo install cargo-tarpaulin

- name: Cache Rust toolchain
uses: Swatinem/rust-cache@23bce251a8cd2ffc3c1075eaa2367cf899916d84 # v2

- name: Generate code coverage
run: |
cargo +nightly tarpaulin --workspace --benches --follow-exec --timeout 120 --out Xml
cargo-tarpaulin --tests --bins --follow-exec --timeout 120 --out Xml

- uses: actions/upload-artifact@v4
with:
name: TarpaulinCodeCoverage.xml
path: cobertura.xml

- name: Upload coverage reports to Codecov
uses: codecov/[email protected]
with:
token: ${{ secrets.CODECOV_TOKEN }}



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