Skip to content
Open
Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
116 commits
Select commit Hold shift + click to select a range
3528e93
Updating to include a small rust library
hannah275 Aug 19, 2026
83a6126
Editing so that rust code is now stored under tiatoolbox/rust-library
hannah275 Aug 19, 2026
13c5bb8
Altering contrast_enhancer to use rust
hannah275 Aug 19, 2026
f566c81
Update patch_predictions_as_qupath_json to use rust code
hannah275 Aug 19, 2026
440709d
Editing patch_predictions_as_annotations to use rust code
hannah275 Aug 19, 2026
b1914f3
In rust created library equilviant to json.dump
hannah275 Aug 19, 2026
1c3dd84
Updated patch predictions as annotations to have preds of type f64
hannah275 Aug 19, 2026
ca5e25b
Corrected types on patch_predictions_as_annotations
hannah275 Aug 20, 2026
4bc7c1f
Corrected types on patch-predictions-as-qupath-json
hannah275 Aug 20, 2026
d92f501
Corrected misc.py for types
hannah275 Aug 20, 2026
7972393
Corrected misc.py for types
hannah275 Aug 20, 2026
73a8b0b
Updated patch_predictions_as_annotations
hannah275 Aug 20, 2026
078f464
Merge branch 'develop' into add-rust-library
shaneahmed Aug 20, 2026
9c0bc63
Added benchmarking
hannah275 Aug 20, 2026
6a80537
Changed name from miscrust to rust-misc
hannah275 Aug 20, 2026
0fedda4
Corrected to find mypy error
hannah275 Aug 20, 2026
ccb4833
Corrected to fix mypy error
hannah275 Aug 20, 2026
10a9605
Corrected types error
hannah275 Aug 21, 2026
882a859
Edited so that json.dump using rust instead of python
hannah275 Aug 24, 2026
2f41cf0
Removed rust code from tiatoolbox/utils
hannah275 Aug 24, 2026
5c8b580
Merge branch 'develop' into rust-json
hannah275 Aug 24, 2026
2983348
Edited contrast_enhancer to use rust code
hannah275 Aug 24, 2026
d78f4c7
Updated benchmarking
hannah275 Aug 24, 2026
f3e8022
Added new tests to cover all branches
hannah275 Aug 24, 2026
60bf98e
Updated test_utils to include a new test for contrast enhancer
hannah275 Aug 24, 2026
8d4529c
Updated test_utils to include a new test for contrast enhancer
hannah275 Aug 24, 2026
f058b4d
Updated test_utils to include a new test for contrast enhancer
hannah275 Aug 24, 2026
1690951
Updated test_utils to include a new test for contrast enhancer
hannah275 Aug 24, 2026
0756577
Removed github workflows
hannah275 Aug 24, 2026
ea28f76
Added in workflow for test
hannah275 Aug 25, 2026
615caf8
Updated rust-library/lib.rs to have proper formatting
hannah275 Aug 25, 2026
c60d41f
Edited rust-library/lib.rs to have better formatting
hannah275 Aug 25, 2026
13cd226
Edited to ignore too many arguments
hannah275 Aug 25, 2026
8ff5bba
Moved location of test_misc.rs
hannah275 Aug 25, 2026
615e23b
Merge branch 'rust-json' of https://github.com/hannah275/tiatoolbox i…
hannah275 Aug 25, 2026
c3ee9a3
Corrected import error
hannah275 Aug 25, 2026
94449e1
Added codecov to cover rust code too
hannah275 Aug 25, 2026
f7e09a4
Updated to include a codecov workflow so that it waits till both the …
hannah275 Aug 25, 2026
11a8fb8
Updated workflows
hannah275 Aug 25, 2026
6cf5469
Updated workflows
hannah275 Aug 25, 2026
7d1d627
Updated workflows
hannah275 Aug 25, 2026
d2513a3
Updated workflows
hannah275 Aug 25, 2026
7484198
Updated workflows
hannah275 Aug 25, 2026
e0a0a8c
Updated workflows
hannah275 Aug 25, 2026
5212cab
Updated workflows
hannah275 Aug 25, 2026
f7490c0
Updated workflows
hannah275 Aug 25, 2026
65db8e3
Updated workflows
hannah275 Aug 25, 2026
40b188c
Updated workflows
hannah275 Aug 25, 2026
8e93c34
Updated pyproject.toml
hannah275 Aug 25, 2026
d518142
Edited workflows
hannah275 Aug 25, 2026
351269e
Edited workflows
hannah275 Aug 25, 2026
ec95b40
Edited workflows
hannah275 Aug 25, 2026
e792219
Edited workflows
hannah275 Aug 25, 2026
6b7d1fd
Edited tests
hannah275 Aug 25, 2026
da75c91
Edited workflow
hannah275 Aug 25, 2026
6f69197
Edited workflow
hannah275 Aug 25, 2026
5149674
Edited workflow
hannah275 Aug 25, 2026
1eb9459
Edited workflow
hannah275 Aug 25, 2026
fd3caf0
Edited tests
hannah275 Aug 25, 2026
858b5be
Edited workflow
hannah275 Aug 25, 2026
f7bc02d
Edited workflow
hannah275 Aug 25, 2026
3695250
Edited tests
hannah275 Aug 25, 2026
84d6195
Corrected test
hannah275 Aug 25, 2026
7850da3
Corrected test
hannah275 Aug 25, 2026
ef52cb8
Updated workflow to ensure test utils as well
hannah275 Aug 25, 2026
4e033c1
Updated tests
hannah275 Aug 25, 2026
49a1036
Test for patch predictions as annotations
hannah275 Aug 25, 2026
6d5f94c
Edited rust library for formatting
hannah275 Aug 25, 2026
3702dd9
Edited rust library for formatting
hannah275 Aug 25, 2026
b579f3f
Edited rust library for formatting
hannah275 Aug 25, 2026
20a8940
Added two new tests for semantic_segmentations_as_qupath_json and jso…
hannah275 Aug 26, 2026
a7a1de7
Corrected formatting for rust
hannah275 Aug 26, 2026
cc6a42b
Corrected formatting for rust-library/lib.rs
hannah275 Aug 26, 2026
c5a98d2
Improved formatting
hannah275 Aug 26, 2026
4c6e236
Improved formatting
hannah275 Aug 26, 2026
e11538f
Altered misc.py to include rust code
hannah275 Aug 26, 2026
55c8e30
Altered misc.py for type checking
hannah275 Aug 26, 2026
9f4b879
Altered misc.py for type checking
hannah275 Aug 26, 2026
05f9c19
Corrected to speed up rust code
hannah275 Aug 26, 2026
015f157
Corrected to allow for codecov to run
hannah275 Aug 26, 2026
2503580
Removed slow rust code from misc
hannah275 Aug 26, 2026
f72ef17
Updated benchmarking
hannah275 Aug 26, 2026
d6191f0
Updated benchmarks folder
hannah275 Aug 26, 2026
e4f2e22
Updated benchmarking to remove asserts
hannah275 Aug 26, 2026
5e61c6d
Updated patch_predictions_as_annotations test to cover all branches
hannah275 Aug 26, 2026
0f56312
Updated to have json.dump use rust
hannah275 Aug 26, 2026
8aec6c5
Updated to have json.dump use rust
hannah275 Aug 26, 2026
2a26831
Improved benchmarking
hannah275 Aug 27, 2026
847989c
Edited to allow for multiple rust libraries
hannah275 Aug 27, 2026
a21bd78
Edited to allow for multiple rust libraries
hannah275 Aug 27, 2026
22c5998
Improved benchmarking
hannah275 Aug 27, 2026
775fac8
Corrected types
hannah275 Aug 27, 2026
cd895cf
Edited so that it can locate rust tests
hannah275 Aug 27, 2026
715d08e
Added new test
hannah275 Aug 27, 2026
b48cd68
Added new tests for save_qupath_json
hannah275 Aug 27, 2026
8a6f9c7
Added rust to readthedocs
hannah275 Aug 27, 2026
c60584b
Edited to have a new test for multitask rust
hannah275 Aug 27, 2026
652b152
Edited to have more tests for patch_predictions_as_annotations
hannah275 Aug 27, 2026
3366d60
Improved tests
hannah275 Aug 27, 2026
91f268f
Improved tests to cover all possibilities
hannah275 Aug 27, 2026
74133da
Correct to ignore error message
hannah275 Aug 27, 2026
01e7794
Updated formatting
hannah275 Aug 27, 2026
a316826
Merge branch 'develop' into rust-json
shaneahmed Aug 27, 2026
87cc4df
Edited to have build single qupath feature to use rust
hannah275 Aug 27, 2026
5841098
Updated build_single_qupath_feature to have improved formatting
hannah275 Aug 27, 2026
7c4fb06
Updated types in build single qupath feature
hannah275 Aug 27, 2026
6b6578d
Updated formatting of multitask rust library
hannah275 Aug 27, 2026
3a20764
Updated formatting
hannah275 Aug 27, 2026
fe54f6b
Improved benchmarking to include more tests
hannah275 Aug 28, 2026
79c05a7
Improved benchmarking to pass pre-commit tests
hannah275 Aug 28, 2026
d623ae6
Added in benchmarking for comparing multitask functions
hannah275 Aug 28, 2026
80ac12e
Updated rmultitask to improve formatting
hannah275 Aug 28, 2026
57eba22
Added compute_annotations to rmultitask
hannah275 Aug 31, 2026
b3c3a6c
Updated formatting
hannah275 Aug 31, 2026
fef4a2e
Updated formatting for rmultitask
hannah275 Aug 31, 2026
0d2ad81
Removed unused import
hannah275 Aug 31, 2026
File filter

Filter by extension

Filter by extension


Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
52 changes: 52 additions & 0 deletions .github/workflows/rust.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,52 @@
name: Rust
on:
push:
branches: [ develop, main, master ]
pull_request:
branches: [ develop, main, master ]
jobs:
rust:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4

- name: Set up Python
uses: actions/setup-python@v7
with:
python-version: "3.12"
- name: Install dependencies
run: |
sudo apt update
sudo apt-get install -y libopenjp2-7 libopenjp2-tools
python -m pip install --upgrade pip
python -m pip install ruff==0.16.1 pytest pytest-cov pytest-runner
pip install uv
uv pip install --system torch torchvision --index-url https://download.pytorch.org/whl/cpu
uv pip install --system -e .
- name: Install Rust
uses: dtolnay/rust-toolchain@stable
with:
components: rustfmt, clippy
- name: Install cargo-llvm-cov
uses: taiki-e/install-action@cargo-llvm-cov
- name: Check formatting
run: cargo fmt --all -- --check
- name: Run Clippy
run: cargo clippy --all-targets --all-features -- -D warnings -A clippy::too_many_arguments
- name: Run Rust coverage
shell: bash
run: |
source <(cargo llvm-cov show-env --sh)
cargo llvm-cov clean --workspace
python -m pip install --force-reinstall --no-deps -e .
python -m pytest tests/test_rust.py -v
cargo test --all-features
cargo llvm-cov report --lcov --output-path lcov.info
- name: Upload Rust coverage to Codecov
uses: codecov/codecov-action@v4
env:
CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
with:
files: lcov.info
flags: rust
fail_ci_if_error: false
1 change: 1 addition & 0 deletions .readthedocs.yml
Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@ build:
os: ubuntu-24.04
tools:
python: "3.12"
rust: "latest"
apt_packages:
- libopenjp2-7-dev
- libopenjp2-tools
Expand Down
13 changes: 13 additions & 0 deletions Cargo.toml
Original file line number Diff line number Diff line change
@@ -0,0 +1,13 @@
[workspace]
resolver = "3"
members = [
"tiatoolbox/rust-library/misc",
"tiatoolbox/rust-library/multitask",
]

[workspace.package]
version = "0.1.0"
edition = "2024"

[workspace.dependencies]
pyo3 = "0.29.2"
51,641 changes: 51,641 additions & 0 deletions benchmarks/comparing_misc_functions_in_rust_v_python.ipynb

Large diffs are not rendered by default.

Loading
Loading