feat(lib): add compute_paths method for image method and "coherence…

…" of paths example (#117) * chore(lib): warn about overflow and add Rust coverage * fix(ci): setup Python inside container * chore(ci): does it work? * chore(ci): setup-python reads `.python-version` * fix(ci): `.python-version` * fix(ci): install cargo-tarpaulin manually * WIP on coherence * chore(lib): add masked vertices * chore(deps): bump JAX and Python>=3.10 * chore(lib): upgrade Python 3.10 and add fibonacci lattice * chore(lint): some fixes * fix(docs): typos * chore(docs): improve * fix(docs): typo * chore(tests): improved coverage * fix(docs): explicit variable name * chore(fmt): run ruff * try(docs): comment code * chore(docs): add reference to paper * wip(lib): ray casting for visibility check * chore(lib): avoid unnecessary broadcasting * chore(docs): cleanup * chore(lib): avoid unnecessary broadcasting * wip: addressing last issues * chore(lib): are we done with broadcasting? * chore(tests): improve PLY parsing and test logging * feat(lib): support reading materials from OBJ files * chore(lint): happy linting * chore(ci): codedoc ignore pyo3 modules * chore(docs): clear nb * fix(ci): justfile * fix(tests): remove materials * fix(lib): use re-entrant lock and add more tests * fix(ci): tests and justfile * chore(ci): disable xdist in CI * try(ci): or this? * chore(tests): one more test * feat(lib): use IndexMap to have reproducible results * fix(tests): lots of fixes and better naming * fix(ci): remove post-install * chore(lib): better defaults for hit tolerance and epsilon value * feat(lib): allow to iterate over chunks * chore(ci): remove fail on warning * chore(tests): add new benchmarks * fix(ci): fixes * chore(ci): codspeed * fix(ci): oops * fix(ci): use uv? * fix(tests): import * try(ci): fix? * try(ci): use real pip? * fix(ci): don't use uv * try(ci): :-( * fix(ci): oops * fix(deps): pin `numpy<2` See PyO3/rust-numpy#409 * chore(deps): update lock file * chore(tests): cleanup * chore(ci): disable xdist when benchmarking * chore(ci): force set `-n0` * chore(ci): remove Rust bench from comments * chore(ci): update * try(ci): add stupid benchmark * try... * fix(ci): install from local packages, not remote * fix(ci): missing interpolation * fix(ci): pip install actually * fix(ci): actually it was installing from remote :o * wip * fix(ci): finally * fix(ci): apt_packages are no longer installed * can we sudo? * :-( * fix(ci): rtd build * fix(ci): point to venv * chore(ci): use asdf install instead * fix(ci): must also install self
jeertmans · Sep 27, 2024 · 06cade7 · 06cade7
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commit 06cade7
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diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
@@ -63,7 +63,7 @@ jobs:
       run: uv run pre-commit run --all-files
 
     - name: Apply fixes when present
-      uses: pre-commit-ci/[email protected].2
+      uses: pre-commit-ci/[email protected].3
       if: always()
       with:
         msg: 'chore(fmt): auto fixes from pre-commit hooks'
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -47,7 +47,7 @@ jobs:
       uses: dtolnay/rust-toolchain@stable
 
     - name: Install dependencies
-      run: uv sync --no-dev --extra tests
+      run: uv sync --locked --no-dev --extra tests
 
     - name: Run tests
       run: uv run pytest
@@ -63,7 +63,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [macos-latest, ubuntu-latest, windows-latest]
-        pyversion: ['3.9', '3.10', '3.11', '3.12']
+        pyversion: ['3.10', '3.11', '3.12']
     runs-on: ${{ matrix.os }}
     steps:
     - name: Checkout repository
@@ -120,28 +120,30 @@ jobs:
       uses: actions/checkout@v4
 
     - uses: actions/setup-python@v5
+      id: setup-python
       with:
         cache: pip
         cache-dependency-path: uv.lock
 
+    - name: Setup uv
+      uses: astral-sh/setup-uv@v2
+
     - name: Install Rust
       uses: dtolnay/rust-toolchain@stable
       with:
         components: llvm-tools
 
-    - name: Install dependencies
-      run: pip install ".[tests]"
+    - name: Cache Rust
+      uses: Swatinem/rust-cache@v2
 
-    - name: Run Benchmarks on changes
-      run: pytest --benchmark-only --benchmark-save=changes differt-core/tests/benchmarks
+    - name: Install dependencies
+      run: uv pip install -r pyproject.toml --extra tests --python '${{ steps.setup-python.outputs.python-path }}'
 
-    - name: Build wheel with profiling profile
-      uses: PyO3/maturin-action@v1
-      with:
-        args: >
-          --release
-          --out pgo-wheel
-        working-directory: differt-core
+    - name: Build differt-core for profiling
+      run: |
+        rm -f python/differt_core/*.so
+        pip install -e . --config-settings=build-args='--profile profiling'
+      working-directory: differt-core
       env:
         RUSTFLAGS: -Cprofile-generate=${{ github.workspace }}/profdata
 
@@ -150,79 +152,23 @@ jobs:
       shell: bash
 
     - name: Generate profile data
-      run: |
-        python -m ensurepip
-        python -m pip install differt-core --no-index --no-deps --find-links differt-core/pgo-wheel --force-reinstall
-        pytest --benchmark-only differt-core/tests/benchmarks
-        rustup run stable bash -c 'echo LLVM_PROFDATA=$RUSTUP_HOME/toolchains/$RUSTUP_TOOLCHAIN/lib/rustlib/${{ env.RUST_HOST }}/bin/llvm-profdata >> "$GITHUB_ENV"'
+      run: pytest --dist=no -n0 --benchmark-enable differt/tests/benchmarks
 
-    - name: Merge GO data
-      run: ${{ env.LLVM_PROFDATA }} merge -o ${{ github.workspace }}/merged.profdata ${{ github.workspace }}/profdata
+    - name: Merge PGO data
+      run: rustup run stable bash -c '$RUSTUP_HOME/toolchains/$RUSTUP_TOOLCHAIN/lib/rustlib/${{ env.RUST_HOST }}/bin/llvm-profdata merge -o ${{ github.workspace }}/merged.profdata ${{ github.workspace }}/profdata'
 
-    - name: Build PGO-optimized wheel
-      uses: PyO3/maturin-action@v1
-      with:
-        args: >
-          --release
-          --out opt-wheel
-        working-directory: differt-core
+    - name: Build differt-core for benchmarking
+      run: |
+        rm -f python/differt_core/*.so
+        pip install -e . --config-settings=build-args='--profile profiling'
+      working-directory: differt-core
       env:
         RUSTFLAGS: -Cprofile-use=${{ github.workspace }}/merged.profdata
 
-    - name: Run Benchmarks on changes with PGO-optimized wheel
-      run: |
-        python -m pip install differt-core --no-index --no-deps --find-links differt-core/opt-wheel --force-reinstall
-        pytest --benchmark-only --benchmark-save=pgo differt-core/tests/benchmarks
-
-    - name: Checkout base branch
-      uses: actions/checkout@v4
-      with:
-        ref: ${{ github.event.pull_request.base.sha }}
-        clean: false
-
-    - name: Install dependencies (before changes)
-      run: pip install ".[tests]"
-
-    - name: Build wheel before changes
-      uses: PyO3/maturin-action@v1
+    - name: Run CodSpeed benchmarks
+      uses: CodSpeedHQ/action@v3
       with:
-        args: >
-          --release
-          --out dist
-        working-directory: differt-core
-
-    - name: Run Benchmarks before changes
-      run: |
-        python -m pip install differt-core --no-index --no-deps --find-links differt-core/dist --force-reinstall
-        pytest --benchmark-only --benchmark-save=before differt-core/tests/benchmarks
-
-    - name: Compare benchmarks
-      run: |
-        echo 'results<<EOF' >> $GITHUB_OUTPUT
-        pytest-benchmark compare --group-by=name --columns="mean,stddev,ops" >> $GITHUB_OUTPUT
-        echo 'EOF' >> $GITHUB_OUTPUT
-      id: compare
-
-    - name: Comment PR with benchmarks
-      uses: thollander/actions-comment-pull-request@v2
-      continue-on-error: true
-      with:
-        message: |
-          Python benchmark results:
-          ```
-          ${{ steps.compare.outputs.results }}
-          ```
-        comment_tag: python-benchmarks
-
-      id: comment
-
-    - name: If PR comment failed, write to PR summary
-      if: steps.comment.outcome != 'success'
-      run: |
-        echo '### Python benchmark results' >> $GITHUB_STEP_SUMMARY
-        echo '```' >> $GITHUB_STEP_SUMMARY
-        echo '${{ steps.compare.outputs.results }}' >> $GITHUB_STEP_SUMMARY
-        echo '```' >> $GITHUB_STEP_SUMMARY
+        run: pytest differt/tests/benchmarks --codspeed
 
   rust-benchmark:
     runs-on: ubuntu-latest
@@ -232,57 +178,20 @@ jobs:
     - name: Checkout repository
       uses: actions/checkout@v4
 
-    - uses: actions/setup-python@v5
+    - name: Setup Python
+      uses: actions/setup-python@v5
 
     - name: Install NumPy
-      run: pip install numpy
+      run: pip install "numpy<2"
 
     - name: Install Rust
       uses: dtolnay/rust-toolchain@stable
 
-    - uses: taiki-e/install-action@v2
-      with:
-        tool: [email protected]
-
-    - name: Run Benchmarks on changes
-      run: cargo bench --bench bench_main -- --save-baseline changes
-
-    - name: Checkout base branch
-      uses: actions/checkout@v4
-      with:
-        ref: ${{ github.event.pull_request.base.sha }}
-        clean: false
-
-    - name: Run Benchmarks before changes
-      run: cargo bench --bench bench_main -- --save-baseline before
+    - name: Cache Rust
+      uses: Swatinem/rust-cache@v2
 
-    - name: Compare benchmarks
-      run: |
-        echo 'results<<EOF' >> $GITHUB_OUTPUT
-        critcmp before changes >> $GITHUB_OUTPUT
-        echo 'EOF' >> $GITHUB_OUTPUT
-      id: compare
-
-    - name: Comment PR with benchmarks
-      uses: thollander/actions-comment-pull-request@v2
-      continue-on-error: true
-      with:
-        message: |
-          Rust benchmark results:
-          ```
-          ${{ steps.compare.outputs.results }}
-          ```
-        comment_tag: rust-benchmarks
-
-      id: comment
-
-    - name: If PR comment failed, write to PR summary
-      if: steps.comment.outcome != 'success'
-      run: |
-        echo '### Rust benchmark results' >> $GITHUB_STEP_SUMMARY
-        echo '```' >> $GITHUB_STEP_SUMMARY
-        echo '${{ steps.compare.outputs.results }}' >> $GITHUB_STEP_SUMMARY
-        echo '```' >> $GITHUB_STEP_SUMMARY
+    - name: Run Benchmarks
+      run: cargo bench
 
   linkcheck-docs:
     runs-on: ubuntu-latest
@@ -296,7 +205,7 @@ jobs:
         enable-cache: true
 
     - name: Install dependencies
-      run: uv sync --no-dev --extra docs
+      run: uv sync --locked --no-dev --extra docs
 
     - name: Install Just
       uses: taiki-e/install-action@just

diff --git a/.gitignore b/.gitignore
@@ -24,5 +24,6 @@ differt/src/differt/scene/scenes/
 
 # Tools
 
-.coverage
+.benchmarks/
+.coverage*
 coverage.xml
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -11,13 +11,12 @@ build:
   jobs:
     post_system_dependencies:
     - nohup Xvfb $DISPLAY -screen 0 1400x900x24 -dpi 96 +extension RANDR +render &
+    post_create_environment:
+    - asdf plugin add uv
+    - asdf install uv latest
+    - asdf global uv latest
+    - uv pip install . -r pyproject.toml --extra docs --no-cache --python $READTHEDOCS_VIRTUALENV_PATH
 sphinx:
   builder: html
   configuration: docs/source/conf.py
-  fail_on_warning: true
-python:
-  install:
-  - method: pip
-    path: .
-    extra_requirements:
-    - docs
+  fail_on_warning: false  # TODO: enable me
diff --git a/.rustfmt.toml b/.rustfmt.toml
@@ -10,6 +10,6 @@ imports_granularity = "Crate"
 match_block_trailing_comma = true
 normalize_doc_attributes = true
 reorder_modules = true
+style_edition = "2024"
 unstable_features = true
-version = "Two"
 wrap_comments = true
diff --git a/Cargo.lock b/Cargo.lock
diff --git a/Cargo.toml b/Cargo.toml
@@ -2,6 +2,11 @@
 debug = true
 strip = false
 
+[profile.profiling]
+debug = true
+inherits = "release"
+strip = false
+
 [profile.release]
 codegen-units = 1
 lto = "fat"

diff --git a/README.md b/README.md
@@ -51,7 +51,7 @@ but performant program. It also heavily uses the capabilities brought by
 
 To run build this package locally, you need:
 
-- [Python 3.9](https://www.python.org/) or above;
+- [Python 3.10](https://www.python.org/) or above;
 - [Rust](https://www.rust-lang.org/) stable toolchain;
 - any modern C compiler;
 - [just](https://github.com/casey/just) to easily run commands listed in `justfile`s;
@@ -120,7 +120,7 @@ pytest
 or benchmark it:
 
 ```bash
-pytest --benchmark-only
+pytest --benchmark-enable differt/tests/benchmarks
 ```
 
 [pypi-version-badge]: https://img.shields.io/pypi/v/DiffeRT?label=DiffeRT&color=blueviolet

diff --git a/ROADMAP.md b/ROADMAP.md
@@ -43,3 +43,4 @@ If you feel something is missing, please create
 ## GitHub
 
 - Add CITATION.cff file
+- Build PGO wheels for release too
diff --git a/differt-core/Cargo.toml b/differt-core/Cargo.toml
@@ -3,13 +3,14 @@ harness = false
 name = "bench_main"
 
 [dependencies]
+indexmap = {version = "2.5.0", features = ["serde"]}
 log = "0.4.21"
 nalgebra = "0.32.3"
 ndarray = {version = "0.15", features = ["rayon"]}
 numpy = "0.21"
 obj-rs = "0.7.1"
 ply-rs = "0.1.3"
-pyo3 = "0.21"
+pyo3 = {version = "0.21", features = ["indexmap"]}
 pyo3-log = "0.10"
 quick-xml = {version = "0.31.0", features = ["serialize"]}
 serde = {version = "1.0.197", features = ["derive"]}
@@ -28,6 +29,9 @@ crate-type = ["cdylib", "rlib"]
 doctest = false
 name = "differt_core"
 
+[lints.rust]
+unexpected_cfgs = {level = "warn", check-cfg = ['cfg(tarpaulin_include)']}
+
 [package]
 edition = "2021"
 name = "differt-core"

diff --git a/differt-core/benches/benchmarks/graph_iterators.rs b/differt-core/benches/benchmarks/graph_iterators.rs
@@ -1,4 +1,4 @@
-use criterion::{black_box, criterion_group, Criterion, Throughput};
+use criterion::{Criterion, Throughput, black_box, criterion_group};
 use differt_core::rt::graph::{complete::CompleteGraph, directed::DiGraph};
 
 const NUM_NODES: usize = 1000;
Original file line number	Diff line number	Diff line change
Expand Up		@@ -43,3 +43,4 @@ If you feel something is missing, please create
		## GitHub

		- Add CITATION.cff file
		- Build PGO wheels for release too