diff --git a/.cargo/config b/.cargo/config.toml similarity index 100% rename from .cargo/config rename to .cargo/config.toml diff --git a/.github/workflows/build-publish.yml b/.github/workflows/build-publish.yml index 624d400..fa3801f 100644 --- a/.github/workflows/build-publish.yml +++ b/.github/workflows/build-publish.yml @@ -11,112 +11,239 @@ jobs: name: Next version runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 - - uses: actions/setup-node@v3 + - uses: actions/checkout@v4 + - uses: actions/setup-node@v4 with: cache: npm - node-version: 16 + node-version: lts/Iron - run: npm install - run: npx semantic-release --dry-run id: semantic_release env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - - uses: actions/upload-artifact@v3 + - uses: actions/upload-artifact@v4 with: name: semantic-release path: | Cargo.toml + pyproject.toml + CITATION.cff retention-days: 1 outputs: version: ${{ steps.semantic_release.outputs.version }} test_rust: - name: Build Rust + name: Test Rust needs: semantic_release_next_version if: needs.semantic_release_next_version.outputs.version != '' runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 - - uses: actions-rs/toolchain@v1 + - uses: actions/checkout@v4 + - uses: actions-rust-lang/setup-rust-toolchain@v1 with: toolchain: stable - - uses: actions-rs/cargo@v1 + - run: + cargo test --release --all-features + + build_linux: + needs: test_rust + runs-on: ${{ matrix.platform.runner }} + strategy: + matrix: + platform: + - runner: ubuntu-latest + target: x86_64 + python-version: + - '3.8' + - '3.9' + - '3.10' + - '3.11' + - '3.12' + steps: + - uses: actions/checkout@v4 + - uses: actions/download-artifact@v4 + with: + name: semantic-release + - uses: actions/setup-python@v5 with: - command: test - args: --release --all-features + python-version: ${{ matrix.python-version }} + - name: Build wheel + uses: PyO3/maturin-action@v1 + with: + target: ${{ matrix.platform.target }} + args: --release --out dist -j 1 --all-features --strip --interpreter python${{ matrix.python-version }} + sccache: 'true' + manylinux: auto + - name: Test wheel + run: | + echo "((A:1,B:2):1,(C:1,(D:3,E:4):2):2);" > test.tree + python -m pip install dendropy + python -m pip install dist/*.whl --force-reinstall + python -c "from phylodm import PhyloDM; PhyloDM.load_from_newick_path('test.tree')" + - name: Upload wheels + uses: actions/upload-artifact@v4 + with: + name: wheels-linux-${{ matrix.platform.runner }}-${{ matrix.platform.target }}-${{ matrix.python-version }} + path: dist + retention-days: 1 - build_python_wheels: - name: Python ${{ matrix.pyver }}@${{ matrix.os }}.whl - needs: semantic_release_next_version - if: needs.semantic_release_next_version.outputs.version != '' - runs-on: ${{ matrix.os }} + musllinux: + needs: test_rust + runs-on: ${{ matrix.platform.runner }} strategy: matrix: - os: [ubuntu-20.04, macos-11] - pyver: [cp37, cp38, cp39, cp310, cp311] + platform: + - runner: ubuntu-latest + target: x86_64 + python-version: + - '3.8' + - '3.9' + - '3.10' + - '3.11' + - '3.12' + steps: + - uses: actions/checkout@v4 + - uses: actions/download-artifact@v4 + with: + name: semantic-release + - uses: actions/setup-python@v5 + with: + python-version: ${{ matrix.python-version }} + - name: Build wheel + uses: PyO3/maturin-action@v1 + with: + target: ${{ matrix.platform.target }} + args: --release --out dist -j 1 --all-features --strip --interpreter python${{ matrix.python-version }} + sccache: 'true' + manylinux: musllinux_1_2 + - name: Upload wheels + uses: actions/upload-artifact@v4 + with: + name: wheels-musllinux-${{ matrix.platform.runner }}-${{ matrix.platform.target }}-${{ matrix.python-version }} + path: dist + retention-days: 1 + + windows: + needs: test_rust + runs-on: ${{ matrix.platform.runner }} + strategy: + matrix: + platform: + - runner: windows-latest + target: x64 + python-version: + - '3.8' + - '3.9' + - '3.10' + - '3.11' + - '3.12' steps: - - uses: actions/checkout@v3 - - uses: actions/download-artifact@v3 + - uses: actions/checkout@v4 + - uses: actions/download-artifact@v4 with: name: semantic-release - - uses: pypa/cibuildwheel@v2.10.0 - env: - CIBW_BUILD: ${{matrix.pyver}}-* - - uses: actions/upload-artifact@v3 + - uses: actions/setup-python@v5 with: - name: pypi - path: wheelhouse/*.whl + python-version: ${{ matrix.python-version }} + - name: Build wheel + uses: PyO3/maturin-action@v1 + with: + target: ${{ matrix.platform.target }} + args: --release --out dist -j 1 --all-features --strip --interpreter python${{ matrix.python-version }} + sccache: 'true' + - name: Test wheel + run: | + echo "((A:1,B:2):1,(C:1,(D:3,E:4):2):2);" > test.tree + python -m pip install dendropy + python -m pip install (get-item .\dist\*.whl) --force-reinstall + python -c "from phylodm import PhyloDM; PhyloDM.load_from_newick_path('test.tree')" + - name: Upload wheels + uses: actions/upload-artifact@v4 + with: + name: wheels-windows-${{ matrix.platform.runner }}-${{ matrix.platform.target }}-${{ matrix.python-version }} + path: dist retention-days: 1 - build_python_dist: - name: Python build *.tar.gz - runs-on: ubuntu-latest - needs: semantic_release_next_version - if: needs.semantic_release_next_version.outputs.version != '' + osx: + needs: test_rust + runs-on: ${{ matrix.platform.runner }} + strategy: + matrix: + platform: + - runner: macos-12 + target: x86_64 + - runner: macos-14 + target: aarch64 + python-version: + - '3.8' + - '3.9' + - '3.10' + - '3.11' + - '3.12' steps: - - uses: actions/checkout@v3 - - uses: actions/download-artifact@v3 + - uses: actions/checkout@v4 + - uses: actions/download-artifact@v4 with: name: semantic-release - - name: Build sdist - run: pipx run build --sdist - - uses: actions/upload-artifact@v3 + - uses: actions/setup-python@v5 with: - name: pypi - path: dist/*.tar.gz + python-version: ${{ matrix.python-version }} + - name: Build wheel + uses: PyO3/maturin-action@v1 + with: + target: ${{ matrix.platform.target }} + args: --release --out dist -j 1 --all-features --strip --interpreter python${{ matrix.python-version }} + sccache: 'true' + - name: Test wheel + run: | + echo "((A:1,B:2):1,(C:1,(D:3,E:4):2):2);" > test.tree + python -m pip install dendropy + python -m pip install dist/*.whl --force-reinstall + python -c "from phylodm import PhyloDM; PhyloDM.load_from_newick_path('test.tree')" + - name: Upload wheels + uses: actions/upload-artifact@v4 + with: + name: wheels-osx-${{ matrix.platform.runner }}-${{ matrix.platform.target }}-${{ matrix.python-version }} + path: dist retention-days: 1 - test_python_dist: - name: Python test *.tar.gz + sdist: + needs: test_rust runs-on: ubuntu-latest - needs: build_python_dist steps: - - uses: actions-rs/toolchain@v1 + - uses: actions/checkout@v4 + - uses: actions/download-artifact@v4 with: - toolchain: stable - - uses: actions/download-artifact@v3 + name: semantic-release + - name: Build wheel + uses: PyO3/maturin-action@v1 with: - name: pypi - path: dist - - uses: actions/setup-python@v4 + command: sdist + args: --out dist + - name: Test dist + run: | + echo "((A:1,B:2):1,(C:1,(D:3,E:4):2):2);" > test.tree + python -m pip install dendropy + python -m pip install dist/*.tar.gz --force-reinstall + python -c "from phylodm import PhyloDM; PhyloDM.load_from_newick_path('test.tree')" + - name: Upload wheels + uses: actions/upload-artifact@v4 with: - python-version: '3.10' - - run: echo "((A:1,B:2):1,(C:1,(D:3,E:4):2):2);" > test.tree - - run: python -m pip install dendropy - - run: python -m pip install dist/*.tar.gz - - run: python -c "from phylodm import PhyloDM; PhyloDM.load_from_newick_path('test.tree')" + name: wheels-sdist + path: dist + retention-days: 1 semantic_release_publish: name: Publish to GitHub - needs: [test_rust, test_python_dist, build_python_wheels] + needs: [build_linux, musllinux, windows, osx, sdist] runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 - - uses: actions/setup-node@v3 + - uses: actions/checkout@v4 + - uses: actions/setup-node@v4 with: cache: npm - node-version: 16 + node-version: lts/Iron - run: npm install - run: npx semantic-release env: @@ -126,27 +253,29 @@ jobs: name: Publish to PyPI needs: [semantic_release_publish] runs-on: ubuntu-latest + environment: + name: pypi + url: https://pypi.org/p/phylodm + permissions: + id-token: write steps: - - uses: actions/download-artifact@v3 + - uses: actions/download-artifact@v4 with: - name: pypi path: dist - + pattern: wheels-* + merge-multiple: true - uses: pypa/gh-action-pypi-publish@release/v1 - with: - user: __token__ - password: ${{ secrets.PYPI_TOKEN }} upload_crates: name: Publish to crates.io needs: [semantic_release_publish] runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 - - uses: actions/download-artifact@v3 + - uses: actions/checkout@v4 + - uses: actions/download-artifact@v4 with: name: semantic-release - - uses: actions-rs/toolchain@v1 + - uses: actions-rust-lang/setup-rust-toolchain@v1 with: toolchain: stable - run: cargo publish --allow-dirty --token ${CRATES_TOKEN} diff --git a/.gitignore b/.gitignore index af9f770..c5c8477 100644 --- a/.gitignore +++ b/.gitignore @@ -145,3 +145,7 @@ wheelhouse/ # Node modules node_modules/ + +# venv +bin/* +pyvenv.cfg diff --git a/.releaserc b/.releaserc index 2626ac6..3ca3de5 100644 --- a/.releaserc +++ b/.releaserc @@ -1,7 +1,8 @@ { "tagFormat": "v${version}", "branches": [ - "main" + "main", + {"name": "dev", "prerelease": true} ], "plugins": [ "@semantic-release/commit-analyzer", @@ -9,7 +10,7 @@ [ "@semantic-release/exec", { - "verifyReleaseCmd": "./version.sh ${nextRelease.version} && echo ::set-output name=version::${nextRelease.version}" + "verifyReleaseCmd": "./version.sh ${nextRelease.version} && echo version=${nextRelease.version} >> $GITHUB_OUTPUT" } ], [ diff --git a/Cargo.lock b/Cargo.lock index 389ad7f..fc2635f 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -20,6 +20,55 @@ dependencies = [ "winapi", ] +[[package]] +name = "anstream" +version = "0.6.14" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "418c75fa768af9c03be99d17643f93f79bbba589895012a80e3452a19ddda15b" +dependencies = [ + "anstyle", + "anstyle-parse", + "anstyle-query", + "anstyle-wincon", + "colorchoice", + "is_terminal_polyfill", + "utf8parse", +] + +[[package]] +name = "anstyle" +version = "1.0.7" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "038dfcf04a5feb68e9c60b21c9625a54c2c0616e79b72b0fd87075a056ae1d1b" + +[[package]] +name = "anstyle-parse" +version = "0.2.4" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "c03a11a9034d92058ceb6ee011ce58af4a9bf61491aa7e1e59ecd24bd40d22d4" +dependencies = [ + "utf8parse", +] + +[[package]] +name = "anstyle-query" +version = "1.1.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "ad186efb764318d35165f1758e7dcef3b10628e26d41a44bc5550652e6804391" +dependencies = [ + "windows-sys", +] + +[[package]] +name = "anstyle-wincon" +version = "3.0.3" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "61a38449feb7068f52bb06c12759005cf459ee52bb4adc1d5a7c4322d716fb19" +dependencies = [ + "anstyle", + "windows-sys", +] + [[package]] name = "atty" version = "0.2.14" @@ -64,6 +113,12 @@ dependencies = [ "vec_map", ] +[[package]] +name = "colorchoice" +version = "1.0.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "0b6a852b24ab71dffc585bcb46eaf7959d175cb865a7152e35b348d1b2960422" + [[package]] name = "convert_case" version = "0.4.0" @@ -72,15 +127,15 @@ checksum = "6245d59a3e82a7fc217c5828a6692dbc6dfb63a0c8c90495621f7b9d79704a0e" [[package]] name = "derive_more" -version = "0.99.17" +version = "0.99.18" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "4fb810d30a7c1953f91334de7244731fc3f3c10d7fe163338a35b9f640960321" +checksum = "5f33878137e4dafd7fa914ad4e259e18a4e8e532b9617a2d0150262bf53abfce" dependencies = [ "convert_case", "proc-macro2", "quote", "rustc_version", - "syn", + "syn 2.0.20", ] [[package]] @@ -89,17 +144,27 @@ version = "1.8.1" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "7fcaabb2fef8c910e7f4c7ce9f67a1283a1715879a7c230ca9d6d1ae31f16d91" +[[package]] +name = "env_filter" +version = "0.1.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "a009aa4810eb158359dda09d0c87378e4bbb89b5a801f016885a4707ba24f7ea" +dependencies = [ + "log", + "regex", +] + [[package]] name = "env_logger" -version = "0.8.4" +version = "0.11.3" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "a19187fea3ac7e84da7dacf48de0c45d63c6a76f9490dae389aead16c243fce3" +checksum = "38b35839ba51819680ba087cd351788c9a3c476841207e0b8cee0b04722343b9" dependencies = [ - "atty", + "anstream", + "anstyle", + "env_filter", "humantime", "log", - "regex", - "termcolor", ] [[package]] @@ -110,9 +175,9 @@ checksum = "ee1289e6cb1ae7c28a9b9776bd599f8afb31c20965ff257a8ea20eaa4da5e3c7" [[package]] name = "getrandom" -version = "0.1.16" +version = "0.2.15" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "8fc3cb4d91f53b50155bdcfd23f6a4c39ae1969c2ae85982b135750cccaf5fce" +checksum = "c4567c8db10ae91089c99af84c68c38da3ec2f087c3f82960bcdbf3656b6f4d7" dependencies = [ "cfg-if", "libc", @@ -128,6 +193,12 @@ dependencies = [ "unicode-segmentation", ] +[[package]] +name = "heck" +version = "0.4.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "95505c38b4572b2d910cecb0281560f54b440a19336cbbcb27bf6ce6adc6f5a8" + [[package]] name = "hermit-abi" version = "0.1.19" @@ -145,15 +216,21 @@ checksum = "9a3a5bfb195931eeb336b2a7b4d761daec841b97f947d34394601737a7bba5e4" [[package]] name = "indoc" -version = "1.0.9" +version = "2.0.5" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "bfa799dd5ed20a7e349f3b4639aa80d74549c81716d9ec4f994c9b5815598306" +checksum = "b248f5224d1d606005e02c97f5aa4e88eeb230488bcc03bc9ca4d7991399f2b5" + +[[package]] +name = "is_terminal_polyfill" +version = "1.70.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "f8478577c03552c21db0e2724ffb8986a5ce7af88107e6be5d2ee6e158c12800" [[package]] name = "itertools" -version = "0.10.5" +version = "0.13.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "b0fd2260e829bddf4cb6ea802289de2f86d6a7a690192fbe91b3f46e0f2c8473" +checksum = "413ee7dfc52ee1a4949ceeb7dbc8a33f2d6c088194d9f922fb8318faf1f01186" dependencies = [ "either", ] @@ -166,15 +243,15 @@ checksum = "e2abad23fbc42b3700f2f279844dc832adb2b2eb069b2df918f455c4e18cc646" [[package]] name = "libc" -version = "0.2.146" +version = "0.2.155" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "f92be4933c13fd498862a9e02a3055f8a8d9c039ce33db97306fd5a6caa7f29b" +checksum = "97b3888a4aecf77e811145cadf6eef5901f4782c53886191b2f693f24761847c" [[package]] name = "light_phylogeny" -version = "2.1.5" +version = "2.2.7" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "b05b6cc82499caacbc149f9a79c29564151f93c45f049999f0da7657fa4c10ad" +checksum = "a34ea165196fb6f7783bffcea43d0532fcf4ebca003e3f71dba61be8165b9e3d" dependencies = [ "env_logger", "getopt", @@ -197,9 +274,9 @@ dependencies = [ [[package]] name = "log" -version = "0.4.19" +version = "0.4.22" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "b06a4cde4c0f271a446782e3eff8de789548ce57dbc8eca9292c27f4a42004b4" +checksum = "a7a70ba024b9dc04c27ea2f0c0548feb474ec5c54bba33a7f72f873a39d07b24" [[package]] name = "matrixmultiply" @@ -269,9 +346,9 @@ dependencies = [ [[package]] name = "numpy" -version = "0.19.0" +version = "0.21.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "437213adf41bbccf4aeae535fbfcdad0f6fed241e1ae182ebe97fa1f3ce19389" +checksum = "ec170733ca37175f5d75a5bea5911d6ff45d2cd52849ce98b685394e4f2f37f4" dependencies = [ "libc", "ndarray", @@ -308,7 +385,7 @@ dependencies = [ "libc", "redox_syscall", "smallvec", - "windows-targets", + "windows-targets 0.48.0", ] [[package]] @@ -323,6 +400,12 @@ dependencies = [ "pyo3", ] +[[package]] +name = "portable-atomic" +version = "1.6.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "7170ef9988bc169ba16dd36a7fa041e5c4cbeb6a35b76d4c03daded371eae7c0" + [[package]] name = "ppv-lite86" version = "0.2.17" @@ -338,7 +421,7 @@ dependencies = [ "proc-macro-error-attr", "proc-macro2", "quote", - "syn", + "syn 1.0.109", "version_check", ] @@ -364,15 +447,16 @@ dependencies = [ [[package]] name = "pyo3" -version = "0.19.0" +version = "0.21.2" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "cffef52f74ec3b1a1baf295d9b8fcc3070327aefc39a6d00656b13c1d0b8885c" +checksum = "a5e00b96a521718e08e03b1a622f01c8a8deb50719335de3f60b3b3950f069d8" dependencies = [ "cfg-if", "indoc", "libc", "memoffset", "parking_lot", + "portable-atomic", "pyo3-build-config", "pyo3-ffi", "pyo3-macros", @@ -381,9 +465,9 @@ dependencies = [ [[package]] name = "pyo3-build-config" -version = "0.19.0" +version = "0.21.2" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "713eccf888fb05f1a96eb78c0dbc51907fee42b3377272dc902eb38985f418d5" +checksum = "7883df5835fafdad87c0d888b266c8ec0f4c9ca48a5bed6bbb592e8dedee1b50" dependencies = [ "once_cell", "target-lexicon", @@ -391,9 +475,9 @@ dependencies = [ [[package]] name = "pyo3-ffi" -version = "0.19.0" +version = "0.21.2" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "5b2ecbdcfb01cbbf56e179ce969a048fd7305a66d4cdf3303e0da09d69afe4c3" +checksum = "01be5843dc60b916ab4dad1dca6d20b9b4e6ddc8e15f50c47fe6d85f1fb97403" dependencies = [ "libc", "pyo3-build-config", @@ -401,25 +485,27 @@ dependencies = [ [[package]] name = "pyo3-macros" -version = "0.19.0" +version = "0.21.2" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "b78fdc0899f2ea781c463679b20cb08af9247febc8d052de941951024cd8aea0" +checksum = "77b34069fc0682e11b31dbd10321cbf94808394c56fd996796ce45217dfac53c" dependencies = [ "proc-macro2", "pyo3-macros-backend", "quote", - "syn", + "syn 2.0.20", ] [[package]] name = "pyo3-macros-backend" -version = "0.19.0" +version = "0.21.2" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "60da7b84f1227c3e2fe7593505de274dcf4c8928b4e0a1c23d551a14e4e80a0f" +checksum = "08260721f32db5e1a5beae69a55553f56b99bd0e1c3e6e0a5e8851a9d0f5a85c" dependencies = [ + "heck 0.4.1", "proc-macro2", + "pyo3-build-config", "quote", - "syn", + "syn 2.0.20", ] [[package]] @@ -433,23 +519,20 @@ dependencies = [ [[package]] name = "rand" -version = "0.7.3" +version = "0.8.5" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "6a6b1679d49b24bbfe0c803429aa1874472f50d9b363131f0e89fc356b544d03" +checksum = "34af8d1a0e25924bc5b7c43c079c942339d8f0a8b57c39049bef581b46327404" dependencies = [ - "getrandom", "libc", "rand_chacha", "rand_core", - "rand_hc", - "rand_pcg", ] [[package]] name = "rand_chacha" -version = "0.2.2" +version = "0.3.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "f4c8ed856279c9737206bf725bf36935d8666ead7aa69b52be55af369d193402" +checksum = "e6c10a63a0fa32252be49d21e7709d4d4baf8d231c2dbce1eaa8141b9b127d88" dependencies = [ "ppv-lite86", "rand_core", @@ -457,36 +540,18 @@ dependencies = [ [[package]] name = "rand_core" -version = "0.5.1" +version = "0.6.4" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "90bde5296fc891b0cef12a6d03ddccc162ce7b2aff54160af9338f8d40df6d19" +checksum = 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+version = "0.52.6" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "4d25c75bf9ea12c4040a97f829154768bbbce366287e2dc044af160cd79a13fd" +checksum = "589f6da84c646204747d1270a2a5661ea66ed1cced2631d546fdfb155959f9ec" diff --git a/Cargo.toml b/Cargo.toml index 63dcf81..b115246 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -7,7 +7,7 @@ description = "Efficient calculation of phylogenetic distance matrices." readme = "README.md" repository = "https://github.com/aaronmussig/PhyloDM" license = "GPL-3.0" -rust-version = "1.65.0" +rust-version = "1.71.1" [lib] crate-type = ["cdylib", "rlib"] @@ -16,12 +16,12 @@ crate-type = ["cdylib", "rlib"] python = ["pyo3", "numpy"] [dependencies] -light_phylogeny = "2.1" -derive_more = "0.99" -itertools = "0.10" -pyo3 = { version = "0.19.0", features = ["extension-module"], optional = true } -numpy = { version = "0.19.0", optional = true } -ndarray = "0.15" +light_phylogeny = "2.2.7" +derive_more = "0.99.18" +itertools = "0.13" +pyo3 = { version = "0.21.0", features = ["extension-module"], optional = true } +numpy = { version = "0.21.0", optional = true } +ndarray = "0.15.6" [profile.release] lto = true diff --git a/MANIFEST.in b/MANIFEST.in index c2af147..47d9c7d 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -1,3 +1,4 @@ include Cargo.toml include Cargo.lock +include .cargo/config.toml recursive-include src * diff --git a/README.md b/README.md index e8078cf..8ca4cd2 100644 --- a/README.md +++ b/README.md @@ -17,7 +17,7 @@ can be used in either Python or Rust, however, the documentation below is writte ## ⚙ Installation -*Requires Python 3.7+* +*Requires Python 3.9+* ### PyPI diff --git a/package-lock.json b/package-lock.json index 4b584bc..1a33135 100644 --- a/package-lock.json +++ b/package-lock.json @@ -5,45 +5,47 @@ "packages": { "": { "devDependencies": { - "@semantic-release/changelog": "^6.0.1", - "@semantic-release/commit-analyzer": "^9.0.2", + "@semantic-release/changelog": "^6.0.3", + 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"inBundle": true, - "license": "ISC", + "license": "Apache-2.0", "dependencies": { - "@npmcli/node-gyp": "^2.0.0", - "@npmcli/promise-spawn": "^3.0.0", - "node-gyp": "^9.0.0", - "read-package-json-fast": "^2.0.3" + "@sigstore/bundle": "^2.3.2", + "@sigstore/core": "^1.1.0", + "@sigstore/protobuf-specs": "^0.3.2" }, "engines": { - "node": "^12.13.0 || ^14.15.0 || >=16.0.0" + "node": "^16.14.0 || >=18.0.0" } }, - "node_modules/npm/node_modules/@tootallnate/once": { + "node_modules/npm/node_modules/@tufjs/canonical-json": { "version": "2.0.0", "dev": true, "inBundle": true, "license": "MIT", "engines": { - "node": ">= 10" + "node": "^16.14.0 || >=18.0.0" } }, - "node_modules/npm/node_modules/abbrev": { - "version": "1.1.1", - "dev": true, - "inBundle": true, - "license": "ISC" - }, - "node_modules/npm/node_modules/agent-base": { - "version": "6.0.2", + "node_modules/npm/node_modules/@tufjs/models": { + "version": "2.0.1", "dev": true, "inBundle": true, "license": "MIT", "dependencies": { - "debug": "4" + "@tufjs/canonical-json": "2.0.0", + "minimatch": "^9.0.4" }, "engines": { - "node": ">= 6.0.0" + "node": "^16.14.0 || >=18.0.0" } }, - "node_modules/npm/node_modules/agentkeepalive": { - "version": "4.2.1", + "node_modules/npm/node_modules/abbrev": { + "version": "2.0.0", + "dev": true, + "inBundle": true, + "license": "ISC", + "engines": { + "node": "^14.17.0 || ^16.13.0 || >=18.0.0" + } + }, + "node_modules/npm/node_modules/agent-base": { + "version": "7.1.1", "dev": true, "inBundle": true, "license": "MIT", "dependencies": { - "debug": "^4.1.0", - "depd": "^1.1.2", - "humanize-ms": "^1.2.1" + "debug": "^4.3.4" }, "engines": { - "node": ">= 8.0.0" + "node": ">= 14" } }, "node_modules/npm/node_modules/aggregate-error": { @@ -2685,15 +3032,12 @@ } }, "node_modules/npm/node_modules/ansi-styles": { - "version": "4.3.0", + "version": "6.2.1", "dev": true, "inBundle": true, "license": "MIT", - "dependencies": { - "color-convert": "^2.0.1" - }, "engines": { - "node": ">=8" + "node": ">=12" }, "funding": { "url": "https://github.com/chalk/ansi-styles?sponsor=1" @@ -2711,25 +3055,6 @@ "inBundle": true, "license": "MIT" }, - "node_modules/npm/node_modules/are-we-there-yet": { - "version": "3.0.0", - "dev": true, - "inBundle": true, - "license": "ISC", - "dependencies": { - "delegates": "^1.0.0", - "readable-stream": "^3.6.0" - }, - "engines": { - "node": "^12.13.0 || ^14.15.0 || >=16" - } - }, - "node_modules/npm/node_modules/asap": { - "version": "2.0.6", - "dev": true, - "inBundle": true, - "license": "MIT" - }, "node_modules/npm/node_modules/balanced-match": { "version": "1.0.2", "dev": true, @@ -2737,29 +3062,30 @@ "license": "MIT" }, "node_modules/npm/node_modules/bin-links": { - "version": "3.0.1", + "version": "4.0.4", "dev": true, "inBundle": true, "license": "ISC", "dependencies": { - "cmd-shim": "^5.0.0", - "mkdirp-infer-owner": "^2.0.0", - "npm-normalize-package-bin": "^1.0.0", - "read-cmd-shim": "^3.0.0", - "rimraf": "^3.0.0", - "write-file-atomic": "^4.0.0" + "cmd-shim": "^6.0.0", + "npm-normalize-package-bin": "^3.0.0", + "read-cmd-shim": "^4.0.0", + "write-file-atomic": "^5.0.0" }, "engines": { - "node": "^12.13.0 || ^14.15.0 || >=16.0.0" + "node": "^14.17.0 || ^16.13.0 || >=18.0.0" } }, "node_modules/npm/node_modules/binary-extensions": { - "version": "2.2.0", + "version": "2.3.0", "dev": true, "inBundle": true, "license": "MIT", "engines": { "node": ">=8" + }, + "funding": { + "url": "https://github.com/sponsors/sindresorhus" } }, "node_modules/npm/node_modules/brace-expansion": { @@ -2771,55 +3097,36 @@ "balanced-match": "^1.0.0" } }, - "node_modules/npm/node_modules/builtins": { - "version": "5.0.1", - "dev": true, - "inBundle": true, - "license": "MIT", - "dependencies": { - "semver": "^7.0.0" - } - }, "node_modules/npm/node_modules/cacache": { - "version": "16.1.0", + "version": "18.0.3", "dev": true, "inBundle": true, "license": "ISC", "dependencies": { - "@npmcli/fs": "^2.1.0", - "@npmcli/move-file": "^2.0.0", - "chownr": "^2.0.0", - "fs-minipass": "^2.1.0", - "glob": "^8.0.1", - "infer-owner": "^1.0.4", - "lru-cache": "^7.7.1", - "minipass": "^3.1.6", - "minipass-collect": "^1.0.2", + "@npmcli/fs": "^3.1.0", + "fs-minipass": "^3.0.0", + "glob": "^10.2.2", + "lru-cache": "^10.0.1", + "minipass": "^7.0.3", + "minipass-collect": "^2.0.1", "minipass-flush": "^1.0.5", "minipass-pipeline": "^1.2.4", - "mkdirp": "^1.0.4", "p-map": "^4.0.0", - "promise-inflight": "^1.0.1", - "rimraf": "^3.0.2", - "ssri": "^9.0.0", + "ssri": "^10.0.0", "tar": "^6.1.11", - "unique-filename": "^1.1.1" + "unique-filename": "^3.0.0" }, "engines": { - "node": "^12.13.0 || ^14.15.0 || >=16.0.0" + "node": "^16.14.0 || >=18.0.0" } }, "node_modules/npm/node_modules/chalk": { - "version": "4.1.2", + "version": "5.3.0", "dev": true, "inBundle": true, "license": "MIT", - "dependencies": { - "ansi-styles": "^4.1.0", - "supports-color": "^7.1.0" - }, "engines": { - "node": ">=10" + "node": "^12.17.0 || ^14.13 || >=16.0.0" }, "funding": { "url": "https://github.com/chalk/chalk?sponsor=1" @@ -2834,16 +3141,31 @@ "node": ">=10" } }, + "node_modules/npm/node_modules/ci-info": { + "version": "4.0.0", + "dev": true, + "funding": [ + { + "type": "github", + "url": "https://github.com/sponsors/sibiraj-s" + } + ], + "inBundle": true, + "license": "MIT", + "engines": { + "node": ">=8" + } + }, "node_modules/npm/node_modules/cidr-regex": { - "version": "3.1.1", + "version": "4.1.1", "dev": true, "inBundle": true, "license": "BSD-2-Clause", "dependencies": { - "ip-regex": "^4.1.0" + "ip-regex": "^5.0.0" }, "engines": { - "node": ">=10" + "node": ">=14" } }, "node_modules/npm/node_modules/clean-stack": { @@ -2868,40 +3190,13 @@ "node": ">= 10" } }, - "node_modules/npm/node_modules/cli-table3": { - "version": "0.6.2", - "dev": true, - "inBundle": true, - "license": "MIT", - "dependencies": { - "string-width": "^4.2.0" - }, - "engines": { - "node": "10.* || >= 12.*" - }, - "optionalDependencies": { - "@colors/colors": "1.5.0" - } - }, - "node_modules/npm/node_modules/clone": { - "version": "1.0.4", - "dev": true, - "inBundle": true, - "license": "MIT", - "engines": { - "node": ">=0.8" - } - }, "node_modules/npm/node_modules/cmd-shim": { - "version": "5.0.0", + "version": "6.0.3", "dev": true, "inBundle": true, "license": "ISC", - "dependencies": { - "mkdirp-infer-owner": "^2.0.0" - }, "engines": { - "node": "^12.13.0 || ^14.15.0 || >=16.0.0" + "node": "^14.17.0 || ^16.13.0 || >=18.0.0" } }, "node_modules/npm/node_modules/color-convert": { @@ -2922,48 +3217,55 @@ "inBundle": true, "license": "MIT" }, - "node_modules/npm/node_modules/color-support": { - "version": "1.1.3", + "node_modules/npm/node_modules/common-ancestor-path": { + "version": "1.0.1", "dev": true, "inBundle": true, - "license": "ISC", - "bin": { - "color-support": "bin.js" - } + "license": "ISC" }, - "node_modules/npm/node_modules/columnify": { - "version": "1.6.0", + "node_modules/npm/node_modules/cross-spawn": { + "version": "7.0.3", "dev": true, "inBundle": true, "license": "MIT", "dependencies": { - "strip-ansi": "^6.0.1", - "wcwidth": "^1.0.0" + "path-key": "^3.1.0", + "shebang-command": "^2.0.0", + "which": "^2.0.1" }, "engines": { - "node": ">=8.0.0" + "node": ">= 8" } }, - "node_modules/npm/node_modules/common-ancestor-path": { - "version": "1.0.1", - "dev": true, - "inBundle": true, - "license": "ISC" - }, - "node_modules/npm/node_modules/concat-map": { - "version": "0.0.1", + "node_modules/npm/node_modules/cross-spawn/node_modules/which": { + "version": "2.0.2", "dev": true, "inBundle": true, - "license": "MIT" + "license": "ISC", + "dependencies": { + "isexe": "^2.0.0" + }, + "bin": { + "node-which": "bin/node-which" + }, + "engines": { + "node": ">= 8" + } }, - "node_modules/npm/node_modules/console-control-strings": { - "version": "1.1.0", + "node_modules/npm/node_modules/cssesc": { + "version": "3.0.0", "dev": true, "inBundle": true, - "license": "ISC" + "license": "MIT", + "bin": { + "cssesc": "bin/cssesc" + }, + "engines": { + "node": ">=4" + } }, "node_modules/npm/node_modules/debug": { - "version": "4.3.4", + "version": "4.3.5", "dev": true, "inBundle": true, "license": "MIT", @@ -2985,58 +3287,21 @@ "inBundle": true, "license": "MIT" }, - "node_modules/npm/node_modules/debuglog": { - "version": "1.0.1", + "node_modules/npm/node_modules/diff": { + "version": "5.2.0", "dev": true, "inBundle": true, - "license": "MIT", + "license": "BSD-3-Clause", "engines": { - "node": "*" - } - }, - "node_modules/npm/node_modules/defaults": { - "version": "1.0.3", - "dev": true, - "inBundle": true, - "license": "MIT", - "dependencies": { - "clone": "^1.0.2" + "node": ">=0.3.1" } }, - "node_modules/npm/node_modules/delegates": { - "version": "1.0.0", + "node_modules/npm/node_modules/eastasianwidth": { + "version": "0.2.0", "dev": true, "inBundle": true, "license": "MIT" }, - "node_modules/npm/node_modules/depd": { - "version": "1.1.2", - "dev": true, - "inBundle": true, - "license": "MIT", - "engines": { - "node": ">= 0.6" - } - }, - "node_modules/npm/node_modules/dezalgo": { - "version": "1.0.4", - "dev": true, - "inBundle": true, - "license": "ISC", - "dependencies": { - "asap": "^2.0.0", - "wrappy": "1" - } - }, - "node_modules/npm/node_modules/diff": { - "version": "5.0.0", - "dev": true, - "inBundle": true, - "license": "BSD-3-Clause", - "engines": { - "node": ">=0.3.1" - } - }, "node_modules/npm/node_modules/emoji-regex": { "version": "8.0.0", "dev": true, @@ -3068,160 +3333,120 @@ "inBundle": true, "license": "MIT" }, - "node_modules/npm/node_modules/fastest-levenshtein": { - "version": "1.0.12", - "dev": true, - "inBundle": true, - "license": "MIT" - }, - "node_modules/npm/node_modules/fs-minipass": { - "version": "2.1.0", - "dev": true, - "inBundle": true, - "license": "ISC", - "dependencies": { - "minipass": "^3.0.0" - }, - "engines": { - "node": ">= 8" - } - }, - "node_modules/npm/node_modules/fs.realpath": { - "version": "1.0.0", - "dev": true, - "inBundle": true, - "license": "ISC" - }, - "node_modules/npm/node_modules/function-bind": { - "version": "1.1.1", + "node_modules/npm/node_modules/exponential-backoff": { + "version": "3.1.1", "dev": true, "inBundle": true, - "license": "MIT" + "license": "Apache-2.0" }, - "node_modules/npm/node_modules/gauge": { - "version": "4.0.4", + "node_modules/npm/node_modules/fastest-levenshtein": { + "version": "1.0.16", "dev": true, "inBundle": true, - "license": "ISC", - "dependencies": { - "aproba": "^1.0.3 || ^2.0.0", - "color-support": "^1.1.3", - "console-control-strings": "^1.1.0", - "has-unicode": "^2.0.1", - "signal-exit": "^3.0.7", - "string-width": "^4.2.3", - "strip-ansi": "^6.0.1", - "wide-align": "^1.1.5" - }, + "license": "MIT", "engines": { - "node": "^12.13.0 || ^14.15.0 || >=16.0.0" + "node": ">= 4.9.1" } }, - "node_modules/npm/node_modules/glob": { - "version": "8.0.1", + "node_modules/npm/node_modules/foreground-child": { + "version": "3.2.1", "dev": true, "inBundle": true, "license": "ISC", "dependencies": { - "fs.realpath": "^1.0.0", - "inflight": "^1.0.4", - "inherits": "2", - "minimatch": "^5.0.1", - "once": "^1.3.0", - "path-is-absolute": "^1.0.0" + "cross-spawn": "^7.0.0", + "signal-exit": "^4.0.1" }, "engines": { - "node": ">=12" + "node": ">=14" }, "funding": { "url": "https://github.com/sponsors/isaacs" } }, - "node_modules/npm/node_modules/graceful-fs": { - "version": "4.2.10", - "dev": true, - "inBundle": true, - "license": "ISC" - }, - "node_modules/npm/node_modules/has": { - "version": "1.0.3", + "node_modules/npm/node_modules/fs-minipass": { + "version": "3.0.3", "dev": true, "inBundle": true, - "license": "MIT", + "license": "ISC", "dependencies": { - "function-bind": "^1.1.1" + "minipass": "^7.0.3" }, "engines": { - "node": ">= 0.4.0" + "node": "^14.17.0 || ^16.13.0 || >=18.0.0" } }, - "node_modules/npm/node_modules/has-flag": { - "version": "4.0.0", + "node_modules/npm/node_modules/glob": { + "version": "10.4.2", "dev": true, "inBundle": true, - "license": "MIT", + "license": "ISC", + "dependencies": { + "foreground-child": "^3.1.0", + "jackspeak": "^3.1.2", + "minimatch": "^9.0.4", + "minipass": "^7.1.2", + "package-json-from-dist": "^1.0.0", + "path-scurry": "^1.11.1" + }, + "bin": { + "glob": "dist/esm/bin.mjs" + }, "engines": { - "node": ">=8" + "node": ">=16 || 14 >=14.18" + }, + "funding": { + "url": "https://github.com/sponsors/isaacs" } }, - "node_modules/npm/node_modules/has-unicode": { - "version": "2.0.1", + "node_modules/npm/node_modules/graceful-fs": { + "version": "4.2.11", "dev": true, "inBundle": true, "license": "ISC" }, "node_modules/npm/node_modules/hosted-git-info": { - "version": "5.0.0", + "version": "7.0.2", "dev": true, "inBundle": true, "license": "ISC", "dependencies": { - "lru-cache": "^7.5.1" + "lru-cache": "^10.0.1" }, "engines": { - "node": "^12.13.0 || ^14.15.0 || >=16" + "node": "^16.14.0 || >=18.0.0" } }, "node_modules/npm/node_modules/http-cache-semantics": { - "version": "4.1.0", + "version": "4.1.1", "dev": true, "inBundle": true, "license": "BSD-2-Clause" }, "node_modules/npm/node_modules/http-proxy-agent": { - "version": "5.0.0", + "version": "7.0.2", "dev": true, "inBundle": true, "license": "MIT", "dependencies": { - "@tootallnate/once": "2", - "agent-base": "6", - "debug": "4" + "agent-base": "^7.1.0", + "debug": "^4.3.4" }, "engines": { - "node": ">= 6" + "node": ">= 14" } }, "node_modules/npm/node_modules/https-proxy-agent": { - "version": "5.0.1", + "version": "7.0.5", "dev": true, "inBundle": true, "license": "MIT", "dependencies": { - "agent-base": "6", + "agent-base": "^7.0.2", "debug": "4" }, "engines": { - "node": ">= 6" - } - }, - "node_modules/npm/node_modules/humanize-ms": { - "version": "1.2.1", - "dev": true, - "inBundle": true, - "license": "MIT", - "dependencies": { - "ms": "^2.0.0" + "node": ">= 14" } }, "node_modules/npm/node_modules/iconv-lite": { @@ -3238,15 +3463,15 @@ } }, "node_modules/npm/node_modules/ignore-walk": { - "version": "5.0.1", + "version": "6.0.5", "dev": true, "inBundle": true, "license": "ISC", "dependencies": { - "minimatch": "^5.0.1" + "minimatch": "^9.0.0" }, "engines": { - "node": "^12.13.0 || ^14.15.0 || >=16.0.0" + "node": "^14.17.0 || ^16.13.0 || >=18.0.0" } }, "node_modules/npm/node_modules/imurmurhash": { @@ -3267,92 +3492,68 @@ "node": ">=8" } }, - "node_modules/npm/node_modules/infer-owner": { - "version": "1.0.4", - "dev": true, - "inBundle": true, - "license": "ISC" - }, - "node_modules/npm/node_modules/inflight": { - "version": "1.0.6", - "dev": true, - "inBundle": true, - "license": "ISC", - "dependencies": { - "once": "^1.3.0", - "wrappy": "1" - } - }, - "node_modules/npm/node_modules/inherits": { - "version": "2.0.4", - "dev": true, - "inBundle": true, - "license": "ISC" - }, "node_modules/npm/node_modules/ini": { - "version": "3.0.0", + "version": "4.1.3", "dev": true, "inBundle": true, "license": "ISC", "engines": { - "node": "^12.13.0 || ^14.15.0 || >=16.0.0" + "node": "^14.17.0 || ^16.13.0 || >=18.0.0" } }, "node_modules/npm/node_modules/init-package-json": { - "version": "3.0.2", + "version": "6.0.3", "dev": true, "inBundle": true, "license": "ISC", "dependencies": { - "npm-package-arg": "^9.0.1", - "promzard": "^0.3.0", - "read": "^1.0.7", - "read-package-json": "^5.0.0", + "@npmcli/package-json": "^5.0.0", + "npm-package-arg": "^11.0.0", + "promzard": "^1.0.0", + "read": "^3.0.1", "semver": "^7.3.5", "validate-npm-package-license": "^3.0.4", - "validate-npm-package-name": "^4.0.0" + "validate-npm-package-name": "^5.0.0" }, "engines": { - "node": "^12.13.0 || ^14.15.0 || >=16.0.0" + "node": "^16.14.0 || >=18.0.0" } }, - "node_modules/npm/node_modules/ip": { - "version": "1.1.8", + "node_modules/npm/node_modules/ip-address": { + "version": "9.0.5", "dev": true, "inBundle": true, - "license": "MIT" + "license": "MIT", + "dependencies": { + "jsbn": "1.1.0", + "sprintf-js": "^1.1.3" + }, + "engines": { + "node": ">= 12" + } }, "node_modules/npm/node_modules/ip-regex": { - "version": "4.3.0", + "version": "5.0.0", "dev": true, "inBundle": true, "license": "MIT", "engines": { - "node": ">=8" + "node": "^12.20.0 || ^14.13.1 || >=16.0.0" + }, + "funding": { + "url": "https://github.com/sponsors/sindresorhus" } }, "node_modules/npm/node_modules/is-cidr": { - "version": "4.0.2", + "version": "5.1.0", "dev": true, "inBundle": true, "license": "BSD-2-Clause", "dependencies": { - "cidr-regex": "^3.1.1" + "cidr-regex": "^4.1.1" }, "engines": { - "node": ">=10" - } - }, - "node_modules/npm/node_modules/is-core-module": { - "version": "2.9.0", - "dev": true, - "inBundle": true, - "license": "MIT", - "dependencies": { - "has": "^1.0.3" - }, - "funding": { - "url": "https://github.com/sponsors/ljharb" + "node": ">=14" } }, "node_modules/npm/node_modules/is-fullwidth-code-point": { @@ -3376,12 +3577,39 @@ "inBundle": true, "license": "ISC" }, - "node_modules/npm/node_modules/json-parse-even-better-errors": { - "version": "2.3.1", + "node_modules/npm/node_modules/jackspeak": { + "version": "3.4.0", + "dev": true, + "inBundle": true, + "license": "BlueOak-1.0.0", + "dependencies": { + "@isaacs/cliui": "^8.0.2" + }, + "engines": { + "node": ">=14" + }, + "funding": { + "url": "https://github.com/sponsors/isaacs" + }, + "optionalDependencies": { + "@pkgjs/parseargs": "^0.11.0" + } + }, + "node_modules/npm/node_modules/jsbn": { + "version": "1.1.0", "dev": true, "inBundle": true, "license": "MIT" }, + "node_modules/npm/node_modules/json-parse-even-better-errors": { + "version": "3.0.2", + "dev": true, + "inBundle": true, + "license": "MIT", + "engines": { + "node": "^14.17.0 || ^16.13.0 || >=18.0.0" + } + }, "node_modules/npm/node_modules/json-stringify-nice": { "version": "1.1.4", "dev": true, @@ -3401,221 +3629,217 @@ "license": "MIT" }, "node_modules/npm/node_modules/just-diff": { - "version": "5.0.2", + "version": "6.0.2", "dev": true, "inBundle": true, "license": "MIT" }, "node_modules/npm/node_modules/just-diff-apply": { - "version": "5.2.0", + "version": "5.5.0", "dev": true, "inBundle": true, "license": "MIT" }, "node_modules/npm/node_modules/libnpmaccess": { - "version": "6.0.3", + "version": "8.0.6", "dev": true, "inBundle": true, "license": "ISC", "dependencies": { - "aproba": "^2.0.0", - "minipass": "^3.1.1", - "npm-package-arg": "^9.0.1", - "npm-registry-fetch": "^13.0.0" + "npm-package-arg": "^11.0.2", + "npm-registry-fetch": "^17.0.1" }, "engines": { - "node": "^12.13.0 || ^14.15.0 || >=16.0.0" + "node": "^16.14.0 || >=18.0.0" } }, "node_modules/npm/node_modules/libnpmdiff": { - "version": "4.0.3", + "version": "6.1.4", "dev": true, "inBundle": true, "license": "ISC", "dependencies": { - "@npmcli/disparity-colors": "^2.0.0", - "@npmcli/installed-package-contents": "^1.0.7", - "binary-extensions": "^2.2.0", - "diff": "^5.0.0", - "minimatch": "^5.0.1", - "npm-package-arg": "^9.0.1", - "pacote": "^13.0.5", - "tar": "^6.1.0" + "@npmcli/arborist": "^7.5.4", + "@npmcli/installed-package-contents": "^2.1.0", + "binary-extensions": "^2.3.0", + "diff": "^5.1.0", + "minimatch": "^9.0.4", + "npm-package-arg": "^11.0.2", + "pacote": "^18.0.6", + "tar": "^6.2.1" }, "engines": { - "node": "^12.13.0 || ^14.15.0 || >=16.0.0" + "node": "^16.14.0 || >=18.0.0" } }, "node_modules/npm/node_modules/libnpmexec": { - "version": "4.0.5", + "version": "8.1.3", "dev": true, "inBundle": true, "license": "ISC", "dependencies": { - "@npmcli/arborist": "^5.0.0", - "@npmcli/ci-detect": "^2.0.0", - "@npmcli/run-script": "^3.0.0", - "chalk": "^4.1.0", - "mkdirp-infer-owner": "^2.0.0", - "npm-package-arg": "^9.0.1", - "npmlog": "^6.0.2", - "pacote": "^13.0.5", - "proc-log": "^2.0.0", - "read": "^1.0.7", - "read-package-json-fast": "^2.0.2", - "walk-up-path": "^1.0.0" + "@npmcli/arborist": "^7.5.4", + "@npmcli/run-script": "^8.1.0", + "ci-info": "^4.0.0", + "npm-package-arg": "^11.0.2", + "pacote": "^18.0.6", + "proc-log": "^4.2.0", + "read": "^3.0.1", + "read-package-json-fast": "^3.0.2", + "semver": "^7.3.7", + "walk-up-path": "^3.0.1" }, "engines": { - "node": "^12.13.0 || ^14.15.0 || >=16.0.0" + "node": "^16.14.0 || >=18.0.0" } }, "node_modules/npm/node_modules/libnpmfund": { - "version": "3.0.2", + "version": "5.0.12", "dev": true, "inBundle": true, "license": "ISC", "dependencies": { - "@npmcli/arborist": "^5.0.0" + "@npmcli/arborist": "^7.5.4" }, "engines": { - "node": "^12.13.0 || ^14.15.0 || >=16.0.0" + "node": "^16.14.0 || >=18.0.0" } }, "node_modules/npm/node_modules/libnpmhook": { - "version": "8.0.3", + "version": "10.0.5", "dev": true, "inBundle": true, "license": "ISC", "dependencies": { "aproba": "^2.0.0", - "npm-registry-fetch": "^13.0.0" + "npm-registry-fetch": "^17.0.1" }, "engines": { - "node": "^12.13.0 || ^14.15.0 || >=16.0.0" + "node": "^16.14.0 || >=18.0.0" } }, "node_modules/npm/node_modules/libnpmorg": { - "version": "4.0.3", + "version": "6.0.6", "dev": true, "inBundle": true, "license": "ISC", "dependencies": { "aproba": "^2.0.0", - "npm-registry-fetch": "^13.0.0" + "npm-registry-fetch": "^17.0.1" }, "engines": { - "node": "^12.13.0 || ^14.15.0 || >=16.0.0" + "node": "^16.14.0 || >=18.0.0" } }, "node_modules/npm/node_modules/libnpmpack": { - "version": "4.1.0", + "version": "7.0.4", "dev": true, "inBundle": true, "license": "ISC", "dependencies": { - "@npmcli/run-script": "^3.0.0", - "npm-package-arg": "^9.0.1", - "pacote": "^13.5.0" + "@npmcli/arborist": "^7.5.4", + "@npmcli/run-script": "^8.1.0", + "npm-package-arg": "^11.0.2", + "pacote": "^18.0.6" }, "engines": { - "node": "^12.13.0 || ^14.15.0 || >=16.0.0" + "node": "^16.14.0 || >=18.0.0" } }, "node_modules/npm/node_modules/libnpmpublish": { - "version": "6.0.4", + "version": "9.0.9", "dev": true, "inBundle": true, "license": "ISC", "dependencies": { - "normalize-package-data": "^4.0.0", - "npm-package-arg": "^9.0.1", - "npm-registry-fetch": "^13.0.0", + "ci-info": "^4.0.0", + "normalize-package-data": "^6.0.1", + "npm-package-arg": "^11.0.2", + "npm-registry-fetch": "^17.0.1", + "proc-log": "^4.2.0", "semver": "^7.3.7", - "ssri": "^9.0.0" + "sigstore": "^2.2.0", + "ssri": "^10.0.6" }, "engines": { - "node": "^12.13.0 || ^14.15.0 || >=16.0.0" + "node": "^16.14.0 || >=18.0.0" } }, "node_modules/npm/node_modules/libnpmsearch": { - "version": "5.0.3", + "version": "7.0.6", "dev": true, "inBundle": true, "license": "ISC", "dependencies": { - "npm-registry-fetch": "^13.0.0" + "npm-registry-fetch": "^17.0.1" }, "engines": { - "node": "^12.13.0 || ^14.15.0 || >=16.0.0" + "node": "^16.14.0 || >=18.0.0" } }, "node_modules/npm/node_modules/libnpmteam": { - "version": "4.0.3", + "version": "6.0.5", "dev": true, "inBundle": true, "license": "ISC", "dependencies": { "aproba": "^2.0.0", - "npm-registry-fetch": "^13.0.0" + "npm-registry-fetch": "^17.0.1" }, "engines": { - "node": "^12.13.0 || ^14.15.0 || >=16.0.0" + "node": "^16.14.0 || >=18.0.0" } }, "node_modules/npm/node_modules/libnpmversion": { - "version": "3.0.4", + "version": "6.0.3", "dev": true, "inBundle": true, "license": "ISC", "dependencies": { - "@npmcli/git": "^3.0.0", - "@npmcli/run-script": "^3.0.0", - "json-parse-even-better-errors": "^2.3.1", - "proc-log": "^2.0.0", + "@npmcli/git": "^5.0.7", + "@npmcli/run-script": "^8.1.0", + "json-parse-even-better-errors": "^3.0.2", + "proc-log": "^4.2.0", "semver": "^7.3.7" }, "engines": { - "node": "^12.13.0 || ^14.15.0 || >=16.0.0" + "node": "^16.14.0 || >=18.0.0" } }, "node_modules/npm/node_modules/lru-cache": { - "version": "7.9.0", + "version": "10.2.2", "dev": true, "inBundle": true, "license": "ISC", "engines": { - "node": ">=12" + "node": "14 || >=16.14" } }, "node_modules/npm/node_modules/make-fetch-happen": { - "version": "10.1.5", + "version": "13.0.1", "dev": true, "inBundle": true, "license": "ISC", "dependencies": { - "agentkeepalive": "^4.2.1", - "cacache": "^16.1.0", - "http-cache-semantics": "^4.1.0", - "http-proxy-agent": "^5.0.0", - "https-proxy-agent": "^5.0.0", + "@npmcli/agent": "^2.0.0", + "cacache": "^18.0.0", + "http-cache-semantics": "^4.1.1", "is-lambda": "^1.0.1", - "lru-cache": "^7.7.1", - "minipass": "^3.1.6", - "minipass-collect": "^1.0.2", - "minipass-fetch": "^2.0.3", + "minipass": "^7.0.2", + "minipass-fetch": "^3.0.0", "minipass-flush": "^1.0.5", "minipass-pipeline": "^1.2.4", "negotiator": "^0.6.3", + "proc-log": "^4.2.0", "promise-retry": "^2.0.1", - "socks-proxy-agent": "^6.1.1", - "ssri": "^9.0.0" + "ssri": "^10.0.0" }, "engines": { - "node": "^12.13.0 || ^14.15.0 || >=16.0.0" + "node": "^16.14.0 || >=18.0.0" } }, "node_modules/npm/node_modules/minimatch": { - "version": "5.0.1", + "version": "9.0.5", "dev": true, "inBundle": true, "license": "ISC", @@ -3623,45 +3847,45 @@ "brace-expansion": "^2.0.1" }, "engines": { - "node": ">=10" + "node": ">=16 || 14 >=14.17" + }, + "funding": { + "url": "https://github.com/sponsors/isaacs" } }, "node_modules/npm/node_modules/minipass": { - "version": "3.1.6", + "version": "7.1.2", "dev": true, "inBundle": true, "license": "ISC", - "dependencies": { - "yallist": "^4.0.0" - }, "engines": { - "node": ">=8" + "node": ">=16 || 14 >=14.17" } }, "node_modules/npm/node_modules/minipass-collect": { - "version": "1.0.2", + "version": "2.0.1", "dev": true, "inBundle": true, "license": "ISC", "dependencies": { - "minipass": "^3.0.0" + "minipass": "^7.0.3" }, "engines": { - "node": ">= 8" + "node": ">=16 || 14 >=14.17" } }, "node_modules/npm/node_modules/minipass-fetch": { - "version": "2.1.0", + "version": "3.0.5", "dev": true, "inBundle": true, "license": "MIT", "dependencies": { - "minipass": "^3.1.6", + "minipass": "^7.0.3", "minipass-sized": "^1.0.3", "minizlib": "^2.1.2" }, "engines": { - "node": "^12.13.0 || ^14.15.0 || >=16.0.0" + "node": "^14.17.0 || ^16.13.0 || >=18.0.0" }, "optionalDependencies": { "encoding": "^0.1.13" @@ -3679,14 +3903,16 @@ "node": ">= 8" } }, - "node_modules/npm/node_modules/minipass-json-stream": { - "version": "1.0.1", + "node_modules/npm/node_modules/minipass-flush/node_modules/minipass": { + "version": "3.3.6", "dev": true, "inBundle": true, - "license": "MIT", + "license": "ISC", "dependencies": { - "jsonparse": "^1.3.1", - "minipass": "^3.0.0" + "yallist": "^4.0.0" + }, + "engines": { + "node": ">=8" } }, "node_modules/npm/node_modules/minipass-pipeline": { @@ -3701,6 +3927,18 @@ "node": ">=8" } }, + "node_modules/npm/node_modules/minipass-pipeline/node_modules/minipass": { + "version": "3.3.6", + "dev": true, + "inBundle": true, + "license": "ISC", + "dependencies": { + "yallist": "^4.0.0" + }, + "engines": { + "node": ">=8" + } + }, "node_modules/npm/node_modules/minipass-sized": { "version": "1.0.3", "dev": true, @@ -3713,6 +3951,18 @@ "node": ">=8" } }, + "node_modules/npm/node_modules/minipass-sized/node_modules/minipass": { + "version": "3.3.6", + "dev": true, + "inBundle": true, + "license": "ISC", + "dependencies": { + "yallist": "^4.0.0" + }, + "engines": { + "node": ">=8" + } + }, "node_modules/npm/node_modules/minizlib": { "version": "2.1.2", "dev": true, @@ -3726,27 +3976,25 @@ "node": ">= 8" } }, - "node_modules/npm/node_modules/mkdirp": { - "version": "1.0.4", + "node_modules/npm/node_modules/minizlib/node_modules/minipass": { + "version": "3.3.6", "dev": true, "inBundle": true, - "license": "MIT", - "bin": { - "mkdirp": "bin/cmd.js" + "license": "ISC", + "dependencies": { + "yallist": "^4.0.0" }, "engines": { - "node": ">=10" + "node": ">=8" } }, - "node_modules/npm/node_modules/mkdirp-infer-owner": { - "version": "2.0.0", + "node_modules/npm/node_modules/mkdirp": { + "version": "1.0.4", "dev": true, "inBundle": true, - "license": "ISC", - "dependencies": { - "chownr": "^2.0.0", - "infer-owner": "^1.0.4", - "mkdirp": "^1.0.3" + "license": "MIT", + "bin": { + "mkdirp": "bin/cmd.js" }, "engines": { "node": ">=10" @@ -3759,10 +4007,13 @@ "license": "MIT" }, "node_modules/npm/node_modules/mute-stream": { - "version": "0.0.8", + "version": "1.0.0", "dev": true, "inBundle": true, - "license": "ISC" + "license": "ISC", + "engines": { + "node": "^14.17.0 || ^16.13.0 || >=18.0.0" + } }, "node_modules/npm/node_modules/negotiator": { "version": "0.6.3", @@ -3774,124 +4025,90 @@ } }, "node_modules/npm/node_modules/node-gyp": { - "version": "9.0.0", + "version": "10.1.0", "dev": true, "inBundle": true, "license": "MIT", "dependencies": { "env-paths": "^2.2.0", - "glob": "^7.1.4", + "exponential-backoff": "^3.1.1", + "glob": "^10.3.10", "graceful-fs": "^4.2.6", - "make-fetch-happen": "^10.0.3", - "nopt": "^5.0.0", - "npmlog": "^6.0.0", - "rimraf": "^3.0.2", + "make-fetch-happen": "^13.0.0", + "nopt": "^7.0.0", + "proc-log": "^3.0.0", "semver": "^7.3.5", "tar": "^6.1.2", - "which": "^2.0.2" + "which": "^4.0.0" }, "bin": { "node-gyp": "bin/node-gyp.js" }, "engines": { - "node": "^12.22 || ^14.13 || >=16" - } - }, - "node_modules/npm/node_modules/node-gyp/node_modules/brace-expansion": { - "version": "1.1.11", - "dev": true, - "inBundle": true, - "license": "MIT", - "dependencies": { - "balanced-match": "^1.0.0", - "concat-map": "0.0.1" - } - }, - "node_modules/npm/node_modules/node-gyp/node_modules/glob": { - "version": "7.2.0", - "dev": true, - "inBundle": true, - "license": "ISC", - "dependencies": { - "fs.realpath": "^1.0.0", - "inflight": "^1.0.4", - "inherits": "2", - "minimatch": "^3.0.4", - "once": "^1.3.0", - "path-is-absolute": "^1.0.0" - }, - "engines": { - "node": "*" - }, - "funding": { - "url": "https://github.com/sponsors/isaacs" + "node": "^16.14.0 || >=18.0.0" } }, - "node_modules/npm/node_modules/node-gyp/node_modules/minimatch": { - "version": "3.1.2", + "node_modules/npm/node_modules/node-gyp/node_modules/proc-log": { + "version": "3.0.0", "dev": true, "inBundle": true, "license": "ISC", - "dependencies": { - "brace-expansion": "^1.1.7" - }, "engines": { - "node": "*" + "node": "^14.17.0 || ^16.13.0 || >=18.0.0" } }, "node_modules/npm/node_modules/nopt": { - "version": "5.0.0", + "version": "7.2.1", "dev": true, "inBundle": true, "license": "ISC", "dependencies": { - "abbrev": "1" + "abbrev": "^2.0.0" }, "bin": { "nopt": "bin/nopt.js" }, "engines": { - "node": ">=6" + "node": "^14.17.0 || ^16.13.0 || >=18.0.0" } }, "node_modules/npm/node_modules/normalize-package-data": { - "version": "4.0.0", + "version": "6.0.2", "dev": true, "inBundle": true, "license": "BSD-2-Clause", "dependencies": { - "hosted-git-info": "^5.0.0", - "is-core-module": "^2.8.1", + "hosted-git-info": "^7.0.0", "semver": "^7.3.5", "validate-npm-package-license": "^3.0.4" }, "engines": { - "node": "^12.13.0 || ^14.15.0 || >=16" + "node": "^16.14.0 || >=18.0.0" } }, "node_modules/npm/node_modules/npm-audit-report": { - "version": "3.0.0", + "version": "5.0.0", "dev": true, "inBundle": true, "license": "ISC", - "dependencies": { - "chalk": "^4.0.0" - }, "engines": { - "node": "^12.13.0 || ^14.15.0 || >=16.0.0" + "node": "^14.17.0 || ^16.13.0 || >=18.0.0" } }, "node_modules/npm/node_modules/npm-bundled": { - "version": "1.1.2", + "version": "3.0.1", "dev": true, "inBundle": true, "license": "ISC", "dependencies": { - "npm-normalize-package-bin": "^1.0.1" + "npm-normalize-package-bin": "^3.0.0" + }, + "engines": { + "node": "^14.17.0 || ^16.13.0 || >=18.0.0" } }, "node_modules/npm/node_modules/npm-install-checks": { - "version": "5.0.0", + "version": "6.3.0", "dev": true, "inBundle": true, "license": "BSD-2-Clause", @@ -3899,130 +4116,99 @@ "semver": "^7.1.1" }, "engines": { - "node": "^12.13.0 || ^14.15.0 || >=16.0.0" + "node": "^14.17.0 || ^16.13.0 || >=18.0.0" } }, "node_modules/npm/node_modules/npm-normalize-package-bin": { - "version": "1.0.1", + "version": "3.0.1", "dev": true, "inBundle": true, - "license": "ISC" + "license": "ISC", + "engines": { + "node": "^14.17.0 || ^16.13.0 || >=18.0.0" + } }, "node_modules/npm/node_modules/npm-package-arg": { - "version": "9.0.2", + "version": "11.0.2", "dev": true, "inBundle": true, "license": "ISC", "dependencies": { - "hosted-git-info": "^5.0.0", + "hosted-git-info": "^7.0.0", + "proc-log": "^4.0.0", "semver": "^7.3.5", - "validate-npm-package-name": "^4.0.0" + "validate-npm-package-name": "^5.0.0" }, "engines": { - "node": "^12.13.0 || ^14.15.0 || >=16.0.0" + "node": "^16.14.0 || >=18.0.0" } }, "node_modules/npm/node_modules/npm-packlist": { - "version": "5.1.0", + "version": "8.0.2", "dev": true, "inBundle": true, "license": "ISC", "dependencies": { - "glob": "^8.0.1", - "ignore-walk": "^5.0.1", - "npm-bundled": "^1.1.2", - "npm-normalize-package-bin": "^1.0.1" - }, - "bin": { - "npm-packlist": "bin/index.js" + "ignore-walk": "^6.0.4" }, "engines": { - "node": "^12.13.0 || ^14.15.0 || >=16.0.0" + "node": "^14.17.0 || ^16.13.0 || >=18.0.0" } }, "node_modules/npm/node_modules/npm-pick-manifest": { - "version": "7.0.1", + "version": "9.1.0", "dev": true, "inBundle": true, "license": "ISC", "dependencies": { - "npm-install-checks": "^5.0.0", - "npm-normalize-package-bin": "^1.0.1", - "npm-package-arg": "^9.0.0", + "npm-install-checks": "^6.0.0", + "npm-normalize-package-bin": "^3.0.0", + "npm-package-arg": "^11.0.0", "semver": "^7.3.5" }, "engines": { - "node": "^12.13.0 || ^14.15.0 || >=16.0.0" + "node": "^16.14.0 || >=18.0.0" } }, "node_modules/npm/node_modules/npm-profile": { - "version": "6.0.3", - "dev": true, - "inBundle": true, - "license": "ISC", - "dependencies": { - "npm-registry-fetch": "^13.0.1", - "proc-log": "^2.0.0" - }, - "engines": { - "node": "^12.13.0 || ^14.15.0 || >=16.0.0" - } - }, - "node_modules/npm/node_modules/npm-registry-fetch": { - "version": "13.1.1", - "dev": true, - "inBundle": true, - "license": "ISC", - "dependencies": { - "make-fetch-happen": "^10.0.6", - "minipass": "^3.1.6", - "minipass-fetch": "^2.0.3", - "minipass-json-stream": "^1.0.1", - "minizlib": "^2.1.2", - "npm-package-arg": "^9.0.1", - "proc-log": "^2.0.0" - }, - "engines": { - "node": "^12.13.0 || ^14.15.0 || >=16.0.0" - } - }, - "node_modules/npm/node_modules/npm-user-validate": { - "version": "1.0.1", - "dev": true, - "inBundle": true, - "license": "BSD-2-Clause" - }, - "node_modules/npm/node_modules/npmlog": { - "version": "6.0.2", + "version": "10.0.0", "dev": true, "inBundle": true, "license": "ISC", "dependencies": { - "are-we-there-yet": "^3.0.0", - "console-control-strings": "^1.1.0", - "gauge": "^4.0.3", - "set-blocking": "^2.0.0" + "npm-registry-fetch": "^17.0.1", + "proc-log": "^4.0.0" }, "engines": { - "node": "^12.13.0 || ^14.15.0 || >=16.0.0" + "node": ">=18.0.0" } }, - "node_modules/npm/node_modules/once": { - "version": "1.4.0", + "node_modules/npm/node_modules/npm-registry-fetch": { + "version": "17.1.0", "dev": true, "inBundle": true, "license": "ISC", "dependencies": { - "wrappy": "1" + "@npmcli/redact": "^2.0.0", + "jsonparse": "^1.3.1", + "make-fetch-happen": "^13.0.0", + "minipass": "^7.0.2", + "minipass-fetch": "^3.0.0", + "minizlib": "^2.1.2", + "npm-package-arg": "^11.0.0", + "proc-log": "^4.0.0" + }, + "engines": { + "node": "^16.14.0 || >=18.0.0" } }, - "node_modules/npm/node_modules/opener": { - "version": "1.5.2", + "node_modules/npm/node_modules/npm-user-validate": { + "version": "2.0.1", "dev": true, "inBundle": true, - "license": "(WTFPL OR MIT)", - "bin": { - "opener": "bin/opener-bin.js" + "license": "BSD-2-Clause", + "engines": { + "node": "^14.17.0 || ^16.13.0 || >=18.0.0" } }, "node_modules/npm/node_modules/p-map": { @@ -4040,71 +4226,111 @@ "url": "https://github.com/sponsors/sindresorhus" } }, + "node_modules/npm/node_modules/package-json-from-dist": { + "version": "1.0.0", + "dev": true, + "inBundle": true, + "license": "BlueOak-1.0.0" + }, "node_modules/npm/node_modules/pacote": { - "version": "13.5.0", + "version": "18.0.6", "dev": true, "inBundle": true, "license": "ISC", "dependencies": { - "@npmcli/git": "^3.0.0", - "@npmcli/installed-package-contents": "^1.0.7", - "@npmcli/promise-spawn": "^3.0.0", - "@npmcli/run-script": "^3.0.1", - "cacache": "^16.0.0", - "chownr": "^2.0.0", - "fs-minipass": "^2.1.0", - "infer-owner": "^1.0.4", - "minipass": "^3.1.6", - "mkdirp": "^1.0.4", - "npm-package-arg": "^9.0.0", - "npm-packlist": "^5.1.0", - "npm-pick-manifest": "^7.0.0", - "npm-registry-fetch": "^13.0.1", - "proc-log": "^2.0.0", + "@npmcli/git": "^5.0.0", + "@npmcli/installed-package-contents": "^2.0.1", + "@npmcli/package-json": "^5.1.0", + "@npmcli/promise-spawn": "^7.0.0", + "@npmcli/run-script": "^8.0.0", + "cacache": "^18.0.0", + "fs-minipass": "^3.0.0", + "minipass": "^7.0.2", + "npm-package-arg": "^11.0.0", + "npm-packlist": "^8.0.0", + "npm-pick-manifest": "^9.0.0", + "npm-registry-fetch": "^17.0.0", + "proc-log": "^4.0.0", "promise-retry": "^2.0.1", - "read-package-json": "^5.0.0", - "read-package-json-fast": "^2.0.3", - "rimraf": "^3.0.2", - "ssri": "^9.0.0", + "sigstore": "^2.2.0", + "ssri": "^10.0.0", "tar": "^6.1.11" }, "bin": { - "pacote": "lib/bin.js" + "pacote": "bin/index.js" }, "engines": { - "node": "^12.13.0 || ^14.15.0 || >=16.0.0" + "node": "^16.14.0 || >=18.0.0" } }, "node_modules/npm/node_modules/parse-conflict-json": { - "version": "2.0.2", + "version": "3.0.1", "dev": true, "inBundle": true, "license": "ISC", "dependencies": { - "json-parse-even-better-errors": "^2.3.1", - "just-diff": "^5.0.1", + "json-parse-even-better-errors": "^3.0.0", + "just-diff": "^6.0.0", "just-diff-apply": "^5.2.0" }, "engines": { - "node": "^12.13.0 || ^14.15.0 || >=16.0.0" + "node": "^14.17.0 || ^16.13.0 || >=18.0.0" } }, - "node_modules/npm/node_modules/path-is-absolute": { - "version": "1.0.1", + "node_modules/npm/node_modules/path-key": { + "version": "3.1.1", "dev": true, "inBundle": true, "license": "MIT", "engines": { - "node": ">=0.10.0" + "node": ">=8" + } + }, + "node_modules/npm/node_modules/path-scurry": { + "version": "1.11.1", + "dev": true, + "inBundle": true, + "license": "BlueOak-1.0.0", + "dependencies": { + "lru-cache": "^10.2.0", + "minipass": "^5.0.0 || ^6.0.2 || ^7.0.0" + }, + "engines": { + "node": ">=16 || 14 >=14.18" + }, + "funding": { + "url": "https://github.com/sponsors/isaacs" + } + }, + "node_modules/npm/node_modules/postcss-selector-parser": { + "version": "6.1.0", + "dev": true, + "inBundle": true, + "license": "MIT", + "dependencies": { + "cssesc": "^3.0.0", + "util-deprecate": "^1.0.2" + }, + "engines": { + "node": ">=4" } }, "node_modules/npm/node_modules/proc-log": { - "version": "2.0.1", + "version": "4.2.0", + "dev": true, + "inBundle": true, + "license": "ISC", + "engines": { + "node": "^14.17.0 || ^16.13.0 || >=18.0.0" + } + }, + "node_modules/npm/node_modules/proggy": { + "version": "2.0.0", "dev": true, "inBundle": true, "license": "ISC", "engines": { - "node": "^12.13.0 || ^14.15.0 || >=16.0.0" + "node": "^14.17.0 || ^16.13.0 || >=18.0.0" } }, "node_modules/npm/node_modules/promise-all-reject-late": { @@ -4117,7 +4343,7 @@ } }, "node_modules/npm/node_modules/promise-call-limit": { - "version": "1.0.1", + "version": "3.0.1", "dev": true, "inBundle": true, "license": "ISC", @@ -4145,12 +4371,15 @@ } }, "node_modules/npm/node_modules/promzard": { - "version": "0.3.0", + "version": "1.0.2", "dev": true, "inBundle": true, "license": "ISC", "dependencies": { - "read": "1" + "read": "^3.0.1" + }, + "engines": { + "node": "^14.17.0 || ^16.13.0 || >=18.0.0" } }, "node_modules/npm/node_modules/qrcode-terminal": { @@ -4162,78 +4391,37 @@ } }, "node_modules/npm/node_modules/read": { - "version": "1.0.7", + "version": "3.0.1", "dev": true, "inBundle": true, "license": "ISC", "dependencies": { - "mute-stream": "~0.0.4" + "mute-stream": "^1.0.0" }, "engines": { - "node": ">=0.8" + "node": "^14.17.0 || ^16.13.0 || >=18.0.0" } }, "node_modules/npm/node_modules/read-cmd-shim": { - "version": "3.0.0", - "dev": true, - "inBundle": true, - "license": "ISC", - "engines": { - "node": "^12.13.0 || ^14.15.0 || >=16.0.0" - } - }, - "node_modules/npm/node_modules/read-package-json": { - "version": "5.0.1", + "version": "4.0.0", "dev": true, "inBundle": true, "license": "ISC", - "dependencies": { - "glob": "^8.0.1", - "json-parse-even-better-errors": "^2.3.1", - "normalize-package-data": "^4.0.0", - "npm-normalize-package-bin": "^1.0.1" - }, "engines": { - "node": "^12.13.0 || ^14.15.0 || >=16.0.0" + "node": "^14.17.0 || ^16.13.0 || >=18.0.0" } }, "node_modules/npm/node_modules/read-package-json-fast": { - "version": "2.0.3", + "version": "3.0.2", "dev": true, "inBundle": true, "license": "ISC", "dependencies": { - "json-parse-even-better-errors": "^2.3.0", - "npm-normalize-package-bin": "^1.0.1" - }, - "engines": { - "node": ">=10" - } - }, - "node_modules/npm/node_modules/readable-stream": { - "version": "3.6.0", - "dev": true, - "inBundle": true, - "license": "MIT", - "dependencies": { - "inherits": "^2.0.3", - "string_decoder": "^1.1.1", - "util-deprecate": "^1.0.1" + "json-parse-even-better-errors": "^3.0.0", + "npm-normalize-package-bin": "^3.0.0" }, "engines": { - "node": ">= 6" - } - }, - "node_modules/npm/node_modules/readdir-scoped-modules": { - "version": "1.1.0", - "dev": true, - "inBundle": true, - "license": "ISC", - "dependencies": { - "debuglog": "^1.0.1", - "dezalgo": "^1.0.0", - "graceful-fs": "^4.1.2", - "once": "^1.3.0" + "node": "^14.17.0 || ^16.13.0 || >=18.0.0" } }, "node_modules/npm/node_modules/retry": { @@ -4245,129 +4433,75 @@ "node": ">= 4" } }, - "node_modules/npm/node_modules/rimraf": { - "version": "3.0.2", - "dev": true, - "inBundle": true, - "license": "ISC", - "dependencies": { - "glob": "^7.1.3" - }, - "bin": { - "rimraf": "bin.js" - }, - "funding": { - "url": "https://github.com/sponsors/isaacs" - } - }, - "node_modules/npm/node_modules/rimraf/node_modules/brace-expansion": { - "version": "1.1.11", + "node_modules/npm/node_modules/safer-buffer": { + "version": "2.1.2", "dev": true, "inBundle": true, "license": "MIT", - "dependencies": { - "balanced-match": "^1.0.0", - "concat-map": "0.0.1" - } + "optional": true }, - "node_modules/npm/node_modules/rimraf/node_modules/glob": { - "version": "7.2.0", + "node_modules/npm/node_modules/semver": { + "version": "7.6.2", "dev": true, "inBundle": true, "license": "ISC", - "dependencies": { - "fs.realpath": "^1.0.0", - "inflight": "^1.0.4", - "inherits": "2", - "minimatch": "^3.0.4", - "once": "^1.3.0", - "path-is-absolute": "^1.0.0" + "bin": { + "semver": "bin/semver.js" }, "engines": { - "node": "*" - }, - "funding": { - "url": "https://github.com/sponsors/isaacs" + "node": ">=10" } }, - "node_modules/npm/node_modules/rimraf/node_modules/minimatch": { - "version": "3.1.2", + "node_modules/npm/node_modules/shebang-command": { + "version": "2.0.0", "dev": true, "inBundle": true, - "license": "ISC", + "license": "MIT", "dependencies": { - "brace-expansion": "^1.1.7" + "shebang-regex": "^3.0.0" }, "engines": { - "node": "*" + "node": ">=8" } }, - "node_modules/npm/node_modules/safe-buffer": { - "version": "5.2.1", - "dev": true, - "funding": [ - { - "type": "github", - "url": "https://github.com/sponsors/feross" - }, - { - "type": "patreon", - "url": "https://www.patreon.com/feross" - }, - { - "type": "consulting", - "url": "https://feross.org/support" - } - ], - "inBundle": true, - "license": "MIT" - }, - "node_modules/npm/node_modules/safer-buffer": { - "version": "2.1.2", + "node_modules/npm/node_modules/shebang-regex": { + "version": "3.0.0", "dev": true, "inBundle": true, "license": "MIT", - "optional": true + "engines": { + "node": ">=8" + } }, - "node_modules/npm/node_modules/semver": { - "version": "7.3.7", + "node_modules/npm/node_modules/signal-exit": { + "version": "4.1.0", "dev": true, "inBundle": true, "license": "ISC", - "dependencies": { - "lru-cache": "^6.0.0" - }, - "bin": { - "semver": "bin/semver.js" - }, "engines": { - "node": ">=10" + "node": ">=14" + }, + "funding": { + "url": "https://github.com/sponsors/isaacs" } }, - "node_modules/npm/node_modules/semver/node_modules/lru-cache": { - "version": "6.0.0", + "node_modules/npm/node_modules/sigstore": { + "version": "2.3.1", "dev": true, "inBundle": true, - "license": "ISC", + "license": "Apache-2.0", "dependencies": { - "yallist": "^4.0.0" + "@sigstore/bundle": "^2.3.2", + "@sigstore/core": "^1.0.0", + "@sigstore/protobuf-specs": "^0.3.2", + "@sigstore/sign": "^2.3.2", + "@sigstore/tuf": "^2.3.4", + "@sigstore/verify": "^1.2.1" }, "engines": { - "node": ">=10" + "node": "^16.14.0 || >=18.0.0" } }, - "node_modules/npm/node_modules/set-blocking": { - "version": "2.0.0", - "dev": true, - "inBundle": true, - "license": "ISC" - }, - "node_modules/npm/node_modules/signal-exit": { - "version": "3.0.7", - "dev": true, - "inBundle": true, - "license": "ISC" - }, "node_modules/npm/node_modules/smart-buffer": { "version": "4.2.0", "dev": true, @@ -4379,35 +4513,35 @@ } }, "node_modules/npm/node_modules/socks": { - "version": "2.6.2", + "version": "2.8.3", "dev": true, "inBundle": true, "license": "MIT", "dependencies": { - "ip": "^1.1.5", + "ip-address": "^9.0.5", "smart-buffer": "^4.2.0" }, "engines": { - "node": ">= 10.13.0", + "node": ">= 10.0.0", "npm": ">= 3.0.0" } }, "node_modules/npm/node_modules/socks-proxy-agent": { - "version": "6.2.0", + "version": "8.0.4", "dev": true, "inBundle": true, "license": "MIT", "dependencies": { - "agent-base": "^6.0.2", - "debug": "^4.3.3", - "socks": "^2.6.2" + "agent-base": "^7.1.1", + "debug": "^4.3.4", + "socks": "^2.8.3" }, "engines": { - "node": ">= 10" + "node": ">= 14" } }, "node_modules/npm/node_modules/spdx-correct": { - "version": "3.1.1", + "version": "3.2.0", "dev": true, "inBundle": true, "license": "Apache-2.0", @@ -4416,14 +4550,24 @@ "spdx-license-ids": "^3.0.0" } }, + "node_modules/npm/node_modules/spdx-correct/node_modules/spdx-expression-parse": { + "version": "3.0.1", + "dev": true, + "inBundle": true, + "license": "MIT", + "dependencies": { + "spdx-exceptions": "^2.1.0", + "spdx-license-ids": "^3.0.0" + } + }, "node_modules/npm/node_modules/spdx-exceptions": { - "version": "2.3.0", + "version": "2.5.0", "dev": true, "inBundle": true, "license": "CC-BY-3.0" }, "node_modules/npm/node_modules/spdx-expression-parse": { - "version": "3.0.1", + "version": "4.0.0", "dev": true, "inBundle": true, "license": "MIT", @@ -4433,85 +4577,143 @@ } }, "node_modules/npm/node_modules/spdx-license-ids": { - "version": "3.0.11", + "version": "3.0.18", "dev": true, "inBundle": true, "license": "CC0-1.0" }, + "node_modules/npm/node_modules/sprintf-js": { + "version": "1.1.3", + "dev": true, + "inBundle": true, + "license": "BSD-3-Clause" + }, "node_modules/npm/node_modules/ssri": { - "version": "9.0.1", + "version": "10.0.6", "dev": true, "inBundle": true, "license": "ISC", "dependencies": { - "minipass": "^3.1.1" + "minipass": "^7.0.3" }, "engines": { - "node": "^12.13.0 || ^14.15.0 || >=16.0.0" + "node": "^14.17.0 || ^16.13.0 || >=18.0.0" } }, - "node_modules/npm/node_modules/string_decoder": { - "version": "1.3.0", + "node_modules/npm/node_modules/string-width": { + "version": "4.2.3", "dev": true, "inBundle": true, "license": "MIT", "dependencies": { - "safe-buffer": "~5.2.0" + "emoji-regex": "^8.0.0", + "is-fullwidth-code-point": "^3.0.0", + "strip-ansi": "^6.0.1" + }, + "engines": { + "node": ">=8" } }, - "node_modules/npm/node_modules/string-width": { + "node_modules/npm/node_modules/string-width-cjs": { + "name": "string-width", "version": "4.2.3", "dev": true, "inBundle": true, "license": "MIT", "dependencies": { - "emoji-regex": "^8.0.0", - "is-fullwidth-code-point": "^3.0.0", - "strip-ansi": "^6.0.1" + "emoji-regex": "^8.0.0", + "is-fullwidth-code-point": "^3.0.0", + "strip-ansi": "^6.0.1" + }, + "engines": { + "node": ">=8" + } + }, + "node_modules/npm/node_modules/strip-ansi": { + "version": "6.0.1", + "dev": true, + "inBundle": true, + "license": "MIT", + "dependencies": { + "ansi-regex": "^5.0.1" + }, + "engines": { + "node": ">=8" + } + }, + "node_modules/npm/node_modules/strip-ansi-cjs": { + "name": "strip-ansi", + "version": "6.0.1", + "dev": true, + "inBundle": true, + "license": "MIT", + "dependencies": { + "ansi-regex": "^5.0.1" + }, + "engines": { + "node": ">=8" + } + }, + "node_modules/npm/node_modules/supports-color": { + "version": "9.4.0", + "dev": true, + "inBundle": true, + "license": "MIT", + "engines": { + "node": ">=12" + }, + "funding": { + "url": "https://github.com/chalk/supports-color?sponsor=1" + } + }, + "node_modules/npm/node_modules/tar": { + "version": "6.2.1", + "dev": true, + "inBundle": true, + "license": "ISC", + "dependencies": { + "chownr": "^2.0.0", + "fs-minipass": "^2.0.0", + "minipass": "^5.0.0", + "minizlib": "^2.1.1", + "mkdirp": "^1.0.3", + "yallist": "^4.0.0" }, "engines": { - "node": ">=8" + "node": ">=10" } }, - "node_modules/npm/node_modules/strip-ansi": { - "version": "6.0.1", + "node_modules/npm/node_modules/tar/node_modules/fs-minipass": { + "version": "2.1.0", "dev": true, "inBundle": true, - "license": "MIT", + "license": "ISC", "dependencies": { - "ansi-regex": "^5.0.1" + "minipass": "^3.0.0" }, "engines": { - "node": ">=8" + "node": ">= 8" } }, - "node_modules/npm/node_modules/supports-color": { - "version": "7.2.0", + "node_modules/npm/node_modules/tar/node_modules/fs-minipass/node_modules/minipass": { + "version": "3.3.6", "dev": true, "inBundle": true, - "license": "MIT", + "license": "ISC", "dependencies": { - "has-flag": "^4.0.0" + "yallist": "^4.0.0" }, "engines": { "node": ">=8" } }, - "node_modules/npm/node_modules/tar": { - "version": "6.1.11", + "node_modules/npm/node_modules/tar/node_modules/minipass": { + "version": "5.0.0", "dev": true, "inBundle": true, "license": "ISC", - "dependencies": { - "chownr": "^2.0.0", - "fs-minipass": "^2.0.0", - "minipass": "^3.0.0", - "minizlib": "^2.1.1", - "mkdirp": "^1.0.3", - "yallist": "^4.0.0" - }, "engines": { - "node": ">= 10" + "node": ">=8" } }, "node_modules/npm/node_modules/text-table": { @@ -4527,30 +4729,50 @@ "license": "MIT" }, "node_modules/npm/node_modules/treeverse": { - "version": "2.0.0", + "version": "3.0.0", "dev": true, "inBundle": true, "license": "ISC", "engines": { - "node": "^12.13.0 || ^14.15.0 || >=16.0.0" + "node": "^14.17.0 || ^16.13.0 || >=18.0.0" + } + }, + "node_modules/npm/node_modules/tuf-js": { + "version": "2.2.1", + "dev": true, + "inBundle": true, + "license": "MIT", + "dependencies": { + "@tufjs/models": "2.0.1", + "debug": "^4.3.4", + "make-fetch-happen": "^13.0.1" + }, + "engines": { + "node": "^16.14.0 || >=18.0.0" } }, "node_modules/npm/node_modules/unique-filename": { - "version": "1.1.1", + "version": "3.0.0", "dev": true, "inBundle": true, "license": "ISC", "dependencies": { - "unique-slug": "^2.0.0" + "unique-slug": "^4.0.0" + }, + "engines": { + "node": "^14.17.0 || ^16.13.0 || >=18.0.0" } }, "node_modules/npm/node_modules/unique-slug": { - "version": "2.0.2", + "version": "4.0.0", 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true, + "requires": { + "debug": "^4.3.4" + } }, - "are-we-there-yet": { - "version": "3.0.0", + "aggregate-error": { + "version": "3.1.0", "bundled": true, "dev": true, "requires": { - "delegates": "^1.0.0", - "readable-stream": "^3.6.0" + "clean-stack": "^2.0.0", + "indent-string": "^4.0.0" } }, - "asap": { - "version": "2.0.6", + "ansi-regex": { + "version": "5.0.1", + "bundled": true, + "dev": true + }, + "ansi-styles": { + "version": "6.2.1", + "bundled": true, + "dev": true + }, + "aproba": { + "version": "2.0.0", + "bundled": true, + "dev": true + }, + "archy": { + "version": "1.0.0", "bundled": true, "dev": true }, @@ -7933,20 +8453,18 @@ "dev": true }, "bin-links": { - "version": "3.0.1", + "version": "4.0.4", "bundled": true, "dev": true, "requires": { - "cmd-shim": "^5.0.0", - "mkdirp-infer-owner": "^2.0.0", - "npm-normalize-package-bin": "^1.0.0", - "read-cmd-shim": "^3.0.0", - "rimraf": "^3.0.0", - "write-file-atomic": "^4.0.0" + "cmd-shim": "^6.0.0", + "npm-normalize-package-bin": "^3.0.0", + "read-cmd-shim": "^4.0.0", + "write-file-atomic": "^5.0.0" } }, "binary-extensions": { - "version": "2.2.0", + "version": "2.3.0", "bundled": true, "dev": true }, @@ -7958,59 +8476,46 @@ "balanced-match": "^1.0.0" } }, - "builtins": { - "version": "5.0.1", - "bundled": true, - "dev": true, - "requires": { - "semver": "^7.0.0" - } - }, "cacache": { - "version": "16.1.0", + "version": "18.0.3", "bundled": true, "dev": true, "requires": { - "@npmcli/fs": "^2.1.0", - "@npmcli/move-file": "^2.0.0", - "chownr": "^2.0.0", - "fs-minipass": "^2.1.0", - "glob": "^8.0.1", - "infer-owner": "^1.0.4", - "lru-cache": "^7.7.1", - "minipass": "^3.1.6", - "minipass-collect": "^1.0.2", + "@npmcli/fs": "^3.1.0", + "fs-minipass": "^3.0.0", + "glob": "^10.2.2", + "lru-cache": "^10.0.1", + "minipass": "^7.0.3", + "minipass-collect": "^2.0.1", "minipass-flush": "^1.0.5", "minipass-pipeline": "^1.2.4", - "mkdirp": "^1.0.4", "p-map": "^4.0.0", - "promise-inflight": "^1.0.1", - "rimraf": "^3.0.2", - "ssri": "^9.0.0", + "ssri": "^10.0.0", "tar": "^6.1.11", - "unique-filename": "^1.1.1" + "unique-filename": "^3.0.0" } }, "chalk": { - "version": "4.1.2", + "version": "5.3.0", "bundled": true, - "dev": true, - "requires": { - "ansi-styles": "^4.1.0", - "supports-color": "^7.1.0" - } + "dev": true }, "chownr": { "version": "2.0.0", "bundled": true, "dev": true }, + "ci-info": { + "version": "4.0.0", + "bundled": true, + "dev": true + }, "cidr-regex": { - "version": "3.1.1", + "version": "4.1.1", "bundled": true, "dev": true, "requires": { - "ip-regex": "^4.1.0" + "ip-regex": "^5.0.0" } }, "clean-stack": { @@ -8027,27 +8532,10 @@ "strip-ansi": "^6.0.1" } }, - "cli-table3": { - "version": "0.6.2", - "bundled": true, - "dev": true, - "requires": { - "@colors/colors": "1.5.0", - "string-width": "^4.2.0" - } - }, - "clone": { - "version": "1.0.4", - "bundled": true, - "dev": true - }, "cmd-shim": { - "version": "5.0.0", + "version": "6.0.3", "bundled": true, - "dev": true, - "requires": { - "mkdirp-infer-owner": "^2.0.0" - } + "dev": true }, "color-convert": { "version": "2.0.1", @@ -8062,37 +8550,38 @@ "bundled": true, "dev": true }, - "color-support": { - "version": "1.1.3", + "common-ancestor-path": { + "version": "1.0.1", "bundled": true, "dev": true }, - "columnify": { - "version": "1.6.0", + "cross-spawn": { + "version": "7.0.3", "bundled": true, "dev": true, "requires": { - "strip-ansi": "^6.0.1", - "wcwidth": "^1.0.0" + "path-key": "^3.1.0", + "shebang-command": "^2.0.0", + "which": "^2.0.1" + }, + "dependencies": { + "which": { + "version": "2.0.2", + "bundled": true, + "dev": true, + "requires": { + "isexe": "^2.0.0" + } + } } }, - "common-ancestor-path": { - "version": "1.0.1", - "bundled": true, - "dev": true - }, - "concat-map": { - "version": "0.0.1", - "bundled": true, - "dev": true - }, - "console-control-strings": { - "version": "1.1.0", + "cssesc": { + "version": "3.0.0", "bundled": true, "dev": true }, "debug": { - "version": "4.3.4", + "version": "4.3.5", "bundled": true, "dev": true, "requires": { @@ -8106,40 +8595,13 @@ } } }, - "debuglog": { - "version": "1.0.1", - "bundled": true, - "dev": true - }, - "defaults": { - "version": "1.0.3", - "bundled": true, - "dev": true, - "requires": { - "clone": "^1.0.2" - } - }, - "delegates": { - "version": "1.0.0", - "bundled": true, - "dev": true - }, - "depd": { - "version": "1.1.2", + "diff": { + "version": "5.2.0", "bundled": true, "dev": true }, - "dezalgo": { - "version": "1.0.4", - "bundled": true, - "dev": true, - "requires": { - "asap": "^2.0.0", - "wrappy": "1" - } - }, - "diff": { - "version": "5.0.0", + "eastasianwidth": { + "version": "0.2.0", "bundled": true, "dev": true }, @@ -8167,120 +8629,82 @@ "bundled": true, "dev": true }, - "fastest-levenshtein": { - "version": "1.0.12", - "bundled": true, - "dev": true - }, - "fs-minipass": { - "version": "2.1.0", - "bundled": true, - "dev": true, - "requires": { - "minipass": "^3.0.0" - } - }, - "fs.realpath": { - "version": "1.0.0", + "exponential-backoff": { + "version": "3.1.1", "bundled": true, "dev": true }, - "function-bind": { - "version": "1.1.1", + "fastest-levenshtein": { + "version": "1.0.16", "bundled": true, "dev": true }, - "gauge": { - "version": "4.0.4", + "foreground-child": { + "version": "3.2.1", "bundled": true, "dev": true, "requires": { - "aproba": "^1.0.3 || ^2.0.0", - "color-support": "^1.1.3", - "console-control-strings": "^1.1.0", - "has-unicode": "^2.0.1", - "signal-exit": "^3.0.7", - "string-width": "^4.2.3", - "strip-ansi": "^6.0.1", - "wide-align": "^1.1.5" + "cross-spawn": "^7.0.0", + "signal-exit": "^4.0.1" } }, - "glob": { - "version": "8.0.1", + "fs-minipass": { + "version": "3.0.3", "bundled": true, "dev": true, "requires": { - "fs.realpath": "^1.0.0", - "inflight": "^1.0.4", - "inherits": "2", - "minimatch": "^5.0.1", - "once": "^1.3.0", - "path-is-absolute": "^1.0.0" + "minipass": "^7.0.3" } }, - "graceful-fs": { - "version": "4.2.10", - "bundled": true, - "dev": true - }, - "has": { - "version": "1.0.3", + "glob": { + "version": "10.4.2", "bundled": true, "dev": true, "requires": { - "function-bind": "^1.1.1" + "foreground-child": "^3.1.0", + "jackspeak": "^3.1.2", + "minimatch": "^9.0.4", + "minipass": "^7.1.2", + "package-json-from-dist": "^1.0.0", + "path-scurry": "^1.11.1" } }, - "has-flag": { - "version": "4.0.0", - "bundled": true, - "dev": true - }, - "has-unicode": { - "version": "2.0.1", + "graceful-fs": { + "version": "4.2.11", "bundled": true, "dev": true }, "hosted-git-info": { - "version": "5.0.0", + "version": "7.0.2", "bundled": true, "dev": true, "requires": { - "lru-cache": "^7.5.1" + "lru-cache": "^10.0.1" } }, "http-cache-semantics": { - "version": "4.1.0", + "version": "4.1.1", "bundled": true, "dev": true }, "http-proxy-agent": { - "version": "5.0.0", + "version": "7.0.2", "bundled": true, "dev": true, "requires": { - "@tootallnate/once": "2", - "agent-base": "6", - "debug": "4" + "agent-base": "^7.1.0", + "debug": "^4.3.4" } }, "https-proxy-agent": { - "version": "5.0.1", + "version": "7.0.5", "bundled": true, "dev": true, "requires": { - "agent-base": "6", + "agent-base": "^7.0.2", "debug": "4" } }, - "humanize-ms": { - "version": "1.2.1", - "bundled": true, - "dev": true, - "requires": { - "ms": "^2.0.0" - } - }, "iconv-lite": { "version": "0.6.3", "bundled": true, @@ -8291,11 +8715,11 @@ } }, "ignore-walk": { - "version": "5.0.1", + "version": "6.0.5", "bundled": true, "dev": true, "requires": { - "minimatch": "^5.0.1" + "minimatch": "^9.0.0" } }, "imurmurhash": { @@ -8308,68 +8732,45 @@ "bundled": true, "dev": true }, - "infer-owner": { - "version": "1.0.4", - "bundled": true, - "dev": true - }, - "inflight": { - "version": "1.0.6", - "bundled": true, - "dev": true, - "requires": { - "once": "^1.3.0", - "wrappy": "1" - } - }, - "inherits": { - "version": "2.0.4", - "bundled": true, - "dev": true - }, "ini": { - "version": "3.0.0", + "version": "4.1.3", "bundled": true, "dev": true }, "init-package-json": { - "version": "3.0.2", + "version": "6.0.3", "bundled": true, "dev": true, "requires": { - "npm-package-arg": "^9.0.1", - "promzard": "^0.3.0", - "read": "^1.0.7", - "read-package-json": "^5.0.0", + "@npmcli/package-json": "^5.0.0", + "npm-package-arg": "^11.0.0", + "promzard": "^1.0.0", + "read": "^3.0.1", "semver": "^7.3.5", "validate-npm-package-license": "^3.0.4", - "validate-npm-package-name": "^4.0.0" + "validate-npm-package-name": "^5.0.0" } }, - "ip": { - "version": "1.1.8", + "ip-address": { + "version": "9.0.5", "bundled": true, - "dev": true + "dev": true, + "requires": { + "jsbn": "1.1.0", + "sprintf-js": "^1.1.3" + } }, "ip-regex": { - "version": "4.3.0", + "version": "5.0.0", "bundled": true, "dev": true }, "is-cidr": { - "version": "4.0.2", - "bundled": true, - "dev": true, - "requires": { - "cidr-regex": "^3.1.1" - } - }, - "is-core-module": { - "version": "2.9.0", + "version": "5.1.0", "bundled": true, "dev": true, "requires": { - "has": "^1.0.3" + "cidr-regex": "^4.1.1" } }, "is-fullwidth-code-point": { @@ -8387,8 +8788,22 @@ "bundled": true, "dev": true }, + "jackspeak": { + "version": "3.4.0", + "bundled": true, + "dev": true, + "requires": { + "@isaacs/cliui": "^8.0.2", + "@pkgjs/parseargs": "^0.11.0" + } + }, + "jsbn": { + "version": "1.1.0", + "bundled": true, + "dev": true + }, "json-parse-even-better-errors": { - "version": "2.3.1", + "version": "3.0.2", "bundled": true, "dev": true }, @@ -8403,167 +8818,163 @@ "dev": true }, "just-diff": { - "version": "5.0.2", + "version": "6.0.2", "bundled": true, "dev": true }, "just-diff-apply": { - "version": "5.2.0", + "version": "5.5.0", "bundled": true, "dev": true }, "libnpmaccess": { - "version": "6.0.3", + "version": "8.0.6", "bundled": true, "dev": true, "requires": { - "aproba": "^2.0.0", - "minipass": "^3.1.1", - "npm-package-arg": "^9.0.1", - "npm-registry-fetch": "^13.0.0" + "npm-package-arg": "^11.0.2", + "npm-registry-fetch": "^17.0.1" } }, "libnpmdiff": { - "version": "4.0.3", + "version": "6.1.4", "bundled": true, "dev": true, "requires": { - "@npmcli/disparity-colors": "^2.0.0", - "@npmcli/installed-package-contents": "^1.0.7", - "binary-extensions": "^2.2.0", - "diff": "^5.0.0", - "minimatch": "^5.0.1", - "npm-package-arg": "^9.0.1", - "pacote": "^13.0.5", - "tar": "^6.1.0" + "@npmcli/arborist": "^7.5.4", + "@npmcli/installed-package-contents": "^2.1.0", + "binary-extensions": "^2.3.0", + "diff": "^5.1.0", + "minimatch": "^9.0.4", + "npm-package-arg": "^11.0.2", + "pacote": "^18.0.6", + "tar": "^6.2.1" } }, "libnpmexec": { - "version": "4.0.5", + "version": "8.1.3", "bundled": true, "dev": true, "requires": { - "@npmcli/arborist": "^5.0.0", - "@npmcli/ci-detect": "^2.0.0", - "@npmcli/run-script": "^3.0.0", - "chalk": "^4.1.0", - "mkdirp-infer-owner": "^2.0.0", - "npm-package-arg": "^9.0.1", - "npmlog": "^6.0.2", - "pacote": "^13.0.5", - "proc-log": "^2.0.0", - "read": "^1.0.7", - "read-package-json-fast": "^2.0.2", - "walk-up-path": "^1.0.0" + "@npmcli/arborist": "^7.5.4", + "@npmcli/run-script": "^8.1.0", + "ci-info": "^4.0.0", + "npm-package-arg": "^11.0.2", + "pacote": "^18.0.6", + "proc-log": "^4.2.0", + "read": "^3.0.1", + "read-package-json-fast": "^3.0.2", + "semver": "^7.3.7", + "walk-up-path": "^3.0.1" } }, "libnpmfund": { - "version": "3.0.2", + "version": "5.0.12", "bundled": true, "dev": true, "requires": { - "@npmcli/arborist": "^5.0.0" + "@npmcli/arborist": "^7.5.4" } }, "libnpmhook": { - "version": "8.0.3", + "version": "10.0.5", "bundled": true, "dev": true, "requires": { "aproba": "^2.0.0", - "npm-registry-fetch": "^13.0.0" + "npm-registry-fetch": "^17.0.1" } }, "libnpmorg": { - "version": "4.0.3", + "version": "6.0.6", "bundled": true, "dev": true, "requires": { "aproba": "^2.0.0", - "npm-registry-fetch": "^13.0.0" + "npm-registry-fetch": "^17.0.1" } }, "libnpmpack": { - "version": "4.1.0", + "version": "7.0.4", "bundled": true, "dev": true, "requires": { - "@npmcli/run-script": "^3.0.0", - "npm-package-arg": "^9.0.1", - "pacote": "^13.5.0" + "@npmcli/arborist": "^7.5.4", + "@npmcli/run-script": "^8.1.0", + "npm-package-arg": "^11.0.2", + "pacote": "^18.0.6" } }, "libnpmpublish": { - "version": "6.0.4", + "version": "9.0.9", "bundled": true, "dev": true, "requires": { - "normalize-package-data": "^4.0.0", - "npm-package-arg": "^9.0.1", - "npm-registry-fetch": "^13.0.0", + "ci-info": "^4.0.0", + "normalize-package-data": "^6.0.1", + "npm-package-arg": "^11.0.2", + "npm-registry-fetch": "^17.0.1", + "proc-log": "^4.2.0", "semver": "^7.3.7", - "ssri": "^9.0.0" + "sigstore": "^2.2.0", + "ssri": "^10.0.6" } }, "libnpmsearch": { - "version": "5.0.3", + "version": "7.0.6", "bundled": true, "dev": true, "requires": { - "npm-registry-fetch": "^13.0.0" + "npm-registry-fetch": "^17.0.1" } }, "libnpmteam": { - "version": "4.0.3", + "version": "6.0.5", "bundled": true, "dev": true, "requires": { "aproba": "^2.0.0", - "npm-registry-fetch": "^13.0.0" + "npm-registry-fetch": "^17.0.1" } }, "libnpmversion": { - "version": "3.0.4", + "version": "6.0.3", "bundled": true, "dev": true, "requires": { - "@npmcli/git": "^3.0.0", - "@npmcli/run-script": "^3.0.0", - "json-parse-even-better-errors": "^2.3.1", - "proc-log": "^2.0.0", + "@npmcli/git": "^5.0.7", + "@npmcli/run-script": "^8.1.0", + "json-parse-even-better-errors": "^3.0.2", + "proc-log": "^4.2.0", "semver": "^7.3.7" } }, "lru-cache": { - "version": "7.9.0", + "version": "10.2.2", "bundled": true, "dev": true }, "make-fetch-happen": { - "version": "10.1.5", + "version": "13.0.1", "bundled": true, "dev": true, "requires": { - "agentkeepalive": "^4.2.1", - "cacache": "^16.1.0", - "http-cache-semantics": "^4.1.0", - "http-proxy-agent": "^5.0.0", - "https-proxy-agent": "^5.0.0", + "@npmcli/agent": "^2.0.0", + "cacache": "^18.0.0", + "http-cache-semantics": "^4.1.1", "is-lambda": "^1.0.1", - "lru-cache": "^7.7.1", - "minipass": "^3.1.6", - "minipass-collect": "^1.0.2", - "minipass-fetch": "^2.0.3", + "minipass": "^7.0.2", + "minipass-fetch": "^3.0.0", "minipass-flush": "^1.0.5", "minipass-pipeline": "^1.2.4", "negotiator": "^0.6.3", + "proc-log": "^4.2.0", "promise-retry": "^2.0.1", - "socks-proxy-agent": "^6.1.1", - "ssri": "^9.0.0" + "ssri": "^10.0.0" } }, "minimatch": { - "version": "5.0.1", + "version": "9.0.5", "bundled": true, "dev": true, "requires": { @@ -8571,28 +8982,25 @@ } }, "minipass": { - "version": "3.1.6", + "version": "7.1.2", "bundled": true, - "dev": true, - "requires": { - "yallist": "^4.0.0" - } + "dev": true }, "minipass-collect": { - "version": "1.0.2", + "version": "2.0.1", "bundled": true, "dev": true, "requires": { - "minipass": "^3.0.0" + "minipass": "^7.0.3" } }, "minipass-fetch": { - "version": "2.1.0", + "version": "3.0.5", "bundled": true, "dev": true, "requires": { "encoding": "^0.1.13", - "minipass": "^3.1.6", + "minipass": "^7.0.3", "minipass-sized": "^1.0.3", "minizlib": "^2.1.2" } @@ -8603,15 +9011,16 @@ "dev": true, "requires": { "minipass": "^3.0.0" - } - }, - "minipass-json-stream": { - "version": "1.0.1", - "bundled": true, - "dev": true, - "requires": { - "jsonparse": "^1.3.1", - "minipass": "^3.0.0" + }, + "dependencies": { + "minipass": { + "version": "3.3.6", + "bundled": true, + "dev": true, + "requires": { + "yallist": "^4.0.0" + } + } } }, "minipass-pipeline": { @@ -8620,6 +9029,16 @@ "dev": true, "requires": { "minipass": "^3.0.0" + }, + "dependencies": { + "minipass": { + "version": "3.3.6", + "bundled": true, + "dev": true, + "requires": { + "yallist": "^4.0.0" + } + } } }, "minipass-sized": { @@ -8628,6 +9047,16 @@ "dev": true, "requires": { "minipass": "^3.0.0" + }, + "dependencies": { + "minipass": { + "version": "3.3.6", + "bundled": true, + "dev": true, + "requires": { + "yallist": "^4.0.0" + } + } } }, "minizlib": { @@ -8637,6 +9066,16 @@ "requires": { "minipass": "^3.0.0", "yallist": "^4.0.0" + }, + "dependencies": { + "minipass": { + "version": "3.3.6", + "bundled": true, + "dev": true, + "requires": { + "yallist": "^4.0.0" + } + } } }, "mkdirp": { @@ -8644,23 +9083,13 @@ "bundled": true, "dev": true }, - "mkdirp-infer-owner": { - "version": "2.0.0", - "bundled": true, - "dev": true, - "requires": { - "chownr": "^2.0.0", - "infer-owner": "^1.0.4", - "mkdirp": "^1.0.3" - } - }, "ms": { "version": "2.1.3", "bundled": true, "dev": true }, "mute-stream": { - "version": "0.0.8", + "version": "1.0.0", "bundled": true, "dev": true }, @@ -8670,91 +9099,62 @@ "dev": true }, "node-gyp": { - "version": "9.0.0", + "version": "10.1.0", "bundled": true, "dev": true, "requires": { "env-paths": "^2.2.0", - "glob": "^7.1.4", + "exponential-backoff": "^3.1.1", + "glob": "^10.3.10", "graceful-fs": "^4.2.6", - "make-fetch-happen": "^10.0.3", - "nopt": "^5.0.0", - "npmlog": "^6.0.0", - "rimraf": "^3.0.2", + "make-fetch-happen": "^13.0.0", + "nopt": "^7.0.0", + "proc-log": "^3.0.0", "semver": "^7.3.5", "tar": "^6.1.2", - "which": "^2.0.2" + "which": "^4.0.0" }, "dependencies": { - "brace-expansion": { - "version": "1.1.11", + "proc-log": { + "version": "3.0.0", "bundled": true, - "dev": true, - "requires": { - "balanced-match": "^1.0.0", - "concat-map": "0.0.1" - } - }, - "glob": { - "version": "7.2.0", - "bundled": true, - "dev": true, - "requires": { - "fs.realpath": "^1.0.0", - "inflight": "^1.0.4", - "inherits": "2", - "minimatch": "^3.0.4", - "once": "^1.3.0", - "path-is-absolute": "^1.0.0" - } - }, - "minimatch": { - "version": "3.1.2", - "bundled": true, - "dev": true, - "requires": { - "brace-expansion": "^1.1.7" - } + "dev": true } } }, "nopt": { - "version": "5.0.0", + "version": "7.2.1", "bundled": true, "dev": true, "requires": { - "abbrev": "1" + "abbrev": "^2.0.0" } }, "normalize-package-data": { - "version": "4.0.0", + "version": "6.0.2", "bundled": true, "dev": true, "requires": { - "hosted-git-info": "^5.0.0", - "is-core-module": "^2.8.1", + "hosted-git-info": "^7.0.0", "semver": "^7.3.5", "validate-npm-package-license": "^3.0.4" } }, "npm-audit-report": { - "version": "3.0.0", + "version": "5.0.0", "bundled": true, - "dev": true, - "requires": { - "chalk": "^4.0.0" - } + "dev": true }, "npm-bundled": { - "version": "1.1.2", + "version": "3.0.1", "bundled": true, "dev": true, "requires": { - "npm-normalize-package-bin": "^1.0.1" + "npm-normalize-package-bin": "^3.0.0" } }, "npm-install-checks": { - "version": "5.0.0", + "version": "6.3.0", "bundled": true, "dev": true, "requires": { @@ -8762,147 +9162,146 @@ } }, "npm-normalize-package-bin": { - "version": "1.0.1", + "version": "3.0.1", "bundled": true, "dev": true }, "npm-package-arg": { - "version": "9.0.2", + "version": "11.0.2", "bundled": true, "dev": true, "requires": { - "hosted-git-info": "^5.0.0", + "hosted-git-info": "^7.0.0", + "proc-log": "^4.0.0", "semver": "^7.3.5", - "validate-npm-package-name": "^4.0.0" + "validate-npm-package-name": "^5.0.0" } }, "npm-packlist": { - "version": "5.1.0", + "version": "8.0.2", "bundled": true, "dev": true, "requires": { - "glob": "^8.0.1", - "ignore-walk": "^5.0.1", - "npm-bundled": "^1.1.2", - "npm-normalize-package-bin": "^1.0.1" + "ignore-walk": "^6.0.4" } }, "npm-pick-manifest": { - "version": "7.0.1", + "version": "9.1.0", "bundled": true, "dev": true, "requires": { - "npm-install-checks": "^5.0.0", - "npm-normalize-package-bin": "^1.0.1", - "npm-package-arg": "^9.0.0", + "npm-install-checks": "^6.0.0", + "npm-normalize-package-bin": "^3.0.0", + "npm-package-arg": "^11.0.0", "semver": "^7.3.5" } }, "npm-profile": { - "version": "6.0.3", + "version": "10.0.0", "bundled": true, "dev": true, "requires": { - "npm-registry-fetch": "^13.0.1", - "proc-log": "^2.0.0" + "npm-registry-fetch": "^17.0.1", + "proc-log": "^4.0.0" } }, "npm-registry-fetch": { - "version": "13.1.1", + "version": "17.1.0", "bundled": true, "dev": true, "requires": { - "make-fetch-happen": "^10.0.6", - "minipass": "^3.1.6", - "minipass-fetch": "^2.0.3", - "minipass-json-stream": "^1.0.1", + "@npmcli/redact": "^2.0.0", + "jsonparse": "^1.3.1", + "make-fetch-happen": "^13.0.0", + "minipass": "^7.0.2", + "minipass-fetch": "^3.0.0", "minizlib": "^2.1.2", - "npm-package-arg": "^9.0.1", - "proc-log": "^2.0.0" + "npm-package-arg": "^11.0.0", + "proc-log": "^4.0.0" } }, "npm-user-validate": { - "version": "1.0.1", + "version": "2.0.1", "bundled": true, "dev": true }, - "npmlog": { - "version": "6.0.2", - "bundled": true, - "dev": true, - "requires": { - "are-we-there-yet": "^3.0.0", - "console-control-strings": "^1.1.0", - "gauge": "^4.0.3", - "set-blocking": "^2.0.0" - } - }, - "once": { - "version": "1.4.0", + "p-map": { + "version": "4.0.0", "bundled": true, "dev": true, "requires": { - "wrappy": "1" + "aggregate-error": "^3.0.0" } }, - "opener": { - "version": "1.5.2", + "package-json-from-dist": { + "version": "1.0.0", "bundled": true, "dev": true }, - "p-map": { - "version": "4.0.0", + "pacote": { + "version": "18.0.6", + "bundled": true, + "dev": true, + "requires": { + "@npmcli/git": "^5.0.0", + "@npmcli/installed-package-contents": "^2.0.1", + "@npmcli/package-json": "^5.1.0", + "@npmcli/promise-spawn": "^7.0.0", + "@npmcli/run-script": "^8.0.0", + "cacache": "^18.0.0", + "fs-minipass": "^3.0.0", + "minipass": "^7.0.2", + "npm-package-arg": "^11.0.0", + "npm-packlist": "^8.0.0", + "npm-pick-manifest": "^9.0.0", + "npm-registry-fetch": "^17.0.0", + "proc-log": "^4.0.0", + "promise-retry": "^2.0.1", + "sigstore": "^2.2.0", + "ssri": "^10.0.0", + "tar": "^6.1.11" + } + }, + "parse-conflict-json": { + "version": "3.0.1", "bundled": true, "dev": true, "requires": { - "aggregate-error": "^3.0.0" + "json-parse-even-better-errors": "^3.0.0", + "just-diff": "^6.0.0", + "just-diff-apply": "^5.2.0" } }, - "pacote": { - "version": "13.5.0", + "path-key": { + "version": "3.1.1", + "bundled": true, + "dev": true + }, + "path-scurry": { + "version": "1.11.1", "bundled": true, "dev": true, "requires": { - "@npmcli/git": "^3.0.0", - "@npmcli/installed-package-contents": "^1.0.7", - "@npmcli/promise-spawn": "^3.0.0", - "@npmcli/run-script": "^3.0.1", - "cacache": "^16.0.0", - "chownr": "^2.0.0", - "fs-minipass": "^2.1.0", - "infer-owner": "^1.0.4", - "minipass": "^3.1.6", - "mkdirp": "^1.0.4", - "npm-package-arg": "^9.0.0", - "npm-packlist": "^5.1.0", - "npm-pick-manifest": "^7.0.0", - "npm-registry-fetch": "^13.0.1", - "proc-log": "^2.0.0", - "promise-retry": "^2.0.1", - "read-package-json": "^5.0.0", - "read-package-json-fast": "^2.0.3", - "rimraf": "^3.0.2", - "ssri": "^9.0.0", - "tar": "^6.1.11" + "lru-cache": "^10.2.0", + "minipass": "^5.0.0 || ^6.0.2 || ^7.0.0" } }, - "parse-conflict-json": { - "version": "2.0.2", + "postcss-selector-parser": { + "version": "6.1.0", "bundled": true, "dev": true, "requires": { - "json-parse-even-better-errors": "^2.3.1", - "just-diff": "^5.0.1", - "just-diff-apply": "^5.2.0" + "cssesc": "^3.0.0", + "util-deprecate": "^1.0.2" } }, - "path-is-absolute": { - "version": "1.0.1", + "proc-log": { + "version": "4.2.0", "bundled": true, "dev": true }, - "proc-log": { - "version": "2.0.1", + "proggy": { + "version": "2.0.0", "bundled": true, "dev": true }, @@ -8912,7 +9311,7 @@ "dev": true }, "promise-call-limit": { - "version": "1.0.1", + "version": "3.0.1", "bundled": true, "dev": true }, @@ -8931,11 +9330,11 @@ } }, "promzard": { - "version": "0.3.0", + "version": "1.0.2", "bundled": true, "dev": true, "requires": { - "read": "1" + "read": "^3.0.1" } }, "qrcode-terminal": { @@ -8944,57 +9343,25 @@ "dev": true }, "read": { - "version": "1.0.7", + "version": "3.0.1", "bundled": true, "dev": true, "requires": { - "mute-stream": "~0.0.4" + "mute-stream": "^1.0.0" } }, "read-cmd-shim": { - "version": "3.0.0", + "version": "4.0.0", "bundled": true, "dev": true }, - "read-package-json": { - "version": "5.0.1", - "bundled": true, - "dev": true, - "requires": { - "glob": "^8.0.1", - "json-parse-even-better-errors": "^2.3.1", - "normalize-package-data": "^4.0.0", - "npm-normalize-package-bin": "^1.0.1" - } - }, "read-package-json-fast": { - "version": "2.0.3", - "bundled": true, - "dev": true, - "requires": { - "json-parse-even-better-errors": "^2.3.0", - "npm-normalize-package-bin": "^1.0.1" - } - }, - "readable-stream": { - "version": "3.6.0", - "bundled": true, - "dev": true, - "requires": { - "inherits": "^2.0.3", - "string_decoder": "^1.1.1", - "util-deprecate": "^1.0.1" - } - }, - "readdir-scoped-modules": { - "version": "1.1.0", + "version": "3.0.2", "bundled": true, "dev": true, "requires": { - "debuglog": "^1.0.1", - "dezalgo": "^1.0.0", - "graceful-fs": "^4.1.2", - "once": "^1.3.0" + "json-parse-even-better-errors": "^3.0.0", + "npm-normalize-package-bin": "^3.0.0" } }, "retry": { @@ -9002,51 +9369,6 @@ "bundled": true, "dev": true }, - "rimraf": { - "version": "3.0.2", - "bundled": true, - "dev": true, - "requires": { - "glob": "^7.1.3" - }, - "dependencies": { - "brace-expansion": { - "version": "1.1.11", - "bundled": true, - "dev": true, - "requires": { - "balanced-match": "^1.0.0", - "concat-map": "0.0.1" - } - }, - "glob": { - "version": "7.2.0", - "bundled": true, - "dev": true, - "requires": { - "fs.realpath": "^1.0.0", - "inflight": "^1.0.4", - "inherits": "2", - "minimatch": "^3.0.4", - "once": "^1.3.0", - "path-is-absolute": "^1.0.0" - } - }, - "minimatch": { - "version": "3.1.2", - "bundled": true, - "dev": true, - "requires": { - "brace-expansion": "^1.1.7" - } - } - } - }, - "safe-buffer": { - "version": "5.2.1", - "bundled": true, - "dev": true - }, "safer-buffer": { "version": "2.1.2", "bundled": true, @@ -9054,73 +9376,92 @@ "optional": true }, "semver": { - "version": "7.3.7", + "version": "7.6.2", + "bundled": true, + "dev": true + }, + "shebang-command": { + "version": "2.0.0", "bundled": true, "dev": true, "requires": { - "lru-cache": "^6.0.0" - }, - "dependencies": { - "lru-cache": { - "version": "6.0.0", - "bundled": true, - "dev": true, - "requires": { - "yallist": "^4.0.0" - } - } + "shebang-regex": "^3.0.0" } }, - "set-blocking": { - "version": "2.0.0", + "shebang-regex": { + "version": "3.0.0", "bundled": true, "dev": true }, "signal-exit": { - "version": "3.0.7", + "version": "4.1.0", "bundled": true, "dev": true }, + "sigstore": { + "version": "2.3.1", + "bundled": true, + "dev": true, + "requires": { + "@sigstore/bundle": "^2.3.2", + "@sigstore/core": "^1.0.0", + "@sigstore/protobuf-specs": "^0.3.2", + "@sigstore/sign": "^2.3.2", + "@sigstore/tuf": "^2.3.4", + "@sigstore/verify": "^1.2.1" + } + }, "smart-buffer": { "version": "4.2.0", "bundled": true, "dev": true }, "socks": { - "version": "2.6.2", + "version": "2.8.3", "bundled": true, "dev": true, "requires": { - "ip": "^1.1.5", + "ip-address": "^9.0.5", "smart-buffer": "^4.2.0" } }, "socks-proxy-agent": { - "version": "6.2.0", + "version": "8.0.4", "bundled": true, "dev": true, "requires": { - "agent-base": "^6.0.2", - "debug": "^4.3.3", - "socks": "^2.6.2" + "agent-base": "^7.1.1", + "debug": "^4.3.4", + "socks": "^2.8.3" } }, "spdx-correct": { - "version": "3.1.1", + "version": "3.2.0", "bundled": true, "dev": true, "requires": { "spdx-expression-parse": "^3.0.0", "spdx-license-ids": "^3.0.0" + }, + "dependencies": { + "spdx-expression-parse": { + "version": "3.0.1", + "bundled": true, + "dev": true, + "requires": { + "spdx-exceptions": "^2.1.0", + "spdx-license-ids": "^3.0.0" + } + } } }, "spdx-exceptions": { - "version": "2.3.0", + "version": "2.5.0", "bundled": true, "dev": true }, "spdx-expression-parse": { - "version": "3.0.1", + "version": "4.0.0", "bundled": true, "dev": true, "requires": { @@ -9129,28 +9470,35 @@ } }, "spdx-license-ids": { - "version": "3.0.11", + "version": "3.0.18", + "bundled": true, + "dev": true + }, + "sprintf-js": { + "version": "1.1.3", "bundled": true, "dev": true }, "ssri": { - "version": "9.0.1", + "version": "10.0.6", "bundled": true, "dev": true, "requires": { - "minipass": "^3.1.1" + "minipass": "^7.0.3" } }, - "string_decoder": { - "version": "1.3.0", + "string-width": { + "version": "4.2.3", "bundled": true, "dev": true, "requires": { - "safe-buffer": "~5.2.0" + "emoji-regex": "^8.0.0", + "is-fullwidth-code-point": "^3.0.0", + "strip-ansi": "^6.0.1" } }, - "string-width": { - "version": "4.2.3", + "string-width-cjs": { + "version": "npm:string-width@4.2.3", "bundled": true, "dev": true, "requires": { @@ -9167,25 +9515,55 @@ "ansi-regex": "^5.0.1" } }, - "supports-color": { - "version": "7.2.0", + "strip-ansi-cjs": { + "version": "npm:strip-ansi@6.0.1", "bundled": true, "dev": true, "requires": { - "has-flag": "^4.0.0" + "ansi-regex": "^5.0.1" } }, + "supports-color": { + "version": "9.4.0", + "bundled": true, + "dev": true + }, "tar": { - "version": "6.1.11", + "version": "6.2.1", "bundled": true, "dev": true, "requires": { "chownr": "^2.0.0", "fs-minipass": "^2.0.0", - "minipass": "^3.0.0", + "minipass": "^5.0.0", "minizlib": "^2.1.1", "mkdirp": "^1.0.3", "yallist": "^4.0.0" + }, + "dependencies": { + "fs-minipass": { + "version": "2.1.0", + "bundled": true, + "dev": true, + "requires": { + "minipass": "^3.0.0" + }, + "dependencies": { + "minipass": { + "version": "3.3.6", + "bundled": true, + "dev": true, + "requires": { + "yallist": "^4.0.0" + } + } + } + }, + "minipass": { + "version": "5.0.0", + "bundled": true, + "dev": true + } } }, "text-table": { @@ -9199,20 +9577,30 @@ "dev": true }, "treeverse": { - "version": "2.0.0", + "version": "3.0.0", "bundled": true, "dev": true }, + "tuf-js": { + "version": "2.2.1", + "bundled": true, + "dev": true, + "requires": { + "@tufjs/models": "2.0.1", + "debug": "^4.3.4", + "make-fetch-happen": "^13.0.1" + } + }, "unique-filename": { - "version": "1.1.1", + "version": "3.0.0", "bundled": true, "dev": true, "requires": { - "unique-slug": "^2.0.0" + "unique-slug": "^4.0.0" } }, "unique-slug": { - "version": "2.0.2", + "version": "4.0.0", "bundled": true, "dev": true, "requires": { @@ -9231,57 +9619,111 @@ "requires": { "spdx-correct": "^3.0.0", "spdx-expression-parse": "^3.0.0" + }, + "dependencies": { + "spdx-expression-parse": { + "version": "3.0.1", + "bundled": true, + "dev": true, + "requires": { + "spdx-exceptions": "^2.1.0", + "spdx-license-ids": "^3.0.0" + } + } } }, "validate-npm-package-name": { - "version": "4.0.0", + "version": "5.0.1", "bundled": true, - "dev": true, - "requires": { - "builtins": "^5.0.0" - } + "dev": true }, "walk-up-path": { - "version": "1.0.0", + "version": "3.0.1", "bundled": true, "dev": true }, - "wcwidth": { - "version": "1.0.1", + "which": { + "version": "4.0.0", "bundled": true, "dev": true, "requires": { - "defaults": "^1.0.3" + "isexe": "^3.1.1" + }, + "dependencies": { + "isexe": { + "version": "3.1.1", + "bundled": true, + "dev": true + } } }, - "which": { - "version": "2.0.2", + "wrap-ansi": { + "version": "8.1.0", "bundled": true, "dev": true, "requires": { - "isexe": "^2.0.0" + "ansi-styles": "^6.1.0", + "string-width": "^5.0.1", + "strip-ansi": "^7.0.1" + }, + "dependencies": { + "ansi-regex": { + "version": "6.0.1", + "bundled": 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true, "requires": { "imurmurhash": "^0.1.4", - "signal-exit": "^3.0.7" + "signal-exit": "^4.0.1" } }, "yallist": { @@ -9300,14 +9742,11 @@ "path-key": "^3.0.0" } }, - "once": { - "version": "1.4.0", - "resolved": "https://registry.npmjs.org/once/-/once-1.4.0.tgz", - "integrity": "sha1-WDsap3WWHUsROsF9nFC6753Xa9E=", - "dev": true, - "requires": { - "wrappy": "1" - } + "object-assign": { + "version": "4.1.1", + "resolved": "https://registry.npmjs.org/object-assign/-/object-assign-4.1.1.tgz", + "integrity": "sha512-rJgTQnkUnH1sFw8yT6VSU3zD3sWmu6sZhIseY8VX+GRu3P6F7Fu+JNDoXfklElbLJSnc3FUQHVe4cU5hj+BcUg==", + "dev": true }, "onetime": { "version": "5.1.2", @@ -9319,18 +9758,18 @@ } }, "p-each-series": { - "version": "2.2.0", - "resolved": "https://registry.npmjs.org/p-each-series/-/p-each-series-2.2.0.tgz", - "integrity": "sha512-ycIL2+1V32th+8scbpTvyHNaHe02z0sjgh91XXjAk+ZeXoPN4Z46DVUnzdso0aX4KckKw0FNNFHdjZ2UsZvxiA==", + "version": "3.0.0", + "resolved": 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"@semantic-release/commit-analyzer": "^13.0.0", "@semantic-release/exec": "^6.0.3", "@semantic-release/git": "^10.0.1", - "@semantic-release/release-notes-generator": "^10.0.3", - "semantic-release": "^19.0.5" + "@semantic-release/release-notes-generator": "^14.0.1", + "semantic-release": "^24.0.0" } } diff --git a/pyproject.toml b/pyproject.toml index 14d9a17..c9cf2be 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,9 +1,46 @@ -[tool.cibuildwheel] -before-all = "curl https://sh.rustup.rs -sSf | sh -s -- --default-toolchain stable -y" -skip = "cp27-* cp34-* cp35-* cp36-* pp* *-win32 *-musllinux* *_i686*" -environment = 'PATH="$PATH:$HOME/.cargo/bin"' -test-command = "python -m unittest discover {project}/test" -test-requires = ["dendropy", "numpy"] +[project] +name = "phylodm" +version = "3.0.0" +dependencies = ["dendropy", "numpy"] +requires-python = ">=3.8" +description = "Efficient calculation of phylogenetic distance matrices." +readme = "README.md" +authors = [ + { name = "Aaron Mussig", email = "aaronmussig@gmail.com" } +] +license = { file = "LICENSE" } +keywords = ["phylogenetic", "distance", "matrix", "symmetric"] +classifiers = [ + "Development Status :: 5 - Production/Stable", + "Intended Audience :: Science/Research", + "License :: OSI Approved :: GNU General Public License v3 (GPLv3)", + "Natural Language :: English", + "Operating System :: OS Independent", + "Programming Language :: Python :: 3.8", + "Programming Language :: Python :: 3.9", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: 3.12", + "Programming Language :: Rust", + "Topic :: Scientific/Engineering :: Bio-Informatics", +] + +[project.urls] +Homepage = "https://github.com/aaronmussig/PhyloDM" +Documentation = "https://github.com/aaronmussig/PhyloDM" +Repository = "https://github.com/aaronmussig/PhyloDM" +Issues = "https://github.com/aaronmussig/PhyloDM/issues" +Changelog = "https://github.com/aaronmussig/PhyloDM/blob/main/CHANGELOG.md" [build-system] -requires = ["setuptools", "wheel", "setuptools-rust"] +requires = ["maturin>=1.0,<2.0"] +build-backend = "maturin" + +[tool.maturin] +features = ["pyo3", "numpy", "python"] +python-source = "python" +module-name = "phylodm.pdm" +include = [ + { format = "sdist", path = ".cargo/*" }, + { format = "sdist", path = "Cargo.lock" }, +] diff --git a/phylodm/__init__.py b/python/phylodm/__init__.py similarity index 91% rename from phylodm/__init__.py rename to python/phylodm/__init__.py index 7923940..1c8d82d 100644 --- a/phylodm/__init__.py +++ b/python/phylodm/__init__.py @@ -1,12 +1,9 @@ from __future__ import annotations from typing import Optional, List -from typing import TYPE_CHECKING import dendropy - -if TYPE_CHECKING: - import numpy as np +import numpy as np from .pdm import PhyloDM as PDM @@ -80,6 +77,12 @@ def add_edge(self, parent_id: int, child_id: int, length: float): """ return self._rs.add_edge(parent_id=parent_id, child_id=child_id, length=length) + def update_edge_lengths(self, child_nodes: np.ndarray, new_edge_lengths: np.ndarray): + return self._rs.update_edge_lengths(child_nodes=child_nodes, lengths=new_edge_lengths) + + def update_all_edge_lengths(self, length: float): + return self._rs.update_all_edge_lengths(length=length) + def get_nodes(self) -> List[int]: """Return all node indexes in the tree.""" return self._rs.get_nodes() diff --git a/python/phylodm/py.typed b/python/phylodm/py.typed new file mode 100644 index 0000000..e69de29 diff --git a/setup.py b/setup.py deleted file mode 100644 index c453bd6..0000000 --- a/setup.py +++ /dev/null @@ -1,71 +0,0 @@ -import sys - -# Restrict to Python 3.7+ -if sys.version_info < (3, 7): - sys.exit('Only Python 3.7+ is supported') - -# Check setuptools is installed -try: - from setuptools import setup -except ImportError: - sys.exit('Please install setuptools before installing this package.') - -# Check setuptools_rust is installed -try: - from setuptools_rust import Binding, RustExtension -except ImportError: - sys.exit('Please install setuptools-rust before installing this package.') - - -# Read the long description from the README file -def readme(): - with open('README.md', encoding='utf-8') as f: - return f.read() - - -# Read the version from the Cargo.toml file -def get_package_version(): - with open('Cargo.toml') as f: - for line in f: - if line.startswith('version ='): - return line.split('=')[1].strip().strip('"').strip("'") - - -# Create the package -setup(name='phylodm', - version=get_package_version(), - description='Efficient calculation of phylogenetic distance matrices.', - long_description=readme(), - long_description_content_type='text/markdown', - author='Aaron Mussig', - author_email='aaronmussig@gmail.com', - url='https://github.com/aaronmussig/PhyloDM', - license='GPL3', - project_urls={ - "Bug Tracker": "https://github.com/aaronmussig/PhyloDM/issues", - "Documentation": "https://github.com/aaronmussig/PhyloDM", - "Source Code": "https://github.com/aaronmussig/PhyloDM", - }, - classifiers=[ - 'Development Status :: 5 - Production/Stable', - 'Intended Audience :: Science/Research', - 'License :: OSI Approved :: GNU General Public License v3 (GPLv3)', - 'Natural Language :: English', - 'Operating System :: OS Independent', - 'Programming Language :: Python :: 3.7', - 'Programming Language :: Python :: 3.8', - 'Programming Language :: Python :: 3.9', - 'Programming Language :: Python :: 3.10', - 'Programming Language :: Python :: 3.11', - 'Programming Language :: Rust', - 'Topic :: Scientific/Engineering :: Bio-Informatics', - ], - keywords='phylogenetic distance matrix symmetric', - packages=['phylodm'], - install_requires=['numpy'], - setup_requires=['setuptools-rust', 'setuptools', 'wheel', 'dendropy'], - python_requires='>=3.7', - data_files=[("", ["LICENSE"])], - rust_extensions=[RustExtension("phylodm.pdm", binding=Binding.PyO3, features=['python'])], - zip_safe=False, - ) diff --git a/src/lib.rs b/src/lib.rs index 39d4350..ce8b50b 100644 --- a/src/lib.rs +++ b/src/lib.rs @@ -1,6 +1,6 @@ pub use self::pdm::PDM; -mod pdm; +pub mod pdm; #[cfg(feature = "python")] pub mod python; diff --git a/src/pdm.rs b/src/pdm.rs index a6f9197..a668df9 100644 --- a/src/pdm.rs +++ b/src/pdm.rs @@ -25,19 +25,19 @@ use crate::util::{create_row_vec_from_mat_dims, row_idx_from_mat_coords, row_vec /// ``` #[derive(Default)] pub struct PDM { - pub(crate) nodes: Vec, - pub(crate) taxon_to_node_id: HashMap, - pub(crate) leaf_idx_to_row_idx: HashMap, - pub(crate) leaf_idx_to_row_idx_vec: Vec, - pub(crate) row_idx_to_leaf_idx: Vec, - pub(crate) nodes_at_depth: HashMap>, - pub(crate) row_vec: Option>, + pub nodes: Vec, + pub taxon_to_node_id: HashMap, + pub leaf_idx_to_row_idx: HashMap, + pub leaf_idx_to_row_idx_vec: Vec, + pub row_idx_to_leaf_idx: Vec, + pub nodes_at_depth: HashMap>, + pub row_vec: Option>, } impl PDM { /// Return the number of nodes (leaf + internal) in the tree. #[must_use] - fn n_nodes(&self) -> usize { + pub fn n_nodes(&self) -> usize { self.nodes.len() } @@ -57,6 +57,16 @@ impl PDM { } Ok(out) } + + /// Return all node IDs in the tree. + #[must_use] + pub fn node_ids(&self) -> Vec { + let mut out = Vec::with_capacity(self.nodes.len()); + for node in &self.nodes { + out.push(node.id); + } + out + } /// Return the sum of all branches in the tree. #[must_use] @@ -68,7 +78,7 @@ impl PDM { } /// Returns a vector of node indices at a specific depth. Errors if depth doesn't exist. - fn get_node_idxs_at_depth(&self, depth: NodeDepth) -> Result, PhyloErr> { + pub fn get_node_idxs_at_depth(&self, depth: NodeDepth) -> Result, PhyloErr> { if self.nodes_at_depth.get(&depth).is_none() { return Err(PhyloErr("No nodes at depth! Please report this error.".to_string())); } @@ -90,13 +100,13 @@ impl PDM { /// Returns the row vector index for a given leaf node id. #[must_use] - fn get_row_vec_idx_from_leaf_idx(&self, leaf_id: NodeId) -> usize { + pub fn get_row_vec_idx_from_leaf_idx(&self, leaf_id: NodeId) -> usize { self.leaf_idx_to_row_idx_vec[leaf_id.0] } /// Get the row vector index for two taxa in the tree. #[must_use] - fn get_row_vec_idx_dist_between_leaf_idx(&self, i: NodeId, j: NodeId) -> usize { + pub fn get_row_vec_idx_dist_between_leaf_idx(&self, i: NodeId, j: NodeId) -> usize { let n_taxa = self.n_leaf_nodes(); let i_idx = self.get_row_vec_idx_from_leaf_idx(i); let j_idx = self.get_row_vec_idx_from_leaf_idx(j); @@ -105,7 +115,7 @@ impl PDM { /// Add a new leaf node to the tree. /// Returns the ID of the new node. - fn add_leaf_node(&mut self, taxon: &Taxon) -> Result { + pub fn add_leaf_node(&mut self, taxon: &Taxon) -> Result { // Panic if the taxon is already in the tree. if self.taxon_to_node_id.contains_key(taxon) { return Err(PhyloErr(format!("Taxon already exists in the tree: '{taxon:?}'"))); @@ -121,14 +131,14 @@ impl PDM { } /// Add a new internal node to the tree. - fn add_internal_node(&mut self) -> NodeId { + pub fn add_internal_node(&mut self) -> NodeId { let node_id = NodeId(self.n_nodes()); self.nodes.push(Node::new(node_id, None)); return self.nodes.last().unwrap().id; } /// Add a node to the tree. - pub(crate) fn add_node(&mut self, taxon: Option<&Taxon>) -> Result { + pub fn add_node(&mut self, taxon: Option<&Taxon>) -> Result { match taxon { Some(t) => self.add_leaf_node(t), None => Ok(self.add_internal_node()), @@ -137,13 +147,13 @@ impl PDM { /// Retrieve a node from the tree. #[must_use] - fn get_node(&self, node_id: NodeId) -> &Node { + pub fn get_node(&self, node_id: NodeId) -> &Node { &self.nodes[node_id.0] } /// Retrieve a mutable node from the tree. #[must_use] - fn get_node_mut(&mut self, node_id: NodeId) -> &mut Node { + pub fn get_node_mut(&mut self, node_id: NodeId) -> &mut Node { &mut self.nodes[node_id.0] } @@ -155,13 +165,56 @@ impl PDM { /// * `child`: - `NodeId` of the child node. /// * `length`: - The branch length between these nodes. /// - pub(crate) fn add_edge(&mut self, parent: NodeId, child: NodeId, length: Edge) { + pub fn add_edge(&mut self, parent: NodeId, child: NodeId, length: Edge) { self.get_node_mut(parent).add_child(child); self.get_node_mut(child).set_parent(parent, length); } - /// Set the depth of each node in the tree. - fn assign_node_depth(&mut self) -> Result<(), PhyloErr> { + /// Update edge lengths of a tree + /// + /// # Arguments + /// + /// * `child_nodes`: - Slice of `NodeId`s + /// * `lengths`: - Slice of `Edge`s + /// + pub fn update_edge_lengths(&mut self, child_nodes: &[NodeId], lengths: &[Edge]) -> Result<(), PhyloErr> { + + // Find the root node and skip it + let root_node_id = self.root_node()?; + + // Check the vectors are the same length + if child_nodes.len() != lengths.len() { + return Err(PhyloErr("Lengths vector does not match the number of nodes!".to_string())); + } + + // Update the values + for (child_node_id, length) in child_nodes.iter().zip(lengths.iter()) { + if child_node_id == &root_node_id { + return Err(PhyloErr("Root node cannot have an edge length!".to_string())); + } + self.get_node_mut(*child_node_id).set_parent_distance(*length); + } + + self.compute_row_vec()?; // For distance matrix calculation + Ok(()) + } + + /// Update all edge lengths of a tree to the same value. + pub fn update_all_edge_lengths(&mut self, length: Edge) -> Result<(), PhyloErr> { + let root_node_id = self.root_node()?; + let node_ids = self.node_ids(); + + for node_id in node_ids { + if node_id != root_node_id { + self.get_node_mut(node_id).set_parent_distance(length); + } + } + self.compute_row_vec()?; // For distance matrix calculation + Ok(()) + } + + /// Return the root node of the tree. + pub fn root_node(&self) -> Result { // Iterate over each node to make sure there is only one root node. let mut root = None; for node in &self.nodes { @@ -172,18 +225,24 @@ impl PDM { root = Some(node.id); } } - if root.is_none() { return Err(PhyloErr("No root node detected!".to_string())); } + Ok(root.unwrap()) + } + + /// Set the depth of each node in the tree. + pub fn assign_node_depth(&mut self) -> Result<(), PhyloErr> { + // Iterate over each node to make sure there is only one root node. + let root = self.root_node()?; // Set the depth of all nodes - self.set_node_depth_dfs(root.unwrap())?; + self.set_node_depth_dfs(root)?; Ok(()) } /// Set the depth of all nodes using a depth first search. - fn set_node_depth_dfs(&mut self, root_id: NodeId) -> Result<(), PhyloErr> { + pub fn set_node_depth_dfs(&mut self, root_id: NodeId) -> Result<(), PhyloErr> { let mut nodes_at_depth: HashMap> = HashMap::new(); // Seed the stack with the root node. @@ -236,8 +295,8 @@ impl PDM { } /// Wrapper method to calculate the pairwise distances at a given depth. - fn calculate_distances_at_depth(&mut self, depth: NodeDepth, row_vec: &mut [f64]) -> Result<(), PhyloErr> { - // Iterate over all nodes a this depth + pub fn calculate_distances_at_depth(&mut self, depth: NodeDepth, row_vec: &mut [f64]) -> Result<(), PhyloErr> { + // Iterate over all nodes at this depth for &node_id in &self.get_node_idxs_at_depth(depth)? { let node = self.get_node(node_id); @@ -274,7 +333,7 @@ impl PDM { /// For a given node, iterate over its children and unset the descendant distances. /// This is mainly to free memory during distance matrix calculation. - fn unset_node_child_distances(&mut self, node_id: NodeId) { + pub fn unset_node_child_distances(&mut self, node_id: NodeId) { self.get_node(node_id) .children .clone() @@ -287,7 +346,7 @@ impl PDM { /// This function sets the descendant distances for a given node. /// Note: This is only the distances to all descendant nodes (including leaf nodes). /// The pairwise leaf distances are calculated in another method. - fn set_node_descendant_distance(&mut self, node_id: NodeId) { + pub fn set_node_descendant_distance(&mut self, node_id: NodeId) { let mut node_desc_distances: HashMap = HashMap::new(); let node = self.get_node(node_id); @@ -311,7 +370,7 @@ impl PDM { /// This function calculates the pairwise distances to all leaf nodes. /// Assumes that the memory has not been freed for the mapping. - fn calc_pairwise_distances_to_leaf_nodes(&self, node_id: NodeId, row_vec: &mut [f64]) { + pub fn calc_pairwise_distances_to_leaf_nodes(&self, node_id: NodeId, row_vec: &mut [f64]) { let node = self.get_node(node_id); let children_idxs = &node.children; @@ -353,7 +412,7 @@ impl PDM { } /// Orders the leaf nodes for reproducibility. - fn order_leaf_node_idx(&mut self) { + pub fn order_leaf_node_idx(&mut self) { let mut new_leaf_idx_to_row_idx: HashMap = HashMap::with_capacity(self.n_leaf_nodes()); let mut new_row_idx_to_leaf_idx: Vec = vec![NodeId::default(); self.n_leaf_nodes()]; @@ -465,7 +524,7 @@ impl PDM { Ok(()) } - fn get_taxon_node_idx(&self, taxon: &Taxon) -> NodeId { + pub fn get_taxon_node_idx(&self, taxon: &Taxon) -> NodeId { self.taxon_to_node_id[taxon] } diff --git a/src/python.rs b/src/python.rs index 5b1ea35..e2ca7a0 100644 --- a/src/python.rs +++ b/src/python.rs @@ -1,5 +1,5 @@ -use numpy::{PyArray2, ToPyArray}; -use pyo3::{Py, pyclass, pymethods, pymodule, PyResult, Python, types::PyModule}; +use numpy::{PyArray1, PyArray2, PyArrayMethods, ToPyArray}; +use pyo3::{Py, pyclass, pymethods, pymodule, PyResult, Python, types::PyModule, Bound}; use pyo3::exceptions::PyValueError; use crate::pdm::PDM as RustPhyloDM; @@ -46,6 +46,31 @@ impl PhyloDM { ); } + pub fn update_edge_lengths(&mut self, child_nodes: &Bound<'_, PyArray1>, lengths: &Bound<'_, PyArray1>) -> PyResult<()> { + + let binding = lengths.to_vec().unwrap(); + let new_lengths_vec: Vec = binding.iter().map(|x| Edge(*x)).collect(); + + let child_nodes_binding = child_nodes.to_vec().unwrap(); + let child_nodes_vec: Vec = child_nodes_binding.iter().map(|x| NodeId(*x)).collect(); + + let result = self.tree.update_edge_lengths(&child_nodes_vec, &new_lengths_vec); + + if result.is_err() { + return Err(PyValueError::new_err("Unable to update edge lengths.")); + } + + Ok(()) + } + + pub fn update_all_edge_lengths(&mut self, length: f64) -> PyResult<()> { + let result = self.tree.update_all_edge_lengths(Edge(length)); + if result.is_err() { + return Err(PyValueError::new_err("Unable to update all edge lengths.")); + } + Ok(()) + } + pub fn get_nodes(&self) -> Vec { let mut out = Vec::new(); for node in &self.tree.nodes { @@ -61,7 +86,7 @@ impl PhyloDM { } let (_, array) = matrix.unwrap(); Ok(Python::with_gil(|py| { - return Py::from(array.to_pyarray(py)); + return Py::from(array.to_pyarray_bound(py)); })) } @@ -96,7 +121,7 @@ impl PhyloDM { } #[pymodule] -fn pdm(_py: Python<'_>, m: &PyModule) -> PyResult<()> { +fn pdm(_py: Python<'_>, m: &Bound<'_, PyModule>) -> PyResult<()> { m.add_class::()?; Ok(()) } diff --git a/src/tree/node.rs b/src/tree/node.rs index 1664492..9ac970f 100644 --- a/src/tree/node.rs +++ b/src/tree/node.rs @@ -54,6 +54,12 @@ impl Node { self.parent_distance = Some(length); } + // Set the distance to parent. + // Can the root have a distance? + pub fn set_parent_distance(&mut self, length: Edge) { + self.parent_distance = Some(length); + } + /// Set the depth of this node. pub fn set_depth(&mut self, depth: NodeDepth) { self.depth = Some(depth); diff --git a/test/test_phylodm.py b/test/test_phylodm.py index 1dee788..e8569cf 100644 --- a/test/test_phylodm.py +++ b/test/test_phylodm.py @@ -146,6 +146,32 @@ def test_load_from_dendropy_with_trifurication(self): self.assertTrue(test_tree['taxa'] == tuple(pdm.taxa())) return + def test_tree_set_branch_lengths(self): + test_tree = get_test_tree(10, trifurication=True) + pdm = PhyloDM.load_from_dendropy(test_tree['tree']) + + print('\n\n') + print('default') + dm = pdm.dm(norm=False) + print(dm) + print('pdm length ', pdm.length()) + print('test length', test_tree['length']) + + print('\nset 1') + num_nodes = len(pdm.get_nodes()) + pdm.update_edge_lengths(np.ones((num_nodes))) + dm2 = pdm.dm(norm=False) + print('pdm length ', pdm.length()) + print(dm2) + + print('\nset 0') + num_nodes = len(pdm.get_nodes()) + pdm.update_edge_lengths(np.zeros((num_nodes))) + dm3 = pdm.dm(norm=False) + print('pdm length ', pdm.length()) + print(dm3) + + # def test_tree_with_bootstraps_from_newick(self): # with tempfile.TemporaryDirectory() as tmp_dir: # tmp_dir = Path(tmp_dir) diff --git a/tests/test_bl_7.tree b/tests/test_bl_7.tree new file mode 100644 index 0000000..fd144a9 --- /dev/null +++ b/tests/test_bl_7.tree @@ -0,0 +1 @@ +((T8:7,T2:7):7,((T9:7,(T10:7,T4:7):7):7,((T6:7,((T3:7,T1:7):7,T7:7):7):7,T5:7):7):7):7; diff --git a/tests/tree.rs b/tests/tree.rs index 06e55a6..af1a262 100644 --- a/tests/tree.rs +++ b/tests/tree.rs @@ -1,7 +1,7 @@ #[cfg(test)] mod tests { use phylodm::PDM; - use phylodm::tree::Taxon; + use phylodm::tree::{Taxon, Edge}; #[test] fn test_tree_dm_twice() { @@ -169,4 +169,83 @@ mod tests { ] ); } + + #[test] + fn test_set_lengths() { + + // Load in the default tree from test.tree + // Then calculate the distance matrix as arr_normal + let mut tree_normal = PDM::default(); + let _ = tree_normal.load_from_newick_path("tests/test.tree"); + let (_taxon, arr_normal) = tree_normal.matrix(false).unwrap(); + let tree_normal_length = tree_normal.length(); + + // Load in the modified tree with all branch lengths = 7 + // Then calculate the distance matrix as arr_bl7 + let mut tree_bl7 = PDM::default(); + let _ = tree_bl7.load_from_newick_path("tests/test_bl_7.tree"); + let (_taxon, arr_bl7) = tree_bl7.matrix(false).unwrap(); + let tree_bl7_length = tree_bl7.length(); + + // Use the default tree and modify all branch lengths to be 7 + // Then calculate the distance matrix as arr_modified_7 + let _ = tree_normal.update_all_edge_lengths(Edge(7.0)); + let (_taxon, arr_modified_7) = tree_normal.matrix(false).unwrap(); + let tree_modified_7_length: Edge = tree_normal.length(); + + println!("\n\nNormal"); + println!("{:?}", arr_normal); + println!("{:?}", tree_normal_length); + + println!("Branch lengths 7 (from file)"); + println!("{:?}", arr_bl7); + println!("{:?}", tree_bl7_length); + + println!("Branch lengths 7 (modified)"); + println!("{:?}", arr_modified_7); + println!("{:?}", tree_modified_7_length); + + // Somehow the modified tree is 7 units longer that the one read from file. + assert_eq!(arr_bl7, arr_modified_7); + assert_eq!(tree_bl7_length.0, tree_modified_7_length.0); + + } + + + #[test] + fn test_update_edge_lengths() { + let mut tree = PDM::default(); + + let taxon_b = Taxon("B".to_string()); + let taxon_c = Taxon("C".to_string()); + let taxon_d = Taxon("D".to_string()); + + let root_node = tree.add_node(None).unwrap(); + let node_a = tree.add_node(None).unwrap(); + let node_b = tree.add_node(Some(&taxon_b)).unwrap(); + let node_c = tree.add_node(Some(&taxon_c)).unwrap(); + let node_d = tree.add_node(Some(&taxon_d)).unwrap(); + + tree.add_edge(root_node, node_a, Edge(1.0)); + tree.add_edge(root_node, node_b, Edge(2.0)); + tree.add_edge(node_a, node_c, Edge(3.0)); + tree.add_edge(node_a, node_d, Edge(7.0)); + + tree.compute_row_vec().unwrap(); + + let dist_b_to_c_before = tree.distance(&taxon_b, &taxon_c, false); + + let node_ids = vec![node_a, node_c]; + let lengths = vec![Edge(11.0), Edge(12.0)]; + + let _ = tree.update_edge_lengths(&node_ids, &lengths); + + let dist_b_to_c_after = tree.distance(&taxon_b, &taxon_c, false); + + assert_eq!(dist_b_to_c_before, 6.0); + assert_eq!(dist_b_to_c_after, 25.0); + + } + + } diff --git a/version.sh b/version.sh index 997cefd..2bef5b6 100755 --- a/version.sh +++ b/version.sh @@ -8,7 +8,9 @@ RELEASE_DATE=$(date +"%Y-%m-%d") # Update Cargo version sed -i "s/^version = .*$/version = \"$VERSION\"/" Cargo.toml +# Update Python version +sed -i "s/^version = .*$/version = \"$VERSION\"/" pyproject.toml + # Update citation version and date sed -i "s/^version: .*$/version: $VERSION/" CITATION.cff sed -i "s/^date-released: .*$/date-released: $RELEASE_DATE/" CITATION.cff -