Create v0.2.2 #65
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Create v0.2.2 #65
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* Proposal to deal with explicit infinite edges Addresses issue #37 * Use if-continue as suggested by @MonkeyBreaker * [TEST] Add regression test for issue #37 Signed-off-by: julian <julian.burellaperez@heig-vd.ch> * [CPP] Slight format and move comment to new relevant section Signed-off-by: julian <monkeybreaker@protonmail.com> * Replace all numeric... by a inf variable at the top of the file Much easier to write :) Signed-off-by: julian <monkeybreaker@protonmail.com> * [CPP] Remove unecessary variables and apply format Signed-off-by: julian <monkeybreaker@protonmail.com> * Revert deletion of death variable and use it when necessary Signed-off-by: julian <monkeybreaker@protonmail.com> Co-authored-by: julian <julian.burellaperez@heig-vd.ch> Co-authored-by: julian <monkeybreaker@protonmail.com>
* [CPP] Update compressed_distance_matrix to support diagonals Signed-off-by: julian <julian.burellaperez@heig-vd.ch> * [PY] Update DParam to include diagonals value Signed-off-by: julian <julian.burellaperez@heig-vd.ch> * [CPP] Update get_vertex_birth to return the diagonal value Signed-off-by: julian <julian.burellaperez@heig-vd.ch> * [PY] Updade backend used when non 0 values are present in the distance matrix Signed-off-by: julian <julian.burellaperez@heig-vd.ch> * [PY] Update logic for threshold in dense case Signed-off-by: julian <monkeybreaker@protonmail.com> * [PY] Remove unused imports Signed-off-by: julian <monkeybreaker@protonmail.com> * [CPP] Refactor to use std::minmax and remove code duplication This could be even further cleaned if we support C++17 if constexpr (...) ... Signed-off-by: julian <monkeybreaker@protonmail.com> * [CPP] Apply Format Signed-off-by: julian <monkeybreaker@protonmail.com> * [CPP] Revert some changes, add diagonal attribute for dense After discussion with ulupo, it is better to keep the code as similar as possible with ripser, so to keep changes minimal, I added an attribute containing the diagonal Signed-off-by: julian <monkeybreaker@protonmail.com> * [BDG] Add diagonal parameter for dense case and removed N parameter Signed-off-by: julian <monkeybreaker@protonmail.com> * [PY] Retrieve diagonal and forward it when computing dense Signed-off-by: julian <monkeybreaker@protonmail.com> * [TST] Add test for extended backend compares the result of the same input matrix in dense and sparse format Signed-off-by: julian <monkeybreaker@protonmail.com> * Update gph/python/test/test_ripser.py Co-authored-by: Umberto Lupo <46537483+ulupo@users.noreply.github.com> * [PY] Remove non-zero diagonal check for enclosing radius computation Signed-off-by: julian <monkeybreaker@protonmail.com> * Fix test with invalid input passed to ripser Signed-off-by: julian <monkeybreaker@protonmail.com> * Fix linter warnings Signed-off-by: julian <monkeybreaker@protonmail.com> * [PY] Refactor collapse edges logic for dense case Signed-off-by: julian <monkeybreaker@protonmail.com> * Update gph/python/ripser_interface.py * [BIN,PY] Include diagonal in collapser bindings Add again diagonal after collapsing Signed-off-by: julian <monkeybreaker@protonmail.com> * [BIN] Revert collapser binding changes Signed-off-by: julian <monkeybreaker@protonmail.com> * Update gph/python/test/test_ripser.py * [PY] Create collapse edge function, remove diags Signed-off-by: julian <monkeybreaker@protonmail.com> * [CPP] Add inline comments to document behavior Signed-off-by: julian <monkeybreaker@protonmail.com> * Update gph/python/ripser_interface.py * [PY] Update collapse_dense as suggested by @ulupo Co-authored-by: Umberto Lupo <46537483+ulupo@users.noreply.github.com> * [PY] Update collapse_dense function as suggested by @ulupo Signed-off-by: julian <monkeybreaker@protonmail.com> * [PY] Tiny linting change Co-authored-by: Umberto Lupo <46537483+ulupo@users.noreply.github.com>
* Implement suggestion in https://stackoverflow.com/questions/13079563/how-does-condensed-distance-matrix-work-pdist/36867493#36867493 adapted ti lower-diagonal compressed format. Thanks to the IEEE 754 standard's strong guarantees on basic arithmetic operations (including square root), finite precision using doubles does not lead to incorrect results whenever 8 * num_edges + 1 does not exceed the largest integer exactly representable as a double, i.e. 2^53. So, one is guaranteed correct results whenever there are fewer than 2^25 = 33'554'432 vertices. Correctness can be tested for even larger values but is not guaranteed there.
…3.10, upgrade to manylinux2014 (#62) * [CI] Enable ARM wheels for MacOS for Python version 3.8, 3.9 and 3.10 Signed-off-by: julian <monkeybreaker@protonmail.com> * [CI] Add arm64 to CIBW_ARCHS_MACOS option * [PY] Remove unused import * Try adding install options for ARM Signed-off-by: julian <monkeybreaker@protonmail.com> * Try adding install options for ARM Signed-off-by: julian <monkeybreaker@protonmail.com> * Try adding install options for ARM Signed-off-by: julian <monkeybreaker@protonmail.com> * Disable arm64 and x86 Signed-off-by: julian <monkeybreaker@protonmail.com> * Trying build arm wheels Signed-off-by: julian <monkeybreaker@protonmail.com> * setup.py arm wheels Signed-off-by: julian <monkeybreaker@protonmail.com> * setup.py arm wheels Signed-off-by: julian <monkeybreaker@protonmail.com> * Clean setup.py and only build universal2 wheels Signed-off-by: julian <monkeybreaker@protonmail.com> * Drop support to Python 3.6 Signed-off-by: julian <monkeybreaker@protonmail.com> * Add CI and wheels for Python 3.11, upgrade to manylinux2014 throughout * Drop Python 3.11 from CI and wheels * Fix YAML typo Signed-off-by: julian <monkeybreaker@protonmail.com> Co-authored-by: Umberto Lupo <46537483+ulupo@users.noreply.github.com> Co-authored-by: Umberto Lupo <umberto.lupo@gmail.com>
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