Use dependabot to auto-update GitHub Actions versions#632
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https://docs.github.com/en/code-security/tutorials/secure-your-dependencies/dependabot-quickstart-guide https://docs.github.com/en/code-security/how-tos/secure-your-supply-chain/secure-your-dependencies/configuring-dependabot-version-updates https://docs.github.com/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
yihui
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https://docs.github.com/en/code-security/tutorials/secure-your-dependencies/dependabot-quickstart-guide https://docs.github.com/en/code-security/how-tos/secure-your-supply-chain/secure-your-dependencies/configuring-dependabot-version-updates https://docs.github.com/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
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* perf: replace object.size() with numhash() in prune_hash object.size() walks the entire hash table structure on every cache_fun() call, taking ~2ms per invocation. Since cache_fun is called 15+ times per gs_design_ahr run (via expected_time/ahr and gs_power_npe), this adds up to significant overhead. Replace with numhash() which returns the entry count in O(1), and use clrhash() for a simple eviction strategy when the limit is exceeded. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com> * perf: replace dplyr full_join/select/arrange with base R in gs_design_npe The output assembly in gs_design_npe used full_join (to merge H0 and H1 probabilities), select, rename, and arrange from dplyr. Since gs_design_npe is called once per gs_design_ahr and these operations are on small data frames (6 rows), base R merge() and column subsetting are much faster. Combined with the gs_power_npe change, this yields ~50% overall improvement for multi-analysis designs. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com> * perf: replace dplyr operations with base R in gs_design_ahr output Replace mutate, full_join, select, arrange, and filter operations in the output assembly section of gs_design_ahr with equivalent base R operations (direct column assignment, merge, column subsetting, order). This eliminates the dplyr overhead for the final output formatting which previously involved multiple tibble round-trips on small data frames. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com> * perf: remove dplyr from hot-path functions (expected_time, gs_info_ahr) Replace select(-n) with base R column removal, and replace mutate/transmute in the info_frac loop of gs_design_ahr with direct column assignment. These functions are called repeatedly during uniroot iterations, so even small per-call savings add up. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com> * perf: preserve tibble output type and fix row ordering Exported functions gs_power_npe and gs_design_npe must return tibbles for backward compatibility. Add tibble::as_tibble() at the return point to convert the base R data.frame used for fast internal computation back to the expected output type. Also fix row ordering in gs_design_npe to maintain upper-before-lower within each analysis (matching the original arrange(analysis) with upper-first convention). Refine prune_hash to use a 100-entry limit per function, giving predictable memory bounds (each entry is typically a few KB, so ~100KB per cached function). Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com> * perf: redesign cache pruning based on empirical measurement Profiling revealed that object.size() overcounts gs_power_npe cache entries by ~600x (reports 1.8 MB per entry when true incremental cost is ~3 KB). This is because object.size() walks into shared namespace environments of function arguments, counting the same gsDesign2 namespace (833 KB) and gsDesign namespace (75 KB) for every entry. Changes: - Remove object.size() from the pruning path (both slow and inaccurate) - Only check entry count before insertions, not on cache hits - Set max_entries = 1024, justified by: - True cost: ~3 KB (gs_power_npe) to ~5 KB (ahr) per entry - 1024 entries ≈ 3-5 MB real memory - Supports ~200 cached designs in a session - A single design creates only 5-28 entries Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com> * return data frame instead * update the change point in the calculation of expected accrual (#628) * Migrate GitHub Actions to Node 24 (#626) * Use dependabot to auto-update GitHub Actions versions (#632) https://docs.github.com/en/code-security/tutorials/secure-your-dependencies/dependabot-quickstart-guide https://docs.github.com/en/code-security/how-tos/secure-your-supply-chain/secure-your-dependencies/configuring-dependabot-version-updates https://docs.github.com/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file * Fix test-coverage workflow inputs for codecov/codecov-action@v6 (#634) * Bump yihui/actions from 1.1.0 to 1.1.2 (#633) Bumps [yihui/actions](https://github.com/yihui/actions) from 1.1.0 to 1.1.2. - [Release notes](https://github.com/yihui/actions/releases) - [Commits](yihui/actions@v1.1.0...v1.1.2) --- updated-dependencies: - dependency-name: yihui/actions dependency-version: 1.1.2 dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Unify test names for consistency (#639) * Increase tolerance for test of gsDesign::gsSurv() vs gs_power_ahr() (#637) --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: Xie <xieyih@lctcvp7913.merck.com> Co-authored-by: Claude Opus 4.6 (1M context) <noreply@anthropic.com> Co-authored-by: Yujie Zhao <43153957+LittleBeannie@users.noreply.github.com> Co-authored-by: John Blischak <jdblischak@gmail.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
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xref: Merck/simtrial#363, Merck/simtrial#362, #626