pysam-developers / pysam

Коли додано кожну зірку й форк — зібрано з GitHub і згруповано за днями. Кумулятивне зростання розміщено просто над денними додаваннями, з яких воно складається, тож їх видно одне проти одного: рівномірне органічне накопичення виглядає зовсім інакше, ніж різкий короткочасний сплеск. Там, де цю різницю можна виміряти, її подано як автентичність росту.

Кожна точка охоплює 12 днів.

Повний розв'язаний набір залежностей із графа залежностей GitHub: 0 прямих і 4 непрямих (транзитивних) пакетів. Транзитивне замикання є повним, коли в репозиторії закомічено lockfile.

Цей репозиторій не публікує пакета, який розпізнає індекс, тож оцінено його власний граф залежностей — 2 пакетів, серед яких є й піниї розробки та тестування, що ніколи не постачаються: 0 мають відомі сповіщення, з них 0 прямі. 2 не вдалося оцінити — немає резолвленої версії, непідтримувана екосистема або поза наведеним переліком пакетів.

Жодне відоме сповіщення не стосується оцінених залежностей.

Сповіщення означає, що версія, записана в графі залежностей, потрапляє в уражений діапазон. Досяжність не аналізується, а граф містить піниї розробки й тестування — знахідка може стосуватися інструментів, а не поставленого коду.

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          "headline": "Set REF_PATH=: automatically during pytest initialisation",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
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        {
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          "body": null,
          "is_bot": false,
          "headline": "Update to cross-platform-actions/action v1.1-style usage",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2026-05-20T10:39:41Z",
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          "oid": "55ad2c6dcb1baa9a5825e6690f32ff91898e1fd4",
          "body": null,
          "is_bot": false,
          "headline": "Build the documentation on a subset of CI configurations",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2026-05-14T10:07:33Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "d7315358ab2a1cee2c5c3db6eca757197aeb3060",
          "body": null,
          "is_bot": false,
          "headline": "Add pysam.reverse_complement_inplace() utility function",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2026-05-14T08:55:57Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "e8b08a71d0e0f8ec6072c92e194c0c1debeccee1",
          "body": "Implement it via low-level code for str, bytes, and int.\nA small script was used to generate pysam_seq_comp_table:\n\n    import pysam\n    iupac = \"=ACMGRSVTWYHKDBN\"\n    for c in range(256):\n\tif c % 16 == 0: print(\"\\n   \", end='')\n\tbase = chr(c).upper()\n\tif base == 'U': base = 'T'\n\tif (b := iupac.find\n[…]\nomplement(b)]\n\t    if chr(c).islower(): comp = comp.lower()\n\t    print(f\" '{comp}', \", end='')\n\telse:\n\t    print(f\" 0x{c:02x},\", end='')\n\nUse the new function in AlignedSegment.get_forward_sequence().",
          "is_bot": false,
          "headline": "Add pysam.reverse_complement() utility function",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2026-05-13T11:52:50Z",
          "body_truncated": true,
          "is_coding_agent": false
        },
        {
          "oid": "aadf7dc2354546ba82c0f19b9a5cb945ce7dc7f6",
          "body": null,
          "is_bot": false,
          "headline": "Rename tests with duplicate names",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2026-05-12T09:21:15Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "c3d8be192dd70e40bc8936b5435951750684e268",
          "body": "I originally wrote these tests as pytest but recoded them to fit in with\nthe rest of AlignedSegment_test.py. But the new intention is to move the\ntestsuite as a whole towards being pytest-native and using fixtures more.",
          "is_bot": false,
          "headline": "Parametrise tests by recoding against the pytest API",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2026-05-12T09:04:37Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "2baef1602eb2606615386766b2f73812892ef330",
          "body": null,
          "is_bot": false,
          "headline": "Belated happy new year",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2026-05-10T08:32:12Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "11dea5e656ca2806e0f83436a5c56d0bcfb25634",
          "body": "…ties\n\nPyUnicode_MAX_CHAR_VALUE() is not declared by Cython's cpython/unicode.pxd\nso these wrappers around PyUnicode_New() encapsulate its use.",
          "is_bot": false,
          "headline": "Add PysamUnicode_NewClone() and PysamUnicode_NewCloneWithSize() utili…",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2026-05-10T04:09:31Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "3fcfcf28f5125a9c2830bdf0d09f7decfb7e04fe",
          "body": null,
          "is_bot": false,
          "headline": "Remove unused cpython imports, and cimport from approriate sub-modules",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2026-05-10T03:23:15Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "4c612926d36d6f5209e9f1114f0e6346ce10156d",
          "body": "AlignmentFile has bespoke code for file descriptors et al, but in fact\nVariantFile also supports them due to HTSFile._open_htsfile()'s special\nhandling. Fixes #1406.\n\nAdd test cases exercising all possibilities for AlignmentFile and\nVariantFile filenames. Only check .closed if the property exists.",
          "is_bot": false,
          "headline": "Fix VariantFile type hints to allow file descriptors",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2026-05-08T08:26:13Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "d1c86903e38431dfcf15cde1c52dcc457004ed79",
          "body": "These should have been removed when `sys.version_info` was removed\nwhen we dropped Python 3.8.",
          "is_bot": false,
          "headline": "Remove now-unused imports etc from stub files",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2026-05-08T05:52:38Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "2bf94ad19fe771f73df3345231bb0953b96caec2",
          "body": "Sadly Cirrus CI will soon shut down. Instead test BSD on GitHub Actions\nunder emulation via cross-platform-actions/action. This has x86-64 running\non x86-64, so performs about as well as the native jobs.\n\nOn FreeBSD, we need to add /usr/local/include to the search path for\nlibcurl headers to be found. NetBSD Python's sysconfig.CFLAGS uses -I\nfor its system header directories, but we don't want those to override\npysam's own -I options so we downgrade them to -isystem.",
          "is_bot": false,
          "headline": "Migrate FreeBSD CI to GH actions, and add NetBSD",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2026-05-07T05:47:36Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "38b94a847cb7adca3eea49f910662e8b7b212334",
          "body": null,
          "is_bot": false,
          "headline": "Bump version number to 0.24.0 and add release notes",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2026-04-27T11:51:56Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "7067acf8097224fc3266e368b387edd210261007",
          "body": null,
          "is_bot": false,
          "headline": "The Profiling section should not be a subsection of PyPI installation",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2026-04-27T11:49:36Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "0d39f2ffd077f3fe4a650a5102873035cb518547",
          "body": null,
          "is_bot": false,
          "headline": "The htslib.org website has not been updated for this point release",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2026-04-27T10:02:37Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "09c3dc6b68b3111632f09eec3ce2744d346f8f90",
          "body": null,
          "is_bot": false,
          "headline": "Move the VCF/BCF documentation up alongside SAM/BAM/CRAM",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2026-04-27T08:59:29Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "3f2aaf8e9eb20249745d012e77fb08d41328c235",
          "body": null,
          "is_bot": false,
          "headline": "Rearrange Variant* class documentation",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2026-04-27T08:33:43Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "8a96ea0b91bb7327748cef5b7860631ed1de398f",
          "body": null,
          "is_bot": false,
          "headline": "Further clarify VariantRecord properties documentation",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2026-04-27T02:46:54Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "8a9f7f8dd0aefdafb96262c4bdb4bd68d32ec2c7",
          "body": "The filenames should also take pathlib.Path; VariantFile does not currently\nsupport file descriptors. HTSlib modes can include comma-separated format\noptions, so Literal is too limited and we should (TODO) remove pysam's\nruntime restrictions on this argument. Fixes #1405.",
          "is_bot": false,
          "headline": "Correct the AlignmentFile/VariantFile filename/mode type hints",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2026-04-26T07:05:38Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "9aa4d1a1cd6eee0483c8f1fc45479f83705a3cdb",
          "body": null,
          "is_bot": false,
          "headline": "Add documentation for all VariantHeader-related classes (PR #1394)",
          "author_name": "Tim Dunn",
          "author_login": "TimD1",
          "committed_at": "2026-04-25T22:36:58Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "48688fc3f4e2b7f58c1cdf250a2097833d142e87",
          "body": "The data is contiguous so we can use [::1] to omit stride calculations.\nUsing explicit memoryviews rather than the previous array indexing code \nleads to a 100x speedup within this function.",
          "is_bot": false,
          "headline": "Use memoryviews to optimize array_to_qualitystring (PR #1363)",
          "author_name": "Josh Chorlton",
          "author_login": "jchorl",
          "committed_at": "2026-04-17T10:08:11Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "d12398616afaa3ca4f2ad86592dcabba74a4b1b0",
          "body": null,
          "is_bot": false,
          "headline": "Add VariantContig and VariantMetadata documentation (PR #1361)",
          "author_name": "Tim Dunn",
          "author_login": "TimD1",
          "committed_at": "2026-04-12T12:49:49Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "6aa975c485a2678d99c685698b6c53981c15eeb6",
          "body": "Fixes #882; fixes #1368.",
          "is_bot": false,
          "headline": "Add documentation for all VariantRecord-related classes (PR #1359)",
          "author_name": "Tim Dunn",
          "author_login": "TimD1",
          "committed_at": "2026-04-12T01:27:45Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "427650a8bf5ff38eb6d035f8085d0e488df9ec67",
          "body": null,
          "is_bot": false,
          "headline": "Adjust for FreeBSD py311-cython package name change",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2026-04-07T12:27:32Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "7f508219393604218fab9b5e54715d9401bd339c",
          "body": "Also remove setup-miniconda's unnecessary auto-activate-base override.",
          "is_bot": false,
          "headline": "Update to node24-based GitHub Actions",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2026-04-07T11:48:51Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "a91efe36089dcdc1b2eebee2916643d68499cab6",
          "body": "Mypy 1.20.0 was released today and reports types such as int\nas \"int\" rather than \"builtins.int\" as in previous versions.",
          "is_bot": false,
          "headline": "Handle mypy 1.20.0's changed output in typechecking testcases",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2026-04-01T10:54:25Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "ec689af1918406185773b5a2cdf3645f6317ff6f",
          "body": null,
          "is_bot": false,
          "headline": "Reformat get_tag() documentation to our usual NumPy style and tidy up",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2026-04-01T08:23:38Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "32752e938adc67c86d9f29c8d7b5c22ed6f3b151",
          "body": "Apply similar changes as made previously to VariantRecordSample.update().",
          "is_bot": false,
          "headline": "Fix other update() methods with iterables and keyword args only",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2026-03-31T10:47:36Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "ce2242855f83fdc8d57ee6033c46153e65fa46a4",
          "body": "Add documentation for the class and its methods.\nFixes #407; fixes #720.",
          "is_bot": false,
          "headline": "Add VariantRecordSample documentation (PR #1358)",
          "author_name": "Tim Dunn",
          "author_login": "TimD1",
          "committed_at": "2026-03-31T09:15:16Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "0f5a36a157f412d7ad943c7fdc148d14c2dc342a",
          "body": "This is documented as accepting an iterable or solely keyword arguments,\nso check before using `items.items()`. Changing the default argument value\ncauses changes only within pysam/libcbcf.c, so has no ABI implications.",
          "is_bot": false,
          "headline": "Fix VariantRecordSample.update() with iterables and keyword args only",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2026-03-31T07:29:04Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "2a3911171f3c6b3b4d907566cf0380edc77e7b62",
          "body": "Link from the AlignmentFile(format_options) and HTSFile.add_hts_options()\nentries. Bring the AlignmentFile constructor signature docstring uptodate.",
          "is_bot": false,
          "headline": "Add link to samtools --input/output-fmt-option keyword documentation",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2026-03-25T12:45:04Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "a417ba16ef7c4bcb4bc08db86c6653a859388e65",
          "body": "Add force_bytes() to convert the input str to bytes as hts_opt_add()\nis expecting.\n\nSimplify the function's signature by making format_options non-optional:\nthere is no point calling this function without specifying format_options,\nand [] is a more suitable no-op.\n\nSimplify the function's implementation by using `finally` for cleanup.\n(Both hts_opt_free() and hts_opt_apply() accept NULL as a no-op.)\nRaise ValueError rather than the more generic RuntimeError.",
          "is_bot": false,
          "headline": "Fix HTSFile.add_hts_options() str vs bytes handling",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2026-03-24T11:38:09Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "4c50e83be0e787fe0c3dd179cc6dd4c32de50e75",
          "body": "For each package:\n\nrm -rf htslib;   python3 devtools/import.py htslib   .../htslib-1.23.1\nrm -rf samtools; python3 devtools/import.py samtools .../samtools-1.23.1\nrm -rf bcftools; python3 devtools/import.py bcftools .../bcftools-1.23.1\n\nTake care to preserve these additional manual changes:\n\n* remov\n[…]\nom htslib/Makefile\n* the wheel-building PKI workaround in htslib/hfile_libcurl.c\n* the #define additions to bcftools/regidx.h\n\nand don't bother adding {sam,bcf}tools/htslib-1.23.1/{LICENSE,**/README}.",
          "is_bot": false,
          "headline": "Import upstream htslib/samtools/bcftools 1.23.1",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2026-03-19T07:00:23Z",
          "body_truncated": true,
          "is_coding_agent": false
        },
        {
          "oid": "54f3d41f380f095e8bfb16fd430b00fe02fb5063",
          "body": "Regularise pysam/*.pyx directives to include `language_level=3` and exclude\n`profile=True`. Reactivate profiling if a PYSAM_PROFILE environment variable\nis set to a true value for both sdist and build_ext commands. Fixes #1350.\n\n(We could set `force` if PYSAM_PROFILE is set differently from the previous\nbuild, but it seems better to leave that to Cython's build_ext and require\nclean_ext when changing settings.)",
          "is_bot": false,
          "headline": "Update cython directives, turning profiling off by default",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2026-03-15T08:52:47Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "e03c4e31dc8b6d2d3f1c81e3b666b4bf4f2a4dc7",
          "body": "… HACK]\n\nLinux wheels are (currently) built on AlmaLinux, so the libcurl.so\nbundled into the wheel follows Alma/Red Hat/Fedora conventions for the\nlocation of its certificate bundle. This fails when the wheel is used on\na Debian/Ubuntu platform with a different convention for this location.\nWhen not\n[…]\nbian bundle location if the Red Hat one isn't present.\n\nReinstates b18dde87, which was inadvertently removed when importing 1.22.\nTake more care to preserve this patch when importing HTSlib in future!",
          "is_bot": false,
          "headline": "Fix wheels' bundled libcurl.so incompatibility with Debian [REINSTATE…",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2026-03-09T07:36:03Z",
          "body_truncated": true,
          "is_coding_agent": false
        },
        {
          "oid": "79293854c45889bedef09491ee7d20de3dbc76a6",
          "body": null,
          "is_bot": false,
          "headline": "Update cibuildwheel and use the new GH Actions case() function",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2026-01-31T06:04:57Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "b7bf2cf7cb5e5263863d444223c63c150ec75eb2",
          "body": null,
          "is_bot": false,
          "headline": "Update imports to htslib/samtools/bcftools 1.23 (PR #1372)",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2026-01-12T07:31:21Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "0a1997ea122541e6f00cc32f1dfa16a8fe42a820",
          "body": "Remove pkg_resources, which is deprecated and slated for removal soon:\n_get_egg_name() has been unused since 2017 anyway.\n\nTake Extension from setuptools instead of distutils.\n\nUse sysconfig.get_config_var[s]() instead of distutils's wrappers.\nOverride LDSHARED properly in cy_build_ext.run() instead\n[…]\nig's own config_vars.\n\nThis linker_tests/link_pre_489/* test is unused anyway, and is present\nin the codebase for reference only. All of linker_tests/* deserves an\noverhaul; see also PR #489 and #503.",
          "is_bot": false,
          "headline": "Apply setup.py's modernisation to (unused) linker_tests/link_pre_489",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2026-01-11T09:34:39Z",
          "body_truncated": true,
          "is_coding_agent": false
        },
        {
          "oid": "0e05d9456fbd22432fa929b844eab7e442a0b992",
          "body": "This symbol check is intended for detecting duplicate *pysam* symbols.\nIgnore any __pyx_* etc symbols, not just the particular function that\nCython 3.1.2 inadvertently left non-static, in case similar mistakes\noccur again in future.\n\nRemove the `License :: OSI Approved` classifier; License classifiers\nare apparently deprecated and cause warnings with recent setuptools.",
          "is_bot": false,
          "headline": "Generalise workaround for non-static Cython internal symbols",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2025-12-24T10:37:53Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "da8e5fee23ef9b30a3808fd331deb81d2281073c",
          "body": "No longer need to be miserly with macOS actions runners, but continue to\nsuppress 3.8 to avoid a spurious error annotation. Update Python versions\nused for sdist and conda CI tests, and use newish setup-miniconda facility\nto suppress the defaults channel and avoid another annotation.\n\nBuild the release sdist on the latest Python release.",
          "is_bot": false,
          "headline": "Add Python 3.14 to CI and test most Python versions on macOS",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2025-12-18T18:22:49Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "ac06a2152046806ed12c1d7e73ad728ac85b80eb",
          "body": null,
          "is_bot": false,
          "headline": "Update pysam/libchtslib.pxd to HTSlib 1.23 htslib/*.h declarations",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2025-12-18T10:23:50Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "24c2b31cdbebd190f0bf36026e05015d2cf0a720",
          "body": "For each package:\n\nrm -rf htslib;   python3 devtools/import.py htslib   .../htslib-1.23\nrm -rf samtools; python3 devtools/import.py samtools .../samtools-1.23\nrm -rf bcftools; python3 devtools/import.py bcftools .../bcftools-1.23\n\nTake care to preserve the #define additions to bcftools/regidx.h.\n(Don't bother adding {sam,bcf}tools/htslib-1.23/{LICENSE,**/README}.)\n\nAlso take care to preserve removing the regeneration of htscodecs.mk\nfrom htslib/Makefile.",
          "is_bot": false,
          "headline": "Import upstream htslib/samtools/bcftools 1.23",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2025-12-18T10:18:47Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "30475d23723df8ff19df6a20df1996d57df496bd",
          "body": null,
          "is_bot": false,
          "headline": "Update Cirrus FreeBSD image (freebsd-14-2 is no longer available on GCP)",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2025-12-18T09:33:21Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "caf56b2617472243e9a64a81de1a7f6846247703",
          "body": null,
          "is_bot": false,
          "headline": "Update imports to htslib/samtools 1.22.1 and bcftools 1.22 (PR #1343)",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2025-11-25T09:36:11Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "3db05f9e7e8be9718cd8008af012010fba65f4c8",
          "body": "Add Python 3.14 to release workflows and update cibuildwheel to a release\nthat uses 3.14-final. Use the new macos-15-intel image instead of macos-13,\nwhich is obsolete.\n\nReorganise the build matrix to separate the manylinux and musllinux jobs\nso they run in parallel.\n\nMove all wheel building to GitH\n[…]\ne's\ndefault Python can no longer run current cibuildwheel (which requires 3.11),\nso it is time to move the ARM wheels to be built on GitHub Actions, now that\nthat supports both Linux and macOS on ARM.",
          "is_bot": false,
          "headline": "Update release workflows for Python 3.14, Intel macOS runner, etc",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2025-11-22T06:04:37Z",
          "body_truncated": true,
          "is_coding_agent": false
        },
        {
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          "body": "Store the output of `force_bytes(stdout_f)` in a live object to ensure\nit is not garbage-collected before it is used within samtools_dispatch().\nThis fixes a test failure on i386 (SamtoolsTest/PysamTest for calmd).",
          "is_bot": false,
          "headline": "Ensure stdout filename object is not garbage-collected while in use in C",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2025-11-17T05:41:22Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "23d81183ad9c00467bdafbb359abffada5797f15",
          "body": null,
          "is_bot": false,
          "headline": "Update pysam/libchtslib.pxd to HTSlib 1.22.1 htslib/*.h declarations",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2025-11-15T07:23:17Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "1de219ab4a66ee35e485e47e78ed659a6069bad7",
          "body": "These tests fail on e.g. i386 because scalar types and layout differ\non this platform. Restrict the tests to run only on the common 64-bit\nplatforms -- we care mostly about incompatibilities on these platforms,\nand failures here will be generally indicative anyway. Fixes #1367.",
          "is_bot": false,
          "headline": "Run class size tests only on aarch64 and x86_64",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2025-11-14T22:50:07Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "c4c0f8d5d50f8b8ed2ab39353029f480d0b7de17",
          "body": "For each package:\n\nrm -rf htslib;   python3 devtools/import.py htslib   .../htslib-1.22.1\nrm -rf samtools; python3 devtools/import.py samtools .../samtools-1.22.1\n\nTake care to preserve removing the regeneration of htscodecs.mk\nfrom htslib/Makefile.",
          "is_bot": false,
          "headline": "Import upstream htslib/samtools 1.22.1",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2025-11-08T04:54:08Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "1190ab7e0c22a5fa63bcacd2f995a165b63c90ec",
          "body": null,
          "is_bot": false,
          "headline": "Add new `samtools checksum` command",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2025-11-08T04:32:57Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "a4a502880718b28a23ef999310933410cb360959",
          "body": "For each package:\n\nrm -rf htslib;   python3 devtools/import.py htslib   .../htslib-1.22\nrm -rf samtools; python3 devtools/import.py samtools .../samtools-1.22\nrm -rf bcftools; python3 devtools/import.py bcftools .../bcftools-1.22\n\nTake care to preserve the #define additions to bcftools/regidx.h.\n(Don't bother adding {sam,bcf}tools/htslib-1.22/{LICENSE,**/README}.)\n\nAlso take care to preserve removing the regeneration of htscodecs.mk\nfrom htslib/Makefile.",
          "is_bot": false,
          "headline": "Import upstream htslib/samtools/bcftools 1.22",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2025-11-08T04:32:57Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "345625eb43bc3974c671f78a0097294a523053d3",
          "body": "Omit the htslib/ref_cache/ source code, and hard-code a configure\n--disable-ref-cache argument accordingly.\n\nBCFtools's mpileup2/* is currently used only by plugins/vrfs.c which\nwe don't wrap, so we can (for now) omit this mpileup2/* code too.",
          "is_bot": false,
          "headline": "Don't import ref_cache/ external tool source code or mpileup2/*.[ch]",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2025-11-08T04:32:57Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "bbad7c553341b63cace60bce0302e30094a2d7a7",
          "body": null,
          "is_bot": false,
          "headline": "Update common GitHub Actions to their Node24-based versions",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2025-11-07T10:08:27Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "6a78ccad576ae5b973998a9b25a0b8f84623b0eb",
          "body": "These operate by adjusting for clipping, so when there is no CIGAR there\nis no adjustment from 0 and query_length. Documentation fixes #1319.",
          "is_bot": false,
          "headline": "Clarify query_alignment_start/_end/_length values for unmapped reads",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2025-10-16T07:09:28Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "b59a459cfac40f74451ca4f5b29665057f159646",
          "body": "Use bam_mods_recorded() to query how many mods may be returned\nby bam_next_basemod() and allocate accordingly. Fixes #1348.",
          "is_bot": false,
          "headline": "Remove AlignedSegment.modified_bases's limit on number of mods",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2025-10-12T02:38:04Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "529ec4289c628294c5cfbfc870d824d8861b16e5",
          "body": "Cython 3.0 was released two years ago and is now available in the system\npackage repositories of all major distributions as well as via pip etc.\n\nThe `globals().update(getattr(CIGAR_OPS, \"__members__\"))` work-around for\nCython 3.1.0's non-global enumerator behaviour change in fact does not work\nwith Cython 0.x so 3.x is already required for pysam.",
          "is_bot": false,
          "headline": "Require Cython 3.x",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2025-10-12T02:21:36Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "ea43c089e572ecbe914aa29fafb27c5fac2877bf",
          "body": null,
          "is_bot": false,
          "headline": "Merge pysam/libchtslib.pxd declaration updates (PR #1362)",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2025-10-12T02:03:24Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "4f45505aed209254ccd8b0e5279de1416501f2f9",
          "body": "Use the full form of source_suffix, which has long been supported,\nas the simple form produces a warning with recent Sphinx versions.",
          "is_bot": false,
          "headline": "Update to current Sphinx and ReadTheDocs theme",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2025-10-08T10:03:37Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "4c563185e8708a6691b413d7fc937ee75a157e03",
          "body": "We intend to make these structs opaque in future: their fields are\npresent in the C declarations for implementation reasons but should\nnot be used by user code, so there is no reason why the corresponding\nCython declarations should not be as incomplete structs.\n\nCython needs named types for some fields that can be anonymous structs\nin C. Rename some of these pysam-local structs so that they follow\nhts_opt_val_union's pattern and avoid polluting the namespace.",
          "is_bot": false,
          "headline": "Deprecate future opaque structs and rename member structs/unions",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2025-09-27T09:29:23Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "c7d83cba39e86ade79994ce44e42ee2eefd99000",
          "body": "Some BGZF, htsFile, hts_itr_t, and sam_hdr_t struct fields are omitted\nfrom these Cython declarations. This commit updates the types of existing\nfields but generally does not add new or previously omitted fields, as we\naim in future to make these structs (and some others) properly opaque.\n\nMark depr\n[…]\nmay be removed\nat a later date.\n\nFix bam_cigar_gen() arguments (`l` is the length) and use `int` for\nCIGAR opcodes in these functions.\n\nExpose only the HTSlib 1.12+ cram_block_method enumerator items.",
          "is_bot": false,
          "headline": "Update pysam/libchtslib.pxd to HTSlib 1.21 htslib/*.h declarations",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2025-09-26T09:48:45Z",
          "body_truncated": true,
          "is_coding_agent": false
        },
        {
          "oid": "2f9d50dde8eea7ddcdb643dcde0a088380f4549a",
          "body": null,
          "is_bot": false,
          "headline": "Minor documentation wordsmithing and alphabetising [trivial]",
          "author_name": "Tim Dunn",
          "author_login": "TimD1",
          "committed_at": "2025-09-18T20:16:23Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "5ac440fa55179133d55c3f3251e9fa82ac378873",
          "body": "We need to search /usr/local/include to find curl/curl.h etc.\nHowever it needs to be searched AFTER ./htslib et al so that pysam\nis compiled against headers from ./htslib/htslib/*.h rather than\nany system-installed HTSlib headers in /usr/local/include.",
          "is_bot": false,
          "headline": "Ensure -I./htslib takes priority over /usr/local/include",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2025-09-15T11:52:48Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "94b24cb3d9abf278d7e54e59c89a392807f14926",
          "body": "Add `const`; apply bam_hdr_t to sam_hdr_t renaming; rewrite most SAM_hdr\ntypedef usage; use samFile typedef; use array parameter forms.",
          "is_bot": false,
          "headline": "Apply trivial differences w.r.t. htslib/*.h declarations",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2025-09-04T09:45:36Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "bfa5a41a2e1f226c91ecb2baa63b9f1f0881582a",
          "body": "Prevents \"Casting a GIL-requiring function into a nogil function\" warnings.",
          "is_bot": false,
          "headline": "Mark callback functions used from C as nogil and (mostly) noexcept",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2025-08-26T07:31:15Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "89380af7c06118a91ad48065d6fbfd2c3627679b",
          "body": "…ormat",
          "is_bot": false,
          "headline": "Use hts_get_format() accessor instead of directly accessing htsFile.f…",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2025-08-23T11:25:15Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "8354e1213325132e9bf39363aa1ec2ee5a634eaf",
          "body": "…b/*.h",
          "is_bot": false,
          "headline": "Reorder existing declarations similarly to upcoming import from htsli…",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2025-07-27T11:09:29Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "c479b720e7ed1bb6e9a59d61555d14385d3a4101",
          "body": "Keep hfile.h, bgzf.h, hts.h, sam.h first as other headers require types\ndeclared therein, but alphabetise the remaining header sections.",
          "is_bot": false,
          "headline": "Reorder cram.h alphabetically within pysam/libchtslib.pxd sections",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2025-07-03T06:57:12Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "34e36247c2f5c1cc0ceef0f866009b70541809ea",
          "body": "Tidy up whitepace, canonicalise pointer declarations as `int *p`,\nreformat onto a single line where appropriate. Fix `bed` typos\nfor `beg`, spell out parameter names as per htslib/*.h declarations.\n\nPrefix struct/union/enum with cdef or ctypedef as appropriate.\nThis PyFile_AsFile declaration from Python.h is long-since unused.",
          "is_bot": false,
          "headline": "Canonicalise whitespace, declaration styles, and other trivia",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2025-07-02T07:23:45Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "3333dd7d2241b23969a657334751b1da082358d2",
          "body": "…/*.h\n\nThis reformatted function documentation duplicates that in htslib/*.h\nand is not easily updated when the original documentation changes.\nMoreover it'll be easier to keep pysam/libchtslib.pxd updated for\nhtslib/*.h API additions when it solely contains declarations.",
          "is_bot": false,
          "headline": "Remove pysam/libchtslib.pxd function documentation copied from htslib…",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2025-07-02T05:15:11Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "bb20683c76127c3db75668c553242fc12505cad5",
          "body": null,
          "is_bot": false,
          "headline": "Update language level implications for the new py3.8 baseline",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2025-06-21T08:19:22Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "4dfc9e99c31df0dc6fe54357731e5a185dd330f2",
          "body": "c{sam,bcf}tools_util.h are long since replaced by {sam,bcf}tools.pysam.h.\nOnly this commented-out libctabix.pyx code used getline(), so remove its\nfallback definition in pysam_utils.c and hence remove the now-empty\npysam_util.[ch]. Remove unused header inclusions from htslib_util.c.",
          "is_bot": false,
          "headline": "Remove obsolete source files and unnecessary includes",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2025-06-16T10:00:40Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "41f6b1974a6c7f14ef9f8e24d54aa03e626b9f0f",
          "body": "Remove kstream_t, so <htslib/kseq.h> is used only by libcfaidx.pyx.",
          "is_bot": false,
          "headline": "Simplify libctabix.pyx by using bgzf_getline() directly",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2025-06-16T09:18:06Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "0c5e147a594683d9206330c14af6568056e9abf4",
          "body": "Rearrange so that KSTREAM_INIT/KSEQ_INIT is used only in *.pyx files\nrather than *.pxd headers, so that the functions don't pollute other\nextension modules. Declare only the needed types in the *.pxd headers.",
          "is_bot": false,
          "headline": "Refactor htslib/kseq.h usage to avoid unused function warnings",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2025-06-16T06:50:39Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "0781b20da207bef7a1715c155642b24a615cdae3",
          "body": null,
          "is_bot": false,
          "headline": "Merge v0.23.3 release branch",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2025-06-10T10:47:49Z",
          "body_truncated": false,
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        },
        {
          "oid": "cefbaa9079b0b2ad65dd8d60a532bc3eb31389ee",
          "body": null,
          "is_bot": false,
          "headline": "Bump version number to 0.23.3 and add release notes",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2025-06-10T10:37:29Z",
          "body_truncated": false,
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          "body": null,
          "is_bot": false,
          "headline": "Cherry-pick work-around for Cython 3.1.2 bug",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2025-06-10T10:26:26Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "96e26524f378ec0958e225499bd754129e730c74",
          "body": "Cython recently added __pyx_CommonTypesMetaclass_get_module() but\nneglected to make it static; cf cython/cython#6957. Remove it from\nthe lists of defined symbols to be checked for collisions.\n\nAlso ensure that we only strip one leading underscore on macOS,\nso that this function's name is as expected.",
          "is_bot": false,
          "headline": "Work around Cython 3.1.2 non-static internal function bug",
          "author_name": "John Marshall",
          "author_login": "jmarshall",
          "committed_at": "2025-06-10T09:50:47Z",
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          "is_coding_agent": false
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            "Intended Audience :: Developers",
            "Intended Audience :: Science/Research",
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            "Operating System :: POSIX",
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            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#branch-protection"
          },
          {
            "name": "CI-Tests",
            "score": 10,
            "reason": "2 out of 2 merged PRs checked by a CI test -- score normalized to 10",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#ci-tests"
          },
          {
            "name": "CII-Best-Practices",
            "score": 0,
            "reason": "no effort to earn an OpenSSF best practices badge detected",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#cii-best-practices"
          },
          {
            "name": "Code-Review",
            "score": 0,
            "reason": "Found 1/27 approved changesets -- score normalized to 0",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#code-review"
          },
          {
            "name": "Contributors",
            "score": 10,
            "reason": "project has 27 contributing companies or organizations",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#contributors"
          },
          {
            "name": "Dangerous-Workflow",
            "score": null,
            "reason": "no workflows found",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#dangerous-workflow"
          },
          {
            "name": "Dependency-Update-Tool",
            "score": 0,
            "reason": "no update tool detected",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#dependency-update-tool"
          },
          {
            "name": "Fuzzing",
            "score": 0,
            "reason": "project is not fuzzed",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#fuzzing"
          },
          {
            "name": "License",
            "score": 10,
            "reason": "license file detected",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#license"
          },
          {
            "name": "Maintained",
            "score": 10,
            "reason": "30 commit(s) and 10 issue activity found in the last 90 days -- score normalized to 10",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#maintained"
          },
          {
            "name": "Packaging",
            "score": null,
            "reason": "packaging workflow not detected",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#packaging"
          },
          {
            "name": "Pinned-Dependencies",
            "score": null,
            "reason": "no dependencies found",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#pinned-dependencies"
          },
          {
            "name": "SAST",
            "score": 0,
            "reason": "SAST tool is not run on all commits -- score normalized to 0",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#sast"
          },
          {
            "name": "Security-Policy",
            "score": 0,
            "reason": "security policy file not detected",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#security-policy"
          },
          {
            "name": "Signed-Releases",
            "score": null,
            "reason": "no releases found",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#signed-releases"
          },
          {
            "name": "Token-Permissions",
            "score": null,
            "reason": "No tokens found",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#token-permissions"
          },
          {
            "name": "Vulnerabilities",
            "score": 10,
            "reason": "0 existing vulnerabilities detected",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#vulnerabilities"
          }
        ],
        "commit": "6a40751c8c9278a3f5be6904437d92ee619377f4",
        "ran_at": "2026-07-21T20:29:53Z",
        "aggregate_score": 4.9,
        "scorecard_version": "v5.5.0"
      },
      "has_codeql_workflow": false,
      "has_security_policy": false,
      "has_dependabot_config": false
    }
  },
  "config": {
    "disabled_metrics": [],
    "disabled_categories": [],
    "disabled_components": {}
  },
  "source": {
    "url": "https://github.com/pysam-developers/pysam",
    "host": "github.com",
    "name": "pysam",
    "owner": "pysam-developers"
  },
  "metrics": {
    "overall": {
      "key": "overall",
      "band": "good",
      "name": "Overall health",
      "note": null,
      "notes": [],
      "value": 73,
      "inputs": {
        "security": 59,
        "vitality": 85,
        "community": 74,
        "governance": 63,
        "engineering": 81
      },
      "components": []
    },
    "categories": [
      {
        "key": "vitality",
        "band": "excellent",
        "name": "Vitality",
        "value": 85,
        "weight": 0.22,
        "metrics": [
          {
            "key": "development_activity",
            "band": "excellent",
            "name": "Development activity",
            "note": null,
            "notes": [],
            "value": 86,
            "inputs": {
              "commits_last_year": 84,
              "human_commit_share": 1,
              "days_since_last_push": 2,
              "active_weeks_last_year": 33
            },
            "components": [
              {
                "key": "push_recency",
                "name": "Push recency",
                "detail": "last push 2 days ago",
                "points": 36,
                "status": "met",
                "details": [
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                    "code": "push_recency",
                    "params": {
                      "days": 2
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                ],
                "max_points": 36
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              {
                "key": "commit_cadence",
                "name": "Commit cadence",
                "detail": "33/52 weeks with commits",
                "points": 22.8,
                "status": "partial",
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                    "code": "commit_cadence_weeks",
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                      "weeks": 33
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                ],
                "max_points": 36
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              {
                "key": "commit_volume",
                "name": "Commit volume",
                "detail": "84 commits in the last year",
                "points": 17.3,
                "status": "partial",
                "details": [
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                    "code": "commits_last_year",
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                      "count": 84
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                "max_points": 18
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              {
                "key": "openssf_scorecard_maintained",
                "name": "OpenSSF Scorecard: Maintained",
                "detail": "30 commit(s) and 10 issue activity found in the last 90 days -- score normalized to 10",
                "points": 10,
                "status": "met",
                "details": [],
                "max_points": 10
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            ]
          },
          {
            "key": "release_discipline",
            "band": "good",
            "name": "Release discipline",
            "note": "Excluded from scoring (no data or not applicable): OpenSSF Scorecard: Signed-Releases. Remaining weights renormalized.",
            "notes": [
              {
                "code": "excluded_no_data",
                "params": {
                  "components": [
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                }
              },
              {
                "code": "weights_renormalized",
                "params": {}
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            "value": 84,
            "inputs": {
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              "days_since_latest_release": 85,
              "mean_days_between_releases": 159.1
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            "components": [
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                "key": "ships_releases",
                "name": "Ships releases",
                "detail": "41 releases published",
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                "status": "met",
                "details": [
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                "name": "Release recency",
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                "key": "release_cadence",
                "name": "Release cadence",
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                "key": "openssf_scorecard_signed_releases",
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                "status": "excluded",
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          {
            "key": "abandonment",
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            "note": null,
            "notes": [],
            "value": 100,
            "inputs": {
              "cap": null,
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              "guards": [],
              "signals": [],
              "red_flag": false,
              "multiplier_pct": 100,
              "declared_reason": null,
              "unverified_reason": null,
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              "unanswered_open_issues": null,
              "days_since_last_merged_pr": null,
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            "components": [
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                "key": "project_is_still_maintained",
                "name": "Project is still maintained",
                "detail": "last human commit 2 days ago",
                "points": 100,
                "status": "met",
                "details": [
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                    "code": "abandonment_maintained",
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                "max_points": 100
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        ],
        "description": "Is the project alive — is code being written and are releases shipping?"
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      {
        "key": "community",
        "band": "good",
        "name": "Community & Adoption",
        "value": 74,
        "weight": 0.18,
        "metrics": [
          {
            "key": "popularity",
            "band": "good",
            "name": "Popularity & adoption",
            "note": null,
            "notes": [],
            "value": 78,
            "inputs": {
              "forks": 297,
              "stars": 900,
              "watchers": 42,
              "growth_state": "organic",
              "growth_factor_pct": 100
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            "components": [
              {
                "key": "stars",
                "name": "Stars",
                "detail": "900 stars",
                "points": 47.9,
                "status": "partial",
                "details": [
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                    "code": "stars",
                    "params": {
                      "count": 900
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                "max_points": 60
              },
              {
                "key": "forks",
                "name": "Forks",
                "detail": "297 forks",
                "points": 20.6,
                "status": "partial",
                "details": [
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                    "code": "forks",
                    "params": {
                      "count": 297
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                ],
                "max_points": 25
              },
              {
                "key": "watchers",
                "name": "Watchers",
                "detail": "42 watchers",
                "points": 9,
                "status": "partial",
                "details": [
                  {
                    "code": "watchers",
                    "params": {
                      "count": 42
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                  }
                ],
                "max_points": 15
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            ]
          },
          {
            "key": "community_health",
            "band": "moderate",
            "name": "Community health",
            "note": null,
            "notes": [],
            "value": 50,
            "inputs": {
              "has_readme": true,
              "has_license": true,
              "has_contributing": false,
              "has_issue_template": false,
              "has_code_of_conduct": false,
              "has_pull_request_template": false
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            "components": [
              {
                "key": "readme",
                "name": "README",
                "detail": null,
                "points": 22.5,
                "status": "met",
                "details": [],
                "max_points": 22.5
              },
              {
                "key": "license",
                "name": "License",
                "detail": "recognized license (MIT)",
                "points": 22.5,
                "status": "met",
                "details": [
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                    "code": "license_standard",
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                  },
                  {
                    "code": "license_spdx",
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                "max_points": 22.5
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              {
                "key": "contributing_guide",
                "name": "CONTRIBUTING guide",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 18
              },
              {
                "key": "code_of_conduct",
                "name": "Code of conduct",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 13.5
              },
              {
                "key": "issue_template",
                "name": "Issue template",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 7.2
              },
              {
                "key": "pr_template",
                "name": "PR template",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 6.3
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            ]
          },
          {
            "key": "ecosystem_adoption",
            "band": "excellent",
            "name": "Ecosystem adoption (downloads)",
            "note": "Excluded from scoring (no data or not applicable): Registry dependents. Remaining weights renormalized.",
            "notes": [
              {
                "code": "excluded_no_data",
                "params": {
                  "components": [
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                }
              },
              {
                "code": "weights_renormalized",
                "params": {}
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            ],
            "value": 100,
            "inputs": {
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              "dependents": null,
              "ecosystems": "pypi",
              "total_downloads": null,
              "monthly_downloads": 1150697
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            "components": [
              {
                "key": "monthly_downloads",
                "name": "Monthly downloads",
                "detail": "1,150,697 downloads/month across pypi",
                "points": 80,
                "status": "met",
                "details": [
                  {
                    "code": "downloads_monthly",
                    "params": {
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                      "ecosystems": "pypi"
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                  }
                ],
                "max_points": 80
              },
              {
                "key": "registry_dependents",
                "name": "Registry dependents",
                "detail": "not reported by this ecosystem",
                "points": 0,
                "status": "excluded",
                "details": [
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                    "code": "not_reported_by_this_ecosystem",
                    "params": {}
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                ],
                "max_points": 20
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            ]
          }
        ],
        "description": "Does the project have users, downloads, attention, and a welcoming setup for contributors?"
      },
      {
        "key": "governance",
        "band": "moderate",
        "name": "Sustainability & Governance",
        "value": 63,
        "weight": 0.24,
        "metrics": [
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            "key": "maintainer_resilience",
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            "note": null,
            "notes": [],
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            "inputs": {
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              "contributors_sampled": 100,
              "top_contributor_share": 0.589
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            "components": [
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                "key": "bus_factor",
                "name": "Bus factor",
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                "status": "partial",
                "details": [
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                ],
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                "key": "commit_distribution",
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                "detail": "top contributor authored 59% of commits",
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                "status": "partial",
                "details": [
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                    "code": "top_contributor_share",
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                "max_points": 22.5
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                "key": "contributor_breadth",
                "name": "Contributor breadth",
                "detail": "100 contributors",
                "points": 13.5,
                "status": "met",
                "details": [
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                    "code": "contributors_sampled",
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                ],
                "max_points": 13.5
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              {
                "key": "openssf_scorecard_contributors",
                "name": "OpenSSF Scorecard: Contributors",
                "detail": "project has 27 contributing companies or organizations",
                "points": 10,
                "status": "met",
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                "max_points": 10
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            ]
          },
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            "key": "responsiveness",
            "band": "moderate",
            "name": "Issue & PR responsiveness",
            "note": null,
            "notes": [],
            "value": 67,
            "inputs": {
              "merged_prs": 344,
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              "closed_issues": 734,
              "issue_closed_ratio": 0.752,
              "closed_unmerged_prs": 67
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            "components": [
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                "key": "issue_resolution",
                "name": "Issue resolution",
                "detail": "75% of issues closed",
                "points": 35.2,
                "status": "partial",
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                    "code": "issues_closed_share",
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                      "share": 75
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                "max_points": 46.75
              },
              {
                "key": "pr_acceptance",
                "name": "PR acceptance",
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                "points": 32,
                "status": "partial",
                "details": [
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                    "code": "decided_prs_merged",
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                ],
                "max_points": 38.25
              },
              {
                "key": "openssf_scorecard_code_review",
                "name": "OpenSSF Scorecard: Code-Review",
                "detail": "Found 1/27 approved changesets -- score normalized to 0",
                "points": 0,
                "status": "missed",
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                "max_points": 15
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            ]
          },
          {
            "key": "stewardship",
            "band": "moderate",
            "name": "Ownership & stewardship",
            "note": null,
            "notes": [],
            "value": 54,
            "inputs": {
              "followers": 10,
              "owner_type": "Organization",
              "is_verified": null,
              "owner_login": "pysam-developers",
              "public_repos": 3,
              "account_age_days": 4548
            },
            "components": [
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                "key": "ownership_backing",
                "name": "Ownership backing",
                "detail": "organization-owned",
                "points": 30,
                "status": "met",
                "details": [
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                    "code": "owner_organization",
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                ],
                "max_points": 30
              },
              {
                "key": "verified_domain",
                "name": "Verified domain",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 20
              },
              {
                "key": "owner_reach",
                "name": "Owner reach",
                "detail": "10 followers of pysam-developers",
                "points": 7.5,
                "status": "partial",
                "details": [
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                    "code": "owner_followers",
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                      "login": "pysam-developers"
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                  }
                ],
                "max_points": 25
              },
              {
                "key": "track_record",
                "name": "Track record",
                "detail": "3 public repos, account ~12 yr old",
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                "status": "partial",
                "details": [
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                  },
                  {
                    "code": "account_age_years",
                    "params": {
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                ],
                "max_points": 25
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            ]
          },
          {
            "key": "package_maintenance",
            "band": "excellent",
            "name": "Package maintenance",
            "note": null,
            "notes": [],
            "value": 100,
            "inputs": {
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              "ecosystems": "pypi",
              "any_deprecated": false,
              "min_days_since_publish": 85
            },
            "components": [
              {
                "key": "published_resolvable",
                "name": "Published & resolvable",
                "detail": "1 package(s) on pypi",
                "points": 25,
                "status": "met",
                "details": [
                  {
                    "code": "packages_published",
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                      "ecosystems": "pypi"
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                  }
                ],
                "max_points": 25
              },
              {
                "key": "publish_recency",
                "name": "Publish recency",
                "detail": "latest publish 85 days ago",
                "points": 35,
                "status": "met",
                "details": [
                  {
                    "code": "publish_recency",
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                ],
                "max_points": 35
              },
              {
                "key": "version_history",
                "name": "Version history",
                "detail": "48 published versions",
                "points": 20,
                "status": "met",
                "details": [
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                    "code": "published_versions",
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                ],
                "max_points": 20
              },
              {
                "key": "not_deprecated",
                "name": "Not deprecated",
                "detail": "active, not deprecated or yanked",
                "points": 20,
                "status": "met",
                "details": [
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                    "code": "package_not_deprecated",
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                ],
                "max_points": 20
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            ]
          }
        ],
        "description": "Will the project survive its people — bus factor, responsiveness, who backs it, and package upkeep?"
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      {
        "key": "engineering",
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        "weight": 0.2,
        "metrics": [
          {
            "key": "engineering_practices",
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            "name": "Engineering practices",
            "note": null,
            "notes": [],
            "value": 68,
            "inputs": {
              "has_ci": true,
              "has_tests": true,
              "has_editorconfig": false,
              "has_linter_config": false,
              "has_precommit_config": false
            },
            "components": [
              {
                "key": "ci_workflows",
                "name": "CI workflows",
                "detail": "2 workflow(s)",
                "points": 24,
                "status": "met",
                "details": [
                  {
                    "code": "ci_workflows",
                    "params": {
                      "count": 2
                    }
                  }
                ],
                "max_points": 24
              },
              {
                "key": "tests_present",
                "name": "Tests present",
                "detail": null,
                "points": 24,
                "status": "met",
                "details": [],
                "max_points": 24
              },
              {
                "key": "linter_config",
                "name": "Linter config",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 16
              },
              {
                "key": "pre_commit_hooks",
                "name": "Pre-commit hooks",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 9.6
              },
              {
                "key": "editorconfig",
                "name": ".editorconfig",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 6.4
              },
              {
                "key": "openssf_scorecard_ci_tests",
                "name": "OpenSSF Scorecard: CI-Tests",
                "detail": "2 out of 2 merged PRs checked by a CI test -- score normalized to 10",
                "points": 20,
                "status": "met",
                "details": [],
                "max_points": 20
              }
            ]
          },
          {
            "key": "documentation",
            "band": "excellent",
            "name": "Documentation",
            "note": null,
            "notes": [],
            "value": 100,
            "inputs": {
              "topics": [
                "bioinformatics",
                "ngs",
                "python",
                "htslib"
              ],
              "has_wiki": true,
              "homepage": "https://pysam.readthedocs.io/en/latest/",
              "has_readme": true,
              "has_docs_dir": true,
              "has_description": true
            },
            "components": [
              {
                "key": "readme",
                "name": "README",
                "detail": null,
                "points": 30,
                "status": "met",
                "details": [],
                "max_points": 30
              },
              {
                "key": "documentation_directory",
                "name": "Documentation directory",
                "detail": null,
                "points": 25,
                "status": "met",
                "details": [],
                "max_points": 25
              },
              {
                "key": "documentation_homepage_site",
                "name": "Documentation / homepage site",
                "detail": "https://pysam.readthedocs.io/en/latest/",
                "points": 15,
                "status": "met",
                "details": [],
                "max_points": 15
              },
              {
                "key": "repository_description",
                "name": "Repository description",
                "detail": null,
                "points": 10,
                "status": "met",
                "details": [],
                "max_points": 10
              },
              {
                "key": "topics",
                "name": "Topics",
                "detail": "4 topics",
                "points": 10,
                "status": "met",
                "details": [
                  {
                    "code": "topics_count",
                    "params": {
                      "count": 4
                    }
                  }
                ],
                "max_points": 10
              },
              {
                "key": "wiki",
                "name": "Wiki",
                "detail": null,
                "points": 10,
                "status": "met",
                "details": [],
                "max_points": 10
              }
            ]
          }
        ],
        "description": "Are baseline engineering and documentation practices in place?"
      },
      {
        "key": "security",
        "band": "moderate",
        "name": "Security",
        "value": 59,
        "weight": 0.16,
        "metrics": [
          {
            "key": "security_posture",
            "band": "at_risk",
            "name": "Security posture",
            "note": "Excluded from scoring (no data or not applicable): Dangerous-Workflow, Packaging, Pinned-Dependencies, Signed-Releases, Token-Permissions. Remaining weights renormalized.",
            "notes": [
              {
                "code": "excluded_no_data",
                "params": {
                  "components": [
                    "dangerous_workflow",
                    "packaging",
                    "pinned_dependencies",
                    "signed_releases",
                    "token_permissions"
                  ]
                }
              },
              {
                "code": "weights_renormalized",
                "params": {}
              }
            ],
            "value": 49,
            "inputs": {
              "source": "openssf_scorecard",
              "checks_evaluated": 13,
              "scorecard_version": "v5.5.0",
              "checks_inconclusive": 5,
              "scorecard_aggregate": 4.9
            },
            "components": [
              {
                "key": "binary_artifacts",
                "name": "Binary-Artifacts",
                "detail": "no binaries found in the repo",
                "points": 7.5,
                "status": "met",
                "details": [],
                "max_points": 7.5
              },
              {
                "key": "branch_protection",
                "name": "Branch-Protection",
                "detail": "branch protection is not maximal on development and all release branches",
                "points": 4.5,
                "status": "partial",
                "details": [],
                "max_points": 7.5
              },
              {
                "key": "ci_tests",
                "name": "CI-Tests",
                "detail": "2 out of 2 merged PRs checked by a CI test -- score normalized to 10",
                "points": 2.5,
                "status": "met",
                "details": [],
                "max_points": 2.5
              },
              {
                "key": "cii_best_practices",
                "name": "CII-Best-Practices",
                "detail": "no effort to earn an OpenSSF best practices badge detected",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 2.5
              },
              {
                "key": "code_review",
                "name": "Code-Review",
                "detail": "Found 1/27 approved changesets -- score normalized to 0",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 7.5
              },
              {
                "key": "contributors",
                "name": "Contributors",
                "detail": "project has 27 contributing companies or organizations",
                "points": 2.5,
                "status": "met",
                "details": [],
                "max_points": 2.5
              },
              {
                "key": "dangerous_workflow",
                "name": "Dangerous-Workflow",
                "detail": "no workflows found",
                "points": 0,
                "status": "excluded",
                "details": [
                  {
                    "code": "no_data",
                    "params": {}
                  }
                ],
                "max_points": 10
              },
              {
                "key": "dependency_update_tool",
                "name": "Dependency-Update-Tool",
                "detail": "no update tool detected",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 7.5
              },
              {
                "key": "fuzzing",
                "name": "Fuzzing",
                "detail": "project is not fuzzed",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 5
              },
              {
                "key": "license",
                "name": "License",
                "detail": "license file detected",
                "points": 2.5,
                "status": "met",
                "details": [],
                "max_points": 2.5
              },
              {
                "key": "maintained",
                "name": "Maintained",
                "detail": "30 commit(s) and 10 issue activity found in the last 90 days -- score normalized to 10",
                "points": 7.5,
                "status": "met",
                "details": [],
                "max_points": 7.5
              },
              {
                "key": "packaging",
                "name": "Packaging",
                "detail": "packaging workflow not detected",
                "points": 0,
                "status": "excluded",
                "details": [
                  {
                    "code": "no_data",
                    "params": {}
                  }
                ],
                "max_points": 5
              },
              {
                "key": "pinned_dependencies",
                "name": "Pinned-Dependencies",
                "detail": "no dependencies found",
                "points": 0,
                "status": "excluded",
                "details": [
                  {
                    "code": "no_data",
                    "params": {}
                  }
                ],
                "max_points": 5
              },
              {
                "key": "sast",
                "name": "SAST",
                "detail": "SAST tool is not run on all commits -- score normalized to 0",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 5
              },
              {
                "key": "security_policy",
                "name": "Security-Policy",
                "detail": "security policy file not detected",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 5
              },
              {
                "key": "signed_releases",
                "name": "Signed-Releases",
                "detail": "no releases found",
                "points": 0,
                "status": "excluded",
                "details": [
                  {
                    "code": "no_data",
                    "params": {}
                  }
                ],
                "max_points": 7.5
              },
              {
                "key": "token_permissions",
                "name": "Token-Permissions",
                "detail": "No tokens found",
                "points": 0,
                "status": "excluded",
                "details": [
                  {
                    "code": "no_data",
                    "params": {}
                  }
                ],
                "max_points": 7.5
              },
              {
                "key": "vulnerabilities",
                "name": "Vulnerabilities",
                "detail": "0 existing vulnerabilities detected",
                "points": 7.5,
                "status": "met",
                "details": [],
                "max_points": 7.5
              }
            ]
          },
          {
            "key": "dependency_advisories",
            "band": "excellent",
            "name": "Dependency advisories",
            "note": "Excluded from scoring (no data or not applicable): Indirect dependencies free of known advisories, No advisories left outstanding. Remaining weights renormalized. Matched 2 resolved dependencies against OSV; 2 could not be assessed (no resolved version, an unsupported ecosystem, or beyond the reported package list). This repository publishes no package the index resolves, so the repository dependency graph was assessed instead. That graph mixes development and test pins with shipped dependencies, so only the declared runtime dependencies are scored; transitive findings are reported as context and excluded from the score. Reachability is not analyzed.",
            "notes": [
              {
                "code": "excluded_no_data",
                "params": {
                  "components": [
                    "indirect_dependencies_free_of_known_advisories",
                    "no_advisories_left_outstanding"
                  ]
                }
              },
              {
                "code": "weights_renormalized",
                "params": {}
              },
              {
                "code": "advisories_scope_repository",
                "params": {
                  "assessed": 2
                }
              },
              {
                "code": "advisories_unassessed",
                "params": {
                  "count": 2
                }
              },
              {
                "code": "advisories_repo_graph_caveat",
                "params": {}
              },
              {
                "code": "advisories_reachability",
                "params": {}
              }
            ],
            "value": 100,
            "inputs": {
              "source": "osv",
              "advisories": 0,
              "affected_packages": 0,
              "assessed_packages": 2,
              "unassessed_packages": 2,
              "affected_by_severity": "none",
              "direct_affected_packages": 0
            },
            "components": [
              {
                "key": "direct_dependencies_free_of_known_advisories",
                "name": "Direct dependencies free of known advisories",
                "detail": "no direct dependency carries a known advisory",
                "points": 35,
                "status": "met",
                "details": [
                  {
                    "code": "no_direct_advisories",
                    "params": {}
                  }
                ],
                "max_points": 35
              },
              {
                "key": "indirect_dependencies_free_of_known_advisories",
                "name": "Indirect dependencies free of known advisories",
                "detail": "transitive set not separable from development and test dependencies in this scope",
                "points": 0,
                "status": "excluded",
                "details": [
                  {
                    "code": "advisories_scope_not_separable",
                    "params": {}
                  }
                ],
                "max_points": 25
              },
              {
                "key": "no_advisories_left_outstanding",
                "name": "No advisories left outstanding",
                "detail": "no advisory carries a publication date",
                "points": 0,
                "status": "excluded",
                "details": [
                  {
                    "code": "advisories_no_publication_date",
                    "params": {}
                  }
                ],
                "max_points": 40
              }
            ]
          },
          {
            "key": "malicious_dependencies",
            "band": "excellent",
            "name": "Malicious dependencies",
            "note": null,
            "notes": [],
            "value": 100,
            "inputs": {
              "source": "osv",
              "meaning": "reported as a malicious package by the OpenSSF corpus; the remedy is removal or moving off the compromised name, never an upgrade of the same artifact. Versions the registry has since pulled are listed but not scored",
              "packages": [],
              "red_flag": false,
              "assessed_packages": 2,
              "malicious_packages": 0,
              "direct_malicious_packages": 0,
              "withdrawn_malicious_packages": 0,
              "installable_malicious_packages": 0
            },
            "components": [
              {
                "key": "no_dependency_reported_as_a_malicious_package",
                "name": "No dependency reported as a malicious package",
                "detail": "no dependency is reported as a malicious package",
                "points": 100,
                "status": "met",
                "details": [
                  {
                    "code": "no_malicious_dependencies",
                    "params": {}
                  }
                ],
                "max_points": 100
              }
            ]
          },
          {
            "key": "high_risk_jurisdiction_exposure",
            "band": "excellent",
            "name": "High-Risk Jurisdiction Exposure",
            "note": "Only high-confidence self-published location evidence affects this multiplier. Ambiguous matches are review-only; country evidence is not proof of nationality, citizenship, legal registration, malicious intent, or sanctions status.",
            "notes": [
              {
                "code": "jurisdiction_evidence_limits",
                "params": {}
              }
            ],
            "value": 100,
            "inputs": {
              "meaning": "self-published location evidence; not nationality or citizenship",
              "red_flag": false,
              "exposures": [],
              "policy_countries": [
                "Russia",
                "Iran",
                "North Korea"
              ],
              "review_only_matches": 0,
              "assessed_self_published_locations": 12
            },
            "components": [
              {
                "key": "policy_exposure_multiplier",
                "name": "Policy exposure multiplier",
                "detail": "no confirmed policy-scope location match",
                "points": 100,
                "status": "met",
                "details": [
                  {
                    "code": "jurisdiction_no_match",
                    "params": {}
                  }
                ],
                "max_points": 100
              }
            ]
          }
        ],
        "description": "Are visible security and supply-chain practices strong, with no malicious dependency and no unresolved high-risk jurisdiction exposure?"
      },
      {
        "key": "ai_readiness",
        "band": "moderate",
        "name": "AI Readiness",
        "value": 51,
        "weight": 0,
        "metrics": [
          {
            "key": "ai_agent_context",
            "band": "at_risk",
            "name": "Agent context & guidance",
            "note": null,
            "notes": [],
            "value": 32,
            "inputs": {
              "has_llms_txt": false,
              "legible_history_share": 0.59,
              "agent_instruction_files": [],
              "agent_instruction_max_bytes": null
            },
            "components": [
              {
                "key": "agent_instructions",
                "name": "Agent instructions",
                "detail": "no CLAUDE.md / AGENTS.md / editor rules",
                "points": 0,
                "status": "missed",
                "details": [
                  {
                    "code": "no_agent_instructions",
                    "params": {}
                  }
                ],
                "max_points": 45
              },
              {
                "key": "machine_readable_docs_llms_txt",
                "name": "Machine-readable docs (llms.txt)",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 15
              },
              {
                "key": "legible_commit_history",
                "name": "Legible commit history",
                "detail": "59 of 100 human commits state their intent (structured subject or explanatory body)",
                "points": 31.5,
                "status": "partial",
                "details": [
                  {
                    "code": "legible_history",
                    "params": {
                      "legible": 59,
                      "sampled": 100
                    }
                  }
                ],
                "max_points": 40
              }
            ]
          },
          {
            "key": "ai_verify_loop",
            "band": "moderate",
            "name": "Verify loop (build / test / typecheck)",
            "note": "Excluded from scoring (no data or not applicable): OpenSSF Scorecard: Pinned-Dependencies. Remaining weights renormalized.",
            "notes": [
              {
                "code": "excluded_no_data",
                "params": {
                  "components": [
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                }
              },
              {
                "code": "weights_renormalized",
                "params": {}
              }
            ],
            "value": 57,
            "inputs": {
              "has_nix": false,
              "has_tests": true,
              "lockfiles": [],
              "has_dockerfile": false,
              "typed_language": false,
              "bootstrap_files": [
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                "tests/pysam_data/Makefile",
                "tests/tabix_data/Makefile"
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              "has_devcontainer": false,
              "has_linter_config": false,
              "typecheck_configs": [
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              "agent_commit_share": 0,
              "toolchain_manifests": [],
              "dependency_bot_commit_share": 0
            },
            "components": [
              {
                "key": "one_command_bootstrap",
                "name": "One-command bootstrap",
                "detail": "doc/Makefile, htslib/Makefile, tests/cbcf_data/Makefile, tests/pysam_data/Makefile, tests/tabix_data/Makefile",
                "points": 18,
                "status": "met",
                "details": [
                  {
                    "code": "file_list",
                    "params": {
                      "files": "doc/Makefile, htslib/Makefile, tests/cbcf_data/Makefile, tests/pysam_data/Makefile, tests/tabix_data/Makefile"
                    }
                  }
                ],
                "max_points": 18
              },
              {
                "key": "automated_tests",
                "name": "Automated tests",
                "detail": null,
                "points": 22,
                "status": "met",
                "details": [],
                "max_points": 22
              },
              {
                "key": "lint_format_config",
                "name": "Lint / format config",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 11
              },
              {
                "key": "static_type_checking",
                "name": "Static type checking",
                "detail": "pysam/py.typed",
                "points": 11,
                "status": "met",
                "details": [
                  {
                    "code": "file_list",
                    "params": {
                      "files": "pysam/py.typed"
                    }
                  }
                ],
                "max_points": 11
              },
              {
                "key": "reproducible_environment",
                "name": "Reproducible environment",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 10
              },
              {
                "key": "demonstrated_agent_practice",
                "name": "Demonstrated agent practice",
                "detail": "no agent-authored commits among the last 100",
                "points": 0,
                "status": "missed",
                "details": [
                  {
                    "code": "no_agent_authored_commits",
                    "params": {
                      "sampled": 100
                    }
                  }
                ],
                "max_points": 10
              },
              {
                "key": "automated_maintenance",
                "name": "Automated maintenance",
                "detail": "no automated dependency updates observed",
                "points": 0,
                "status": "missed",
                "details": [
                  {
                    "code": "no_dependency_automation",
                    "params": {}
                  }
                ],
                "max_points": 8
              },
              {
                "key": "openssf_scorecard_pinned_dependencies",
                "name": "OpenSSF Scorecard: Pinned-Dependencies",
                "detail": "no dependencies found",
                "points": 0,
                "status": "excluded",
                "details": [
                  {
                    "code": "no_data",
                    "params": {}
                  }
                ],
                "max_points": 10
              }
            ]
          },
          {
            "key": "ai_code_legibility",
            "band": "good",
            "name": "Code legibility for models",
            "note": null,
            "notes": [],
            "value": 75,
            "inputs": {
              "primary_language": "Cython",
              "largest_source_bytes": 230215,
              "source_files_sampled": 458,
              "oversized_source_files": 56
            },
            "components": [
              {
                "key": "type_checkable_code",
                "name": "Type-checkable code",
                "detail": "Cython with type-check config (pysam/py.typed)",
                "points": 27,
                "status": "partial",
                "details": [
                  {
                    "code": "typecheck_config_language",
                    "params": {
                      "files": "pysam/py.typed",
                      "language": "Cython"
                    }
                  }
                ],
                "max_points": 45
              },
              {
                "key": "manageable_file_sizes",
                "name": "Manageable file sizes",
                "detail": "56/458 source files over 60KB",
                "points": 48.3,
                "status": "partial",
                "details": [
                  {
                    "code": "oversized_source_files",
                    "params": {
                      "kb": 60,
                      "sampled": 458,
                      "oversized": 56
                    }
                  }
                ],
                "max_points": 55
              }
            ]
          }
        ],
        "description": "How well is the repo equipped to be developed and maintained with AI coding agents? An independent, experimental badge — weight 0.0, so it is surfaced on its own and does not affect the overall health score."
      }
    ],
    "metrics_version": "1.13.0"
  },
  "warnings": [
    "Could not fetch pypi package 'pysam.libchtslib' from its registry"
  ],
  "report_type": "repository",
  "generated_at": "2026-07-21T20:30:14.249715Z",
  "schema_version": "0.23.0",
  "badge_url": "https://raw.githubusercontent.com/inspect-software/badges/main/v1/p/pysam-developers/pysam.svg",
  "full_name": "pysam-developers/pysam",
  "license_state": "standard",
  "license_spdx": "MIT"
}