Public recordGood
Software health reportschema 0.27.0 · metrics 1.13.0 · 2026-07-27 22:27 UTC
CompOmics / ms2rescore
Modular and user-friendly platform for AI-assisted rescoring of peptide identifications
CompOmics/ms2rescore holds a health index of 72 out of 100, placing it in the Good band. It scores highest on Engineering Quality (90/100) and lowest on AI Readiness (43/100). It was last updated 3 days ago. 2 contributors account for most of its recent work.
72
overall / 100Software health index
Metrics are grouped into weighted categories on one standardized 1–100 scale. Overall starts as their weighted mean; when public evidence triggers the High-Risk Jurisdiction Policy, the rating is adjusted and receives an At risk ceiling of 49. AI Readiness sits outside the overall score.
72
Excellent85-100Exemplary; meets essentially all checked criteria
Good70-84Healthy; minor gaps
Moderate50-69Acceptable with notable gaps; review recommended
At risk30-49Significant weaknesses; adoption warrants caution
Critical1-29Severe problems (abandoned, single-maintainer, no hygiene)
Score profile
Each axis is a category. The shape matters more than the average — a healthy subject fills the whole shape, while a spike-and-crater profile means strength in one dimension is masking risk in another.
Ownership
Computational Omics and Systems Biology GroupOrganization
129 followers114 public repossince Mar 2015
This repository is backed by an organization — shared, accountable stewardship that can outlive any single maintainer.
Package ecosystems
| Registry | Package | Version | Downloads / mo | Versions | Last publish | Tags |
|---|---|---|---|---|---|---|
| PyPI | ms2rescore | 4.0.1 | - | 45 | 3 days ago | ms2rescorems2pipdeeplcproteomicsmass-spectrometrypeptide-identificationrescoringmachine-learning |
Metrics by category
Vitality
Is the project alive — is code being written and are releases shipping?
79
Development activity
77Good
How it's scored
| 36/36 | Push recency — last push 3 days ago |
| 13.2/36 | Commit cadence — 19/52 weeks with commits |
| 18/18 | Commit volume — 210 commits in the last year |
| 10/10 | OpenSSF Scorecard: Maintained — 30 commit(s) and 5 issue activity found in the last 90 days -- score normalized to 10 |
Inputs used
| commits_last_year | 210 |
| human_commit_share | 1 |
| days_since_last_push | 3 |
| active_weeks_last_year | 19 |
Release discipline
83Good
How it's scored
| 27/27 | Ships releases — 43 releases published |
| 36/36 | Release recency — latest release 3 days ago |
| 19.8/27 | Release cadence — a release every ~78.8 days |
| 0/10 | OpenSSF Scorecard: Signed-Releases — Project has not signed or included provenance with any releases. |
Inputs used
| releases_count | 43 |
| latest_release_tag | v4.0.1 |
| releases_from_tags | no |
| days_since_latest_release | 3 |
| mean_days_between_releases | 78.8 |
Community & Adoption
Does the project have users, downloads, attention, and a welcoming setup for contributors?
56
Popularity & adoption
44At risk
How it's scored
| 29.4/60 | Stars — 66 stars |
| 11/25 | Forks — 22 forks |
| 3.9/15 | Watchers — 6 watchers |
Inputs used
| forks | 22 |
| stars | 66 |
| watchers | 6 |
| growth_state | unverified |
| growth_factor_pct | 100 |
| growth_unverified_reason | no_history |
Community health
70Good
How it's scored
| 22.5/22.5 | README |
| 22.5/22.5 | License — recognized license (Apache-2.0) |
| 18/18 | CONTRIBUTING guide |
| 0/13.5 | Code of conduct |
| 0/7.2 | Issue template |
| 0/6.3 | PR template |
Inputs used
| has_readme | yes |
| has_license | yes |
| has_contributing | yes |
| has_issue_template | no |
| has_code_of_conduct | no |
| has_pull_request_template | no |
Sustainability & Governance
Will the project survive its people — bus factor, responsiveness, who backs it, and package upkeep?
73
Maintainer resilience (bus factor)
56Moderate
How it's scored
| 25.2/54 | Bus factor — 2 contributor(s) cover half of all commits |
| 11.5/22.5 | Commit distribution — top contributor authored 49% of commits |
| 9.5/13.5 | Contributor breadth — 7 contributors |
| 10/10 | OpenSSF Scorecard: Contributors — project has 6 contributing companies or organizations |
Inputs used
| bus_factor | 2 |
| contributors_sampled | 7 |
| top_contributor_share | 0.489 |
How it's scored
| 41.4/46.8 | Issue resolution — 89% of issues closed |
| 32.1/38.3 | PR acceptance — 110/131 decided PRs merged |
| 1.5/15 | OpenSSF Scorecard: Code-Review — Found 1/7 approved changesets -- score normalized to 1 |
Inputs used
| merged_prs | 110 |
| open_issues | 14 |
| closed_issues | 109 |
| issue_closed_ratio | 0.886 |
| closed_unmerged_prs | 21 |
Ownership & stewardship
70Good
How it's scored
| 30/30 | Ownership backing — organization-owned |
| 0/20 | Verified domain |
| 15.2/25 | Owner reach — 129 followers of CompOmics |
| 25/25 | Track record — 114 public repos, account ~11 yr old |
Inputs used
| followers | 129 |
| owner_type | Organization |
| is_verified | — |
| owner_login | CompOmics |
| public_repos | 114 |
| account_age_days | 4,143 |
Package maintenance
100Excellent
How it's scored
| 25/25 | Published & resolvable — 1 package(s) on pypi |
| 35/35 | Publish recency — latest publish 3 days ago |
| 20/20 | Version history — 45 published versions |
| 20/20 | Not deprecated — active, not deprecated or yanked |
Inputs used
| packages | ms2rescore |
| ecosystems | pypi |
| any_deprecated | no |
| min_days_since_publish | 3 |
Engineering Quality
Are baseline engineering and documentation practices in place?
90
Engineering practices
90Excellent
How it's scored
| 24/24 | CI workflows — 2 workflow(s) |
| 24/24 | Tests present |
| 16/16 | Linter config |
| 9.6/9.6 | Pre-commit hooks |
| 0/6.4 | .editorconfig |
| 16/20 | OpenSSF Scorecard: CI-Tests — 4 out of 5 merged PRs checked by a CI test -- score normalized to 8 |
Inputs used
| has_ci | yes |
| has_tests | yes |
| has_editorconfig | no |
| has_linter_config | yes |
| has_precommit_config | yes |
Documentation
90Excellent
How it's scored
| 30/30 | README |
| 25/25 | Documentation directory |
| 15/15 | Documentation / homepage site — https://ms2rescore.readthedocs.io |
| 10/10 | Repository description |
| 10/10 | Topics — 5 topics |
| 0/10 | Wiki |
Inputs used
| topics | proteomics, ms2pip, percolator, deeplc, peptide-identification |
| has_wiki | no |
| homepage | https://ms2rescore.readthedocs.io |
| has_readme | yes |
| has_docs_dir | yes |
| has_description | yes |
Security
Are visible security and supply-chain practices strong, without unresolved high-risk jurisdiction exposure?
58
Security posture
47At risk
How it's scored
| 7.5/7.5 | Binary-Artifacts — no binaries found in the repo |
| 0/7.5 | Branch-Protection — no data |
| 2/2.5 | CI-Tests — 4 out of 5 merged PRs checked by a CI test -- score normalized to 8 |
| 0/2.5 | CII-Best-Practices — no effort to earn an OpenSSF best practices badge detected |
| 0.8/7.5 | Code-Review — Found 1/7 approved changesets -- score normalized to 1 |
| 2.5/2.5 | Contributors — project has 6 contributing companies or organizations |
| 10/10 | Dangerous-Workflow — no dangerous workflow patterns detected |
| 0/7.5 | Dependency-Update-Tool — no update tool detected |
| 0/5 | Fuzzing — project is not fuzzed |
| 2.5/2.5 | License — license file detected |
| 7.5/7.5 | Maintained — 30 commit(s) and 5 issue activity found in the last 90 days -- score normalized to 10 |
| 5/5 | Packaging — packaging workflow detected |
| 0.5/5 | Pinned-Dependencies — dependency not pinned by hash detected -- score normalized to 1 |
| 0/5 | SAST — SAST tool is not run on all commits -- score normalized to 0 |
| 0/5 | Security-Policy — security policy file not detected |
| 0/7.5 | Signed-Releases — Project has not signed or included provenance with any releases. |
| 0/7.5 | Token-Permissions — detected GitHub workflow tokens with excessive permissions |
| 7.5/7.5 | Vulnerabilities — 0 existing vulnerabilities detected |
Inputs used
| source | openssf_scorecard |
| checks_evaluated | 17 |
| scorecard_version | v5.5.0 |
| checks_inconclusive | 1 |
| scorecard_aggregate | 4.7 |
Excluded from scoring (no data or not applicable): branch_protection. Remaining weights renormalized.
Dependency advisories
100Excellent
How it's scored
| 35/35 | Direct dependencies free of known advisories — no direct dependency carries a known advisory |
| 25/25 | Indirect dependencies free of known advisories — no indirect dependency carries a known advisory |
| 0/40 | No advisories left outstanding — no advisory carries a publication date |
Inputs used
| source | osv |
| advisories | 0 |
| affected_packages | 0 |
| assessed_packages | 69 |
| unassessed_packages | 0 |
| affected_by_severity | none |
| direct_affected_packages | 0 |
Excluded from scoring (no data or not applicable): No advisories left outstanding. Remaining weights renormalized. Matched the pypi:ms2rescore@4.0.1 runtime dependency closure — what installing the published package pulls in — 69 packages. Reachability is not analyzed.
AI Readiness
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.
43
Agent context & guidance
32At risk
How it's scored
| 0/45 | Agent instructions — no CLAUDE.md / AGENTS.md / editor rules |
| 0/15 | Machine-readable docs (llms.txt) |
| 32/40 | Legible commit history — 60 of 100 human commits state their intent (structured subject or explanatory body) |
Inputs used
| has_llms_txt | no |
| legible_history_share | 0.6 |
| agent_instruction_files | — |
| agent_instruction_max_bytes | — |
How it's scored
| 0/18 | One-command bootstrap |
| 22/22 | Automated tests |
| 11/11 | Lint / format config |
| 0/11 | Static type checking |
| 10/10 | Reproducible environment — Dockerfile, lockfile |
| 4/10 | Demonstrated agent practice — 2 of the last 100 commits agent-authored or agent-credited |
| 0/8 | Automated maintenance — no automated dependency updates observed |
| 1/10 | OpenSSF Scorecard: Pinned-Dependencies — dependency not pinned by hash detected -- score normalized to 1 |
Inputs used
| has_nix | no |
| has_tests | yes |
| lockfiles | uv.lock |
| has_dockerfile | yes |
| typed_language | no |
| bootstrap_files | — |
| has_devcontainer | no |
| has_linter_config | yes |
| typecheck_configs | — |
| agent_commit_share | 0.02 |
| toolchain_manifests | — |
| dependency_bot_commit_share | 0 |
Code legibility for models
54Moderate
How it's scored
| 0/45 | Type-checkable code — Python without a type-check config |
| 53.9/55 | Manageable file sizes — 1/49 source files over 60KB |
Inputs used
| primary_language | Python |
| largest_source_bytes | 116,571 |
| source_files_sampled | 49 |
| oversized_source_files | 1 |
Machine-readable interfaces
40At risk
How it's scored
| 0/40 | API schema (OpenAPI/GraphQL/proto) |
| 0/20 | MCP server |
| 40/40 | Runnable examples — examples, notebooks |
Inputs used
| example_dirs | examples, notebooks |
| has_mcp_signal | no |
| api_schema_files | — |
Key facts
66GitHub stars
7contributors
210commits, last 12 months
3days since last push
43releases
2bus factor
14open issues
PyPIpackage ecosystems
Data collection warnings
- Star history unavailable: GitHub GraphQL error: Resource not accessible by personal access token
More detail
Star and fork history 0 ★ / 22 ⇿
0Stars
22Forks
41Releases
When each star and fork was added, collected from GitHub and bucketed by day. Cumulative growth sits directly above the daily additions it is made of, so the two read against each other: steady organic accretion looks nothing like an abrupt, short-lived burst. Where that difference is measurable, it is reported as growth authenticity.
Major 2Minor 3Patch 13
Each point covers 7 days.
OpenSSF Scorecard 4.7 / 10
4.7aggregate
Independent, tool-agnostic security assessment from the open-source OpenSSF Scorecard. Each check rewards a security practice, not a specific vendor's tool. Checks Scorecard could not determine are marked n/a and excluded from the security score (never counted as zero).
| 10 | Binary-Artifacts | no binaries found in the repo |
| n/a | Branch-Protection | internal error: error during branchesHandler.setup: internal error: some github tokens can't read classic branch protection rules: https://github.com/ossf/scorecard-action/blob/main/docs/authentication/fine-grained-auth-token.md |
| 8 | CI-Tests | 4 out of 5 merged PRs checked by a CI test -- score normalized to 8 |
| 0 | CII-Best-Practices | no effort to earn an OpenSSF best practices badge detected |
| 1 | Code-Review | Found 1/7 approved changesets -- score normalized to 1 |
| 10 | Contributors | project has 6 contributing companies or organizations |
| 10 | Dangerous-Workflow | no dangerous workflow patterns detected |
| 0 | Dependency-Update-Tool | no update tool detected |
| 0 | Fuzzing | project is not fuzzed |
| 10 | License | license file detected |
| 10 | Maintained | 30 commit(s) and 5 issue activity found in the last 90 days -- score normalized to 10 |
| 10 | Packaging | packaging workflow detected |
| 1 | Pinned-Dependencies | dependency not pinned by hash detected -- score normalized to 1 |
| 0 | SAST | SAST tool is not run on all commits -- score normalized to 0 |
| 0 | Security-Policy | security policy file not detected |
| 0 | Signed-Releases | Project has not signed or included provenance with any releases. |
| 0 | Token-Permissions | detected GitHub workflow tokens with excessive permissions |
| 10 | Vulnerabilities | 0 existing vulnerabilities detected |
Direct dependencies 18
| Registry | Package | Version constraint | Manifest |
|---|---|---|---|
| PyPI | cascade-config | >=0.4.0 | pyproject.toml |
| PyPI | click | >=7 | pyproject.toml |
| PyPI | customtkinter | >=5,<6 | pyproject.toml |
| PyPI | deeplc | >=4.0.0 | pyproject.toml |
| PyPI | im2deep | >=2.0.1 | pyproject.toml |
| PyPI | jinja2 | >=3 | pyproject.toml |
| PyPI | lxml | >=4.5 | pyproject.toml |
| PyPI | ms2pip | >=4.2.0 | pyproject.toml |
| PyPI | ms2rescore_rs | >=0.5.0 | pyproject.toml |
| PyPI | numpy | >=1.25,<3.0 | pyproject.toml |
| PyPI | packaging | >=25.0 | pyproject.toml |
| PyPI | pandas | >=1 | pyproject.toml |
| PyPI | plotly | >=5 | pyproject.toml |
| PyPI | psm_utils | >=1.1 | pyproject.toml |
| PyPI | pyarrow | >=14 | pyproject.toml |
| PyPI | pyteomics | >=4.7.2 | pyproject.toml |
| PyPI | rich | >=12 | pyproject.toml |
| PyPI | ristretto-ms | >=0.3.0 | pyproject.toml |
All dependencies 210
Full resolved dependency set from the GitHub dependency graph: 19 direct and 191 indirect (transitive) packages. The transitive closure is complete when the repository commits a lockfile.
| Registry | Package | Version | Relation |
|---|---|---|---|
| PyPI | cascade-config | 0.4.0 | direct |
| PyPI | click | 8.4.2 | direct |
| PyPI | customtkinter | 5.2.2 | direct |
| PyPI | deeplc | 4.0.0 | direct |
| PyPI | im2deep | 2.0.2 | direct |
| PyPI | jinja2 | 3.1.6 | direct |
| PyPI | lxml | 6.1.1 | direct |
| PyPI | ms2pip | 4.2.0 | direct |
| PyPI | ms2rescore-rs | 0.5.0 | direct |
| PyPI | numpy | 2.4.6 | direct |
| PyPI | numpy | 2.5.1 | direct |
| PyPI | packaging | 26.2 | direct |
| PyPI | pandas | 2.3.3 | direct |
| PyPI | plotly | 6.9.0 | direct |
| PyPI | psm-utils | 1.5.5 | direct |
| PyPI | pyarrow | 25.0.0 | direct |
| PyPI | pyteomics | 4.7.5 | direct |
| PyPI | rich | 14.3.4 | direct |
| PyPI | ristretto-ms | 0.3.0 | direct |
| PyPI | aiohappyeyeballs | 2.7.1 | indirect |
| PyPI | aiohttp | 3.14.3 | indirect |
| PyPI | aiosignal | 1.4.0 | indirect |
| PyPI | alabaster | 1.0.0 | indirect |
| PyPI | altgraph | 0.17.5 | indirect |
| PyPI | annotated-types | 0.8.0 | indirect |
| PyPI | anyio | 4.14.2 | indirect |
| PyPI | appnope | 0.1.4 | indirect |
| PyPI | asttokens | 3.0.2 | indirect |
| PyPI | attrs | 26.1.0 | indirect |
| PyPI | babel | 2.18.0 | indirect |
| PyPI | beautifulsoup4 | 4.15.0 | indirect |
| PyPI | black | 26.5.1 | indirect |
| PyPI | bleach | 6.4.0 | indirect |
| PyPI | cbor2 | 6.1.3 | indirect |
| PyPI | certifi | 2026.7.22 | indirect |
| PyPI | cffi | 2.1.0 | indirect |
| PyPI | cfgv | 3.5.0 | indirect |
| PyPI | charset-normalizer | 3.4.9 | indirect |
| PyPI | colorama | 0.4.6 | indirect |
| PyPI | comm | 0.2.3 | indirect |
| PyPI | contourpy | 1.3.3 | indirect |
| PyPI | coverage | 7.15.2 | indirect |
| PyPI | cuda-bindings | 13.3.1 | indirect |
| PyPI | cuda-pathfinder | 1.6.0 | indirect |
| PyPI | cuda-toolkit | 13.0.3.0 | indirect |
| PyPI | cycler | 0.12.1 | indirect |
| PyPI | darkdetect | 0.8.0 | indirect |
| PyPI | debugpy | 1.8.21 | indirect |
| PyPI | decorator | 5.3.1 | indirect |
| PyPI | defusedxml | 0.7.1 | indirect |
| PyPI | distlib | 0.4.3 | indirect |
| PyPI | docutils | 0.22.4 | indirect |
| PyPI | executing | 2.2.1 | indirect |
| PyPI | fastjsonschema | 2.21.2 | indirect |
| PyPI | filelock | 3.32.0 | indirect |
| PyPI | fonttools | 4.63.0 | indirect |
| PyPI | frozenlist | 1.8.0 | indirect |
| PyPI | fsspec | 2026.6.0 | indirect |
| PyPI | greenlet | 3.5.4 | indirect |
| PyPI | h11 | 0.16.0 | indirect |
| PyPI | identify | 2.6.19 | indirect |
| PyPI | idna | 3.18 | indirect |
| PyPI | imagesize | 2.0.0 | indirect |
| PyPI | iniconfig | 2.3.0 | indirect |
| PyPI | ipykernel | 7.3.0 | indirect |
| PyPI | ipython | 9.15.0 | indirect |
| PyPI | ipython-pygments-lexers | 1.1.1 | indirect |
| PyPI | ipywidgets | 8.1.8 | indirect |
| PyPI | jedi | 0.20.0 | indirect |
| PyPI | joblib | 1.5.3 | indirect |
| PyPI | jsonschema | 4.26.0 | indirect |
| PyPI | jsonschema-specifications | 2025.9.1 | indirect |
| PyPI | jupyter-client | 8.9.1 | indirect |
| PyPI | jupyter-core | 5.9.1 | indirect |
| PyPI | jupyterlab-pygments | 0.3.0 | indirect |
| PyPI | jupyterlab-widgets | 3.0.16 | indirect |
| PyPI | kiwisolver | 1.5.0 | indirect |
| PyPI | lightning | 2.6.5 | indirect |
| PyPI | lightning-utilities | 0.15.3 | indirect |
| PyPI | macholib | 1.16.4 | indirect |
| PyPI | markdown-it-py | 4.2.0 | indirect |
| PyPI | markupsafe | 3.0.3 | indirect |
| PyPI | matplotlib | 3.11.1 | indirect |
| PyPI | matplotlib-inline | 0.2.2 | indirect |
| PyPI | mdit-py-plugins | 0.6.1 | indirect |
| PyPI | mdurl | 0.1.2 | indirect |
| PyPI | mistune | 3.3.4 | indirect |
| PyPI | ml-dtypes | 0.5.4 | indirect |
| PyPI | mpmath | 1.3.0 | indirect |
| PyPI | ms2rescore | 4.0.1 | indirect |
| PyPI | multidict | 6.7.1 | indirect |
| PyPI | mumble | 0.3.0 | indirect |
| PyPI | mypy-extensions | 1.1.0 | indirect |
| PyPI | myst-parser | 5.1.0 | indirect |
| PyPI | narwhals | 2.24.0 | indirect |
| PyPI | nbclient | 0.11.0 | indirect |
| PyPI | nbconvert | 7.17.1 | indirect |
| PyPI | nbformat | 5.10.4 | indirect |
| PyPI | nbsphinx | 0.9.8 | indirect |
| PyPI | nest-asyncio2 | 1.7.2 | indirect |
| PyPI | networkx | 3.6.1 | indirect |
| PyPI | nodeenv | 1.10.0 | indirect |
| PyPI | numpydoc | 1.10.0 | indirect |
| PyPI | nvidia-cublas | 13.1.1.3 | indirect |
| PyPI | nvidia-cuda-cupti | 13.0.85 | indirect |
| PyPI | nvidia-cuda-nvrtc | 13.0.88 | indirect |
| PyPI | nvidia-cuda-runtime | 13.0.96 | indirect |
| PyPI | nvidia-cudnn-cu13 | 9.20.0.48 | indirect |
| PyPI | nvidia-cufft | 12.0.0.61 | indirect |
| PyPI | nvidia-cufile | 1.15.1.6 | indirect |
| PyPI | nvidia-curand | 10.4.0.35 | indirect |
| PyPI | nvidia-cusolver | 12.0.4.66 | indirect |
| PyPI | nvidia-cusparse | 12.6.3.3 | indirect |
| PyPI | nvidia-cusparselt-cu13 | 0.8.1 | indirect |
| PyPI | nvidia-nccl-cu12 | 2.30.7 | indirect |
| PyPI | nvidia-nccl-cu13 | 2.29.7 | indirect |
| PyPI | nvidia-nvjitlink | 13.3.33 | indirect |
| PyPI | nvidia-nvshmem-cu13 | 3.4.5 | indirect |
| PyPI | nvidia-nvtx | 13.0.85 | indirect |
| PyPI | onnx | 1.22.0 | indirect |
| PyPI | onnx2torch | 1.5.15 | indirect |
| PyPI | pandocfilters | 1.5.1 | indirect |
| PyPI | parso | 0.8.7 | indirect |
| PyPI | pathspec | 1.1.1 | indirect |
| PyPI | pefile | 2024.8.26 | indirect |
| PyPI | pexpect | 4.9.0 | indirect |
| PyPI | pillow | 12.3.0 | indirect |
| PyPI | platformdirs | 4.11.0 | indirect |
| PyPI | pluggy | 1.6.0 | indirect |
| PyPI | pre-commit | 4.6.1 | indirect |
| PyPI | prompt-toolkit | 3.0.52 | indirect |
| PyPI | propcache | 0.5.2 | indirect |
| PyPI | protobuf | 7.35.1 | indirect |
| PyPI | psims | 1.3.6 | indirect |
| PyPI | psutil | 7.2.2 | indirect |
| PyPI | ptyprocess | 0.7.0 | indirect |
| PyPI | pure-eval | 0.2.3 | indirect |
| PyPI | pycparser | 3.0 | indirect |
| PyPI | pydantic | 2.13.4 | indirect |
| PyPI | pydantic-core | 2.46.4 | indirect |
| PyPI | pygments | 2.20.0 | indirect |
| PyPI | pyinstaller | 6.21.0 | indirect |
| PyPI | pyinstaller-hooks-contrib | 2026.6 | indirect |
| PyPI | pyopenms | 3.5.0 | indirect |
| PyPI | pyparsing | 3.3.2 | indirect |
| PyPI | pytest | 9.1.1 | indirect |
| PyPI | pytest-cov | 7.1.0 | indirect |
| PyPI | python-dateutil | 2.9.0.post0 | indirect |
| PyPI | python-discovery | 1.5.0 | indirect |
| PyPI | pytokens | 0.4.1 | indirect |
| PyPI | pytorch-lightning | 2.6.5 | indirect |
| PyPI | pytz | 2026.2 | indirect |
| PyPI | pywin32-ctypes | 0.2.3 | indirect |
| PyPI | pyyaml | 6.0.3 | indirect |
| PyPI | pyzmq | 27.1.0 | indirect |
| PyPI | referencing | 0.37.0 | indirect |
| PyPI | requests | 2.34.2 | indirect |
| PyPI | roman-numerals | 4.1.0 | indirect |
| PyPI | rpds-py | 2026.6.3 | indirect |
| PyPI | ruff | 0.16.0 | indirect |
| PyPI | rustyms | 0.10.0 | indirect |
| PyPI | scikit-learn | 1.9.0 | indirect |
| PyPI | scipy | 1.17.1 | indirect |
| PyPI | scipy | 1.18.0 | indirect |
| PyPI | semver | 3.0.4 | indirect |
| PyPI | setuptools | 83.0.0 | indirect |
| PyPI | six | 1.17.0 | indirect |
| PyPI | snowballstemmer | 3.1.1 | indirect |
| PyPI | soupsieve | 2.9.1 | indirect |
| PyPI | sphinx | 9.0.4 | indirect |
| PyPI | sphinx | 9.1.0 | indirect |
| PyPI | sphinx-argparse | 0.6.0 | indirect |
| PyPI | sphinx-autobuild | 2025.8.25 | indirect |
| PyPI | sphinx-inline-tabs | 2025.12.21.14 | indirect |
| PyPI | sphinx-rtd-theme | 3.1.0 | indirect |
| PyPI | sphinxcontrib-applehelp | 2.0.0 | indirect |
| PyPI | sphinxcontrib-devhelp | 2.0.0 | indirect |
| PyPI | sphinxcontrib-htmlhelp | 2.1.0 | indirect |
| PyPI | sphinxcontrib-jquery | 4.1 | indirect |
| PyPI | sphinxcontrib-jsmath | 1.0.1 | indirect |
| PyPI | sphinxcontrib-qthelp | 2.0.0 | indirect |
| PyPI | sphinxcontrib-serializinghtml | 2.0.0 | indirect |
| PyPI | sqlalchemy | 2.0.51 | indirect |
| PyPI | stack-data | 0.6.3 | indirect |
| PyPI | starlette | 1.3.1 | indirect |
| PyPI | sympy | 1.14.0 | indirect |
| PyPI | threadpoolctl | 3.6.0 | indirect |
| PyPI | tinycss2 | 1.5.1 | indirect |
| PyPI | tomli | 2.4.1 | indirect |
| PyPI | torch | 2.13.0 | indirect |
| PyPI | torchmetrics | 1.9.0 | indirect |
| PyPI | torchvision | 0.28.0 | indirect |
| PyPI | tornado | 6.5.7 | indirect |
| PyPI | tqdm | 4.69.1 | indirect |
| PyPI | traitlets | 5.15.1 | indirect |
| PyPI | triton | 3.7.1 | indirect |
| PyPI | typing-extensions | 4.16.0 | indirect |
| PyPI | typing-inspection | 0.4.2 | indirect |
| PyPI | tzdata | 2026.3 | indirect |
| PyPI | urllib3 | 2.7.0 | indirect |
| PyPI | uvicorn | 0.51.0 | indirect |
| PyPI | virtualenv | 21.7.0 | indirect |
| PyPI | watchfiles | 1.2.0 | indirect |
| PyPI | wcwidth | 0.8.2 | indirect |
| PyPI | webencodings | 0.5.1 | indirect |
| PyPI | websockets | 16.1.1 | indirect |
| PyPI | werkzeug | 3.1.8 | indirect |
| PyPI | widgetsnbextension | 4.0.15 | indirect |
| PyPI | xgboost | 2.1.4 | indirect |
| PyPI | yarl | 1.24.5 | indirect |
Dependency advisories 0
Installing pypi:ms2rescore@4.0.1 pulls in 69 packages, direct and transitive: 0 carry known advisories, of which 0 are direct dependencies.
No known advisories affect the assessed dependencies.
An advisory means the version recorded in the dependency graph falls inside an advisory’s affected range. Reachability is not analysed, and the graph includes development and test pins — a finding may concern tooling rather than shipped software.
Raw JSON report machine-readable
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"committed_at": "2026-07-17T15:08:00Z",
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{
"oid": "ee8a1c83f5db86e7f7e977546b6569c2c3175707",
"body": "Move package-level private rescoring functions to new module _ristretto_utils.py",
"is_bot": false,
"headline": "Merge pull request #269 from CompOmics/fix/rescoring-module",
"author_name": "ArthurDeclercq",
"author_login": "ArthurDeclercq",
"committed_at": "2026-07-17T14:51:02Z",
"body_truncated": false,
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{
"oid": "58f3c47bab9207a942233b5eadf5d550d75ecbe4",
"body": null,
"is_bot": false,
"headline": "fix: correct test import",
"author_name": "RalfG",
"author_login": "RalfG",
"committed_at": "2026-07-17T14:37:20Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "ac1e427e50717701b80bd3a662a3acf789a487f4",
"body": null,
"is_bot": false,
"headline": "docs: add rescoring module",
"author_name": "RalfG",
"author_login": "RalfG",
"committed_at": "2026-07-17T13:57:10Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "0f1f5231272cc9de4003dca08104a053af2814c9",
"body": "…s2rescore into fix/docs-after-ristretto",
"is_bot": false,
"headline": "Merge branch 'fix/rescoring-module' of https://github.com/CompOmics/m…",
"author_name": "RalfG",
"author_login": "RalfG",
"committed_at": "2026-07-17T13:54:18Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "e09fb2137af2ec341d131b98b317e2f5204cbc26",
"body": null,
"is_bot": false,
"headline": "fix: update tests",
"author_name": "RalfG",
"author_login": "RalfG",
"committed_at": "2026-07-17T13:52:38Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "adeb0ec94e5761aa92f9fb73f054eab2f4f61bc1",
"body": null,
"is_bot": false,
"headline": "Move back some functions only used in rescoring.py",
"author_name": "RalfG",
"author_login": "RalfG",
"committed_at": "2026-07-17T13:47:50Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "bcd475395ae8cc3e41c00a3336bb450cd5adbddd",
"body": "… into fix/rescoring-module",
"is_bot": false,
"headline": "Merge branch 'release/4.0' of https://github.com/CompOmics/ms2rescore…",
"author_name": "RalfG",
"author_login": "RalfG",
"committed_at": "2026-07-17T13:39:43Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "7a52505fbf5d000501632f8e54153751a30aaa83",
"body": "…to_utils.py",
"is_bot": false,
"headline": "Move package-level private rescoring functions to new module _ristret…",
"author_name": "RalfG",
"author_login": "RalfG",
"committed_at": "2026-07-17T13:39:33Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "45c45ae90c959631c34a17b0a5a73c997f10d302",
"body": null,
"is_bot": false,
"headline": "end to end test",
"author_name": "ArthurDeclercq",
"author_login": null,
"committed_at": "2026-07-17T10:57:21Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "24fadb75b22e88d41258b33d973fe6524f07bc61",
"body": null,
"is_bot": false,
"headline": "docs: update in-depth-python-api and userguide",
"author_name": "RalfG",
"author_login": "RalfG",
"committed_at": "2026-07-17T10:23:12Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "0ab30b69551e98415c44dc7ed42af0991ad3719e",
"body": "Replace mokapot rescoring engine with ristretto",
"is_bot": false,
"headline": "Merge pull request #268 from CompOmics/feat/add-ristretto",
"author_name": "ArthurDeclercq",
"author_login": "ArthurDeclercq",
"committed_at": "2026-07-17T09:03:16Z",
"body_truncated": false,
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},
{
"oid": "c255a3fcfd7fa6f8f0d4e05509e7dceba0ac7fdc",
"body": null,
"is_bot": false,
"headline": "fix import error for python 3.12",
"author_name": "ArthurDeclercq",
"author_login": null,
"committed_at": "2026-07-17T08:40:04Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "59de3f31e2cda5fc086e12d11048967cb955805c",
"body": "Review findings from the cumulative-diff review, addressed:\n\n- rescoring: null never actually disabled rescoring (CascadeConfig's\n none_overrides_value=False silently ignores it), and the \"skip\n rescoring\" path that was reachable only in principle would have\n written no output at all. Rather than\n[…]\nreference).\n\nAlso reformats CHANGELOG.md's \"Breaking changes\" section (non-standard\nKeep a Changelog category) into the canonical Added/Changed/Removed\nsections, with breaking items tagged [BREAKING].",
"is_bot": false,
"headline": "Remove ability to skip rescoring; run infer_score_direction per-run",
"author_name": "RalfG",
"author_login": "RalfG",
"committed_at": "2026-07-16T16:18:24Z",
"body_truncated": true,
"is_coding_agent": false
},
{
"oid": "0f24e598a48cca9c51664b8af7140fcdd1e5711f",
"body": "Cumulative summary of the mokapot -> ristretto rescoring engine\nmigration (report_fdr, model choice, auto score-direction inference,\noutput-file renames, GUI log.html fix, and the resulting config/API\nremovals), merged into the existing Unreleased section.",
"is_bot": false,
"headline": "Add ristretto migration entries to CHANGELOG",
"author_name": "RalfG",
"author_login": "RalfG",
"committed_at": "2026-07-16T15:50:30Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "fba6411e330732d1456e1d74b3f18ec60e7bd5a1",
"body": "…of-date",
"is_bot": false,
"headline": "docs: minor cleanup; temporarily remove overview figure as it is out-…",
"author_name": "RalfG",
"author_login": "RalfG",
"committed_at": "2026-07-16T15:34:56Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "95a9ee6928ed58e02447e5976d956eee0a0ea214",
"body": "The GUI's logging setup only ever attached a plain FileHandler for\n<prefix>.log.txt -- unlike the CLI, it never used a recording Rich console\nor called save_html(), so <prefix>.log.html (documented as always written)\nwas silently never created for GUI-launched runs. Added the same\nConsole(record=Tru\n[…]\naises.\n\nAlso add an INFO-level log line when rescoring actually starts, since the\nper-fold/rollup/competition detail ristretto itself logs is moving to\nDEBUG level (fixed at the source, in ristretto).",
"is_bot": false,
"headline": "Fix missing HTML log file in GUI runs; log when rescoring starts",
"author_name": "RalfG",
"author_login": "RalfG",
"committed_at": "2026-07-16T15:07:55Z",
"body_truncated": true,
"is_coding_agent": false
},
{
"oid": "617cec085aabe9688be7903546a398aa21330356",
"body": "…nal API surface\n\n- Fix rescore() always returning empty feature_weights/n_iterations: it\n rebuilds the final result via ristretto.evaluate() (no training, so those\n fields come back empty), discarding the real values from the earlier\n ristretto.rescore() call. Now carried over explicitly, includ\n[…]\ne that explicit rather than presenting it as public API. Also\n privatized build_features_dataframe and fix_constant_pep, which were\n only ever called internally within the rescoring workflow itself.",
"is_bot": false,
"headline": "Fix empty feature weights, simplify output naming, and minimize inter…",
"author_name": "RalfG",
"author_login": "RalfG",
"committed_at": "2026-07-16T14:55:43Z",
"body_truncated": true,
"is_coding_agent": false
},
{
"oid": "dc62a277fad5dce4ed1b70d317dd237a5f3bf71e",
"body": "A user-provided rescoring dict (e.g. \"rescoring\": {} or {\"model\": \"lda\"})\nis passed through as-is by the config cascade -- same as feature_generators\nand psm_generator, where an override is taken at face value rather than\nmerged with defaults (CascadeConfig's max_recursion_depth stops it from\nreachi\n[…]\nig[\"rescoring\"] to ristretto.rescore()\nvia **kwargs instead of naming train_fdr/model explicitly, so ristretto's\nown defaults (train_fdr=0.01, model=\"svm\") apply to whatever the user's\nconfig omitted.",
"is_bot": false,
"headline": "Fix KeyError on partial/empty rescoring config",
"author_name": "RalfG",
"author_login": "RalfG",
"committed_at": "2026-07-16T13:10:51Z",
"body_truncated": true,
"is_coding_agent": false
},
{
"oid": "49104a38ba6de291222a2d0afb7b84d97f3c69a5",
"body": "Clarifies alongside the existing null (skip rescoring) note that\nrescoring: {} is equivalent to omitting the key, since cascade_config\ndeep-merges schema defaults into a partial dict. Also fixes a stale\nmention that rescoring only exposed train_fdr (model was added earlier).",
"is_bot": false,
"headline": "Document that an empty rescoring object uses the schema defaults",
"author_name": "RalfG",
"author_login": "RalfG",
"committed_at": "2026-07-16T12:51:32Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "aa7a2c013d105819b3e32cb160a4ee28f97ea26e",
"body": "…e-ristretto-fixes",
"is_bot": false,
"headline": "Merge remote-tracking branch 'origin/feat/add-ristretto' into worktre…",
"author_name": "RalfG",
"author_login": "RalfG",
"committed_at": "2026-07-16T12:50:04Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "2610434c03c257e1a540b44e89ed151f902f327d",
"body": "Adds a top-level report_fdr setting (default 0.01) used for console-logged\nidentification counts, HTML report stats/charts, and FlashLFQ output\nfiltering. This is independent of rescoring.train_fdr, which only controls\nristretto's semi-supervised training. Standalone report regeneration\n(ms2rescore-report) gains a --fdr option to override the report_fdr stored\nin the original run's full-config.json, without rerunning rescoring.",
"is_bot": false,
"headline": "Add report_fdr config option to replace hardcoded 1% FDR threshold",
"author_name": "RalfG",
"author_login": "RalfG",
"committed_at": "2026-07-16T12:49:32Z",
"body_truncated": false,
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},
{
"oid": "8d8aec14de9bd1e2498584cf2f6425f3adc136ac",
"body": "… into feat/add-ristretto",
"is_bot": false,
"headline": "Merge branch 'release/4.0' of https://github.com/CompOmics/ms2rescore…",
"author_name": "RalfG",
"author_login": "RalfG",
"committed_at": "2026-07-16T12:35:36Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "7d8ed98782fb24870f9dd2259246c95dc9c28a3b",
"body": "Add rescoring.model config option (svm, the default iterative\nPercolator-style SVM; or lda, a single-pass Fisher LDA that's faster\nbut less powerful on hard-to-separate datasets), threaded through to\nristretto.rescore()'s model kwarg. Adds a GUI dropdown alongside the\nexisting training-FDR field.\n\nR\n[…]\nthe jsonschema2md CLI's\npinned Python interpreter is missing on this machine (pre-existing\nenvironment issue, unrelated to this change) -- the generated\nsections were mirrored exactly by hand instead.",
"is_bot": false,
"headline": "Expose ristretto's model choice; always write rescoring tables",
"author_name": "RalfG",
"author_login": "RalfG",
"committed_at": "2026-07-16T12:28:34Z",
"body_truncated": true,
"is_coding_agent": false
},
{
"oid": "519a3bce4dadd38f3bbae60bbce0325c38d94e76",
"body": "ristretto-ms>=0.3.0 is now on PyPI, so the local ../ironbrew editable\npath override is no longer needed. Removes the now-empty\n[tool.uv.sources] override and its TODO, and regenerates uv.lock to\nresolve ristretto-ms from the registry.",
"is_bot": false,
"headline": "Depend on published ristretto-ms instead of the local editable path",
"author_name": "RalfG",
"author_login": "RalfG",
"committed_at": "2026-07-16T12:13:13Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "cfe700f86ce527f199509d02908d2949192a6e55",
"body": "Rescoring result tables are now plain TSV (not Parquet) at every\nidentification level, and only the post-rescoring (\"after\") result is\nwritten -- \"before\" is reconstructed on demand from the main PSM\nlist's provenance data, so it's never persisted. Also documents the\nmax_psm_rank_output > 1 caveat (multi-rank rows, not statistically\nrigorous FDR) and drops the now-obsolete after_report paragraph.",
"is_bot": false,
"headline": "Update output-files.rst for the TSV-only, after-only rescoring tables",
"author_name": "RalfG",
"author_login": "RalfG",
"committed_at": "2026-07-16T11:28:32Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "b153875ecc24fcf27c8c128467c138ad4cf65e6c",
"body": "max_psm_rank_output is a special feature for surfacing ambiguous\nresults (e.g. mumble's multiple candidate peptidoforms per spectrum),\nnot for statistically rigorous FDR control when > 1 -- that trade-off\nis now explicit and applied consistently everywhere, instead of\ncomputing a separate always-ran\n[…]\nindexing returns the same underlying PSM\nobject references, not copies, so evaluate_before_from_provenance now\ntakes a real deep copy before mutating scores, to avoid corrupting\nthe caller's psm_list.",
"is_bot": false,
"headline": "Rework max_psm_rank_output and report reconstruction",
"author_name": "RalfG",
"author_login": "RalfG",
"committed_at": "2026-07-16T11:27:32Z",
"body_truncated": true,
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},
{
"oid": "6e425d19010c4fe6c40c969728a239c44523df98",
"body": "build_features_dataframe now includes a \"run\" column, and every\nristretto.rescore()/evaluate() call passes run_col=\"run\" (requires\nristretto-ms>=0.3.0). Competition and CV splitting now group by\n(run, spectrum_id) at the source, instead of spectrum_id alone --\npreviously, two different physical spec\n[…]\nntirely: \"run\" now\ncomes back natively on every RescoreResult.psms from ristretto itself,\nso there's no more index-alignment hack needed on the ms2rescore side.\n\nBumps the ristretto-ms pin to >=0.3.0.",
"is_bot": false,
"headline": "Fix multi-run spectrum_id collisions via ristretto's new run_col",
"author_name": "RalfG",
"author_login": "RalfG",
"committed_at": "2026-07-16T09:49:38Z",
"body_truncated": true,
"is_coding_agent": false
},
{
"oid": "5a7706a3a105beba66ece6bb14458bddb7d61145",
"body": "write_rescoring_tables() writes an additional set of *_after_report\nParquet tables when max_psm_rank_output > 1 (the rank-1 report view,\ndistinct from the multi-rank *_after files), which wasn't mentioned\nanywhere in the output-files reference.",
"is_bot": false,
"headline": "Document after_report Parquet output files",
"author_name": "RalfG",
"author_login": "RalfG",
"committed_at": "2026-07-16T09:11:06Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "723a9a09d380ce588140dc97a62a400bd190202a",
"body": "…n report\n\ncompute_id_stats/identification_overlap consumed before_result unmasked,\nunlike core.py's console-log count, which excludes mumble-generated\nalternate candidates via psm.metadata['original_psm']. Attach that\nmask onto before_result.psms itself (evaluate_before), the same way\nrun already i\n[…]\nfor that level.\n\nAdds direct unit coverage for both: _n_identified's masking behavior,\nand identification_overlap's run-based disambiguation (which the old\nbare-spectrum_id grouping would undercount).",
"is_bot": false,
"headline": "Apply mumble original_psm mask and run+spectrum_id key consistently i…",
"author_name": "RalfG",
"author_login": "RalfG",
"committed_at": "2026-07-16T09:10:35Z",
"body_truncated": true,
"is_coding_agent": false
},
{
"oid": "96b8dc0ac4362a22dbcbb746b022ac17ce9245ee",
"body": "fix_constant_pep previously only filtered result.psms, leaving\npeptidoform/peptide/protein rollups computed on the decoy-contaminated\npopulation -- _write_group_metadata would then look up stale\nscores/qvalues/PEPs for surviving PSMs. Now recomputes q-values, PEP,\nand rollups from scratch via ristre\n[…]\nt while the\nreal output looked fine. Split the fix into a result-only core\n(_fix_constant_pep_result) plus the existing psm_list-aware wrapper,\nand apply the core check to report_result independently.",
"is_bot": false,
"headline": "Refresh rollups in fix_constant_pep and apply it to report_result too",
"author_name": "RalfG",
"author_login": "RalfG",
"committed_at": "2026-07-16T09:05:14Z",
"body_truncated": true,
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},
{
"oid": "98c5d51e0dc150b5eddb4afd283f1d3f94a189d7",
"body": null,
"is_bot": false,
"headline": "commit new lock file",
"author_name": "ArthurDeclercq",
"author_login": null,
"committed_at": "2026-07-16T08:13:47Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "4726d4d10685d9d9181b5b9849d85e48ae357a0b",
"body": "fix_constant_pep now takes/returns a (PSMList, RescoreResult) pair;\nrescore() returns (psm_list, after_result, after_report_result).\nRescoreResult.psms now always carries a run column. Adds coverage for\nthe new report_result (rank-1 view, distinct from a multi-rank final\nresult) and the after_report Parquet table written when they differ.\nAlso asserts rescoring_tables_unavailable is set when the ristretto\nParquet tables are missing.",
"is_bot": false,
"headline": "Update tests for rescore()'s 3-tuple return and RescoreResult schema",
"author_name": "RalfG",
"author_login": "RalfG",
"committed_at": "2026-07-15T22:14:47Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "9abf1c917111df815ddc0c3c881fb1acf1663019",
"body": "The \"Rescoring result tables\" table had inconsistent column-divider\npositions across its border/header/content rows (four different\nwidths), which docutils/Sphinx rejects as a malformed table. Rebuilt\nit with consistent column widths (verified programmatically: every\nrow shares identical +/| column positions).",
"is_bot": false,
"headline": "Fix malformed RST grid table in output-files.rst",
"author_name": "RalfG",
"author_login": "RalfG",
"committed_at": "2026-07-15T22:11:37Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "f6af833dac16dc1bec5b28bc6c25b4b5aec45672",
"body": "…p levels\n\ncreate_psm_dataframe: filter psm_list to rank==1 (the report is always\na single-best-PSM-per-spectrum view, regardless of max_psm_rank_output)\nand merge before/after by (run, spectrum_id) instead of (spectrum_id,\npeptidoform). The old peptidoform-keyed merge produced NaN\nscore_before/qval\n[…]\n after_report table (rank-1 view) over after (which may be\nmulti-rank) when both exist. The overview tab shows an explicit notice\nwhen tables are unavailable instead of silently rendering empty stats.",
"is_bot": false,
"headline": "Rework report before/after comparison to (run, spectrum_id) + 4 rollu…",
"author_name": "RalfG",
"author_login": "RalfG",
"committed_at": "2026-07-15T22:09:00Z",
"body_truncated": true,
"is_coding_agent": false
},
{
"oid": "27c4c4c98371b91736ed060ffb7cba8857223cf9",
"body": "ristretto's RescoreResult schema has no room for a passthrough run\ncolumn, so attach it after the fact (index-aligned against the\noriginal PSMList) on before_result, final_result, and report_result.\nEnables merging before/after by (run, spectrum_id) in the report,\nguarding against spectrum_id collis\n[…]\nset when it differs from after (i.e. max_psm_rank_output > 1), so\nstandalone report regeneration (ms2rescore-report) can use the same\nalways-rank-1 view as a live run instead of the multi-rank result.",
"is_bot": false,
"headline": "Attach run to RescoreResult.psms; persist a separate after_report table",
"author_name": "RalfG",
"author_login": "RalfG",
"committed_at": "2026-07-15T22:03:35Z",
"body_truncated": true,
"is_coding_agent": false
},
{
"oid": "b6093887be54e585d636f6ca6f53b28b68e77171",
"body": "psm.get_usi() bakes the peptidoform into the string. Once\nrename_to_usi overwrote psm_list's spectrum_id (before rescore()),\nristretto's spectrum-grouped competition -- keyed on spectrum_id --\nsaw every candidate peptidoform for a spectrum as its own singleton\ngroup, breaking competition whenever ma\n[…]\nd from psm_list).\n\nRestore the mumble-candidate exclusion (via the original_psm metadata\nflag) when counting identified PSMs before rescoring, matching what\nthe deleted _log_id_psms_before used to do.",
"is_bot": false,
"headline": "Fix USI/spectrum-grouping bug and always report at rank-1",
"author_name": "RalfG",
"author_login": "RalfG",
"committed_at": "2026-07-15T21:44:37Z",
"body_truncated": true,
"is_coding_agent": false
},
{
"oid": "d46c24d4acc6dd65d03edde28a5241cfbe51c503",
"body": null,
"is_bot": false,
"headline": "removed local paths",
"author_name": "ArthurDeclercq",
"author_login": null,
"committed_at": "2026-07-15T16:01:14Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "fe4573eedf3ce3de6568933c014d1431135915e1",
"body": "_write_group_metadata crashed with KeyError for decoy PSMs whenever\nprotein-level FDR used picked-protein competition (id_decoy_pattern\nset): ristretto's picked_rollup strips the decoy pattern from group\nkeys, so strip it the same way before the lookup. Log a warning when\nplain rollup runs instead (\n[…]\nw, and correctly\ncompetes multiple candidate PSMs per spectrum (relevant since this\nruns before rank filtering). Warn when the inferred direction is\nlower-is-better, since that's the less common case.",
"is_bot": false,
"headline": "Fix protein rollup KeyError and improve score-direction inference",
"author_name": "RalfG",
"author_login": "RalfG",
"committed_at": "2026-07-15T16:00:03Z",
"body_truncated": true,
"is_coding_agent": false
},
{
"oid": "84cf197f5cfa4899e280ee8dc10828eb35692e17",
"body": null,
"is_bot": false,
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{
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{
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{
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},
{
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],
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{
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{
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]
},
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{
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{
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]
}
],
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{
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{
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{
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"points": 0,
"status": "missed",
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{
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"points": 10,
"status": "met",
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},
{
"key": "dependency_update_tool",
"name": "Dependency-Update-Tool",
"detail": "no update tool detected",
"points": 0,
"status": "missed",
"details": [],
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},
{
"key": "fuzzing",
"name": "Fuzzing",
"detail": "project is not fuzzed",
"points": 0,
"status": "missed",
"details": [],
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},
{
"key": "license",
"name": "License",
"detail": "license file detected",
"points": 2.5,
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"details": [],
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},
{
"key": "maintained",
"name": "Maintained",
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"points": 7.5,
"status": "met",
"details": [],
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{
"key": "packaging",
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"points": 5,
"status": "met",
"details": [],
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},
{
"key": "pinned_dependencies",
"name": "Pinned-Dependencies",
"detail": "dependency not pinned by hash detected -- score normalized to 1",
"points": 0.5,
"status": "partial",
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},
{
"key": "sast",
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"points": 0,
"status": "missed",
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},
{
"key": "security_policy",
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"points": 0,
"status": "missed",
"details": [],
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},
{
"key": "signed_releases",
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"points": 0,
"status": "missed",
"details": [],
"max_points": 7.5
},
{
"key": "token_permissions",
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"points": 0,
"status": "missed",
"details": [],
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},
{
"key": "vulnerabilities",
"name": "Vulnerabilities",
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]
},
{
"key": "dependency_advisories",
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"notes": [
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{
"code": "weights_renormalized",
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"code": "advisories_scope_published",
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"components": [
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{
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{
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},
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"inputs": {
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},
{
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"notes": [
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],
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],
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"components": [
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{
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{
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{
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"inputs": {
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"components": [
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"points": 0,
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{
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{
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"status": "met",
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],
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"warnings": [
"Star history unavailable: GitHub GraphQL error: Resource not accessible by personal access token"
],
"report_type": "repository",
"generated_at": "2026-07-27T22:27:21.075230Z",
"schema_version": "0.27.0",
"badge_url": "https://raw.githubusercontent.com/inspect-software/badges/main/v1/c/CompOmics/ms2rescore.svg",
"full_name": "CompOmics/ms2rescore",
"license_state": "standard",
"license_spdx": "Apache-2.0"
}Scores are signals, not warranties. They reflect publicly visible practices on GitHub — not a code audit, and not a security guarantee.
Missing data is excluded and weights renormalized, never scored as zero. Methodology is versioned and open: metrics v1.13.0, schema v0.27.0 — full methodology · metrics wiki.
How one result sits in the wider record: aggregate statistics — PyPI.