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OpenMS/agentomics

A repository of agentic created tools in proteomics using pyopenms

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  • Python
  • ★ 0
  • commit 253b99aef22e
  • scored 2026-11-14
  • scoring prov-5+qual-2+sec-2

AI provenance

100%

explicit

Confidence
82%
Coverage
100%

Estimated share of AI-generated code. Explicit attribution is a lower bound.

Code quality

68/100

adequate

Confidence
90%
Coverage
100%

Complexity, duplication, lint density, tests, CI, docs and review process.

Security

78/100

adequate

Confidence
85%
Coverage
100%

Secrets, static analysis, vulnerable dependencies, CI and supply-chain posture.

Dispute or request a re-score Full report JSON RepoTrust ai badgeRepoTrust quality badgeRepoTrust security badge

AI provenance

100% explicit

Explicit AI attribution on 100% of first-party code added; an estimated 100% including velocity signals.

How the score is built

  • Explicitly attributed share100%
  • Unattributed share in AI-pace bursts0%
  • Estimated AI-generated share100%
  • AI tool configuration files4
  • Work sessions at AI pace1
  • Releases at AI pacenot measured
  • Coding-style index (1.0+ means possible)0.07

Attributed AI tools

ToolCommitsLines addedFirst seenLast seen
Claude Code4253,4082026-03-242026-03-26
GitHub Copilot coding agent41,4102026-03-252026-03-25

Lines added per month all AI-attributed share

  1. 2026-0355,025 · 100% AI

Findings in AI-attributed lines vs the rest

From git blame: 28,092 lines trace to AI-attributed commits, 0 to others. Too few lines in one group for a fair comparison. Reported, not scored.

Findings per 1,000 linesAI-attributedOtherRatio
Code quality7.12——
Security0.50——

Evidence by analyzer

Explicit AI attributionok27 items
attributed_commit_share
93.9%
attributed_commits
46
attributed_loc
54,818
attributed_loc_share
99.6%
commits
49
effective_loc
55,025
tools_detected
2
AI tool configurationok4 items
artifacts
4
earliest_adoption
2026-03-24
tools_configured
2
workflow_agents
0
Commit velocityok1 item
excluded_import_loc
37,116
flagged_loc
13,075
flagged_loc_share
73.0%
flagged_units
1
max_loc_per_hour
2,875.73
measured_loc
17,909
median_loc_per_hour
351
pr_timed_units
0
pre_ai_era_burst_loc
0
pre_ai_era_bursts
0
pre_ai_era_measured_loc
0
work_units
6
Release velocityskipped
Coding styleok2 items
count:assistant_voice
0
count:emoji_in_code
0
count:narrated_steps
2
count:placeholder
0
files:assistant_voice
0
files:emoji_in_code
0
files:narrated_steps
1
files:placeholder
0
index
0.07
lines_scanned
28,092
per_kloc:assistant_voice
0
per_kloc:emoji_in_code
0
per_kloc:narrated_steps
0.07
per_kloc:placeholder
0
Findings in AI-written linesok
ai_lines
28,092
blame_failures
0
files_blamed
170
other_lines
0
quality:ai_findings
200
quality:ai_per_kloc
7.12
quality:other_findings
0
security:ai_findings
14
security:ai_per_kloc
0.50
security:other_findings
0

Code quality

68 adequate

Code quality is adequate: test-to-source ratio 0.64, CI runs tests; 3% of function code in complex or long functions; 11% duplicated lines. Weakest area: lint.

How the score is built

  • Complexity92
  • Duplication52
  • Lint and smells12
  • Tests and CI100
  • Documentation65
  • Type safety40
  • Review processnot measured

Evidence by analyzer

Complexity (lizard)ok7 items
complex_functions
7
function_nloc
11,541
functions
750
long_functions
0
many_param_functions
8
mean_ccn
3.79
p90_ccn
8
risky_nloc_share
2.7%
Duplication (jscpd)ok10 items
compared_lines
20,905
duplicated_lines
2,270
duplicated_share
10.9%
files
170
Lintok
category:best-practice
225
category:correctness
15
findings
240
scanned_lines
28,092
weighted_findings
240
Tests and CIok3 items
  • CI config: .github/workflows/validate.yml .github/workflows/validate.yml
  • CI runs tests (pytest)
  • CI runs linters (ruff)
check:ci_present
yes
check:ci_runs_lint
yes
check:ci_runs_tests
yes
check:has_tests
yes
check:test_ratio
yes
check:tests_cochange
yes
ci_files
1
cochange_commits
31
cochange_share
90.3%
source_lines
28,092
test_lines
17,945
test_ratio
0.64
Documentationok2 items
  • README.md README.md
  • LICENSE LICENSE
check:changelog
no
check:contributing
no
check:license
yes
check:readme
yes
readme_lines
256
Type safetyok
check:low_escape_density
yes
check:strict_config
no
escapes
0
escapes_per_kloc
0

Security

78 adequate

Security posture is adequate: 4 high-severity workflow issues. Weakest area: posture.

How the score is built

  • Secrets100
  • Static analysis (SAST)99
  • Vulnerable dependencies100
  • CI workflows38
  • Security posture0
  • OpenSSF Scorecardnot measured

Evidence by analyzer

OpenSSF Scorecardskipped

no published OpenSSF Scorecard result for this repo

Package registriesok
checked
4
declared
4
lookup_errors
0
missing
0
recent
0
Secrets (gitleaks)ok
secrets_current
0
secrets_history
0
secrets_low_confidence
0
secrets_nonprod
0
Static analysis (opengrep)ok
findings
14
findings_high
0
findings_low
14
findings_medium
0
parse_errors
0
scanned_lines
28,092
weighted_findings
0.88
Dependencies (osv-scanner)ok
penalty
0
vulnerabilities
0
vulnerable_packages
0
vulns_critical
0
vulns_high
0
vulns_low
0
vulns_medium
0
vulns_unknown
0
CI workflows (zizmor)ok
findings
12
findings_high
4
findings_low
3
findings_medium
5
penalty
57.60
workflows
1
Security postureok
check:dependency_updates
no
check:lockfiles
yes
check:security_policy
no
check:signed_commits
no
signed_commit_share
6.1%
unpinned_manifests
0
Release downloadsok
binary_assets
0
signals
0
suspicious
0

Findings

4 high205 medium14 low3 info

SeverityRuleLocationMessageTool
high zizmor/unpinned-uses .github/workflows/validate.yml:15 unpinned action reference [confidence high] CI workflows (zizmor)
high zizmor/template-injection .github/workflows/validate.yml:25 code injection via template expansion [confidence high] CI workflows (zizmor)
high zizmor/unpinned-uses .github/workflows/validate.yml:44 unpinned action reference [confidence high] CI workflows (zizmor)
high zizmor/unpinned-uses .github/workflows/validate.yml:46 unpinned action reference [confidence high] CI workflows (zizmor)
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/compound_annotation/kendrick_mass_defect_analyzer/kendrick_mass_defect_analyzer.py:139 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/compound_annotation/kendrick_mass_defect_analyzer/kendrick_mass_defect_analyzer.py:154 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/compound_annotation/metabolite_class_predictor/metabolite_class_predictor.py:251 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/compound_annotation/metabolite_class_predictor/metabolite_class_predictor.py:259 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/compound_annotation/metabolite_class_predictor/metabolite_class_predictor.py:263 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/compound_annotation/suspect_screener/suspect_screener.py:108 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/compound_annotation/suspect_screener/suspect_screener.py:186 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/compound_annotation/suspect_screener/suspect_screener.py:190 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/compound_annotation/suspect_screener/suspect_screener.py:78 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/compound_annotation/van_krevelen_data_generator/van_krevelen_data_generator.py:118 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/compound_annotation/van_krevelen_data_generator/van_krevelen_data_generator.py:129 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/drug_metabolism/drug_metabolite_screener/drug_metabolite_screener.py:170 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/drug_metabolism/mass_difference_network_builder/mass_difference_network_builder.py:136 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/drug_metabolism/mass_difference_network_builder/mass_difference_network_builder.py:144 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/drug_metabolism/mass_difference_network_builder/mass_difference_network_builder.py:63 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/export/gnps_fbmn_exporter/gnps_fbmn_exporter.py:146 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/export/gnps_fbmn_exporter/gnps_fbmn_exporter.py:179 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/export/gnps_fbmn_exporter/gnps_fbmn_exporter.py:195 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/export/gnps_fbmn_exporter/gnps_fbmn_exporter.py:59 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/export/kovats_ri_calculator/kovats_ri_calculator.py:166 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/export/kovats_ri_calculator/kovats_ri_calculator.py:170 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/export/kovats_ri_calculator/kovats_ri_calculator.py:42 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/export/sirius_exporter/sirius_exporter.py:36 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/export/sirius_exporter/sirius_exporter.py:85 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/feature_processing/adduct_group_analyzer/adduct_group_analyzer.py:125 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/feature_processing/adduct_group_analyzer/adduct_group_analyzer.py:134 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/feature_processing/blank_subtraction_tool/blank_subtraction_tool.py:112 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/feature_processing/blank_subtraction_tool/blank_subtraction_tool.py:93 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/feature_processing/blank_subtraction_tool/blank_subtraction_tool.py:99 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/feature_processing/duplicate_feature_detector/duplicate_feature_detector.py:134 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/feature_processing/duplicate_feature_detector/duplicate_feature_detector.py:142 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/feature_processing/isf_detector/isf_detector.py:189 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/feature_processing/isf_detector/isf_detector.py:199 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/feature_processing/mass_defect_filter/mass_defect_filter.py:141 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/feature_processing/mass_defect_filter/mass_defect_filter.py:159 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/feature_processing/mass_defect_filter/mass_defect_filter.py:164 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/feature_processing/targeted_feature_extractor/targeted_feature_extractor.py:153 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/feature_processing/targeted_feature_extractor/targeted_feature_extractor.py:160 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/formula_tools/adduct_calculator/adduct_calculator.py:119 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/formula_tools/formula_mass_calculator/formula_mass_calculator.py:117 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/formula_tools/formula_mass_calculator/formula_mass_calculator.py:126 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/formula_tools/formula_mass_calculator/formula_mass_calculator.py:133 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/formula_tools/formula_validator_golden_rules/formula_validator_golden_rules.py:244 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/formula_tools/formula_validator_golden_rules/formula_validator_golden_rules.py:252 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/formula_tools/mass_decomposition_tool/mass_decomposition_tool.py:183 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/formula_tools/mass_decomposition_tool/mass_decomposition_tool.py:188 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/formula_tools/metabolite_formula_annotator/metabolite_formula_annotator.py:180 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/formula_tools/metabolite_formula_annotator/metabolite_formula_annotator.py:187 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/formula_tools/molecular_formula_finder/molecular_formula_finder.py:260 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/formula_tools/molecular_formula_finder/molecular_formula_finder.py:265 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/formula_tools/rdbe_calculator/rdbe_calculator.py:103 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/formula_tools/rdbe_calculator/rdbe_calculator.py:95 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/identification/accurate_mass_searcher/accurate_mass_searcher.py:129 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/identification/accurate_mass_searcher/accurate_mass_searcher.py:133 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/identification/accurate_mass_searcher/accurate_mass_searcher.py:69 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/identification/accurate_mass_searcher/accurate_mass_searcher.py:92 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/identification/metabolite_spectral_matcher/metabolite_spectral_matcher.py:73 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/isotope_labeling/isotope_label_detector/isotope_label_detector.py:157 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/isotope_labeling/isotope_label_detector/isotope_label_detector.py:168 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/isotope_labeling/mid_natural_abundance_corrector/mid_natural_abundance_corrector.py:156 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/isotope_labeling/mid_natural_abundance_corrector/mid_natural_abundance_corrector.py:169 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/lipidomics/lipid_ecn_rt_predictor/lipid_ecn_rt_predictor.py:164 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/lipidomics/lipid_ecn_rt_predictor/lipid_ecn_rt_predictor.py:168 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/lipidomics/lipid_ecn_rt_predictor/lipid_ecn_rt_predictor.py:62 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/lipidomics/lipid_species_resolver/lipid_species_resolver.py:224 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/lipidomics/lipid_species_resolver/lipid_species_resolver.py:232 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/lipidomics/lipid_species_resolver/lipid_species_resolver.py:236 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/spectral_analysis/isotope_pattern_analyzer/isotope_pattern_analyzer.py:400 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/spectral_analysis/isotope_pattern_analyzer/isotope_pattern_analyzer.py:409 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/spectral_analysis/massql_query_tool/massql_query_tool.py:146 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/spectral_analysis/neutral_loss_scanner/neutral_loss_scanner.py:143 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/spectral_analysis/spectral_entropy_scorer/spectral_entropy_scorer.py:213 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/metabolomics/spectral_analysis/spectral_entropy_scorer/spectral_entropy_scorer.py:254 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/dia_analysis/chromatogram_extractor/chromatogram_extractor.py:50 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/dia_analysis/dia_scorer/dia_scorer.py:187 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/dia_analysis/dia_scorer/dia_scorer.py:42 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/dia_analysis/mrm_decoy_generator/mrm_decoy_generator.py:128 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/dia_analysis/mrm_decoy_generator/mrm_decoy_generator.py:183 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/dia_analysis/mrm_feature_finder/mrm_feature_finder.py:48 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/dia_analysis/mrm_rt_normalizer/mrm_rt_normalizer.py:100 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/dia_analysis/mrm_rt_normalizer/mrm_rt_normalizer.py:133 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.correctness.common-mistakes.string-concat-in-list tools/proteomics/fasta_utils/contaminant_database_merger/contaminant_database_merger.py:25 Detected strings that are implicitly concatenated inside a list. Python will implicitly concatenate strings when not explicitly delimited. Was this supposed to be individual elements of the list? Lint
medium opengrep/python.lang.correctness.common-mistakes.string-concat-in-list tools/proteomics/fasta_utils/contaminant_database_merger/contaminant_database_merger.py:27 Detected strings that are implicitly concatenated inside a list. Python will implicitly concatenate strings when not explicitly delimited. Was this supposed to be individual elements of the list? Lint
medium opengrep/python.lang.correctness.common-mistakes.string-concat-in-list tools/proteomics/fasta_utils/contaminant_database_merger/contaminant_database_merger.py:29 Detected strings that are implicitly concatenated inside a list. Python will implicitly concatenate strings when not explicitly delimited. Was this supposed to be individual elements of the list? Lint
medium opengrep/python.lang.correctness.common-mistakes.string-concat-in-list tools/proteomics/fasta_utils/contaminant_database_merger/contaminant_database_merger.py:31 Detected strings that are implicitly concatenated inside a list. Python will implicitly concatenate strings when not explicitly delimited. Was this supposed to be individual elements of the list? Lint
medium opengrep/python.lang.correctness.common-mistakes.string-concat-in-list tools/proteomics/fasta_utils/contaminant_database_merger/contaminant_database_merger.py:33 Detected strings that are implicitly concatenated inside a list. Python will implicitly concatenate strings when not explicitly delimited. Was this supposed to be individual elements of the list? Lint
medium opengrep/python.lang.correctness.common-mistakes.string-concat-in-list tools/proteomics/fasta_utils/contaminant_database_merger/contaminant_database_merger.py:35 Detected strings that are implicitly concatenated inside a list. Python will implicitly concatenate strings when not explicitly delimited. Was this supposed to be individual elements of the list? Lint
medium opengrep/python.lang.correctness.common-mistakes.string-concat-in-list tools/proteomics/fasta_utils/contaminant_database_merger/contaminant_database_merger.py:37 Detected strings that are implicitly concatenated inside a list. Python will implicitly concatenate strings when not explicitly delimited. Was this supposed to be individual elements of the list? Lint
medium opengrep/python.lang.correctness.common-mistakes.string-concat-in-list tools/proteomics/fasta_utils/contaminant_database_merger/contaminant_database_merger.py:39 Detected strings that are implicitly concatenated inside a list. Python will implicitly concatenate strings when not explicitly delimited. Was this supposed to be individual elements of the list? Lint
medium opengrep/python.lang.correctness.common-mistakes.string-concat-in-list tools/proteomics/fasta_utils/contaminant_database_merger/contaminant_database_merger.py:41 Detected strings that are implicitly concatenated inside a list. Python will implicitly concatenate strings when not explicitly delimited. Was this supposed to be individual elements of the list? Lint
medium opengrep/python.lang.correctness.common-mistakes.string-concat-in-list tools/proteomics/fasta_utils/contaminant_database_merger/contaminant_database_merger.py:47 Detected strings that are implicitly concatenated inside a list. Python will implicitly concatenate strings when not explicitly delimited. Was this supposed to be individual elements of the list? Lint
medium opengrep/python.lang.correctness.common-mistakes.string-concat-in-list tools/proteomics/fasta_utils/contaminant_database_merger/contaminant_database_merger.py:49 Detected strings that are implicitly concatenated inside a list. Python will implicitly concatenate strings when not explicitly delimited. Was this supposed to be individual elements of the list? Lint
medium opengrep/python.lang.correctness.common-mistakes.string-concat-in-list tools/proteomics/fasta_utils/contaminant_database_merger/contaminant_database_merger.py:51 Detected strings that are implicitly concatenated inside a list. Python will implicitly concatenate strings when not explicitly delimited. Was this supposed to be individual elements of the list? Lint
medium opengrep/python.lang.correctness.common-mistakes.string-concat-in-list tools/proteomics/fasta_utils/contaminant_database_merger/contaminant_database_merger.py:53 Detected strings that are implicitly concatenated inside a list. Python will implicitly concatenate strings when not explicitly delimited. Was this supposed to be individual elements of the list? Lint
medium opengrep/python.lang.correctness.common-mistakes.string-concat-in-list tools/proteomics/fasta_utils/contaminant_database_merger/contaminant_database_merger.py:55 Detected strings that are implicitly concatenated inside a list. Python will implicitly concatenate strings when not explicitly delimited. Was this supposed to be individual elements of the list? Lint
medium opengrep/python.lang.correctness.common-mistakes.string-concat-in-list tools/proteomics/fasta_utils/contaminant_database_merger/contaminant_database_merger.py:58 Detected strings that are implicitly concatenated inside a list. Python will implicitly concatenate strings when not explicitly delimited. Was this supposed to be individual elements of the list? Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/fasta_utils/fasta_decoy_validator/fasta_decoy_validator.py:111 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/fasta_utils/fasta_in_silico_digest_stats/fasta_in_silico_digest_stats.py:103 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/fasta_utils/fasta_statistics_reporter/fasta_statistics_reporter.py:109 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/fasta_utils/fasta_subset_extractor/fasta_subset_extractor.py:99 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/file_conversion/consensus_map_to_matrix/consensus_map_to_matrix.py:72 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/file_conversion/idxml_to_tsv_exporter/idxml_to_tsv_exporter.py:45 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/file_conversion/mgf_mzml_converter/mgf_mzml_converter.py:319 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/file_conversion/mgf_mzml_converter/mgf_mzml_converter.py:74 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/file_conversion/ms_data_ml_exporter/ms_data_ml_exporter.py:101 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/file_conversion/ms_data_to_csv_exporter/ms_data_to_csv_exporter.py:46 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/file_conversion/ms_data_to_csv_exporter/ms_data_to_csv_exporter.py:69 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/file_conversion/ms_data_to_csv_exporter/ms_data_to_csv_exporter.py:96 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/file_conversion/mztab_summarizer/mztab_summarizer.py:136 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/file_conversion/mztab_summarizer/mztab_summarizer.py:37 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/identification/mzml_metadata_extractor/mzml_metadata_extractor.py:122 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/identification/peptide_spectral_match_validator/peptide_spectral_match_validator.py:122 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/identification/peptide_spectral_match_validator/peptide_spectral_match_validator.py:193 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/identification/psm_feature_extractor/psm_feature_extractor.py:212 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/identification/psm_feature_extractor/psm_feature_extractor.py:39 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/identification/semi_tryptic_peptide_finder/semi_tryptic_peptide_finder.py:189 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/identification/semi_tryptic_peptide_finder/semi_tryptic_peptide_finder.py:208 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/identification/sequence_tag_generator/sequence_tag_generator.py:182 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/peptide_analysis/amino_acid_composition_analyzer/amino_acid_composition_analyzer.py:124 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/peptide_analysis/amino_acid_composition_analyzer/amino_acid_composition_analyzer.py:127 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/peptide_analysis/charge_state_predictor/charge_state_predictor.py:148 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/peptide_analysis/isoelectric_point_calculator/isoelectric_point_calculator.py:210 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/peptide_analysis/isoelectric_point_calculator/isoelectric_point_calculator.py:213 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/peptide_analysis/modification_mass_calculator/modification_mass_calculator.py:150 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/peptide_analysis/modification_mass_calculator/modification_mass_calculator.py:160 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/peptide_analysis/modification_mass_calculator/modification_mass_calculator.py:168 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/peptide_analysis/modified_peptide_generator/modified_peptide_generator.py:172 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/peptide_analysis/modified_peptide_generator/modified_peptide_generator.py:175 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/peptide_analysis/peptide_detectability_predictor/peptide_detectability_predictor.py:160 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/peptide_analysis/peptide_detectability_predictor/peptide_detectability_predictor.py:167 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/peptide_analysis/peptide_mass_fingerprint/peptide_mass_fingerprint.py:156 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/peptide_analysis/peptide_modification_analyzer/peptide_modification_analyzer.py:100 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/peptide_analysis/peptide_modification_analyzer/peptide_modification_analyzer.py:97 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/peptide_analysis/peptide_property_calculator/peptide_property_calculator.py:232 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/peptide_analysis/peptide_property_calculator/peptide_property_calculator.py:241 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/peptide_analysis/peptide_property_calculator/peptide_property_calculator.py:244 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/peptide_analysis/peptide_uniqueness_checker/peptide_uniqueness_checker.py:103 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/peptide_analysis/peptide_uniqueness_checker/peptide_uniqueness_checker.py:91 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/peptide_analysis/rt_prediction_additive/rt_prediction_additive.py:127 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/peptide_analysis/rt_prediction_additive/rt_prediction_additive.py:133 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/peptide_analysis/rt_prediction_additive/rt_prediction_additive.py:142 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/peptide_analysis/rt_prediction_additive/rt_prediction_additive.py:145 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/protein_analysis/peptide_to_protein_mapper/peptide_to_protein_mapper.py:148 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/protein_analysis/peptide_to_protein_mapper/peptide_to_protein_mapper.py:57 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/protein_analysis/protein_coverage_calculator/protein_coverage_calculator.py:104 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/protein_analysis/protein_coverage_calculator/protein_coverage_calculator.py:114 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/protein_analysis/protein_group_reporter/protein_group_reporter.py:171 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/protein_analysis/protein_group_reporter/protein_group_reporter.py:190 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/protein_analysis/spectral_counting_quantifier/spectral_counting_quantifier.py:170 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/protein_analysis/spectral_counting_quantifier/spectral_counting_quantifier.py:207 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/protein_analysis/spectral_counting_quantifier/spectral_counting_quantifier.py:210 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/ptm_analysis/glycopeptide_mass_calculator/glycopeptide_mass_calculator.py:141 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/ptm_analysis/phospho_enrichment_qc/phospho_enrichment_qc.py:158 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/ptm_analysis/phospho_enrichment_qc/phospho_enrichment_qc.py:167 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/ptm_analysis/phospho_motif_analyzer/phospho_motif_analyzer.py:200 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/ptm_analysis/phospho_motif_analyzer/phospho_motif_analyzer.py:215 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/ptm_analysis/phospho_motif_analyzer/phospho_motif_analyzer.py:222 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/ptm_analysis/phosphosite_class_filter/phosphosite_class_filter.py:173 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/ptm_analysis/phosphosite_class_filter/phosphosite_class_filter.py:196 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/ptm_analysis/phosphosite_class_filter/phosphosite_class_filter.py:204 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/ptm_analysis/ptm_site_localization_scorer/ptm_site_localization_scorer.py:230 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/ptm_analysis/ptm_site_localization_scorer/ptm_site_localization_scorer.py:233 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/quality_control/acquisition_rate_analyzer/acquisition_rate_analyzer.py:97 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/quality_control/collision_energy_analyzer/collision_energy_analyzer.py:109 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/quality_control/identification_qc_reporter/identification_qc_reporter.py:113 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/quality_control/identification_qc_reporter/identification_qc_reporter.py:127 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/quality_control/injection_time_analyzer/injection_time_analyzer.py:113 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/quality_control/lc_ms_qc_reporter/lc_ms_qc_reporter.py:94 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/quality_control/mass_error_distribution_analyzer/mass_error_distribution_analyzer.py:129 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/quality_control/mass_error_distribution_analyzer/mass_error_distribution_analyzer.py:139 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/quality_control/missed_cleavage_analyzer/missed_cleavage_analyzer.py:110 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/quality_control/missed_cleavage_analyzer/missed_cleavage_analyzer.py:113 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/quality_control/missed_cleavage_analyzer/missed_cleavage_analyzer.py:99 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/quality_control/ms1_feature_intensity_tracker/ms1_feature_intensity_tracker.py:211 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/quality_control/ms1_feature_intensity_tracker/ms1_feature_intensity_tracker.py:44 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/quality_control/mzqc_generator/mzqc_generator.py:130 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/quality_control/precursor_charge_distribution/precursor_charge_distribution.py:121 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/quality_control/precursor_isolation_purity/precursor_isolation_purity.py:121 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/quality_control/precursor_recurrence_analyzer/precursor_recurrence_analyzer.py:165 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/quality_control/run_comparison_reporter/run_comparison_reporter.py:126 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/quality_control/sample_complexity_estimator/sample_complexity_estimator.py:115 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/quantification/peptide_protein_quantifier/peptide_protein_quantifier.py:99 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/rna/rna_digest/rna_digest.py:120 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/rna/rna_fragment_spectrum_generator/rna_fragment_spectrum_generator.py:209 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/rna/rna_mass_calculator/rna_mass_calculator.py:150 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/signal_processing/peak_type_estimator/peak_type_estimator.py:63 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/signal_processing/signal_to_noise_estimator/signal_to_noise_estimator.py:60 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/specialized/cleavage_site_profiler/cleavage_site_profiler.py:230 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/specialized/cleavage_site_profiler/cleavage_site_profiler.py:245 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/specialized/cleavage_site_profiler/cleavage_site_profiler.py:251 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/specialized/immunopeptide_filter/immunopeptide_filter.py:115 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/specialized/immunopeptide_filter/immunopeptide_filter.py:134 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/specialized/immunopeptide_filter/immunopeptide_filter.py:138 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/specialized/immunopeptidome_qc/immunopeptidome_qc.py:220 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/specialized/immunopeptidome_qc/immunopeptidome_qc.py:233 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/specialized/immunopeptidome_qc/immunopeptidome_qc.py:249 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/specialized/metapeptide_lca_assigner/metapeptide_lca_assigner.py:219 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/specialized/metapeptide_lca_assigner/metapeptide_lca_assigner.py:231 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/specialized/metapeptide_lca_assigner/metapeptide_lca_assigner.py:68 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium opengrep/python.lang.best-practice.unspecified-open-encoding tools/proteomics/specialized/nterm_modification_annotator/nterm_modification_annotator.py:249 Missing 'encoding' parameter. 'open()' uses device locale encodings by default, corrupting files with special characters. Specify the encoding to ensure cross-platform support when opening files in text mode (e.g. encoding="utf-8"). Lint
medium zizmor/excessive-permissions .github/workflows/validate.yml:1 overly broad permissions [confidence medium] CI workflows (zizmor)
medium zizmor/artipacked .github/workflows/validate.yml:15 credential persistence through GitHub Actions artifacts [confidence low] CI workflows (zizmor)
medium zizmor/excessive-permissions .github/workflows/validate.yml:39 overly broad permissions [confidence medium] CI workflows (zizmor)
medium zizmor/artipacked .github/workflows/validate.yml:44 credential persistence through GitHub Actions artifacts [confidence low] CI workflows (zizmor)
medium zizmor/excessive-permissions .github/workflows/validate.yml:9 overly broad permissions [confidence medium] CI workflows (zizmor)
low opengrep/python.lang.security.use-defusedcsv tools/metabolomics/formula_tools/metabolite_formula_annotator/metabolite_formula_annotator.py:188 Detected the generation of a CSV file using the built-in `csv` module. If user data is used to generate the data in this file, it is possible that an attacker could inject a formula when the CSV is imported into a spreadsheet... Static analysis (opengrep)
low opengrep/python.lang.security.use-defusedcsv tools/proteomics/fasta_utils/fasta_in_silico_digest_stats/fasta_in_silico_digest_stats.py:104 Detected the generation of a CSV file using the built-in `csv` module. If user data is used to generate the data in this file, it is possible that an attacker could inject a formula when the CSV is imported into a spreadsheet... Static analysis (opengrep)
low opengrep/python.lang.security.use-defusedcsv tools/proteomics/file_conversion/consensus_map_to_matrix/consensus_map_to_matrix.py:73 Detected the generation of a CSV file using the built-in `csv` module. If user data is used to generate the data in this file, it is possible that an attacker could inject a formula when the CSV is imported into a spreadsheet... Static analysis (opengrep)
low opengrep/python.lang.security.use-defusedcsv tools/proteomics/file_conversion/idxml_to_tsv_exporter/idxml_to_tsv_exporter.py:46 Detected the generation of a CSV file using the built-in `csv` module. If user data is used to generate the data in this file, it is possible that an attacker could inject a formula when the CSV is imported into a spreadsheet... Static analysis (opengrep)
low opengrep/python.lang.security.use-defusedcsv tools/proteomics/file_conversion/ms_data_to_csv_exporter/ms_data_to_csv_exporter.py:47 Detected the generation of a CSV file using the built-in `csv` module. If user data is used to generate the data in this file, it is possible that an attacker could inject a formula when the CSV is imported into a spreadsheet... Static analysis (opengrep)
low opengrep/python.lang.security.use-defusedcsv tools/proteomics/file_conversion/ms_data_to_csv_exporter/ms_data_to_csv_exporter.py:70 Detected the generation of a CSV file using the built-in `csv` module. If user data is used to generate the data in this file, it is possible that an attacker could inject a formula when the CSV is imported into a spreadsheet... Static analysis (opengrep)
low opengrep/python.lang.security.use-defusedcsv tools/proteomics/file_conversion/ms_data_to_csv_exporter/ms_data_to_csv_exporter.py:97 Detected the generation of a CSV file using the built-in `csv` module. If user data is used to generate the data in this file, it is possible that an attacker could inject a formula when the CSV is imported into a spreadsheet... Static analysis (opengrep)
low opengrep/python.lang.security.use-defusedcsv tools/proteomics/file_conversion/mztab_summarizer/mztab_summarizer.py:137 Detected the generation of a CSV file using the built-in `csv` module. If user data is used to generate the data in this file, it is possible that an attacker could inject a formula when the CSV is imported into a spreadsheet... Static analysis (opengrep)
low opengrep/python.lang.security.use-defusedcsv tools/proteomics/quantification/peptide_protein_quantifier/peptide_protein_quantifier.py:100 Detected the generation of a CSV file using the built-in `csv` module. If user data is used to generate the data in this file, it is possible that an attacker could inject a formula when the CSV is imported into a spreadsheet... Static analysis (opengrep)
low opengrep/python.lang.security.use-defusedcsv tools/proteomics/specialized/immunopeptidome_qc/immunopeptidome_qc.py:234 Detected the generation of a CSV file using the built-in `csv` module. If user data is used to generate the data in this file, it is possible that an attacker could inject a formula when the CSV is imported into a spreadsheet... Static analysis (opengrep)
low opengrep/python.lang.security.use-defusedcsv tools/proteomics/specialized/immunopeptidome_qc/immunopeptidome_qc.py:250 Detected the generation of a CSV file using the built-in `csv` module. If user data is used to generate the data in this file, it is possible that an attacker could inject a formula when the CSV is imported into a spreadsheet... Static analysis (opengrep)
low opengrep/python.lang.security.use-defusedcsv tools/proteomics/specialized/proteoform_delta_annotator/proteoform_delta_annotator.py:153 Detected the generation of a CSV file using the built-in `csv` module. If user data is used to generate the data in this file, it is possible that an attacker could inject a formula when the CSV is imported into a spreadsheet... Static analysis (opengrep)
low opengrep/python.lang.security.use-defusedcsv tools/proteomics/specialized/topdown_coverage_calculator/topdown_coverage_calculator.py:186 Detected the generation of a CSV file using the built-in `csv` module. If user data is used to generate the data in this file, it is possible that an attacker could inject a formula when the CSV is imported into a spreadsheet... Static analysis (opengrep)
low opengrep/python.lang.security.use-defusedcsv tools/proteomics/targeted_proteomics/library_coverage_estimator/library_coverage_estimator.py:170 Detected the generation of a CSV file using the built-in `csv` module. If user data is used to generate the data in this file, it is possible that an attacker could inject a formula when the CSV is imported into a spreadsheet... Static analysis (opengrep)
info zizmor/template-injection .github/workflows/validate.yml:54 code injection via template expansion [confidence low] CI workflows (zizmor)
info zizmor/template-injection .github/workflows/validate.yml:63 code injection via template expansion [confidence low] CI workflows (zizmor)
info zizmor/template-injection .github/workflows/validate.yml:74 code injection via template expansion [confidence low] CI workflows (zizmor)

Tools and coverage

Every analyzer that ran on this commit. A failed or skipped tool is a coverage gap: its share of the score is left out and the coverage figure drops.

AnalyzerPillarStatusVersionFindingsNote
AI tool configurationAI provenanceoksignatures-v10
Explicit AI attributionAI provenanceoksignatures-v10
Release velocityAI provenanceskipped—0
Coding styleAI provenanceok—0
Commit velocityAI provenanceokprov-40
Findings in AI-written linesAI provenanceokgit-blame0
Complexity (lizard)Code qualityoklizard 1.25.10
DocumentationCode qualityok—0
Duplication (jscpd)Code qualityokrepotrust-dup-w60
LintCode qualityokopengrep 1.33.1; rules f1d2b562b414200
Tests and CICode qualityok—0
Type safetyCode qualityok—0
CI workflows (zizmor)Securityokzizmor 1.32.012
Dependencies (osv-scanner)Securityokosv-scanner version: 2.7.10
Release downloadsSecurityok—0
Security postureSecurityok—0
Package registriesSecurityok—0
Static analysis (opengrep)Securityokopengrep 1.33.1; rules f1d2b562b41414
OpenSSF ScorecardSecurityskipped—0no published OpenSSF Scorecard result for this repo
Secrets (gitleaks)Securityokgitleaks 8.30.10

Score history

Scores from different scoring versions aren't directly comparable.

ScoredCommitScoringAI provenanceQualitySecurity
2026-11-14253b99aef22eprov-5+qual-2+sec-2100%6878
2026-11-14253b99aef22eprov-4+qual-2+sec-2100%6878

Embed a badge

Maintainers can show these in a README. Badges update when the repository is re-scored.

[![RepoTrust ai](https://repotrust.synapticcyber.com/badge/github.com/OpenMS/agentomics/ai.svg)](https://repotrust.synapticcyber.com/r/github.com/OpenMS/agentomics/)
[![RepoTrust quality](https://repotrust.synapticcyber.com/badge/github.com/OpenMS/agentomics/quality.svg)](https://repotrust.synapticcyber.com/r/github.com/OpenMS/agentomics/)
[![RepoTrust security](https://repotrust.synapticcyber.com/badge/github.com/OpenMS/agentomics/security.svg)](https://repotrust.synapticcyber.com/r/github.com/OpenMS/agentomics/)
Full text report
  • Repository: https://github.com/OpenMS/agentomics
  • Commit: 253b99aef22e0522d4039b009ace4a1cbd83434e
  • Generated: 2026-11-14T14:52:01+00:00
  • Scorer 0.1.0, scoring prov-5+qual-2+sec-2, report schema v2

Scores

Pillar Score Signal Confidence Coverage
AI provenance (estimated AI-generated share) 100 explicit 82% 100%
Code quality 68 adequate 90% 100%
Security 78 adequate 85% 100%

AI provenance

Explicit AI attribution on 100% of first-party code added; an estimated 100% including velocity signals.

  • Explicitly attributed share (lower bound): 99.6%
  • Unattributed share in AI-consistent velocity bursts: 0.0%
  • Estimated AI-generated share: 99.6%
AI tool Attributed commits Lines added
Claude Code 42 53,408
GitHub Copilot coding agent 4 1,410
  • AI tooling configured in repo: claude-code, generic-agent

Current source lines last changed by AI-attributed commits: 28,092 of 28,092.

Too few lines in one group to compare finding densities.

  • Stylometry index: 0.07 per 1,000 lines (narrated steps 2, placeholders 0, assistant phrasing 0, emoji 0). Reported as a signal, not scored.
Month Lines added Attributed to AI
2026-03 55,025 100%

Evidence

  • Claude Code: trailer 'Co-Authored-By: Claude' (8a8e0df89b5b)
  • Claude Code: trailer 'Co-Authored-By: Claude' (2e594314654e)
  • Claude Code: trailer 'Co-Authored-By: Claude' (e15d3566e341)
  • Claude Code: trailer 'Co-Authored-By: Claude' (dbddefa0ed95)
  • Claude Code: trailer 'Co-Authored-By: Claude' (8603f9d46fc8)
  • Claude Code: trailer 'Co-Authored-By: Claude' (da55a4091772)
  • Claude Code: trailer 'Co-Authored-By: Claude' (8212aeb2af14)
  • Claude Code: trailer 'Co-Authored-By: Claude' (fbdc057c7a26)
  • Claude Code: trailer 'Co-Authored-By: Claude' (7b0551ad69fb)
  • Claude Code: trailer 'Co-Authored-By: Claude' (fb71ed9c60fb)
  • Claude Code: trailer 'Co-Authored-By: Claude' (d0fa79c347e6)
  • Claude Code: trailer 'Co-Authored-By: Claude' (479b718f6d80)
  • Claude Code: trailer 'Co-Authored-By: Claude' (4abd6402c306)
  • Claude Code: trailer 'Co-Authored-By: Claude' (be3c3d4481fd)
  • Claude Code: trailer 'Co-Authored-By: Claude' (8ae997071657)

AI provenance describes how code was produced; it is not a quality judgment. Unless attribution is explicit, these are signals consistent with AI generation, not proof. Squash/rebase workflows, imported code, and rewritten history reduce accuracy.

Code quality

Code quality is adequate: test-to-source ratio 0.64, CI runs tests; 3% of function code in complex or long functions; 11% duplicated lines. Weakest area: lint.

Area Score
Complexity (lizard) 92
Duplication 52
Code smells (Opengrep) 12
Tests and CI 100
Documentation 65
Type safety 40
Process (Scorecard review/maintenance) n/a
  • Functions: 750; mean complexity 3.8, 90th percentile 8; 7 complex and 0 long functions
  • Duplicated lines: 10.9% of 20,905 compared
  • Tests: 17,945 test lines for 28,092 source lines (ratio 0.64); CI test commands: pytest; 90% of recent source commits also change tests
  • Docs missing or thin: contributing, changelog

Most complex functions:

Security

Security posture is adequate: 4 high-severity workflow issues. Weakest area: posture.

Area Score
Secrets (gitleaks, tree + history) 100
Static analysis (Opengrep) 99
Vulnerable dependencies (OSV) 100
CI workflows (zizmor) 38
Posture (policy, updates, signing, lockfiles) 0
OpenSSF Scorecard n/a
  • Posture checks passed: lockfiles; missing: security policy, dependency updates, signed commits

Top findings

Severity Finding Location
high zizmor/template-injection: code injection via template expansion [confidence high] .github/workflows/validate.yml:25
high zizmor/unpinned-uses: unpinned action reference [confidence high] .github/workflows/validate.yml:15
high zizmor/unpinned-uses: unpinned action reference [confidence high] .github/workflows/validate.yml:44
high zizmor/unpinned-uses: unpinned action reference [confidence high] .github/workflows/validate.yml:46
medium zizmor/artipacked: credential persistence through GitHub Actions artifacts [confidence low] .github/workflows/validate.yml:15
medium zizmor/artipacked: credential persistence through GitHub Actions artifacts [confidence low] .github/workflows/validate.yml:44
medium zizmor/excessive-permissions: overly broad permissions [confidence medium] .github/workflows/validate.yml:1
medium zizmor/excessive-permissions: overly broad permissions [confidence medium] .github/workflows/validate.yml:9
medium zizmor/excessive-permissions: overly broad permissions [confidence medium] .github/workflows/validate.yml:39
low opengrep/python.lang.security.use-defusedcsv: Detected the generation of a CSV file using the built-in csv module. If user data is used to generate the data in this file, it is possible that an attacker could inject a formula when the CSV is imported into a spreadsheet application that runs an attacker script, which could steal data from the [confidence low] tools/metabolomics/formula_tools/metabolite_formula_annotator/metabolite_formula_annotator.py:188
low opengrep/python.lang.security.use-defusedcsv: Detected the generation of a CSV file using the built-in csv module. If user data is used to generate the data in this file, it is possible that an attacker could inject a formula when the CSV is imported into a spreadsheet application that runs an attacker script, which could steal data from the [confidence low] tools/proteomics/fasta_utils/fasta_in_silico_digest_stats/fasta_in_silico_digest_stats.py:104
low opengrep/python.lang.security.use-defusedcsv: Detected the generation of a CSV file using the built-in csv module. If user data is used to generate the data in this file, it is possible that an attacker could inject a formula when the CSV is imported into a spreadsheet application that runs an attacker script, which could steal data from the [confidence low] tools/proteomics/file_conversion/consensus_map_to_matrix/consensus_map_to_matrix.py:73
low opengrep/python.lang.security.use-defusedcsv: Detected the generation of a CSV file using the built-in csv module. If user data is used to generate the data in this file, it is possible that an attacker could inject a formula when the CSV is imported into a spreadsheet application that runs an attacker script, which could steal data from the [confidence low] tools/proteomics/file_conversion/idxml_to_tsv_exporter/idxml_to_tsv_exporter.py:46
low opengrep/python.lang.security.use-defusedcsv: Detected the generation of a CSV file using the built-in csv module. If user data is used to generate the data in this file, it is possible that an attacker could inject a formula when the CSV is imported into a spreadsheet application that runs an attacker script, which could steal data from the [confidence low] tools/proteomics/file_conversion/ms_data_to_csv_exporter/ms_data_to_csv_exporter.py:47
low opengrep/python.lang.security.use-defusedcsv: Detected the generation of a CSV file using the built-in csv module. If user data is used to generate the data in this file, it is possible that an attacker could inject a formula when the CSV is imported into a spreadsheet application that runs an attacker script, which could steal data from the [confidence low] tools/proteomics/file_conversion/ms_data_to_csv_exporter/ms_data_to_csv_exporter.py:70
low opengrep/python.lang.security.use-defusedcsv: Detected the generation of a CSV file using the built-in csv module. If user data is used to generate the data in this file, it is possible that an attacker could inject a formula when the CSV is imported into a spreadsheet application that runs an attacker script, which could steal data from the [confidence low] tools/proteomics/file_conversion/ms_data_to_csv_exporter/ms_data_to_csv_exporter.py:97
low opengrep/python.lang.security.use-defusedcsv: Detected the generation of a CSV file using the built-in csv module. If user data is used to generate the data in this file, it is possible that an attacker could inject a formula when the CSV is imported into a spreadsheet application that runs an attacker script, which could steal data from the [confidence low] tools/proteomics/file_conversion/mztab_summarizer/mztab_summarizer.py:137
low opengrep/python.lang.security.use-defusedcsv: Detected the generation of a CSV file using the built-in csv module. If user data is used to generate the data in this file, it is possible that an attacker could inject a formula when the CSV is imported into a spreadsheet application that runs an attacker script, which could steal data from the [confidence low] tools/proteomics/quantification/peptide_protein_quantifier/peptide_protein_quantifier.py:100
low opengrep/python.lang.security.use-defusedcsv: Detected the generation of a CSV file using the built-in csv module. If user data is used to generate the data in this file, it is possible that an attacker could inject a formula when the CSV is imported into a spreadsheet application that runs an attacker script, which could steal data from the [confidence low] tools/proteomics/specialized/immunopeptidome_qc/immunopeptidome_qc.py:234
low opengrep/python.lang.security.use-defusedcsv: Detected the generation of a CSV file using the built-in csv module. If user data is used to generate the data in this file, it is possible that an attacker could inject a formula when the CSV is imported into a spreadsheet application that runs an attacker script, which could steal data from the [confidence low] tools/proteomics/specialized/immunopeptidome_qc/immunopeptidome_qc.py:250
low opengrep/python.lang.security.use-defusedcsv: Detected the generation of a CSV file using the built-in csv module. If user data is used to generate the data in this file, it is possible that an attacker could inject a formula when the CSV is imported into a spreadsheet application that runs an attacker script, which could steal data from the [confidence low] tools/proteomics/specialized/proteoform_delta_annotator/proteoform_delta_annotator.py:153
low opengrep/python.lang.security.use-defusedcsv: Detected the generation of a CSV file using the built-in csv module. If user data is used to generate the data in this file, it is possible that an attacker could inject a formula when the CSV is imported into a spreadsheet application that runs an attacker script, which could steal data from the [confidence low] tools/proteomics/specialized/topdown_coverage_calculator/topdown_coverage_calculator.py:186
low opengrep/python.lang.security.use-defusedcsv: Detected the generation of a CSV file using the built-in csv module. If user data is used to generate the data in this file, it is possible that an attacker could inject a formula when the CSV is imported into a spreadsheet application that runs an attacker script, which could steal data from the [confidence low] tools/proteomics/targeted_proteomics/library_coverage_estimator/library_coverage_estimator.py:170
info zizmor/template-injection: code injection via template expansion [confidence low] .github/workflows/validate.yml:54
info zizmor/template-injection: code injection via template expansion [confidence low] .github/workflows/validate.yml:63

Static signals only: the scorer never runs the project's code. Secret findings are pattern matches that were not verified, and secret values are never stored.

Repository profile

  • Source lines: 28,092; test lines: 17,945
Language Lines
Python 46,037