@litfamily/litopencode 1.0.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/.gitattributes +8 -0
- package/ATTRIBUTION.md +56 -0
- package/CHANGELOG.md +267 -0
- package/CODE_OF_CONDUCT.md +30 -0
- package/CONTRIBUTING.md +82 -0
- package/LICENSE +21 -0
- package/README-Ko-KR.md +252 -0
- package/README.md +252 -0
- package/SECURITY.md +36 -0
- package/SUPPORT.md +37 -0
- package/bin/litopencode +3 -0
- package/bin/litopencode.cjs +10 -0
- package/dist/activation-managed-prompts.d.ts +2 -0
- package/dist/activation-managed-prompts.js +51 -0
- package/dist/activation-primary-prompts.d.ts +2 -0
- package/dist/activation-primary-prompts.js +176 -0
- package/dist/activation-probe.d.ts +3 -0
- package/dist/activation-probe.js +19 -0
- package/dist/activation-prompt-utils.d.ts +6 -0
- package/dist/activation-prompt-utils.js +36 -0
- package/dist/activation-routing.d.ts +5 -0
- package/dist/activation-routing.js +340 -0
- package/dist/activation-workflow-prompts.d.ts +26 -0
- package/dist/activation-workflow-prompts.js +295 -0
- package/dist/activation.d.ts +24 -0
- package/dist/activation.js +152 -0
- package/dist/agents/defaults.d.ts +15 -0
- package/dist/agents/defaults.js +112 -0
- package/dist/agents/registry.d.ts +65 -0
- package/dist/agents/registry.js +319 -0
- package/dist/agents/specialists.d.ts +49 -0
- package/dist/agents/specialists.js +307 -0
- package/dist/agents/types.d.ts +55 -0
- package/dist/agents/types.js +4 -0
- package/dist/agents.d.ts +4 -0
- package/dist/agents.js +3 -0
- package/dist/benchmark.d.ts +94 -0
- package/dist/benchmark.js +172 -0
- package/dist/bounded-authority-hooks.d.ts +19 -0
- package/dist/bounded-authority-hooks.js +157 -0
- package/dist/bounded-authority.d.ts +184 -0
- package/dist/bounded-authority.js +825 -0
- package/dist/cache-metrics.d.ts +54 -0
- package/dist/cache-metrics.js +81 -0
- package/dist/cli/args.d.ts +5 -0
- package/dist/cli/args.js +415 -0
- package/dist/cli/auto-update.d.ts +117 -0
- package/dist/cli/auto-update.js +604 -0
- package/dist/cli/command-alias-ownership.d.ts +2 -0
- package/dist/cli/command-alias-ownership.js +14 -0
- package/dist/cli/command-aliases.d.ts +12 -0
- package/dist/cli/command-aliases.js +112 -0
- package/dist/cli/doctor.d.ts +2 -0
- package/dist/cli/doctor.js +175 -0
- package/dist/cli/host-capabilities.d.ts +12 -0
- package/dist/cli/host-capabilities.js +25 -0
- package/dist/cli/host-limits.d.ts +21 -0
- package/dist/cli/host-limits.js +83 -0
- package/dist/cli/install-config.d.ts +13 -0
- package/dist/cli/install-config.js +201 -0
- package/dist/cli/install-report.d.ts +2 -0
- package/dist/cli/install-report.js +180 -0
- package/dist/cli/install-tui.d.ts +12 -0
- package/dist/cli/install-tui.js +174 -0
- package/dist/cli/install.d.ts +2 -0
- package/dist/cli/install.js +264 -0
- package/dist/cli/json.d.ts +4 -0
- package/dist/cli/json.js +31 -0
- package/dist/cli/loop.d.ts +3 -0
- package/dist/cli/loop.js +135 -0
- package/dist/cli/lsp-capability.d.ts +17 -0
- package/dist/cli/lsp-capability.js +92 -0
- package/dist/cli/managed-skill-assets.d.ts +23 -0
- package/dist/cli/managed-skill-assets.js +117 -0
- package/dist/cli/model-catalog.d.ts +21 -0
- package/dist/cli/model-catalog.js +107 -0
- package/dist/cli/model-policy.d.ts +3 -0
- package/dist/cli/model-policy.js +143 -0
- package/dist/cli/model-routing.d.ts +5 -0
- package/dist/cli/model-routing.js +208 -0
- package/dist/cli/native-canonical-backup.d.ts +9 -0
- package/dist/cli/native-canonical-backup.js +96 -0
- package/dist/cli/native-canonical-cache.d.ts +9 -0
- package/dist/cli/native-canonical-cache.js +37 -0
- package/dist/cli/native-skill-install.d.ts +2 -0
- package/dist/cli/native-skill-install.js +128 -0
- package/dist/cli/native-skill-integrity.d.ts +25 -0
- package/dist/cli/native-skill-integrity.js +178 -0
- package/dist/cli/native-skill-tree.d.ts +12 -0
- package/dist/cli/native-skill-tree.js +104 -0
- package/dist/cli/native-skills.d.ts +22 -0
- package/dist/cli/native-skills.js +105 -0
- package/dist/cli/plugin-mutation.d.ts +4 -0
- package/dist/cli/plugin-mutation.js +89 -0
- package/dist/cli/scientific-visualization-dependencies.d.ts +18 -0
- package/dist/cli/scientific-visualization-dependencies.js +91 -0
- package/dist/cli/skill-loop.d.ts +3 -0
- package/dist/cli/skill-loop.js +649 -0
- package/dist/cli/types.d.ts +188 -0
- package/dist/cli/types.js +1 -0
- package/dist/cli/update-check.d.ts +2 -0
- package/dist/cli/update-check.js +15 -0
- package/dist/cli/update-notifier.d.ts +70 -0
- package/dist/cli/update-notifier.js +717 -0
- package/dist/cli/vendor-path-migration.d.ts +9 -0
- package/dist/cli/vendor-path-migration.js +96 -0
- package/dist/cli.d.ts +7 -0
- package/dist/cli.js +250 -0
- package/dist/commands.d.ts +331 -0
- package/dist/commands.js +600 -0
- package/dist/config-parser.d.ts +5 -0
- package/dist/config-parser.js +274 -0
- package/dist/config.d.ts +72 -0
- package/dist/config.js +157 -0
- package/dist/deliverable-hedge-guard.d.ts +26 -0
- package/dist/deliverable-hedge-guard.js +302 -0
- package/dist/durable-plan.d.ts +23 -0
- package/dist/durable-plan.js +349 -0
- package/dist/features.d.ts +828 -0
- package/dist/features.js +1109 -0
- package/dist/hooks.d.ts +17 -0
- package/dist/hooks.js +83 -0
- package/dist/ignition.d.ts +14 -0
- package/dist/ignition.js +33 -0
- package/dist/index.d.ts +30 -0
- package/dist/index.js +30 -0
- package/dist/inert-data.d.ts +2 -0
- package/dist/inert-data.js +13 -0
- package/dist/knowledge.d.ts +98 -0
- package/dist/knowledge.js +961 -0
- package/dist/ledger.d.ts +181 -0
- package/dist/ledger.js +1179 -0
- package/dist/lit-fetch-classify.d.ts +8 -0
- package/dist/lit-fetch-classify.js +107 -0
- package/dist/lit-fetch-content.d.ts +2 -0
- package/dist/lit-fetch-content.js +43 -0
- package/dist/lit-fetch-http.d.ts +10 -0
- package/dist/lit-fetch-http.js +82 -0
- package/dist/lit-fetch-result.d.ts +2 -0
- package/dist/lit-fetch-result.js +65 -0
- package/dist/lit-fetch-ssrf.d.ts +9 -0
- package/dist/lit-fetch-ssrf.js +77 -0
- package/dist/lit-fetch-url.d.ts +3 -0
- package/dist/lit-fetch-url.js +28 -0
- package/dist/lit-fetch.d.ts +69 -0
- package/dist/lit-fetch.js +84 -0
- package/dist/lit-mark.d.ts +17 -0
- package/dist/lit-mark.js +129 -0
- package/dist/logger.d.ts +9 -0
- package/dist/logger.js +21 -0
- package/dist/model-route-policy.d.ts +25 -0
- package/dist/model-route-policy.js +129 -0
- package/dist/reader-facing-output.d.ts +3 -0
- package/dist/reader-facing-output.js +28 -0
- package/dist/rules/discovery.d.ts +36 -0
- package/dist/rules/discovery.js +270 -0
- package/dist/rules/engine.d.ts +43 -0
- package/dist/rules/engine.js +236 -0
- package/dist/rules/frontmatter.d.ts +16 -0
- package/dist/rules/frontmatter.js +179 -0
- package/dist/rules/glob.d.ts +12 -0
- package/dist/rules/glob.js +233 -0
- package/dist/rules/hooks.d.ts +25 -0
- package/dist/rules/hooks.js +75 -0
- package/dist/rules/output-style.d.ts +1 -0
- package/dist/rules/output-style.js +20 -0
- package/dist/scientific-visualization-banner.d.ts +1 -0
- package/dist/scientific-visualization-banner.js +2 -0
- package/dist/search-workflow-ideas.d.ts +67 -0
- package/dist/search-workflow-ideas.js +128 -0
- package/dist/secret-shapes.d.ts +9 -0
- package/dist/secret-shapes.js +63 -0
- package/dist/server.d.ts +6 -0
- package/dist/server.js +129 -0
- package/dist/session-lineage.d.ts +8 -0
- package/dist/session-lineage.js +12 -0
- package/dist/skill-loop/apply.d.ts +19 -0
- package/dist/skill-loop/apply.js +483 -0
- package/dist/skill-loop/config.d.ts +50 -0
- package/dist/skill-loop/config.js +215 -0
- package/dist/skill-loop/curator.d.ts +18 -0
- package/dist/skill-loop/curator.js +232 -0
- package/dist/skill-loop/ledger.d.ts +39 -0
- package/dist/skill-loop/ledger.js +344 -0
- package/dist/skill-loop/proposals.d.ts +48 -0
- package/dist/skill-loop/proposals.js +290 -0
- package/dist/skill-loop/storage.d.ts +72 -0
- package/dist/skill-loop/storage.js +817 -0
- package/dist/skill-loop/time.d.ts +2 -0
- package/dist/skill-loop/time.js +23 -0
- package/dist/skill-loop/transaction.d.ts +62 -0
- package/dist/skill-loop/transaction.js +836 -0
- package/dist/skill-loop/usage.d.ts +31 -0
- package/dist/skill-loop/usage.js +146 -0
- package/dist/skill-observer.d.ts +22 -0
- package/dist/skill-observer.js +1154 -0
- package/dist/skill-renames.d.ts +5 -0
- package/dist/skill-renames.js +8 -0
- package/dist/skills.d.ts +307 -0
- package/dist/skills.js +450 -0
- package/dist/stable-identity.d.ts +14 -0
- package/dist/stable-identity.js +15 -0
- package/dist/state.d.ts +25 -0
- package/dist/state.js +38 -0
- package/dist/strict-json.d.ts +2 -0
- package/dist/strict-json.js +94 -0
- package/dist/tool-guards.d.ts +34 -0
- package/dist/tool-guards.js +210 -0
- package/dist/tool-kit.d.ts +32 -0
- package/dist/tool-kit.js +75 -0
- package/dist/tools.d.ts +43 -0
- package/dist/tools.js +381 -0
- package/dist/uiux-visual-catalog.d.ts +50 -0
- package/dist/uiux-visual-catalog.js +103 -0
- package/dist/user-facing-markdown.d.ts +5 -0
- package/dist/user-facing-markdown.js +93 -0
- package/dist/workflow-families.d.ts +16 -0
- package/dist/workflow-families.js +95 -0
- package/docs/assets/cover.webp +0 -0
- package/docs/assets/litopencode-continuity-1600.webp +0 -0
- package/docs/assets/litopencode-ignition-1600.webp +0 -0
- package/docs/assets/readme/badge-license.svg +1 -0
- package/docs/assets/readme/badge-version.svg +1 -0
- package/docs/assets/readme/litopencode-clay-icon.png +0 -0
- package/docs/assets/readme/litopencode-wordmark.svg +5 -0
- package/docs/lit-mark.md +46 -0
- package/docs/migration.md +162 -0
- package/docs/privacy.md +82 -0
- package/docs/reference-Ko-KR.md +309 -0
- package/docs/reference.md +444 -0
- package/output-styles/asd-ste100-ko.md +41 -0
- package/output-styles/asd-ste100.md +40 -0
- package/output-styles/eli5-ko.md +13 -0
- package/output-styles/eli5.md +11 -0
- package/package.json +57 -0
- package/qa/fixtures/litfamily-harness-speed-v1.json +38 -0
- package/qa/harness-speed-contract.mjs +209 -0
- package/qa/harness-speed-v2-contract.mjs +213 -0
- package/qa/harness-speed-verdict.mjs +105 -0
- package/skills/agent-roster/SKILL.md +262 -0
- package/skills/autoconference/LICENSE +21 -0
- package/skills/autoconference/PROVENANCE.md +20 -0
- package/skills/autoconference/SKILL.md +125 -0
- package/skills/autoconference/assets/conference_template.md +76 -0
- package/skills/autoconference/assets/report_template.md +53 -0
- package/skills/autoconference/assets/synthesis_template.md +39 -0
- package/skills/autoconference/modes/analyze.md +255 -0
- package/skills/autoconference/modes/core.md +112 -0
- package/skills/autoconference/modes/debate.md +373 -0
- package/skills/autoconference/modes/plan.md +310 -0
- package/skills/autoconference/modes/resume.md +48 -0
- package/skills/autoconference/modes/ship.md +57 -0
- package/skills/autoconference/modes/survey.md +109 -0
- package/skills/autoconference/references/agent-prompts.md +134 -0
- package/skills/autoconference/references/conference-protocol.md +102 -0
- package/skills/autoconference/references/convergence-guide.md +167 -0
- package/skills/autoconference/references/core-principles.md +83 -0
- package/skills/autoconference/references/crash-recovery.md +104 -0
- package/skills/autoconference/references/results-logging.md +198 -0
- package/skills/autoconference/references/upstream-family-contract.md +130 -0
- package/skills/autoconference/references/visualization-guide.md +105 -0
- package/skills/autoconference/scripts/check_conference.sh +371 -0
- package/skills/autoconference/scripts/init_conference.py +625 -0
- package/skills/autoconference/scripts/style_presets.py +104 -0
- package/skills/autoresearch/LICENSE +21 -0
- package/skills/autoresearch/PROVENANCE.md +20 -0
- package/skills/autoresearch/SKILL.md +131 -0
- package/skills/autoresearch/assets/report_template.md +50 -0
- package/skills/autoresearch/assets/research_template.md +38 -0
- package/skills/autoresearch/assets/results_template.tsv +1 -0
- package/skills/autoresearch/modes/core.md +216 -0
- package/skills/autoresearch/modes/debug.md +235 -0
- package/skills/autoresearch/modes/fix.md +173 -0
- package/skills/autoresearch/modes/learn.md +91 -0
- package/skills/autoresearch/modes/plan.md +291 -0
- package/skills/autoresearch/modes/predict.md +266 -0
- package/skills/autoresearch/modes/reason.md +170 -0
- package/skills/autoresearch/modes/scenario.md +164 -0
- package/skills/autoresearch/modes/security.md +282 -0
- package/skills/autoresearch/modes/ship.md +49 -0
- package/skills/autoresearch/references/core-principles.md +80 -0
- package/skills/autoresearch/references/evaluator-contract.md +126 -0
- package/skills/autoresearch/references/investigation-techniques.md +205 -0
- package/skills/autoresearch/references/owasp-checklist.md +161 -0
- package/skills/autoresearch/references/persona-templates.md +232 -0
- package/skills/autoresearch/references/results-logging.md +96 -0
- package/skills/autoresearch/references/scenario-dimensions.md +178 -0
- package/skills/autoresearch/references/stride-model.md +196 -0
- package/skills/autoresearch/references/stuck-detection.md +107 -0
- package/skills/autoresearch/references/type-checklists.md +163 -0
- package/skills/autoresearch/references/upstream-family-contract.md +125 -0
- package/skills/autoresearch/references/visualization-guide.md +95 -0
- package/skills/autoresearch/scripts/check_progress.sh +272 -0
- package/skills/autoresearch/scripts/init_research.py +330 -0
- package/skills/autoresearch/scripts/run_with_deadline.py +164 -0
- package/skills/autoresearch/scripts/style_presets.py +104 -0
- package/skills/browser-drive/SKILL.md +133 -0
- package/skills/browser-drive/references/snapshot-act-loop.md +37 -0
- package/skills/browser-drive/scripts/capability-probe.mjs +262 -0
- package/skills/comment-checker/SKILL.md +171 -0
- package/skills/debugging/SKILL.md +202 -0
- package/skills/debugging/references/README.md +15 -0
- package/skills/debugging/references/escalation.md +43 -0
- package/skills/debugging/references/runtimes/README.md +17 -0
- package/skills/debugging/references/runtimes/bundled-js-binary.md +44 -0
- package/skills/debugging/references/runtimes/go.md +37 -0
- package/skills/debugging/references/runtimes/native-binary.md +44 -0
- package/skills/debugging/references/runtimes/node.md +43 -0
- package/skills/debugging/references/runtimes/python.md +41 -0
- package/skills/debugging/references/runtimes/rust.md +37 -0
- package/skills/debugging/references/tools.md +72 -0
- package/skills/deep-interview/SKILL.md +201 -0
- package/skills/doctor-installer/SKILL.md +252 -0
- package/skills/durable-litgoal/SKILL.md +248 -0
- package/skills/frontend-ui-ux/SKILL.md +70 -0
- package/skills/frontend-ui-ux/data/LICENSE +21 -0
- package/skills/frontend-ui-ux/data/PROVENANCE.json +1088 -0
- package/skills/frontend-ui-ux/data/THIRD-PARTY-NOTICE.txt +14 -0
- package/skills/frontend-ui-ux/data/design-intelligence.json +1 -0
- package/skills/frontend-ui-ux/references/_canonical-corpus/ATTRIBUTION.md +217 -0
- package/skills/frontend-ui-ux/references/_canonical-corpus/LICENSE +21 -0
- package/skills/frontend-ui-ux/references/_canonical-corpus/LICENSE-Apache-2.0.txt +201 -0
- package/skills/frontend-ui-ux/references/_canonical-corpus/manifest.json +867 -0
- package/skills/frontend-ui-ux/references/adaptive-layout.md +85 -0
- package/skills/frontend-ui-ux/references/brand-and-imagery.md +79 -0
- package/skills/frontend-ui-ux/references/complete-contract.md +282 -0
- package/skills/frontend-ui-ux/references/composition.md +87 -0
- package/skills/frontend-ui-ux/references/creative-directions.md +83 -0
- package/skills/frontend-ui-ux/references/design/README.md +248 -0
- package/skills/frontend-ui-ux/references/design/_INDEX.md +191 -0
- package/skills/frontend-ui-ux/references/design/airbnb.md +393 -0
- package/skills/frontend-ui-ux/references/design/airtable.md +92 -0
- package/skills/frontend-ui-ux/references/design/apple.md +250 -0
- package/skills/frontend-ui-ux/references/design/aside.md +209 -0
- package/skills/frontend-ui-ux/references/design/binance.md +348 -0
- package/skills/frontend-ui-ux/references/design/bmw.md +183 -0
- package/skills/frontend-ui-ux/references/design/brutalist-skill.md +92 -0
- package/skills/frontend-ui-ux/references/design/bugatti.md +271 -0
- package/skills/frontend-ui-ux/references/design/cal.md +262 -0
- package/skills/frontend-ui-ux/references/design/claude.md +315 -0
- package/skills/frontend-ui-ux/references/design/clay.md +307 -0
- package/skills/frontend-ui-ux/references/design/clickhouse.md +284 -0
- package/skills/frontend-ui-ux/references/design/clone-from-url.md +65 -0
- package/skills/frontend-ui-ux/references/design/cohere.md +269 -0
- package/skills/frontend-ui-ux/references/design/coinbase.md +132 -0
- package/skills/frontend-ui-ux/references/design/composio.md +310 -0
- package/skills/frontend-ui-ux/references/design/cursor.md +312 -0
- package/skills/frontend-ui-ux/references/design/design-system-architecture.md +244 -0
- package/skills/frontend-ui-ux/references/design/elevenlabs.md +268 -0
- package/skills/frontend-ui-ux/references/design/expo.md +284 -0
- package/skills/frontend-ui-ux/references/design/ferrari.md +317 -0
- package/skills/frontend-ui-ux/references/design/figma.md +223 -0
- package/skills/frontend-ui-ux/references/design/framer.md +249 -0
- package/skills/frontend-ui-ux/references/design/gpt-tasteskill.md +74 -0
- package/skills/frontend-ui-ux/references/design/hashicorp.md +281 -0
- package/skills/frontend-ui-ux/references/design/ibm.md +335 -0
- package/skills/frontend-ui-ux/references/design/image-to-code-skill.md +1228 -0
- package/skills/frontend-ui-ux/references/design/imagegen-brandkit.md +798 -0
- package/skills/frontend-ui-ux/references/design/imagegen-frontend-mobile.md +1465 -0
- package/skills/frontend-ui-ux/references/design/imagegen-frontend-web.md +987 -0
- package/skills/frontend-ui-ux/references/design/intercom.md +149 -0
- package/skills/frontend-ui-ux/references/design/kraken.md +128 -0
- package/skills/frontend-ui-ux/references/design/lamborghini.md +291 -0
- package/skills/frontend-ui-ux/references/design/layout-skill.md +107 -0
- package/skills/frontend-ui-ux/references/design/lazyweb.md +77 -0
- package/skills/frontend-ui-ux/references/design/linear.app.md +370 -0
- package/skills/frontend-ui-ux/references/design/lovable.md +301 -0
- package/skills/frontend-ui-ux/references/design/mastercard.md +368 -0
- package/skills/frontend-ui-ux/references/design/meta.md +369 -0
- package/skills/frontend-ui-ux/references/design/minimalist-skill.md +85 -0
- package/skills/frontend-ui-ux/references/design/minimax.md +260 -0
- package/skills/frontend-ui-ux/references/design/mintlify.md +329 -0
- package/skills/frontend-ui-ux/references/design/miro.md +111 -0
- package/skills/frontend-ui-ux/references/design/mistral.ai.md +264 -0
- package/skills/frontend-ui-ux/references/design/mongodb.md +269 -0
- package/skills/frontend-ui-ux/references/design/nike.md +366 -0
- package/skills/frontend-ui-ux/references/design/notion.md +312 -0
- package/skills/frontend-ui-ux/references/design/nvidia.md +296 -0
- package/skills/frontend-ui-ux/references/design/ollama.md +270 -0
- package/skills/frontend-ui-ux/references/design/opencode.ai.md +284 -0
- package/skills/frontend-ui-ux/references/design/output-skill.md +49 -0
- package/skills/frontend-ui-ux/references/design/pinterest.md +233 -0
- package/skills/frontend-ui-ux/references/design/playstation.md +367 -0
- package/skills/frontend-ui-ux/references/design/posthog.md +259 -0
- package/skills/frontend-ui-ux/references/design/raycast.md +271 -0
- package/skills/frontend-ui-ux/references/design/react-dev-tooling-skill.md +230 -0
- package/skills/frontend-ui-ux/references/design/redesign-skill.md +178 -0
- package/skills/frontend-ui-ux/references/design/renault.md +314 -0
- package/skills/frontend-ui-ux/references/design/replicate.md +264 -0
- package/skills/frontend-ui-ux/references/design/resend.md +306 -0
- package/skills/frontend-ui-ux/references/design/revolut.md +188 -0
- package/skills/frontend-ui-ux/references/design/runwayml.md +247 -0
- package/skills/frontend-ui-ux/references/design/sanity.md +360 -0
- package/skills/frontend-ui-ux/references/design/sentry.md +265 -0
- package/skills/frontend-ui-ux/references/design/shopify.md +353 -0
- package/skills/frontend-ui-ux/references/design/soft-skill.md +98 -0
- package/skills/frontend-ui-ux/references/design/spacex.md +197 -0
- package/skills/frontend-ui-ux/references/design/spotify.md +249 -0
- package/skills/frontend-ui-ux/references/design/starbucks.md +583 -0
- package/skills/frontend-ui-ux/references/design/stitch-design-example.md +121 -0
- package/skills/frontend-ui-ux/references/design/stitch-skill.md +184 -0
- package/skills/frontend-ui-ux/references/design/stripe.md +325 -0
- package/skills/frontend-ui-ux/references/design/supabase.md +258 -0
- package/skills/frontend-ui-ux/references/design/superhuman.md +255 -0
- package/skills/frontend-ui-ux/references/design/taste-skill.md +1206 -0
- package/skills/frontend-ui-ux/references/design/tesla.md +289 -0
- package/skills/frontend-ui-ux/references/design/theverge.md +342 -0
- package/skills/frontend-ui-ux/references/design/together.ai.md +266 -0
- package/skills/frontend-ui-ux/references/design/uber.md +298 -0
- package/skills/frontend-ui-ux/references/design/vercel.md +313 -0
- package/skills/frontend-ui-ux/references/design/vodafone.md +426 -0
- package/skills/frontend-ui-ux/references/design/voltagent.md +326 -0
- package/skills/frontend-ui-ux/references/design/warp.md +256 -0
- package/skills/frontend-ui-ux/references/design/webflow.md +95 -0
- package/skills/frontend-ui-ux/references/design/wired.md +281 -0
- package/skills/frontend-ui-ux/references/design/wise.md +176 -0
- package/skills/frontend-ui-ux/references/design/x.ai.md +260 -0
- package/skills/frontend-ui-ux/references/design/zapier.md +331 -0
- package/skills/frontend-ui-ux/references/designpowers/EVIDENCE.md +97 -0
- package/skills/frontend-ui-ux/references/designpowers/README.md +48 -0
- package/skills/frontend-ui-ux/references/designpowers/UPSTREAM.md +80 -0
- package/skills/frontend-ui-ux/references/designpowers/lane-a-direction.md +64 -0
- package/skills/frontend-ui-ux/references/designpowers/lane-b-execution.md +65 -0
- package/skills/frontend-ui-ux/references/designpowers/lane-c-review.md +65 -0
- package/skills/frontend-ui-ux/references/designpowers/lane-d-memory.md +83 -0
- package/skills/frontend-ui-ux/references/designpowers/orchestration.md +80 -0
- package/skills/frontend-ui-ux/references/designpowers/routing.md +79 -0
- package/skills/frontend-ui-ux/references/designpowers/vendor/LICENSE +21 -0
- package/skills/frontend-ui-ux/references/designpowers/vendor/agents/accessibility-reviewer.md +83 -0
- package/skills/frontend-ui-ux/references/designpowers/vendor/agents/content-writer.md +132 -0
- package/skills/frontend-ui-ux/references/designpowers/vendor/agents/design-builder.md +109 -0
- package/skills/frontend-ui-ux/references/designpowers/vendor/agents/design-critic.md +89 -0
- package/skills/frontend-ui-ux/references/designpowers/vendor/agents/design-lead.md +113 -0
- package/skills/frontend-ui-ux/references/designpowers/vendor/agents/design-scout.md +78 -0
- package/skills/frontend-ui-ux/references/designpowers/vendor/agents/design-strategist.md +121 -0
- package/skills/frontend-ui-ux/references/designpowers/vendor/agents/heuristic-evaluator.md +268 -0
- package/skills/frontend-ui-ux/references/designpowers/vendor/agents/inspiration-scout.md +107 -0
- package/skills/frontend-ui-ux/references/designpowers/vendor/agents/motion-designer.md +120 -0
- package/skills/frontend-ui-ux/references/designpowers/vendor/skills/accessible-content/reference.md +101 -0
- package/skills/frontend-ui-ux/references/designpowers/vendor/skills/adaptive-interfaces/reference.md +109 -0
- package/skills/frontend-ui-ux/references/designpowers/vendor/skills/cognitive-accessibility/reference.md +107 -0
- package/skills/frontend-ui-ux/references/designpowers/vendor/skills/design-debate/reference.md +199 -0
- package/skills/frontend-ui-ux/references/designpowers/vendor/skills/design-debt-tracker/reference.md +174 -0
- package/skills/frontend-ui-ux/references/designpowers/vendor/skills/design-handoff/reference.md +125 -0
- package/skills/frontend-ui-ux/references/designpowers/vendor/skills/design-md/reference.md +106 -0
- package/skills/frontend-ui-ux/references/designpowers/vendor/skills/design-retrospective/reference.md +266 -0
- package/skills/frontend-ui-ux/references/designpowers/vendor/skills/design-review/reference.md +123 -0
- package/skills/frontend-ui-ux/references/designpowers/vendor/skills/design-system-alignment/reference.md +120 -0
- package/skills/frontend-ui-ux/references/designpowers/vendor/skills/designpowers-critique/reference.md +164 -0
- package/skills/frontend-ui-ux/references/designpowers/vendor/skills/heuristic-evaluation/reference.md +85 -0
- package/skills/frontend-ui-ux/references/designpowers/vendor/skills/inclusive-personas/reference.md +98 -0
- package/skills/frontend-ui-ux/references/designpowers/vendor/skills/inspiration-scouting/reference.md +165 -0
- package/skills/frontend-ui-ux/references/designpowers/vendor/skills/interaction-design/reference.md +122 -0
- package/skills/frontend-ui-ux/references/designpowers/vendor/skills/motion-choreography/reference.md +81 -0
- package/skills/frontend-ui-ux/references/designpowers/vendor/skills/research-planning/reference.md +96 -0
- package/skills/frontend-ui-ux/references/designpowers/vendor/skills/responsive-patterns/reference.md +77 -0
- package/skills/frontend-ui-ux/references/designpowers/vendor/skills/synthetic-user-testing/reference.md +192 -0
- package/skills/frontend-ui-ux/references/designpowers/vendor/skills/taste-feedback/reference.md +165 -0
- package/skills/frontend-ui-ux/references/designpowers/vendor/skills/taste-report/reference.md +78 -0
- package/skills/frontend-ui-ux/references/designpowers/vendor/skills/token-architecture/reference.md +75 -0
- package/skills/frontend-ui-ux/references/designpowers/vendor/skills/ui-composition/reference.md +117 -0
- package/skills/frontend-ui-ux/references/designpowers/vendor/skills/usability-testing/reference.md +78 -0
- package/skills/frontend-ui-ux/references/designpowers/vendor/skills/verification-before-shipping/reference.md +125 -0
- package/skills/frontend-ui-ux/references/designpowers/vendor/skills/voice-and-tone/reference.md +79 -0
- package/skills/frontend-ui-ux/references/designpowers/vendor/skills/writing-design-plans/reference.md +119 -0
- package/skills/frontend-ui-ux/references/evidence-review.md +103 -0
- package/skills/frontend-ui-ux/references/implementation-platforms.md +94 -0
- package/skills/frontend-ui-ux/references/inclusive-interface.md +85 -0
- package/skills/frontend-ui-ux/references/interaction-motion.md +93 -0
- package/skills/frontend-ui-ux/references/operating-lanes.md +80 -0
- package/skills/frontend-ui-ux/references/perfection/README.md +160 -0
- package/skills/frontend-ui-ux/references/perfection/react-perf-tooling.md +127 -0
- package/skills/frontend-ui-ux/references/performance-delivery.md +77 -0
- package/skills/frontend-ui-ux/references/product-direction.md +84 -0
- package/skills/frontend-ui-ux/references/redesign-playbook.md +88 -0
- package/skills/frontend-ui-ux/references/system-foundations.md +86 -0
- package/skills/frontend-ui-ux/references/taste-direction.md +55 -0
- package/skills/frontend-ui-ux/references/ui-ux-db/README.md +659 -0
- package/skills/frontend-ui-ux/references/ui-ux-db/data/charts.csv +26 -0
- package/skills/frontend-ui-ux/references/ui-ux-db/data/colors.csv +162 -0
- package/skills/frontend-ui-ux/references/ui-ux-db/data/icons.csv +106 -0
- package/skills/frontend-ui-ux/references/ui-ux-db/data/landing.csv +35 -0
- package/skills/frontend-ui-ux/references/ui-ux-db/data/products.csv +162 -0
- package/skills/frontend-ui-ux/references/ui-ux-db/data/react-performance.csv +45 -0
- package/skills/frontend-ui-ux/references/ui-ux-db/data/stacks/astro.csv +54 -0
- package/skills/frontend-ui-ux/references/ui-ux-db/data/stacks/flutter.csv +53 -0
- package/skills/frontend-ui-ux/references/ui-ux-db/data/stacks/html-tailwind.csv +56 -0
- package/skills/frontend-ui-ux/references/ui-ux-db/data/stacks/jetpack-compose.csv +53 -0
- package/skills/frontend-ui-ux/references/ui-ux-db/data/stacks/nextjs.csv +53 -0
- package/skills/frontend-ui-ux/references/ui-ux-db/data/stacks/nuxt-ui.csv +51 -0
- package/skills/frontend-ui-ux/references/ui-ux-db/data/stacks/nuxtjs.csv +59 -0
- package/skills/frontend-ui-ux/references/ui-ux-db/data/stacks/react-native.csv +52 -0
- package/skills/frontend-ui-ux/references/ui-ux-db/data/stacks/react.csv +54 -0
- package/skills/frontend-ui-ux/references/ui-ux-db/data/stacks/shadcn.csv +61 -0
- package/skills/frontend-ui-ux/references/ui-ux-db/data/stacks/svelte.csv +54 -0
- package/skills/frontend-ui-ux/references/ui-ux-db/data/stacks/swiftui.csv +51 -0
- package/skills/frontend-ui-ux/references/ui-ux-db/data/stacks/vue.csv +50 -0
- package/skills/frontend-ui-ux/references/ui-ux-db/data/styles.csv +85 -0
- package/skills/frontend-ui-ux/references/ui-ux-db/data/typography.csv +74 -0
- package/skills/frontend-ui-ux/references/ui-ux-db/data/ui-reasoning.csv +162 -0
- package/skills/frontend-ui-ux/references/ui-ux-db/data/ux-guidelines.csv +100 -0
- package/skills/frontend-ui-ux/references/ui-ux-db/data/web-interface.csv +31 -0
- package/skills/frontend-ui-ux/references/ui-ux-db/scripts/core.py +262 -0
- package/skills/frontend-ui-ux/references/ui-ux-db/scripts/design_system.py +1148 -0
- package/skills/frontend-ui-ux/references/ui-ux-db/scripts/search.py +114 -0
- package/skills/frontend-ui-ux/references/visual-language.md +84 -0
- package/skills/frontend-ui-ux/references/visual-reconstruction.md +87 -0
- package/skills/frontend-ui-ux/schemas/design-contract-v1alpha1.json +570 -0
- package/skills/frontend-ui-ux/schemas/design-contract-v1beta1.json +32 -0
- package/skills/frontend-ui-ux/schemas/design-contract-v1beta2.json +34 -0
- package/skills/frontend-ui-ux/scripts/bounded-json.mjs +45 -0
- package/skills/frontend-ui-ux/scripts/canonical-json.mjs +26 -0
- package/skills/frontend-ui-ux/scripts/contract-error.mjs +15 -0
- package/skills/frontend-ui-ux/scripts/csv.mjs +64 -0
- package/skills/frontend-ui-ux/scripts/dataset.mjs +65 -0
- package/skills/frontend-ui-ux/scripts/design-contract.mjs +609 -0
- package/skills/frontend-ui-ux/scripts/import-design-intelligence.mjs +193 -0
- package/skills/frontend-ui-ux/scripts/retrieval.mjs +92 -0
- package/skills/frontend-ui-ux/scripts/stable-file-read.mjs +237 -0
- package/skills/frontend-ui-ux/scripts/stdin-json.mjs +16 -0
- package/skills/frontend-ui-ux/scripts/strict-json.mjs +102 -0
- package/skills/frontend-ui-ux/scripts/uiux.mjs +86 -0
- package/skills/frontend-ui-ux/scripts/verify-canonical-corpus.mjs +266 -0
- package/skills/lit-burnoff/SKILL.md +227 -0
- package/skills/lit-burnoff-file/SKILL.md +175 -0
- package/skills/lit-code/SKILL.md +266 -0
- package/skills/lit-code/references/README.md +18 -0
- package/skills/lit-code/references/go/README.md +12 -0
- package/skills/lit-code/references/go/concurrency.md +42 -0
- package/skills/lit-code/references/go/error-handling.md +47 -0
- package/skills/lit-code/references/go/testing.md +55 -0
- package/skills/lit-code/references/go/tooling.md +35 -0
- package/skills/lit-code/references/go/type-patterns.md +50 -0
- package/skills/lit-code/references/python/README.md +12 -0
- package/skills/lit-code/references/python/async.md +50 -0
- package/skills/lit-code/references/python/error-handling.md +44 -0
- package/skills/lit-code/references/python/testing.md +50 -0
- package/skills/lit-code/references/python/tooling.md +38 -0
- package/skills/lit-code/references/python/type-patterns.md +46 -0
- package/skills/lit-code/references/rust/README.md +12 -0
- package/skills/lit-code/references/rust/concurrency.md +45 -0
- package/skills/lit-code/references/rust/error-handling.md +43 -0
- package/skills/lit-code/references/rust/tooling.md +36 -0
- package/skills/lit-code/references/rust/type-patterns.md +46 -0
- package/skills/lit-code/references/rust/unsafe.md +47 -0
- package/skills/lit-code/references/typescript/README.md +11 -0
- package/skills/lit-code/references/typescript/error-handling.md +56 -0
- package/skills/lit-code/references/typescript/testing.md +42 -0
- package/skills/lit-code/references/typescript/tsconfig-strict.md +40 -0
- package/skills/lit-code/references/typescript/type-patterns.md +60 -0
- package/skills/lit-commit/SKILL.md +222 -0
- package/skills/lit-comprehend/SKILL.md +278 -0
- package/skills/lit-comprehend/assets/explainer-scaffold.html +104 -0
- package/skills/lit-comprehend/references/artifact-template.md +114 -0
- package/skills/lit-comprehend/references/micro-worlds.md +115 -0
- package/skills/lit-comprehend/scripts/verify-explainer.ts +339 -0
- package/skills/lit-crucible/SKILL.md +212 -0
- package/skills/lit-fetch/SKILL.md +242 -0
- package/skills/lit-handoff/SKILL.md +199 -0
- package/skills/lit-init/SKILL.md +214 -0
- package/skills/lit-korean/SKILL.md +231 -0
- package/skills/lit-plan/SKILL.md +351 -0
- package/skills/lit-plan/scripts/scaffold-plan.mjs +275 -0
- package/skills/lit-recap/SKILL.md +233 -0
- package/skills/lit-scientific-visualization/SKILL.md +175 -0
- package/skills/litresearch/SKILL.md +436 -0
- package/skills/litwork/SKILL.md +227 -0
- package/skills/lsp/SKILL.md +186 -0
- package/skills/lsp-setup/SKILL.md +187 -0
- package/skills/lsp-setup/references/README.md +40 -0
- package/skills/lsp-setup/references/bash.md +31 -0
- package/skills/lsp-setup/references/c-cpp.md +43 -0
- package/skills/lsp-setup/references/csharp.md +29 -0
- package/skills/lsp-setup/references/dart.md +25 -0
- package/skills/lsp-setup/references/elixir.md +30 -0
- package/skills/lsp-setup/references/go.md +33 -0
- package/skills/lsp-setup/references/haskell.md +27 -0
- package/skills/lsp-setup/references/java.md +28 -0
- package/skills/lsp-setup/references/julia.md +28 -0
- package/skills/lsp-setup/references/kotlin.md +25 -0
- package/skills/lsp-setup/references/lua.md +26 -0
- package/skills/lsp-setup/references/php.md +30 -0
- package/skills/lsp-setup/references/python.md +33 -0
- package/skills/lsp-setup/references/ruby.md +34 -0
- package/skills/lsp-setup/references/rust.md +34 -0
- package/skills/lsp-setup/references/swift.md +26 -0
- package/skills/lsp-setup/references/terraform.md +26 -0
- package/skills/lsp-setup/references/typescript.md +35 -0
- package/skills/lsp-setup/references/yaml.md +27 -0
- package/skills/lsp-setup/references/zig.md +28 -0
- package/skills/managed-skill-manifest.json +1386 -0
- package/skills/native-goal-verdict/SKILL.md +216 -0
- package/skills/refactor/SKILL.md +221 -0
- package/skills/reference-benchmark-claims/SKILL.md +204 -0
- package/skills/release-guardrails/SKILL.md +245 -0
- package/skills/review-work/SKILL.md +301 -0
- package/skills/rules/SKILL.md +196 -0
- package/skills/search-workflow-ideas/SKILL.md +223 -0
- package/skills/skill-observer/SKILL.md +148 -0
- package/skills/skill-observer/references/review-contract.md +95 -0
- package/skills/skill-rename-aliases.json +10 -0
- package/skills/start-work/SKILL.md +334 -0
- package/skills/structural-search/SKILL.md +234 -0
- package/skills/tool-guards/SKILL.md +223 -0
- package/skills/visual-qa/SKILL.md +61 -0
- package/skills/visual-qa/references/capture-playbook.md +105 -0
- package/skills/visual-qa/references/complete-contract.md +411 -0
- package/skills/visual-qa/schemas/evidence-manifest-v1alpha1.json +201 -0
- package/skills/visual-qa/schemas/evidence-manifest-v1beta1.json +141 -0
- package/skills/visual-qa/schemas/review-receipt-v1alpha1.json +113 -0
- package/skills/visual-qa/scripts/artifact.mjs +123 -0
- package/skills/visual-qa/scripts/bounded-json.mjs +47 -0
- package/skills/visual-qa/scripts/canonical-json.mjs +28 -0
- package/skills/visual-qa/scripts/capabilities.mjs +66 -0
- package/skills/visual-qa/scripts/contract-text.mjs +15 -0
- package/skills/visual-qa/scripts/design-contract.mjs +611 -0
- package/skills/visual-qa/scripts/evidence-evaluate.mjs +521 -0
- package/skills/visual-qa/scripts/evidence.mjs +271 -0
- package/skills/visual-qa/scripts/png-decode.mjs +146 -0
- package/skills/visual-qa/scripts/png.mjs +154 -0
- package/skills/visual-qa/scripts/review.mjs +188 -0
- package/skills/visual-qa/scripts/stdin-json.mjs +16 -0
- package/skills/visual-qa/scripts/strict-json.mjs +102 -0
- package/skills/visual-qa/scripts/tui.mjs +149 -0
- package/skills/visual-qa/scripts/visual-qa.mjs +90 -0
- package/skills/wikify/LICENSE +21 -0
- package/skills/wikify/PROVENANCE.md +18 -0
- package/skills/wikify/SKILL.md +176 -0
- package/skills/wikify/assets/home-template.md +44 -0
- package/skills/wikify/assets/maintenance-report-template.md +46 -0
- package/skills/wikify/assets/paper-source-note-template.md +137 -0
- package/skills/wikify/assets/source-note-template.md +45 -0
- package/skills/wikify/assets/wiki-rules-template.md +117 -0
- package/skills/wikify/modes/ingest.md +57 -0
- package/skills/wikify/modes/init.md +44 -0
- package/skills/wikify/modes/lint.md +60 -0
- package/skills/wikify/modes/query.md +38 -0
- package/skills/wikify/modes/save.md +45 -0
- package/skills/wikify/references-upstream-contract.md +758 -0
- package/skills/workflow-loop/SKILL.md +387 -0
- package/tools/check-pack-payload.mjs +410 -0
- package/tools/check-payload-substance.mjs +738 -0
- package/tools/check-version-lockstep.mjs +238 -0
- package/tools/gen-canonical-frontend-manifest.mjs +66 -0
- package/tools/gen-managed-skill-manifest.mjs +135 -0
- package/tools/harness-speed-local.mjs +261 -0
- package/tools/payload-reference-exemptions.json +49 -0
- package/tools/payload-substance-allowlist.json +46 -0
- package/tools/payload-substance-parity.json +571 -0
- package/tools/qa-real-surface-fixtures.mjs +428 -0
- package/tools/qa-real-surface-harness.mjs +173 -0
- package/tools/run-behavior-replacement-probes.mjs +296 -0
- package/tools/run-build.mjs +101 -0
- package/tools/run-harness-speed-local.mjs +52 -0
- package/tools/run-harness-speed-v2.mjs +36 -0
- package/tools/run-installed-resource-tamper-probe.mjs +62 -0
- package/tools/run-negative-gate-matrix.mjs +516 -0
- package/tools/run-rules-glob-differential.mjs +232 -0
- package/tools/run-typecheck.mjs +25 -0
- package/tools/run-uiux-visual-qa-scenarios.mjs +234 -0
- package/tools/run-wikify-surface-probe.mjs +170 -0
- package/tools/scan-legacy-tokens.mjs +431 -0
- package/tools/version-manifests.json +60 -0
- package/tsconfig.build.json +12 -0
- package/tsconfig.json +13 -0
- package/vendor/NOTICE.md +21 -0
- package/vendor/handoff/SKILL.md +199 -0
- package/vendor/handoff/evals/evals.json +154 -0
- package/vendor/handoff/examples/HANDOFF-example-generic-auth-refactor.md +97 -0
- package/vendor/handoff/templates/HANDOFF.md +121 -0
- package/vendor/licenses/022_handoff-MIT.txt +21 -0
- package/vendor/licenses/045_scientific-visualization-MIT.txt +21 -0
- package/vendor/provenance/022_handoff.md +19 -0
- package/vendor/provenance/045_scientific-visualization.md +36 -0
- package/vendor/scientific-visualization/SKILL.md +283 -0
- package/vendor/scientific-visualization/assets/color_palettes.py +197 -0
- package/vendor/scientific-visualization/assets/nature.mplstyle +75 -0
- package/vendor/scientific-visualization/assets/presentation.mplstyle +74 -0
- package/vendor/scientific-visualization/assets/publication.mplstyle +78 -0
- package/vendor/scientific-visualization/evals/evals.json +158 -0
- package/vendor/scientific-visualization/references/color_palettes.md +380 -0
- package/vendor/scientific-visualization/references/journal_requirements.md +359 -0
- package/vendor/scientific-visualization/references/matplotlib_examples.md +608 -0
- package/vendor/scientific-visualization/references/mdanalysis_martini_visualization.md +85 -0
- package/vendor/scientific-visualization/references/publication_guidelines.md +217 -0
- package/vendor/scientific-visualization/references/seaborn_for_publications.md +293 -0
- package/vendor/scientific-visualization/scripts/figure_export.py +238 -0
- package/vendor/scientific-visualization/scripts/style_presets.py +467 -0
- package/vendor/scientific-visualization/tests/test_figure_export.py +51 -0
- package/vendor/scientific-visualization/tests/test_style_presets.py +114 -0
|
@@ -0,0 +1,238 @@
|
|
|
1
|
+
#!/usr/bin/env python3
|
|
2
|
+
"""
|
|
3
|
+
Figure Export Utilities for Publication-Ready Scientific Figures
|
|
4
|
+
|
|
5
|
+
Exports matplotlib figures in publication-ready formats.
|
|
6
|
+
Default raster DPI is 600 (must be > 500 per project requirements). Vector
|
|
7
|
+
formats remain editable; DPI only affects rasterized artists embedded in them.
|
|
8
|
+
"""
|
|
9
|
+
|
|
10
|
+
import matplotlib.pyplot as plt
|
|
11
|
+
from pathlib import Path
|
|
12
|
+
from typing import List, Optional, Union
|
|
13
|
+
|
|
14
|
+
|
|
15
|
+
def save_publication_figure(
|
|
16
|
+
fig: plt.Figure,
|
|
17
|
+
filename: Union[str, Path],
|
|
18
|
+
formats: Optional[List[str]] = None,
|
|
19
|
+
dpi: int = 600,
|
|
20
|
+
transparent: bool = True,
|
|
21
|
+
bbox_inches: str = 'tight',
|
|
22
|
+
pad_inches: float = 0.1,
|
|
23
|
+
facecolor: str = 'white',
|
|
24
|
+
**kwargs
|
|
25
|
+
) -> List[Path]:
|
|
26
|
+
"""
|
|
27
|
+
Save a matplotlib figure in multiple formats with publication-quality settings.
|
|
28
|
+
|
|
29
|
+
Parameters
|
|
30
|
+
----------
|
|
31
|
+
fig : matplotlib.figure.Figure
|
|
32
|
+
The figure to save
|
|
33
|
+
filename : str or Path
|
|
34
|
+
Base filename (without extension)
|
|
35
|
+
formats : list of str, default ['pdf', 'png']
|
|
36
|
+
List of file formats to save. Options: 'pdf', 'png', 'eps', 'svg', 'tiff'
|
|
37
|
+
dpi : int, default 600
|
|
38
|
+
Resolution for raster formats (png, tiff). Must be > 500.
|
|
39
|
+
transparent : bool, default True
|
|
40
|
+
If True, save with transparent background. Journal-specific exports
|
|
41
|
+
override this to False unless explicitly changed.
|
|
42
|
+
bbox_inches : str, default 'tight'
|
|
43
|
+
Bounding box specification. 'tight' removes excess whitespace
|
|
44
|
+
pad_inches : float, default 0.1
|
|
45
|
+
Padding around the figure when bbox_inches='tight'
|
|
46
|
+
facecolor : str, default 'white'
|
|
47
|
+
Background color (ignored if transparent=True)
|
|
48
|
+
**kwargs
|
|
49
|
+
Additional keyword arguments passed to fig.savefig()
|
|
50
|
+
|
|
51
|
+
Returns
|
|
52
|
+
-------
|
|
53
|
+
list of Path
|
|
54
|
+
List of paths to saved files
|
|
55
|
+
"""
|
|
56
|
+
if formats is None:
|
|
57
|
+
formats = ['pdf', 'png']
|
|
58
|
+
|
|
59
|
+
filename = Path(filename)
|
|
60
|
+
base_name = filename.stem
|
|
61
|
+
output_dir = filename.parent
|
|
62
|
+
if not output_dir.exists():
|
|
63
|
+
raise FileNotFoundError(f"Output directory does not exist: {output_dir}")
|
|
64
|
+
|
|
65
|
+
saved_files = []
|
|
66
|
+
|
|
67
|
+
for fmt in formats:
|
|
68
|
+
output_file = output_dir / f"{base_name}.{fmt}"
|
|
69
|
+
|
|
70
|
+
save_kwargs = {
|
|
71
|
+
'dpi': dpi,
|
|
72
|
+
'bbox_inches': bbox_inches,
|
|
73
|
+
'pad_inches': pad_inches,
|
|
74
|
+
'facecolor': facecolor if not transparent else 'none',
|
|
75
|
+
'edgecolor': 'none',
|
|
76
|
+
'transparent': transparent,
|
|
77
|
+
'format': fmt,
|
|
78
|
+
}
|
|
79
|
+
|
|
80
|
+
save_kwargs.update(kwargs)
|
|
81
|
+
|
|
82
|
+
try:
|
|
83
|
+
fig.savefig(output_file, **save_kwargs)
|
|
84
|
+
saved_files.append(output_file)
|
|
85
|
+
print(f"Saved: {output_file}")
|
|
86
|
+
except Exception as e:
|
|
87
|
+
print(f"Failed to save {output_file}: {e}")
|
|
88
|
+
|
|
89
|
+
return saved_files
|
|
90
|
+
|
|
91
|
+
|
|
92
|
+
def save_for_journal(
|
|
93
|
+
fig: plt.Figure,
|
|
94
|
+
filename: Union[str, Path],
|
|
95
|
+
journal: str,
|
|
96
|
+
figure_type: str = 'combination'
|
|
97
|
+
) -> List[Path]:
|
|
98
|
+
"""
|
|
99
|
+
Save figure with journal-specific requirements.
|
|
100
|
+
|
|
101
|
+
Parameters
|
|
102
|
+
----------
|
|
103
|
+
fig : matplotlib.figure.Figure
|
|
104
|
+
The figure to save
|
|
105
|
+
filename : str or Path
|
|
106
|
+
Base filename (without extension)
|
|
107
|
+
journal : str
|
|
108
|
+
Journal name. Options: 'nature', 'science', 'cell', 'plos', 'acs', 'ieee'
|
|
109
|
+
figure_type : str, default 'combination'
|
|
110
|
+
Type of figure. Options: 'line_art', 'photo', 'combination'
|
|
111
|
+
|
|
112
|
+
Returns
|
|
113
|
+
-------
|
|
114
|
+
list of Path
|
|
115
|
+
List of paths to saved files
|
|
116
|
+
"""
|
|
117
|
+
journal = journal.lower()
|
|
118
|
+
|
|
119
|
+
journal_specs = {
|
|
120
|
+
'nature': {
|
|
121
|
+
'line_art': {'formats': ['pdf', 'eps'], 'dpi': 1000},
|
|
122
|
+
'photo': {'formats': ['tiff'], 'dpi': 600},
|
|
123
|
+
'combination': {'formats': ['pdf'], 'dpi': 600},
|
|
124
|
+
},
|
|
125
|
+
'science': {
|
|
126
|
+
'line_art': {'formats': ['eps', 'pdf'], 'dpi': 1000},
|
|
127
|
+
'photo': {'formats': ['tiff'], 'dpi': 600},
|
|
128
|
+
'combination': {'formats': ['eps'], 'dpi': 600},
|
|
129
|
+
},
|
|
130
|
+
'cell': {
|
|
131
|
+
'line_art': {'formats': ['pdf', 'eps'], 'dpi': 1000},
|
|
132
|
+
'photo': {'formats': ['tiff'], 'dpi': 600},
|
|
133
|
+
'combination': {'formats': ['pdf'], 'dpi': 600},
|
|
134
|
+
},
|
|
135
|
+
'plos': {
|
|
136
|
+
'line_art': {'formats': ['pdf', 'eps'], 'dpi': 600},
|
|
137
|
+
'photo': {'formats': ['tiff', 'png'], 'dpi': 600},
|
|
138
|
+
'combination': {'formats': ['tiff'], 'dpi': 600},
|
|
139
|
+
},
|
|
140
|
+
'acs': {
|
|
141
|
+
'line_art': {'formats': ['tiff', 'pdf'], 'dpi': 600},
|
|
142
|
+
'photo': {'formats': ['tiff'], 'dpi': 600},
|
|
143
|
+
'combination': {'formats': ['tiff'], 'dpi': 600},
|
|
144
|
+
},
|
|
145
|
+
'ieee': {
|
|
146
|
+
'line_art': {'formats': ['pdf', 'eps'], 'dpi': 600},
|
|
147
|
+
'photo': {'formats': ['tiff'], 'dpi': 600},
|
|
148
|
+
'combination': {'formats': ['pdf'], 'dpi': 600},
|
|
149
|
+
},
|
|
150
|
+
}
|
|
151
|
+
|
|
152
|
+
if journal not in journal_specs:
|
|
153
|
+
available = ', '.join(journal_specs.keys())
|
|
154
|
+
raise ValueError(f"Journal '{journal}' not recognized. Available: {available}")
|
|
155
|
+
|
|
156
|
+
if figure_type not in journal_specs[journal]:
|
|
157
|
+
available = ', '.join(journal_specs[journal].keys())
|
|
158
|
+
raise ValueError(f"Figure type '{figure_type}' not valid. Available: {available}")
|
|
159
|
+
|
|
160
|
+
specs = journal_specs[journal][figure_type]
|
|
161
|
+
|
|
162
|
+
return save_publication_figure(
|
|
163
|
+
fig=fig,
|
|
164
|
+
filename=filename,
|
|
165
|
+
formats=specs['formats'],
|
|
166
|
+
dpi=specs['dpi'],
|
|
167
|
+
transparent=False,
|
|
168
|
+
facecolor='white'
|
|
169
|
+
)
|
|
170
|
+
|
|
171
|
+
|
|
172
|
+
def check_figure_size(fig: plt.Figure, journal: str = 'nature') -> dict:
|
|
173
|
+
"""
|
|
174
|
+
Check if figure dimensions are appropriate for journal requirements.
|
|
175
|
+
|
|
176
|
+
Parameters
|
|
177
|
+
----------
|
|
178
|
+
fig : matplotlib.figure.Figure
|
|
179
|
+
The figure to check
|
|
180
|
+
journal : str, default 'nature'
|
|
181
|
+
Journal name
|
|
182
|
+
|
|
183
|
+
Returns
|
|
184
|
+
-------
|
|
185
|
+
dict
|
|
186
|
+
Dictionary with figure dimensions and compliance status
|
|
187
|
+
"""
|
|
188
|
+
journal = journal.lower()
|
|
189
|
+
|
|
190
|
+
width_inches, height_inches = fig.get_size_inches()
|
|
191
|
+
width_mm = width_inches * 25.4
|
|
192
|
+
height_mm = height_inches * 25.4
|
|
193
|
+
|
|
194
|
+
specs = {
|
|
195
|
+
'nature': {'single': 89, 'one_half': 120, 'double': 183, 'max_height': 247},
|
|
196
|
+
'science': {'single': 55, 'one_half': 120, 'double': 175, 'max_height': 233},
|
|
197
|
+
'cell': {'single': 85, 'double': 178, 'max_height': 230},
|
|
198
|
+
'plos': {'single': 83, 'one_half': 114, 'double': 173, 'max_height': 233},
|
|
199
|
+
'acs': {'single': 82.5, 'double': 178, 'max_height': 247},
|
|
200
|
+
'ieee': {'single': 89, 'double': 182, 'max_height': 247},
|
|
201
|
+
}
|
|
202
|
+
|
|
203
|
+
if journal not in specs:
|
|
204
|
+
journal_spec = specs['nature']
|
|
205
|
+
else:
|
|
206
|
+
journal_spec = specs[journal]
|
|
207
|
+
|
|
208
|
+
column_type = None
|
|
209
|
+
width_ok = False
|
|
210
|
+
|
|
211
|
+
tolerance = 5 # mm
|
|
212
|
+
for width_name in ('single', 'one_half', 'double'):
|
|
213
|
+
if width_name in journal_spec and abs(width_mm - journal_spec[width_name]) < tolerance:
|
|
214
|
+
column_type = width_name
|
|
215
|
+
width_ok = True
|
|
216
|
+
break
|
|
217
|
+
|
|
218
|
+
height_ok = height_mm <= journal_spec['max_height']
|
|
219
|
+
|
|
220
|
+
result = {
|
|
221
|
+
'width_inches': width_inches,
|
|
222
|
+
'height_inches': height_inches,
|
|
223
|
+
'width_mm': width_mm,
|
|
224
|
+
'height_mm': height_mm,
|
|
225
|
+
'journal': journal,
|
|
226
|
+
'column_type': column_type,
|
|
227
|
+
'width_ok': width_ok,
|
|
228
|
+
'height_ok': height_ok,
|
|
229
|
+
'compliant': width_ok and height_ok,
|
|
230
|
+
'recommendations': {
|
|
231
|
+
'single_column_mm': journal_spec['single'],
|
|
232
|
+
'one_half_column_mm': journal_spec.get('one_half'),
|
|
233
|
+
'double_column_mm': journal_spec['double'],
|
|
234
|
+
'max_height_mm': journal_spec['max_height'],
|
|
235
|
+
}
|
|
236
|
+
}
|
|
237
|
+
|
|
238
|
+
return result
|
|
@@ -0,0 +1,467 @@
|
|
|
1
|
+
#!/usr/bin/env python3
|
|
2
|
+
"""
|
|
3
|
+
Matplotlib Style Presets for Publication-Ready Scientific Figures
|
|
4
|
+
|
|
5
|
+
Primary style is set via rcparams(), which configures Pretendard first, Arial
|
|
6
|
+
fallback second, emergency system font fallbacks after that, inward ticks with
|
|
7
|
+
minor ticks visible, grids off, transparent tight generic export, and
|
|
8
|
+
publication-appropriate sizing.
|
|
9
|
+
"""
|
|
10
|
+
|
|
11
|
+
import matplotlib.pyplot as plt
|
|
12
|
+
import matplotlib as mpl
|
|
13
|
+
from matplotlib import rcParams
|
|
14
|
+
from matplotlib import font_manager
|
|
15
|
+
from typing import Optional, Dict, Any, Tuple
|
|
16
|
+
|
|
17
|
+
|
|
18
|
+
# Okabe-Ito colorblind-friendly palette
|
|
19
|
+
OKABE_ITO_COLORS = [
|
|
20
|
+
'#E69F00', # Orange
|
|
21
|
+
'#56B4E9', # Sky Blue
|
|
22
|
+
'#009E73', # Bluish Green
|
|
23
|
+
'#F0E442', # Yellow
|
|
24
|
+
'#0072B2', # Blue
|
|
25
|
+
'#D55E00', # Vermillion
|
|
26
|
+
'#CC79A7', # Reddish Purple
|
|
27
|
+
'#000000' # Black
|
|
28
|
+
]
|
|
29
|
+
|
|
30
|
+
# Paul Tol palettes
|
|
31
|
+
TOL_BRIGHT = ['#4477AA', '#EE6677', '#228833', '#CCBB44', '#66CCEE', '#AA3377', '#BBBBBB']
|
|
32
|
+
TOL_MUTED = ['#332288', '#88CCEE', '#44AA99', '#117733', '#999933', '#DDCC77', '#CC6677', '#882255', '#AA4499']
|
|
33
|
+
TOL_HIGH_CONTRAST = ['#004488', '#DDAA33', '#BB5566']
|
|
34
|
+
|
|
35
|
+
# Wong palette
|
|
36
|
+
WONG_COLORS = ['#000000', '#E69F00', '#56B4E9', '#009E73', '#F0E442', '#0072B2', '#D55E00', '#CC79A7']
|
|
37
|
+
|
|
38
|
+
PREFERRED_FONT_STACK = [
|
|
39
|
+
'Pretendard',
|
|
40
|
+
'Arial',
|
|
41
|
+
'Helvetica',
|
|
42
|
+
'DejaVu Sans',
|
|
43
|
+
'AppleGothic',
|
|
44
|
+
'Noto Sans CJK KR',
|
|
45
|
+
'Noto Sans CJK SC',
|
|
46
|
+
'Noto Sans CJK JP',
|
|
47
|
+
'Malgun Gothic',
|
|
48
|
+
]
|
|
49
|
+
|
|
50
|
+
JOURNAL_CONFIGS = {
|
|
51
|
+
'nature': {
|
|
52
|
+
'widths': {'single': 89, 'one_half': 120, 'double': 183},
|
|
53
|
+
'max_height': 247,
|
|
54
|
+
'style': 'nature',
|
|
55
|
+
},
|
|
56
|
+
'science': {
|
|
57
|
+
'widths': {'single': 55, 'one_half': 120, 'double': 175},
|
|
58
|
+
'max_height': 233,
|
|
59
|
+
'style': 'science',
|
|
60
|
+
},
|
|
61
|
+
'cell': {
|
|
62
|
+
'widths': {'single': 85, 'double': 178},
|
|
63
|
+
'max_height': 230,
|
|
64
|
+
'style': 'cell',
|
|
65
|
+
},
|
|
66
|
+
'plos': {
|
|
67
|
+
'widths': {'single': 83, 'one_half': 114, 'double': 173},
|
|
68
|
+
'max_height': 233,
|
|
69
|
+
'style': 'default',
|
|
70
|
+
},
|
|
71
|
+
'acs': {
|
|
72
|
+
'widths': {'single': 82.5, 'double': 178},
|
|
73
|
+
'max_height': 247,
|
|
74
|
+
'style': 'default',
|
|
75
|
+
},
|
|
76
|
+
'ieee': {
|
|
77
|
+
'widths': {'single': 89, 'double': 182},
|
|
78
|
+
'max_height': 247,
|
|
79
|
+
'style': 'default',
|
|
80
|
+
},
|
|
81
|
+
}
|
|
82
|
+
|
|
83
|
+
|
|
84
|
+
def _available_preferred_fonts() -> list:
|
|
85
|
+
"""Return installed fonts from the preferred publication fallback stack."""
|
|
86
|
+
available_fonts = {f.name for f in font_manager.fontManager.ttflist}
|
|
87
|
+
installed = [name for name in PREFERRED_FONT_STACK if name in available_fonts]
|
|
88
|
+
return installed or PREFERRED_FONT_STACK
|
|
89
|
+
|
|
90
|
+
|
|
91
|
+
def rcparams():
|
|
92
|
+
"""
|
|
93
|
+
Apply the canonical publication style. This is the primary style function
|
|
94
|
+
that must be called at the start of every figure script.
|
|
95
|
+
|
|
96
|
+
Sets Pretendard first and Arial fallback second, then emergency system
|
|
97
|
+
fallbacks, inward ticks with minor ticks, and publication-appropriate font
|
|
98
|
+
sizes.
|
|
99
|
+
"""
|
|
100
|
+
rcParams['figure.figsize'] = 5, 4
|
|
101
|
+
rcParams['font.family'] = 'sans-serif'
|
|
102
|
+
|
|
103
|
+
rcParams['font.sans-serif'] = _available_preferred_fonts()
|
|
104
|
+
rcParams['pdf.fonttype'] = 42
|
|
105
|
+
rcParams['ps.fonttype'] = 42
|
|
106
|
+
rcParams['svg.fonttype'] = 'none'
|
|
107
|
+
|
|
108
|
+
# Label should be far away from the axes
|
|
109
|
+
rcParams['axes.labelpad'] = 8
|
|
110
|
+
rcParams['xtick.major.pad'] = 7
|
|
111
|
+
rcParams['ytick.major.pad'] = 7
|
|
112
|
+
|
|
113
|
+
# Add minor ticks
|
|
114
|
+
rcParams['xtick.minor.visible'] = True
|
|
115
|
+
rcParams['ytick.minor.visible'] = True
|
|
116
|
+
|
|
117
|
+
# Tick width
|
|
118
|
+
rcParams['xtick.major.width'] = 1
|
|
119
|
+
rcParams['ytick.major.width'] = 1
|
|
120
|
+
rcParams['xtick.minor.width'] = 0.5
|
|
121
|
+
rcParams['ytick.minor.width'] = 0.5
|
|
122
|
+
|
|
123
|
+
# Tick length
|
|
124
|
+
rcParams['xtick.major.size'] = 5
|
|
125
|
+
rcParams['ytick.major.size'] = 5
|
|
126
|
+
rcParams['xtick.minor.size'] = 3
|
|
127
|
+
rcParams['ytick.minor.size'] = 3
|
|
128
|
+
|
|
129
|
+
# Tick color
|
|
130
|
+
rcParams['xtick.color'] = 'black'
|
|
131
|
+
rcParams['ytick.color'] = 'black'
|
|
132
|
+
|
|
133
|
+
rcParams['font.size'] = 14
|
|
134
|
+
rcParams['axes.titlepad'] = 10
|
|
135
|
+
rcParams['axes.titleweight'] = 'normal'
|
|
136
|
+
rcParams['axes.titlesize'] = 18
|
|
137
|
+
|
|
138
|
+
# Axes settings
|
|
139
|
+
rcParams['axes.labelweight'] = 'normal'
|
|
140
|
+
rcParams['xtick.labelsize'] = 12
|
|
141
|
+
rcParams['ytick.labelsize'] = 12
|
|
142
|
+
rcParams['axes.labelsize'] = 16
|
|
143
|
+
rcParams['xtick.direction'] = 'in'
|
|
144
|
+
rcParams['ytick.direction'] = 'in'
|
|
145
|
+
|
|
146
|
+
# Additional publication defaults
|
|
147
|
+
rcParams['axes.linewidth'] = 1
|
|
148
|
+
rcParams['axes.edgecolor'] = 'black'
|
|
149
|
+
rcParams['axes.labelcolor'] = 'black'
|
|
150
|
+
rcParams['axes.axisbelow'] = True
|
|
151
|
+
rcParams['axes.grid'] = False
|
|
152
|
+
rcParams['axes.prop_cycle'] = mpl.cycler(color=OKABE_ITO_COLORS)
|
|
153
|
+
|
|
154
|
+
# Figure
|
|
155
|
+
rcParams['figure.dpi'] = 100
|
|
156
|
+
rcParams['figure.facecolor'] = 'white'
|
|
157
|
+
rcParams['figure.autolayout'] = False
|
|
158
|
+
|
|
159
|
+
# Lines
|
|
160
|
+
rcParams['lines.linewidth'] = 1.5
|
|
161
|
+
rcParams['lines.markersize'] = 5
|
|
162
|
+
rcParams['lines.markeredgewidth'] = 0.5
|
|
163
|
+
|
|
164
|
+
# Legend — black border, fully opaque
|
|
165
|
+
rcParams['legend.fontsize'] = 12
|
|
166
|
+
rcParams['legend.frameon'] = True
|
|
167
|
+
rcParams['legend.edgecolor'] = 'black'
|
|
168
|
+
rcParams['legend.framealpha'] = 1
|
|
169
|
+
rcParams['legend.loc'] = 'best'
|
|
170
|
+
|
|
171
|
+
# Savefig — DPI > 500
|
|
172
|
+
rcParams['savefig.dpi'] = 600
|
|
173
|
+
rcParams['savefig.format'] = 'pdf'
|
|
174
|
+
rcParams['savefig.bbox'] = 'tight'
|
|
175
|
+
rcParams['savefig.pad_inches'] = 0.05
|
|
176
|
+
rcParams['savefig.transparent'] = True
|
|
177
|
+
rcParams['savefig.facecolor'] = 'none'
|
|
178
|
+
|
|
179
|
+
# Image
|
|
180
|
+
rcParams['image.cmap'] = 'viridis'
|
|
181
|
+
rcParams['image.aspect'] = 'auto'
|
|
182
|
+
|
|
183
|
+
|
|
184
|
+
# Keep backward compatibility
|
|
185
|
+
def apply_publication_style(style_name: str = 'default') -> None:
|
|
186
|
+
"""
|
|
187
|
+
Apply a pre-configured publication style.
|
|
188
|
+
|
|
189
|
+
Calls rcparams() first, then applies journal-specific overrides.
|
|
190
|
+
|
|
191
|
+
Parameters
|
|
192
|
+
----------
|
|
193
|
+
style_name : str, default 'default'
|
|
194
|
+
Name of the style to apply. Options:
|
|
195
|
+
- 'default': General publication style (rcparams)
|
|
196
|
+
- 'nature': Nature journal style
|
|
197
|
+
- 'science': Science journal style
|
|
198
|
+
- 'cell': Cell Press style
|
|
199
|
+
- 'minimal': Minimal clean style
|
|
200
|
+
- 'presentation': Larger fonts for presentations
|
|
201
|
+
"""
|
|
202
|
+
# Always start from rcparams base
|
|
203
|
+
rcparams()
|
|
204
|
+
|
|
205
|
+
# Style-specific modifications (overlaid on rcparams)
|
|
206
|
+
if style_name == 'nature':
|
|
207
|
+
mpl.rcParams.update({
|
|
208
|
+
'font.size': 7,
|
|
209
|
+
'axes.labelsize': 8,
|
|
210
|
+
'axes.titlesize': 8,
|
|
211
|
+
'xtick.labelsize': 6,
|
|
212
|
+
'ytick.labelsize': 6,
|
|
213
|
+
'legend.fontsize': 6,
|
|
214
|
+
'savefig.transparent': False,
|
|
215
|
+
'savefig.facecolor': 'white',
|
|
216
|
+
})
|
|
217
|
+
|
|
218
|
+
elif style_name == 'science':
|
|
219
|
+
mpl.rcParams.update({
|
|
220
|
+
'font.size': 7,
|
|
221
|
+
'axes.labelsize': 8,
|
|
222
|
+
'xtick.labelsize': 6,
|
|
223
|
+
'ytick.labelsize': 6,
|
|
224
|
+
'legend.fontsize': 6,
|
|
225
|
+
'savefig.transparent': False,
|
|
226
|
+
'savefig.facecolor': 'white',
|
|
227
|
+
})
|
|
228
|
+
|
|
229
|
+
elif style_name == 'cell':
|
|
230
|
+
mpl.rcParams.update({
|
|
231
|
+
'font.size': 8,
|
|
232
|
+
'axes.labelsize': 9,
|
|
233
|
+
'xtick.labelsize': 7,
|
|
234
|
+
'ytick.labelsize': 7,
|
|
235
|
+
'legend.fontsize': 7,
|
|
236
|
+
'savefig.transparent': False,
|
|
237
|
+
'savefig.facecolor': 'white',
|
|
238
|
+
})
|
|
239
|
+
|
|
240
|
+
elif style_name == 'minimal':
|
|
241
|
+
mpl.rcParams.update({
|
|
242
|
+
'axes.linewidth': 0.8,
|
|
243
|
+
'lines.linewidth': 2,
|
|
244
|
+
})
|
|
245
|
+
|
|
246
|
+
elif style_name == 'presentation':
|
|
247
|
+
mpl.rcParams.update({
|
|
248
|
+
'font.size': 14,
|
|
249
|
+
'axes.labelsize': 16,
|
|
250
|
+
'axes.titlesize': 18,
|
|
251
|
+
'xtick.labelsize': 12,
|
|
252
|
+
'ytick.labelsize': 12,
|
|
253
|
+
'legend.fontsize': 12,
|
|
254
|
+
'axes.linewidth': 1.5,
|
|
255
|
+
'lines.linewidth': 2.5,
|
|
256
|
+
'lines.markersize': 8,
|
|
257
|
+
})
|
|
258
|
+
|
|
259
|
+
elif style_name != 'default':
|
|
260
|
+
print(f"Warning: Style '{style_name}' not recognized. Using 'default'.")
|
|
261
|
+
|
|
262
|
+
|
|
263
|
+
def set_color_palette(palette_name: str = 'okabe_ito') -> None:
|
|
264
|
+
"""
|
|
265
|
+
Set a colorblind-friendly color palette.
|
|
266
|
+
|
|
267
|
+
Parameters
|
|
268
|
+
----------
|
|
269
|
+
palette_name : str, default 'okabe_ito'
|
|
270
|
+
Name of the palette. Options:
|
|
271
|
+
'okabe_ito', 'wong', 'tol_bright', 'tol_muted', 'tol_high_contrast'
|
|
272
|
+
"""
|
|
273
|
+
palettes = {
|
|
274
|
+
'okabe_ito': OKABE_ITO_COLORS,
|
|
275
|
+
'wong': WONG_COLORS,
|
|
276
|
+
'tol_bright': TOL_BRIGHT,
|
|
277
|
+
'tol_muted': TOL_MUTED,
|
|
278
|
+
'tol_high_contrast': TOL_HIGH_CONTRAST,
|
|
279
|
+
}
|
|
280
|
+
|
|
281
|
+
if palette_name not in palettes:
|
|
282
|
+
available = ', '.join(palettes.keys())
|
|
283
|
+
print(f"Warning: Palette '{palette_name}' not found. Available: {available}")
|
|
284
|
+
palette_name = 'okabe_ito'
|
|
285
|
+
|
|
286
|
+
colors = palettes[palette_name]
|
|
287
|
+
plt.rcParams['axes.prop_cycle'] = plt.cycler(color=colors)
|
|
288
|
+
|
|
289
|
+
|
|
290
|
+
def figure_size_for_journal(
|
|
291
|
+
journal: str,
|
|
292
|
+
figure_width: str = 'single',
|
|
293
|
+
aspect: float = 0.75,
|
|
294
|
+
) -> Tuple[float, float]:
|
|
295
|
+
"""
|
|
296
|
+
Return a journal-safe figure size in inches.
|
|
297
|
+
|
|
298
|
+
Parameters
|
|
299
|
+
----------
|
|
300
|
+
journal : str
|
|
301
|
+
Journal name: 'nature', 'science', 'cell', 'plos', 'acs', 'ieee'
|
|
302
|
+
figure_width : str, default 'single'
|
|
303
|
+
Figure width: 'single', 'one_half' where supported, or 'double'
|
|
304
|
+
aspect : float, default 0.75
|
|
305
|
+
Height / width ratio before max-height clipping.
|
|
306
|
+
"""
|
|
307
|
+
journal = journal.lower()
|
|
308
|
+
if journal not in JOURNAL_CONFIGS:
|
|
309
|
+
available = ', '.join(JOURNAL_CONFIGS.keys())
|
|
310
|
+
raise ValueError(f"Journal '{journal}' not recognized. Available: {available}")
|
|
311
|
+
|
|
312
|
+
config = JOURNAL_CONFIGS[journal]
|
|
313
|
+
widths = config['widths']
|
|
314
|
+
if figure_width not in widths:
|
|
315
|
+
available = ', '.join(widths.keys())
|
|
316
|
+
raise ValueError(f"Figure width '{figure_width}' not valid for {journal}. Available: {available}")
|
|
317
|
+
|
|
318
|
+
width_inches = widths[figure_width] / 25.4
|
|
319
|
+
max_height_inches = config['max_height'] / 25.4
|
|
320
|
+
height_inches = min(width_inches * aspect, max_height_inches)
|
|
321
|
+
return width_inches, height_inches
|
|
322
|
+
|
|
323
|
+
|
|
324
|
+
def configure_for_journal(journal: str, figure_width: str = 'single', aspect: float = 0.75) -> None:
|
|
325
|
+
"""
|
|
326
|
+
Configure matplotlib for a specific journal.
|
|
327
|
+
|
|
328
|
+
Calls rcparams() first, then applies journal-specific size and font overrides.
|
|
329
|
+
|
|
330
|
+
Parameters
|
|
331
|
+
----------
|
|
332
|
+
journal : str
|
|
333
|
+
Journal name: 'nature', 'science', 'cell', 'plos', 'acs', 'ieee'
|
|
334
|
+
figure_width : str, default 'single'
|
|
335
|
+
Figure width: 'single', 'one_half' where supported, or 'double' column
|
|
336
|
+
aspect : float, default 0.75
|
|
337
|
+
Height / width ratio before max-height clipping
|
|
338
|
+
"""
|
|
339
|
+
journal = journal.lower()
|
|
340
|
+
|
|
341
|
+
if journal not in JOURNAL_CONFIGS:
|
|
342
|
+
available = ', '.join(JOURNAL_CONFIGS.keys())
|
|
343
|
+
raise ValueError(f"Journal '{journal}' not recognized. Available: {available}")
|
|
344
|
+
|
|
345
|
+
config = JOURNAL_CONFIGS[journal]
|
|
346
|
+
|
|
347
|
+
# Apply style (which calls rcparams() internally)
|
|
348
|
+
apply_publication_style(config['style'])
|
|
349
|
+
|
|
350
|
+
plt.rcParams['figure.figsize'] = figure_size_for_journal(journal, figure_width, aspect)
|
|
351
|
+
|
|
352
|
+
|
|
353
|
+
def ensure_zero_origin_ticks(ax, x: bool = False, y: bool = False, nbins: int = 5) -> None:
|
|
354
|
+
"""Ensure axes that start at zero also have their first major tick at zero."""
|
|
355
|
+
locator = mpl.ticker.MaxNLocator(nbins=max(1, nbins - 1))
|
|
356
|
+
|
|
357
|
+
def ticks_from_zero(upper):
|
|
358
|
+
if upper <= 0:
|
|
359
|
+
return [0]
|
|
360
|
+
ticks = [tick for tick in locator.tick_values(0, upper) if 0 <= tick <= upper]
|
|
361
|
+
if not ticks or abs(ticks[0]) > 1e-12:
|
|
362
|
+
ticks.insert(0, 0)
|
|
363
|
+
if ticks[-1] < upper and len(ticks) < nbins + 1:
|
|
364
|
+
ticks.append(upper)
|
|
365
|
+
return ticks
|
|
366
|
+
|
|
367
|
+
if x:
|
|
368
|
+
left, right = ax.get_xlim()
|
|
369
|
+
if abs(left) <= 1e-12:
|
|
370
|
+
ax.set_xticks(ticks_from_zero(right))
|
|
371
|
+
ax.set_xlim(0, right)
|
|
372
|
+
|
|
373
|
+
if y:
|
|
374
|
+
bottom, top = ax.get_ylim()
|
|
375
|
+
if abs(bottom) <= 1e-12:
|
|
376
|
+
ax.set_yticks(ticks_from_zero(top))
|
|
377
|
+
ax.set_ylim(0, top)
|
|
378
|
+
|
|
379
|
+
|
|
380
|
+
def _artist_color(artist):
|
|
381
|
+
if hasattr(artist, 'get_color'):
|
|
382
|
+
return artist.get_color()
|
|
383
|
+
if hasattr(artist, 'get_facecolor'):
|
|
384
|
+
colors = artist.get_facecolor()
|
|
385
|
+
try:
|
|
386
|
+
if len(colors) == 4 and not hasattr(colors[0], '__len__'):
|
|
387
|
+
return tuple(colors)
|
|
388
|
+
if len(colors):
|
|
389
|
+
first = colors[0]
|
|
390
|
+
return tuple(first) if hasattr(first, '__len__') else tuple(colors)
|
|
391
|
+
except TypeError:
|
|
392
|
+
return colors
|
|
393
|
+
return 'black'
|
|
394
|
+
|
|
395
|
+
|
|
396
|
+
def style_legend(ax, color_text: bool = False, outside: bool = False, **kwargs):
|
|
397
|
+
"""
|
|
398
|
+
Create a publication-safe legend with black border and optional colored text.
|
|
399
|
+
|
|
400
|
+
Nature-style output should keep legend text black and use colored handles;
|
|
401
|
+
set ``color_text=True`` only when the target style explicitly wants colored
|
|
402
|
+
legend labels.
|
|
403
|
+
"""
|
|
404
|
+
legend_kwargs = {
|
|
405
|
+
'frameon': True,
|
|
406
|
+
'edgecolor': 'black',
|
|
407
|
+
'framealpha': 1,
|
|
408
|
+
}
|
|
409
|
+
if outside:
|
|
410
|
+
legend_kwargs.update({'loc': 'center left', 'bbox_to_anchor': (1.02, 0.5), 'borderaxespad': 0})
|
|
411
|
+
legend_kwargs.update(kwargs)
|
|
412
|
+
|
|
413
|
+
legend = ax.legend(**legend_kwargs)
|
|
414
|
+
legend.get_frame().set_edgecolor('black')
|
|
415
|
+
legend.get_frame().set_alpha(1)
|
|
416
|
+
handles = getattr(legend, 'legend_handles', None) or getattr(legend, 'legendHandles', None)
|
|
417
|
+
if handles is None:
|
|
418
|
+
handles, _ = ax.get_legend_handles_labels()
|
|
419
|
+
for text, handle in zip(legend.get_texts(), handles):
|
|
420
|
+
text.set_color(_artist_color(handle) if color_text else 'black')
|
|
421
|
+
return legend
|
|
422
|
+
|
|
423
|
+
|
|
424
|
+
def plot_scatter_only(ax, x, y, **kwargs):
|
|
425
|
+
"""
|
|
426
|
+
Plot independent observations as scatter only, with no connecting lines.
|
|
427
|
+
|
|
428
|
+
Use this for unordered observations, replicate clouds, correlations,
|
|
429
|
+
embeddings, and other point data where connecting observations would imply
|
|
430
|
+
a trajectory or interpolation that is not scientifically justified.
|
|
431
|
+
"""
|
|
432
|
+
kwargs.setdefault('edgecolors', 'none')
|
|
433
|
+
return ax.scatter(x, y, **kwargs)
|
|
434
|
+
|
|
435
|
+
|
|
436
|
+
def reset_to_default() -> None:
|
|
437
|
+
"""Reset matplotlib to default settings."""
|
|
438
|
+
mpl.rcdefaults()
|
|
439
|
+
|
|
440
|
+
|
|
441
|
+
def show_color_palettes() -> None:
|
|
442
|
+
"""Display available color palettes for visual inspection."""
|
|
443
|
+
palettes = {
|
|
444
|
+
'Okabe-Ito': OKABE_ITO_COLORS,
|
|
445
|
+
'Wong': WONG_COLORS,
|
|
446
|
+
'Tol Bright': TOL_BRIGHT,
|
|
447
|
+
'Tol Muted': TOL_MUTED,
|
|
448
|
+
'Tol High Contrast': TOL_HIGH_CONTRAST,
|
|
449
|
+
}
|
|
450
|
+
|
|
451
|
+
fig, axes = plt.subplots(len(palettes), 1, figsize=(8, len(palettes) * 0.5))
|
|
452
|
+
|
|
453
|
+
for ax, (name, colors) in zip(axes, palettes.items()):
|
|
454
|
+
ax.set_xlim(0, len(colors))
|
|
455
|
+
ax.set_ylim(0, 1)
|
|
456
|
+
ax.set_yticks([])
|
|
457
|
+
ax.set_xticks([])
|
|
458
|
+
ax.set_ylabel(name, fontsize=10)
|
|
459
|
+
|
|
460
|
+
for i, color in enumerate(colors):
|
|
461
|
+
ax.add_patch(plt.Rectangle((i, 0), 1, 1, facecolor=color, edgecolor='black', linewidth=0.5))
|
|
462
|
+
ax.text(i + 0.5, 0.5, color, ha='center', va='center',
|
|
463
|
+
fontsize=7, color='white' if i >= len(colors) - 1 else 'black')
|
|
464
|
+
|
|
465
|
+
fig.suptitle('Colorblind-Friendly Palettes', fontsize=12, fontweight='bold')
|
|
466
|
+
plt.tight_layout()
|
|
467
|
+
plt.show()
|