diff-grok 1.1.0 → 1.3.0
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/LICENSE +1 -1
- package/README.MD +80 -31
- package/dist/index.d.ts +6 -0
- package/{index.js → dist/index.js} +2 -1
- package/dist/index.js.map +1 -0
- package/dist/src/examples/basic-use.d.ts +10 -0
- package/dist/src/examples/basic-use.js.map +1 -0
- package/dist/src/examples/check-methods.d.ts +1 -0
- package/{src → dist/src}/examples/check-methods.js +15 -3
- package/dist/src/examples/check-methods.js.map +1 -0
- package/dist/src/examples/corr-probs.d.ts +15 -0
- package/{src → dist/src}/examples/corr-probs.js +2 -2
- package/dist/src/examples/corr-probs.js.map +1 -0
- package/dist/src/examples/cyclic-model.d.ts +6 -0
- package/dist/src/examples/cyclic-model.js.map +1 -0
- package/dist/src/examples/e5.d.ts +15 -0
- package/dist/src/examples/e5.js.map +1 -0
- package/dist/src/examples/hires.d.ts +15 -0
- package/dist/src/examples/hires.js.map +1 -0
- package/dist/src/examples/index.d.ts +22 -0
- package/dist/src/examples/index.js.map +1 -0
- package/dist/src/examples/model-updates.d.ts +6 -0
- package/dist/src/examples/model-updates.js.map +1 -0
- package/dist/src/examples/orego.d.ts +15 -0
- package/dist/src/examples/orego.js.map +1 -0
- package/dist/src/examples/pipeline-use.d.ts +6 -0
- package/dist/src/examples/pipeline-use.js.map +1 -0
- package/dist/src/examples/pollution.d.ts +15 -0
- package/dist/src/examples/pollution.js.map +1 -0
- package/{src/examples/print-benchmark.ts → dist/src/examples/print-benchmark.d.ts} +8 -58
- package/dist/src/examples/print-benchmark.js.map +1 -0
- package/dist/src/examples/robertson.d.ts +15 -0
- package/{src → dist/src}/examples/robertson.js +2 -2
- package/dist/src/examples/robertson.js.map +1 -0
- package/dist/src/examples/scripting.d.ts +1 -0
- package/dist/src/examples/scripting.js.map +1 -0
- package/dist/src/examples/vdpol.d.ts +15 -0
- package/dist/src/examples/vdpol.js.map +1 -0
- package/dist/src/latex-export/examples/advanced-to-latex.d.ts +2 -0
- package/dist/src/latex-export/examples/advanced-to-latex.js +41 -0
- package/dist/src/latex-export/examples/advanced-to-latex.js.map +1 -0
- package/dist/src/latex-export/examples/basic-to-latex.d.ts +2 -0
- package/dist/src/latex-export/examples/basic-to-latex.js +17 -0
- package/dist/src/latex-export/examples/basic-to-latex.js.map +1 -0
- package/dist/src/latex-export/examples/bioreactor-to-latex-selective.d.ts +2 -0
- package/dist/src/latex-export/examples/bioreactor-to-latex-selective.js +145 -0
- package/dist/src/latex-export/examples/bioreactor-to-latex-selective.js.map +1 -0
- package/dist/src/latex-export/examples/chem-react-to-latex-no-cdot.d.ts +2 -0
- package/dist/src/latex-export/examples/chem-react-to-latex-no-cdot.js +41 -0
- package/dist/src/latex-export/examples/chem-react-to-latex-no-cdot.js.map +1 -0
- package/dist/src/latex-export/examples/energy-n-control-to-markdown.d.ts +2 -0
- package/dist/src/latex-export/examples/energy-n-control-to-markdown.js +58 -0
- package/dist/src/latex-export/examples/energy-n-control-to-markdown.js.map +1 -0
- package/dist/src/latex-export/examples/extended-to-markdown.d.ts +2 -0
- package/dist/src/latex-export/examples/extended-to-markdown.js +37 -0
- package/dist/src/latex-export/examples/extended-to-markdown.js.map +1 -0
- package/dist/src/latex-export/examples/fermentation-to-latex.d.ts +2 -0
- package/dist/src/latex-export/examples/fermentation-to-latex.js +32 -0
- package/dist/src/latex-export/examples/fermentation-to-latex.js.map +1 -0
- package/dist/src/latex-export/examples/ga-production-to-markdown.d.ts +2 -0
- package/dist/src/latex-export/examples/ga-production-to-markdown.js +58 -0
- package/dist/src/latex-export/examples/ga-production-to-markdown.js.map +1 -0
- package/dist/src/latex-export/examples/nimotuzumab-to-latex.d.ts +2 -0
- package/dist/src/latex-export/examples/nimotuzumab-to-latex.js +53 -0
- package/dist/src/latex-export/examples/nimotuzumab-to-latex.js.map +1 -0
- package/dist/src/latex-export/examples/pk-pd-to-markdown-minimal.d.ts +2 -0
- package/dist/src/latex-export/examples/pk-pd-to-markdown-minimal.js +50 -0
- package/dist/src/latex-export/examples/pk-pd-to-markdown-minimal.js.map +1 -0
- package/dist/src/latex-export/examples/pk-to-markdown.d.ts +2 -0
- package/dist/src/latex-export/examples/pk-to-markdown.js +35 -0
- package/dist/src/latex-export/examples/pk-to-markdown.js.map +1 -0
- package/dist/src/latex-export/examples/pollution-to-latex.d.ts +2 -0
- package/dist/src/latex-export/examples/pollution-to-latex.js +141 -0
- package/dist/src/latex-export/examples/pollution-to-latex.js.map +1 -0
- package/dist/src/latex-export/examples/robertson-to-latex-no-meta.d.ts +2 -0
- package/dist/src/latex-export/examples/robertson-to-latex-no-meta.js +25 -0
- package/dist/src/latex-export/examples/robertson-to-latex-no-meta.js.map +1 -0
- package/dist/src/latex-export/generator/bracket-manager.d.ts +19 -0
- package/dist/src/latex-export/generator/bracket-manager.js +58 -0
- package/dist/src/latex-export/generator/bracket-manager.js.map +1 -0
- package/dist/src/latex-export/generator/document-builder.d.ts +13 -0
- package/dist/src/latex-export/generator/document-builder.js +433 -0
- package/dist/src/latex-export/generator/document-builder.js.map +1 -0
- package/dist/src/latex-export/generator/latex-generator.d.ts +23 -0
- package/dist/src/latex-export/generator/latex-generator.js +176 -0
- package/dist/src/latex-export/generator/latex-generator.js.map +1 -0
- package/dist/src/latex-export/index.d.ts +8 -0
- package/dist/src/latex-export/index.js +25 -0
- package/dist/src/latex-export/index.js.map +1 -0
- package/dist/src/latex-export/output/md-formatter.d.ts +16 -0
- package/dist/src/latex-export/output/md-formatter.js +27 -0
- package/dist/src/latex-export/output/md-formatter.js.map +1 -0
- package/dist/src/latex-export/output/tex-formatter.d.ts +5 -0
- package/dist/src/latex-export/output/tex-formatter.js +20 -0
- package/dist/src/latex-export/output/tex-formatter.js.map +1 -0
- package/dist/src/latex-export/parser/ast-parser.d.ts +7 -0
- package/dist/src/latex-export/parser/ast-parser.js +153 -0
- package/dist/src/latex-export/parser/ast-parser.js.map +1 -0
- package/dist/src/latex-export/parser/ivp-parser.d.ts +6 -0
- package/dist/src/latex-export/parser/ivp-parser.js +219 -0
- package/dist/src/latex-export/parser/ivp-parser.js.map +1 -0
- package/dist/src/latex-export/parser/line-joiner.d.ts +25 -0
- package/dist/src/latex-export/parser/line-joiner.js +80 -0
- package/dist/src/latex-export/parser/line-joiner.js.map +1 -0
- package/dist/src/latex-export/parser/tokenizer.d.ts +7 -0
- package/dist/src/latex-export/parser/tokenizer.js +143 -0
- package/dist/src/latex-export/parser/tokenizer.js.map +1 -0
- package/dist/src/latex-export/transformer/functions.d.ts +12 -0
- package/dist/src/latex-export/transformer/functions.js +47 -0
- package/dist/src/latex-export/transformer/functions.js.map +1 -0
- package/dist/src/latex-export/transformer/identifier.d.ts +23 -0
- package/dist/src/latex-export/transformer/identifier.js +194 -0
- package/dist/src/latex-export/transformer/identifier.js.map +1 -0
- package/dist/src/latex-export/transformer/operators.d.ts +9 -0
- package/dist/src/latex-export/transformer/operators.js +41 -0
- package/dist/src/latex-export/transformer/operators.js.map +1 -0
- package/dist/src/latex-export/types.d.ts +122 -0
- package/dist/src/latex-export/types.js +10 -0
- package/dist/src/latex-export/types.js.map +1 -0
- package/{src/pipeline/basic-pipeline-creator.ts → dist/src/pipeline/basic-pipeline-creator.d.ts} +11 -28
- package/dist/src/pipeline/basic-pipeline-creator.js.map +1 -0
- package/dist/src/pipeline/constants.d.ts +14 -0
- package/dist/src/pipeline/constants.js.map +1 -0
- package/dist/src/pipeline/index.d.ts +7 -0
- package/dist/src/pipeline/index.js.map +1 -0
- package/dist/src/pipeline/input.d.ts +3 -0
- package/dist/src/pipeline/input.js.map +1 -0
- package/dist/src/pipeline/loops-pipeline-creator.d.ts +124 -0
- package/dist/src/pipeline/loops-pipeline-creator.js.map +1 -0
- package/dist/src/pipeline/output.d.ts +10 -0
- package/{src → dist/src}/pipeline/output.js +1 -1
- package/dist/src/pipeline/output.js.map +1 -0
- package/dist/src/pipeline/pipeline-creator.d.ts +12 -0
- package/{src → dist/src}/pipeline/pipeline-creator.js +2 -0
- package/dist/src/pipeline/pipeline-creator.js.map +1 -0
- package/{src/pipeline/pipeline.ts → dist/src/pipeline/pipeline.d.ts} +10 -97
- package/dist/src/pipeline/pipeline.js.map +1 -0
- package/{src/pipeline/updates-pipeline-creator.ts → dist/src/pipeline/updates-pipeline-creator.d.ts} +15 -131
- package/dist/src/pipeline/updates-pipeline-creator.js.map +1 -0
- package/dist/src/scripting-tools/constants.d.ts +59 -0
- package/dist/src/scripting-tools/constants.js.map +1 -0
- package/dist/src/scripting-tools/index.d.ts +3 -0
- package/dist/src/scripting-tools/index.js.map +1 -0
- package/dist/src/scripting-tools/model-error.d.ts +10 -0
- package/{src → dist/src}/scripting-tools/model-error.js +2 -1
- package/dist/src/scripting-tools/model-error.js.map +1 -0
- package/dist/src/scripting-tools/scripting-tools.d.ts +277 -0
- package/{src → dist/src}/scripting-tools/scripting-tools.js +2 -4
- package/dist/src/scripting-tools/scripting-tools.js.map +1 -0
- package/dist/src/solver-tools/ab4-method.d.ts +46 -0
- package/{src → dist/src}/solver-tools/ab4-method.js +3 -3
- package/dist/src/solver-tools/ab4-method.js.map +1 -0
- package/dist/src/solver-tools/ab5-method.d.ts +46 -0
- package/{src → dist/src}/solver-tools/ab5-method.js +3 -3
- package/dist/src/solver-tools/ab5-method.js.map +1 -0
- package/dist/src/solver-tools/callbacks/callback-base.d.ts +8 -0
- package/dist/src/solver-tools/callbacks/callback-base.js.map +1 -0
- package/dist/src/solver-tools/callbacks/callback-tools.d.ts +6 -0
- package/dist/src/solver-tools/callbacks/callback-tools.js.map +1 -0
- package/dist/src/solver-tools/callbacks/iter-checker-callback.d.ts +12 -0
- package/{src → dist/src}/solver-tools/callbacks/iter-checker-callback.js +2 -0
- package/dist/src/solver-tools/callbacks/iter-checker-callback.js.map +1 -0
- package/dist/src/solver-tools/callbacks/time-checker-callback.d.ts +12 -0
- package/{src → dist/src}/solver-tools/callbacks/time-checker-callback.js +2 -2
- package/dist/src/solver-tools/callbacks/time-checker-callback.js.map +1 -0
- package/dist/src/solver-tools/cvode/common.d.ts +395 -0
- package/dist/src/solver-tools/cvode/common.js +483 -0
- package/dist/src/solver-tools/cvode/common.js.map +1 -0
- package/dist/src/solver-tools/cvode/cvode.d.ts +23 -0
- package/dist/src/solver-tools/cvode/cvode.js +1062 -0
- package/dist/src/solver-tools/cvode/cvode.js.map +1 -0
- package/dist/src/solver-tools/cvode/cvode_adams.d.ts +22 -0
- package/dist/src/solver-tools/cvode/cvode_adams.js +124 -0
- package/dist/src/solver-tools/cvode/cvode_adams.js.map +1 -0
- package/dist/src/solver-tools/cvode/cvode_bdf.d.ts +37 -0
- package/dist/src/solver-tools/cvode/cvode_bdf.js +153 -0
- package/dist/src/solver-tools/cvode/cvode_bdf.js.map +1 -0
- package/dist/src/solver-tools/cvode/cvode_class.d.ts +116 -0
- package/dist/src/solver-tools/cvode/cvode_class.js +163 -0
- package/dist/src/solver-tools/cvode/cvode_class.js.map +1 -0
- package/dist/src/solver-tools/cvode/cvode_hin.d.ts +24 -0
- package/dist/src/solver-tools/cvode/cvode_hin.js +119 -0
- package/dist/src/solver-tools/cvode/cvode_hin.js.map +1 -0
- package/dist/src/solver-tools/cvode/cvode_io.d.ts +98 -0
- package/dist/src/solver-tools/cvode/cvode_io.js +202 -0
- package/dist/src/solver-tools/cvode/cvode_io.js.map +1 -0
- package/dist/src/solver-tools/cvode/cvode_ls.d.ts +23 -0
- package/dist/src/solver-tools/cvode/cvode_ls.js +210 -0
- package/dist/src/solver-tools/cvode/cvode_ls.js.map +1 -0
- package/dist/src/solver-tools/cvode/cvode_nls.d.ts +25 -0
- package/dist/src/solver-tools/cvode/cvode_nls.js +220 -0
- package/dist/src/solver-tools/cvode/cvode_nls.js.map +1 -0
- package/dist/src/solver-tools/cvode/cvode_root.d.ts +64 -0
- package/dist/src/solver-tools/cvode/cvode_root.js +415 -0
- package/dist/src/solver-tools/cvode/cvode_root.js.map +1 -0
- package/dist/src/solver-tools/cvode/dense_linalg.d.ts +50 -0
- package/dist/src/solver-tools/cvode/dense_linalg.js +131 -0
- package/dist/src/solver-tools/cvode/dense_linalg.js.map +1 -0
- package/dist/src/solver-tools/cvode/index.d.ts +24 -0
- package/dist/src/solver-tools/cvode/index.js +26 -0
- package/dist/src/solver-tools/cvode/index.js.map +1 -0
- package/dist/src/solver-tools/cvode-method.d.ts +47 -0
- package/dist/src/solver-tools/cvode-method.js +114 -0
- package/dist/src/solver-tools/cvode-method.js.map +1 -0
- package/dist/src/solver-tools/index.d.ts +16 -0
- package/{src → dist/src}/solver-tools/index.js +1 -0
- package/dist/src/solver-tools/index.js.map +1 -0
- package/dist/src/solver-tools/lin-alg-tools.d.ts +6 -0
- package/dist/src/solver-tools/lin-alg-tools.js.map +1 -0
- package/dist/src/solver-tools/lsoda/blas.d.ts +59 -0
- package/{src → dist/src}/solver-tools/lsoda/blas.js +11 -0
- package/dist/src/solver-tools/lsoda/blas.js.map +1 -0
- package/dist/src/solver-tools/lsoda/cfode.d.ts +18 -0
- package/{src → dist/src}/solver-tools/lsoda/cfode.js +11 -0
- package/dist/src/solver-tools/lsoda/cfode.js.map +1 -0
- package/dist/src/solver-tools/lsoda/common.d.ts +85 -0
- package/dist/src/solver-tools/lsoda/common.js +96 -0
- package/dist/src/solver-tools/lsoda/common.js.map +1 -0
- package/dist/src/solver-tools/lsoda/corfailure.d.ts +18 -0
- package/{src → dist/src}/solver-tools/lsoda/corfailure.js +11 -0
- package/dist/src/solver-tools/lsoda/corfailure.js.map +1 -0
- package/dist/src/solver-tools/lsoda/correction.d.ts +23 -0
- package/{src → dist/src}/solver-tools/lsoda/correction.js +11 -0
- package/dist/src/solver-tools/lsoda/correction.js.map +1 -0
- package/dist/src/solver-tools/lsoda/dense.d.ts +47 -0
- package/{src → dist/src}/solver-tools/lsoda/dense.js +13 -0
- package/dist/src/solver-tools/lsoda/dense.js.map +1 -0
- package/dist/src/solver-tools/lsoda/index.d.ts +16 -0
- package/dist/src/solver-tools/lsoda/index.js +15 -0
- package/dist/src/solver-tools/lsoda/index.js.map +1 -0
- package/dist/src/solver-tools/lsoda/intdy.d.ts +19 -0
- package/{src → dist/src}/solver-tools/lsoda/intdy.js +11 -0
- package/dist/src/solver-tools/lsoda/intdy.js.map +1 -0
- package/dist/src/solver-tools/lsoda/lsoda.d.ts +66 -0
- package/{src → dist/src}/solver-tools/lsoda/lsoda.js +24 -5
- package/dist/src/solver-tools/lsoda/lsoda.js.map +1 -0
- package/dist/src/solver-tools/lsoda/methodswitch.d.ts +21 -0
- package/{src → dist/src}/solver-tools/lsoda/methodswitch.js +11 -0
- package/dist/src/solver-tools/lsoda/methodswitch.js.map +1 -0
- package/dist/src/solver-tools/lsoda/orderswitch.d.ts +21 -0
- package/{src → dist/src}/solver-tools/lsoda/orderswitch.js +11 -0
- package/dist/src/solver-tools/lsoda/orderswitch.js.map +1 -0
- package/dist/src/solver-tools/lsoda/prja.d.ts +18 -0
- package/{src → dist/src}/solver-tools/lsoda/prja.js +11 -0
- package/dist/src/solver-tools/lsoda/prja.js.map +1 -0
- package/dist/src/solver-tools/lsoda/scaleh.d.ts +16 -0
- package/{src → dist/src}/solver-tools/lsoda/scaleh.js +11 -0
- package/dist/src/solver-tools/lsoda/scaleh.js.map +1 -0
- package/dist/src/solver-tools/lsoda/solsy.d.ts +17 -0
- package/dist/src/solver-tools/lsoda/solsy.js +25 -0
- package/dist/src/solver-tools/lsoda/solsy.js.map +1 -0
- package/dist/src/solver-tools/lsoda/stoda.d.ts +19 -0
- package/{src → dist/src}/solver-tools/lsoda/stoda.js +11 -0
- package/dist/src/solver-tools/lsoda/stoda.js.map +1 -0
- package/dist/src/solver-tools/lsoda-method.d.ts +46 -0
- package/{src → dist/src}/solver-tools/lsoda-method.js +23 -9
- package/dist/src/solver-tools/lsoda-method.js.map +1 -0
- package/dist/src/solver-tools/mrt-method.d.ts +47 -0
- package/{src → dist/src}/solver-tools/mrt-method.js +2 -2
- package/dist/src/solver-tools/mrt-method.js.map +1 -0
- package/dist/src/solver-tools/rk3-method.d.ts +46 -0
- package/{src → dist/src}/solver-tools/rk3-method.js +2 -2
- package/dist/src/solver-tools/rk3-method.js.map +1 -0
- package/dist/src/solver-tools/rk4-method.d.ts +46 -0
- package/{src → dist/src}/solver-tools/rk4-method.js +2 -2
- package/dist/src/solver-tools/rk4-method.js.map +1 -0
- package/dist/src/solver-tools/rkdp-method.d.ts +46 -0
- package/{src → dist/src}/solver-tools/rkdp-method.js +2 -2
- package/dist/src/solver-tools/rkdp-method.js.map +1 -0
- package/dist/src/solver-tools/ros34prw-method.d.ts +46 -0
- package/{src → dist/src}/solver-tools/ros34prw-method.js +2 -2
- package/dist/src/solver-tools/ros34prw-method.js.map +1 -0
- package/dist/src/solver-tools/ros3prw-method.d.ts +46 -0
- package/{src → dist/src}/solver-tools/ros3prw-method.js +2 -2
- package/dist/src/solver-tools/ros3prw-method.js.map +1 -0
- package/{src/solver-tools/solver-defs.ts → dist/src/solver-tools/solver-defs.d.ts} +45 -84
- package/{src → dist/src}/solver-tools/solver-defs.js +1 -0
- package/dist/src/solver-tools/solver-defs.js.map +1 -0
- package/dist/src/worker-tools/index.d.ts +2 -0
- package/dist/src/worker-tools/index.js.map +1 -0
- package/{src/worker-tools/scripting.ts → dist/src/worker-tools/scripting.d.ts} +9 -91
- package/dist/src/worker-tools/scripting.js.map +1 -0
- package/dist/src/worker-tools/solving.d.ts +7 -0
- package/{src → dist/src}/worker-tools/solving.js +3 -1
- package/dist/src/worker-tools/solving.js.map +1 -0
- package/package.json +13 -12
- package/.claude/settings.local.json +0 -11
- package/.eslintrc.json +0 -45
- package/.github/ISSUE_TEMPLATE/bug_report.md +0 -29
- package/.github/ISSUE_TEMPLATE/feature_request.md +0 -20
- package/.github/PULL_REQUEST_TEMPLATE.md +0 -22
- package/.github/scripts/bump-js-api-version.sh +0 -106
- package/.github/scripts/check-output.sh +0 -20
- package/.github/scripts/iac-cfn-deploy.sh +0 -90
- package/.github/scripts/slack_api_request.sh +0 -65
- package/.github/scripts/test_package.sh +0 -270
- package/.github/workflows/deploy-docs.yml +0 -15
- package/.github/workflows/libraries.yaml +0 -305
- package/.github/workflows/test.yaml +0 -19
- package/CLAUDE.md +0 -98
- package/CONTRIBUTING.md +0 -74
- package/eslintrc.json +0 -45
- package/images/E5.png +0 -0
- package/images/HIRES.png +0 -0
- package/images/OREGO.png +0 -0
- package/images/POLL-full.png +0 -0
- package/images/POLL.png +0 -0
- package/images/ROBER.png +0 -0
- package/images/VDP0L.png +0 -0
- package/images/VDPOL.png +0 -0
- package/images/acid-prod.gif +0 -0
- package/index.js.map +0 -1
- package/index.ts +0 -17
- package/jest.config.js +0 -13
- package/src/examples/basic-use.js.map +0 -1
- package/src/examples/basic-use.ts +0 -44
- package/src/examples/bioreactor.js +0 -125
- package/src/examples/bioreactor.js.map +0 -1
- package/src/examples/bioreactor.ts +0 -132
- package/src/examples/check-methods.js.map +0 -1
- package/src/examples/check-methods.ts +0 -81
- package/src/examples/corr-probs.js.map +0 -1
- package/src/examples/corr-probs.ts +0 -155
- package/src/examples/cyclic-model.js.map +0 -1
- package/src/examples/cyclic-model.ts +0 -112
- package/src/examples/e5.js.map +0 -1
- package/src/examples/e5.ts +0 -36
- package/src/examples/hires.js.map +0 -1
- package/src/examples/hires.ts +0 -40
- package/src/examples/index.js.map +0 -1
- package/src/examples/index.ts +0 -34
- package/src/examples/model-updates.js.map +0 -1
- package/src/examples/model-updates.ts +0 -122
- package/src/examples/orego.js.map +0 -1
- package/src/examples/orego.ts +0 -25
- package/src/examples/pipeline-use.js.map +0 -1
- package/src/examples/pipeline-use.ts +0 -98
- package/src/examples/pollution.js.map +0 -1
- package/src/examples/pollution.ts +0 -133
- package/src/examples/print-benchmark.js.map +0 -1
- package/src/examples/robertson.js.map +0 -1
- package/src/examples/robertson.ts +0 -19
- package/src/examples/scripting.js.map +0 -1
- package/src/examples/scripting.ts +0 -35
- package/src/examples/vdpol.js.map +0 -1
- package/src/examples/vdpol.ts +0 -17
- package/src/pipeline/basic-pipeline-creator.js.map +0 -1
- package/src/pipeline/constants.js.map +0 -1
- package/src/pipeline/constants.ts +0 -21
- package/src/pipeline/index.js.map +0 -1
- package/src/pipeline/index.ts +0 -7
- package/src/pipeline/input.js.map +0 -1
- package/src/pipeline/input.ts +0 -55
- package/src/pipeline/loops-pipeline-creator.js.map +0 -1
- package/src/pipeline/loops-pipeline-creator.ts +0 -252
- package/src/pipeline/output.js.map +0 -1
- package/src/pipeline/output.ts +0 -201
- package/src/pipeline/pipeline-creator.js.map +0 -1
- package/src/pipeline/pipeline-creator.ts +0 -20
- package/src/pipeline/pipeline.js.map +0 -1
- package/src/pipeline/updates-pipeline-creator.js.map +0 -1
- package/src/scripting-tools/constants.js.map +0 -1
- package/src/scripting-tools/constants.ts +0 -69
- package/src/scripting-tools/index.js.map +0 -1
- package/src/scripting-tools/index.ts +0 -8
- package/src/scripting-tools/model-error.js.map +0 -1
- package/src/scripting-tools/model-error.ts +0 -21
- package/src/scripting-tools/scripting-tools.js.map +0 -1
- package/src/scripting-tools/scripting-tools.ts +0 -1582
- package/src/solver-tools/ab4-method.js.map +0 -1
- package/src/solver-tools/ab4-method.ts +0 -395
- package/src/solver-tools/ab5-method.js.map +0 -1
- package/src/solver-tools/ab5-method.ts +0 -397
- package/src/solver-tools/callbacks/callback-base.js.map +0 -1
- package/src/solver-tools/callbacks/callback-base.ts +0 -12
- package/src/solver-tools/callbacks/callback-tools.js.map +0 -1
- package/src/solver-tools/callbacks/callback-tools.ts +0 -22
- package/src/solver-tools/callbacks/iter-checker-callback.js.map +0 -1
- package/src/solver-tools/callbacks/iter-checker-callback.ts +0 -25
- package/src/solver-tools/callbacks/time-checker-callback.js.map +0 -1
- package/src/solver-tools/callbacks/time-checker-callback.ts +0 -23
- package/src/solver-tools/index.js.map +0 -1
- package/src/solver-tools/index.ts +0 -15
- package/src/solver-tools/lin-alg-tools.js.map +0 -1
- package/src/solver-tools/lin-alg-tools.ts +0 -75
- package/src/solver-tools/lsoda/blas.js.map +0 -1
- package/src/solver-tools/lsoda/blas.ts +0 -267
- package/src/solver-tools/lsoda/cfode.js.map +0 -1
- package/src/solver-tools/lsoda/cfode.ts +0 -83
- package/src/solver-tools/lsoda/common.js +0 -94
- package/src/solver-tools/lsoda/common.js.map +0 -1
- package/src/solver-tools/lsoda/common.ts +0 -135
- package/src/solver-tools/lsoda/corfailure.js.map +0 -1
- package/src/solver-tools/lsoda/corfailure.ts +0 -30
- package/src/solver-tools/lsoda/correction.js.map +0 -1
- package/src/solver-tools/lsoda/correction.ts +0 -119
- package/src/solver-tools/lsoda/dense.js.map +0 -1
- package/src/solver-tools/lsoda/dense.ts +0 -129
- package/src/solver-tools/lsoda/index.js +0 -4
- package/src/solver-tools/lsoda/index.js.map +0 -1
- package/src/solver-tools/lsoda/index.ts +0 -5
- package/src/solver-tools/lsoda/intdy.js.map +0 -1
- package/src/solver-tools/lsoda/intdy.ts +0 -50
- package/src/solver-tools/lsoda/lsoda.js.map +0 -1
- package/src/solver-tools/lsoda/lsoda.ts +0 -632
- package/src/solver-tools/lsoda/methodswitch.js.map +0 -1
- package/src/solver-tools/lsoda/methodswitch.ts +0 -107
- package/src/solver-tools/lsoda/orderswitch.js.map +0 -1
- package/src/solver-tools/lsoda/orderswitch.ts +0 -95
- package/src/solver-tools/lsoda/prja.js.map +0 -1
- package/src/solver-tools/lsoda/prja.ts +0 -49
- package/src/solver-tools/lsoda/scaleh.js.map +0 -1
- package/src/solver-tools/lsoda/scaleh.ts +0 -33
- package/src/solver-tools/lsoda/solsy.js +0 -14
- package/src/solver-tools/lsoda/solsy.js.map +0 -1
- package/src/solver-tools/lsoda/solsy.ts +0 -18
- package/src/solver-tools/lsoda/stoda.js.map +0 -1
- package/src/solver-tools/lsoda/stoda.ts +0 -286
- package/src/solver-tools/lsoda-method.js.map +0 -1
- package/src/solver-tools/lsoda-method.ts +0 -136
- package/src/solver-tools/mrt-method.js.map +0 -1
- package/src/solver-tools/mrt-method.ts +0 -398
- package/src/solver-tools/rk3-method.js.map +0 -1
- package/src/solver-tools/rk3-method.ts +0 -257
- package/src/solver-tools/rk4-method.js.map +0 -1
- package/src/solver-tools/rk4-method.ts +0 -286
- package/src/solver-tools/rkdp-method.js.map +0 -1
- package/src/solver-tools/rkdp-method.ts +0 -300
- package/src/solver-tools/ros34prw-method.js.map +0 -1
- package/src/solver-tools/ros34prw-method.ts +0 -373
- package/src/solver-tools/ros3prw-method.js.map +0 -1
- package/src/solver-tools/ros3prw-method.ts +0 -342
- package/src/solver-tools/solver-defs.js.map +0 -1
- package/src/tests/correctness.test.js +0 -15
- package/src/tests/correctness.test.js.map +0 -1
- package/src/tests/correctness.test.ts +0 -16
- package/src/tests/lsoda-lib-correctness.test.js +0 -223
- package/src/tests/lsoda-lib-correctness.test.js.map +0 -1
- package/src/tests/lsoda-lib-correctness.test.ts +0 -283
- package/src/tests/lsoda-lib-performance.test.js +0 -95
- package/src/tests/lsoda-lib-performance.test.js.map +0 -1
- package/src/tests/lsoda-lib-performance.test.ts +0 -126
- package/src/tests/performance.test.js +0 -16
- package/src/tests/performance.test.js.map +0 -1
- package/src/tests/performance.test.ts +0 -17
- package/src/tests/pipeline.test.js +0 -10
- package/src/tests/pipeline.test.js.map +0 -1
- package/src/tests/pipeline.test.ts +0 -11
- package/src/tests/test-defs.js +0 -207
- package/src/tests/test-defs.js.map +0 -1
- package/src/tests/test-defs.ts +0 -225
- package/src/tests/test-utils.js +0 -28
- package/src/tests/test-utils.js.map +0 -1
- package/src/tests/test-utils.ts +0 -37
- package/src/worker-tools/index.js.map +0 -1
- package/src/worker-tools/index.ts +0 -2
- package/src/worker-tools/scripting.js.map +0 -1
- package/src/worker-tools/solving.js.map +0 -1
- package/src/worker-tools/solving.ts +0 -83
- package/tsconfig.json +0 -71
- package/typedoc.json +0 -8
- /package/{src → dist/src}/examples/basic-use.js +0 -0
- /package/{src → dist/src}/examples/cyclic-model.js +0 -0
- /package/{src → dist/src}/examples/e5.js +0 -0
- /package/{src → dist/src}/examples/hires.js +0 -0
- /package/{src → dist/src}/examples/index.js +0 -0
- /package/{src → dist/src}/examples/model-updates.js +0 -0
- /package/{src → dist/src}/examples/orego.js +0 -0
- /package/{src → dist/src}/examples/pipeline-use.js +0 -0
- /package/{src → dist/src}/examples/pollution.js +0 -0
- /package/{src → dist/src}/examples/print-benchmark.js +0 -0
- /package/{src → dist/src}/examples/scripting.js +0 -0
- /package/{src → dist/src}/examples/vdpol.js +0 -0
- /package/{src → dist/src}/pipeline/basic-pipeline-creator.js +0 -0
- /package/{src → dist/src}/pipeline/constants.js +0 -0
- /package/{src → dist/src}/pipeline/index.js +0 -0
- /package/{src → dist/src}/pipeline/input.js +0 -0
- /package/{src → dist/src}/pipeline/loops-pipeline-creator.js +0 -0
- /package/{src → dist/src}/pipeline/pipeline.js +0 -0
- /package/{src → dist/src}/pipeline/updates-pipeline-creator.js +0 -0
- /package/{src → dist/src}/scripting-tools/constants.js +0 -0
- /package/{src → dist/src}/scripting-tools/index.js +0 -0
- /package/{src → dist/src}/solver-tools/callbacks/callback-base.js +0 -0
- /package/{src → dist/src}/solver-tools/callbacks/callback-tools.js +0 -0
- /package/{src → dist/src}/solver-tools/lin-alg-tools.js +0 -0
- /package/{src → dist/src}/worker-tools/index.js +0 -0
- /package/{src → dist/src}/worker-tools/scripting.js +0 -0
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/** Example: GA production model (multi-stage) → Markdown, no cdot. */
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import { convertIvpToLatex } from '../index';
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const MODEL = `#name: Acid Production
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#description: Gluconic acid (GA) production by Aspergillus niger modeling
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#equations:
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dX/dt = rX
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dS/dt = -gamma * rX - lambda * X
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dO/dt = Kla * (Cod - O) - delta * rX - phi * X
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dP/dt = alpha * rX + beta * X
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#expressions:
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mu = muM * S / (Ks + S) * O / (Ko + O)
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rX = mu * X
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#argument: t, 1-st stage
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start = 0 {units: h; caption: initial; category: Misc}
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stage1 = 60 {units: h; caption: 1-st stage; category: Durations; min: 20; max: 80}
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step = 0.1 {units: h; caption: step; category: Misc; min: 0.01; max: 1}
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#update: 2-nd stage
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duration = overall - _t1
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S += 70
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#inits:
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X = 5 {units: kg/m³; caption: biomass; category: Initial concentrations; min: 1; max: 10}
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S = 150 {units: kg/m³; caption: glucose; category: Initial concentrations; min: 50; max: 200}
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O = 7 {units: kg/m³; caption: oxygen; category: Initial concentrations; min: 1; max: 10}
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P = 0 {units: kg/m³; caption: acid; category: Initial concentrations; min: 0; max: 0.1}
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#output:
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t {caption: time}
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X {caption: biomass}
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S {caption: glucose}
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O {caption: oxygen}
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P {caption: acid}
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#parameters:
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overall = 100 {units: h; category: Durations; min: 100; max: 140}
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muM = 0.668 {units: 1/h; category: Parameters}
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alpha = 2.92 {category: Parameters}
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beta = 0.131 {units: 1/h; category: Parameters}
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gamma = 2.12 {category: Parameters}
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lambda = 0.232 {units: 1/h; category: Parameters}
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delta = 0.278 {category: Parameters}
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phi = 4.87e-3 {units: 1/h; category: Parameters}
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Ks = 1.309e2 {units: g/L; category: Parameters}
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Ko = 3.63e-4 {units: g/L; category: Parameters}
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Kla = 1.7e-2 {units: 1/s; category: Parameters}
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Cod = 15 {units: kg/m³; category: Parameters}
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#tolerance: 1e-9`;
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// Markdown with juxtaposition — good for multi-stage models
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const markdown = convertIvpToLatex(MODEL, {
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format: 'markdown',
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useCdot: false,
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});
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console.log(markdown);
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//# sourceMappingURL=ga-production-to-markdown.js.map
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{"version":3,"file":"ga-production-to-markdown.js","sourceRoot":"","sources":["../../../../src/latex-export/examples/ga-production-to-markdown.ts"],"names":[],"mappings":"AAAA,sEAAsE;AAEtE,OAAO,EAAC,iBAAiB,EAAC,MAAM,UAAU,CAAC;AAE3C,MAAM,KAAK,GAAG;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;iBAgDG,CAAC;AAElB,4DAA4D;AAC5D,MAAM,QAAQ,GAAG,iBAAiB,CAAC,KAAK,EAAE;IACxC,MAAM,EAAE,UAAU;IAClB,OAAO,EAAE,KAAK;CACf,CAAC,CAAC;AACH,OAAO,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAC"}
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/** Example: nimotuzumab model → LaTeX, no inits, no cdot. */
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import { convertIvpToLatex } from '../index';
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const MODEL = `#name: Nimotuzumab
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#description: Nimotuzumab disposition model
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#comment:
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Source: https://www.mdpi.com/1999-4923/12/12/1147
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#equations:
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dA1/dt = (-(CL * A3 / V1 + Q / V1) * A1 + Q / V2 * A2 - kint * Rtot * A1 / (Kss + A1 / V1))
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/ (1 + Rtot * Kss / (Kss + A1 / V1)**2)
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dA2/dt = (Q / V1 * A1 - Q / V2 * A2) / (1 + Rtotp * Kss / (Kss + A2 / V2)**2)
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dA3/dt = Kin * (1 + Smax * A1**gamma / (S50**gamma + A1**gamma)) - Kout * A3
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#argument: t
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start = 0 {caption: Initial; category: Time; min: 0; max: 10}
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finish = 70 {caption: Final; category: Time; min: 50; max: 100}
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step = 0.01 {caption: Step; category: Time; min: 0.01; max: 1}
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#inits:
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A1 = 0.43 {category: Initials; min: 0.2; max: 0.6}
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A2 = 0.55 {category: Initials; min: 0.3; max: 0.8}
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A3 = 10.32 {category: Initials; min: 5; max: 15}
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#output:
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t {caption: Time, h}
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A1 {caption: Central}
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A2 {caption: Periferal}
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#parameters:
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CL = 9.64E-3 {category: Parameters; min: 0.005; max: 0.015}
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V1 = 2.63 {category: Parameters; min: 0.7; max: 3}
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Q = 2.88E-2 {category: Parameters; min: 0.015; max: 0.035}
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V2 = 9.92E-3 {category: Parameters; min: 0.0067; max: 0.0265}
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35
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Kss = 15.5 {category: Parameters; min: 10; max: 45}
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36
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kint = 1E-2 {category: Parameters; min: 0.01; max: 0.05}
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Rtot = 1.05E-2 {category: Parameters; min: 0.007; max: 0.032}
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Rtotp = 956 {category: Parameters; min: 120; max: 3500}
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39
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Kin = 1.33E-2 {category: Parameters; min: 0.01; max: 0.05}
|
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40
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Kout = 1.33E-2 {category: Parameters; min: 0.001; max: 0.02}
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41
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S50 = 8.57 {category: Parameters; min: 5; max: 12}
|
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42
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Smax = 3.18 {category: Parameters; min: 1; max: 5}
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gamma = 0.5 {category: Parameters; min: 0.1; max: 1}
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#tolerance: 1E-7`;
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// Compact LaTeX, suppress initial conditions, juxtaposition
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const latex = convertIvpToLatex(MODEL, {
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compact: true,
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includeInits: false,
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useCdot: false,
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});
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console.log(latex);
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//# sourceMappingURL=nimotuzumab-to-latex.js.map
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{"version":3,"file":"nimotuzumab-to-latex.js","sourceRoot":"","sources":["../../../../src/latex-export/examples/nimotuzumab-to-latex.ts"],"names":[],"mappings":"AAAA,6DAA6D;AAE7D,OAAO,EAAC,iBAAiB,EAAC,MAAM,UAAU,CAAC;AAE3C,MAAM,KAAK,GAAG;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;iBA0CG,CAAC;AAElB,4DAA4D;AAC5D,MAAM,KAAK,GAAG,iBAAiB,CAAC,KAAK,EAAE;IACrC,OAAO,EAAE,IAAI;IACb,YAAY,EAAE,KAAK;IACnB,OAAO,EAAE,KAAK;CACf,CAAC,CAAC;AACH,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC"}
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/** Example: PK-PD model → Markdown with only equations (no inits, parameters, constants). */
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2
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import { convertIvpToLatex } from '../index';
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const MODEL = `#name: PK-PD
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#description: Pharmacokinetic-pharmacodynamic (PK-PD) simulation: two-compartment model
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#equations:
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6
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d(depot)/dt = -KA * depot
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7
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d(centr)/dt = KA * depot - CL * C2 - Q * C2 + Q * C3
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d(peri)/dt = Q * C2 - Q * C3
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9
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d(eff)/dt = Kin - Kout * (1 - C2/(EC50 + C2)) * eff
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#expressions:
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C2 = centr / V2
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C3 = peri / V3
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#loop:
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count = 10 {caption: count; category: Dosing; min: 1; max: 20}
|
|
17
|
+
depot += dose
|
|
18
|
+
|
|
19
|
+
#argument: t
|
|
20
|
+
start = 0 {units: h; caption: begin; category: Dosing; min: 0; max: 1}
|
|
21
|
+
final = 12 {units: h; caption: end; category: Dosing; min: 5; max: 15}
|
|
22
|
+
step = 0.1 {units: h; caption: step; category: Dosing; min: 0.01; max: 0.1}
|
|
23
|
+
|
|
24
|
+
#inits:
|
|
25
|
+
depot = 0 {category: Initial values}
|
|
26
|
+
centr = 0 {category: Initial values}
|
|
27
|
+
peri = 0 {category: Initial values}
|
|
28
|
+
eff = 0.2 {category: Initial values}
|
|
29
|
+
|
|
30
|
+
#parameters:
|
|
31
|
+
dose = 1E4 {category: Dosing; min: 1E3; max: 2E4; step: 1E3}
|
|
32
|
+
KA = 0.3 {caption: rate constant; category: Parameters; min: 0.1; max: 1}
|
|
33
|
+
CL = 2 {caption: clearance; category: Parameters; min: 1; max: 5}
|
|
34
|
+
V2 = 4 {caption: central volume; category: Parameters; min: 1; max: 10}
|
|
35
|
+
Q = 1 {caption: inter rate; category: Parameters; min: 0.1; max: 1}
|
|
36
|
+
V3 = 30 {caption: peri volume; category: Parameters; min: 20; max: 40}
|
|
37
|
+
EC50 = 8 {caption: effect; category: Parameters; min: 1; max: 10}
|
|
38
|
+
Kin = 0.2 {caption: Kin; category: Parameters; min: 0.1; max: 0.5}
|
|
39
|
+
Kout = 0.2 {caption: Kout; category: Parameters; min: 0.1; max: 0.5}
|
|
40
|
+
|
|
41
|
+
#tolerance: 1E-9`;
|
|
42
|
+
// Markdown, equations only — suppress inits, parameters, and constants tables
|
|
43
|
+
const markdown = convertIvpToLatex(MODEL, {
|
|
44
|
+
format: 'markdown',
|
|
45
|
+
includeInits: false,
|
|
46
|
+
includeParameters: false,
|
|
47
|
+
includeConstants: false,
|
|
48
|
+
});
|
|
49
|
+
console.log(markdown);
|
|
50
|
+
//# sourceMappingURL=pk-pd-to-markdown-minimal.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"pk-pd-to-markdown-minimal.js","sourceRoot":"","sources":["../../../../src/latex-export/examples/pk-pd-to-markdown-minimal.ts"],"names":[],"mappings":"AAAA,6FAA6F;AAE7F,OAAO,EAAC,iBAAiB,EAAC,MAAM,UAAU,CAAC;AAE3C,MAAM,KAAK,GAAG;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;iBAsCG,CAAC;AAElB,8EAA8E;AAC9E,MAAM,QAAQ,GAAG,iBAAiB,CAAC,KAAK,EAAE;IACxC,MAAM,EAAE,UAAU;IAClB,YAAY,EAAE,KAAK;IACnB,iBAAiB,EAAE,KAAK;IACxB,gBAAgB,EAAE,KAAK;CACxB,CAAC,CAAC;AACH,OAAO,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAC"}
|
|
@@ -0,0 +1,35 @@
|
|
|
1
|
+
/** Example: PK model (with loop) → Markdown with default options. */
|
|
2
|
+
import { convertIvpToLatex } from '../index';
|
|
3
|
+
const MODEL = `#name: PK
|
|
4
|
+
#description: Pharmacokinetic (PK) simulation: one-compartment model
|
|
5
|
+
#equations:
|
|
6
|
+
d(depot)/dt = -KA * depot
|
|
7
|
+
d(centr)/dt = KA * depot - CL * C2
|
|
8
|
+
|
|
9
|
+
#expressions:
|
|
10
|
+
C2 = centr / V2
|
|
11
|
+
|
|
12
|
+
#loop:
|
|
13
|
+
count = 1 {category: Dosing; min: 1; max: 10}
|
|
14
|
+
depot += dose
|
|
15
|
+
|
|
16
|
+
#argument: t
|
|
17
|
+
start = 0 {units: h; caption: begin; category: Dosing; min: 0; max: 1}
|
|
18
|
+
final = 12 {units: h; caption: end; category: Dosing; min: 5; max: 15}
|
|
19
|
+
step = 0.01 {units: h; caption: step; category: Dosing; min: 0.01; max: 0.1}
|
|
20
|
+
|
|
21
|
+
#inits:
|
|
22
|
+
depot = 0 {category: Initial values}
|
|
23
|
+
centr = 0 {category: Initial values}
|
|
24
|
+
|
|
25
|
+
#parameters:
|
|
26
|
+
dose = 1E4 {category: Dosing; min: 1E3; max: 2E4; step: 1E3}
|
|
27
|
+
KA = 0.3 {caption: rate constant; category: Parameters; min: 0.1; max: 1}
|
|
28
|
+
CL = 2 {caption: clearance; category: Parameters; min: 1; max: 5}
|
|
29
|
+
V2 = 4 {caption: central volume; category: Parameters; min: 1; max: 10}
|
|
30
|
+
|
|
31
|
+
#tolerance: 1E-9`;
|
|
32
|
+
// Compact Markdown — loop model
|
|
33
|
+
const markdown = convertIvpToLatex(MODEL, { format: 'markdown', compact: true });
|
|
34
|
+
console.log(markdown);
|
|
35
|
+
//# sourceMappingURL=pk-to-markdown.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"pk-to-markdown.js","sourceRoot":"","sources":["../../../../src/latex-export/examples/pk-to-markdown.ts"],"names":[],"mappings":"AAAA,qEAAqE;AAErE,OAAO,EAAC,iBAAiB,EAAC,MAAM,UAAU,CAAC;AAE3C,MAAM,KAAK,GAAG;;;;;;;;;;;;;;;;;;;;;;;;;;;;iBA4BG,CAAC;AAElB,gCAAgC;AAChC,MAAM,QAAQ,GAAG,iBAAiB,CAAC,KAAK,EAAE,EAAC,MAAM,EAAE,UAAU,EAAE,OAAO,EAAE,IAAI,EAAC,CAAC,CAAC;AAC/E,OAAO,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAC"}
|
|
@@ -0,0 +1,141 @@
|
|
|
1
|
+
/** Example: pollution model (20 species) → LaTeX, no metadata, no inits. */
|
|
2
|
+
import { convertIvpToLatex } from '../index';
|
|
3
|
+
const MODEL = `#name: Pollution
|
|
4
|
+
#description: The chemical reaction part of the air pollution model developed at The Dutch National Institute of Public Health and Environmental Protection
|
|
5
|
+
#comment:
|
|
6
|
+
Source: https://archimede.uniba.it/~testset/report/pollu.pdf
|
|
7
|
+
#equations:
|
|
8
|
+
dy1/dt = -(r1 + r10 + r14 + r23 + r24) + (r2 + r3 + r9 + r11 + r12 + r22 + r25)
|
|
9
|
+
|
|
10
|
+
dy2/dt = -r2 - r3 - r9 - r12 + r1 + r21
|
|
11
|
+
|
|
12
|
+
dy3/dt = -r15 + r1 + r17 + r19 + r22
|
|
13
|
+
|
|
14
|
+
dy4/dt = -r2 - r16 - r17 - r23 + r15
|
|
15
|
+
|
|
16
|
+
dy5/dt = -r3 +2 * r4 + r6 +r7 +r13 + r20
|
|
17
|
+
|
|
18
|
+
dy6/dt = -r6 - r8 - r14 - r20 + r3 + 2 * r18
|
|
19
|
+
|
|
20
|
+
dy7/dt = -r4 - r5 - r6 + r13
|
|
21
|
+
|
|
22
|
+
dy8/dt = r4 + r5 + r6 + r7
|
|
23
|
+
|
|
24
|
+
dy9/dt = -r7 - r8
|
|
25
|
+
|
|
26
|
+
dy10/dt = -r12 +r7 + r9
|
|
27
|
+
|
|
28
|
+
dy11/dt = -r9 - r10 + r8 + r11
|
|
29
|
+
|
|
30
|
+
dy12/dt = r9
|
|
31
|
+
|
|
32
|
+
dy13/dt = -r11 + r10
|
|
33
|
+
|
|
34
|
+
dy14/dt = -r13 + r12
|
|
35
|
+
|
|
36
|
+
dy15/dt = r14
|
|
37
|
+
|
|
38
|
+
dy16/dt = -r18 - r19 + r16
|
|
39
|
+
|
|
40
|
+
dy17/dt = -r20
|
|
41
|
+
|
|
42
|
+
dy18/dt = r20
|
|
43
|
+
|
|
44
|
+
dy19/dt = -r21 - r22 - r24 + r23 + r25
|
|
45
|
+
|
|
46
|
+
dy20/dt = -r25 + r24
|
|
47
|
+
|
|
48
|
+
#expressions:
|
|
49
|
+
r1 = k1 * y1
|
|
50
|
+
r2 = k2 * y2 * y4
|
|
51
|
+
r3 = k3 * y5 * y2
|
|
52
|
+
r4 = k4 * y7
|
|
53
|
+
r5 = k5 * y7
|
|
54
|
+
r6 = k6 * y7 * y6
|
|
55
|
+
r7 = k7 * y9
|
|
56
|
+
r8 = k8 * y9 * y6
|
|
57
|
+
r9 = k9 * y11 * y2
|
|
58
|
+
r10 = k10 * y11 * y1
|
|
59
|
+
r11 = k11 * y13
|
|
60
|
+
r12 = k12 * y10 * y2
|
|
61
|
+
r13 = k13 * y14
|
|
62
|
+
r14 = k14 * y1 * y6
|
|
63
|
+
r15 = k15 * y3
|
|
64
|
+
r16 = k16 * y4
|
|
65
|
+
r17 = k17 * y4
|
|
66
|
+
r18 = k18 * y16
|
|
67
|
+
r19 = k19 * y16
|
|
68
|
+
r20 = k20 * y17 * y6
|
|
69
|
+
r21 = k21 * y19
|
|
70
|
+
r22 = k22 * y19
|
|
71
|
+
r23 = k23 * y1 * y4
|
|
72
|
+
r24 = k24 * y19 * y1
|
|
73
|
+
r25 = k25 * y20
|
|
74
|
+
|
|
75
|
+
#argument: t
|
|
76
|
+
t0 = 0 {units: min; caption: Initial; category: Time; min: 0; max: 0.9}
|
|
77
|
+
t1 = 60 {units: min; caption: Final; category: Time; min: 1; max: 100; step: 1}
|
|
78
|
+
h = 0.1 {units: min; caption: Step; category: Time; min: 0.001; max: 0.1; step: 0.001}
|
|
79
|
+
|
|
80
|
+
#inits:
|
|
81
|
+
y1 = 0 {caption: NO2; category: Initial concentrations; min: 0; max: 0.1}
|
|
82
|
+
y2 = 0.2 {caption: NO; category: Initial concentrations; min: 0; max: 0.4}
|
|
83
|
+
y3 = 0 {caption: O3P; category: Initial concentrations; min: 0; max: 0.1}
|
|
84
|
+
y4 = 0.04 {caption: O3; category: Initial concentrations; min: 0; max: 0.1}
|
|
85
|
+
y5 = 0 {caption: HO2; category: Initial concentrations}
|
|
86
|
+
y6 = 0 {caption: OH; category: Initial concentrations}
|
|
87
|
+
y7 = 0.1 {caption: HCHO; category: Initial concentrations}
|
|
88
|
+
y8 = 0.3 {caption: CO; category: Initial concentrations}
|
|
89
|
+
y9 = 0.01 {caption: ALD; category: Initial concentrations}
|
|
90
|
+
y10 = 0 {caption: MEO2; category: Initial concentrations}
|
|
91
|
+
y11 = 0 {caption: C2O3; category: Initial concentrations}
|
|
92
|
+
y12 = 0 {caption: CO2; category: Initial concentrations}
|
|
93
|
+
y13 = 0 {caption: PAN; category: Initial concentrations}
|
|
94
|
+
y14 = 0 {caption: CH3O; category: Initial concentrations}
|
|
95
|
+
y15 = 0 {caption: HNO3; category: Initial concentrations}
|
|
96
|
+
y16 = 0 {caption: O1D; category: Initial concentrations}
|
|
97
|
+
y17 = 0.007 {caption: SO2; category: Initial concentrations}
|
|
98
|
+
y18 = 0 {caption: SO4; category: Initial concentrations}
|
|
99
|
+
y19 = 0 {caption: NO3; category: Initial concentrations}
|
|
100
|
+
y20 = 0 {caption: N2O5; category: Initial concentrations}
|
|
101
|
+
|
|
102
|
+
#output:
|
|
103
|
+
t {caption: t, min}
|
|
104
|
+
y1 {caption: NO2}
|
|
105
|
+
y2 {caption: NO}
|
|
106
|
+
|
|
107
|
+
#parameters:
|
|
108
|
+
k1 = 0.35 {category: Reaction constants}
|
|
109
|
+
k2 = 26.6 {category: Reaction constants}
|
|
110
|
+
k3 = 1.23e4 {category: Reaction constants}
|
|
111
|
+
k4 = 8.6e-4 {category: Reaction constants}
|
|
112
|
+
k5 = 8.2e-4 {category: Reaction constants}
|
|
113
|
+
k6 = 1.5e4 {category: Reaction constants}
|
|
114
|
+
k7 = 1.3e-4 {category: Reaction constants}
|
|
115
|
+
k8 = 2.4e4 {category: Reaction constants}
|
|
116
|
+
k9 = 1.65e4 {category: Reaction constants}
|
|
117
|
+
k10 = 9e3 {category: Reaction constants}
|
|
118
|
+
k11 = 0.022 {category: Reaction constants}
|
|
119
|
+
k12 = 1.2e4 {category: Reaction constants}
|
|
120
|
+
k13 = 1.88 {category: Reaction constants}
|
|
121
|
+
k14 = 1.63e4 {category: Reaction constants}
|
|
122
|
+
k15 = 4.8e6 {category: Reaction constants}
|
|
123
|
+
k16 = 3.5e-4 {category: Reaction constants}
|
|
124
|
+
k17 = 0.0175 {category: Reaction constants}
|
|
125
|
+
k18 = 1e8 {category: Reaction constants}
|
|
126
|
+
k19 = 4.44e11 {category: Reaction constants}
|
|
127
|
+
k20 = 1240 {category: Reaction constants}
|
|
128
|
+
k21 = 2.1 {category: Reaction constants}
|
|
129
|
+
k22 = 5.78 {category: Reaction constants}
|
|
130
|
+
k23 = 0.0474 {category: Reaction constants}
|
|
131
|
+
k24 = 1780 {category: Reaction constants}
|
|
132
|
+
k25 = 3.12 {category: Reaction constants}
|
|
133
|
+
|
|
134
|
+
#tolerance: 1e-6`;
|
|
135
|
+
// Large model: no metadata, no inits — focus on equations & parameters
|
|
136
|
+
const latex = convertIvpToLatex(MODEL, {
|
|
137
|
+
includeMetadata: false,
|
|
138
|
+
includeInits: false,
|
|
139
|
+
});
|
|
140
|
+
console.log(latex);
|
|
141
|
+
//# sourceMappingURL=pollution-to-latex.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"pollution-to-latex.js","sourceRoot":"","sources":["../../../../src/latex-export/examples/pollution-to-latex.ts"],"names":[],"mappings":"AAAA,4EAA4E;AAE5E,OAAO,EAAC,iBAAiB,EAAC,MAAM,UAAU,CAAC;AAE3C,MAAM,KAAK,GAAG;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;iBAmIG,CAAC;AAElB,uEAAuE;AACvE,MAAM,KAAK,GAAG,iBAAiB,CAAC,KAAK,EAAE;IACrC,eAAe,EAAE,KAAK;IACtB,YAAY,EAAE,KAAK;CACpB,CAAC,CAAC;AACH,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC"}
|
|
@@ -0,0 +1,25 @@
|
|
|
1
|
+
/** Example: Robertson model → LaTeX without metadata (name, description, comment). */
|
|
2
|
+
import { convertIvpToLatex } from '../index';
|
|
3
|
+
const MODEL = `#name: Robertson
|
|
4
|
+
#description: Robertson's chemical reaction model
|
|
5
|
+
#comment: This is classic example of stiff ODEs.
|
|
6
|
+
#equations:
|
|
7
|
+
dA/dt = -0.04 * A + 1e4 * B * C
|
|
8
|
+
dB/dt = 0.04 * A - 1e4 * B * C - 3e7 * B**2
|
|
9
|
+
dC/dt = 3e7 * B**2
|
|
10
|
+
|
|
11
|
+
#inits:
|
|
12
|
+
A = 1 {units: mol/L; category: Initial concentrations; min: 0; max: 5}
|
|
13
|
+
B = 0 {units: mol/L; category: Initial concentrations; min: 0; max: 5}
|
|
14
|
+
C = 0 {units: mol/L; category: Initial concentrations; min: 0; max: 5}
|
|
15
|
+
|
|
16
|
+
#argument: t
|
|
17
|
+
start = 0 {units: sec; caption: Initial; category: Time; min: 0; max: 1}
|
|
18
|
+
finish = 40 {units: sec; caption: Final; category: Time; min: 2; max: 50}
|
|
19
|
+
step = 0.01 {units: sec; caption: Step; category: Time; min: 0.01; max: 0.1}
|
|
20
|
+
|
|
21
|
+
#tolerance: 1e-7`;
|
|
22
|
+
// Compact, no metadata
|
|
23
|
+
const latex = convertIvpToLatex(MODEL, { compact: true, includeMetadata: false });
|
|
24
|
+
console.log(latex);
|
|
25
|
+
//# sourceMappingURL=robertson-to-latex-no-meta.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"robertson-to-latex-no-meta.js","sourceRoot":"","sources":["../../../../src/latex-export/examples/robertson-to-latex-no-meta.ts"],"names":[],"mappings":"AAAA,sFAAsF;AAEtF,OAAO,EAAC,iBAAiB,EAAC,MAAM,UAAU,CAAC;AAE3C,MAAM,KAAK,GAAG;;;;;;;;;;;;;;;;;;iBAkBG,CAAC;AAElB,uBAAuB;AACvB,MAAM,KAAK,GAAG,iBAAiB,CAAC,KAAK,EAAE,EAAC,OAAO,EAAE,IAAI,EAAE,eAAe,EAAE,KAAK,EAAC,CAAC,CAAC;AAChF,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC"}
|
|
@@ -0,0 +1,19 @@
|
|
|
1
|
+
/** Get the precedence level of an operator.
|
|
2
|
+
* Higher number = higher precedence = binds tighter.
|
|
3
|
+
* @param op operator string
|
|
4
|
+
* @returns numeric precedence level (0–6)
|
|
5
|
+
*/
|
|
6
|
+
export declare function getPrecedence(op: string): number;
|
|
7
|
+
/** Determine if a child expression needs parentheses given the parent operator context.
|
|
8
|
+
* @param childOp operator of the child node (or undefined for atoms)
|
|
9
|
+
* @param parentOp operator of the parent node
|
|
10
|
+
* @param position 'left' or 'right' child
|
|
11
|
+
* @returns true if parentheses are needed
|
|
12
|
+
*/
|
|
13
|
+
export declare function needsParentheses(childOp: string | undefined, parentOp: string, position: 'left' | 'right'): boolean;
|
|
14
|
+
/** Wrap a LaTeX string in \left( \right) if needed.
|
|
15
|
+
* @param latex LaTeX string to wrap
|
|
16
|
+
* @param needed whether wrapping is required
|
|
17
|
+
* @returns wrapped or original string
|
|
18
|
+
*/
|
|
19
|
+
export declare function wrapParens(latex: string, needed: boolean): string;
|
|
@@ -0,0 +1,58 @@
|
|
|
1
|
+
/* Bracket manager: determines when parentheses are needed based on operator precedence. */
|
|
2
|
+
/** Get the precedence level of an operator.
|
|
3
|
+
* Higher number = higher precedence = binds tighter.
|
|
4
|
+
* @param op operator string
|
|
5
|
+
* @returns numeric precedence level (0–6)
|
|
6
|
+
*/
|
|
7
|
+
export function getPrecedence(op) {
|
|
8
|
+
switch (op) {
|
|
9
|
+
case '?': return 1;
|
|
10
|
+
case '<':
|
|
11
|
+
case '>':
|
|
12
|
+
case '<=':
|
|
13
|
+
case '>=':
|
|
14
|
+
case '==':
|
|
15
|
+
case '!=':
|
|
16
|
+
return 2;
|
|
17
|
+
case '+':
|
|
18
|
+
case '-':
|
|
19
|
+
return 3;
|
|
20
|
+
case '*':
|
|
21
|
+
case '/':
|
|
22
|
+
return 4;
|
|
23
|
+
case 'unary': return 5;
|
|
24
|
+
case '**': return 6;
|
|
25
|
+
default: return 0;
|
|
26
|
+
}
|
|
27
|
+
}
|
|
28
|
+
/** Determine if a child expression needs parentheses given the parent operator context.
|
|
29
|
+
* @param childOp operator of the child node (or undefined for atoms)
|
|
30
|
+
* @param parentOp operator of the parent node
|
|
31
|
+
* @param position 'left' or 'right' child
|
|
32
|
+
* @returns true if parentheses are needed
|
|
33
|
+
*/
|
|
34
|
+
export function needsParentheses(childOp, parentOp, position) {
|
|
35
|
+
if (childOp === undefined)
|
|
36
|
+
return false;
|
|
37
|
+
const childPrec = getPrecedence(childOp);
|
|
38
|
+
const parentPrec = getPrecedence(parentOp);
|
|
39
|
+
if (childPrec < parentPrec)
|
|
40
|
+
return true;
|
|
41
|
+
if (childPrec > parentPrec)
|
|
42
|
+
return false;
|
|
43
|
+
// Same precedence: right child of non-commutative ops needs parens
|
|
44
|
+
if (position === 'right' && (parentOp === '-' || parentOp === '/'))
|
|
45
|
+
return true;
|
|
46
|
+
return false;
|
|
47
|
+
}
|
|
48
|
+
/** Wrap a LaTeX string in \left( \right) if needed.
|
|
49
|
+
* @param latex LaTeX string to wrap
|
|
50
|
+
* @param needed whether wrapping is required
|
|
51
|
+
* @returns wrapped or original string
|
|
52
|
+
*/
|
|
53
|
+
export function wrapParens(latex, needed) {
|
|
54
|
+
if (needed)
|
|
55
|
+
return `\\left(${latex}\\right)`;
|
|
56
|
+
return latex;
|
|
57
|
+
}
|
|
58
|
+
//# sourceMappingURL=bracket-manager.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
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|
|
@@ -0,0 +1,13 @@
|
|
|
1
|
+
import { ParsedModel, ConvertOptions } from '../types';
|
|
2
|
+
/** Build a complete LaTeX document from a parsed model.
|
|
3
|
+
* @param model parsed IVP model
|
|
4
|
+
* @param options conversion options
|
|
5
|
+
* @returns LaTeX document string
|
|
6
|
+
*/
|
|
7
|
+
export declare function buildLatexDocument(model: ParsedModel, options?: Partial<ConvertOptions>): string;
|
|
8
|
+
/** Build a complete Markdown document from a parsed model.
|
|
9
|
+
* @param model parsed IVP model
|
|
10
|
+
* @param options conversion options
|
|
11
|
+
* @returns Markdown document string
|
|
12
|
+
*/
|
|
13
|
+
export declare function buildMarkdownDocument(model: ParsedModel, options?: Partial<ConvertOptions>): string;
|