diff --git a/app/scripts/nmr-cli/Dockerfile b/app/scripts/nmr-cli/Dockerfile index e6dfe1e..182b144 100644 --- a/app/scripts/nmr-cli/Dockerfile +++ b/app/scripts/nmr-cli/Dockerfile @@ -1,18 +1,7 @@ # build the image ` docker build --tag nmr-cli . ` # run the container ` docker run -it nmr-cli bash ` -# NOTE: if `docker run` prints -# "Error while loading conda entry point: conda-libmamba-solver (module 'libmambapy' has no attribute 'QueryFormat')" -# this is unrelated to this image/container — it comes from a version mismatch between -# conda-libmamba-solver and libmambapy in your HOST shell's conda (base) environment. -# It does not affect the container. To fix it on the host, run: -# conda update -n base -c conda-forge conda conda-libmamba-solver libmambapy -# or, if that doesn't resolve it: -# conda install -n base -c conda-forge --force-reinstall conda-libmamba-solver libmambapy -# or, to bypass libmamba entirely: -# conda config --set solver classic - -FROM mcr.microsoft.com/playwright:v1.62.1-noble +FROM mcr.microsoft.com/playwright:v1.63.0-noble SHELL ["/bin/bash", "-o", "pipefail", "-c"] diff --git a/app/scripts/nmr-cli/package-lock.json b/app/scripts/nmr-cli/package-lock.json index 1693735..cbb4051 100644 --- a/app/scripts/nmr-cli/package-lock.json +++ b/app/scripts/nmr-cli/package-lock.json @@ -9,31 +9,31 @@ "version": "1.0.0", "license": "ISC", "dependencies": { - "@zakodium/nmr-types": "^0.5.26", - "@zakodium/nmrium-core": "0.7.65", - "@zakodium/nmrium-core-plugins": "0.7.87", - "axios": "^1.19.0", + "@zakodium/nmr-types": "^0.5.33", + "@zakodium/nmrium-core": "0.7.77", + "@zakodium/nmrium-core-plugins": "0.7.109", + 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{ "playwright": "cli.js" }, "engines": { "node": ">=20" - }, - "optionalDependencies": { - "fsevents": "2.3.2" } }, "node_modules/playwright-core": { - "version": "1.62.1", - "resolved": "https://registry.npmjs.org/playwright-core/-/playwright-core-1.62.1.tgz", - "integrity": "sha512-wPYSwEBJY9GHraISXqyqtx0na0LpO3XEX7jNDhntbex7tzUS7kLnZsOlFruFJB4Hi/rhDMjXGqHewDZ68nYZVw==", + "version": "1.63.0", + "resolved": "https://registry.npmjs.org/playwright-core/-/playwright-core-1.63.0.tgz", + "integrity": "sha512-rYCsBF/M5HjUch52bbtVONEFjv6Xu8sm8h72dNlR5bzIE1fvC/bxgspzkjSfU+MweEMmPM8KJebG6nnyxo5mCg==", "license": "Apache-2.0", "bin": { "playwright-core": "cli.js" @@ -1503,17 +1826,38 @@ "license": "MIT" }, "node_modules/typescript": { - "version": "5.9.3", - "resolved": "https://registry.npmjs.org/typescript/-/typescript-5.9.3.tgz", - "integrity": "sha512-jl1vZzPDinLr9eUt3J/t7V6FgNEw9QjvBPdysz9KfQDD41fQrC2Y4vKQdiaUpFT4bXlb1RHhLpp8wtm6M5TgSw==", + "version": "7.0.2", + "resolved": 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"@typescript/typescript-linux-x64": "7.0.2", + "@typescript/typescript-netbsd-arm64": "7.0.2", + "@typescript/typescript-netbsd-x64": "7.0.2", + "@typescript/typescript-openbsd-arm64": "7.0.2", + "@typescript/typescript-openbsd-x64": "7.0.2", + "@typescript/typescript-sunos-x64": "7.0.2", + "@typescript/typescript-win32-arm64": "7.0.2", + "@typescript/typescript-win32-x64": "7.0.2" } }, "node_modules/typescript-event-target": { @@ -1563,9 +1907,9 @@ } }, "node_modules/yargs": { - "version": "18.1.0", - "resolved": "https://registry.npmjs.org/yargs/-/yargs-18.1.0.tgz", - "integrity": "sha512-2rAgRKu54VsHkqI0/tYkmluGXHD4KW7yZoycuqDQ15QOTnc2VVfy0nN/1eMhnQLO00A+dwtK20xuCnc1YGeUyg==", + "version": "18.2.0", + "resolved": "https://registry.npmjs.org/yargs/-/yargs-18.2.0.tgz", + "integrity": "sha512-9OpKOLeaoNFecEp7P6iYbzze/5CqWoH7N3SMs/6y1XF4nMvFMspEGZzJ6uFi9MmQwXhyzqYoSEKO3tvA3Z/o2w==", "license": "MIT", "dependencies": { "cliui": "^9.0.1", @@ -1615,9 +1959,9 @@ } }, "node_modules/zod": { - "version": "4.4.3", - "resolved": "https://registry.npmjs.org/zod/-/zod-4.4.3.tgz", - "integrity": "sha512-ytENFjIJFl2UwYglde2jchW2Hwm4GJFLDiSXWdTrJQBIN9Fcyp7n4DhxJEiWNAJMV1/BqWfW/kkg71UDcHJyTQ==", + "version": "4.6.5", + "resolved": "https://registry.npmjs.org/zod/-/zod-4.6.5.tgz", + "integrity": "sha512-v5l/aFXZQeai4awLbOpSoHecE9UiMrnfx75tEXLjNonXVARxQ5mOeipTjROUchszUNCqnE+hqAMujRsRHsut2Q==", "license": "MIT", "funding": { "url": "https://github.com/sponsors/colinhacks" diff --git a/app/scripts/nmr-cli/package.json b/app/scripts/nmr-cli/package.json index 3d93e43..57a1072 100644 --- a/app/scripts/nmr-cli/package.json +++ b/app/scripts/nmr-cli/package.json @@ -17,27 +17,27 @@ "nmr-cli": "./build/index.js" }, "dependencies": { - "@zakodium/nmr-types": "^0.5.26", - "@zakodium/nmrium-core": "0.7.65", - "@zakodium/nmrium-core-plugins": "0.7.87", - "axios": "^1.19.0", + "@zakodium/nmr-types": "^0.5.33", + "@zakodium/nmrium-core": "0.7.77", + "@zakodium/nmrium-core-plugins": "0.7.109", + "axios": "^1.20.0", "fifo-logger": "^2.0.1", "file-collection": "^6.7.0", "json-stream-stringify": "^3.1.7", "lodash.merge": "^4.6.2", - "mf-parser": "^3.9.2", - "ml-spectra-processing": "^14.34.0", + "mf-parser": "^3.9.3", + "ml-spectra-processing": "^14.35.1", "nmr-correlation": "^3.0.2", - "nmr-processing": "^22.23.6", - "openchemlib": "^9.25.0", - "playwright": "1.62.1", - "yargs": "^18.1.0" + "nmr-processing": "^22.25.2", + "openchemlib": "^9.25.1", + "playwright": "1.63.0", + "yargs": "^18.2.0" }, "devDependencies": { "@types/lodash.merge": "^4.6.9", - "@types/node": "^26.6.3", + "@types/node": "^26.6.4", "@types/yargs": "^17.0.35", "ts-node": "^10.9.2", - "typescript": "^5.9.3" + "typescript": "^7.0.2" } } diff --git a/app/scripts/nmr-cli/src/correlation.ts b/app/scripts/nmr-cli/src/correlation.ts index b12b8b0..6537493 100644 --- a/app/scripts/nmr-cli/src/correlation.ts +++ b/app/scripts/nmr-cli/src/correlation.ts @@ -104,7 +104,10 @@ export async function generateCorrelationData(input: CorrelationInput) { let correlationData try { - correlationData = buildCorrelationData(spectra as Spectra, options) + correlationData = buildCorrelationData( + spectra as unknown as Spectra, + options + ) } catch (error) { throw new Error( `Failed to build correlation data: ${error instanceof Error ? error.message : String(error)}` diff --git a/app/scripts/nmr-cli/tsconfig.json b/app/scripts/nmr-cli/tsconfig.json index 45db58d..8b17471 100644 --- a/app/scripts/nmr-cli/tsconfig.json +++ b/app/scripts/nmr-cli/tsconfig.json @@ -4,6 +4,8 @@ "module": "NodeNext", "strict": true, "esModuleInterop": true, + "types": ["node"], + "rootDir": "./src", "outDir": "./build", "skipLibCheck": true },