Development

.github/workflows/dev-build.yml

@@ -35,35 +35,35 @@ jobs:
     steps:
       # Clone repository code to runner
       - name: Check out the repo
-        uses: actions/checkout@v4
+        uses: actions/checkout@v7
 
       # Enable multi-architecture builds via QEMU emulation
       - name: Set up QEMU
-        uses: docker/setup-qemu-action@v3
+        uses: docker/setup-qemu-action@v4
 
       # Enable advanced Docker build features (required for caching)
       - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v3
+        uses: docker/setup-buildx-action@v4
 
       # Authenticate with Docker Hub for image push access
       - name: Log in to Docker Hub
-        uses: docker/login-action@v3
+        uses: docker/login-action@v4
         with:
           username: ${{ secrets.DOCKER_USERNAME }}
           password: ${{ secrets.DOCKER_PASSWORD }}
 
       # Detect changes in nmr-cli folder to skip unnecessary builds
       - name: Check for file changes
         id: changes
-        uses: dorny/paths-filter@v3
+        uses: dorny/paths-filter@v4
         with:
           filters: |
             nmr-cli:
               - 'app/scripts/nmr-cli/**'
 
       # Build main nmrKit image with registry caching for faster builds
       - name: Build and push nmrKit Docker image
-        uses: docker/build-push-action@v6
+        uses: docker/build-push-action@v7
         with:
           context: .
           file: ./Dockerfile
@@ -77,7 +77,7 @@ jobs:
       # Build nmr-cli image only if files in app/scripts/nmr-cli/ changed
       - name: Build and push nmr-cli Docker image
         if: steps.changes.outputs.nmr-cli == 'true'
-        uses: docker/build-push-action@v6
+        uses: docker/build-push-action@v7
         with:
           context: ./app/scripts/nmr-cli/
           file: ./app/scripts/nmr-cli/Dockerfile

.github/workflows/doc-deploy.yml

@@ -29,7 +29,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v7
         with:
           fetch-depth: 0 # Not needed if lastUpdated is not enabled
       # - uses: pnpm/action-setup@v2 # Uncomment this if you're using pnpm

.github/workflows/prod-build.yml

@@ -71,27 +71,27 @@ jobs:
     steps:
       # Clone repository code to runner
       - name: Check out the repo
-        uses: actions/checkout@v4
+        uses: actions/checkout@v7
 
       # Enable multi-architecture builds via QEMU emulation
       - name: Set up QEMU
-        uses: docker/setup-qemu-action@v3
+        uses: docker/setup-qemu-action@v4
 
       # Enable advanced Docker build features (required for caching)
       - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v3
+        uses: docker/setup-buildx-action@v4
 
       # Authenticate with Docker Hub for image push access
       - name: Log in to Docker Hub
-        uses: docker/login-action@v3
+        uses: docker/login-action@v4
         with:
           username: ${{ secrets.DOCKER_USERNAME }}
           password: ${{ secrets.DOCKER_PASSWORD }}
 
       # Detect changes in nmr-cli folder to skip unnecessary builds
       - name: Check for file changes
         id: changes
-        uses: dorny/paths-filter@v3
+        uses: dorny/paths-filter@v4
         with:
           filters: |
             nmr-cli:
@@ -107,7 +107,7 @@ jobs:
 
       # Build main nmrKit image with registry caching for faster builds
       - name: Build and push nmrKit Docker image
-        uses: docker/build-push-action@v6
+        uses: docker/build-push-action@v7
         with:
           context: .
           file: ./Dockerfile
@@ -123,7 +123,7 @@ jobs:
       # Build nmr-cli image only if files in app/scripts/nmr-cli/ changed
       - name: Build and push nmr-cli Docker image
         if: steps.changes.outputs.nmr-cli == 'true'
-        uses: docker/build-push-action@v6
+        uses: docker/build-push-action@v7
         with:
           context: ./app/scripts/nmr-cli/
           file: ./app/scripts/nmr-cli/Dockerfile

.github/workflows/test.yml

@@ -31,7 +31,7 @@ jobs:
         python-version: ["3.10"]
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v7
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v5
       with:

Dockerfile

@@ -1,4 +1,4 @@
-FROM continuumio/miniconda3:24.1.2-0 AS nmrkit-ms
+FROM continuumio/miniconda3:25.3.1-1 AS nmrkit-ms
 ARG TARGETARCH=amd64
 
 ENV PYTHON_VERSION=3.10
@@ -24,8 +24,13 @@ RUN apt-get update && \
 
 RUN apt-get update && apt-get -y install docker.io
 
-RUN conda install -c conda-forge python>=PYTHON_VERSION
-RUN conda install -c conda-forge openbabel>=OPENBABEL_VERSION
+RUN conda config --remove-key channels && \
+    conda config --add channels conda-forge && \
+    conda config --set channel_priority strict
+
+RUN conda install -y \
+    "python=${PYTHON_VERSION}" \
+    "openbabel>=${OPENBABEL_VERSION}"
 
 RUN pip3 install rdkit
 
@@ -51,8 +56,11 @@ RUN python3 -m pip install uvicorn[standard]
 
 COPY ./app /code/app
 
-RUN curl -sL https://deb.nodesource.com/setup_current.x | bash -
-RUN apt-get install -y nodejs
+# Download the setup script first so a failure fails the build instead of being masked by the pipe
+RUN curl -fsSL https://deb.nodesource.com/setup_24.x -o /tmp/nodesource_setup.sh && \
+    bash /tmp/nodesource_setup.sh && \
+    apt-get install -y nodejs && \
+    rm -rf /var/lib/apt/lists/* /tmp/nodesource_setup.sh
 RUN npm install -g npm@latest
 
 RUN npm install -g /code/app/scripts/nmr-cli

README.md

@@ -1,9 +1,9 @@
-<p align="center"><a href="#" target="_blank"><img src="/public/img/logo.svg" width="400" alt="NMRKit Logo"></a></p> 
+<p align="center"><a href="#" target="_blank"><img src="/public/img/logo.svg" width="400" alt="NMRKit Logo"></a></p>
 
 [![License](https://img.shields.io/badge/License-MIT%202.0-blue.svg)](https://opensource.org/licenses/MIT)
 [![Maintenance](https://img.shields.io/badge/Maintained%3F-yes-blue.svg)](https://github.com/NFDI4Chem/nmrkit/graphs/commit-activity)
 [![GitHub issues](https://img.shields.io/github/issues/NFDI4Chem/nmrkit.svg)](https://github.com/NFDI4Chem/nmrkit/issues)
-[![GitHub contributors](https://img.shields.io/github/contributors/NFDI4Chem/nmrkit.svg)]([https://GitHub.com/Steinbeck-Lab/cheminformatics-python-microservice/graphs/contributors/](https://github.com/NFDI4Chem/nmrkit/graphs/contributors))
+[![GitHub contributors](https://img.shields.io/github/contributors/NFDI4Chem/nmrkit.svg)](<[https://GitHub.com/Steinbeck-Lab/cheminformatics-python-microservice/graphs/contributors/](https://github.com/NFDI4Chem/nmrkit/graphs/contributors)>)
 [![Powered by CDK](https://img.shields.io/badge/Powered%20by-CDK-blue.svg?style=flat&logo=chem)](https://cdk.github.io)
 [![RDKit badge](https://img.shields.io/badge/Powered%20by-RDKit-3838ff.svg?logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQBAMAAADt3eJSAAAABGdBTUEAALGPC/xhBQAAACBjSFJNAAB6JgAAgIQAAPoAAACA6AAAdTAAAOpgAAA6mAAAF3CculE8AAAAFVBMVEXc3NwUFP8UPP9kZP+MjP+0tP////9ZXZotAAAAAXRSTlMAQObYZgAAAAFiS0dEBmFmuH0AAAAHdElNRQfmAwsPGi+MyC9RAAAAQElEQVQI12NgQABGQUEBMENISUkRLKBsbGwEEhIyBgJFsICLC0iIUdnExcUZwnANQWfApKCK4doRBsKtQFgKAQC5Ww1JEHSEkAAAACV0RVh0ZGF0ZTpjcmVhdGUAMjAyMi0wMy0xMVQxNToyNjo0NyswMDowMDzr2J4AAAAldEVYdGRhdGU6bW9kaWZ5ADIwMjItMDMtMTFUMTU6MjY6NDcrMDA6MDBNtmAiAAAAAElFTkSuQmCC)](https://www.rdkit.org/)
 ![Workflow](https://github.com/NFDI4Chem/nmrkit/actions/workflows/dev-build.yml/badge.svg)
@@ -12,7 +12,6 @@
 [![framework](https://img.shields.io/badge/Framework-FastAPI-blue?style)](https://fastapi.tiangolo.com/)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.8112749.svg)](https://doi.org/10.5281/zenodo.8211374)
 
-
 # Welcome to NMRKit 🚀
 
 NMRKit features a collection of powerful microservices designed to simplify your NMR data processing and analysis. Whether you're a seasoned researcher or a curious chemist, our suite of tools offers NMR Prediction, Validation, and Depiction via the nmrium library, along with seamless Format Conversion using the nmr-load-save package. With our robust API, functionalities, and developer-friendly documentation, exploring and interpreting NMR spectra has never been easier.
@@ -27,7 +26,7 @@ Key Features:
 API Reference (Scalar) - https://dev.nmrkit.nmrxiv.org/latest/docs
 📢 Found a bug or have a feature request? We'd love to hear from you! Please open an issue: [https://github.com/NFDI4Chem/nmrkit/issues]
 
-Happy NMR exploring! 🧪🌟"
+Happy NMR exploring..! 🧪🌟"
 
 ## Help Desk
 
@@ -46,9 +45,9 @@ Licensed under the [MIT license](https://opensource.org/licenses/MIT).
 Venkata, C., Sharma, N. , Stefan Kuhn, Hamed Musallam nmrKit [Computer software]. https://doi.org/10.5281/zenodo.8211374
 
 ## Maintained by
-NMRKit is developed and maintained by the [NFDI4Chem partners](https://www.nfdi4chem.de/) at the [Friedrich Schiller University](https://www.uni-jena.de/en/) Jena, Germany. 
-The code for this web application is released under the [MIT license](https://opensource.org/licenses/MIT).
 
+NMRKit is developed and maintained by the [NFDI4Chem partners](https://www.nfdi4chem.de/) at the [Friedrich Schiller University](https://www.uni-jena.de/en/) Jena, Germany.
+The code for this web application is released under the [MIT license](https://opensource.org/licenses/MIT).
 
 <p align="left"><a href="https://nfdi4chem.de/" target="_blank"><img src="https://www.nfdi4chem.de/wp-content/themes/wptheme/assets/img/logo.svg" width="30%" alt="NFDI4Chem Logo"></a></p>
 <p align="left"><a href="https://cheminf.uni-jena.de/" target="_blank"><img src="/public/img/fsu-jena.jpg" width="30%" alt="NFDI4Chem Logo"></a></p>

app/routers/spectra.py

@@ -3,7 +3,7 @@
 import io
 from app.schemas import HealthCheck
 from pydantic import BaseModel, HttpUrl, Field
-from typing import Optional
+from typing import Optional, List
 import subprocess
 import tempfile
 import os
@@ -50,6 +50,10 @@ class UrlParseRequest(BaseModel):
     )
     raw_data: bool = Field(
         False, description="Include raw data in the output (default: data source)")
+    include: Optional[List[str]] = Field(
+        None, description="Only include files matching pattern(s) (glob/regex string)")
+    exclude: Optional[List[str]] = Field(
+        None, description="Exclude files matching pattern(s) (glob/regex string)")
 
     model_config = {
         "json_schema_extra": {
@@ -95,6 +99,8 @@ def run_command(
     auto_processing: bool = False,
     auto_detection: bool = False,
     raw_data: bool = False,
+    include: Optional[List[str]] = None,
+    exclude: Optional[List[str]] = None,
 ) -> StreamingResponse:
     """Execute nmr-cli parse-spectra command in Docker container."""
 
@@ -113,6 +119,12 @@ def run_command(
         cmd.append("-d")
     if raw_data:
         cmd.append("-r")
+    if include:
+        cmd.append("--include")
+        cmd.extend(include)
+    if exclude:
+        cmd.append("--exclude")
+        cmd.extend(exclude)
 
     try:
         result = subprocess.run(
@@ -362,7 +374,11 @@ async def parse_spectra_from_file(
         description="Enable ranges and zones automatic detection",
     ),
     raw_data: bool = Form(
-        False, description="Include raw data in the output (default: data source references)")
+        False, description="Include raw data in the output (default: data source references)"),
+    include: Optional[List[str]] = Form(
+        None, description="Only include files matching pattern(s) (glob/regex string)"),
+    exclude: Optional[List[str]] = Form(
+        None, description="Exclude files matching pattern(s) (glob/regex string)"),
 ):
     """
     ## Parse spectra from an uploaded file
@@ -376,6 +392,8 @@ async def parse_spectra_from_file(
     | `auto_processing` | Automatically process FID → FT spectra |
     | `auto_detection` | Automatically detect ranges and zones |
     | `raw_data` | Include raw data in the output (default: data source) |
+    | `include` | Only include files matching pattern(s) |
+    | `exclude` | Exclude files matching pattern(s) |
     ### Returns
     Parsed spectra data in NMRium-compatible JSON format.
     """
@@ -405,6 +423,8 @@ async def parse_spectra_from_file(
             auto_processing=auto_processing,
             auto_detection=auto_detection,
             raw_data=raw_data,
+            include=include,
+            exclude=exclude,
         )
 
     except HTTPException:
@@ -452,6 +472,8 @@ async def parse_spectra_from_url(request: UrlParseRequest):
     | `auto_processing` | Automatically process FID → FT spectra |
     | `auto_detection` | Automatically detect ranges and zones |
     | `raw_data` | Include raw data in the output (default: data source) |
+    | `include` | Only include files matching pattern(s) |
+    | `exclude` | Exclude files matching pattern(s) |
 
     ### Returns
     Parsed spectra data in NMRium-compatible JSON format.
@@ -463,6 +485,8 @@ async def parse_spectra_from_url(request: UrlParseRequest):
             auto_processing=request.auto_processing,
             auto_detection=request.auto_detection,
             raw_data=request.raw_data,
+            include=request.include,
+            exclude=request.exclude,
         )
 
     except HTTPException:

app/scripts/nmr-cli/Dockerfile

@@ -1,13 +1,21 @@
 # build the image ` docker build --tag nmr-cli  . ` 
 # run the container ` docker run -it nmr-cli bash `
 
-FROM mcr.microsoft.com/playwright:v1.58.2-noble
+# 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
 
 SHELL ["/bin/bash", "-o", "pipefail", "-c"]
 
-# Downgrade to Node 22
-RUN npm install -g n && n 22 && hash -r
-
 WORKDIR /app
 
 #ENV BASE_NMRIUM_URL=https://nmrium.nmrxiv.org/