CoreMS 3.1.0__tar.gz → 4.0.0__tar.gz

{CoreMS-3.1.0 → corems-4.0.0/CoreMS.egg-info}/PKG-INFO

@@ -1,18 +1,62 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: CoreMS
-Version: 3.1.0
+Version: 4.0.0
 Summary: Mass Spectrometry Framework for Small Molecules Analysis
-Home-page: https://github.com/EMSL-Computing/CoreMS
-Author: Corilo, Yuri
-Author-email: corilo@pnnl.gov
+Author-email: "Corilo, Yuri" <corilo@pnnl.gov>
+License: BSD
+Project-URL: Homepage, https://github.com/EMSL-Computing/CoreMS
+Project-URL: Repository, https://github.com/EMSL-Computing/CoreMS
+Project-URL: Issues, https://github.com/EMSL-Computing/CoreMS/issues
 Classifier: License :: OSI Approved :: BSD License
-Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
 Classifier: Development Status :: 4 - Beta
+Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
+Requires-Dist: beautifulsoup4>=4.12.3
+Requires-Dist: chardet>=5.2.0
+Requires-Dist: h5py>=3.13.0
+Requires-Dist: IsoSpecPy>=2.2.2
+Requires-Dist: lmfit>=1.3.0
+Requires-Dist: lxml>=5.2.0
+Requires-Dist: matplotlib>=3.9.0
+Requires-Dist: ms-entropy>=1.2.2
+Requires-Dist: netCDF4>=1.7.0
+Requires-Dist: numpy>=2.1.0
+Requires-Dist: openpyxl>=3.1.2
+Requires-Dist: pandas>=2.2.2
+Requires-Dist: psycopg2-binary>=2.9.10
+Requires-Dist: pyswarm>=0.6
+Requires-Dist: pythonnet>=3.0.3
+Requires-Dist: pymzml>=2.5.11
+Requires-Dist: requests>=2.32.0
+Requires-Dist: ripser>=0.6.4
+Requires-Dist: s3path>=0.5.0
+Requires-Dist: scikit_learn>=1.5.0
+Requires-Dist: scipy>=1.14.0
+Requires-Dist: seaborn>=0.13.2
+Requires-Dist: setuptools>=72.0.0
+Requires-Dist: SQLAlchemy>=2.0.0
+Requires-Dist: packaging>=23.0
+Requires-Dist: toml>=0.10.2
+Requires-Dist: tqdm>=4.66.0
+Provides-Extra: dev
+Requires-Dist: pylint; extra == "dev"
+Requires-Dist: pytest>=8.3.2; extra == "dev"
+Requires-Dist: pytest-cov>=5.0.0; extra == "dev"
+Requires-Dist: pytest-xdist>=3.6.1; extra == "dev"
+Requires-Dist: pyprof2calltree; extra == "dev"
+Requires-Dist: memory_profiler; extra == "dev"
+Requires-Dist: twine; extra == "dev"
+Requires-Dist: bump2version; extra == "dev"
+Requires-Dist: psutil>=5.6.6; extra == "dev"
+Requires-Dist: PyWavelets; extra == "dev"
+Requires-Dist: pdoc>=14.1.0; extra == "dev"
+Dynamic: license-file
 
 ![CoreMS Logo](https://github.com/EMSL-Computing/CoreMS/blob/master/docs/CoreMS.COLOR_small.png?raw=true)  
 
@@ -20,7 +64,10 @@ License-File: LICENSE
 
 <br>
 <br>
-<a href="https://doi.org/10.5281/zenodo.14009575"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.14009575.svg" alt="DOI"></a>
+<a href="https://doi.org/10.5281/zenodo.4641552"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.4641552.svg" alt="DOI"></a>
+<a href="https://github.com/EMSL-Computing/CoreMS/actions/workflows/ci.yml"><img src="https://github.com/EMSL-Computing/CoreMS/actions/workflows/ci.yml/badge.svg" alt="CI"></a>
+<a href="https://pypi.org/project/CoreMS/"><img src="https://img.shields.io/pypi/v/CoreMS.svg" alt="PyPI"></a>
+<a href="https://pypi.org/project/CoreMS/"><img src="https://img.shields.io/pypi/pyversions/CoreMS.svg" alt="Python versions"></a>
 <br>
 </div>
 
@@ -39,9 +86,8 @@ License-File: LICENSE
   - [Installation](#corems-installation)  
   - [Thermo Raw File on Mac and Linux](#thermo-raw-file-access)  
 - Execution     
-  - [Jupyter Notebook and Docker containers](#docker-stack)  
+  - [Building and Running the Docker Image](#docker-image)
   - [Example for FT-ICR Data Processing](#simple-script-example)  
-  - [Python Examples](examples/scripts)
   - [Jupyter Notebook Examples](examples/notebooks)  
 - Sibling Projects    
     - [EnviroMS](https://github.com/EMSL-Computing/EnviroMS)  
@@ -65,7 +111,7 @@ CoreMS aims to provide
 
 ## Current Version
 
- `3.1.0`
+ `4.0.0`
 
 ***
 
@@ -167,6 +213,7 @@ As an open source project, CoreMS welcomes contributions of all forms. Before co
 - Calculated ICR Resolving Power based on magnetic field (B), and transient time(T)
 
 ### LC-MS Signal Processing, Molecular Formula Search and Assignment, and Spectral Similarity Searches
+See walkthrough in [this notebook](examples/notebooks/LCMS_Tutorial.ipynb)
 - Two dimensional (m/z and retention time) peak picking using persistent homology
 - Smoothing, cetroid detection, and integration of extracted ion chromatograms
 - Peak shape metric calculations including half peak height, tailing factor, and dispersity index
@@ -183,16 +230,24 @@ As an open source project, CoreMS welcomes contributions of all forms. Before co
 pip install corems
 ```
 
-By default the molecular formula database will be generated using SQLite
+Corems requires **Python 3.9 or later** (including Python 3.13) and is compatible with **NumPy 2.x**, **pandas 2.x**, and **SQLAlchemy 2.x**.
 
-To use Postgresql the easiest way is to build a docker container:
+To install with development and testing extras:
+
+```bash
+pip install "corems[dev]"
+```
+
+By default the molecular formula database will be generated using SQLite.
+
+To use PostgreSQL the easiest way is to build a docker container:
 
 ```bash
 docker-compose up -d
 ```
 
--  Change the url_database on MSParameters.molecular_search.url_database to: "postgresql+psycopg2://coremsappdb:coremsapppnnl@localhost:5432/coremsapp"
--  Set the url_database env variable COREMS_DATABASE_URL to: "postgresql+psycopg2://coremsappdb:coremsapppnnl@localhost:5432/coremsapp"
+- Change the url_database on `MSParameters.molecular_search.url_database` to: `"postgresql+psycopg2://coremsappdb:coremsapppnnl@localhost:5432/coremsapp"`
+- Set the env variable `COREMS_DATABASE_URL` to: `"postgresql+psycopg2://coremsappdb:coremsapppnnl@localhost:5432/coremsapp"`
 
 ### Thermo Raw File Access:
 
@@ -210,66 +265,103 @@ To be able to open thermo file a installation of pythonnet is needed:
 
 ***
 
-## Docker stack 
+## Building and Running the CoreMS Docker Image <a name="docker-image"></a>
 
-Another option to use CoreMS is to run the docker stack that will start the CoreMS containers
+CoreMS provides a Dockerfile that packages the entire application (including .NET 8 runtime for Thermo .raw file support) into a self-contained image. This is useful for running CoreMS in a reproducible environment without installing dependencies on your host system.
 
-### Molecular Database and Jupyter Notebook Docker Containers
+### Prerequisites
+- Docker installed and running on your system.
+- The CoreMS repository cloned locally.
+- Navigate to the root of the CoreMS repository before running any commands.
 
-A docker container containing:
-- A custom python distribution will all dependencies installed
-- A Jupyter notebook server with workflow examples
-- A PostgreSQL database for the molecular formulae assignment
+### Building the Docker Image
 
-If you don't have docker installed, the easiest way is to [install docker for desktop](https://hub.docker.com/?overlay=onboarding)
+The Makefile provides convenience targets for building the image. The image is tagged with the current version from `.bumpversion.cfg`.
 
-1. Start the containers using docker-compose (easiest way): 
+**On Linux/Windows (standard build):**
+```bash
+make build-image-local
+```
 
-    On docker-compose-jupyter.yml there is a volume mapping for the tests_data directory with the data provided for testing, to change to your data location: 
-    
-    - locate the volumes on docker-compose-jupyter.yml:
+**On macOS (cross-platform build for linux/amd64):**
+```bash
+make build-image-mac-local
+```
 
-    ```bash
-    volumes:
-      - ./tests/tests_data:/home/CoreMS/data
-    ```
-    - change "./tests/tests_data" to your data directory location
+This runs `docker build` with the `--platform linux/amd64` flag, which is necessary when building on Apple Silicon (M1/M2/M3) Macs to ensure compatibility.
 
-    ```bash
-    volumes:
-      - path_to_your_data_directory:/home/corems/data
-    ```
-    - save the file and then call:
-    
-    ```bash
-    docker-compose -f docker-compose-jupyter.yml up
-    ```
+Alternatively, you can build manually with:
+```bash
+docker build -t corems:<version> .
+```
+Replace `<version>` with your desired tag (e.g., `4.0.0`).
 
-2. Another option is to manually build the containers: 
-
-    - Build the corems image:
-        ```bash
-        docker build -t corems:local .
-        ```
-    - Start the database container:
-        ```bash
-        docker-compose up -d   
-        ```
-    - Start the Jupyter Notebook:
-        ```bash
-        docker run --rm -v ./data:/home/CoreMS/data corems:local
-        ```
-    
-    - Open your browser, copy and past the URL address provided in the terminal: `http://localhost:8888/?token=<token>.`
+### What the Dockerfile Does
 
-    - Open the CoreMS-Tutorial.ipynb
+The Dockerfile performs the following steps:
+1. Starts from a `python:3.13-slim` base image.
+2. Installs the .NET 8 runtime (required for Thermo .raw file support via PythonNET).
+3. Copies the CoreMS source code into the image.
+4. Installs CoreMS and all its dependencies via `pip install .`.
+5. Installs `pytest-xdist` and `pytest-cov` for running tests.
+6. Removes build-time dependencies (gcc, python3-dev) to keep the image lean.
 
+### Running the Docker Image
+
+**On Linux/Windows:**
+```bash
+make image-run-local
+```
+
+**On macOS:**
+```bash
+make image-run-mac-local
+```
+
+This launches an interactive bash shell inside the container:
+```bash
+docker run -it corems:<version>
+```
+
+From within the container, you can import and use CoreMS directly:
+```python
+python3 -c "import corems; print(corems.__version__)"
+```
+
+### Mounting Data into the Container
+
+To process your own data files, mount a local directory into the container:
+```bash
+docker run -it -v /path/to/your/data:/data corilo/corems:<version>
+```
+Your files will then be accessible at `/data` inside the container.
+
+### Managing the PostgreSQL Database with Docker Compose
+
+The `docker-compose.yml` file defines a PostgreSQL database service for CoreMS. The Makefile provides targets to manage it:
+
+**Start the database:**
+```bash
+make db-up
+```
+
+**Stop the database:**
+```bash
+make db-down
+```
+
+**View database logs:**
+```bash
+make db-logs
+```
+
+These are equivalent to running `docker-compose up -d`, `docker-compose down`, and `docker-compose logs -f` respectively.
 
 ***
 
 ## Example for FT-ICR Data Processing
 
-More examples can be found under the directory examples/scripts, examples/notebooks
+More examples can be found in the [examples/notebooks](examples/notebooks) directory
 
 - Basic functionality example
 
@@ -349,15 +441,11 @@ UML (unified modeling language) diagrams for Direct Infusion FT-MS and GC-MS cla
 
 ## Citing CoreMS
 
-If you use CoreMS in your work, please use the following citation:
+If you use CoreMS in your work, please cite the archived release on Zenodo. The badge below is the *concept DOI* — it always resolves to the latest archived release, and each archived release also has its own version-specific DOI listed on that page.
 
-Version [3.1.0 Release on GitHub](https://github.com/EMSL-Computing/CoreMS/releases/tag/v3.1.0), archived on Zenodo:  
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4641552.svg)](https://doi.org/10.5281/zenodo.4641552)
 
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.14009575.svg)](https://doi.org/10.5281/zenodo.14009575)
-
-Yuri E. Corilo, William R. Kew, Lee Ann McCue, Katherine R . Heal, James C. Carr (2024, October 29). EMSL-Computing/CoreMS: CoreMS 3.1.0 (Version v3.1.0), as developed on Github. Zenodo. http://doi.org/10.5281/zenodo.14009575
-
-```
+For citation metadata (BibTeX, RIS, etc.), use the "Cite this repository" button on the GitHub sidebar, click "Export" on the Zenodo page above, or see [`CITATION.cff`](CITATION.cff) in the repository root.
 
 ***
 

{CoreMS-3.1.0 → corems-4.0.0}/CoreMS.egg-info/SOURCES.txt

@@ -3,7 +3,7 @@ LICENSE
 MANIFEST.in
 README.md
 disclaimer.txt
-requirements.txt
+pyproject.toml
 setup.py
 CoreMS.egg-info/PKG-INFO
 CoreMS.egg-info/SOURCES.txt
@@ -14,6 +14,7 @@ corems/__init__.py
 corems/chroma_peak/__init__.py
 corems/chroma_peak/calc/ChromaPeakCalc.py
 corems/chroma_peak/calc/__init__.py
+corems/chroma_peak/calc/subset.py
 corems/chroma_peak/factory/__init__.py
 corems/chroma_peak/factory/chroma_peak_classes.py
 corems/encapsulation/__init__.py
@@ -34,6 +35,7 @@ corems/mass_spectra/calc/MZSearch.py
 corems/mass_spectra/calc/SignalProcessing.py
 corems/mass_spectra/calc/__init__.py
 corems/mass_spectra/calc/lc_calc.py
+corems/mass_spectra/calc/lc_calc_operations.py
 corems/mass_spectra/factory/GC_Class.py
 corems/mass_spectra/factory/__init__.py
 corems/mass_spectra/factory/chromat_data.py
@@ -42,6 +44,7 @@ corems/mass_spectra/input/__init__.py
 corems/mass_spectra/input/andiNetCDF.py
 corems/mass_spectra/input/boosterHDF5.py
 corems/mass_spectra/input/brukerSolarix.py
+corems/mass_spectra/input/brukerSolarix_utils.py
 corems/mass_spectra/input/corems_hdf5.py
 corems/mass_spectra/input/massList.py
 corems/mass_spectra/input/mzml.py
@@ -84,6 +87,8 @@ corems/molecular_id/calc/MolecularFilter.py
 corems/molecular_id/calc/SpectralSimilarity.py
 corems/molecular_id/calc/__init__.py
 corems/molecular_id/calc/math_distance.py
+corems/molecular_id/data/FAMES_REF.msp
+corems/molecular_id/data/PNNLMetV20191015.msp
 corems/molecular_id/factory/EI_SQL.py
 corems/molecular_id/factory/MolecularLookupTable.py
 corems/molecular_id/factory/__init__.py
@@ -113,6 +118,19 @@ corems/transient/factory/__init__.py
 corems/transient/input/__init__.py
 corems/transient/input/brukerSolarix.py
 corems/transient/input/midasDatFile.py
+examples/test_notebooks.py
+examples/archive/scripts/CoreMS_tutorial.py
+examples/archive/scripts/DI HR-MS Halogens Bruker.py
+examples/archive/scripts/DI HR-MS MassList.py
+examples/archive/scripts/GC-MS MetabRef.py
+examples/archive/scripts/GC-MS NetCDF.py
+examples/archive/scripts/HR-MS Thermo Raw 21T.py
+examples/archive/scripts/LC-ICPMS_metal_peaks.py
+examples/archive/scripts/LCMS-Thermo.py
+examples/archive/scripts/LCMS_isotopes.py
+examples/archive/scripts/MSParams_example.py
+examples/archive/scripts/Molecular Formula Data Aggreation.py
+examples/archive/scripts/Single Mz Search.py
 ext_lib/ChemstationMSFileReader.dll
 ext_lib/ChemstationMSFileReader.xml
 ext_lib/RawFileReaderLicense.doc
@@ -143,17 +161,36 @@ ext_lib/dotnet/ThermoFisher.CommonCore.MassPrecisionEstimator.dll
 ext_lib/dotnet/ThermoFisher.CommonCore.MassPrecisionEstimator.xml
 ext_lib/dotnet/ThermoFisher.CommonCore.RawFileReader.dll
 ext_lib/dotnet/ThermoFisher.CommonCore.RawFileReader.xml
+support_code/atom_parsers/AtomsDescription.py
+support_code/atom_parsers/CreateAtomsDescription.py
+support_code/nmdc/filefinder.py
+support_code/nmdc/lipidomics/lipidomics_workflow.py
+support_code/nmdc/lipidomics/manifest_examples.py
+support_code/nmdc/metabolomics/gcms_workflow.py
+support_code/nmdc/metabolomics/lcms_metabolomics_targeted_search.py
+support_code/nmdc/metabolomics/lcms_metabolomics_workflow.py
+support_code/nmdc/metabolomics/metabolomics_collection.py
+support_code/nmdc/metadata/dms_api.py
+support_code/nmdc/nom/nom_workflow.py
+support_code/nmdc/nom/archived_scripts/nmdc_metadata_gen.py
+support_code/nmdc/nom/archived_scripts/nom_grow_workflow.py
+support_code/windows_only_importers/BrukerCompassXtract.py
+support_code/windows_only_importers/ThermoMSFileReader.py
 tests/test_calibration.py
 tests/test_classification.py
 tests/test_gcms.py
 tests/test_input.py
+tests/test_lcms_collection.py
+tests/test_lcms_metabolomics.py
 tests/test_mass_spectrum.py
 tests/test_mass_spectrum_export_import.py
 tests/test_molecular_formula.py
 tests/test_molecular_formula_db_factory.py
 tests/test_molecular_formula_search.py
 tests/test_mspeak.py
+tests/test_noise_calc.py
 tests/test_output.py
 tests/test_search_mass_list.py
 tests/test_setting_settings.py
+tests/test_time_range_filtering.py
 tests/test_wf_lipidomics.py

corems-4.0.0/CoreMS.egg-info/requires.txt

@@ -0,0 +1,40 @@
+beautifulsoup4>=4.12.3
+chardet>=5.2.0
+h5py>=3.13.0
+IsoSpecPy>=2.2.2
+lmfit>=1.3.0
+lxml>=5.2.0
+matplotlib>=3.9.0
+ms-entropy>=1.2.2
+netCDF4>=1.7.0
+numpy>=2.1.0
+openpyxl>=3.1.2
+pandas>=2.2.2
+psycopg2-binary>=2.9.10
+pyswarm>=0.6
+pythonnet>=3.0.3
+pymzml>=2.5.11
+requests>=2.32.0
+ripser>=0.6.4
+s3path>=0.5.0
+scikit_learn>=1.5.0
+scipy>=1.14.0
+seaborn>=0.13.2
+setuptools>=72.0.0
+SQLAlchemy>=2.0.0
+packaging>=23.0
+toml>=0.10.2
+tqdm>=4.66.0
+
+[dev]
+pylint
+pytest>=8.3.2
+pytest-cov>=5.0.0
+pytest-xdist>=3.6.1
+pyprof2calltree
+memory_profiler
+twine
+bump2version
+psutil>=5.6.6
+PyWavelets
+pdoc>=14.1.0

corems-4.0.0/CoreMS.egg-info/top_level.txt

@@ -0,0 +1,7 @@
+corems
+db
+dist
+docs
+examples
+ext_lib
+support_code

corems-4.0.0/Dockerfile

@@ -0,0 +1,37 @@
+FROM python:3.13-slim AS base
+WORKDIR /home/corems
+
+# Install .NET 8 runtime via official install script (avoids APT keyring SHA1 issue)
+RUN apt-get update && apt-get install -y --no-install-recommends \
+        curl ca-certificates libssl3 libkrb5-3 zlib1g && \
+    curl -sSL https://dot.net/v1/dotnet-install.sh -o /tmp/dotnet-install.sh && \
+    chmod +x /tmp/dotnet-install.sh && \
+    /tmp/dotnet-install.sh --runtime dotnet --channel 8.0 --install-dir /usr/local/dotnet && \
+    rm /tmp/dotnet-install.sh && \
+    apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/*
+
+ENV DOTNET_ROOT=/usr/local/dotnet
+ENV PATH="${PATH}:/usr/local/dotnet"
+ENV PYTHONNET_RUNTIME=coreclr
+ENV DOTNET_SYSTEM_GLOBALIZATION_INVARIANT=1
+
+# Install the corems package (pyproject.toml defines all dependencies)
+# gcc is needed to compile ms-entropy's Cython extension; purged afterwards to keep the image lean
+COPY pyproject.toml README.md disclaimer.txt ./
+COPY ./ ./
+RUN apt-get update && apt-get install -y --no-install-recommends gcc python3-dev && \
+    python3 -m pip install --upgrade pip && \
+    python3 -m pip install --no-cache-dir . && \
+    python -m pip install pytest-xdist && \
+    python -m pip install pytest-cov && \
+    apt-get purge -y gcc python3-dev && apt-get autoremove -y && \
+    apt-get clean && rm -rf /var/lib/apt/lists/*
+
+FROM base AS build
+WORKDIR /home/corems
+
+#COPY examples/notebooks/*.ipynb README.md ./
+
+CMD ["/bin/bash"]
+
+

{CoreMS-3.1.0 → corems-4.0.0}/MANIFEST.in

@@ -1,5 +1,5 @@
-include requirements.txt
 include disclaimer.txt
 include Dockerfile
 include ext_lib/*
 include ext_lib/dotnet/*
+include corems/molecular_id/data/*.msp