lcmodel-wrapper 0.2.0__tar.gz → 0.3.1__tar.gz

lcmodel_wrapper-0.3.1/NOTICE

@@ -0,0 +1,24 @@
+PyLCModel (lcmodel_wrapper)
+Copyright (c) 2024 Julian P. Merkofer and contributors
+
+Licensed under the Apache License, Version 2.0 (see LICENSE).
+
+------------------------------------------------------------------------------
+LCModel
+------------------------------------------------------------------------------
+
+LCModel is NOT part of this project's copyright. It is a separate program by
+Dr. Stephen Provencher, distributed under the BSD 3-Clause License
+(Copyright (c) 1992-2021, Stephen Provencher); see LICENSE.lcmodel for the
+full text. Home page: https://s-provencher.com/lcmodel.shtml
+
+This wrapper bundles no LCModel code or binary. At run time it may obtain one
+from these sources, and the BSD 3-Clause license applies to every one of them:
+
+  - the community binary collection at https://github.com/schorschinho/LCModel
+    (maintained by Georg Oeltzschner and contributors),
+  - binaries and the container image ghcr.io/julianmer/lcmodel built by this
+    repository's CI (.github/workflows/lcmodel-binaries.yml) from the pinned
+    upstream source, unmodified, using the compilation flags documented there;
+    LICENSE.lcmodel and this NOTICE are published alongside them,
+  - a local build from the same source via gfortran.

{lcmodel_wrapper-0.2.0 → lcmodel_wrapper-0.3.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: lcmodel_wrapper
-Version: 0.2.0
+Version: 0.3.1
 Summary: Lightweight Python wrapper for LCModel MRS fitting
 Author-email: Julian Merkofer <j.p.merkofer@tue.nl>
 License: Apache-2.0
@@ -16,6 +16,7 @@ Requires-Dist: scipy>=1.10
 Requires-Dist: nibabel>=4.0
 Requires-Dist: nifti-mrs>=1.0
 Provides-Extra: test
+Requires-Dist: pytest>=7.0; extra == "test"
 Requires-Dist: pandas>=1.4; extra == "test"
 Requires-Dist: openpyxl>=3.0; extra == "test"
 Dynamic: license-file
@@ -36,7 +37,7 @@ Dynamic: license-file
 
 ## Features
 
-- **Zero-setup binaries** — the LCModel executable is resolved automatically (download, build from source, or your own path); nothing is bundled in the wheel.
+- **Zero-setup binaries** — the LCModel executable is resolved automatically (download, container image, build from source, or your own path); nothing is bundled in the wheel.
 - **Flexible input** — NumPy arrays, NIfTI-MRS, jMRUI text, and LCModel `.RAW`, in time or frequency domain.
 - **Automated control files** — generated to match your data, or templated from an existing one.
 - **Basis conversion (experimental)** — jMRUI, FSL-MRS, LCModel `.RAW`, and Osprey/FID-A basis sets to `.basis`.
@@ -50,7 +51,6 @@ Dynamic: license-file
 ```bash
 pip install lcmodel-wrapper
 ```
-Enter your API token:
 
 ### From Source
 ```bash
@@ -58,19 +58,28 @@ git clone https://github.com/julianmer/PyLCModel.git
 cd PyLCModel
 pip install -e .
 ```
+Add `--recursive` to the clone (or run `git submodule update --init`) to also fetch the
+[ISMRM 2016 fitting challenge](https://www.ismrm.org/workshops/Spectroscopy16/mrs_fitting_challenge/)
+example data used by the tests.
 
 ---
 
 ## How the LCModel binary is handled
 
-The LCModel program is **not** part of this package and is **not** shipped in the wheel. On first use, the binary is resolved in this order:
+LCModel is **not** shipped in the wheel. On first use it is found in this order, and the first one that works is cached:
 
-1. an explicit `path2exec="/path/to/lcmodel"` you pass to `PyLCModel`,
-2. a previously cached download/build (under `~/.cache/lcmodel_wrapper`, or `%LOCALAPPDATA%` on Windows; override with `LCMODEL_CACHE_DIR`),
-3. a download of the matching binary for your OS/architecture from [schorschinho/LCModel](https://github.com/schorschinho/LCModel),
-4. a build from the LCModel Fortran source via `gfortran` (source fetched on demand).
+1. `path2exec` you pass to `PyLCModel`,
+2. the community binary for your OS/architecture from [schorschinho/LCModel](https://github.com/schorschinho/LCModel),
+3. the binary built by this repository's CI for the installed version ([releases](https://github.com/julianmer/PyLCModel/releases); Linux x86_64/aarch64 and macOS arm64/x86_64, all statically linked),
+4. the container image `ghcr.io/julianmer/lcmodel`, if Docker or podman is running,
+5. a build from source with `gfortran`.
 
-There is no git submodule and no bundled `lcmodel/` folder — keeping both the repository and the PyPI wheel small.
+Each candidate is run once before it is accepted, so a binary that cannot run on your machine is skipped rather than cached. Useful switches: `allow_download`, `allow_docker`, `allow_build` on `PyLCModel`, and the `LCMODEL_EXEC` / `LCMODEL_CACHE_DIR` environment variables.
+
+With the container, LCModel sees your working directory and your home directory; keep the basis set and any `save_path` under one of them. The image also works on its own:
+```bash
+docker run --rm -i -v "$PWD:$PWD" -w "$PWD" ghcr.io/julianmer/lcmodel < control.file
+```
 
 ---
 
@@ -130,9 +139,11 @@ This wrapper (the Python code) is released under the **Apache License 2.0** (see
 
 ## Acknowledgements
 
+- LCModel source code: created and made [available](https://s-provencher.com/lcmodel.shtml) free of charge (Stephen Provencher).
 - LCModel binaries: [schorschinho/LCModel](https://github.com/schorschinho/LCModel) (Georg Oeltzschner and contributors)
 - Basis conversion reference: [MRS Basis Set Conversion Toolbox](https://github.com/igweckay/MRS-Basis-Set-Conversion-Toolbox) (Kay Igwe)
-- NIfTI-MRS: [spec2nii](https://github.com/wtclarke/spec2nii), [NIfTI-MRS Pyhton tools](https://github.com/wtclarke/nifti_mrs_tools) (Will Clarke)
+- NIfTI-MRS: [spec2nii](https://github.com/wtclarke/spec2nii), [NIfTI-MRS Python tools](https://github.com/wtclarke/nifti_mrs_tools) (Will Clarke)
+- Example data: [ISMRM 2016 MRS Fitting Challenge](https://www.ismrm.org/workshops/Spectroscopy16/mrs_fitting_challenge/) (Małgorzata Marjańska, Dinesh Deelchand, Roland Kreis), mirrored via [wtclarke/mrs_fitting_challenge](https://github.com/wtclarke/mrs_fitting_challenge)
 
 ---
 

{lcmodel_wrapper-0.2.0 → lcmodel_wrapper-0.3.1}/README.md

@@ -14,7 +14,7 @@
 
 ## Features
 
-- **Zero-setup binaries** — the LCModel executable is resolved automatically (download, build from source, or your own path); nothing is bundled in the wheel.
+- **Zero-setup binaries** — the LCModel executable is resolved automatically (download, container image, build from source, or your own path); nothing is bundled in the wheel.
 - **Flexible input** — NumPy arrays, NIfTI-MRS, jMRUI text, and LCModel `.RAW`, in time or frequency domain.
 - **Automated control files** — generated to match your data, or templated from an existing one.
 - **Basis conversion (experimental)** — jMRUI, FSL-MRS, LCModel `.RAW`, and Osprey/FID-A basis sets to `.basis`.
@@ -28,7 +28,6 @@
 ```bash
 pip install lcmodel-wrapper
 ```
-Enter your API token:
 
 ### From Source
 ```bash
@@ -36,19 +35,28 @@ git clone https://github.com/julianmer/PyLCModel.git
 cd PyLCModel
 pip install -e .
 ```
+Add `--recursive` to the clone (or run `git submodule update --init`) to also fetch the
+[ISMRM 2016 fitting challenge](https://www.ismrm.org/workshops/Spectroscopy16/mrs_fitting_challenge/)
+example data used by the tests.
 
 ---
 
 ## How the LCModel binary is handled
 
-The LCModel program is **not** part of this package and is **not** shipped in the wheel. On first use, the binary is resolved in this order:
+LCModel is **not** shipped in the wheel. On first use it is found in this order, and the first one that works is cached:
 
-1. an explicit `path2exec="/path/to/lcmodel"` you pass to `PyLCModel`,
-2. a previously cached download/build (under `~/.cache/lcmodel_wrapper`, or `%LOCALAPPDATA%` on Windows; override with `LCMODEL_CACHE_DIR`),
-3. a download of the matching binary for your OS/architecture from [schorschinho/LCModel](https://github.com/schorschinho/LCModel),
-4. a build from the LCModel Fortran source via `gfortran` (source fetched on demand).
+1. `path2exec` you pass to `PyLCModel`,
+2. the community binary for your OS/architecture from [schorschinho/LCModel](https://github.com/schorschinho/LCModel),
+3. the binary built by this repository's CI for the installed version ([releases](https://github.com/julianmer/PyLCModel/releases); Linux x86_64/aarch64 and macOS arm64/x86_64, all statically linked),
+4. the container image `ghcr.io/julianmer/lcmodel`, if Docker or podman is running,
+5. a build from source with `gfortran`.
 
-There is no git submodule and no bundled `lcmodel/` folder — keeping both the repository and the PyPI wheel small.
+Each candidate is run once before it is accepted, so a binary that cannot run on your machine is skipped rather than cached. Useful switches: `allow_download`, `allow_docker`, `allow_build` on `PyLCModel`, and the `LCMODEL_EXEC` / `LCMODEL_CACHE_DIR` environment variables.
+
+With the container, LCModel sees your working directory and your home directory; keep the basis set and any `save_path` under one of them. The image also works on its own:
+```bash
+docker run --rm -i -v "$PWD:$PWD" -w "$PWD" ghcr.io/julianmer/lcmodel < control.file
+```
 
 ---
 
@@ -108,9 +116,11 @@ This wrapper (the Python code) is released under the **Apache License 2.0** (see
 
 ## Acknowledgements
 
+- LCModel source code: created and made [available](https://s-provencher.com/lcmodel.shtml) free of charge (Stephen Provencher).
 - LCModel binaries: [schorschinho/LCModel](https://github.com/schorschinho/LCModel) (Georg Oeltzschner and contributors)
 - Basis conversion reference: [MRS Basis Set Conversion Toolbox](https://github.com/igweckay/MRS-Basis-Set-Conversion-Toolbox) (Kay Igwe)
-- NIfTI-MRS: [spec2nii](https://github.com/wtclarke/spec2nii), [NIfTI-MRS Pyhton tools](https://github.com/wtclarke/nifti_mrs_tools) (Will Clarke)
+- NIfTI-MRS: [spec2nii](https://github.com/wtclarke/spec2nii), [NIfTI-MRS Python tools](https://github.com/wtclarke/nifti_mrs_tools) (Will Clarke)
+- Example data: [ISMRM 2016 MRS Fitting Challenge](https://www.ismrm.org/workshops/Spectroscopy16/mrs_fitting_challenge/) (Małgorzata Marjańska, Dinesh Deelchand, Roland Kreis), mirrored via [wtclarke/mrs_fitting_challenge](https://github.com/wtclarke/mrs_fitting_challenge)
 
 ---
 

{lcmodel_wrapper-0.2.0 → lcmodel_wrapper-0.3.1}/lcmodel_wrapper/__init__.py

@@ -4,19 +4,27 @@ LCModel itself is a separate program by Dr. Stephen Provencher, distributed unde
 BSD 3-Clause License (see LICENSE.lcmodel). This package only wraps it.
 """
 
-from .core import PyLCModel
+from ._version import __version__
+from .core import PyLCModel, LCModelError
 from .basis import read_basis, LCModelBasis
+from .binaries import verify_executable
 from .convert import ensure_basis, convert_to_basis, detect_format
-from . import binaries, io, control, coord, convert
+from .io import from_nifti_mrs, load_signals
+from . import binaries, container, io, control, coord, convert
 
 __all__ = [
     "PyLCModel",
+    "LCModelError",
+    "verify_executable",
     "read_basis",
     "LCModelBasis",
     "ensure_basis",
     "convert_to_basis",
     "detect_format",
+    "from_nifti_mrs",
+    "load_signals",
     "binaries",
+    "container",
     "io",
     "control",
     "coord",

lcmodel_wrapper-0.3.1/lcmodel_wrapper/_version.py

@@ -0,0 +1,4 @@
+# Single source of truth for the package version. pyproject.toml reads it at build time,
+# and binaries.py derives the GitHub release / container image tag ("v<version>") from
+# it, so every wheel pairs with the LCModel artifacts built alongside it.
+__version__ = "0.3.1"

{lcmodel_wrapper-0.2.0 → lcmodel_wrapper-0.3.1}/lcmodel_wrapper/basis.py

@@ -6,9 +6,9 @@
 #                                                                                                  #
 # Created: 26/06/26                                                                                #
 #                                                                                                  #
-# Purpose: Lightweight parser for LCModel ".basis" files. Replaces the previous dependency on       #
+# Purpose: Lightweight parser for LCModel ".basis" files. Replaces the previous dependency on      #
 #          fsl_mrs for reading basis metadata. It extracts only what the wrapper needs to build    #
-#          control files and to align fitted concentrations: the field strength (HZPPPM), dwell       #
+#          control files and to align fitted concentrations: the field strength (HZPPPM), dwell    #
 #          time (BADELT), number of points (NDATAB) and the ordered metabolite names (METABO).     #
 #                                                                                                  #
 ####################################################################################################
@@ -77,14 +77,14 @@ def read_basis(path: str) -> LCModelBasis:
     with open(path, "r", errors="ignore") as fh:
         header_lines = []
         for line in fh:
-            header_lines.append(line)
+            if len(header_lines) < 200:        # scalars live near the top
+                header_lines.append(line)
             # "METABO" lines are sparse; keep scanning the whole file for them.
             # Match exactly "METABO =" (not "METABO_CONTAM" / "METABO_SINGLET").
             m = re.match(r"\s*METABO\s*=\s*'(.*?)'", line)
             if m:
                 basis.names.append(m.group(1).strip())
-
-        header = "".join(header_lines[:200])   # scalars live near the top
+        header = "".join(header_lines)
 
     basis.central_freq = _find_scalar(header, "HZPPPM")
     basis.dwell = _find_scalar(header, "BADELT")