thyra 4.6.2__tar.gz → 4.6.3__tar.gz

{thyra-4.6.2 → thyra-4.6.3}/PKG-INFO

@@ -1,7 +1,7 @@
 Metadata-Version: 2.5
 Name: thyra
-Version: 4.6.2
-Summary: A modern Python library for converting Mass Spectrometry Imaging (MSI) data into SpatialData/Zarr format - your portal to spatial omics
+Version: 4.6.3
+Summary: Convert mass spectrometry imaging (MSI) data from Bruker, Waters, PHI and imzML, with ion mobility and MS/MS, into the open SpatialData/Zarr format
 Project-URL: Homepage, https://github.com/M4i-Imaging-Mass-Spectrometry/thyra
 Project-URL: Repository, https://github.com/M4i-Imaging-Mass-Spectrometry/thyra
 Project-URL: Documentation, https://M4i-Imaging-Mass-Spectrometry.github.io/thyra/
@@ -15,11 +15,13 @@ Author-email: Theodoros Visvikis <t.visvikis@maastrichtuniversity.nl>
 Maintainer-email: Theodoros Visvikis <t.visvikis@maastrichtuniversity.nl>
 License-Expression: MIT
 License-File: LICENSE
-Keywords: bioinformatics,bruker,data-conversion,imaging,imzml,ion-mobility,mass-spectrometry,msi,msms,omics,pasef,scientific-computing,spatial-omics,spatialdata,tims,timstof,zarr
+Keywords: anndata,bioinformatics,bruker,data-conversion,desi,imaging,imzml,ion-mobility,lipidomics,maldi,mass-spectrometry,mass-spectrometry-imaging,metabolomics,msi,msms,omics,pasef,scientific-computing,scverse,spatial-omics,spatialdata,tims,timstof,tof-sims,waters,zarr
 Classifier: Development Status :: 4 - Beta
 Classifier: Environment :: Console
 Classifier: Intended Audience :: Science/Research
-Classifier: Operating System :: OS Independent
+Classifier: Operating System :: MacOS
+Classifier: Operating System :: Microsoft :: Windows
+Classifier: Operating System :: POSIX :: Linux
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
@@ -65,12 +67,18 @@ Description-Content-Type: text/markdown
 [![Docs](https://img.shields.io/badge/docs-mkdocs-blue)](https://M4i-Imaging-Mass-Spectrometry.github.io/thyra)
 [![Open in Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/M4i-Imaging-Mass-Spectrometry/thyra/blob/main/notebooks/Thyra_Validation_Workflow.ipynb)
 
-**Thyra converts imaging mass spectrometry data into one open format.** It
-reads the files your instrument writes (Bruker, Waters, PHI, or imzML from any
-vendor) and saves them in [SpatialData](https://spatialdata.scverse.org/),
-which analysis and viewing tools can read. It keeps ion mobility (TIMS 1/K0)
-and MS/MS (PASEF, iprm-PASEF) data, not only the spectra. You do not need to
-know how to program.
+**Thyra converts imaging mass spectrometry data into one open format: the
+spectra, the ion mobility and the MS/MS.** It reads the MSI files your MALDI,
+DESI or ToF-SIMS instrument writes (Bruker, Waters, PHI, or imzML from any
+vendor) and saves them in [SpatialData](https://spatialdata.scverse.org/), the
+open format of the [scverse](https://scverse.org/) tools. Ion mobility (TIMS
+1/K0, Waters drift time) and MS/MS (PASEF, iprm-PASEF) are kept beside the
+spectra, not dropped. Converting needs no programming.
+
+**What you gain:** your data leaves the vendor format and can sit beside the
+microscopy and spatial transcriptomics data of the same tissue, in a format
+built to hold them together. In Python it opens as an AnnData table, one row
+per pixel, with the optical image next to it.
 
 **[Documentation](https://M4i-Imaging-Mass-Spectrometry.github.io/thyra)** | [Install](https://M4i-Imaging-Mass-Spectrometry.github.io/thyra/install/) | [Your first conversion](https://M4i-Imaging-Mass-Spectrometry.github.io/thyra/getting-started/) | [Tutorial](https://M4i-Imaging-Mass-Spectrometry.github.io/thyra/tutorial/) | [Technical reference](https://M4i-Imaging-Mass-Spectrometry.github.io/thyra/technical-reference/)
 
@@ -99,14 +107,15 @@ also converts the published example dataset
 
 ## What you can convert
 
-| Your instrument | Point Thyra at |
-|---|---|
-| Bruker timsTOF or solariX | the folder ending in `.d` |
-| Bruker rapifleX | the acquisition folder |
-| Waters (MassLynx) | the folder ending in `.raw` |
-| PHI nanoTOF (ToF-SIMS) | the file ending in `.raw` |
-| Any instrument that exports imzML | the `.imzML` file, with its `.ibd` file next to it |
-| mzPeak (experimental) | the `.mzpeak` file |
+| Your instrument | Point Thyra at | Kept beside the spectra |
+|---|---|---|
+| Bruker timsTOF | the folder ending in `.d` | ion mobility (1/K0), MS/MS (PASEF, iprm-PASEF), optical image and its alignment, regions |
+| Bruker solariX | the folder ending in `.d` | optical image |
+| Bruker rapifleX | the acquisition folder | optical image and its alignment |
+| Waters (MassLynx) | the folder ending in `.raw` | ion mobility (drift time, Synapt and Cyclic IMS), regions |
+| PHI nanoTOF (ToF-SIMS) | the file ending in `.raw` | mosaic tiles joined into one image |
+| Any instrument that exports imzML | the `.imzML` file, with its `.ibd` file next to it | ion mobility array, 3D data |
+| mzPeak (experimental) | the `.mzpeak` file | |
 
 imzML with a mobility array is read too. In continuous mode, as TIMSImaging
 writes it, the mobility is kept as its own table. In processed mode, as
@@ -120,6 +129,20 @@ PHI mosaic, MS/MS and depth-profiling acquisitions have so far been tested
 only on synthetic files. If you have real data in those modes, please get in
 touch.
 
+### Not supported yet, and how to change that
+
+Only the formats in the table are read natively. Other vendor formats
+(Thermo, Shimadzu, Agilent, SCIEX and others) are not: export imzML from the
+vendor software and convert that.
+
+A gap is there because nobody has needed it yet or because time ran out, not
+because it cannot be done. If your instrument, format or acquisition mode is
+missing,
+[tell us in the discussions](https://github.com/M4i-Imaging-Mass-Spectrometry/thyra/discussions).
+A small example dataset is the fastest way to a new reader. Collaborations are
+welcome: on formats, on tools that read the result, and on the metadata
+schema.
+
 ## What you get
 
 One folder ending in `.zarr`, holding:
@@ -128,7 +151,8 @@ One folder ending in `.zarr`, holding:
 - an image of the total ion current (TIC)
 - the optical image of the slide, when the acquisition has one
 - ion mobility and MS/MS data, when the acquisition has them (below)
-- a validated description of the acquisition, ready for METASPACE
+- a validated description of the acquisition, which Thyra can export as a
+  METASPACE submission file
 
 Thyra handles datasets larger than your computer's memory, slides with
 several regions, and 3D data.

{thyra-4.6.2 → thyra-4.6.3}/README.md

@@ -10,12 +10,18 @@
 [![Docs](https://img.shields.io/badge/docs-mkdocs-blue)](https://M4i-Imaging-Mass-Spectrometry.github.io/thyra)
 [![Open in Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/M4i-Imaging-Mass-Spectrometry/thyra/blob/main/notebooks/Thyra_Validation_Workflow.ipynb)
 
-**Thyra converts imaging mass spectrometry data into one open format.** It
-reads the files your instrument writes (Bruker, Waters, PHI, or imzML from any
-vendor) and saves them in [SpatialData](https://spatialdata.scverse.org/),
-which analysis and viewing tools can read. It keeps ion mobility (TIMS 1/K0)
-and MS/MS (PASEF, iprm-PASEF) data, not only the spectra. You do not need to
-know how to program.
+**Thyra converts imaging mass spectrometry data into one open format: the
+spectra, the ion mobility and the MS/MS.** It reads the MSI files your MALDI,
+DESI or ToF-SIMS instrument writes (Bruker, Waters, PHI, or imzML from any
+vendor) and saves them in [SpatialData](https://spatialdata.scverse.org/), the
+open format of the [scverse](https://scverse.org/) tools. Ion mobility (TIMS
+1/K0, Waters drift time) and MS/MS (PASEF, iprm-PASEF) are kept beside the
+spectra, not dropped. Converting needs no programming.
+
+**What you gain:** your data leaves the vendor format and can sit beside the
+microscopy and spatial transcriptomics data of the same tissue, in a format
+built to hold them together. In Python it opens as an AnnData table, one row
+per pixel, with the optical image next to it.
 
 **[Documentation](https://M4i-Imaging-Mass-Spectrometry.github.io/thyra)** | [Install](https://M4i-Imaging-Mass-Spectrometry.github.io/thyra/install/) | [Your first conversion](https://M4i-Imaging-Mass-Spectrometry.github.io/thyra/getting-started/) | [Tutorial](https://M4i-Imaging-Mass-Spectrometry.github.io/thyra/tutorial/) | [Technical reference](https://M4i-Imaging-Mass-Spectrometry.github.io/thyra/technical-reference/)
 
@@ -44,14 +50,15 @@ also converts the published example dataset
 
 ## What you can convert
 
-| Your instrument | Point Thyra at |
-|---|---|
-| Bruker timsTOF or solariX | the folder ending in `.d` |
-| Bruker rapifleX | the acquisition folder |
-| Waters (MassLynx) | the folder ending in `.raw` |
-| PHI nanoTOF (ToF-SIMS) | the file ending in `.raw` |
-| Any instrument that exports imzML | the `.imzML` file, with its `.ibd` file next to it |
-| mzPeak (experimental) | the `.mzpeak` file |
+| Your instrument | Point Thyra at | Kept beside the spectra |
+|---|---|---|
+| Bruker timsTOF | the folder ending in `.d` | ion mobility (1/K0), MS/MS (PASEF, iprm-PASEF), optical image and its alignment, regions |
+| Bruker solariX | the folder ending in `.d` | optical image |
+| Bruker rapifleX | the acquisition folder | optical image and its alignment |
+| Waters (MassLynx) | the folder ending in `.raw` | ion mobility (drift time, Synapt and Cyclic IMS), regions |
+| PHI nanoTOF (ToF-SIMS) | the file ending in `.raw` | mosaic tiles joined into one image |
+| Any instrument that exports imzML | the `.imzML` file, with its `.ibd` file next to it | ion mobility array, 3D data |
+| mzPeak (experimental) | the `.mzpeak` file | |
 
 imzML with a mobility array is read too. In continuous mode, as TIMSImaging
 writes it, the mobility is kept as its own table. In processed mode, as
@@ -65,6 +72,20 @@ PHI mosaic, MS/MS and depth-profiling acquisitions have so far been tested
 only on synthetic files. If you have real data in those modes, please get in
 touch.
 
+### Not supported yet, and how to change that
+
+Only the formats in the table are read natively. Other vendor formats
+(Thermo, Shimadzu, Agilent, SCIEX and others) are not: export imzML from the
+vendor software and convert that.
+
+A gap is there because nobody has needed it yet or because time ran out, not
+because it cannot be done. If your instrument, format or acquisition mode is
+missing,
+[tell us in the discussions](https://github.com/M4i-Imaging-Mass-Spectrometry/thyra/discussions).
+A small example dataset is the fastest way to a new reader. Collaborations are
+welcome: on formats, on tools that read the result, and on the metadata
+schema.
+
 ## What you get
 
 One folder ending in `.zarr`, holding:
@@ -73,7 +94,8 @@ One folder ending in `.zarr`, holding:
 - an image of the total ion current (TIC)
 - the optical image of the slide, when the acquisition has one
 - ion mobility and MS/MS data, when the acquisition has them (below)
-- a validated description of the acquisition, ready for METASPACE
+- a validated description of the acquisition, which Thyra can export as a
+  METASPACE submission file
 
 Thyra handles datasets larger than your computer's memory, slides with
 several regions, and 3D data.

{thyra-4.6.2 → thyra-4.6.3}/pyproject.toml

@@ -4,8 +4,8 @@ build-backend = "hatchling.build"
 
 [project]
 name = "thyra"
-version = "4.6.2"
-description = "A modern Python library for converting Mass Spectrometry Imaging (MSI) data into SpatialData/Zarr format - your portal to spatial omics"
+version = "4.6.3"
+description = "Convert mass spectrometry imaging (MSI) data from Bruker, Waters, PHI and imzML, with ion mobility and MS/MS, into the open SpatialData/Zarr format"
 authors = [{ name = "Theodoros Visvikis", email = "t.visvikis@maastrichtuniversity.nl" }]
 maintainers = [{ name = "Theodoros Visvikis", email = "t.visvikis@maastrichtuniversity.nl" }]
 license = "MIT"
@@ -14,14 +14,23 @@ readme = "README.md"
 requires-python = ">=3.12, <3.15"
 keywords = [
     "mass-spectrometry",
+    "mass-spectrometry-imaging",
     "imaging",
     "spatialdata",
+    "anndata",
+    "scverse",
     "zarr",
     "omics",
+    "metabolomics",
+    "lipidomics",
     "bioinformatics",
     "msi",
+    "maldi",
+    "desi",
+    "tof-sims",
     "imzml",
     "bruker",
+    "waters",
     "timstof",
     "ion-mobility",
     "tims",
@@ -35,7 +44,11 @@ keywords = [
 classifiers = [
     "Development Status :: 4 - Beta",
     "Intended Audience :: Science/Research",
-    "Operating System :: OS Independent",
+    # Not "OS Independent": the timsTOF and Waters readers load vendor
+    # libraries that exist for Windows and Linux only.
+    "Operating System :: Microsoft :: Windows",
+    "Operating System :: POSIX :: Linux",
+    "Operating System :: MacOS",
     "Programming Language :: Python :: 3",
     "Programming Language :: Python :: 3.12",
     "Programming Language :: Python :: 3.13",
@@ -86,7 +99,7 @@ dependencies = [
     # 8.3.1 and passes on what CI resolves. That cost a test on main -- see
     # tests/unit/test_cli_interactive_calibration.py. Green CI is evidence
     # about 8.4.2 and about nothing else in the declared range.
-    "click>=8.1, <9",                 # verified 8.1.8, 8.4.2 and 8.5.0
+    "click>=8.1, <9",                 # verified 8.1.8, 8.4.2 and 8.5.1
     # Secure XML parsing for the shared Bruker `.mis` parser, which every
     # Bruker path goes through: the Rapiflex, timsTOF and solariX readers and
     # BrukerMetadataExtractor. `mis_parser` imports it unconditionally and has
@@ -253,8 +266,7 @@ Paper = "https://doi.org/10.1038/s41592-026-03305-5"
 "Bug Tracker" = "https://github.com/M4i-Imaging-Mass-Spectrometry/thyra/issues"
 Discussions = "https://github.com/M4i-Imaging-Mass-Spectrometry/thyra/discussions"
 Changelog = "https://github.com/M4i-Imaging-Mass-Spectrometry/thyra/blob/main/CHANGELOG.md"
-# There is no CONTRIBUTING.md at the repository root; the guide lives at
-# docs/contributing.md and is published as this page.
+# The full guide lives at docs/contributing.md and is published as this page.
 Contributing = "https://M4i-Imaging-Mass-Spectrometry.github.io/thyra/contributing/"
 
 [project.scripts]

{thyra-4.6.2 → thyra-4.6.3}/thyra/__init__.py

@@ -70,7 +70,7 @@ warnings.filterwarnings(
     category=FutureWarning,
 )
 
-__version__ = "4.6.2"
+__version__ = "4.6.3"
 
 #: Public name -> the module that defines it, imported on first access.
 _LAZY_ATTRS = {

{thyra-4.6.2 → thyra-4.6.3}/thyra/__main__.py

@@ -854,9 +854,17 @@ class GroupedCommand(click.Command):
 
     @staticmethod
     def _collect_options(ctx: click.Context) -> tuple:
-        """Collect options and build name-to-record mapping."""
+        """Collect options and build name-to-record mapping.
+
+        Positional arguments are left out, as ``click.Command.format_options``
+        leaves them out: they are on the usage line and in the help text.
+        From click 8.5.1 an argument always has a help record, so without
+        this they would land in the trailing ``Options:`` section.
+        """
         opts = []
         for param in ctx.command.get_params(ctx):
+            if isinstance(param, click.Argument):
+                continue
             rv = param.get_help_record(ctx)
             if rv is not None:
                 opts.append((param, rv))