Update FAIMS splitter. Update Changelog

Author: mobiusklein

CHANGELOG.md

@@ -18,6 +18,28 @@ The format is based on [Keep a Changelog][Keep a Changelog] and this project adh
 ### Security
 
 
+## [v0.0.33] - 2021-12-05
+
+### Added
+1. Added an example script for splitting a FAIMS file into separate mzML files.
+2. Added an example script for ion mobility and charge state deconvolving Waters HDMSe data.
+3. Added Waters MassLynx SDK bindings for reading Waters .RAW folders directly on Windows
+   when the SDK C library is present.
+4. Added a new command `ms-index maintenance register-waters-masslynx` to register the location
+   of the Waters MassLynx SDK if it is not installed in the expected location.
+5. Improved documentation of `mzMLb` reading and writing.
+
+### Changed
+
+### Deprecated
+
+### Removed
+
+### Fixed
+
+### Security
+
+
 ## [v0.0.32]
 
 ### Added
@@ -332,8 +354,9 @@ The format is based on [Keep a Changelog][Keep a Changelog] and this project adh
 [Semantic Versioning]: https://semver.org/
 
 <!-- Versions -->
-[Unreleased]: https://github.com/mobiusklein/ms_deisotope/compare/v0.0.32...HEAD
+[Unreleased]: https://github.com/mobiusklein/ms_deisotope/compare/v0.0.33...HEAD
 [Released]: https://github.com/mobiusklein/ms_deisotope/releases
+[v0.0.33]: https://github.com/mobiusklein/ms_deisotope/releases/v0.0.33
 [v0.0.32]: https://github.com/mobiusklein/ms_deisotope/releases/v0.0.32
 [v0.0.31]: https://github.com/mobiusklein/ms_deisotope/releases/v0.0.31
 [v0.0.30]: https://github.com/mobiusklein/ms_deisotope/releases/v0.0.30

docker/Dockerfile

@@ -2,7 +2,9 @@ FROM python:3.8-slim-buster
 LABEL description="A container for the ms_deisotope Python package, ms-deisotope CLI tool, and ms-index CLI tool"
 
 # Build requirements
-RUN apt-get update && apt-get install -y --no-install-recommends gcc build-essential procps sudo git
+RUN apt-get update && apt-get install -y --no-install-recommends gcc build-essential procps sudo git \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/*
 
 WORKDIR /app
 

examples/faims_split.py

@@ -1,17 +1,19 @@
+#!/usr/bin/env python
 import click
 import ms_deisotope
-from ms_deisotope import output
 
 from ms_deisotope.output import MzMLSerializer
 from ms_deisotope.data_source import query
 
-from ms_deisotope.tools.utils import register_debug_hook
-
 
 @click.command('faims-split')
 @click.argument("source_file", type=click.Path(exists=True, readable=True))
 @click.argument("output_prefix")
 def main(source_file, output_prefix):
+    '''Read in `source_file` and split it based upon FAIMS compensation voltage into separate
+    mzML files whose path prefix matches `output_prefix` and ends with the compensation voltage
+    dedicated to that stream.
+    '''
     reader = ms_deisotope.MSFileLoader(source_file)
 
     sinks = {}
@@ -34,6 +36,8 @@ def main(source_file, output_prefix):
                     method = writer.build_processing_method(1, False, False, False, ["ion mobility seperation"])
                     writer.add_data_processing(method)
                     sinks[channel] = writer
+                else:
+                    writer = sinks[channel]
                 writer.save_scan(value)
                 i += 1
             else:
@@ -47,7 +51,7 @@ def main(source_file, output_prefix):
 
     click.echo("Closing buffers.")
     for sink in sinks.values():
-        click.echo("Closing %r" % (sink, ))
+        click.echo("Closing %r" % (sink.handle.name, ))
         sink.close()
 
 if __name__ == "__main__":