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Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

[v1.3.3] - 2024-01-25

Name Version Checksum
XLMOD.obo.gz release/2019-10-28 4e577044551d277e4bbd62753fa15e08
gno.obo.gz 2023-12-11 ec47a2eb0af631bca7a40d85a4832ab4
go.obo.gz releases/2024-01-17 7e6b9974184dda306e6e07631f1783af
pato.obo.gz releases/2023-05-18/pato.obo 8a14f0e3b3318c13d029d84d693a01e3
psi-mod.obo.gz - 713e6dd17632d0388802f1b0e06800f0
psi-ms.obo.gz 4.1.139 a7254eb76da9e38c85b9dad624c9f77e
unimod_tables.xml.gz - efc94f333458012a77203d09a64d7d38
unit.obo.gz releases/2023-05-25 5a04e9d871730a1ee04764055e841785

Changed

  1. The Unimod object now uses a thread-safe database session abstraction

v1.3.2 - 2023-12-02

Name Version Checksum
XLMOD.obo.gz release/2019-10-28 4e577044551d277e4bbd62753fa15e08
gno.obo.gz 2023-11-09 078de92750ee4956b705684253a66f97
go.obo.gz releases/2023-11-15 1130d315870d82c1624f87b37305777b
pato.obo.gz releases/2023-05-18/pato.obo 8a14f0e3b3318c13d029d84d693a01e3
psi-mod.obo.gz - 713e6dd17632d0388802f1b0e06800f0
psi-ms.obo.gz 4.1.136 1d5aa08ea57762000d00a9300734a78c
unimod_tables.xml.gz - efc94f333458012a77203d09a64d7d38
unit.obo.gz releases/2023-05-25 5a04e9d871730a1ee04764055e841785

Added

  1. Add by_id method to Unimod for parity with pyteomics

v1.3.1

Changed

  1. Replaced the global import of pkg_resources in psims.validation.validator with importlib.resources

v1.3.0 - 2023-11-03

Name Version Checksum
XLMOD.obo.gz release/2019-10-28 4e577044551d277e4bbd62753fa15e08
gno.obo.gz 2023-08-09 6178d787e38a8a1b5d7506e3c1a880d0
go.obo.gz releases/2023-10-09 a827a54e43185170c973afe1add92941
pato.obo.gz releases/2023-05-18/pato.obo 8a14f0e3b3318c13d029d84d693a01e3
psi-mod.obo.gz - 713e6dd17632d0388802f1b0e06800f0
psi-ms.obo.gz 4.1.135 3f58f845ef728dc3225a5a2df32fff3a
unimod_tables.xml.gz - efc94f333458012a77203d09a64d7d38
unit.obo.gz releases/2023-05-25 5a04e9d871730a1ee04764055e841785

Changed

  1. The default compressor for mzMLb has been reverted to zlib/gzip for compatibility with the forthcoming ProteoWizard release.
  2. The mzMLb version attribute is now stored as a fixed-length string in HDF5 (for spec compatibility), which h5py unilaterally reads as a bytes object, requiring the reader to decode it themselves.

v1.2.9 - 2023-10-26

Name Version Checksum
XLMOD.obo.gz release/2019-10-28 4e577044551d277e4bbd62753fa15e08
gno.obo.gz 2023-08-09 6178d787e38a8a1b5d7506e3c1a880d0
go.obo.gz releases/2023-10-09 a827a54e43185170c973afe1add92941
pato.obo.gz releases/2023-05-18/pato.obo 8a14f0e3b3318c13d029d84d693a01e3
psi-mod.obo.gz - 713e6dd17632d0388802f1b0e06800f0
psi-ms.obo.gz 4.1.134 d3eea6067a44a85dc72fef90acafbfb5
unimod_tables.xml.gz - efc94f333458012a77203d09a64d7d38
unit.obo.gz releases/2023-05-25 5a04e9d871730a1ee04764055e841785

Changed

  1. The compression parameter for mzML and mzMLb spectrum and chromatogram writing methods may now be a Mapping-like object mapping array name to compressor name. This supports using Numpress on m/z arrays and zlib on intensity arrays, for example, or two different Numpress compressors as the linear compression Numpress proposes for m/z isn't appropriate for intensity.
  2. The mzMLb writer will now detect when a compressor has occluded the data type of an array and mark that array as opaque so that the future reading HDF5 library doesn't try to cast that array to its "real" data type. This leaves it up to the caller to properly decode the opaque bytes back into their proper representation.

v1.2.8 - 2023-10-13

Name Version Checksum
XLMOD.obo.gz release/2019-10-28 4e577044551d277e4bbd62753fa15e08
gno.obo.gz 2023-08-09 6178d787e38a8a1b5d7506e3c1a880d0
go.obo.gz releases/2023-10-09 a827a54e43185170c973afe1add92941
pato.obo.gz releases/2023-05-18/pato.obo 8a14f0e3b3318c13d029d84d693a01e3
psi-mod.obo.gz - 713e6dd17632d0388802f1b0e06800f0
psi-ms.obo.gz 4.1.134 d3eea6067a44a85dc72fef90acafbfb5
unimod_tables.xml.gz - efc94f333458012a77203d09a64d7d38
unit.obo.gz releases/2023-05-25 5a04e9d871730a1ee04764055e841785

Changed

  1. load_unimod now uses the automatic caching and vendored CV fallback mechanism that all other load_* methods use.

v1.2.7 - 2023-08-27

Name Version Checksum
XLMOD.obo.gz release/2019-10-28 4e577044551d277e4bbd62753fa15e08
gno.obo.gz 2023-08-09 6178d787e38a8a1b5d7506e3c1a880d0
go.obo.gz releases/2023-07-27 326bc165ad57ee38d87a380098e49ca7
pato.obo.gz releases/2023-05-18/pato.obo 8a14f0e3b3318c13d029d84d693a01e3
psi-mod.obo.gz - 713e6dd17632d0388802f1b0e06800f0
psi-ms.obo.gz 4.1.132 e5520f1823470c3c05b9eb94b0cdd06b
unimod_tables.xml.gz - 7e6f1cffe9ad27fecbf5b394103b9836
unit.obo.gz releases/2023-05-25 5a04e9d871730a1ee04764055e841785

Added

  1. Added a translation cache to ControlledVocabulary objects to avoid repeatedly resolving the same names over and over again.

v1.2.5 - 2023-05-25

Name Version Checksum
XLMOD.obo.gz release/2019-10-28 4e577044551d277e4bbd62753fa15e08
gno.obo.gz 2023-05-08 40808f9d7b3b2589ec272f2d36db80c8
go.obo.gz releases/2023-05-10 e9845499eadaef2418f464cd7e9ac92e
pato.obo.gz releases/2023-05-18/pato.obo 8a14f0e3b3318c13d029d84d693a01e3
psi-mod.obo.gz - 713e6dd17632d0388802f1b0e06800f0
psi-ms.obo.gz 4.1.121 851867a39838c846425fbc96f408506f
unimod_tables.xml.gz - 7e6f1cffe9ad27fecbf5b394103b9836
unit.obo.gz releases/2023-05-25 5a04e9d871730a1ee04764055e841785

Fixed

  1. Entity objects now compare as equal if their ids are equal instead of doing a deep comparison.

v1.2.4 - 2023-04-30

Name Version Checksum
XLMOD.obo.gz release/2019-10-28 4e577044551d277e4bbd62753fa15e08
gno.obo.gz 2022-12-20 2af78cbf0e6256586a5499babe3f59b9
go.obo.gz releases/2023-04-01 299355f7feb050cab4edab556f2e5c7e
pato.obo.gz releases/2023-02-17/pato.obo 3b9bc35244bbb8e9ba9c4952d80980dd
psi-mod.obo.gz - 713e6dd17632d0388802f1b0e06800f0
psi-ms.obo.gz 4.1.119 f646e5364d10e6bac37b43e31debe99a
unimod_tables.xml.gz - 7e6f1cffe9ad27fecbf5b394103b9836
unit.obo.gz - c7d0dedfdc0223d42a9cf66ffb03f2a2

Fixed

  • The SQLAlchemy dependency should no longer issue deprecation warnings when used with SQLAlchemy v2+.
  • More docstrings are formatted properly and cleaned up.

[v1.2.3] - 2023-01-07

Name Version Checksum
XLMOD.obo.gz release/2019-10-28 4e577044551d277e4bbd62753fa15e08
gno.obo.gz 2022-12-20 2af78cbf0e6256586a5499babe3f59b9
go.obo.gz releases/2023-01-01 f2a0667c060b688fa4c4afa59f7a783a
pato.obo.gz releases/2022-12-15/pato.obo 5c67369f32b06e41e9e146d1c768df6d
psi-mod.obo.gz - 713e6dd17632d0388802f1b0e06800f0
psi-ms.obo.gz 4.1.109 afa2e3eab46c82354615595d8ecedf55
unimod_tables.xml.gz - 7e6f1cffe9ad27fecbf5b394103b9836
unit.obo.gz - 1616553109ee3ebc85ffc978d8e39ce8

[v1.2.2] - 2022-11-21

Name Version Checksum
XLMOD.obo.gz release/2019-10-28 4e577044551d277e4bbd62753fa15e08
gno.obo.gz 2022-02-23 a397dc95d8d809acea44209818a0f77f
go.obo.gz releases/2022-11-03 704f04eb6308c28cb2139a9803b7da3a
pato.obo.gz releases/2022-11-09/pato.obo 1b269eb54e4848c56885fa2d66b83b9b
psi-mod.obo.gz - 713e6dd17632d0388802f1b0e06800f0
psi-ms.obo.gz 4.1.108 9e5ffabe9c045ad2078f1bcc49a5214e
unimod_tables.xml.gz - 7e6f1cffe9ad27fecbf5b394103b9836
unit.obo.gz - 1616553109ee3ebc85ffc978d8e39ce8

Added

  • Added more documentation for mzIdentML writing.
  • MzMLTransformer now coerces cvParam and userParam from key-value pairs without requiring cvstr instances for keys.

Changed

Deprecated

Removed

Fixed

Security

[v1.2.1]

Name Version Checksum
XLMOD.obo.gz release/2019-10-28 4e577044551d277e4bbd62753fa15e08
gno.obo.gz 2022-02-23 a397dc95d8d809acea44209818a0f77f
go.obo.gz releases/2022-09-19 8f0f6557c8140bc68af67ac57239236d
pato.obo.gz releases/2022-08-31/pato.obo f84ce80b421e6f693a6e8031a70fe95f
psi-mod.obo.gz - 713e6dd17632d0388802f1b0e06800f0
psi-ms.obo.gz 4.1.104 6b5051c9a66b3c15cf0334920099bac1
unimod_tables.xml.gz - 523d0bb41eeb41bb1554fa405915e310
unit.obo.gz - 1f6e1b5122ea4c2d3797bae72f140ab1

Added

  1. Controlled vocabularies fail to resolve, a more descriptive error message will be used in the error. If failing to import a CV fails, it is not treated as an error.
  2. Wrapped component classes on writer types now expose a register method which is shorthand for writer.register("component type name", identifier).

[v1.2.0] - 2022-07-29

Changed

  1. When giving a Spectrum an ID value which is just an integer, the writer will attempt to convert it into the appropriate nativeID format. To control the nativeID format, set MzMLWriter.native_id_format or include an appropriate cvParam term in the MzMLWriter.file_description parameters.

Fixed

  1. When a CV fails to import another CV, that failure will be noted and it won't attempt to download again.

v1.1.0 - 2022-07-29

Name Version Checksum
XLMOD.obo.gz release/2019-10-28 4e577044551d277e4bbd62753fa15e08
gno.obo.gz 2022-02-23 a397dc95d8d809acea44209818a0f77f
go.obo.gz releases/2022-07-01 1b557078fdb541dbed5ee3fb1f51cbed
pato.obo.gz releases/2022-07-21/pato.obo 1b9d2d654020da497b0ebb5934451acb
psi-mod.obo.gz - 713e6dd17632d0388802f1b0e06800f0
psi-ms.obo.gz 4.1.95 c9a6c38ae4ec451a839f2a200b7bf601
unimod_tables.xml.gz - 523d0bb41eeb41bb1554fa405915e310
unit.obo.gz - 1f6e1b5122ea4c2d3797bae72f140ab1

Added

  1. OBOCache.load wraps the resolve/fallback and OBOParser parsing steps in a single call to produce a ControlledVocabulary instance.

Changed

  1. DocumentContext objects are always truthy, regardless of whether they have any keys.
  2. ControlledVocabulary instances will now also query their imports (restricted to OBO imports for now) when looking up missing terms.
  3. VocabularyResolver instances now cache CVs loaded through them to avoid having multiple copies of the same CV for the same document. This applies to CVs imported indirectly as well.

Deprecated

Removed

Fixed

Security

v1.2.6 - 2023-07-15

Name Version Checksum
XLMOD.obo.gz release/2019-10-28 4e577044551d277e4bbd62753fa15e08
gno.obo.gz 2023-05-08 40808f9d7b3b2589ec272f2d36db80c8
go.obo.gz releases/2023-06-11 b4aafb08e95a7c5c5852872e3d4a8959
pato.obo.gz releases/2023-05-18/pato.obo 8a14f0e3b3318c13d029d84d693a01e3
psi-mod.obo.gz - 713e6dd17632d0388802f1b0e06800f0
psi-ms.obo.gz 4.1.130 693097be4d0d1d16ed1162c4313cb9f5
unimod_tables.xml.gz - 7e6f1cffe9ad27fecbf5b394103b9836
unit.obo.gz releases/2023-05-25 5a04e9d871730a1ee04764055e841785

Fixed

  1. Actually implement parameter-less version of bound Component.write() (GH #20)
  2. Actually implement bound Component.register() (GH #19)

v1.1.0 - 2022-07-07

Added

  • Added MzMLWriter.native_id_format attribute that governs how integers are converted into strings for the spectrum id attribute. This will default to MS:1000774 multiple peak list nativeID format. If fileContents includes a nativeID format term and it is not been explicitly specified, that format will be used. This has no effect when specifying a a spectrum id with a string.

Changed

Deprecated

Removed

Fixed

Security

v1.0.0 - 2022-06-15

Name Version Checksum
XLMOD.obo.gz release/2019-10-28 4e577044551d277e4bbd62753fa15e08
gno.obo.gz 2022-02-23 a397dc95d8d809acea44209818a0f77f
go.obo.gz releases/2022-05-16 3408f54d9b0e2c7a1e71322ee17fda55
pato.obo.gz releases/2019-09-05 443de10a418cba2b0a6f4a9c3b73c60c
psi-mod.obo.gz - 713e6dd17632d0388802f1b0e06800f0
psi-ms.obo.gz 4.1.91 fd8c3970411f47d57ec47c470f5c2db2
unimod_tables.xml.gz - 523d0bb41eeb41bb1554fa405915e310
unit.obo.gz releases/2020-03-10 4e45267605698d1fcda533c27853a8fc

Changed

  1. Breaking The default behavior for all writer classes (MzMLWriter, MzIdentMLWriter, etc.) will now be to close files if they are closable. To preserve the previous behavior, explicitly pass close=False.

v0.1.47 - 2022-04-25

Name Version Checksum
XLMOD.obo.gz release/2019-10-28 4e577044551d277e4bbd62753fa15e08
gno.obo.gz 2022-02-23 a397dc95d8d809acea44209818a0f77f
go.obo.gz releases/2022-03-22 b24ea119f8b86d8ab7c680ec23047f56
pato.obo.gz releases/2019-09-05 443de10a418cba2b0a6f4a9c3b73c60c
psi-mod.obo.gz - 921a87531252fbb49b73c92e0b201ab2
psi-ms.obo.gz 4.1.84 ace0024e6845eec1d375b6e81a3e90e0
unimod_tables.xml.gz - 523d0bb41eeb41bb1554fa405915e310
unit.obo.gz releases/2020-03-10 4e45267605698d1fcda533c27853a8fc

Added

  1. Added an option to test if the environment variable PSIMS_NO_PYNUMPRESS to prevent loading the pynumpress C extension library.

v0.1.46 - 2022-03-02

CV Versions

Name Version Checksum
XLMOD.obo.gz release/2019-10-28 4e577044551d277e4bbd62753fa15e08
gno.obo.gz 2022-02-23 a397dc95d8d809acea44209818a0f77f
go.obo.gz releases/2022-01-13 122d68f6cf380a8cbb1abb4a74624416
pato.obo.gz releases/2019-09-05 443de10a418cba2b0a6f4a9c3b73c60c
psi-mod.obo.gz - 921a87531252fbb49b73c92e0b201ab2
psi-ms.obo.gz 4.1.72 593ed9190e0d657b0eb249efc9a12e77
unimod_tables.xml.gz - 61ac665064dd806b536c609fcb775920
unit.obo.gz releases/2020-03-10 4e45267605698d1fcda533c27853a8fc

Changed

  1. Properly use non-standard array cvParam, setting the value to the custom array name. Still also sets a userParam.

[v0.1.45]

CV Versions

Name Version Checksum
XLMOD.obo.gz release/2019-10-28 6e4b70ba06653e2944a7f4e73e30a42b
gno.obo.gz 2021-08-13 a0365da4060e84703aaec8baeae753d0
go.obo.gz releases/2021-11-16 1cc9921ed933b2de6231cdfa4a0acdf6
pato.obo.gz releases/2019-09-05 443de10a418cba2b0a6f4a9c3b73c60c
psi-mod.obo.gz - 0f6779b432281c47de1f6879262e394d
psi-ms.obo.gz 4.1.64 162f1ab5e81bacd9bfce95088d1f4967
unimod_tables.xml.gz - 61ac665064dd806b536c609fcb775920
unit.obo.gz releases/2020-03-10 4e45267605698d1fcda533c27853a8fc

v0.1.44 - 2021-12-04

CV Versions

Name Version Checksum
XLMOD.obo.gz release/2019-10-28 6e4b70ba06653e2944a7f4e73e30a42b
gno.obo.gz 2021-08-13 a0365da4060e84703aaec8baeae753d0
go.obo.gz releases/2021-11-16 1cc9921ed933b2de6231cdfa4a0acdf6
pato.obo.gz releases/2019-09-05 443de10a418cba2b0a6f4a9c3b73c60c
psi-mod.obo.gz - 0f6779b432281c47de1f6879262e394d
psi-ms.obo.gz 4.1.64 162f1ab5e81bacd9bfce95088d1f4967
unimod_tables.xml.gz - 61ac665064dd806b536c609fcb775920
unit.obo.gz releases/2020-03-10 4e45267605698d1fcda533c27853a8fc

Added

  • Improved documentation of HDF5 compressors

v0.1.43 - 2021-08-06

Added

  1. Properly coerce negative numbers

Fixed

  1. Restored support for Py3.5

v0.1.42 - 2021-08-05

Fixed

  1. Made CV-param binding safe to use for Py2 again.

v0.1.41 - 2021-08-05

Added

  1. Re-wrote the Entity.value_type machinery to better take into account compound or vocabulary-defined types.
  2. Modified the Relationship type to be able to dispatch to sub-classes for named relationship types.

Changed

  1. Updated vendor controlled vocabularies.

v0.1.39 - 2021-06-27

Added

  1. The data model for representing entities in OBO was revised to cover a wider range of cases.
  2. Entity attributes are automatically type-coerced if their primitive types are recognizable. This does not apply to formula-like attributes as these are formatted in a controlled vocabulary-specific manner.

Changed

  1. Updated vendor controlled vocabularies.

Deprecated

Removed

Fixed

Security

v0.1.38 - 2021-05-24

Changed

  1. Updated vendor controlled vocabularies
  2. Extended mzML writer's list of known arrays to match psi-ms.obo v4.1.53's new list
  3. Added additional warnings for when users have h5py but not hdf5plugin

v0.1.37

Added

  1. Added additional in-memory buffering of data arrays to reduce round-trips to HDF5 file when writing mzMLb.

Changed

  1. The MzIdentMLTranslater class was renamed MzIdentMLTranslator for the sake of the English language.
  2. Overhauled large parts of the documentation.
  3. Added clearer error message when attempting to use the mzMLb components without h5py.

Deprecated

Removed

Fixed

  1. Made the README mzML example actually work.
  2. Allowed Mapping types to be used for other_arrays array names so that units may be specified. Previously, only hashable types were supported, though this was not the intent. Also corrected the documentation to indicate this expects a list of (name, array) pairs, not a Mapping of them.

Security

v0.1.35

Added

  1. Added a change log.
  2. Added a mzMLb writer implementation.

Changed

  1. Improved write performance when writing indexedMzML by supporting io.BufferedWriter wrapping the whole write stack.
  2. Vendored controlled vocabularies are now gzip-compressed so they use much less space on disk.

Deprecated

Removed

Fixed

Security

Released