Version 0.1.47

CHANGELOG.md

@@ -3,6 +3,24 @@ All notable changes to this project will be documented in this file.
 
 The format is based on [Keep a Changelog][Keep a Changelog] and this project adheres to [Semantic Versioning][Semantic Versioning].
 
+## [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
@@ -158,8 +176,9 @@ 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/psims/compare/v0.1.46...HEAD
+[Unreleased]: https://github.com/mobiusklein/psims/compare/v0.1.47...HEAD
 [Released]: https://github.com/mobiusklein/psims/releases
+[v0.1.47]: https://github.com/mobiusklein/psims/releases/v0.1.47
 [v0.1.46]: https://github.com/mobiusklein/psims/releases/v0.1.46
 [v0.1.44]: https://github.com/mobiusklein/psims/releases/v0.1.44
 [v0.1.43]: https://github.com/mobiusklein/psims/releases/v0.1.43

psims/controlled_vocabulary/entity.py

@@ -67,6 +67,9 @@ def format(self, value):
         return str(value)
 
 
+class KeyOrAttributeError(KeyError, AttributeError):
+    pass
+
 
 class Entity(Mapping):
     '''Represent a term in a controlled vocabulary.
@@ -106,7 +109,10 @@ def __setitem__(self, key, value):
         self.data[key] = value
 
     def __getattr__(self, key):
-        return self[key]
+        try:
+            return self[key]
+        except KeyError:
+            raise KeyOrAttributeError(key) from None
 
     def __setattr__(self, key, value):
         if key in ("vocabulary", "children", "data"):

psims/controlled_vocabulary/vendor/record.json

@@ -1,34 +1,34 @@
 {
   "XLMOD.obo.gz": {
-    "checksum": "4e577044551d277e4bbd62753fa15e08", 
+    "checksum": "4e577044551d277e4bbd62753fa15e08",
     "version": "release/2019-10-28"
-  }, 
+  },
   "gno.obo.gz": {
-    "checksum": "a397dc95d8d809acea44209818a0f77f", 
+    "checksum": "a397dc95d8d809acea44209818a0f77f",
     "version": "2022-02-23"
-  }, 
+  },
   "go.obo.gz": {
-    "checksum": "122d68f6cf380a8cbb1abb4a74624416", 
-    "version": "releases/2022-01-13"
-  }, 
+    "checksum": "b24ea119f8b86d8ab7c680ec23047f56",
+    "version": "releases/2022-03-22"
+  },
   "pato.obo.gz": {
-    "checksum": "443de10a418cba2b0a6f4a9c3b73c60c", 
+    "checksum": "443de10a418cba2b0a6f4a9c3b73c60c",
     "version": "releases/2019-09-05"
-  }, 
+  },
   "psi-mod.obo.gz": {
-    "checksum": "921a87531252fbb49b73c92e0b201ab2", 
+    "checksum": "921a87531252fbb49b73c92e0b201ab2",
     "version": null
-  }, 
+  },
   "psi-ms.obo.gz": {
-    "checksum": "593ed9190e0d657b0eb249efc9a12e77", 
-    "version": "4.1.72"
-  }, 
+    "checksum": "ace0024e6845eec1d375b6e81a3e90e0",
+    "version": "4.1.84"
+  },
   "unimod_tables.xml.gz": {
-    "checksum": "61ac665064dd806b536c609fcb775920", 
+    "checksum": "523d0bb41eeb41bb1554fa405915e310",
     "version": null
-  }, 
+  },
   "unit.obo.gz": {
-    "checksum": "4e45267605698d1fcda533c27853a8fc", 
+    "checksum": "4e45267605698d1fcda533c27853a8fc",
     "version": "releases/2020-03-10"
   }
 }

psims/mzml/binary_encoding.py

@@ -1,3 +1,4 @@
+import os
 import base64
 import zlib
 
@@ -12,7 +13,10 @@
 
 
 try:
-    import pynumpress
+    if os.environ.get("PSIMS_NO_PYNUMPRESS"):
+        pynumpress = False
+    else:
+        import pynumpress
 except ImportError:
     pynumpress = None
 

psims/mzml/writer.py

@@ -18,20 +18,17 @@
 import numbers
 import warnings
 
-from collections import defaultdict
+from typing import List, Optional, Dict, Tuple, Mapping, Iterable, BinaryIO, TypedDict, Union, DefaultDict
 
-try:
-    from collections.abc import Mapping
-except ImportError:
-    from collections import Mapping
+from collections import defaultdict
 
 import numpy as np
 
-from psims.xml import XMLWriterMixin, XMLDocumentWriter
+from psims.xml import CVParam, XMLWriterMixin, XMLDocumentWriter
 from psims.utils import TableStateMachine
 
 from .components import (
-    ComponentDispatcher, element,
+    ComponentDispatcher, Software, Spectrum, element,
     default_cv_list, MzML, InstrumentConfiguration, IndexedMzML)
 
 from .binary_encoding import (
@@ -85,6 +82,14 @@
 ]
 
 
+class ArrayTypeSpec(TypedDict):
+    name: str
+    unit: Union[Mapping[str, str], CVParam]
+
+
+ArrayType = Union[str, ArrayTypeSpec]
+
+
 class DocumentSection(ComponentDispatcher, XMLWriterMixin):
 
     def __init__(self, section, writer, parent_context, section_args=None, **kwargs):
@@ -268,7 +273,7 @@ def controlled_vocabularies(self):
         self.state_machine.transition("controlled_vocabularies")
         super(PlainMzMLWriter, self).controlled_vocabularies()
 
-    def software_list(self, software_list):
+    def software_list(self, software_list: Iterable[Union[Software, Mapping]]):
         """Writes the ``<softwareList>`` section of the document.
 
         .. note::
@@ -465,11 +470,12 @@ def chromatogram_list(self, count, data_processing_method=None):
             self.writer, self.context, count=count,
             data_processing_method=data_processing_method)
 
-    def spectrum(self, mz_array=None, intensity_array=None, charge_array=None, id=None,
+    def spectrum(self, mz_array: Optional[np.ndarray] = None, intensity_array: Optional[np.ndarray] = None,
+                 charge_array: Optional[np.ndarray] = None, id: Optional[str] = None,
                  polarity='positive scan', centroided=True, precursor_information=None,
                  scan_start_time=None, params=None, compression=COMPRESSION_ZLIB,
                  encoding=None, other_arrays=None, scan_params=None, scan_window_list=None,
-                 instrument_configuration_id=None, intensity_unit=DEFAULT_INTENSITY_UNIT):
+                 instrument_configuration_id=None, intensity_unit=DEFAULT_INTENSITY_UNIT) -> Spectrum:
         '''Create a new :class:`~.Spectrum` instance to be written.
 
         This method does not immediately write and close the spectrum element, leaving it
@@ -546,11 +552,11 @@ def spectrum(self, mz_array=None, intensity_array=None, charge_array=None, id=No
             scan_window_list = list(scan_window_list)
 
         if isinstance(encoding, Mapping):
-            encoding = defaultdict(lambda: np.float32, encoding)
+            encoding = DefaultDict(lambda: np.float32, encoding)
         else:
             # create new variable to capture in closure
             _encoding = encoding
-            encoding = defaultdict(lambda: _encoding)
+            encoding = DefaultDict(lambda: _encoding)
         if polarity is not None:
             if isinstance(polarity, int):
                 if polarity > 0:

psims/version.py

@@ -1,3 +1 @@
-version = '0.1.47'
-
-checkout = "$Id$".replace("Id:", '').replace("$", '').strip()
+version = '0.1.47'