Update docs, changelog, authors, bump version to 4.3.3

AUTHORS

@@ -5,6 +5,7 @@ On Github
 .........
 
 Vladimir Gorshkov [caetera]
+Andrey Rozenberg [alephreish]
 
 
 On Bitbucket (before March 1, 2020)

CHANGELOG

@@ -1,7 +1,21 @@
-dev
----
+4.3.3
+-----
+
+ - Add :py:func:`pyteomics.electrochem.gravy` (`#9 <https://github.com/levitsky/pyteomics/pull/9>`_).
+
+ - Fixes and improvements in :py:func:`pyteomics.pepxml.roc_curve` (`#10 <https://github.com/levitsky/pyteomics/pull/10>`_).
+
+ - Changes in guessing behavior of :py:func:`read` functions.
+
+   In modules that implement :ref:`indexing parsers <indexing>` for non-XML formats (MGF, FASTA, PEFF, ms1/ms2),
+   when a parser is instantiated using :py:func:`read`, the parser class to instantiate is guessed
+   based on the mode of the file object passed to :py:func:`read` (text or binary).
 
-Add :py:func:`pyteomics.electrochem.gravy` (`#9 <https://github.com/levitsky/pyteomics/pull/9>`_).
+   With some file-like objects, mode cannot be easily deduced without consuming some of the data.
+   You will now see more warnings in case `use_index` is not explicitly passed to :py:func:`read` and reading mode is not obvious.
+   There will also be warnings if `use_index` is specified but the file is opened in the wrong mode.
+   To avoid all of this, youy are encouraged to instantiate parser classes directly,
+   or explicitly specify `use_index` to :py:func:`read` in all corner cases.
 
 4.3.2
 -----

VERSION

@@ -1 +1 @@
-4.3.3dev1
+4.3.3

doc/source/data.rst

@@ -6,16 +6,16 @@ The following section is dedicated to data manipulation. **Pyteomics** aims to
 support the most common formats of (LC-)MS/MS data, peptide identification
 results and protein databases.
 
-.. include :: data/notes.rst
+.. include :: data/notes.rst.inc
 
 .. contents:: Document contents
     :backlinks: top
     :depth: 3
 
-.. include :: data/text.rst
+.. include :: data/text.rst.inc
 
-.. include :: data/xml.rst
+.. include :: data/xml.rst.inc
 
-.. include :: data/indexing.rst
+.. include :: data/indexing.rst.inc
 
-.. include :: data/tda.rst
+.. include :: data/tda.rst.inc

doc/source/data/text.rst → doc/source/data/text.rst.inc

@@ -71,56 +71,56 @@ Class-based interface
 Since version 3.4.3, MGF parsing functionality is encapsulated in a class:
 :py:class:`pyteomics.mgf.MGF`. This class can be used for:
 
- - sequential parsing of the file (the same as :py:func:`read`)::
-
- .. code-block:: python
-
-    >>> with mgf.MGF('tests/test.mgf') as reader:
-    ..:     for spectrum in reader:
-    ..:         ...
-
- - accessing the file header (the same as :py:func:`read_header`)::
-
- .. code-block:: python
-
-    >>> f = mgf.MGF('tests/test.mgf')
-    >>> f.header
-    {'charge': [2, 3],
-     'com': 'Based on http://www.matrixscience.com/help/data_file_help.html',
-     'it_mods': 'Oxidation (M)',
-     'itol': '1',
-     'itolu': 'Da',
-     'mass': 'Monoisotopic',
-     'mods': 'Carbamidomethyl (C)',
-     'useremail': 'leu@altered-state.edu',
-     'username': 'Lou Scene'}
-
- - direct access to spectra by title (the same as :py:func:`get_spectrum`)::
-
- .. code-block:: python
-
-    >>> f = mgf.MGF('tests/test.mgf')
-    >>> f['Spectrum 2']
-    {'charge array': masked_array(data = [3 2 1 1 1 1],
-                  mask = False,
-            fill_value = 0),
-     'intensity array': array([  237.,   128.,   108.,  1007.,   974.,    79.]),
-     'm/z array': array([  345.1,   370.2,   460.2,  1673.3,  1674. ,  1675.3]),
-     'params': {'charge': [2, 3],
-      'com': 'Based on http://www.matrixscience.com/help/data_file_help.html',
-      'it_mods': 'Oxidation (M)',
-      'itol': '1',
-      'itolu': 'Da',
-      'mass': 'Monoisotopic',
-      'mods': 'Carbamidomethyl (C)',
-      'pepmass': (1084.9, 1234.0),
-      'rtinseconds': '25',
-      'scans': '3',
-      'title': 'Spectrum 2',
-      'useremail': 'leu@altered-state.edu',
-      'username': 'Lou Scene'}}
-
-.. note ::
+ - sequential parsing of the file (the same as :py:func:`read`):
+
+   .. code-block:: python
+
+      >>> with mgf.MGF('tests/test.mgf') as reader:
+      ..:     for spectrum in reader:
+      ..:         ...
+
+ - accessing the file header (the same as :py:func:`read_header`):
+
+   .. code-block:: python
+
+      >>> f = mgf.MGF('tests/test.mgf')
+      >>> f.header
+      {'charge': [2, 3],
+       'com': 'Based on http://www.matrixscience.com/help/data_file_help.html',
+       'it_mods': 'Oxidation (M)',
+       'itol': '1',
+       'itolu': 'Da',
+       'mass': 'Monoisotopic',
+       'mods': 'Carbamidomethyl (C)',
+       'useremail': 'leu@altered-state.edu',
+       'username': 'Lou Scene'}
+
+ - direct access to spectra by title (the same as :py:func:`get_spectrum`):
+
+   .. code-block:: python
+
+      >>> f = mgf.MGF('tests/test.mgf')
+      >>> f['Spectrum 2']
+      {'charge array': masked_array(data = [3 2 1 1 1 1],
+                    mask = False,
+              fill_value = 0),
+       'intensity array': array([  237.,   128.,   108.,  1007.,   974.,    79.]),
+       'm/z array': array([  345.1,   370.2,   460.2,  1673.3,  1674. ,  1675.3]),
+       'params': {'charge': [2, 3],
+        'com': 'Based on http://www.matrixscience.com/help/data_file_help.html',
+        'it_mods': 'Oxidation (M)',
+        'itol': '1',
+        'itolu': 'Da',
+        'mass': 'Monoisotopic',
+        'mods': 'Carbamidomethyl (C)',
+        'pepmass': (1084.9, 1234.0),
+        'rtinseconds': '25',
+        'scans': '3',
+        'title': 'Spectrum 2',
+        'useremail': 'leu@altered-state.edu',
+        'username': 'Lou Scene'}}
+
+   .. note ::
     :py:class:`MGF`'s support for direct indexing is rudimentary, because it does not in fact keep an index and has
     to search through the file line-wise on every call. :py:class:`pyteomics.mgf.IndexedMGF` is designed for
     random access and more (see `Indexed Parsers`_ for details).

doc/source/data/xml.rst → doc/source/data/xml.rst.inc

@@ -340,7 +340,7 @@ idXML
 **idXML** is an OpenMS format for peptide identifications. It is supported in :py:mod:`pyteomics.openms.idxml`.
 It partially supports indexing (protein information can be indexed and extracted with `retrieve_refs`).
 
-The regular iterative parsing is done through :py:func:`read` or :py:class:`IDXML`, and :py:class:`pandas.DataFrame`s
+The regular iterative parsing is done through :py:func:`read` or :py:class:`IDXML`, and :py:class:`pandas.DataFrame`
 can be created as well.
 
 

doc/source/intro.rst

@@ -1,8 +1,8 @@
 Introduction
 ============
 
-This tutorial covers the basic Pyteomics functionality. For more details, 
-please, check the API reference. You can also access the API docstrings from 
+This tutorial covers the basic Pyteomics functionality. For more details,
+please, check the API reference. You can also access the API docstrings from
 Python shell:
 
 .. code-block:: python
@@ -12,10 +12,12 @@ Python shell:
 
 IPython users can use the following shortcut:
 
-.. code-block:: python
+.. code-block::
+
+    In [1]: from pyteomics.mass import calculate_mass
+
+    In [2]: calculate_mass?
 
-    >>> from pyteomics.mass import calculate_mass
-    >>> calculate_mass?
 
-We expect the reader to be familiar with the basic Python syntax as well as 
+We expect the reader to be familiar with the basic Python syntax as well as
 proteomics concepts.