Merge pull request #234 from pymzml/release/v2.4.7

Release/v2.4.7

.gitattributes

@@ -0,0 +1,2 @@
+# Never modify line endings of mzML files
+*.mzML* -crlf

README.rst

@@ -6,8 +6,8 @@ Introduction
 .. image:: https://travis-ci.org/pymzml/pymzML.svg?branch=master
     :target: https://travis-ci.org/pymzml/pymzML
 
-.. image:: https://ci.appveyor.com/api/projects/status/4nlw52a9qn22921d?svg=true
-   :target: https://ci.appveyor.com/project/fufezan-lab/pymzml
+.. image:: https://ci.appveyor.com/api/projects/status/e5reb5xw74jfqk2v/branch/dev?svg=true
+   :target: https://ci.appveyor.com/api/projects/status/e5reb5xw74jfqk2v/branch/dev?svg=true
    :alt: AppVeyor CI status
 
 .. image:: https://readthedocs.org/projects/pymzml/badge/?version=latest
@@ -82,10 +82,9 @@ pymzML is an extension to Python that offers
 Implementation
 **************
 
-pymzML requires Python3.4+.
+pymzML requires Python3.5+.
 The module is freely available on pymzml.github.com or pypi,
-published under MIT license and requires no additional modules to be installed, but can
-optionally use numpy.
+published under MIT license and only requires numpy and regex, however there are several optional dependencies for extended functionality like interactive plotting and deconvolution.
 
 
 ********
@@ -111,7 +110,7 @@ doi: https://doi.org/10.1093/bioinformatics/bty046
 Installation
 ************
 
-pymzML requires `Python`_ 3.4 or higher.
+pymzML requires `Python`_ 3.5 or higher.
 
 .. note::
 
@@ -134,6 +133,15 @@ Download pymzML using `GitHub`_ **or** the zip file:
 .. _GitHub:
    https://github.com/pymzML/pymzml
 
+* pypi version::
+
+   user@localhost:~$ pip install pymzml # install standard version
+   user@localhost:~$ pip install "pymzml[plot]" # with plotting support
+   user@localhost:~$ pip install "pymzml[pynumpress]" # with pynumpress support
+   user@localhost:~$ pip install "pymzml[deconvolution]" # with deconvolution support using ms_deisotope
+   user@localhost:~$ pip install "pymzml[full]" # full featured
+
+
 If you have troubles installing the dependencies, install numpy first separately,
 since pynumpress requires numpy to be installed.
 
@@ -146,7 +154,7 @@ Testing
 
 To test the package and correct installation::
 
-    nosetests tests/*.py
+    tox
 
 
 *************

docs/requirements.txt

@@ -1,3 +1,3 @@
-sphinx==2.3.1
+sphinx==3.0.3
 sphinx_rtd_theme==0.4.3
 regex

docs/source/quick_start.rst

@@ -33,4 +33,27 @@ no matter if an index was included into the file or not.
     spectrum_with_id_2540 = run[ 2540 ]
 
 
+Reading mzML indices with a custom regular expression
+------------------------------------------------------
+
+When reading mzML files with indices wich is not an integer or contains "scan=1" or similar,
+you can set a custom regex to parse the index when initializing the reader.
+
+Say for example you have an index as in the example file Manuels_customs_ids.mzML:
+    <offset idRef="ManuelsCustomID=1 diesdas">4026</offset>
+
+.. code-block:: python
+
+    #!/usr/bin/env python
+    import pymzml
+    import re
+
+    index_re = re.compile(
+        b'.*idRef="ManuelsCustomID=(?P<ID>.*) diesdas">(?P<offset>[0-9]*)</offset>'
+    )
+    run = pymzml.run.Reader(your_file_path, index_regex=index_re)
+    spec_1 = run[1]
+
+The regular expression has to contain a group called ID and a group called offset.
+Also be aware that your regex need to be a byte string.