[med-svn] [Git][med-team/pycorrfit][upstream] New upstream version 1.1.4+dfsg

[Alexandre Mestiashvili]

Alexandre Mestiashvili pushed to branch upstream at Debian Med / pycorrfit


Commits:
a26dafc8 by Alexandre Mestiashvili at 2018-09-26T11:13:34Z
New upstream version 1.1.4+dfsg
- - - - -


7 changed files:

- CHANGELOG
- README.rst
- docs/conf.py
- docs/extensions/github_changelog.py
- docs/sec_about.rst
- docs/sec_getting_started.rst
- pycorrfit/fit.py


Changes:

=====================================
CHANGELOG
=====================================
@@ -1,3 +1,6 @@
+1.1.2
+ - ci: Automated release to PyPI with appveyor and travis-ci
+ - fix: support lmfit >= 0.9.11
 1.1.1
  - Fix plotting error with LaTeX (thanks @toubol) (#179)
  - Update documentation


=====================================
README.rst
=====================================
@@ -1,7 +1,7 @@
 |PyCorrFit|
 ===========
 
-|PyPI Version| |Build Status Win| |Build Status Travis| |Coverage Status|
+|PyPI Version| |Build Status Win| |Build Status Travis| |Coverage Status| |Docs Status|
 
 
 Documentation
@@ -25,3 +25,5 @@ at the `issues page <https://github.com/FCS-analysis/PyCorrFit/wiki/Creating-a-n
    :target: https://travis-ci.org/FCS-analysis/PyCorrFit
 .. |Coverage Status| image:: https://img.shields.io/codecov/c/github/FCS-analysis/PyCorrFit/master.svg
    :target: https://codecov.io/gh/FCS-analysis/PyCorrFit
+.. |Docs Status| image:: https://readthedocs.org/projects/pycorrfit/badge/?version=latest
+   :target: https://readthedocs.org/projects/pycorrfit/builds/


=====================================
docs/conf.py
=====================================
@@ -81,6 +81,7 @@ master_doc = 'index'
 
 # General information about the project.
 project = 'PyCorrFit'
+github_project = 'FCS-analysis/' + project
 copyright = '2014, Paul Müller'
 author = 'Paul Müller'
 
@@ -184,7 +185,7 @@ man_pages = [
 #  dir menu entry, description, category)
 texinfo_documents = [
     (master_doc, project, project + ' Documentation',
-     author, project, 'Phase imaging analysis software.',
+     author, project, 'Curve fitting in FCS.',
      'Scientific'),
 ]
 


=====================================
docs/extensions/github_changelog.py
=====================================
@@ -29,13 +29,13 @@ class IncludeDirective(Directive):
 
     def run(self):
         full_path = self.arguments[0]
-        project = self.state.document.settings.env.config.project
+        project = self.state.document.settings.env.config.github_project
 
         def insert_github_link(reobj):
             line = reobj.string
             instr = line[reobj.start():reobj.end()]
             issue = instr.strip("#()")
-            link = "https://github.com/RI-imaging/{}/issues/".format(project)
+            link = "https://github.com/{}/issues/".format(project)
             rstlink = "(`#{issue} <{link}{issue}>`_)".format(issue=issue,
                                                              link=link)
             return rstlink
@@ -70,5 +70,6 @@ class IncludeDirective(Directive):
 
 
 def setup(app):
+    app.add_config_value('github_project', "user/project", 'html')
     app.add_directive('include_changelog', IncludeDirective)
     return {'version': '0.1'}   # identifies the version of our extension


=====================================
docs/sec_about.rst
=====================================
@@ -52,5 +52,5 @@ How to cite
 Müller, P., Schwille, P., and Weidemann, T.
 *PyCorrFit - generic data evaluation for fluorescence correlation spectroscopy.*
 Bioinformatics 30(17):2532-2533 (2014).
-DOI:`10.1093/bioinformatics/btu328 <http://dx.doi.org/10.1093/bioinformatics/btu328>`_
+doi:`10.1093/bioinformatics/btu328 <http://dx.doi.org/10.1093/bioinformatics/btu328>`_
 


=====================================
docs/sec_getting_started.rst
=====================================
@@ -4,7 +4,8 @@ Getting started
 
 Installation
 ------------
-- Installers for PyCorrFit are available at the `release page <https://github.com/FCS-analysis/PyCorrFit/releases>`_.
+- Windows installers for PyCorrFit are available at the `release page <https://github.com/FCS-analysis/PyCorrFit/releases>`_.
+- On Debian-based systems, install via ``apt-get install pycorrfit``.
 - If you have Python 3.6 installed, you may install PyCorrFit via ``pip install pycorrfit[GUI]``.
   After the installation, type ``pycorrfit`` in a command shell to start PyCorrFit.
 
@@ -12,7 +13,7 @@ Installation
 Documentation
 -------------
 The documentation is in the process of being transferred entirely to
-readthedocs.org. Currently, the it is scattered across several
+readthedocs.org. Currently, it is scattered across several
 places and it is most-likely outdated:
 
 - Original LaTeX-based PDF file (outdated): https://github.com/FCS-analysis/PyCorrFit/wiki/PyCorrFit_doc.pdf


=====================================
pycorrfit/fit.py
=====================================
@@ -870,12 +870,18 @@ class Fit(object):
         # Only allow physically correct parameters
         self.fit_parm = self.check_parms(self.fit_parm)
         # Compute error estimates for fit (Only "Lev-Mar")
-        if self.fit_algorithm == "Lev-Mar" and result.success:
+        if (self.fit_algorithm == "Lev-Mar"
+            and result.success
+            # If the covariance matrix cannot be computed in
+            # - lmfit <= 0.9.10: result.covar is None
+            # - lmfit >= 0.9.11: result.covar is not set
+            and hasattr(result, "covar")
+            and result.covar is not None):
             # This is the standard way to minimize the data. Therefore,
             # we are a little bit more verbose.
-            self.covar = result.covar
+            covar = result.covar
             try:
-                self.parmoptim_error = np.diag(self.covar)
+                self.parmoptim_error = np.diag(covar)
             except:
                 warnings.warn("PyCorrFit Warning: Error estimate not "+\
                               "possible, because we could not "+\



View it on GitLab: https://salsa.debian.org/med-team/pycorrfit/commit/a26dafc8c0c5601591761217cafa70096b25e962

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