[med-svn] [Git][med-team/pycorrfit][upstream] New upstream version 1.1.4+dfsg
Alexandre Mestiashvili
gitlab at salsa.debian.org
Thu Sep 27 09:01:36 BST 2018
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
--
View it on GitLab: https://salsa.debian.org/med-team/pycorrfit/commit/a26dafc8c0c5601591761217cafa70096b25e962
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