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 You're receiving this email because of your account on salsa.debian.org.
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