CHANGELOG

+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

 |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/

debian/changelog

-pycorrfit (1.1.1+dfsg-1) UNRELEASED; urgency=medium
+pycorrfit (1.1.4+dfsg-1) unstable; urgency=medium
 
   [ Steffen Moeller ]
   * upstream/metadata RRID->SciCrunch
@@ -8,22 +8,30 @@ pycorrfit (1.1.1+dfsg-1) UNRELEASED; urgency=medium
 
   [ Alexandre Mestiashvili ]
   * Add .readthedocs.yml to Files-Excluded list
+  * New upstream version 1.1.1+dfsg
+  * New upstream version 1.1.4+dfsg
   * d/control:
-    - bump policy to 4.1.4
-    - bump debhelper to 11
+    - bump policy to 4.2.1, debhelper to 11
     - update VCS headers to point to salsa
+    - update uploaders email
     - switch to python3
-    - add python3-dev, python3-wxgtk4.0 and python3-matplotlib to build-depends
-  * Update d/rules, use --with python3
-  * New upstream version 1.1.1+dfsg
+    - add python3-dev, python3-wxgtk4.0, python3-matplotlib,
+          python3-simplejson, libpython3-all-dev
+    - use ${python3:Depends}, drop libpython2.7-dev
+  * Update d/rules:
+    - --with python3
+    - don't install modules as public pmodules
+      use PYBUILD_INSTALL_ARGS_python3=--install-lib=/usr/lib/pycorrfit
+    - exclude __pycache and pyc files with dh_install
+    - remove README from modules dir
+    - move and symlink pycorrfit script
+    - archive and install tests to examples
   * Update d/source/options to ignore pycorrfit/_version_save.py
   * Drop obsoleted patch fix_entry_point_for_gui.patch
+  * Update copyright, add new files
+  * Add autopkgtests, skip tests requiring network access
 
-  * TODO:
-    - Upstream requires scipy > 1.0.1
-    - Consider installing python modules to private_dir
-
- -- Alexandre Mestiashvili <mestia@debian.org>  Thu, 14 Jun 2018 11:41:50 +0200
+ -- Alexandre Mestiashvili <mestia@debian.org>  Thu, 27 Sep 2018 07:42:33 +0000
 
 pycorrfit (1.0.1+dfsg-2) unstable; urgency=medium
 
@@ -121,9 +129,9 @@ pycorrfit (0.8.8+dfsg-1) unstable; urgency=medium
      new get-orig-source target, remove duplicated LICENSE file
   * d/watch: add +dfsg suffix
   * d/copyright: add Files-Excluded section
-  * d/patches: deleted 
+  * d/patches: deleted
   * d/get-orig-source: deleted
-  * d/pycorrfit.pyremove: remove, as we need the egg-info directory 
+  * d/pycorrfit.pyremove: remove, as we need the egg-info directory
   * d/source/options: ignore generated files
   * Imported Upstream version 0.8.8+dfsg
 

debian/control

@@ -11,7 +11,6 @@ Build-Depends: cython3,
                imagemagick,
                libpython3-all-dev,
                librsvg2-bin,
-               python3-all,
                python3-dev,
                python3-lmfit (>= 0.9.2),
                python3-matplotlib,
@@ -29,7 +28,7 @@ Build-Depends: cython3,
                texlive-latex-extra,
                texlive-latex-recommended,
                texlive-science
-Standards-Version: 4.1.4
+Standards-Version: 4.2.1
 Vcs-Browser: https://salsa.debian.org/med-team/pycorrfit
 Vcs-Git: https://salsa.debian.org/med-team/pycorrfit.git
 Homepage: http://fcs-analysis.github.io/PyCorrFit/

debian/rules

 #!/usr/bin/make -f
+export DH_VERBOSE=1
 
 export DEB_BUILD_MAINT_OPTIONS=hardening=+BINDNOW
 export PYBUILD_NAME=pycorrfit
-export PYBUILD_TEST_PYTEST=0
+export PYBUILD_TEST_PYTEST=1
 export PYBUILD_INSTALL_ARGS_python3=--install-lib=/usr/lib/${PYBUILD_NAME}
 # see https://wiki.debian.org/ReproducibleBuilds/TimestampsInPDFGeneratedByLaTeX
 DEB_DATE_RFC_2822 := $(shell dpkg-parsechangelog -S date)
@@ -40,12 +41,20 @@ override_dh_install:
 	dh_install -X__pycache__ -X.*pyc
 	mv $(CURDIR)/debian/$(DEB_SOURCE)/usr/bin/pycorrfit \
            $(CURDIR)/debian/$(DEB_SOURCE)/usr/lib/$(DEB_SOURCE)/pycorrfit_run
-	find $(CURDIR) -print
 	cd $(CURDIR)/debian/$(DEB_SOURCE)/usr/bin/; \
         ln -s ../lib/$(DEB_SOURCE)/pycorrfit_run pycorrfit; cd -
 	mv debian/pycorrfit.xpm \
 		debian/$(DEB_SOURCE)/usr/share/pixmaps
 	chmod -R 644 debian/$(DEB_SOURCE)/usr/share/doc/$(DEB_SOURCE)/examples/external_model_functions/
+	rm -vf $(CURDIR)/debian/$(DEB_SOURCE)/usr/lib/$(DEB_SOURCE)/pycorrfit/readfiles/read_pt3_scripts/README
 
 override_dh_compress:
 	dh_compress -Xsample_sessions -Xexternal_model_functions
+
+override_dh_installexamples:
+	tar --sort=name \
+            --mtime="@${SOURCE_DATE_EPOCH}" \
+            --owner=root --group=root --numeric-owner \
+            --mode=go=rX,u+rw,a-s \
+            -cJf $(CURDIR)/debian/$(DEB_SOURCE)/usr/share/doc/$(DEB_SOURCE)/examples/tests.tar.xz  tests/
+	dh_installexamples

debian/tests/control

+Tests: pycorrfit-autopkgtests
+Restrictions: allow-stderr
+Depends: @, python3-pytest

debian/tests/pycorrfit-autopkgtests

+#!/bin/bash
+
+# Use test.tar.xz from /usr/share/doc/pycorrfit/examples/ if executed with
+# autopkgtest
+set -e
+pkg=pycorrfit
+export PYTHONPATH=/usr/lib/${pkg}
+examplesdir=/usr/share/doc/${pkg}/examples
+TMPDIR=$(mktemp -d)
+trap "rm -rf $TMPDIR" 0 INT QUIT ABRT PIPE TERM
+tar -xf ${examplesdir}/tests.tar.xz -C $TMPDIR
+WORKDIR=${TMPDIR}
+
+cd $WORKDIR
+
+# Skip tests which need network access
+
+rm -vf tests/{test_constraints.py,test_file_formats.py,test_session.py}
+find tests -print
+
+python3 -m pytest tests
+
+rm -rf $WORKDIR

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 "+\