[med-svn] [Git][med-team/pycorrfit][master] 13 commits: New upstream version 1.1.4+dfsg
Alexandre Mestiashvili
gitlab at salsa.debian.org
Thu Sep 27 09:01:33 BST 2018
Alexandre Mestiashvili pushed to branch master at Debian Med / pycorrfit
Commits:
a26dafc8 by Alexandre Mestiashvili at 2018-09-26T11:13:34Z
New upstream version 1.1.4+dfsg
- - - - -
b683ed50 by Alexandre Mestiashvili at 2018-09-26T11:13:39Z
Update upstream source from tag 'upstream/1.1.4+dfsg'
Update to upstream version '1.1.4+dfsg'
with Debian dir 282278a7a62be0794206b5caf539576c0ea50da9
- - - - -
9f44f908 by Alexandre Mestiashvili at 2018-09-26T11:20:00Z
Update changelog
- - - - -
5a118263 by Alexandre Mestiashvili at 2018-09-26T12:45:30Z
Enable tests, DH_VERBOSE=1
- - - - -
f36434f8 by Alexandre Mestiashvili at 2018-09-26T13:07:20Z
Archive and install tests to examples dir
- - - - -
8ff258c2 by Alexandre Mestiashvili at 2018-09-26T13:27:12Z
Add d/tests with initial autopkgtest
- - - - -
02a316a6 by Alexandre Mestiashvili at 2018-09-26T13:42:53Z
Tweak dh_installexamples
- - - - -
d6f3aa34 by Alexandre Mestiashvili at 2018-09-26T14:11:36Z
Update d/tests, add python3-pytest to Depends
- - - - -
54f7b6da by Alexandre Mestiashvili at 2018-09-26T14:52:34Z
Skip tests requiring network access
- - - - -
9a918226 by Alexandre Mestiashvili at 2018-09-26T15:06:26Z
Remove README from the modules dir
- - - - -
cad2ffd1 by Alexandre Mestiashvili at 2018-09-26T15:09:18Z
Bump Policy to 4.2.1
- - - - -
05faa4ff by Alexandre Mestiashvili at 2018-09-27T07:31:05Z
Remove python3-dev from Build-Depends
- - - - -
87e3a91f by Alexandre Mestiashvili at 2018-09-27T07:53:17Z
Update changelog
Gbp-Dch: Ignore
- - - - -
12 changed files:
- CHANGELOG
- README.rst
- debian/changelog
- debian/control
- debian/rules
- + debian/tests/control
- + debian/tests/pycorrfit-autopkgtests
- 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/
=====================================
debian/changelog
=====================================
@@ -1,4 +1,4 @@
-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 at debian.org> Thu, 14 Jun 2018 11:41:50 +0200
+ -- Alexandre Mestiashvili <mestia at 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
=====================================
@@ -1,8 +1,9 @@
#!/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/$(DEB_SOURCE)/examples/tests.tar.xz tests/
+ dh_installexamples
=====================================
debian/tests/control
=====================================
@@ -0,0 +1,3 @@
+Tests: pycorrfit-autopkgtests
+Restrictions: allow-stderr
+Depends: @, python3-pytest
=====================================
debian/tests/pycorrfit-autopkgtests
=====================================
@@ -0,0 +1,23 @@
+#!/bin/bash
+
+# Use test.tar.xz from /usr/share/doc/pycorrfit/examples/ if executed with
+# autopkgtest
+set -e
+pkg=pycorrfit
+export PYTHONPATH=/usr/lib/${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 "+\
View it on GitLab: https://salsa.debian.org/med-team/pycorrfit/compare/b95471b38668e88ef07b87d12346504b0ae6e05c...87e3a91f135b5b24057b75928fb47f49f0747ae8
--
View it on GitLab: https://salsa.debian.org/med-team/pycorrfit/compare/b95471b38668e88ef07b87d12346504b0ae6e05c...87e3a91f135b5b24057b75928fb47f49f0747ae8
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