[med-svn] [khmer] 02/04: Imported Upstream version 2.0+dfsg
Michael Crusoe
misterc-guest at moszumanska.debian.org
Tue Sep 8 17:21:26 UTC 2015
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a commit to branch master
in repository khmer.
commit a9e0b6644f22bccdca34a060e876aa3252b112ce
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Date: Tue Sep 8 09:45:20 2015 -0700
Imported Upstream version 2.0+dfsg
---
ChangeLog | 12 ++++++++++++
README.rst | 37 +++++++++----------------------------
doc/index.rst | 4 +---
doc/roadmap.rst | 44 ++++++++++++++++++++++++--------------------
khmer/_version.py | 4 ++--
tests/test_scripts.py | 9 +++++++--
6 files changed, 55 insertions(+), 55 deletions(-)
diff --git a/ChangeLog b/ChangeLog
index 60f459e..40e0967 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,15 @@
+2015-09-07 Michael R. Crusoe <crusoe at ucdavis.edu>
+
+ * doc/roadmap.rst: Updated for 2.0 release.
+ * README.rst: drop unstable badges; fix links
+ * doc/index.rst: point at getting help guide
+
+2015-09-05 Michael R. Crusoe <crusoe at ucdavis.edu>
+
+ * tests/test_scripts.py: make the script version test more specific; double
+ check that script in question is from the 'khmer' project based upon the
+ second line of the file.
+
2015-09-04 Michael R. Crusoe <crusoe at ucdavis.edu>
* tests/khmer_tst_utils.py: look in "EGG-INFO" for scripts before checking
diff --git a/README.rst b/README.rst
index 3ab1ce5..22ed675 100644
--- a/README.rst
+++ b/README.rst
@@ -41,25 +41,7 @@ khmer
Welcome to khmer: k-mer counting, filtering and graph traversal FTW!
-.. image:: https://readthedocs.org/projects/khmer/badge
- :target: https://readthedocs.org/projects/khmer/
- :alt: Documentation Status
-.. image:: https://badge.fury.io/py/khmer.svg
- :target: http://badge.fury.io/py/khmer
- :alt: PyPI Package
-.. image:: https://pypip.in/d/khmer/badge.svg
- :target: https://crate.io/packages/khmer
- :alt: Downloads Counter
-.. image:: https://pypip.in/license/khmer/badge.svg
- :target: https://pypi.python.org/pypi/khmer/
- :alt: License
-.. image:: http://ci.ged.msu.edu/job/khmer-master/badge/icon
- :target: http://ci.ged.msu.edu/job/khmer-master/
-.. image:: https://scan.coverity.com/projects/621/badge.svg
- :target: https://scan.coverity.com/projects/621
- :alt: Coverity Scan Build Status
-
-The official repository is at
+The official source code repository is at
https://github.com/dib-lab/khmer
@@ -78,27 +60,29 @@ them, please visit the following URLs:
We chat at https://gitter.im/dib-lab/khmer and the maintainers can be
contacted at khmer-project at idyll.org.
-For getting help with please see this guide: http://khmer.readthedocs.org/user/getting-help.html
+For getting help please see this guide: http://khmer.readthedocs.org/en/stable/user/getting-help.html
IMPORTANT NOTE: CITE US!
------------------------
khmer is *research software*, so you should cite us when you use it
-in scientific publications! Please see the CITATION file for
+in scientific publications! Please see the `CITATION
+<http://khmer.readthedocs.org/en/stable/citations.html>`__ file for
citation information.
INSTALL INSTRUCTIONS:
---------------------
-khmer requires a 64-bit operating system and Python 2.7.x. Linux users will need
-the Python development libraries and gcc. OS X users may need XCode installed.
+khmer requires a 64-bit operating system and Python version 2.7.x, 3.3.x, or
+3.4.x. Linux users will need the Python development libraries and gcc. OS X
+users may need XCode installed to build from source.
In short:
``pip install khmer`` to download, build, and install the latest stable
version.
-For more details see `doc/install.txt <https://khmer.readthedocs.org/en/latest/user/install.html>`_
+For more details see `doc/install.rst <https://khmer.readthedocs.org/en/stable/user/install.html>`_
The use of a virtualenv is recommended, see
https://virtualenv.readthedocs.org/en/latest/installation.html
@@ -107,7 +91,4 @@ khmer is under the BSD license; see doc/LICENSE.txt. Distribution,
modification and redistribution, incorporation into other software, and
pretty much everything else is allowed.
-MRC 2014-05-14
-
-.. vim: set filetype=rst
-
+MRC 2015-09-07
diff --git a/doc/index.rst b/doc/index.rst
index f419c86..dfa9934 100644
--- a/doc/index.rst
+++ b/doc/index.rst
@@ -66,9 +66,7 @@ common research tasks <https://khmer-recipes.readthedocs.org/>`__.
You might also be interested in :doc:`papers using or citing khmer
<user/biblio>`.
-**To get help**, please ask questions on `the khmer mailing list
-<http://lists.idyll.org/listinfo/khmer>`__ or `post an issue on
-GitHub <https://github.com/dib-lab/khmer/issues/new>`__.
+**To get help**, :doc:`please follow this guide <user/getting-help>`.
We welcome contributions to the khmer project! We are friendly and
supportive of new contributors, and have a :doc:`code of conduct
diff --git a/doc/roadmap.rst b/doc/roadmap.rst
index 45e0c63..deb9842 100644
--- a/doc/roadmap.rst
+++ b/doc/roadmap.rst
@@ -37,7 +37,7 @@
Contact: khmer-project at idyll.org
***************************
-Roadmap to v2.0, v3.0, v4.0
+Roadmap to v3.0, v4.0, v5.0
***************************
Background
@@ -45,42 +45,50 @@ Background
To make the khmer project easier to use and easier to build upon several
fundamental changes need to happen. This document outlines our plan to do so
-while minimizing the impact of these changes on our existing users.
+while minimizing the impact of these changes on our existing users. The
+version numbers are approximate; there may be additional major number
+releases to support needed changes to the API along the way. This document has
+been updated for v2.0 onwards from the `original roadmap
+<http://khmer.readthedocs.org/en/v1.2/roadmap.html>`__.
The discussion that lead to this document can be read at
https://github.com/dib-lab/khmer/issues/389
-Remainder of v1.x series
+Remainder of v2.x series
========================
-Start of transition to a single entrypoint named `oxli`. This will be exempt
-from the project's semantic versioning and will be advertised as experimental
-and unstable.
+Continue transition to a single entrypoint named `oxli
+<https://github.com/dib-lab/khmer/blob/master/oxli/__init__.py#L38>`__ . This
+will be exempt from the project's semantic versioning and will not be
+advertised as it is experimental and unstable. (For the 2.0 version we removed
+the ``oxli`` script just prior to release and restored it afterwards to the
+development tree.)
-Migration of Python script functionality to a Python module named `oxli`. As
-the code moves over there will be no change to external script functionality or
-their command line interfaces.
+The Python script functionality will continue to migrate to a Python module
+named `oxli <https://github.com/dib-lab/khmer/tree/master/oxli>`__. As the code
+moves over there will be no change to external script functionality or their
+command line interfaces (except for new features).
-v2.x series
+v3.x series
===========
-`oxli` command is now under semantic versioning. Scripts are still the
+The ``oxli`` command is now under semantic versioning. Scripts are still the
advertised and preferred entry point for users. Developers and workflow systems
-can start to trial `oxli` but need not switch until 3.0. New functionality is
-added to both the scripts and the `oxli` command.
+can start to trial ``oxli`` but need not switch until 4.0. New functionality is
+added to both the scripts and the ``oxli`` command.
-v3.0 and project renaming
+v4.0 and project renaming
=========================
Project renamed to 'oxli'; all references to 'khmer' removed from the code and
documentation except for a single note in the docs. All scripts dropped as
-their functionality has been moved to the `oxli` command. Websites that we
+their functionality has been moved to the ``oxli`` command. Websites that we
maintain that have 'khmer' in the URL will have redirects installed.
Refinement of the Python API continues, however it is not part of the semantic
versioning of the project.
-v4.0
+v5.0
====
The semantic versioning now extends to the Python API.
@@ -88,12 +96,8 @@ The semantic versioning now extends to the Python API.
Python API wishlist
===================
-Python 3.0 support
-
API for multiple container types and implementation of the same.
Cleanup of Python/C++ class hierarchy to cut down on boilerplate glue code.
Switch to new-style Python objects (see LabelHash & Hashbits)
-
-
diff --git a/khmer/_version.py b/khmer/_version.py
index e7a72b4..b46a20e 100644
--- a/khmer/_version.py
+++ b/khmer/_version.py
@@ -16,8 +16,8 @@ import subprocess
import sys
# these strings will be replaced by git during git-archive
-git_refnames = " (HEAD -> master, tag: v2.0-rc6)"
-git_full = "4c759652ff29dba715bca71f516c6cf6eb756114"
+git_refnames = " (HEAD -> master, tag: v2.0)"
+git_full = "c2cc671127b97083e87989c0822ea036dd8202dc"
# these strings are filled in when 'setup.py versioneer' creates _version.py
tag_prefix = "v"
diff --git a/tests/test_scripts.py b/tests/test_scripts.py
index 8575b08..7df2153 100644
--- a/tests/test_scripts.py
+++ b/tests/test_scripts.py
@@ -3711,7 +3711,7 @@ def test_unique_kmers_multiple_inputs():
assert 'Total estimated number of unique 20-mers: 4170' in err
-def check_version(scriptname):
+def check_version_and_basic_citation(scriptname):
version = re.compile("^khmer .*$", re.MULTILINE)
status, out, err = utils.runscript(scriptname, ["--version"])
assert status == 0, status
@@ -3722,4 +3722,9 @@ def check_version(scriptname):
def test_version():
for entry in os.listdir(utils.scriptpath()):
if entry.endswith(".py"):
- yield check_version, entry
+ with open(os.path.join(utils.scriptpath(), entry)) as script:
+ line = script.readline()
+ line = script.readline()
+ if 'khmer' in line: # simple check of copyright line.
+ yield check_version_and_basic_citation, entry
+ # emit test for each script
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/khmer.git
More information about the debian-med-commit
mailing list