./lib Makefile rewrite, create libkhmer.{a,so} and install target by kdm9 · Pull Request #788 · dib-lab/khmer

kdm9 · 2015-02-20T01:20:38Z

Hi all,

This rehashes the makefile in ./lib, adding a few targets and cleaning up. (mentioned in #776, also ping #751)

Added:

libkhmer.so shared object (how does this work on OSX? will it break due to shared objects being named X.dylib?)
libkhmer.a static archive

removed:

obsolete targets whose dependent source files don't exist any longer
use wildcards for *.o targets where possible

changes:

Use versioneer not python packaging for versioning. If haven't done python setup.py something, the old script spat out a sentence explaining this. Now, you don't need setup.py.
add compiled files to gitignores

All of this stuff probably needs testing, this started as a hack to test a few things. There's probably also some more culling that could happen in the makefile.

Cheers,
K

kdm9 · 2015-02-20T01:21:38Z

Is it mergable?
Did it pass the tests?
~~If it introduces new functionality in scripts/ is it tested? Check for code coverage with make clean diff-cover~~
Is it well formatted? Look at make pep8, make diff_pylint_report,
make cppcheck, and make doc output. Use make format and manual
fixing as needed.
~~Did it change the command-line interface? Only additions are allowed without a major version increment. Changing file formats also requires a major version number increment.~~
Is it documented in the ChangeLog? http://en.wikipedia.org/wiki/Changelog#Format
Was a spellchecker run on the source code and documentation after changes were made?

kdm9 · 2015-02-20T01:22:15Z

Whelp, merge conflict already 😵. Will rebase and push.

kdm9 · 2015-02-20T01:35:35Z

Hmm, are those failures my stuff up or Jenkins'?

EDIT: they're mine. Working on it now.

mr-c · 2015-02-20T02:52:47Z

Yeah, this Makefile hasn't been used in about two years.

The following defines are no longer present in the codebase and can be removed:

TRACE_STATE_CHANGES
TRACE_BUSYWAITS
TRACE_SPINLOCKS
TRACE_MEMCOPIES
TRACE_DATA

kdm9 · 2015-02-23T05:26:04Z

retest this please

kdm9 · 2015-02-23T05:32:29Z

@mr-c Does that mean that lib/trace_logger is also obsolete?

mr-c · 2015-02-23T06:19:44Z

@kdmurray91 Not quite yet :-)

kdm9 · 2015-02-24T07:56:07Z

retest this please

kdm9 · 2015-03-23T04:22:27Z

Can I delete the following files:

test-CacheManager.cc: Functionality has been removed
test-StreamReader.cc: Functionality has been removed

Additionally, test-Colours.cc doesn't compile.

#18

- replace most .o targets with wildcard targets - add libkhmer.so and libkhmer.a targets - Minor tidying

- Allows the version to be obtained without khmer being installed.

They were being called libkhmer.a.a and .so.so due to a copy-paste error

And add more comments

kdm9 · 2015-03-27T11:18:52Z

Jenkins, don't make us call Camille, retest this please!!

kdm9 · 2015-03-27T11:20:20Z

Ah, I think jenkins is having trouble pulling down changes, as github's under a DDOS attack

kdm9 · 2015-03-27T11:26:03Z

retest this please

kdm9 · 2015-03-27T11:39:04Z

Well, closer. git fetch only failed on the OS X node that time. retest this please

kdm9 · 2015-03-27T11:43:08Z

Ah, that's an actual failure. Hacky configure is hacky.

I.e make it work on OS X

kdm9 · 2015-03-27T12:00:56Z

mr-c · 2015-03-27T13:01:08Z

Should your tst.cc be included here to catch issues similar to the Seqan header problem in the future?

mr-c · 2015-03-27T13:10:23Z

This generally looks good to me. Slap a completed checklist on this and I'll merge.

kdm9 · 2015-03-27T22:42:22Z

Is it mergeable?
Did it pass the tests?
If it introduces new functionality in scripts/ is it tested?
Check for code coverage with make clean diff-cover
Is it well formatted? Look at make pep8, make diff_pylint_report,
make cppcheck, and make doc output. Use make format and manual
fixing as needed.
Did it change the command-line interface? Only additions are allowed
without a major version increment. Changing file formats also requires a
major version number increment.
Is it documented in the ChangeLog?
http://en.wikipedia.org/wiki/Changelog#Format
Was a spellchecker run on the source code and documentation after
changes were made?

kdm9 · 2015-03-27T22:49:07Z

retest this please

kdm9 · 2015-03-27T22:51:56Z

All good to go I think @mr-c

./lib Makefile rewrite, create libkhmer.{a,so} and install target

mr-c · 2015-03-28T10:52:56Z

Thanks!

kdm9 force-pushed the libmakefile branch from f1afc0a to 78fcd29 Compare February 20, 2015 01:24

kdm9 added a commit to kdm9/khmer that referenced this pull request Feb 20, 2015

Add changelog entry for PR dib-lab#788

af8c84f

kdm9 force-pushed the libmakefile branch from 383e33a to 0233aaf Compare February 23, 2015 05:34

kdm9 added a commit to kdm9/khmer that referenced this pull request Feb 23, 2015

Add changelog entry for PR dib-lab#788

ecdeec8

kdm9 force-pushed the libmakefile branch from 164e5cd to 3d3b5f3 Compare March 7, 2015 07:22

kdm9 added a commit to kdm9/khmer that referenced this pull request Mar 7, 2015

Add changelog entry for PR dib-lab#788

a837015

kdm9 mentioned this pull request Mar 12, 2015

Refactor C++ Test Drivers #18

Open

kdm9 force-pushed the libmakefile branch from 3d3b5f3 to 679a263 Compare March 23, 2015 04:07

kdm9 added a commit to kdm9/khmer that referenced this pull request Mar 23, 2015

Add changelog entry for PR dib-lab#788

ab1b76c

kdm9 added 10 commits March 23, 2015 16:08

Clean up makefile & add .so/.a targets

06cdc35

- replace most .o targets with wildcard targets - add libkhmer.so and libkhmer.a targets - Minor tidying

Use versioneer for ./lib version

0db4d0f

- Allows the version to be obtained without khmer being installed.

Fix libkhmer target extensions

4593154

They were being called libkhmer.a.a and .so.so due to a copy-paste error

Update gitignores in CPP library and 3rd party dir

f8088b7

Add changelog entry for PR dib-lab#788

29acdd7

Spellcheck lib/Makefile

8f48e9d

Remove obsolete TRACE cflags from lib/Makefile

93a440d

Add versioned .so files to gitignore

1be80bb

More tidying of lib/Makefile

4bd15c4

Fix clean rule in lib/makefile

39433ca

And add more comments

kdm9 force-pushed the libmakefile branch from 679a263 to 39433ca Compare March 23, 2015 05:09

Add lib/ build to jenkins build script

a09bc3d

kdm9 added 3 commits March 27, 2015 22:46

Make the khmer pkgconfig rule more portable

e888b7d

I.e make it work on OS X

Document the addition of khmer.pc.in in changelog

fe15f5b

Remove extraneous makefile rule

d72be06

mr-c reviewed Mar 27, 2015
View reviewed changes

kdm9 added 4 commits March 28, 2015 09:33

Add test-compile.cc and use it in root makefile

7b6dcfd

Update copyright dates in files I've changed

2b7c32c

Wrap long lines in lib/Makefile

39b4b78

Add better description & URL to pkg-config file

3f2204f

Add test-compile to lib/Makefile test progs

5a3c0e2

mr-c added a commit that referenced this pull request Mar 28, 2015

Merge pull request #788 from kdmurray91/libmakefile

2f6e71a

./lib Makefile rewrite, create libkhmer.{a,so} and install target

mr-c merged commit 2f6e71a into dib-lab:master Mar 28, 2015

kdm9 deleted the libmakefile branch March 28, 2015 11:55

kdm9 mentioned this pull request Mar 30, 2015

libkhmer-dev debian package? #885

Closed

21 tasks

wking mentioned this pull request Mar 30, 2015

Proposed change to coding guidelines: squashing commits #660

Closed

mr-c mentioned this pull request Apr 1, 2015

Python API #776

Open

kdm9 mentioned this pull request Apr 1, 2015

C++ library discussion #893

Closed

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