Add doxygen #2135

shadowwalkersb · 2016-12-28T06:44:12Z

Closes #1733 .

Check license info

conda-forge-linter · 2016-12-28T06:44:16Z

Hi! This is the friendly automated conda-forge-linting service.

I just wanted to let you know that I linted all conda-recipes in your PR (recipes/doxygen) and found it was in an excellent condition.

shadowwalkersb · 2016-12-28T18:42:55Z

Need a review and help here.
Windows is set to skip, so isn't it supposed to be skipped for CI?
CMakeLists has flex and bison set as required. When added as build req in the recipe Mac builds fail with conda-forge versions of flex and bison. When removed Mac builds find ones existing in the system and builds successfully, but Linux builds fail. Workaround I found is to remove flex and bison from build requirements and add them into yum_requirements.txt.

jakirkham · 2016-12-30T06:54:34Z

That's unfortunate. Sounds like we may have a bug in cmake then. 😕 Could you please raise an issue on that feedstock with some info about how to reproduce the issue?

shadowwalkersb · 2016-12-30T17:30:52Z

I think cmake is good. When flex and bison are listed in build reqs, they are installed and cmake finds them. If not listed as build req, it cmake finds the system ones on Mac and fails to find them on Linux. But, when they are installed via yum_requirements.txt, then cmake finds them. IMO, problem is with conda-forge's flex and/or bison. Not sure when I can dig up the logs and report on flex and bison feedstocks.

shadowwalkersb · 2016-12-30T17:45:16Z

Or, I could demonstrate the problem here in this PR. Would you rather keep this PR clean and merge it as is, maybe? The failure on Appveyor is another story. conda-build complains about the license. So, I just skipped Windows, but it is still built. I am not sure if that is, yet another problem. So, we got a stack of problems in our hands here. 😜

conda-forge-linter · 2016-12-30T22:15:40Z

Hi! This is the friendly automated conda-forge-linting service.

I wanted to let you know that I linted all conda-recipes in your PR (recipes/doxygen) and found some lint.

Here's what I've got...

For recipes/doxygen:

The license item is expected in the about section.

jakirkham · 2016-12-31T02:51:02Z

recipes/doxygen/build.sh

+	-DCMAKE_INSTALL_PREFIX=$PREFIX          \
+	-DCMAKE_BUILD_TYPE=Release              \
+	..
+make -j


Please add $CPU_COUNT if you wish to build in parallel.

Not building in parallel. Done.

jakirkham · 2016-12-31T02:51:24Z

recipes/doxygen/meta.yaml

+      - vc14   # [win and py35]
+
+requirements:
+  build:


Needs python as a build requirement on Windows for features to work.

And if want to skip Windows, should I remove features? Or can they stay for future use?

They can stay. Just suggesting we get all the pieces in place.

jakirkham · 2016-12-31T02:52:26Z

recipes/doxygen/meta.yaml

+
+test:
+  commands:
+    - test -f "${PREFIX}/bin/doxygen"   # [not win]


Couldn't we just run doxygen --help and drop the selector?

jakirkham · 2016-12-31T02:52:57Z

recipes/doxygen/meta.yaml

+    - test -f "${PREFIX}/bin/doxygen"   # [not win]
+
+about:
+  home: http://www.stack.nl/~dimitri/doxygen/index.html


Please add license. It looks like it is GPL2.

What is the license_family?

That's optional. Sadly it is also GPL2 so a bit redundant. Would skip it if I were you.

jakirkham · 2016-12-31T02:54:40Z

The license complaint is valid. So that needs to be addressed.

I'd really like to understand the issues with flex and bison before we proceed. Right now I don't follow. Could you please demonstrate the issue?

shadowwalkersb · 2016-12-31T02:56:45Z

The license complaint is valid. So that needs to be addressed.

Only Windows complains, the rest passes though. I'll add GPL2 for license field as you suggested.

conda-forge-linter · 2016-12-31T03:01:46Z

Hi! This is the friendly automated conda-forge-linting service.

I just wanted to let you know that I linted all conda-recipes in your PR (recipes/doxygen) and found it was in an excellent condition.

shadowwalkersb · 2016-12-31T03:13:16Z

Mac and Linux fail with this message:
[ 24%] [BISON][constexp] Building parser with bison 3.0.4 /staged-recipes/build_artefacts/doxygen_1483153761659/_b_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/bin/bison: m4 subprocess failed

isuruf · 2017-01-04T03:46:14Z

How about updating test 12 using --updateref --id 12 and then running all the tests?

shadowwalkersb · 2017-01-04T03:51:42Z

I can't follow the code. What is it supposed to do?

shadowwalkersb · 2017-01-04T04:00:38Z

Here's a brainteaser for you. Why does pinning conda-build to 2.0.12 fix builds? I'm pretty sure, I saw successful builds with 2.1 in this PR, but after some point things started getting weird. I'm giving up for now. 😩 😫

isuruf · 2017-01-04T04:01:16Z

It will first update the test 12 with the output from doxygen.
When make tests is run again, it will obviously match because we have updated the expected output.

python runtests.py --updateref --id 12 --inputdir=testing
make tests

isuruf · 2017-01-04T04:19:02Z

.CI/build_all

@@ -19,7 +19,7 @@ conda install --yes --quiet conda-forge-build-setup
 source run_conda_forge_build_setup

 # install conda-build 2.x to build with a long prefix
-conda install --yes --quiet conda-build=2
+conda install --yes --quiet conda-build=2.0.12


I don't think this repo is using conda-build=2, even though that line is there. Previously it was downgraded to 1.21.

The following packages will be DOWNGRADED due to dependency conflicts: conda-build: 2.1.0-py35_0 defaults --> 1.21.14-py35_0 defaults

When pinned to 2.0.12 instead of 2, it actually works.
cc @ocefpaf

That was a mistake, it was downgraded and then upgraded.

Yeah, that's happening when running source run_conda_forge_build_setup. This line is after that so it shouldn't matter what conda-forge-build-setup does.

isuruf · 2017-01-04T04:26:42Z

I couldn't find a build log with conda-build 2.1 that worked.

shadowwalkersb · 2017-01-04T12:09:30Z

You're right, I can't find any either. So, I guess, it is safe to say that conda-build 2.1 breaks things here, but 2.0.12 is OK?

isuruf · 2017-01-04T14:29:23Z

Yes, it's strange though that 2.1 breaks stuff. I've managed to compile with 2.1 by adding,
export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib -liconv" at the top of build.sh (This makes me more puzzled.)

jakirkham · 2017-01-04T16:37:56Z

It is very possible there is a bug or at least an unexpected change of behavior. Could you guys please raise an issue on the conda-build issue tracker? Feel free to xref back to this PR.

isuruf · 2017-01-04T19:14:18Z

This seems to be a bug in doxygen and the bug was hidden in conda-build < 2.1 and came to surface in conda-build 2.1. conda-build 2.1 probably has a change related path (a good change that found this bug.)
Previously it was finding iconv_open function from glibc and iconv.h from glibc as well. Now due to some path related change, iconv.h is found from libiconv conda package, but iconv_open is still found from glibc. I have a PR that fixes this mismatch

This reverts commit 8191e0c.

isuruf · 2017-01-04T19:58:53Z

shadowwalkersb/staged-recipes#2

FindIconv.cmake patch

shadowwalkersb · 2017-01-05T03:50:11Z

@isuruf , would you be interested in being a maintainer? Maybe, even the only maintainer?

isuruf · 2017-01-05T03:55:04Z

Sure, I can help with maintaining

shadowwalkersb · 2017-01-05T04:03:21Z

To be clear, if you don't mind, I'll remove myself.

shadowwalkersb · 2017-01-05T04:11:34Z

@jakirkham , @isuruf played it nicely, and kindly fixed CMakelLists, but I just removed the problematic part from CMakeLists. Even if it works, please, let me know if you want me to back out my changes. Considering @isuruf is going to be the only maintainer, it may be better to go with his solution, but I still wanted to put it out there. 😉

shadowwalkersb · 2017-01-05T04:20:06Z

I, just, need a final confirmation that the license is GPL2, please.

isuruf · 2017-01-05T04:23:13Z

Yes, it's GPL2. Btw, there was a new release doxygen-1.8.13 after this PR was open.

isuruf · 2017-01-05T06:14:05Z

Ready to merge now.

scopatz · 2017-01-05T09:57:43Z

Thanks all!

shadowwalkersb added 3 commits December 28, 2016 00:18

initial commit

f7592f7

license

eb4ec6f

skip win

ff86b66

add tests

9e6f255

remove fields to make conda-build on Windows happy

a524d34

jakirkham reviewed Dec 31, 2016

View reviewed changes

shadowwalkersb added 4 commits December 30, 2016 20:57

license

f180fb7

add license

b9a4e55

add $CPU_COUNT

d94be76

add build req: bison and flex, remove yum_requirements.txt

21e05cb

fix command for parallel make

6b49b03

shadowwalkersb added 6 commits December 30, 2016 21:21

add python as build req for Windows

751e720

update test command

b86ca55

turn off parallel make to make output easier to follow

14fada8

remove bison

cd6c974

remove flex

bbd9329

add flex and bison via yum_requirements.txt to fix Linux

a84d616

isuruf reviewed Jan 4, 2017

View reviewed changes

isuruf added 3 commits January 5, 2017 01:11

patch for iconv.h and lib mismatch

c01ec53

Revert "force conda-build version to 2.0.12"

b782a45

This reverts commit 8191e0c.

Add libiconv as requirements

9a05239

Merge pull request #2 from isuruf/shadowwalkersb-doxygen

cdeecd2

FindIconv.cmake patch

isuruf approved these changes Jan 5, 2017

View reviewed changes

replace maintainer

081de45

alternative patch: completely remove part that checks for iconv_open

f8457cb

update version and download site

65cd5ba

scopatz merged commit 98b4dc7 into conda-forge:master Jan 5, 2017

shadowwalkersb deleted the doxygen branch January 5, 2017 15:06

kyleabeauchamp mentioned this pull request Jan 12, 2017

Try xcode8.2 image to get around doxygen segfault (issue #1714) openmm/openmm#1716

Closed

Add doxygen #2135

Add doxygen #2135

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jakirkham commented Dec 31, 2016

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