Add python-lzo #3370

sebastian-luna-valero · 2017-07-27T11:57:30Z

No description provided.

conda-forge-linter · 2017-07-27T11:57:35Z

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/python-lzo) and found some lint.

Here's what I've got...

For recipes/python-lzo:

There are 1 too many lines. There should be one empty line at the end of the file.

conda-forge-linter · 2017-07-27T11:58:50Z

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/python-lzo) and found it was in an excellent condition.

conda-forge-linter · 2017-07-27T13:12:02Z

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/python-lzo) and found some lint.

Here's what I've got...

For recipes/python-lzo:

Selectors are suggested to take a <two spaces>#<one space>[<expression>] form.

conda-forge-linter · 2017-07-27T13:14:41Z

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/python-lzo) and found it was in an excellent condition.

sebastian-luna-valero · 2017-07-27T14:02:52Z

Please @conda-forge/staged-recipes review.

ocefpaf

Two minor things that can be done later in the feedstock. Thanks @sebastian-luna-valero!

ocefpaf · 2017-07-27T14:04:28Z

recipes/python-lzo/meta.yaml

+    - lzo 2.10.*
+  run:
+    - python
+    - lzo 2.10.*


I think we are using 2.* instead of 2.10.*. The latter is more restrictive and it is fine if your package needs that.

Indeed, thanks!

ocefpaf · 2017-07-27T14:05:19Z

recipes/python-lzo/build.sh

+export CPPFLAGS="-I$PREFIX/include -I$PREFIX/include/lzo $CPPFLAGS"
+export LDFLAGS="-L$PREFIX/lib $LDFLAGS"
+
+$PYTHON setup.py install


This seems to use setuptools, can you add --single-version-externally-managed --record record.txt? (See the example recipe for details on this.)

I got error: option --single-version-externally-managed not recognized. Please see: https://travis-ci.org/conda-forge/staged-recipes/builds/258113000#L243

I guess that the package does not use setuptools then. You can probably remove it from the build section later.

Not sure, sorry. Presumably @jd-boyd can confirm, and I am happy to update the package.

That is a minor thing anyway. You can test that in the next package iteration (updating or bumping the build number for some reason.)

Brilliant, will do. Many thanks!

Python-lzo uses distutils

sebastian-luna-valero · 2017-07-27T15:06:01Z

Silly question, how long do I need to wait for the feedstock to be created?

isuruf · 2017-07-27T15:07:20Z

Until this build, https://travis-ci.org/conda-forge/staged-recipes/builds/258159145 is finished.

ocefpaf · 2017-07-27T15:08:09Z

Silly question, how long do I need to wait for the feedstock to be created?

Not silly. In fact that question comes up to often that we should add it to the FAQ 😄

In theory a few hours. But every now and then there are a few hiccups in the CIs that may cause some delay.

sebastian-luna-valero · 2017-07-27T15:26:53Z

Thanks both!

Indeed, having this information somewhere in the PR process of staged-recipes would help.

It's passing now:
https://travis-ci.org/conda-forge/staged-recipes/builds/258139566

* include conda env export command * use conda environment file instead of meta-package * fix pysam to 0.11.1 * fix CondaValueError: invalid package specification: pysam 0.11.1 * download a copy of the conda spec file before installation * try with r 3.3.1 instead of r 3.3.2 * try with py35 * try r 3.3.2 * remove more deps from conda/environments/scripts-nosetests.yml and add conda/environments/scripts-devel.yml * pybedtools and wigToBigWig required for testing * try adding bedtools * update install-CGAT-tools.sh accordingly * update install-CGAT-tools.sh to test local install properly * bedtools is now a dep for pybedtools; bioconda/bioconda-recipes#5351 * update conda env for scripts-devel * DEXSeq is Py2 only * python-lzo added to conda-forge: conda-forge/staged-recipes#3370 * reorganise devel env file * update env file and install script * make sure scripts are installed in CGAT_HOME/cgat-scripts

* include conda env export command * use conda environment file instead of meta-package * fix pysam to 0.11.1 * fix CondaValueError: invalid package specification: pysam 0.11.1 * download a copy of the conda spec file before installation * try with r 3.3.1 instead of r 3.3.2 * try with py35 * try r 3.3.2 * remove more deps from conda/environments/scripts-nosetests.yml and add conda/environments/scripts-devel.yml * pybedtools and wigToBigWig required for testing * try adding bedtools * update install-CGAT-tools.sh accordingly * update install-CGAT-tools.sh to test local install properly * bedtools is now a dep for pybedtools; bioconda/bioconda-recipes#5351 * update conda env for scripts-devel * DEXSeq is Py2 only * python-lzo added to conda-forge: conda-forge/staged-recipes#3370 * reorganise devel env file * update env file and install script * make sure scripts are installed in CGAT_HOME/cgat-scripts * improve scripts to check for dependencies * use TRAVIS_BRANCH for local installations as well * pysam should still be pinned to 0.11.1 * make --zip the default installation option * unified script to find Python and R deps * before holiday commit * revisit how misc deps are found * improve dependency checking * forgot to comment out debugging section * check deps also for module files in production scripts * update test_import.py to reflect new repository structure * add sqlalchemy to conda env * add mysqlclient to conda env * remove __init__.py * add helper script to match conda package names with versions * start using pinned env files * update rpy2 in env file * make sure cgat-scripts package from bioconda installs fine * try installation on OS X * Update install-CGAT-tools.sh * Update .travis.yml * further updates for OS X * fix .travis.yml * temporarily disable xvfb * INSTALL_PYTHON_VERSION no longer needed * fix curl command * fix curl command * update comments * add bash error trap to installation script * fix curl command to download zip file * fix sed command to work on OS X * install bx-python after enabling conda environment * use INSTALL_BRANCH for git archive * update conda env * {AH} replace zcat with gunzip for OSX compatibility * updated cgat_conda_deps.sh and scripts-nosetests.yml * install bx-python with pip * enable xvfb on Linux only * add additional info to bash trap, and check cgat-scripts installation properly * nosetests and pep8 are not required as deps for production scripts * remove unused import subprocess from cgat_check_deps.py * add comment to output regarding creation * add bx-python warning instead of pip install, which didn't work properly * rename install options * updated README.rst for GitHub * update README.rst * update README.rst * fix conda version * fix bx-python version * update link to paper * unknown input option for install script * parse bash statements with bashlex * parse statement.append * reorder MISC_DEPS * add excluded items to cgat_check_deps.py * clean up parameter interpolation properly * add exceptions to cgat_check_deps.py * added new condition to get the string of statement.append * update conda environments * removes pip install bx-python on match_conda_deps.sh * output env.yml * quiet conda installation * bugfix quiet install * remove pip install from env * update conda env for nosetests * updated conda envs

initial version of the recipe

1703fe5

conda-forge linter: empty line at the end of the file

b22eb10

sebastian-luna-valero added 4 commits July 27, 2017 13:08

error: option --single-version-externally-managed not recognized

049cf32

add build.sh

e5746ec

add -I/include/lzo

d0174a5

skip windows and fix lzo version

130f46b

apply conda-forge-linter suggestion

500e88e

ocefpaf approved these changes Jul 27, 2017

View reviewed changes

ocefpaf merged commit 871a25d into conda-forge:master Jul 27, 2017

sebastian-luna-valero mentioned this pull request Jul 27, 2017

Added python-lzo to conda-forge jd-boyd/python-lzo#32

Closed

sebastian-luna-valero added a commit to CGATOxford/cgat that referenced this pull request Jul 28, 2017

python-lzo added to conda-forge: conda-forge/staged-recipes#3370

4eb9e15

sebastian-luna-valero deleted the python-lzo branch July 28, 2017 08:18

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Add python-lzo #3370

Add python-lzo #3370

sebastian-luna-valero commented Jul 27, 2017

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sebastian-luna-valero commented Jul 27, 2017

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sebastian-luna-valero commented Jul 27, 2017 •

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Add python-lzo #3370

Add python-lzo #3370

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sebastian-luna-valero commented Jul 27, 2017

isuruf commented Jul 27, 2017

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