Add bcolz #2322

alimanfoo · 2017-01-31T09:58:11Z

Here's a recipe for bcolz.

alimanfoo · 2017-01-31T09:59:24Z

@FrancescAlted I've added you as a maintainer. Please could add a comment to confirm this is OK.

alimanfoo · 2017-01-31T10:00:05Z

@CarstVaartjes if you'd like to be added as a maintainer, let me know, happy to add you.

conda-forge-linter · 2017-01-31T10:35:33Z

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/bcolz) and found it was in an excellent condition.

FrancescAlted · 2017-01-31T10:35:47Z

Yes, I am ok with being a maintainer. Thanks!

CarstVaartjes · 2017-01-31T15:33:24Z

For me it's not necessary (up to Francesc really), but would love to help where I can!

alimanfoo · 2017-01-31T21:59:37Z

Currently builds for PY27 are failing because of Blosc/bcolz#322. We need a bcolz 1.1.1 release with the fix for that issue.

FrancescAlted · 2017-02-01T11:39:30Z

bcolz 1.1.1 is out. Could you give it a try?

alimanfoo · 2017-02-01T12:04:57Z

Thanks, will do.

…

On Wednesday, February 1, 2017, Francesc Alted ***@***.***> wrote: bcolz 1.1.1 is out. Could you give it a try? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#2322 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAq8Qh7W9cqUJSJ5OI8VojhdIhYfY_PLks5rYG7ygaJpZM4LybYw> .

-- Alistair Miles Head of Epidemiological Informatics Centre for Genomics and Global Health <http://cggh.org> The Wellcome Trust Centre for Human Genetics Roosevelt Drive Oxford OX3 7BN United Kingdom Email: [email protected] Web: http://purl.org/net/aliman Twitter: https://twitter.com/alimanfoo Tel: +44 (0)1865 287721

alimanfoo · 2017-02-01T13:12:02Z

@FrancescAlted could you release bcolz 1.1.1 on PyPI?

FrancescAlted · 2017-02-01T13:49:42Z

Ooops. Uploaded the version in PyPI!

alimanfoo · 2017-02-01T17:05:36Z

PY36 is failing on circle, error:

conda.exceptions.UnsatisfiableError: The following specifications were found to be in conflict:
  - numpy 1.9* -> python 2.6*|2.7*|3.3*|3.4*|3.5*
  - python 3.6*

Have no idea why it's trying to install numpy 1.9, the builds for PY27 and PY35 both install numpy 1.11 and build fine. Will see what happens on appveyor and travis...

alimanfoo · 2017-02-01T20:29:27Z

Maybe forgot to update my fork of staged-recipes from upstream. Have rebased on upstream/master, see if that fixes the PY36 builds.

alimanfoo · 2017-02-01T20:45:35Z

@conda-forge/core could you please help, builds for PY27 and PY35 are fine but PY36 builds are failing with this message:

conda.exceptions.UnsatisfiableError: The following specifications were found to be in conflict:
  - numpy 1.9* -> python 2.6*|2.7*|3.3*|3.4*|3.5*
  - python 3.6*

It looks like for the PY36 build the CONDA_NPY=19 variable is getting picked up, although it is ignored in other builds.

patricksnape · 2017-02-01T21:32:20Z

If you build against numpy you should have numpy x.x rather than just numpy

alimanfoo · 2017-02-01T22:45:03Z

Thanks @patricksnape, forgot about numpy x.x.

Now builds failing because we don't have a pytables build for numpy 1.12. Have submitted a PR to the pytables feedstock: conda-forge/pytables-feedstock#10

FrancescAlted · 2017-02-02T08:14:58Z

PyTables is an optional requisite, so why not leave it out?

alimanfoo · 2017-02-02T09:28:23Z

Yep, could do. I have a slight preference to keep it as it makes life a bit easier for the user, and also seems to be common practice in other packages (e.g., dask) to include optional dependencies in the conda recipe. Builds for pytables against numpy 1.12 should be arriving very soon so will try a rebuild for bcolz shortly (and will also bump the bcolz version to get zstd).

…

On Thursday, February 2, 2017, Francesc Alted ***@***.***> wrote: PyTables is an optional requisite, so why not leave it out? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#2322 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAq8QvwahoKxIcBpiy97tMtjOO8C4Ugzks5rYZCCgaJpZM4LybYw> .

-- Alistair Miles Head of Epidemiological Informatics Centre for Genomics and Global Health <http://cggh.org> The Wellcome Trust Centre for Human Genetics Roosevelt Drive Oxford OX3 7BN United Kingdom Email: [email protected] Web: http://purl.org/net/aliman Twitter: https://twitter.com/alimanfoo Tel: +44 (0)1865 287721

jakirkham · 2017-02-06T04:21:28Z

As for pytables, it should be a simple matter of re-rendering that feedstock, which appears to already have been done in PR ( conda-forge/pytables-feedstock#9 ).

alimanfoo · 2017-02-06T08:42:42Z

Thanks @jakirkham, the pytables builds are all there now so bcolz is building fine with all dependencies. This is ready to go AFAIC.

jakirkham · 2017-02-08T04:45:53Z

recipes/bcolz/meta.yaml

+    - bcolz
+  commands:
+    - python -c"import bcolz; bcolz.test(heavy=True)"
+    - python -c"import bcolz; assert set(bcolz.blosc_compressor_list()) == set(['blosclz', 'lz4', 'lz4hc', 'snappy', 'zlib', 'zstd'])"


For this sort of stuff, it may be better to move it to run_test.py. Should make it easier to read and follow. Plus it just runs with python. So there is no need for the python -c "...".

jakirkham · 2017-02-08T04:46:31Z

One minor comment. Otherwise LGTM.

alimanfoo · 2017-02-08T08:46:39Z

Thanks @jakirkham. Would you mind if I tidy up the tests section after this is merged? It would be nice to get this in so we can start using it. If we have to wait for another round of CI checks before merge then it could be days given how slow travis is at the moment.

…

On Wednesday, February 8, 2017, jakirkham ***@***.***> wrote: One minor comment. Otherwise LGTM. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#2322 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAq8Qt7j8yRBHgi7a0lvIl6vPf4B51p6ks5raUiogaJpZM4LybYw> .

-- Alistair Miles Head of Epidemiological Informatics Centre for Genomics and Global Health <http://cggh.org> The Wellcome Trust Centre for Human Genetics Roosevelt Drive Oxford OX3 7BN United Kingdom Email: [email protected] Web: http://purl.org/net/aliman Twitter: https://twitter.com/alimanfoo Tel: +44 (0)1865 287721

jakirkham · 2017-02-08T16:58:02Z

Sure. Let's do it. 👍

jakirkham · 2017-02-08T16:59:37Z

Also am working on a longer term fix to the Travis CI issues.

xref: conda-forge/conda-forge-build-setup-feedstock#52

alimanfoo · 2017-02-08T17:43:02Z

Cool, thanks very much.

…

On Wed, Feb 8, 2017 at 4:59 PM, jakirkham ***@***.***> wrote: Also am working on a longer term fix to the Travis CI issues. xref: conda-forge/conda-forge-build-setup-feedstock#52 <conda-forge/conda-forge-build-setup-feedstock#52> — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#2322 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAq8Qg1pgQzv7cjLedfhPMnwEH-B90v6ks5rafR6gaJpZM4LybYw> .

-- Alistair Miles Head of Epidemiological Informatics Centre for Genomics and Global Health <http://cggh.org> The Wellcome Trust Centre for Human Genetics Roosevelt Drive Oxford OX3 7BN United Kingdom Email: [email protected] Web: http://purl.org/net/aliman Twitter: https://twitter.com/alimanfoo Tel: +44 (0)1865 287721

alimanfoo mentioned this pull request Jan 31, 2017

Conda bcolz is out of date (1.0.0) Blosc/bcolz#333

Closed

alimanfoo mentioned this pull request Jan 31, 2017

PY27 bcolz with dask unicode error Blosc/bcolz#322

Closed

alimanfoo added 5 commits February 1, 2017 20:27

initial version of bcolz recipe

b4d4f6a

avoid setuptools download

6c8ecd2

correct pytables dependency

0cc4642

upgrade to 1.1.1

038b31e

add CarstVaartjes as maintainer

bf289de

alimanfoo force-pushed the bcolz branch from 452adcc to bf289de Compare February 1, 2017 20:28

fix numpy x.x

fb2879e

alimanfoo mentioned this pull request Feb 1, 2017

Rerender to get numpy 1.12 build conda-forge/pytables-feedstock#10

Closed

alimanfoo added 2 commits February 2, 2017 09:33

bump to version 1.1.2 to get zstd

d73e7c5

trivial change to trigger rebuild

d147c18

jakirkham reviewed Feb 8, 2017

View reviewed changes

jakirkham merged commit a227f4f into conda-forge:master Feb 8, 2017

alimanfoo mentioned this pull request Feb 9, 2017

Simplify test section of recipe conda-forge/bcolz-feedstock#1

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Add bcolz #2322

Add bcolz #2322

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Add bcolz #2322

Add bcolz #2322

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