mdanalysis v1.0.1 #28

regro-cf-autotick-bot · 2021-02-19T20:02:22Z

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Here is a list of all the pending dependencies (and their versions) for this repo. Please double check all dependencies before merging.

Name	Upstream Version	Current Version
python	3.9.2

Dependency Analysis

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Analysis of the source code shows no discrepancy between the library's imports and the package's stated requirements in the meta.yaml.

conda-forge-linter · 2021-02-19T20:02:25Z

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 (recipe) and found it was in an excellent condition.

I do have some suggestions for making it better though...

For recipe:

License is not an SPDX identifier (or a custom LicenseRef) nor an SPDX license expression.

Documentation on acceptable licenses can be found here.

Picked from https://spdx.org/licenses/ as recommended by linter.

conda-forge-linter · 2021-02-19T20:09:18Z

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 (recipe) and found it was in an excellent condition.

orbeckst

+1

orbeckst

@richardjgowers @IAlibay do we need to restrict the biopython version in the meta.yml?

Blocking until we know.

orbeckst · 2021-02-19T20:17:30Z

From setup.py

          'biopython>=1.71,<1.77', # to support Py 2
          'networkx>=1.0',
          'GridDataFormats>=0.4.0',
          'six>=1.4.0',            # to support Py 2
          'mmtf-python>=1.0.0',
          'joblib>=0.12,<0.15.0',  # to support Py 2
          'scipy>=1.0.0',
          'matplotlib>=1.5.1',
          'mock',
          'tqdm>=4.43.0',
          'funcsigs',              # to support Py 2

I think we need some serious updating of our dependencies in meta.yml, in particular for 1.0.1 anything related to Py 2 support.

orbeckst · 2021-02-19T20:22:12Z

https://docs.conda.io/projects/conda-build/en/stable/resources/define-metadata.html#run states that we can include restrictions on versions
https://docs.conda.io/projects/conda-build/en/stable/resources/define-metadata.html#run-constrained shows how to specify constraints on optional packages (like chemfiles or RDKit)... at least I think that's how this works

orbeckst · 2021-02-19T20:25:05Z

No sure why pip was not able to find numpy for pypy:

    ERROR: Could not find a version that satisfies the requirement numpy<1.17,>=1.13.3
    ERROR: No matching distribution found for numpy<1.17,>=1.13.3

https://dev.azure.com/conda-forge/feedstock-builds/_build/results?buildId=279986&view=logs&j=d0d954b5-f111-5dc4-4d76-03b6c9d0cf7e&t=841356e0-85bb-57d8-dbbc-852e683d1642&l=1199

IAlibay · 2021-02-19T20:26:46Z

Yeah looks like we'll need to at very least pin numpy (seems like it's picking up 1.20?) and biopython?

Future proofing wise, we probably also want to pin on cython < 1.0?

orbeckst · 2021-02-19T20:26:57Z

Same problem with 3.6 cpython

    ERROR: Could not find a version that satisfies the requirement numpy<1.17,>=1.13.3
    ERROR: No matching distribution found for numpy<1.17,>=1.13.3

https://dev.azure.com/conda-forge/feedstock-builds/_build/results?buildId=279986&view=logs&j=d0d954b5-f111-5dc4-4d76-03b6c9d0cf7e&t=841356e0-85bb-57d8-dbbc-852e683d1642&l=1199

orbeckst · 2021-02-19T20:28:35Z

Future proofing wise, we probably also want to pin on cython < 1.0?

I think so (for the build).

For the conda package itself, cython isn't a dep, is it?

IAlibay · 2021-02-19T20:30:00Z

For the conda package itself, cython isn't a dep, is it?

You're right, it isn't (maybe in 2.0 though 🙃 ).

- add constraints from the 1.0.1 setup.py - added funcsigs and mock - gsd was doubled up: removed the version that did not have the `[not win]` comment... not sure about this

orbeckst · 2021-02-19T20:45:10Z

I added package constraints directly to this PR (didn't manage to do a PR against the PR). Please have a look.

@richardjgowers why did we have gsd doubled up in here? Do we have a conda gsd package for win???

orbeckst · 2021-02-19T20:48:41Z

These package constraints are a bit iffy. Anything that was "for Python 2" should really not apply for conda packages built against Python 3. We will almost certainly annoy users when we ship conda packages that tell them that they have to downgrade joblib to < 0.15.0. Can we write the restriction in a way that differentiates between Py 2 and Py 3 builds?

numpy is supposedly handled differently although I don't understand how pin_compatible() really works.

IAlibay · 2021-02-19T21:12:14Z

These package constraints are a bit iffy. Anything that was "for Python 2" should really not apply for conda packages built against Python 3. We will almost certainly annoy users when we ship conda packages that tell them that they have to downgrade joblib to < 0.15.0.

Agreed, although because these restrictions were imposed in setup.py, we haven't tested a version of 1.0.1 that goes outside these limits. For sure numpy 1.19+ is going to fail (I don't think Tyler's fixes were backported?). Joblib and biopython are unlikely to have broken anything, but we'd have to test anyway.

conda-forge-linter · 2021-02-20T13:48:05Z

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 (recipe) and found some lint.

Here's what I've got...

For recipe:

Selectors are suggested to take a <two spaces>#<one space>[<expression>] form. See lines [35, 36, 45]

IAlibay · 2021-02-20T13:57:38Z

We're going to have to explicitly define the python versions here since it seems to have added 3.9 (which we don't support in 1.0.x), it's not immediately clear to me that we can add support back for 3.5 or 2.7 though.

conda-forge-linter · 2021-02-20T14:24:27Z

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 (recipe) and found it was in an excellent condition.

richardjgowers · 2021-02-20T14:53:04Z

Ok so it looks like pypy doesn't work, but I'm not sure we have checked that ourselves, so we can drop that.

Windows is failing complaining about something in MANIFEST being an absolute path which is confusing.

Then 3.9 builds are also failing. what fun!

IAlibay · 2021-02-20T15:00:27Z

Then 3.9 builds are also failing. what fun!

@richardjgowers is there any way we can restrict the maximum python version to 3.8? 3.9 isn't in our CI matrix and if I remember correctly a bunch of optional deps don't work on it yet.

IAlibay · 2021-02-23T16:30:13Z

@richardjgowers and @orbeckst we should probably act on this soon-ish. Do we want to go ahead with it knowing that it won't work on Windows/pypy/some newer versions of some packages, or do we want to kill 1.0.1 and quickly replace it with 1.0.2? I'd be tempted to vote for the former so that it gives us a little bit of time to roll out a stable 1.0.2 that works w/ nsgrid fixed.

If we do go with the 1.0.1 then maybe I should go ahead and release the tests on pypi now?

conda-forge-linter · 2021-02-28T11:58:03Z

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 (recipe) and found some lint.

Here's what I've got...

For recipe:

The build section contained an unexpected subsection name. slip is not a valid subsection name.

conda-forge-linter · 2021-02-28T12:00:59Z

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 (recipe) and found it was in an excellent condition.

richardjgowers · 2021-02-28T12:14:29Z

@conda-forge-admin, please rerender

…da-forge-pinning 2021.02.26.15.36.03

updated v1.0.1

1b95b11

regro-cf-autotick-bot requested review from kain88-de, orbeckst and richardjgowers as code owners February 19, 2021 20:02

updated license specifier

62ac7d0

Picked from https://spdx.org/licenses/ as recommended by linter.

orbeckst approved these changes Feb 19, 2021

View reviewed changes

orbeckst self-requested a review February 19, 2021 20:13

orbeckst requested changes Feb 19, 2021

View reviewed changes

package constraints

e62d541

- add constraints from the 1.0.1 setup.py - added funcsigs and mock - gsd was doubled up: removed the version that did not have the `[not win]` comment... not sure about this

Update meta.yaml

db6948a

Update meta.yaml

4b6cdbe

Update meta.yaml

3483d5f

Update meta.yaml

4792610

richardjgowers mentioned this pull request Feb 21, 2021

abspaths slipping into SOURCES and breaking windows conda build MDAnalysis/mdanalysis#3129

Closed

richardjgowers added 5 commits February 27, 2021 18:10

Update meta.yaml

0f46581

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MNT: Re-rendered with conda-build 3.21.4, conda-smithy 3.9.0, and con…

a21c60c

…da-forge-pinning 2021.02.26.15.36.03

richardjgowers merged commit 3d4cc9c into conda-forge:master Feb 28, 2021

regro-cf-autotick-bot deleted the 1.0.1_h5fe41f branch February 28, 2021 13:13

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mdanalysis v1.0.1 #28

mdanalysis v1.0.1 #28

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mdanalysis v1.0.1 #28

mdanalysis v1.0.1 #28

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