Add support for h5py >=3.0.0.

[bdice]

Description

This PR adds support for h5py major version 3 and should be merged before #409 (to show that the code functions both before and after the upgrade).

The h5py package changed its default handling of strings in version 3. See this page for info: https://docs.h5py.org/en/latest/strings.html

This PR adds a shim to detect string data, so that it can be returned as str and not bytes. I tested this locally with h5py 2.10.0 and 3.0.0, and it should work for older versions of h5py as well (that's why I used the older function check_dtype instead of check_string_dtype, which was added in 2.10).

Types of Changes

• Documentation update
• Bug fix
• New feature
• Breaking change¹

¹The change breaks (or has the potential to break) existing functionality.

Checklist:

• I am familiar with the Contributing Guidelines.
• I agree with the terms of the Contributor Agreement.
• My name is on the list of contributors.
• My code follows the code style guideline of this project.
• The changes introduced by this pull request are covered by existing or newly introduced tests.

If necessary:

• I have updated the API documentation as part of the package doc-strings.
• I have created a separate pull request to update the framework documentation on signac-docs and linked it here.
• I have updated the changelog and added all related issue and pull request numbers for future reference (if applicable). See example below.

Example for a changelog entry: Fix issue with launching rockets to the moon (#101, #212).

[codecov]

Codecov Report

Merging #411 into master will decrease coverage by 0.04%.
The diff coverage is 66.66%.

@@            Coverage Diff             @@
##           master     #411      +/-   ##
==========================================
- Coverage   76.40%   76.35%   -0.05%     
==========================================
  Files          45       45              
  Lines        7136     7139       +3     
==========================================
- Hits         5452     5451       -1     
- Misses       1684     1688       +4     

Impacted Files	Coverage Δ
signac/core/h5store.py	90.75% <66.66%> (-0.26%)	⬇️
signac/contrib/project.py	90.92% <0.00%> (-0.41%)	⬇️

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[jennyfothergill]

Hi!
Pytest is throwing an error for me. Here is a file with the error output:
pytest-error.txt
And just to make sure that I'm not doing something wrong, below are my install steps:
(in signac root dir)

gh pr checkout 411
conda env create -f environment.yml  
conda activate signac-dev
pip install -e .

environment.yml
I also tried changing the line in environment.yml to h5py>=3 and then conda gave me package not found, so I tried installing like this:

conda create -n signac-dev pip
conda activate signac-dev
pip install 'h5py>=3' pytest
pip install -e .

and I get the same error from pytest.
I'm on osx 10.14.6 (18G103)

[bdice]

@jennyfothergill

1. Test failure: thanks for the details, that's helpful. I think this test failure is the same as H5Store pytest is failing on MacOS but passes on Linux #281. This seems to be testing a behavior that isn't very safe across different operating systems. We should probably consider removing this test since it only appears to work on Linux.

2. h5py 3.0 isn't available on conda-forge yet, so adding it to the environment.yml won't work yet. You're an early adopter! 😄 Seems like you got it installed from PyPI and saw the same error as above.

Sounds like the takeaway is that this works except for the known issue in #281. I appreciate the extensive testing!

[jennyfothergill]

@bdice Ah, OK I wasn't sure if that error was already known, but I should've checked the issues first! Haha, I don't know about extensive testing. :) I'm not sure how to check that strings are working correctly. (I assuming that I should test if strings work as statepoint keys/values?) I tried:

signac init myproject
signac job '{"N": 1.0, "type": "heck"}' --create

and it seemed to work fine with both versions of h5py. Is there a better way to test?

[bdice]

@jennyfothergill signac uses h5py for the H5Store class. This can be accessed with job.data, project.data, or as a standalone class signac.H5Store. This is useful for storing large arrays of values (like a big NumPy array) that are too large for a job document (stored as JSON, which is not an efficient way to store large amounts of binary data). See here for API examples: https://docs.signac.io/projects/core/en/latest/api.html#the-h5store

[jennyfothergill]

LGTM. I'm still not sure if I'm checking this correctly, but with h5py==2.10 and h5py>=3 both print <class 'str'>:

from signac import H5Store
with H5Store('file.h5') as h5s:
    h5s['foo'] = 'bar'
    print(type(h5s.foo))

[mikemhenry]

LGTM! Thanks Jenny for that thorough review!