Documentation about contributing #227
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@jakirkham, @mrocklin, @shoyer if you have a moment, I'd appreciate any feedback on this, especially the contributing doc. I've borrowed bits from the dask and pandas contributing guides while trying to keep it fairly short. Any suggestions welcome. |
| $ pip install -r requirements_dev.txt | ||
| $ pip install -r requirements_dev_optional.txt | ||
| $ pip install -e . | ||
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I would suggest also including an example of how to do this with conda. My experience is that this is a common workflow.
$ conda env create -n zarr-dev -f requirements_dev.yml # req file would need to be added
$ source activate zarr-dev
$ pip install -e # or python setup.py develop
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I didn't give a conda example as (last time I looked) you can't use tox with conda, and tox is the best way at the moment to run all the tests (including doctests, coverage, flake8 etc.) and verify support for PY2 and PY3.
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virtualenv has been packaged and exists on defaults and conda-forge. Once that was done tox was added to conda-forge in short order.
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I think I'll leave this as-is for now as I don't have time to verify all the steps to get tox fully up and running all test environments under a conda installation, but if someone wants to do this later and can provide the necessary commands then very happy to add.
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Sure. That was only meant as an informative comment. Happy with this as is.
docs/contributing.rst
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| It's best to create a new, separate branch for each piece of work you want to do. E.g.:: | ||
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| git checkout -b shiny-new-feature |
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I would preface this with:
git fetch upstream
git checkout -b shiny-new-feature upsteam/master
zarr/tests/test_convenience.py
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| @pytest.mark.skipif(h5py is None, reason='h5py not installed') |
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we also ran into this in pydata/xarray#1557. This should work but just for reference, we created our own skipif machinery using unittest.
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Thanks @jhamman for the comments, much appreciated. |
alimanfoo
changed the title
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Looks like readthedocs is happy. |
.github/ISSUE_TEMPLATE.md
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| * How Zarr was installed (e.g., "using pip into virtual environment", or "using conda") | ||
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| Also, if you think it might be relevant, please provide the output from ``pip list`` or | ||
| ``conda list`` depending on which was used to install Zarr. |
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Might suggest conda env export and pip freeze instead. These produce files that can be used to immediately install a user's environment and begin playing with it. While conda list and pip list do provide the same info, there is no one liner that turns them into an environment on a dev's machine.
.github/PULL_REQUEST_TEMPLATE.md
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| TODO: | ||
| * [ ] Unit tests and/or doctests in docstrings | ||
| * [ ] ``tox -e py36`` passes locally | ||
| * [ ] ``tox -e py27`` passes locally |
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Personally I don't think we need to be so formal. Maybe something like this for the first one. Similar for the second.
* [ ] Python 3.6 tests pass (e.g. ``tox -e py36``)
.github/PULL_REQUEST_TEMPLATE.md
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| * [ ] Docstrings and API docs for any new/modified user-facing classes and functions | ||
| * [ ] New/modified features documented in docs/tutorial.rst | ||
| * [ ] Changes documented in docs/release.rst | ||
| * [ ] ``tox -e docs`` passes locally |
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Similar story as above. Here some comment about the docs building ok.
docs/contributing.rst
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| <https://github.com/zarr-developers/zarr/issues/new>`_ including a link to your StackOverflow | ||
| question. We will try to respond to questions as quickly as possible, but please bear | ||
| in mind that there may be periods where we have limited time to answer questions | ||
| due to other commitments. |
.github/ISSUE_TEMPLATE.md
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| <!-- | ||
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| For bug reports, please follow the template below. For enhancement proposals, feel free | ||
| to use whatever template makes sense. |
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This seems good, but it doesn't show up currently (when rendered). Any reason for it to be commented?
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Not really, was just copying another example I'd seen.
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Thanks @jakirkham. I've made some changes which hopefully address all points. Regarding developer best practices, I've added a new section at the end, also including some information about versioning and release policies, let me know what you think. Ideally I was thinking we should at least review and approve each other's PRs, although I don't want to place too heavy a burden so feel free to say "too busy at the moment" and maybe we can try to work around or reschedule. |
docs/contributing.rst
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| ~~~~~~~~~~~~~~~~~~~~~ | ||
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| If at all possible, pull requests submitted by an external contributor should be | ||
| reviewed and approved by all core developers before being merged. Pull requests |
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Do we want to constrain it to all? It may be difficult to achieve due to time constraints and competing demands. Admittedly "all" is small right now though.
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As contrast, scikit-learn requires two approvals for merging (see Pull Request Checklist). Dask has a more informal mechanism by which core developers say they plan to merge in a particular time frame if they get no comments (typical in a day).
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I think I'll edit this to say we'd like to aim for pull requests to be reviewed by at least one other core developer. With only two of us at the moment it amounts to the same thing, but I think it's probably worth saying we'd like to aim for some review of PRs. This will slow things down if either of us is unable to review due to other commitments, but I think it's probably ok to move slowly for a while and focus on consolidation and sharing knowledge between core devs.
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Sure. I completely agree. We also added a lot of features. So we might need to be in maintenance mode for a bit just in case any bugs show up.
docs/contributing.rst
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| function, class or method is usually a backwards compatible change. However, removing a | ||
| function, class or method; removing an argument to a function or method; adding a | ||
| required argument to a function or method; or changing the behaviour of a function or | ||
| method, are examples of **backwards-incompatible API changes**. |
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As we did add a few notes about functions not having a stable API. We should probably include a similar note here.
Also how do you feel about documented API vs. functions found inside Zarr? Some projects only consider the documented part public. In that case even functions that don't have a leading underscore are still considered private as long as they are not in the docs.
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Ah sorry. Just got to the section on not stable API below. Thoughts about moving that section after this one?
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I think I will change the definition of public API to include only what is documented in the API docs, probably safer for now.
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SGTM. We can always expand the scope later.
docs/contributing.rst
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| 2.2.0 -> 2.2.1). If a release contains API changes, but all API changes are | ||
| backwards-compatible, then the minor version number should be incremented | ||
| (e.g., 2.2.1 -> 2.3.0). If a release contains any backwards-incompatible API changes, | ||
| the major version number should be incremented (e.g., 2.3.0 -> 3.0.0). |
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Do we want to go down the road of having release branches? Asking this partially as I would like to get an idea of how we want to handle breaking changes should they be proposed.
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How would we use release branches? Is it to allow work to be going on on the next major version (including breaking API changes) in parallel with bug fixes on the current major version?
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That seems like a reasonable solution to me.
docs/contributing.rst
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| Exceptions can be made for any function, class or method which has been documented as | ||
| an experimental feature, i.e., backwards-incompatible changes can be included in a | ||
| minor release, although this should be avoided wherever possible. |
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As noted above, it would be nice to have this right after the API section as they seem more logically connected.
docs/contributing.rst
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| desirable to maintain data format compatibility wherever possible. However, if a change | ||
| is needed to the storage specification, and that change would break data format | ||
| compatibility in any way, then the storage specification version number should be | ||
| incremented (e.g., 2 -> 3). |
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What happens when we add something to the data format spec which is not breaking? Is there a way to version this?
Also related how do we migrate between these enhancement versions? Lastly do we have a way to check the data format spec version of Zarr and/or the files themselves?
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At the moment, I cannot imagine any change to the data format spec that does not break data format compatibility in some way, in the sense that data written by any one implementation can be read correctly by all others. Hence the storage spec has only a major version number, there is no minor or micro version number. This simplifies the definition of data format compatibility, i.e., all libraries implementing a given spec version number should be fully interoperable. That said, if you have an example of a spec change that does not fit into this model, happy to discuss.
The spec version of the data files is included in the metadata (.zarray or .zgroup). The spec version that zarr implements is currently stored as the ZARR_FORMAT variable in the zarr.meta module. There is a check on reading array or group metadata, if there is a difference between the spec version in the metadata files and the ZARR_FORMAT variable then an exception is raised.
When we moved from spec version 1 to 2 I implemented a function zarr.storage.migrate_1to2 which updates the metadata resources to conform to spec version 2. I imagined that we would do something similar for any future spec changes.
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As an example, we recently opted to not always write metadata files and noted this in the spec. We have also made sure that current Zarr treats this as empty metadata. That said, I'm not sure if an older version of Zarr (claiming to support the same spec version) would handle this correctly. Even though what we added didn't fundamentally break the version 2 spec. Instead it provided a superset of the existing functionality. IOW this seems like a feature we added to the spec that would make it 2.1. Though this could just be me being pedantic. :)
Everything else sounds great. We might want to mention the ZARR_FORMAT variable here.
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It's a fair point, although that change was a bit of a grey area in that zarr 2.1 is happy if .zattrs is missing and the spec did not say whether .zattrs is required or not, so saying that .zattrs is optional was a clarification and did not break compatibility with previous zarr versions implementing spec version 2. I might have been a bit more cautious if I knew there were other zarr implementations out there, but it still would have been a clarification rather than a change to the spec.
We may still come across other cases which are more clear cut, in that some change is required in the spec to support a new feature, and where using something more fine-grained than a single major version number for the spec version could be useful, but I find it hard to think that through without a concrete case in front of me. The questions we would need to answer are things like, what kinds of changes would be allowed in a minor spec change (e.g., 2.0 -> 2.1), how should an implementation behave if it implements spec version 2.0 and encounters data using spec version 2.1, etc. I think we can cross those bridges if and when the need arises.
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We could probably smooth this over by adding one last patch release to 2.1 with this change. Alternatively we could make the behavior something users opt-in to. That said, I'm not too worried about it. In any event, this discussion is diverging from the spec version and can be continued in an issue if we would like.
Sure, make sense. Easy to add once we need it.
docs/contributing.rst
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| number 3.0.0. Note however that the major version number of the Zarr library may not | ||
| always correspond to the spec version number. For example, Zarr versions 2.x, 3.x, and | ||
| 4.x might all implement the same version of the storage spec and thus maintain data | ||
| format compatibility, although they will not maintain API compatibility. |
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Do we store the spec version in a variable somewhere?
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| Ideally, any bug fixes that don't change the public API should be released as soon as | ||
| possible. It is fine for a micro release to contain only a single bug fix. |
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Hence the branching question above. Do we want to branch out 2.2 and allow mater to get enhancements and backport patches to 2.2?
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Ideally this would be great, although given that developer time is limited I think I wouldn't want to make any promises to backport bug fixes.
| Tag the version (where "X.X.X" stands for the version number, e.g., "2.2.0"):: | ||
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| $ version=X.X.X | ||
| $ git tag -a v$version -m v$version |
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Any other rules about the message? Are we allowed to highlight changes or is that undesirable?
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I don't mind about the message, happy with more information if useful.
| Release source code to PyPI:: | ||
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| $ python setup.py register sdist | ||
| $ twine upload dist/zarr-${version}.tar.gz |
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Are there some rules about who gets permissions to PyPI?
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Happy for other core devs to have PyPI permissions.
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Sorry for the slew of questions above. Tried to be thorough. Happy to clarify anything that is unclear. |
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Many thanks @jakirkham, I'll do some editing next week.
…On Fri, Jan 5, 2018 at 7:38 PM, jakirkham ***@***.***> wrote:
Sorry for the slew of questions above. Tried to be thorough. Happy to
clarify anything that is unclear.
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Anything I can help with here? |
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It's OK, thanks, I just need to find a minute to make a few edits. Been
full pelt on other projects the last few weeks.
…On Wed, Jan 24, 2018 at 6:20 PM, jakirkham ***@***.***> wrote:
Anything I can help with here?
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Hi @jakirkham, I've made some edits to the contributing doc, hopefully addresses comments but let me know if any other thoughts. |
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No worries. Know the feeling. :) The edits look great. Had one more comment on the version spec regarding a particular change we made. Happy to go along with whatever you decide. Other than that I think this should be good to merge. |
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Thanks @jakirkham. Will merge on Monday if no further comments then make a
2.2rc1 release.
…On Friday, January 26, 2018, jakirkham ***@***.***> wrote:
***@***.**** commented on this pull request.
------------------------------
In docs/contributing.rst
<#227 (comment)>:
> +
+Here we consider all functions, classes and methods that do not begin with an
+underscore as part of the Zarr public API. Any change to the public API that does **not**
+break existing third party code importing Zarr, or cause third party code to behave in
+a different way, is a **backwards-compatible API change**. For example, adding a new
+function, class or method is usually a backwards compatible change. However, removing a
+function, class or method; removing an argument to a function or method; adding a
+required argument to a function or method; or changing the behaviour of a function or
+method, are examples of **backwards-incompatible API changes**.
+
+If a release contains no changes to the public API (e.g., contains only bug fixes or
+other maintenance work), then the micro version number should be incremented (e.g.,
+2.2.0 -> 2.2.1). If a release contains API changes, but all API changes are
+backwards-compatible, then the minor version number should be incremented
+(e.g., 2.2.1 -> 2.3.0). If a release contains any backwards-incompatible API changes,
+the major version number should be incremented (e.g., 2.3.0 -> 3.0.0).
That seems like a reasonable solution to me.
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FWIW am happy to see this merged whenever you are ready. |
This PR adds some documentation about contributing to Zarr.
Also discovered in working up this PR is that the pytest.mark.skipif usage is broken due to pytest-dev/pytest#568, and so this PR includes a simple workaround for the tests with optional dependencies.
TODO: