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build: Update lower bounds to jsonschema v4.15.0, importlib-resources v1.4.0 #1979

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merged 6 commits into from
Sep 2, 2022

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@matthewfeickert matthewfeickert commented Sep 2, 2022

Description

Following #1976 (comment) this updates the lower bound of supported jsonschema to v4.15.0 given the discussion that @kratsg opened: https://github.com/orgs/python-jsonschema/discussions/995. This also updates the lower bound on importlib-resources to v1.4.0 as

jsonschema 4.15.0 depends on importlib-resources>=1.4.0; python_version < "3.9"

Checklist Before Requesting Reviewer

  • Tests are passing
  • "WIP" removed from the title of the pull request
  • Selected an Assignee for the PR to be responsible for the log summary

Before Merging

For the PR Assignees:

  • Summarize commit messages into a comprehensive review of the PR
* Update lower bound of the supported jsonschema versions to v4.15.0 to use the
  required improvements to jsonschema.RefResolver used in PR #1976.
   - c.f. https://github.com/orgs/python-jsonschema/discussions/995
   - Amends PR #1976.
* Update lower bound of the supported importlib-resources versions to v1.4.0 as
  > jsonschema 4.15.0 depends on importlib-resources>=1.4.0; python_version < "3.9"
* Update tests/constraints.txt to use jsonschema==4.15.0 and importlib_resources==1.4.0.

The conflict is caused by:
    pyhf[test] 0.1.dev1 depends on importlib-resources>=1.3.0; python_version < "3.9"
    jsonschema 4.15.0 depends on importlib-resources>=1.4.0; python_version < "3.9"
    The user requested (constraint) importlib-resources==1.3.0
@matthewfeickert matthewfeickert added fix A bug fix build Changes that affect the build system or external dependencies labels Sep 2, 2022
@matthewfeickert matthewfeickert self-assigned this Sep 2, 2022
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codecov bot commented Sep 2, 2022

Codecov Report

Base: 98.24% // Head: 98.24% // No change to project coverage 👍

Coverage data is based on head (001ce4c) compared to base (925769a).
Patch has no changes to coverable lines.

Additional details and impacted files
@@           Coverage Diff           @@
##           master    #1979   +/-   ##
=======================================
  Coverage   98.24%   98.24%           
=======================================
  Files          68       68           
  Lines        4378     4378           
  Branches      726      726           
=======================================
  Hits         4301     4301           
  Misses         45       45           
  Partials       32       32           
Flag Coverage Δ
contrib 26.58% <ø> (ø)
doctest 60.57% <ø> (ø)
unittests-3.10 96.13% <ø> (ø)
unittests-3.7 96.12% <ø> (ø)
unittests-3.8 96.16% <ø> (ø)
unittests-3.9 96.18% <ø> (ø)

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@kratsg
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kratsg commented Sep 2, 2022

We don't need the lower bounds on jsonschema to be 4.15. The change I made is backwards-compatible.

EDIT: It seems that the issue is because of the fact that in the custom schema, we have

{
    "$schema": "http://json-schema.org/draft-06/schema#",
    "$id": "1.1.0/workspace.json",
    "$ref": "defs.json#/definitions/workspace"
}

which is set with base_uri = path/to/custom_schemas/1.1.0 in #1976 . Since there's a $ref and an $id - the $id is being used to add a 1.1.0 to the base_uri when it shouldn't be. So yes, this is a bug in jsonschema that was resolved in 4.15.0.

We could update this to a newer draft for the validator, and this issue won't occur.

@kratsg kratsg merged commit b1d6bd4 into master Sep 2, 2022
@kratsg kratsg deleted the build/update-jsonschema-lower-bound branch September 2, 2022 19:35
matthewfeickert added a commit that referenced this pull request Sep 12, 2022
…#2000)

* Update jsonschema lower bound to v4.15.0 and importlib-resources lower bound to v1.4.0
  to match their versions in setup.cfg.
   - Amends PR #1979
matthewfeickert added a commit that referenced this pull request Sep 15, 2022
* Add FAQ explaining how reasons why users might have to manually downgrade dependencies.
   - c.f. PR #1979 for context
matthewfeickert added a commit that referenced this pull request Sep 20, 2022
Use fstrings for rtol warning

Use level arg over hardcoded 0.05

add in lru_cache import

fix: Pin codemetapy to v0.3.5 for `--no-extras` functionality (#1995)

* Pin codemetapy to v0.3.5 in the 'current release' test workflow to keep the
  `--no-extras` CLI API option.
   - c.f. proycon/codemetapy#24
* Update lower bounds for scipy and click in codemeta.json and add lower bounds
  for importlib-resources and typing-extensions.

Rename and add to public API

Add in hypotest_kwargs

Add FIXME notice for later. FIX BEFORE MERGE

Update public API repr

ci: Install release candidates for 'current release' test workflow (#1996)

* Use release candidates that are on PyPI for verifiying that the public API
  passes tests. This verifies that the release candidates that users are being
  asked to test reflect the release API.
* Use the latest version of pytest.

refactor: Use urllib.parse.urlsplit over urlparse (#1997)

* Use urllib.parse.urlsplit over urllib.parse.urlparse to avoid having to deal with
  urlparse's 'params' argument which incurs a performance cost.
   - c.f. https://docs.python.org/3/library/urllib.parse.html#urllib.parse.urlsplit
   - c.f. https://youtu.be/ABJvdsIANds

Indent docstrings correctly

Use uncorrelated_background API for docstring example

Use rtol in docstring example to avoid warning

drop lru_cache

fix kwargs for autoscan

Bump version: 0.7.0rc3 → 0.7.0rc4

docs: Add Binder Python runtime environment specification (#1998)

* Add binder/runtime.txt to specify the version of Python that is used for the Binder
  environment. Use Python 3.10 as this is the latest version that all pyhf backends will
  work with.
   - c.f. https://mybinder.readthedocs.io/en/latest/howto/languages.html#python

fix: Update codemeta lower bounds for jsonschema, importlib-resources (#2000)

* Update jsonschema lower bound to v4.15.0 and importlib-resources lower bound to v1.4.0
  to match their versions in setup.cfg.
   - Amends PR #1979

docs: Add milestone for 2000 project GitHub items (#2001)

* Add milestone to README for 2000 project GitHub issues and pull requests.

fix: Use codemetapy v2.2.2+ API (#2002)

* Update codemetapy to v2.2.2+ in 'current release' workflow to have access to
  the `--no-extras` CLI API in v2.0+ and reproducible runs.
   - c.f. proycon/codemetapy#24
   - c.f. proycon/codemetapy#26
   - Amends PR #1995
* Use the codemetapy v2.0 API which requires `--inputtype python` to be added.
* Update codemeta.json to follow codemetapy v2.0+ general spec.

fix: Add filterwarnings ignore for protobuf DeprecationWarning (#2005)

* Add a ignore to filterwarnings to avoid a protobuf DeprecationWarning

> DeprecationWarning: Call to deprecated create function FileDescriptor().
> Note: Create unlinked descriptors is going to go away. Please use get/find
> descriptors from generated code or query the descriptor_pool.

from TensorFlow's use of protobuf.

fix: Specify encoding as utf-8 to enforce PEP 597 (#2007)

* Explicitly specify the encoding as utf-8 while opening a file to enforce PEP 597.
  This is future-proofing work to some degree as Python 3.15+ will make utf-8 the
  default.
   - c.f. https://peps.python.org/pep-0597/
* Add the flake8-encodings pre-commit hook to enforce PEP 597.

docs: Add FAQ on reasons for need to downgrade dependencies (#1529)

* Add FAQ explaining how reasons why users might have to manually downgrade dependencies.
   - c.f. PR #1979 for context

docs: Seperate docstrings semantically

Apply sourcery suggestion for simplification

Rename to cached for clarity

Add test for auto through upperlimit API

Use None instead of auto to simplify API

Avoid function level globals

Use np.asarray to avoid copy

Use lower and upper to match scipy terms

Split warning for readability

Add test for rtol warning

Remove tmpdir fixture as not needed for these tests given no writing of output

Add check for return_results

More verbose

fix: Correct concatenate lists instead of adding float to all list elements

Test bounds expansion

test: Update test_plot_results_no_axis baseline image (#2009)

* matplotlib v3.6.0 results in a slightly different baseline image than
  matplotlib v3.5.x, so regenerate the baseline image using matplotlib v3.6.0
  with `pytest --mpl-generate-path=tests/contrib/baseline tests/contrib/test_viz.py`.
* Mark the test_plot_results_no_axis test as xfail for Python 3.7 as matplotlib v3.6.0
  is Python 3.8+ and so the image is guaranteed to be different as Python 3.7 runtimes
  will install matplotlib v3.5.x.

Add upperlimit_fixed_scan to API docs

Add return_results test

move to test_upperlimit_with_kwargs

Move the pop out before evaluation to make everything very clean and clear

Note what scan

Rename to auto_scan

docs: fix link

Provide better coverage and use np.allclose

docs: Add Beojan Stanislaus to contributor list

change auto_scan to toms748_scan

rename fixed_scan to linear_grid_scan

Make intervals module and change API to upper_limit

Rename to pyhf.infer.intervals.upper_limits

get upper_limits.upper_limit working

Also bring along old API

limit to just upper_limit by default

Rearrange

feat: Add internal API to warn of deprecation and future removal

* Add internal API pyhf.exceptions._deprecated_api_warning to alert users to API deprecation
  by raising a subclass of DeprecationWarning and future removal.
* Add test for pyhf.exceptions._deprecated_api_warning to ensure it gets picked up as
  DeprecationWarning.

Note deprecated API

Seperate into condifence intervals section

fix: Use function scope to avoid altering hypotest_args fixture

Make test name explicit

Use deprecated Sphinx note

Add versionadded directives

feat: Add internal API to warn of deprecation and future removal (#2012)

* Add internal API pyhf.exceptions._deprecated_api_warning to alert users to API deprecation
  by raising a subclass of DeprecationWarning and future removal.
* Add test for pyhf.exceptions._deprecated_api_warning to ensure it gets picked up as
  DeprecationWarning.

Update lower bound on scipy as toms748 added in scipy v1.2.0

fixup from autoscan test changes
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