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FIX: Namespace packaging #42

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merged 13 commits into from
Jul 14, 2023
Merged

FIX: Namespace packaging #42

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13de6b5
FIX: Namespace packaging
effigies Jul 13, 2023
b9d7db1
FIX: Import from bids.ext.reports
effigies Jul 13, 2023
da0eb22
CI: Test package name, not location
effigies Jul 13, 2023
7996d79
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jul 13, 2023
4649028
CI: Check TOML
effigies Jul 13, 2023
c35ce6f
FIX: Point to correct location for script
effigies Jul 13, 2023
20f1a8a
FIX: Update codespell and mypy configuration
effigies Jul 13, 2023
f3bcbaa
CI: Update concurrency so tests do not squash one another
effigies Jul 13, 2023
a760413
MNT: Remove mypy from pre-commit; it does not pass with proper packaging
effigies Jul 13, 2023
68ee83f
FIX: Import from bids.ext.reports in tests
effigies Jul 13, 2023
31ce05d
CI: Configure coverage and run module doctests
effigies Jul 13, 2023
dd91068
DOC: Use fully qualified module names
effigies Jul 13, 2023
38a93d3
MNT: Fix mistyped only-include
effigies Jul 13, 2023
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4 changes: 2 additions & 2 deletions .github/workflows/testing.yml
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Expand Up @@ -10,7 +10,7 @@ on:
- '*'

concurrency:
group: environment-${{ github.ref }}
group: ${{ github.workflow }}-${{ github.ref }}
cancel-in-progress: true

jobs:
Expand Down Expand Up @@ -42,7 +42,7 @@ jobs:
run: pip install .[tests]
- name: Run tests
shell: bash {0}
run: python -m pytest --pyargs bids/ext/reports --cov=bids/ext/reports
run: pytest --pyargs bids.ext.reports --doctest-modules --cov=bids.ext.reports
- name: Upload coverage to CodeCov
uses: codecov/codecov-action@v3
if: success()
2 changes: 1 addition & 1 deletion .github/workflows/testing_cli.yml
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Expand Up @@ -10,7 +10,7 @@ on:
- '*'

concurrency:
group: environment-${{ github.ref }}
group: ${{ github.workflow }}-${{ github.ref }}
cancel-in-progress: true

jobs:
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6 changes: 1 addition & 5 deletions .pre-commit-config.yaml
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Expand Up @@ -11,6 +11,7 @@ repos:
- id: check-ast
- id: check-added-large-files
- id: check-case-conflict
- id: check-toml

- repo: https://github.com/codespell-project/codespell
rev: v2.2.5
Expand Down Expand Up @@ -43,11 +44,6 @@ repos:
- id: black
args: [--config=pyproject.toml, --verbose]

- repo: https://github.com/pre-commit/mirrors-mypy
rev: v1.4.1
hooks:
- id: mypy
Comment on lines -46 to -49
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My guess is this previously worked by accident. Here's what you get now:

$ mypy --explicit-package-bases bids/ext/reports
bids/ext/reports/templates/demos/python/demo.py:5: error: Module "bids" has no attribute "BIDSLayout"  [attr-defined]
bids/ext/reports/templates/demos/python/demo.py:10: error: Function is missing a return type annotation  [no-untyped-def]
bids/ext/reports/templates/demos/python/demo.py:14: error: Function is missing a type annotation  [no-untyped-def]
bids/ext/reports/templates/demos/python/demo.py:21: error: Function is missing a type annotation  [no-untyped-def]
bids/ext/reports/templates/demos/python/demo.py:39: error: Function is missing a return type annotation  [no-untyped-def]
bids/ext/reports/templates/demos/python/demo.py:39: note: Use "-> None" if function does not return a value
bids/ext/reports/utils.py:11: error: Cannot find implementation or library stub for module named "bids.layout"  [import]
bids/ext/reports/parameters.py:9: error: Cannot find implementation or library stub for module named "num2words"  [import]
bids/ext/reports/parameters.py:15: error: Cannot find implementation or library stub for module named "bids.layout"  [import]
bids/ext/reports/parameters.py:56: error: Argument 1 to "append" of "list" has incompatible type "None"; expected "int"  [arg-type]
bids/ext/reports/parameters.py:71: error: Argument 1 to "get_nb_vols" has incompatible type "List[Nifti1Image]"; expected "List[Optional[Nifti1Image]]"  [arg-type]
bids/ext/reports/parameters.py:71: note: "List" is invariant -- see https://mypy.readthedocs.io/en/stable/common_issues.html#variance
bids/ext/reports/parameters.py:71: note: Consider using "Sequence" instead, which is covariant
bids/ext/reports/parameters.py:80: error: Argument 1 to "get_nb_vols" has incompatible type "List[Nifti1Image]"; expected "List[Optional[Nifti1Image]]"  [arg-type]
bids/ext/reports/parameters.py:80: note: "List" is invariant -- see https://mypy.readthedocs.io/en/stable/common_issues.html#variance
bids/ext/reports/parameters.py:80: note: Consider using "Sequence" instead, which is covariant
bids/ext/reports/parsing.py:14: error: Cannot find implementation or library stub for module named "bids.layout"  [import]
bids/ext/reports/parsing.py:107: error: Module has no attribute "func_info"  [attr-defined]
bids/ext/reports/parsing.py:143: error: Module has no attribute "anat_info"  [attr-defined]
bids/ext/reports/parsing.py:174: error: Incompatible types in assignment (expression has type "int", variable has type "str")  [assignment]
bids/ext/reports/parsing.py:185: error: Module has no attribute "dwi_info"  [attr-defined]
bids/ext/reports/parsing.py:228: error: Module has no attribute "fmap_info"  [attr-defined]
bids/ext/reports/parsing.py:253: error: Module has no attribute "meg_info"  [attr-defined]
bids/ext/reports/parsing.py:362: error: Incompatible return value type (got "Optional[FileBasedImage]", expected "Optional[Nifti1Image]")  [return-value]
bids/ext/reports/report.py:14: error: Cannot find implementation or library stub for module named "bids.layout"  [import]
bids/ext/reports/cli.py:15: error: Cannot find implementation or library stub for module named "bids.layout"  [import]
bids/ext/reports/cli.py:15: note: See https://mypy.readthedocs.io/en/stable/running_mypy.html#missing-imports
Found 21 errors in 6 files (checked 10 source files)

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Can be re-added later, but fixing these issues feels out-of-scope for this PR.

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totally outside of the scope indeed


- repo: https://github.com/pycqa/flake8
rev: 6.0.0
hooks:
Expand Down
2 changes: 1 addition & 1 deletion bids/ext/reports/cli.py
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Expand Up @@ -8,10 +8,10 @@
from typing import Sequence

import rich
from reports import BIDSReport

from ._version import __version__
from .logger import pybids_reports_logger
from bids.ext.reports import BIDSReport
from bids.layout import BIDSLayout

# from bids.reports import BIDSReport
Expand Down
3 changes: 2 additions & 1 deletion bids/ext/reports/tests/test_parameters.py
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Expand Up @@ -2,7 +2,8 @@
from __future__ import annotations

import pytest
from ext.reports import parameters

from bids.ext.reports import parameters


@pytest.mark.parametrize(
Expand Down
3 changes: 1 addition & 2 deletions bids/ext/reports/tests/test_parsing.py
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Expand Up @@ -3,9 +3,8 @@

from pathlib import Path

from ext.reports import parsing

from bids import BIDSLayout
from bids.ext.reports import parsing
from bids.tests import get_test_data_path


Expand Down
3 changes: 1 addition & 2 deletions bids/ext/reports/tests/test_report.py
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Expand Up @@ -6,8 +6,7 @@
from os.path import abspath
from os.path import join

from ext.reports import BIDSReport

from bids.ext.reports import BIDSReport
from bids.tests import get_test_data_path


Expand Down
4 changes: 2 additions & 2 deletions bids/ext/reports/tests/test_templates.py
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Expand Up @@ -4,8 +4,8 @@
import json
from pathlib import Path

from ext.reports import parsing
from ext.reports import templates
from bids.ext.reports import parsing
from bids.ext.reports import templates


def test_pet():
Expand Down
24 changes: 12 additions & 12 deletions docs/source/reports.rst
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@@ -1,10 +1,10 @@
reports package
===============
bids.ext.reports package
========================

Module contents
---------------

.. automodule:: reports
.. automodule:: bids.ext.reports
:members:
:undoc-members:
:show-inheritance:
Expand All @@ -13,26 +13,26 @@ Module contents
Submodules
----------

reports.parameters module
-------------------------
bids.ext.reports.parameters module
----------------------------------

.. automodule:: reports.parameters
.. automodule:: bids.ext.reports.parameters
:members:
:undoc-members:
:show-inheritance:

reports.parsing module
----------------------
bids.ext.reports.parsing module
-------------------------------

.. automodule:: reports.parsing
.. automodule:: bids.ext.reports.parsing
:members:
:undoc-members:
:show-inheritance:

reports.report module
---------------------
bids.ext.reports.report module
------------------------------

.. automodule:: reports.report
.. automodule:: bids.ext.reports.report
:members:
:undoc-members:
:show-inheritance:
26 changes: 16 additions & 10 deletions pyproject.toml
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Expand Up @@ -6,11 +6,8 @@ build-backend = "hatchling.build"
source = "vcs"

[tool.hatch.build.targets.wheel]
packages = ["bids/ext/reports"]

[tool.hatch.build.targets.wheel.sources]
"src" = ""
"scripts" = "mypackage/scripts"
packages = ["bids"]
only-include = ["bids/ext/reports"]
Comment on lines +9 to +10
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For your reference, this was the main issue: https://hatch.pypa.io/latest/config/build/#explicit-selection

Everything else just followed from fixing tests


[tool.hatch.build.hooks.vcs]
version-file = "bids/ext/reports/_version.py"
Expand Down Expand Up @@ -44,7 +41,7 @@ classifiers = [
dynamic = ["version"]

[project.scripts]
pybids_reports = "reports.cli:cli"
pybids_reports = "bids.ext.reports.cli:cli"

[project.urls]
Homepage = "http://github.com/bids-standard/pybids-reports"
Expand Down Expand Up @@ -101,7 +98,7 @@ exclude = '''
'''

[tool.codespell]
skip = "./.git,versioneer.py,_version.py,bids/ext/reports/tests/data/*"
skip = "./.git,bids/ext/reports/tests/data/*"
ignore-words-list = "te"

[tool.mypy]
Expand All @@ -116,8 +113,17 @@ warn_unused_ignores = true

[[tool.mypy.overrides]]
module = [
'ext.reports.tests.*',
'ext.reports._version.*',
'ext.reports.due.*',
'bids.ext.reports.tests.*',
'bids.ext.reports._version.*',
'bids.ext.reports.due.*',
]
ignore_errors = true

[tool.coverage.paths]
source = [
"bids/ext/reports",
"**/bids/ext/reports",
]

[tool.coverage.report]
include_namespace_packages = true