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Replacing Setup.py with Pyproject.py #279

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merged 10 commits into from
Feb 23, 2024
Merged

Replacing Setup.py with Pyproject.py #279

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f81c5f4
replaced setup.cfg and setup.py completly with pyproject.toml, remove…
Feb 22, 2024
9ffa8e4
fixed pyproject.toml setuptools package find location
Feb 22, 2024
7cd1b04
fixed dev-requirements.txt updated mypy version
Feb 22, 2024
ff9cd28
Removed setup.py check command, currently no integrated solution to v…
Feb 22, 2024
6b7bcea
updated dev pip install in README.md
Feb 22, 2024
83e711c
minor formatting updates
Feb 22, 2024
db65a8b
minor formatting updates
Feb 22, 2024
63d10d3
updated python support to =>3.9 because 3.7 is no longer being suppor…
Feb 22, 2024
dd4feb0
moved ignore_missing_imports under pytest in pyproject.toml
Feb 22, 2024
29d43f6
minor formatting change
Feb 22, 2024
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3 changes: 0 additions & 3 deletions .github/workflows/pypi_packaging.yml
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Expand Up @@ -80,9 +80,6 @@ jobs:
- name: Setup Env
run: python3 -m pip install --upgrade pip build

- name: Validate setup.py
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There is no integrated solution for validating the pyproject.toml file. There are some third-party application but they are unstable.
I've noticed though that tox run excutting its test automatically does a basic level check of the toml file using not a cli command but via package called "tomli". This has been added to the dev-requirments.txt file

run: python3 setup.py check --metadata

- name: Build
run: python3 -m build

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6 changes: 3 additions & 3 deletions dev-requirements.txt
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@@ -1,13 +1,13 @@
isort==4.3.21
isort==5.13.2
tox
wheel
bumpversion
twine
black
flake8
pylint
tomli==2.0.1
cython
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needed for tox validation of pyproject.toml

sphinx
sphinx-rtd-theme
mypy==0.770
-r requirements.txt
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needed to updated because latest version of Py3.11 did not support this version

mypy==1.8.0
6 changes: 3 additions & 3 deletions developer_docs/runtests.md
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Expand Up @@ -14,13 +14,13 @@ as seen below
tox -e lint

# reformat all project files
black src tests setup.py
black src tests

# sort imports in project files
isort -rc src tests setup.py
isort -rc src tests

# check pep8 against all project files
flake8 src tests setup.py
flake8 src tests

# lint python code for common errors and codestyle issues
pylint src
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51 changes: 49 additions & 2 deletions pyproject.toml
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@@ -1,3 +1,5 @@

ignore_missing_imports = true
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Can you explain this one to me? Don't we need all our imports?

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Thanks for this catch, its suppose to be under [tool.mypy."pytest.*"]
When ignore_missing_imports is set to true, mypy will not report an error when an imported module cannot be found. This is to replicate the setting that was originally found in the setup.cfg file

[build-system]
requires = ["setuptools>=61.0"]
build-backend = "setuptools.build_meta"
Expand All @@ -7,8 +9,53 @@ name = "cromshell"
# Version number is automatically set via bumpversion. DO NOT MODIFY:
version = "2.1.1"
readme = "README.md"

description="Command Line Interface (CLI) for Cromwell servers"
authors=[
{name = "Jonn Smith", email = "[email protected]"},
{name = "Louis Bergelson", email = "[email protected]"},
{name = "Beri Shifaw", email = "[email protected]"},
]
license={text = "BSD 3-Clause"}
requires-python=">=3.7"
classifiers=[
"Development Status :: 5 - Production/Stable",
"Intended Audience :: Science/Research",
"License :: OSI Approved :: BSD License",
"Natural Language :: English",
"Operating System :: OS Independent",
"Programming Language :: Python :: 3.7",
"Programming Language :: Python :: 3.8",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: Implementation :: CPython",
]
keywords = [
"cromwell", "cromshell", "cromwell-cli", "cromwell-client", "cromwell-api",
"cromwell-rest", "cromwell-utilities", "cromwell-tools",
]
dynamic = ["dependencies", "optional-dependencies"]

[project.urls]
"Homepage" = "https://github.com/broadinstitute/cromshell"
Homepage = "https://github.com/broadinstitute/cromshell"
"Bug Tracker" = "https://github.com/broadinstitute/cromshell/issues"

[project.scripts]
cromshell = "cromshell.__main__:main_entry"

# Configuration for the `setuptools` package
[tool.setuptools.dynamic]
dependencies = {file = ["requirements.txt"]}
optional-dependencies = {dev = { file = ["dev-requirements.txt"]}, tests = { file = ["test-requirements.txt"]}}

[tool.setuptools.packages.find]
where = ["src"]
include = ["cromshell*"]

# former dump_setup.cfg configuration for mypy
[tool.mypy."numpy.*"]
ignore_missing_imports = true

[tool.mypy."pysam.*"]
ignore_missing_imports = true

[tool.mypy."pytest.*"]
8 changes: 0 additions & 8 deletions setup.cfg
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54 changes: 0 additions & 54 deletions setup.py
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1 change: 0 additions & 1 deletion test-requirements.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -2,4 +2,3 @@ pytest
pytest-cov
pytest-dependency
coverage>=4.5
-r requirements.txt
16 changes: 10 additions & 6 deletions tox.ini
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Expand Up @@ -15,6 +15,7 @@ ignore = E203, E501, W503

[testenv]
deps = -rtest-requirements.txt
-rrequirements.txt
commands =
pytest tests/unit tests/integration tests/acceptance \
--cov cromshell \
Expand All @@ -28,16 +29,19 @@ setenv =

[testenv:unit]
deps = -rtest-requirements.txt
-rrequirements.txt
commands =
pytest tests/unit {posargs}

[testenv:integration]
deps = -rtest-requirements.txt
-rrequirements.txt
commands =
pytest tests/integration {posargs}

[testenv:acceptance]
deps = -rtest-requirements.txt
-rrequirements.txt
commands =
pytest tests/acceptance {posargs}

Expand All @@ -49,9 +53,9 @@ deps =
flake8

commands =
black --check --diff --target-version py38 src tests setup.py
isort --check-only --profile black --diff -rc tests src setup.py
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-rc for isort is deprecated because options now happen by default

flake8 src tests setup.py
black --check --diff --target-version py38 src tests
isort --check-only --profile black --diff tests src
flake8 src tests
pylint --exit-zero src

[testenv:lint-edit]
Expand All @@ -61,9 +65,9 @@ deps =
flake8

commands =
black --target-version py38 src tests setup.py
isort --profile black -rc tests src setup.py
flake8 src tests setup.py
black --target-version py38 src tests
isort --profile black tests src
flake8 src tests
pylint --exit-zero src

[gh-actions]
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The original thought was to have this be used during github testing, but the github actions list the python version to test so its is not needed here

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