Replacing Setup.py with Pyproject.py (#279)

* replaced setup.cfg and setup.py completely with pyproject.toml, removed recursive packaging from test-requirements.txt and dev-requirements.txt, removed setup* from tox.ini,

* updated mypy and issort version

* In git actions removed setup.py check command, currently no integrated solution to validate pyproject.toml

* updated python support to =>3.9 because 3.7 is no longer being supported and 3.8 support will end this year

---------

Co-authored-by: bshifaw <[email protected]>

.github/workflows/integration_tests.yml

@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python: [ '3.7', '3.8', '3.9', '3.10' ]
+        python: [ '3.9', '3.10', '3.11']
 
     steps:
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it

.github/workflows/pypi_packaging.yml

@@ -80,9 +80,6 @@ jobs:
     - name: Setup Env
       run: python3 -m pip install --upgrade pip build
 
-    - name: Validate setup.py
-      run: python3 setup.py check --metadata
-
     - name: Build
       run: python3 -m build
 

.github/workflows/unit_tests.yml

@@ -12,7 +12,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python: [ '3.7', '3.8', '3.9', '3.10' ]
+        python: [ '3.9', '3.10', '3.11']
 
 
     # Steps represent a sequence of tasks that will be executed as part of the job

dev-requirements.txt

@@ -1,13 +1,13 @@
-isort==4.3.21
+isort==5.13.2
 tox
 wheel
 bumpversion
 twine
 black
 flake8
 pylint
+tomli==2.0.1
 cython
 sphinx
 sphinx-rtd-theme
-mypy==0.770
--r requirements.txt
+mypy==1.8.0

developer_docs/runtests.md

@@ -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

pyproject.toml

@@ -1,3 +1,4 @@
+
 [build-system]
 requires = ["setuptools>=61.0"]
 build-backend = "setuptools.build_meta"
@@ -7,8 +8,53 @@ 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=">=3.9"
+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 :: 3.9",
+        "Programming Language :: Python :: 3.10",
+        "Programming Language :: Python :: 3.11",
+        "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"
 "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 setup.cfg configuration for mypy
+[tool.mypy."numpy.*"]
+ignore_missing_imports = true
+
+[tool.mypy."pysam.*"]
+ignore_missing_imports = true
+
+[tool.mypy."pytest.*"]
+ignore_missing_imports = true

test-requirements.txt

@@ -2,4 +2,3 @@ pytest
 pytest-cov
 pytest-dependency
 coverage>=4.5
--r requirements.txt

tox.ini

@@ -4,7 +4,7 @@
 # and then run "tox" from this directory.
 
 [tox]
-envlist = lint,py37,py38,py39,py310
+envlist = lint,py39,py310,py311
 skip_missing_interpreters =
     true
 
@@ -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 \
@@ -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}
 
@@ -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
-    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]
@@ -61,14 +65,7 @@ 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]
-python =
-    3.7: py37
-    3.8: py38
-    3.9: py39
-    3.10: py310