Merge pull request #7 from shachafl/pypi_description

Missing pypi description fix by adding pyproject.toml
Verified solution by uploading to testpypi after build:
`python3 -m twine upload --repository testpypi dist/*`

Will be resolved on master branch after new release is made and uploaded.

Reference:
https://packaging.python.org/en/latest/guides/modernize-setup-py-project/
https://packaging.python.org/en/latest/guides/writing-pyproject-toml/
https://packaging.python.org/en/latest/specifications/pyproject-toml/
https://setuptools.pypa.io/en/latest/userguide/pyproject_config.html

Makefile

@@ -295,7 +295,7 @@ release-env/bin/make_shell:
 # public: generate the release build
 release-prep: release-check release-ready release-env
 	release-env/bin/python setup.py clean
-	release-env/bin/python setup.py sdist
+	release-env/bin/python -m build
 	release-env/bin/pip install dist/starfish-$(VERSION).tar.gz
 
 ## Sections: 5 - 6

pyproject.toml

@@ -0,0 +1,48 @@
+[build-system]
+requires = ["setuptools >= 66.1.0", "versioneer"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "starfish"
+dynamic = ["version", "dependencies", "optional-dependencies"]
+requires-python = ">= 3.9, <3.13"
+authors = [
+    {name = "Deep Ganguli", email = "dganguli@chanzuckerberg.com"}
+]
+maintainers = [
+  {name = "Lior Shachaf", email = "shachaflior@gmail.com"}
+]
+description = "Pipelines and pipeline components for the analysis of image-based transcriptomics data"
+readme = "README.rst"
+keywords = ["single-cell", "image-based", "transcriptomics"]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Natural Language :: English",
+    "Operating System :: POSIX :: Linux",
+    "Operating System :: Unix",
+    "Operating System :: MacOS :: MacOS X",
+    "Operating System :: Microsoft :: Windows",
+    "License :: OSI Approved :: MIT License",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12"
+]
+
+[tool.versioneer]
+VCS = "git"
+style = "pep440"
+versionfile_source = "starfish/core/_version.py"
+versionfile_build = "starfish/core/_version.py"
+parentdir_prefix = "starfish-"
+tag_prefix = ""
+
+[project.urls]
+Homepage = "https://spacetx-starfish.readthedocs.io/en/latest/"
+Documentation = "https://spacetx-starfish.readthedocs.io/en/latest/"
+Repository = "https://github.com/spacetx/starfish"
+"Bug Tracker" = "https://github.com/spacetx/starfish/issues"
+
+[project.scripts]
+starfish = "starfish.core.starfish:starfish"

requirements/REQUIREMENTS-CI.txt

@@ -1,21 +1,22 @@
 # You should not edit this file directly.  Instead, you should edit one of the following files (requirements/REQUIREMENTS-CI.txt.in) and run make requirements/REQUIREMENTS-CI.txt
 alabaster==0.7.16
-asttokens==2.4.1
+asttokens==3.0.0
 attrs==24.2.0
 babel==2.16.0
 backports.tarfile==1.2.0
 beautifulsoup4==4.12.3
-bleach==6.1.0
+bleach==6.2.0
 boto3==1.35.38
 botocore==1.35.38
+build==1.2.2.post1
 certifi==2024.8.30
 cffi==1.17.1
 charset-normalizer==3.4.0
 click==8.1.7
 commonmark==0.9.1
 contourpy==1.3.0
-coverage==7.6.2
-cryptography==43.0.1
+coverage==7.6.9
+cryptography==44.0.0
 cycler==0.12.1
 decorator==5.1.1
 defusedxml==0.7.1
@@ -25,7 +26,7 @@ entrypoints==0.4
 exceptiongroup==1.2.2
 execnet==2.1.1
 executing==2.1.0
-fastjsonschema==2.20.0
+fastjsonschema==2.21.1
 flake8==7.1.1
 flake8-import-order==0.18.2
 fonttools==4.54.1
@@ -40,7 +41,7 @@ ipython==8.18.1
 jaraco.classes==3.4.0
 jaraco.context==6.0.1
 jaraco.functools==4.1.0
-jedi==0.19.1
+jedi==0.19.2
 jeepney==0.8.0
 Jinja2==3.1.4
 jmespath==1.0.1
@@ -49,15 +50,15 @@ jsonschema==4.17.3
 jupyter_client==8.6.3
 jupyter_core==5.7.2
 jupyterlab_pygments==0.3.0
-keyring==25.4.1
+keyring==25.5.0
 kiwisolver==1.4.7
 lazy_loader==0.4
 looseversion==1.3.0
 lxml==5.3.0
-lxml_html_clean==0.4.0
+lxml_html_clean==0.4.1
 m2r2==0.3.3.post2
 markdown-it-py==3.0.0
-MarkupSafe==3.0.1
+MarkupSafe==3.0.2
 matplotlib==3.7.5
 matplotlib-inline==0.1.7
 mccabe==0.7.0
@@ -67,12 +68,12 @@ more-itertools==10.5.0
 mpmath==1.3.0
 mypy==1.10.1
 mypy-extensions==1.0.0
-nbclient==0.10.0
+nbclient==0.10.1
 nbconvert==6.5.4
 nbencdec==0.0.10
 nbformat==5.10.4
 networkx==3.2.1
-nh3==0.2.18
+nh3==0.2.19
 numpy==1.26.4
 numpydoc==1.8.0
 packaging==24.1
@@ -81,7 +82,7 @@ pandocfilters==1.5.1
 parso==0.8.4
 pexpect==4.9.0
 pillow==10.4.0
-pkginfo==1.10.0
+pkginfo==1.12.0
 platformdirs==4.3.6
 pluggy==1.5.0
 prompt_toolkit==3.0.48
@@ -92,9 +93,10 @@ pycparser==2.22
 pyflakes==3.2.0
 Pygments==2.18.0
 pyparsing==3.1.4
+pyproject_hooks==1.2.0
 pyrsistent==0.20.0
-pytest==8.3.3
-pytest-cov==5.0.0
+pytest==8.3.4
+pytest-cov==6.0.0
 pytest-xdist==3.6.1
 python-dateutil==2.9.0.post0
 pytz==2024.2
@@ -108,7 +110,7 @@ regional==1.1.2
 requests==2.32.3
 requests-toolbelt==1.0.0
 rfc3986==2.0.0
-rich==13.9.2
+rich==13.9.4
 s3transfer==0.10.3
 scikit-image==0.21.0
 scikit-learn==1.5.2
@@ -126,30 +128,30 @@ Sphinx==7.4.7
 sphinx-autodoc-typehints==2.3.0
 sphinx-bootstrap-theme==0.8.1
 sphinx-gallery==0.18.0
-sphinx-rtd-theme==3.0.1
+sphinx-rtd-theme==3.0.2
 sphinxcontrib-applehelp==2.0.0
 sphinxcontrib-devhelp==2.0.0
 sphinxcontrib-htmlhelp==2.1.0
 sphinxcontrib-jquery==4.1
 sphinxcontrib-jsmath==1.0.1
-sphinxcontrib-programoutput==0.17
+sphinxcontrib-programoutput==0.18
 sphinxcontrib-qthelp==2.0.0
 sphinxcontrib-serializinghtml==2.0.0
 stack-data==0.6.3
 sympy==1.13.3
 tabulate==0.9.0
 threadpoolctl==3.5.0
 tifffile==2024.8.30
-tinycss2==1.3.0
-tomli==2.0.2
+tinycss2==1.4.0
+tomli==2.2.1
 tornado==6.4.2
 tqdm==4.66.5
 trackpy==0.6.4
 traitlets==5.14.3
-twine==5.1.1
+twine==6.0.1
 types-PyYAML==6.0.12.20240917
 types-requests==2.31.0.6
-types-setuptools==75.1.0.20240917
+types-setuptools==75.6.0.20241126
 types-urllib3==1.26.25.14
 typing_extensions==4.12.2
 tzdata==2024.2

requirements/REQUIREMENTS-CI.txt.in

@@ -1,6 +1,7 @@
 # requirements to run CI except for napari
 # constrain the CI requirements to packages already in REQUIREMENTS-STRICT.txt
 -r ../starfish/REQUIREMENTS-STRICT.txt
+build
 flake8
 flake8-import-order
 lxml_html_clean

setup.py

@@ -22,13 +22,7 @@
     extras_require={
         'napari': [f"napari[all]>={napari_version}"],
     },
-    entry_points={
-        'console_scripts': [
-            "starfish=starfish.core.starfish:starfish",
-        ]
-    },
     include_package_data=True,
     version=versioneer.get_version(),
     cmdclass=versioneer.get_cmdclass(),
-    python_requires='>=3.9, <3.13'
 )