Update packaging to pyproject.toml

.github/workflows/github-actions-ci.yml

@@ -44,6 +44,7 @@ jobs:
           git config lfs.url 'https://github.com/AllenInstitute/ipfx.git/info/lfs'
           git lfs env
           git lfs pull
+          pip install -e .
           python -m pytest --junitxml=test-results/junit.xml --verbose
 
 

.gitignore

@@ -89,3 +89,6 @@ venv.bak/
 
 # MacOS Finder
 .DS_Store
+
+# hatch-vcs
+ipfx/_version.py

.readthedocs.yml

@@ -10,7 +10,7 @@ sphinx:
 python:
    version: 3.6
    install:
-      - requirements: requirements_docs.txt
+      - requirements: requirements-docs.txt
       - requirements: requirements.txt
 
 formats:

RELEASE_INSTRUCTIONS.md

@@ -5,12 +5,11 @@ or a predetermined release date is approaching
 ## GitHub
 
 - [ ] Assign a developer to be responsible for the release deployment
-- [ ] Create a release branch from dev
+- [ ] Create a release branch from master
 - [ ] Create a draft pull request for the release
   - [ ] Add the Project Owner as a reviewer
   - [ ] Copy this checklist into the draft pull request description
 - [ ] Prepare the official release commit
-  - [ ] Bump version in the version.txt
   - [ ] Move changes from the "Unreleased" section to the proper sections in the CHANGELOG.md
   - [ ] Confirm all GitHub Actions tests pass
   - [ ] Change the draft to pull request to "ready for review"
@@ -24,11 +23,9 @@ or a predetermined release date is approaching
 
 ### PyPI and BKP
 
-- [ ] Reconfirm the version is correct in `version.txt`
-- [ ] Set release version with "git tag v#.#.#" (e.g. "git tag v1.0.0", equivalent to the version you bumped to), this triggers circleci to publish ipfx to PyPI (deprecated, need to move to GitHub Actions)
-- [ ] After release/deployment, merge master branch (bug fixes, document generation, etc.) back into dev and delete the release branch
+- [ ] Set release version with "git tag v#.#.#" (e.g. "git tag v1.0.0"), this triggers circleci to publish ipfx to PyPI (deprecated, need to move to GitHub Actions)
 - [ ] Build and deploy:
-    - [ ] `python setup.py sdist` and `python setup.py bdist_wheel`
+    - [ ] `hatch build`
     - [ ] `twine upload dist/* --verbose --config-file ~/.pypirc`
 - [ ] Announce release on https://community.brain-map.org
 

docker/run_tests_with_docker.sh

@@ -27,4 +27,5 @@ docker run
                     git config lfs.url 'https://github.com/AllenInstitute/ipfx.git/info/lfs'; \
                     git lfs env;                                                              \
                     git lfs pull;                                                             \
+                    pip install -e .;                                                         \
                     python -m pytest --junitxml=test-reports/test.xml --verbose"

ipfx/__init__.py

@@ -1,10 +1,6 @@
 # -*- coding: utf-8 -*-
 
 """Top-level package for ipfx."""
-import os
+from ._version import __version__
 
 __author__ = """Allen Institute for Brain Science"""
-
-version_file_path = os.path.join(os.path.dirname(__file__), "version.txt")
-with open(version_file_path, "r") as version_file:
-    __version__ = version_file.read()

pyproject.toml

@@ -0,0 +1,102 @@
+[build-system]
+requires = ["hatchling >= 1.27", "hatch-vcs"]
+build-backend = "hatchling.build"
+
+[project]
+name = "IPFX"
+dynamic = ["version"]
+description = "Intrinsic Physiology Feature Extractor (IPFX) - tool for computing neuronal features from the intracellular electrophysiological recordings"
+readme = "README.md"
+license = "LicenseRef-Proprietary"
+license-files = ["LICENSE"]
+authors = [
+    { name = "Allen Institute for Brain Science", email = "[email protected]" },
+]
+
+requires-python = ">= 3.9"
+
+keywords = [
+    "bioinformatics",
+    "neuroscience",
+    "scientific",
+]
+
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "Intended Audience :: Science/Research",
+    "License :: Other/Proprietary 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 :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+]
+
+# https://github.com/repo-helper/hatch-requirements-txt looks promising but seems unmaintained
+dependencies = [
+    "argschema",
+    "dictdiffer",
+    "h5py",
+    "marshmallow",
+    "matplotlib",
+    "methodtools",
+    "numpy",
+    "pandas",
+    "pg8000",
+    "pillow",
+    "pyabf",
+    "pynwb==3.1.2",
+    "pyYAML",
+    "python-dateutil",
+    "ruamel.yaml<0.18.0",
+    "scipy",
+    "simplejson",
+    "watchdog",
+]
+
+[project.urls]
+Homepage = "https://github.com/AllenInstitute/ipfx"
+Documentation = "https://ipfx.readthedocs.io/en/latest/"
+"Bug Tracker" = "https://github.com/AllenInstitute/ipfx/issues"
+Changelog = "https://github.com/AllenInstitute/ipfx/blob/master/CHANGELOG.md"
+
+[tool.hatch.version]
+source = "vcs"
+
+[tool.hatch.build.hooks.vcs]
+version-file = "ipfx/_version.py"
+
+[tool.hatch.build.targets.sdist]
+include = [
+    "/ipfx",
+    "/docs",
+    "requirements.txt",
+    "requirements-test.txt",
+    "requirements-docs.txt",
+    "AUTHORS.rst",
+    "CHANGELOG.md",
+    "README.md"]
+exclude = ["/ipfx/bin/*.sh", "docker", "test", ".flake8"]
+
+[tool.hatch.build.targets.wheel]
+include = [
+    "/ipfx",
+    "AUTHORS.rst",
+    "LICENSE"]
+exclude = ["/ipfx/bin/*.sh", "docs", "docker", "test", ".flake8"]
+
+[tool.pytest.ini_options]
+addopts = "--junitxml=test-reports/test.xml"
+markers = ["slow: slow tests",
+           "requires_lims: require connection to LIMS",
+           "requires_inhouse_data: require inhouse data"]
+filterwarnings = ["error",
+                  "ignore:add_child is deprecated. Set the parent attribute instead.:DeprecationWarning",
+                  "ignore::marshmallow.warnings.RemovedInMarshmallow4Warning",
+                  "ignore::marshmallow.warnings.ChangedInMarshmallow4Warning",
+                  "ignore:scipy.misc is deprecated and will be removed in 2.0.0",
+                  "ignore:.*behaviour will change in pandas 3.0!.*:FutureWarning"]

setup.cfg

@@ -1,8 +1,2 @@
-[bdist_wheel]
-universal = 1
-
 [flake8]
 exclude = docs
-
-[tool:pytest]
-addopts = --junitxml=test-reports/test.xml