Add poetry dynamic versioning and update release process (#132)

* add version detection utility

* manage semver with poetry-dynamic-versioning

* comments to further describe what's happening

* update github actions workflows and simplify

* remove version util and lint

* update pre-commit check versions

* add docs on semver for release publishing process

* move setup-poetry appropriately

* correct action location

.github/actions/setup-poetry/action.yml

@@ -0,0 +1,11 @@
+name: Setup Environment and Cache
+description: |
+  Setup poetry for use with GitHub Actions workflows.
+  Note: presumes pre-installed Python.
+runs:
+  using: "composite"
+  steps:
+    - name: Setup poetry and poetry-dynamic-versioning
+      shell: bash
+      run: |
+        python -m pip install poetry poetry-dynamic-versioning

.github/workflows/publish-docs.yml

@@ -19,10 +19,8 @@ jobs:
       - uses: actions/setup-python@v4
         with:
           python-version: "3.10"
-      - name: install poetry
-        uses: abatilo/actions-poetry@v2
-        with:
-          poetry-version: "1.6.1"
+      - name: Setup for poetry
+        uses: ./.github/actions/setup-poetry
       - name: poetry deps
         run: poetry install
       - name: Build documentation

.github/workflows/publish-pypi.yml

@@ -22,10 +22,8 @@ jobs:
       - uses: actions/setup-python@v4
         with:
           python-version: "3.10"
-      - name: install poetry
-        uses: abatilo/actions-poetry@v2
-        with:
-          poetry-version: "1.6.1"
+      - name: Setup for poetry
+        uses: ./.github/actions/setup-poetry
       - name: poetry deps
         run: poetry install
       - name: poetry build distribution content

.github/workflows/test.yml

@@ -24,8 +24,8 @@ jobs:
         uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python_version }}
-      - name: Install poetry
-        run: pip install poetry
+      - name: Setup for poetry
+        uses: ./.github/actions/setup-poetry
       - name: Install environment
         run: poetry install --no-interaction --no-ansi
       - name: Run sphinx-docs build test

.pre-commit-config.yaml

@@ -4,15 +4,15 @@ default_language_version:
   python: python3.10
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.5.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
       - id: check-yaml
       - id: check-added-large-files
       - id: check-toml
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.5
+    rev: v2.2.6
     hooks:
       - id: codespell
         exclude: >
@@ -29,37 +29,37 @@ repos:
           - mdformat-myst
           - mdformat-gfm
   - repo: https://github.com/adrienverge/yamllint
-    rev: v1.32.0
+    rev: v1.33.0
     hooks:
       - id: yamllint
   - repo: https://github.com/psf/black
-    rev: 23.9.1
+    rev: 23.12.0
     hooks:
       - id: black
   - repo: https://github.com/asottile/blacken-docs
     rev: 1.16.0
     hooks:
       - id: blacken-docs
   - repo: https://github.com/PyCQA/bandit
-    rev: 1.7.5
+    rev: 1.7.6
     hooks:
       - id: bandit
         args: ["-c", "pyproject.toml"]
         additional_dependencies: ["bandit[toml]"]
   - repo: https://github.com/PyCQA/isort
-    rev: 5.12.0
+    rev: 5.13.2
     hooks:
       - id: isort
   - repo: https://github.com/jendrikseipp/vulture
-    rev: v2.9.1
+    rev: v2.10
     hooks:
       - id: vulture
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.5.1
+    rev: v1.7.1
     hooks:
       - id: mypy
   - repo: https://github.com/PyCQA/pylint
-    rev: v3.0.0a7
+    rev: v3.0.3
     hooks:
       - id: pylint
         name: pylint

cytotable/__init__.py

@@ -1,6 +1,10 @@
 """
 __init__.py for cytotable
 """
+
+# note: version data is maintained by poetry-dynamic-versioning
+__version__ = "0.0.0"
+
 from .convert import convert
 from .exceptions import (
     CytoTableException,

docs/source/contributing.md

@@ -180,13 +180,16 @@ We utilize [semantic versioning](https://en.wikipedia.org/wiki/Software_versioni
 We publish source code by using [GitHub Releases](https://docs.github.com/en/repositories/releasing-projects-on-github/about-releases) available [here](https://github.com/cytomining/CytoTable/releases).
 We publish Python packages through the [Python Packaging Index (PyPI)](https://pypi.org/) available [here](https://pypi.org/project/cytotable/).
 
-### Publishing Process
+### Release Publishing Process
 
 There are several manual and automated steps involved with publishing CytoTable releases.
 See below for an overview of how this works.
 
-1. Prepare a release in a code contribution which utilizes the command [`poetry version ...`](https://python-poetry.org/docs/cli/#version) to update the version (this updates `pyproject.toml` with automatically incremented versions under `version = "..."`).
+Notes about [semantic version](https://en.wikipedia.org/wiki/Software_versioning#Semantic_versioning) (semver) specifications:
+CytoTable semvers are controlled through [`poetry-dynamic-versioning`](https://github.com/mtkennerly/poetry-dynamic-versioning) which leverages [`dunamai`](https://github.com/mtkennerly/dunamai) to create version data based on [git tags](https://git-scm.com/book/en/v2/Git-Basics-Tagging) and and commits.
+CytoTable release git tags are automatically applied through [GitHub Releases](https://docs.github.com/en/repositories/releasing-projects-on-github/about-releases) and related inferred changes from [`release-drafter`](https://github.com/release-drafter/release-drafter).
+
 1. Open a pull request and use a repository label for `release-<semver release type>` to label the pull request for visibility with [`release-drafter`](https://github.com/release-drafter/release-drafter) (for example, see [CytoTable#108](https://github.com/cytomining/CytoTable/pull/108) as a reference of a semver patch update).
-1. On merging the pull request for the release, a [GitHub Actions workflow](https://docs.github.com/en/actions/using-workflows) defined in `draft-release.yml` leveraging [`release-drafter`](https://github.com/release-drafter/release-drafter) will draft a release for maintainers to modify.
+1. On merging the pull request for the release, a [GitHub Actions workflow](https://docs.github.com/en/actions/using-workflows) defined in `draft-release.yml` leveraging [`release-drafter`](https://github.com/release-drafter/release-drafter) will draft a release for maintainers to modify as needed (double checking on the prepared git tag and content).
 1. Make modifications as necessary to the draft GitHub release, then publish the release.
 1. On publishing the release, another GitHub Actions workflow defined in `publish-pypi.yml` will run to build and deploy the Python package to PyPI (utilizing the earlier modified `pyproject.toml` semantic version reference for labeling the release).

pyproject.toml

@@ -1,6 +1,7 @@
 [tool.poetry]
 name = "CytoTable"
-version = "0.0.3"
+# note: version data is maintained by poetry-dynamic-versioning
+version = "0.0.0"
 description = "Transform CellProfiler and DeepProfiler data for processing image-based profiling readouts with Pycytominer and other Cytomining tools."
 authors = ["Cytomining Community"]
 license = "BSD-3-Clause License"
@@ -10,12 +11,22 @@ repository = "https://github.com/cytomining/CytoTable"
 documentation = "https://cytomining.github.io/CytoTable/"
 keywords = ["python", "cellprofiler","single-cell-analysis", "way-lab"]
 
+[tool.poetry-dynamic-versioning]
+enable = true
+style = "pep440"
+vcs = "git"
+
+[build-system]
+requires = ["poetry-core>=1.0.0", "poetry-dynamic-versioning>=1.0.0,<2.0.0"]
+build-backend = "poetry_dynamic_versioning.backend"
+
 [tool.poetry.dependencies]
 python = ">=3.8,<3.13"
 pyarrow = ">=13.0.0"
 cloudpathlib = {extras = ["all"], version = "^0.15.0"}
 duckdb = ">=0.8.0"
 parsl = ">=2023.9.25"
+dunamai = "^1.19.0"
 
 [tool.poetry.dev-dependencies]
 pytest = "^7.4.0"
@@ -28,9 +39,7 @@ cffconvert = "^2.0.0"
 cytominer-database = "^0.3.4"
 pycytominer = { git = "https://github.com/cytomining/pycytominer.git", rev = "09b2c79aa94908e3520f0931a844db4fba7fd3fb" }
 
-[build-system]
-requires = ["poetry-core"]
-build-backend = "poetry.core.masonry.api"
+
 
 [tool.vulture]
 min_confidence = 80