updated to use poetry to manage pyproject.toml (#4)

* updated to use poetry to manage pyproject.toml

Incremental fixes throughout:
* updated CI.yaml test location given new folder structure
* packages = [ {include = missense_kinase_toolkit, from=src},] in pyproject.toml
* added [tool.pytest.ini_options] pythonpath = [src] in pyproject.toml
* removed __init__.py from src/missense_kinase_toolkit
* build now only depends on package not datetime due to CI error, include missense_kinase_toolkit in src, and updated requests_cache import in hgnc
* fixed extra format-jinja assignment

.github/workflows/CI.yaml

@@ -54,7 +54,7 @@ jobs:
         # conda setup requires this special shell
         shell: bash -l {0}
         run: |
-          pytest -v --cov=missense_kinase_toolkit --cov-report=xml --color=yes missense_kinase_toolkit/tests/
+          pytest -v --cov=missense_kinase_toolkit --cov-report=xml --color=yes tests/
 
       - name: CodeCov
         uses: codecov/codecov-action@v1

pyproject.toml

@@ -1,91 +1,54 @@
-[build-system]
-requires = ["setuptools>=61.0", "versioningit~=2.0"]
-build-backend = "setuptools.build_meta"
-
-# Self-descriptive entries which should always be present
-# https://packaging.python.org/en/latest/specifications/declaring-project-metadata/
-[project]
-name = "missense_kinase_toolkit"
+[tool.poetry]
+name = "missense-kinase-toolkit"
+# https://github.com/mtkennerly/poetry-dynamic-versioning/issues/14
+version = "0.0.0"
 description = "An ETL pipeline package to facilitate structure-based ML for human kinase property prediction"
-dynamic = ["version"]
+authors = ["Jess White <[email protected]>"]
+license = "MIT"
 readme = "README.md"
-authors = [
-    { name = "Jess White", email = "[email protected]" }
-]
-license = { text = "MIT" }
-# See https://pypi.org/classifiers/
+repository = "https://github.com/choderalab/missense_kinase_toolkit/"
 classifiers = [
     "License :: OSI Approved :: MIT License",
     "Programming Language :: Python :: 3",
 ]
-requires-python = ">=3.9"
-# Declare any run-time dependencies that should be installed with the package.
-dependencies = [
-    "importlib-resources;python_version<='3.11'",
-    "setuptools",
-    "pydantic>=1.10,<2",
-    "tqdm>=4.64.0",
-    "pandas>=2,<3",
-    "requests-cache>=0.9.7,<1",
-    "requests>=2.28.1,<3",
+packages = [
+    {include = "missense_kinase_toolkit", from = "src"},
 ]
 
-# Update the urls once the hosting is set up.
-[project.urls]
-"Source" = "https://github.com/choderalab/missense_kinase_toolkit/"
-#"Documentation" = "https://missense_kinase_toolkit.readthedocs.io/"
+[tool.poetry.dependencies]
+python = "^3.9"
+setuptools = "^69.1.0"
+pydantic = ">=1.10,<2"
+tqdm = "4.64.0"
+pandas = ">=2,<3"
+requests = ">=2.28.1,<3"
+requests-cache = ">=0.9.7,<1"
 
-[project.optional-dependencies]
-test = [
-  "pytest>=6.1.2",
-  "pytest-runner"
-]
 
-[tool.setuptools]
-# This subkey is a beta stage development and keys may change in the future, see https://setuptools.pypa.io/en/latest/userguide/pyproject_config.html for more details
-#
-# As of version 0.971, mypy does not support type checking of installed zipped
-# packages (because it does not actually import the Python packages).
-# We declare the package not-zip-safe so that our type hints are also available
-# when checking client code that uses our (installed) package.
-# Ref:
-# https://mypy.readthedocs.io/en/stable/installed_packages.html?highlight=zip#using-installed-packages-with-mypy-pep-561
-zip-safe = false
-# Let setuptools discover the package in the current directory,
-# but be explicit about non-Python files.
-# See also:
-#   https://setuptools.pypa.io/en/latest/userguide/pyproject_config.html#setuptools-specific-configuration
-# Note that behavior is currently evolving with respect to how to interpret the
-# "data" and "tests" subdirectories. As of setuptools 63, both are automatically
-# included if namespaces is true (default), even if the package is named explicitly
-# (instead of using 'find'). With 'find', the 'tests' subpackage is discovered
-# recursively because of its __init__.py file, but the data subdirectory is excluded
-# with include-package-data = false and namespaces = false.
-include-package-data = false
-[tool.setuptools.packages.find]
-namespaces = false
-where = ["."]
 
-# Ref https://setuptools.pypa.io/en/latest/userguide/datafiles.html#package-data
-[tool.setuptools.package-data]
-missense_kinase_toolkit = [
-    "py.typed"
-]
+[tool.poetry.group.dev.dependencies]
+black = "^24.2.0"
+flake8 = "^7.0.0"
 
-[tool.versioningit]
-default-version = "1+unknown"
 
-[tool.versioningit.format]
-distance = "{base_version}+{distance}.{vcs}{rev}"
-dirty = "{base_version}+{distance}.{vcs}{rev}.dirty"
-distance-dirty = "{base_version}+{distance}.{vcs}{rev}.dirty"
+[tool.poetry.group.test.dependencies]
+pytest = "^8.0.1"
+pytest-runner = "^6.0.1"
 
-[tool.versioningit.vcs]
-# The method key:
-method = "git"  # <- The method name
-# Parameters to pass to the method:
-match = ["*"]
-default-tag = "1.0.0"
+[tool.pytest.ini_options]
+pythonpath = ["src"]
 
-[tool.versioningit.write]
-file = "missense_kinase_toolkit/_version.py"
+[tool.poetry-dynamic-versioning]
+enable = true
+vcs = "git"
+pattern  = "^(?P<base>\\d+\\.\\d+\\.\\d+)(-?((?P<stage>[a-zA-Z]+)\\.?(?P<revision>\\d+)?))?"
+format-jinja = """
+    {%- if distance == 0 -%}
+        {{- base -}}
+    {%- else -%}
+        {{- base }}.dev{{ distance }}+g{{commit}}
+    {%- endif -%}
+"""
+[build-system]
+requires = ["poetry-core>=1.0.0", "poetry-dynamic-versioning>=1.0.0,<2.0.0"]
+build-backend = "poetry_dynamic_versioning.backend"

missense_kinase_toolkit/src/hgnc.py → src/missense_kinase_toolkit/hgnc.py

@@ -2,7 +2,7 @@
 
 import requests
 
-import requests_wrapper
+from missense_kinase_toolkit import requests_wrapper
 
 
 def maybe_get_symbol_from_hgnc_search(