diff --git a/.github/workflows/CI.yaml b/.github/workflows/CI.yaml index ec93169..33c3381 100644 --- a/.github/workflows/CI.yaml +++ b/.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 diff --git a/missense_kinase_toolkit/data/README.md b/data/README.md similarity index 100% rename from missense_kinase_toolkit/data/README.md rename to data/README.md diff --git a/missense_kinase_toolkit/__init__.py b/missense_kinase_toolkit/__init__.py deleted file mode 100644 index e3a1673..0000000 --- a/missense_kinase_toolkit/__init__.py +++ /dev/null @@ -1,7 +0,0 @@ -"""An ETL pipeline package to facilitate structure-based ML for human kinase property prediction""" - -# Add imports here -from 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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 "] +license = "MIT" readme = "README.md" -authors = [ - { name = "Jess White", email = "jessica.white@choderalab.org" } -] -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\\d+\\.\\d+\\.\\d+)(-?((?P[a-zA-Z]+)\\.?(?P\\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" diff --git a/missense_kinase_toolkit/src/hgnc.py b/src/missense_kinase_toolkit/hgnc.py similarity index 98% rename from missense_kinase_toolkit/src/hgnc.py rename to src/missense_kinase_toolkit/hgnc.py index a01b7af..101e469 100644 --- a/missense_kinase_toolkit/src/hgnc.py +++ b/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( diff --git a/missense_kinase_toolkit/py.typed b/src/missense_kinase_toolkit/py.typed similarity index 100% rename from missense_kinase_toolkit/py.typed rename to src/missense_kinase_toolkit/py.typed diff --git a/missense_kinase_toolkit/src/requests_wrapper.py b/src/missense_kinase_toolkit/requests_wrapper.py similarity index 100% rename from missense_kinase_toolkit/src/requests_wrapper.py rename to src/missense_kinase_toolkit/requests_wrapper.py diff --git a/missense_kinase_toolkit/tests/__init__.py b/tests/__init__.py similarity index 100% rename from missense_kinase_toolkit/tests/__init__.py rename to tests/__init__.py diff --git a/missense_kinase_toolkit/tests/test_missense_kinase_toolkit.py b/tests/test_missense_kinase_toolkit.py similarity index 100% rename from missense_kinase_toolkit/tests/test_missense_kinase_toolkit.py rename to tests/test_missense_kinase_toolkit.py