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kfrey-idmkfrey-idm
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Update PyPI workflows (#149)
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9 files changed

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‎.github/workflows/build_publish_hiv.yml‎

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uses: actions/setup-python@v5
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with:
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python-version: "3.x"
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- name: Download executable
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uses: actions/download-artifact@v5
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with:
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name: Eradication
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path: pypi_hiv/src/eradication_dir
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- name: Download schema
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uses: actions/download-artifact@v5
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with:
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name: schema.json
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path: pypi_hiv/src/schema_dir
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- name: Download version
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uses: actions/download-artifact@v5
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with:
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name: version
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path: pypi_hiv/src/version_dir
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- name: Prep files
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run: |
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cd pypi_hiv
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cd src
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mv version_dir/version version
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zip -j emod_hiv/Eradication.zip eradication_dir/Eradication
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zip -j emod_hiv/schema.zip schema_dir/schema.json
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rm -r version_dir
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rm -r eradication_dir
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rm -r schema_dir
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- name: Build PyPI distribution
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run: |
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python3 -m pip install build
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cd pypi_hiv
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python3 -m build
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- name: Upload files to PyPI
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uses: pypa/gh-action-pypi-publish@release/v1
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with:
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verbose: true
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packages-dir: pypi_hiv/dist

‎.github/workflows/build_publish_malaria.yml‎

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uses: actions/setup-python@v5
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with:
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python-version: "3.x"
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- name: Download executable
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uses: actions/download-artifact@v5
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with:
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name: Eradication
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path: pypi_malaria/src/eradication_dir
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- name: Download schema
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uses: actions/download-artifact@v5
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with:
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name: schema.json
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path: pypi_malaria/src/schema_dir
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- name: Download version
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uses: actions/download-artifact@v5
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with:
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name: version
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path: pypi_malaria/src/version_dir
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- name: Prep files
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run: |
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cd pypi_malaria
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cd src
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mv version_dir/version version
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zip -j emod_malaria/Eradication.zip eradication_dir/Eradication
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zip -j emod_malaria/schema.zip schema_dir/schema.json
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rm -r version_dir
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rm -r eradication_dir
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rm -r schema_dir
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- name: Build PyPI distribution
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run: |
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python3 -m pip install build
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cd pypi_malaria
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python3 -m build
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- name: Upload files to PyPI
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uses: pypa/gh-action-pypi-publish@release/v1
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with:
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verbose: true
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packages-dir: pypi_malaria/dist

‎pypi_common/pyproject.toml‎

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@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
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[project]
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name = "emod-common"
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dynamic = ["version"]
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description = "PyPI distribution of EMOD files for testing common to all sim types"
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description = "PyPI distribution of EMOD for testing features common to all sim types"
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license = "MIT"
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authors = [
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]

‎pypi_hiv/pyproject.toml‎

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[build-system]
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requires = ["setuptools"]
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build-backend = "setuptools.build_meta"
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[project]
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name = "emod-hiv"
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dynamic = ["version"]
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description = "PyPI distribution of EMOD for the HIV sim type"
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license = "MIT"
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authors = [
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]
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readme = "README.md"
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requires-python = ">=3.9"
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dependencies = [
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]
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classifiers = [
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"Operating System :: POSIX :: Linux",
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"Programming Language :: C++",
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"Topic :: Scientific/Engineering :: Bio-Informatics",
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]
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[project.optional-dependencies]
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docs = [
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]
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tests = [
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]
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[project.urls]
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Documentation = "https://docs.idmod.org/projects/emod/en/latest/"
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Repository = "https://github.com/EMOD-Hub/EMOD"
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Issues = "https://github.com/EMOD-Hub/EMOD/issues"
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[tool.setuptools.package-data]
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"*" = ["*.zip"]
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[tool.setuptools.dynamic]
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version = {file = ["src/version"]}

‎pypi_hiv/src/emod_hiv/__init__.py‎

Whitespace-only changes.

‎pypi_hiv/src/emod_hiv/bootstrap.py‎

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import os
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import sys
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import shutil
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import zipfile
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from glob import glob
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def extract(package_name, local_dir):
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os.makedirs(local_dir, exist_ok=True)
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os.chdir(local_dir)
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pkgdir = sys.modules[package_name].__path__[0]
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# extract all *.zip files in the package, preserve relative file paths
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for fullpath in glob(os.path.join(pkgdir, "**/*.zip"), recursive=True):
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# determine zip relative filepath
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rel_filepath = os.path.relpath(fullpath, pkgdir)
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rel_dir = os.path.dirname(rel_filepath)
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if rel_dir and len(rel_dir) > 0:
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os.makedirs(rel_dir, exist_ok=True)
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# copy archive under current dir
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temp_zip_path = os.path.join(os.getcwd(), rel_filepath)
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shutil.copy(fullpath, temp_zip_path)
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with zipfile.ZipFile(rel_filepath, 'r') as zip_ref:
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zip_ref.extractall(rel_dir)
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os.unlink(temp_zip_path)
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os.chdir("..")
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def setup(local_dir="stash"):
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"""
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Extract binary and schema into a local directory.
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"""
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extract('emod_hiv', local_dir)
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if __name__ == "__main__":
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setup()

‎pypi_malaria/pyproject.toml‎

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[build-system]
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requires = ["setuptools"]
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build-backend = "setuptools.build_meta"
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[project]
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name = "emod-malaria"
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dynamic = ["version"]
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description = "PyPI distribution of EMOD for the Malaria sim type"
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license = "MIT"
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authors = [
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]
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readme = "README.md"
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requires-python = ">=3.9"
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dependencies = [
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]
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classifiers = [
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"Operating System :: POSIX :: Linux",
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"Programming Language :: C++",
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"Topic :: Scientific/Engineering :: Bio-Informatics",
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]
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[project.optional-dependencies]
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docs = [
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]
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tests = [
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]
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[project.urls]
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Documentation = "https://docs.idmod.org/projects/emod/en/latest/"
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Repository = "https://github.com/EMOD-Hub/EMOD"
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Issues = "https://github.com/EMOD-Hub/EMOD/issues"
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[tool.setuptools.package-data]
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"*" = ["*.zip"]
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[tool.setuptools.dynamic]
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version = {file = ["src/version"]}

‎pypi_malaria/src/emod_malaria/__init__.py‎

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‎pypi_malaria/src/emod_malaria/bootstrap.py‎

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import os
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import sys
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import shutil
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import zipfile
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from glob import glob
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def extract(package_name, local_dir):
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os.makedirs(local_dir, exist_ok=True)
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os.chdir(local_dir)
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pkgdir = sys.modules[package_name].__path__[0]
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# extract all *.zip files in the package, preserve relative file paths
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for fullpath in glob(os.path.join(pkgdir, "**/*.zip"), recursive=True):
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# determine zip relative filepath
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rel_filepath = os.path.relpath(fullpath, pkgdir)
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rel_dir = os.path.dirname(rel_filepath)
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if rel_dir and len(rel_dir) > 0:
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os.makedirs(rel_dir, exist_ok=True)
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# copy archive under current dir
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temp_zip_path = os.path.join(os.getcwd(), rel_filepath)
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shutil.copy(fullpath, temp_zip_path)
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with zipfile.ZipFile(rel_filepath, 'r') as zip_ref:
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zip_ref.extractall(rel_dir)
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os.unlink(temp_zip_path)
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os.chdir("..")
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def setup(local_dir="stash"):
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"""
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Extract binary and schema into a local directory.
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"""
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extract('emod_malaria', local_dir)
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if __name__ == "__main__":
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setup()

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