Merge pull request #8 from Ensembl/setup_pyproject

toying with setuptools

.gitignore

@@ -1 +1,4 @@
 **/__pycache__
+**/*.egg-info
+**/pip-wheel-metadata
+**/build

README.md

@@ -8,3 +8,49 @@ A set of ehive pipelines:
 
 The files are in various formats (fasta, gff3, json) following BRC4 specifications.
 
+## Get repo and install
+
+```
+git clone [email protected]:Ensembl/ensembl-genomio.git 
+pip install ./ensembl-genomio
+
+# test
+python -c 'import ensembl.brc4.runnable.read_json'
+```
+
+Update your perl envs (if you need to)
+```
+export PERL5LIB=$(pwd)/ensembl-genomio/lib/perl:$PERL5LIB
+export PATH=$(pwd)/ensembl-genomio/scripts:$PATH
+```
+
+### Optional installation
+If you need to install "editable" python package use '-e' option
+```
+pip install -e ./ensembl-genomio
+```
+
+To install additional dependencies (e.g. `[doc]` or `[dev]`) provide `[<tag>]` string. I.e.
+```
+pip install -e ./ensembl-genomio[dev]
+```
+
+For the list of tags see `[project.optional-dependencies]` in [pyproject.toml](./pyproject.toml). 
+
+### Docs generation
+Install python part with the `[doc]` or `[dev]` tag.
+Change into repo dir
+Run doc build script.
+
+```
+git clone [email protected]:Ensembl/ensembl-genomio.git 
+pip install -e ./ensembl-genomio[doc]
+
+cd ./ensembl-genomio
+
+# build docs
+./scripts/setup/docs/build_sphinx_docs.sh
+```
+
+
+

pyproject.toml

@@ -0,0 +1,95 @@
+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+# pyproject.toml -- Ensembl GenomIO project configuration
+
+[build-system]
+requires = [
+    "setuptools",
+    "setuptools-scm",
+    "wheel"
+]
+build-backend = "setuptools.build_meta"
+
+
+## Generic configuration
+[project]
+name = "ensembl-genomio"
+version = "0.1" # should be assigned dynamically in the future
+requires-python = ">= 3.7"
+
+description = "Ensembl GenomIO -- pipelines to convert basic genomic data into Ensembl cores and back to flatfile"
+readme = "README.md"
+
+authors = [ { name = "Ensembl", email = "[email protected]" } ]
+license = { text = "Apache License 2.0" }
+# for urls see [project.urls] below 
+
+keywords = [
+    "genome_io",
+    "ensembl",
+    "bioinformatics",
+    "annotation",
+    "setup",
+]
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Environment :: Console",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: Apache Software License",
+    "Natural Language :: English",
+    "Programming Language :: Python :: 3 :: Only",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "Topic :: Software Development :: Libraries :: Python Modules",
+]
+
+dependencies = [
+    "bcbio-gff >= 0.6.6",
+    "biopython >= 1.79",
+    "jsonschema >= 4.6.0",
+    "intervaltree >= 3.1.0",
+    "mysql-connector-python >= 8.0.29",
+    "python-redmine >= 2.3.0",
+    "requests >= 2.28.0",
+] # see [project.optional-dependencies] for dev dependencies 
+
+[project.optional-dependencies]
+dev = [
+    "mock",
+    "Sphinx",
+    "toml-validator",
+]
+
+doc = [
+    "mock",
+    "Sphinx",
+]
+
+
+[project.urls]
+homepage = "https://www.ensembl.org"
+repository = "https://github.com/Ensembl/ensembl-genomio"
+
+
+## `setuptools` related section
+[tool.setuptools]
+package-dir = {"" = "lib/python"}
+
+[tool.setuptools.packages.find]
+where = ["lib/python"]  # list of folders that contain the packages (["."] by default)
+
+# For additional information on `setuptools` configuration see
+#    https://setuptools.pypa.io/en/latest/userguide/quickstart.html
+#    https://setuptools.pypa.io/en/latest/userguide/pyproject_config.html
+#    https://packaging.python.org/en/latest/specifications/declaring-project-metadata/

setup.py

@@ -12,44 +12,10 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-"""Build script for setuptools."""
-import sys
+"""setuptools based stub for the "editable" installations"""
 
-from setuptools import setup, find_namespace_packages
+from setuptools import setup
 
-with open('README.md') as f:
-    readme = f.read()
+if __name__ == "__main__":
+    setup()
 
-with open('VERSION') as f:
-    version = f.read()
-
-def import_requirements(requirements_path):
-    """Import file located at the root of the repository."""
-    with open(requirements_path) as file:
-        return [line.rstrip() for line in file.readlines()]
-setup(
-    name='ensembl-genomio',
-    version=version,
-    packages=find_namespace_packages(where='lib/python'),
-    package_dir={"": "lib/python"},
-    description="Ensembl Genome IO",
-    include_package_data=True,
-    install_requires=import_requirements('requirements.txt'),
-    long_description=readme,
-    author='Ensembl',
-    author_email='[email protected]',
-    url='https://www.ensembl.org',
-    download_url='https://github.com/Ensembl/ensembl-genomio',
-    license="Apache License 2.0",
-    python_requires=">=3.7",
-    classifiers=[
-        "Development Status :: 3 - Alpha",
-        "Environment :: Console",
-        "Intended Audience :: Science/Research",
-        "License :: OSI Approved :: Apache Software License",
-        "Natural Language :: English",
-        "Programming Language :: Python :: 3.7",
-        "Topic :: Scientific/Engineering :: Bio-Informatics",
-        "Topic :: Software Development :: Libraries :: Python Modules",
-    ]
-)