Merge pull request #65 from nlesc-nano/rel

REL: Prepare for a flamingo release on pypi

.github/workflows/pypi.yaml

@@ -0,0 +1,34 @@
+name: Publish
+
+on:
+    release:
+        types: [published]
+
+jobs:
+    publish:
+        runs-on: ubuntu-latest
+        steps:
+            -   uses: actions/checkout@v2
+
+            -   name: Set up Python
+                uses: actions/setup-python@v2
+
+            -   name: Install dependencies
+                run: pip install wheel twine
+
+            -   name: Python info
+                run: |
+                    which python
+                    python --version
+
+            -   name: Installed packages
+                run: pip list
+
+            -   name: Build the package
+                run: python setup.py sdist bdist_wheel
+
+            -   name: Publish the package
+                uses: pypa/gh-action-pypi-publish@master
+                with:
+                    user: __token__
+                    password: ${{ secrets.PYPI_TOKEN }}

.github/workflows/pythonpackage.yml

@@ -0,0 +1,66 @@
+name: Tests
+
+on:
+    push:
+        branches:
+            - main
+    pull_request:
+
+jobs:
+    build:
+        name: ${{ matrix.os }} (py ${{ matrix.version }}${{ matrix.special }})
+        runs-on: ${{ matrix.os }}
+        strategy:
+            fail-fast: false
+            matrix:
+                os: [ubuntu-latest, macos-latest]
+                version: ["3.7", "3.8", "3.9"]
+                special: [""]
+                include:
+                    -   os: ubuntu-latest
+                        special: "; pre-release"
+                        version: "3.9"
+        steps:
+            -   name: Cancel Previous Runs
+                uses: styfle/cancel-workflow-action@0.9.1
+                with:
+                    access_token: ${{ github.token }}
+
+            -   uses: actions/checkout@v2
+
+            -   name: Setup Conda
+                uses: s-weigand/setup-conda@v1
+                with:
+                    update-conda: false
+
+            -   name: Install dependencies
+                run: |
+                    conda create -n test -c conda-forge python=${{ matrix.version }} rdkit
+                    source $CONDA/bin/activate test
+                    case "${{ matrix.special }}" in
+                        "; pre-release")
+                            pip install -e .[test,doc] --pre --upgrade --force-reinstall
+                            pip install git+https://github.com/SCM-NV/PLAMS@master --upgrade
+                            ;;
+                        *)
+                            pip install -e .[test,doc] ;;
+                    esac
+
+            -   name: Conda info
+                run: |
+                    source $CONDA/bin/activate test
+                    conda info
+
+            -   name: Installed packages
+                run: conda list -n test
+
+            -   name: Run tests
+                run: |
+                    source $CONDA/bin/activate test
+                    pytest
+
+            -   name: Run codecov
+                uses: codecov/codecov-action@v2
+                with:
+                    file: ./coverage.xml
+                    name: codecov-umbrella

CHANGELOG.rst

@@ -5,19 +5,22 @@ Change Log
 All notable changes to this project will be documented in this file.
 This project adheres to `Semantic Versioning <http://semver.org/>`_.
 
-0.2.2 [Unreleased]
+
+0.3.0 [03/12/2021]
 ******************
+* Release flamingo on pypi (#64)
 * Run all the filters in parallel (#38)
 * Filter molecules with a single functional group (#43)
 * Add interface to cosmo-rs (#5)
-
+
+
 0.2.1 [14/01/2021]
 ******************
 Change
 -----
 * Use all the available CPU to compute bulkiness with CAT by calling the `imap_unordered Pool's method <https://docs.python.org/3/library/multiprocessing.html#multiprocessing.pool.Pool.imap_unordered>`_.
 * Remove the `batch_size` input parameter and fix it to 1000.
-  
+
 
 0.2.0 [03/11/2020]
 ******************

README.rst

@@ -54,7 +54,7 @@ Package installation
 Finally install the package:
 
 - Install **flamingo** using pip:
-  - ``pip install git+https://github.com/nlesc-nano/flamingo.git@master``
+  - ``pip install nlesc-flamingo``
 
 Now you are ready to use *flamingo*.
 

flamingo/__version__.py

@@ -1 +1 @@
-__version__ = "0.2.1"
+__version__ = "0.3.0"

flamingo/log_config.py

@@ -2,26 +2,29 @@
 
 import logging
 import sys
+import importlib
 from pathlib import Path
 
-import pkg_resources
-
 __all__ = ["configure_logger"]
 
 logger = logging.getLogger(__name__)
 
 
 def configure_logger(workdir: Path, package_name: str) -> None:
     """Set the logging infrasctucture."""
+    pkg = sys.modules.get(package_name)
+    if pkg is None:
+        pkg = importlib.import_module(package_name)
+
     file_log = workdir / f'{package_name}_output.log'
     logging.basicConfig(filename=file_log, level=logging.INFO,
                         format='%(asctime)s  %(message)s',
                         datefmt='[%I:%M:%S]')
     handler = logging.StreamHandler()
     handler.terminator = ""
 
-    version = pkg_resources.get_distribution(package_name).version
-    path = pkg_resources.resource_filename(package_name, '')
+    version = getattr(pkg, "__version__", "UNKNOWN")
+    path = Path(pkg.__file__).parent
 
     logger.info(f"Using {package_name} version: {version}\n")
     logger.info(f"{package_name} path is: {path}\n")

setup.cfg

@@ -1,5 +1,6 @@
 [metadata]
-description-file = README.rst
+description_file = README.rst
+license_file = LICENSE
 
 [aliases]
 # Define `python setup.py test`

setup.py

@@ -16,21 +16,20 @@
 
 try:
     importlib.import_module("rdkit")
-    importlib.import_module("h5py")
 except ModuleNotFoundError:
     exc = ModuleNotFoundError(
-        """'flamingo' requires the 'rdkit' package: https://anaconda.org/conda-forge/rdkit
-and the h5py package: https://anaconda.org/conda-forge/h5py"""
+        "'flamingo' requires the 'rdkit' package: https://anaconda.org/conda-forge/rdkit"
     )
     exc.__cause__ = None
     raise exc
 
 
 setup(
-    name='flamingo',
+    name='nlesc-flamingo',
     version=version['__version__'],
     description="Compute and filter molecular properties",
     long_description=README + '\n\n',
+    long_description_content_type='text/x-rst',
     author="Felipe Zapata",
     author_email='f.zapata@esciencecenter.nl',
     url='https://github.com/https://github.com/nlesc-nano/flamingo',
@@ -48,21 +47,34 @@
         'Programming Language :: Python :: 3',
         'Programming Language :: Python :: 3.7',
         'Programming Language :: Python :: 3.8',
+        'Programming Language :: Python :: 3.9',
+        'Typing :: Typed',
     ],
+    python_requires='>=3.7',
     install_requires=[
-        'CAT@git+https://github.com/nlesc-nano/CAT@master',
-        'nano-CAT@git+https://github.com/nlesc-nano/nano-CAT@master',
-        'data-CAT@git+https://github.com/nlesc-nano/data-CAT@master',
-        'more_itertools', 'numpy', 'pandas',
-        'pyyaml>=5.1.1', 'schema', 'typing_extensions'],
+        'nlesc-CAT>=0.10.0',
+        'nano-CAT>=0.7.0',
+        'data-CAT>=0.7.0',
+        'plams>=1.5.1',
+        'more_itertools',
+        'numpy',
+        'pandas',
+        'pyyaml>=5.1.1',
+        'schema!=0.7.5',
+        'typing_extensions',
+        'h5py',
+    ],
     entry_points={
         'console_scripts': [
             'smiles_screener=flamingo.screen:main'
         ]
     },
     package_data={
-        'flamingo': ['data/scscore/full_reaxys_model_1024bool/model.ckpt-10654.as_numpy.json.gz',
-        'data/scscore/full_reaxys_model_2048bool/model.ckpt-10654.as_numpy.json.gz']
+        'flamingo': [
+            'data/scscore/full_reaxys_model_1024bool/model.ckpt-10654.as_numpy.json.gz',
+            'data/scscore/full_reaxys_model_2048bool/model.ckpt-10654.as_numpy.json.gz',
+            'py.typed',
+        ]
     },
     data_files=[('citation/flamingo', ['CITATION.cff'])],
     extras_require={