Add python package (#167)

yannikschaelte · web-flow · commit 797845b8b2cb · 2022-08-16T15:25:12.000+02:00
* add python package

* add unit test

* fix typo

* fix dir

* restrict to push

* address comments from code review

* fixi

* add test

* remove deploy; use full paths

* add install.md

* why does ci fail

* fix intention

* fix sth

* fixup

* Update INSTALL.md
diff --git a/.github/workflows/python.yml b/.github/workflows/python.yml
@@ -0,0 +1,55 @@
+name: Python CI
+
+# trigger
+on: [push]
+
+jobs:
+  base:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.10']
+
+    steps:
+    - name: Check out repository
+      uses: actions/checkout@v2
+
+    - name: Prepare python ${{ matrix.python-version }}
+      uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Run tests from editable install
+      run: |
+        cd src/python
+        pip install --upgrade pip
+        pip install -e .
+        pip install pytest
+        pytest test
+    
+    - name: Run tests from sdist install
+      run: |
+        cd src/python
+        ./build.sh
+        pip install pytest
+        pytest test
+
+  lint:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.10']
+
+    steps:
+    - name: Check out repository
+      uses: actions/checkout@v2
+
+    - name: Prepare python ${{ matrix.python-version }}
+      uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Run pre-commit hooks
+      run: |
+        pip install pre-commit
+        pre-commit run --all-files
diff --git a/.gitignore b/.gitignore
@@ -2,3 +2,5 @@
 *.DS_store
 ~$*
 __pycache__
+*egg-info
+src/python/build
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -0,0 +1,18 @@
+files: src/python
+repos:
+- repo: https://github.com/psf/black
+  rev: 22.3.0
+  hooks:
+  - id: black
+    description: The uncompromising code formatter
+- repo: https://github.com/pycqa/isort
+  rev: 5.10.1
+  hooks:
+  - id: isort
+    name: isort
+- repo: https://github.com/pycqa/flake8
+  rev: 5.0.4
+  additional_dependencies: [flake8-docstrings]
+  hooks:
+  - id: flake8
+    args: [--config, src/python/setup.cfg]
diff --git a/INSTALL.md b/INSTALL.md
@@ -0,0 +1,56 @@
+# Install
+
+There are various ways of installing or downloading the benchmark models:
+
+## Git clone
+
+The repository containing the benchmark models can be cloned from GitHub via:
+
+    git clone git@github.com:Benchmarking-Initiative/Benchmark-Models-PEtab.git
+
+## Download source files
+
+The Benchmark files can be downloaded from GitHub as a
+[ZIP file](https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab/archive/refs/heads/master.zip).
+
+## Python package
+
+We provide a Python utility package that simplifies the installation and
+provides access functionality at [src/python](src/python).
+
+It can be installed directly from GitHub via:
+
+    pip install git+https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab.git@master#subdirectory=src/python
+
+Alternatively, when the whole repository has been cloned (see above),
+the python package can be installed via
+
+    cd src/python
+
+followed by either an in-place develop mode installation:
+
+    pip install -e .
+
+or a packaged installation:
+
+    ./build.sh
+    pip install build/dist/*
+
+Note that when the repository models are updated, also the python package needs
+to be updated, as it does not actively synchronize.
+
+Once installed, the python package can be used via:
+
+```python
+import benchmark_models_petab as models
+   
+# print models base folder
+print(models.MODELS_DIR)
+# print all model names
+print(models.MODELS)
+# generate petab problem
+petab_problem = models.get_problem("Zheng_PNAS2012")
+```
+    
+For provided functionality, see the
+[source code documentation](src/python/benchmark_models_petab).
diff --git a/README.md b/README.md
@@ -43,3 +43,7 @@ Contributions to the collection are very welcome. For this, please create a new
 Any original content in this repository may be used under the terms of the [BSD-3-Clause license](LICENSE).
 Different terms may apply to models and datasets, for which we refer the user to the original publications
 that are referenced in the respective SBML files.
+
+## Installation
+
+See [INSTALL.md](INSTALL.md).
diff --git a/src/python/LICENSE b/src/python/LICENSE
@@ -0,0 +1 @@
+../../LICENSE
diff --git a/src/python/MANIFEST.in b/src/python/MANIFEST.in
@@ -0,0 +1 @@
+include benchmark_models_petab/Benchmark-Models/*/*
diff --git a/src/python/README.md b/src/python/README.md
@@ -0,0 +1 @@
+../../README.md
diff --git a/src/python/benchmark_models_petab/Benchmark-Models b/src/python/benchmark_models_petab/Benchmark-Models
@@ -0,0 +1 @@
+../../../Benchmark-Models
diff --git a/src/python/benchmark_models_petab/C.py b/src/python/benchmark_models_petab/C.py
@@ -0,0 +1,10 @@
+"""Constants."""
+
+import os
+from typing import List
+
+BASE_DIR: str = os.path.abspath(os.path.dirname(__file__))
+MODELS_DIR: str = os.path.join(BASE_DIR, "Benchmark-Models")
+
+MODELS: List[str] = os.listdir(MODELS_DIR)
+MODEL_DIRS: List[str] = [os.path.join(MODELS_DIR, d) for d in MODELS]
diff --git a/src/python/benchmark_models_petab/__init__.py b/src/python/benchmark_models_petab/__init__.py
@@ -0,0 +1,11 @@
+"""
+Benchmark Models PEtab
+======================
+
+Python tool to access the model collection.
+
+"""
+
+from .base import get_problem
+from .C import MODEL_DIRS, MODELS, MODELS_DIR
+from .version import __version__
diff --git a/src/python/benchmark_models_petab/base.py b/src/python/benchmark_models_petab/base.py
@@ -0,0 +1,23 @@
+"""Get a petab problem from the collection."""
+
+import os
+
+import petab
+
+from .C import MODELS_DIR
+
+
+def get_problem(id_: str) -> petab.Problem:
+    """Read PEtab problem from benchmark collection by name.
+
+    Parameters
+    ----------
+    id_: Problem name, as in `benchmark_models_petab.MODELS`.
+
+    Returns
+    -------
+    The PEtab problem.
+    """
+    yaml_file = os.path.join(MODELS_DIR, id_, id_ + ".yaml")
+    petab_problem = petab.Problem.from_yaml(yaml_file)
+    return petab_problem
diff --git a/src/python/benchmark_models_petab/version.py b/src/python/benchmark_models_petab/version.py
@@ -0,0 +1,3 @@
+"""Version."""
+
+__version__ = "0.0.0a1"
diff --git a/src/python/build.sh b/src/python/build.sh
@@ -0,0 +1,40 @@
+# Build library as source distribution with included model files
+
+# Either, call `./build.sh` followed by `pip install build/dist/*`
+# Or directly install from source via `pip install -e .`
+
+# Get script directory
+DIR="$(dirname "${BASH_SOURCE[0]}")"
+DIR="$(realpath "$DIR")"
+
+# Hop into
+cd $DIR
+
+BUILD_DIR="build"
+CODE_DIR="benchmark_models_petab"
+DATA_DIR="Benchmark-Models"
+
+# Create build folder
+if [ -e $BUILD_DIR ]; then
+    echo "Remove build folder $BUILD_DIR"
+    exit 1
+fi
+mkdir $BUILD_DIR
+
+# Copy code
+cp -r \
+  $CODE_DIR \
+  "setup.cfg" "setup.py" "pyproject.toml" "MANIFEST.in" \
+  "../../LICENSE" "../../README.md" \
+  $BUILD_DIR
+# Remove link
+rm -rf $BUILD_DIR/$CODE_DIR/$DATA_DIR
+# Copy data
+cp -r "../../$DATA_DIR" $BUILD_DIR/$CODE_DIR
+
+# Hop into
+cd $BUILD_DIR
+
+# Build
+pip install --upgrade build
+python -m build --sdist
diff --git a/src/python/pyproject.toml b/src/python/pyproject.toml
@@ -0,0 +1,14 @@
+[build-system]
+requires = [
+    "setuptools",
+    "wheel",
+]
+build-backend = "setuptools.build_meta"
+
+[tool.black]
+line-length = 79
+
+[tool.isort]
+profile = "black"
+line_length = 79
+multi_line_output = 3
diff --git a/src/python/setup.cfg b/src/python/setup.cfg
@@ -0,0 +1,29 @@
+# Benchmark-Models-PEtab python package."""
+
+[metadata]
+name = benchmark_models_petab
+version = attr: benchmark_models_petab.version.__version__
+description = "A collection of models with experimental data in the PEtab format"
+long_description = file: README.md
+long_description_content_type = text/markdown
+url = "https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab"
+
+author = "The Benchmark-Models-PEtab maintainers"
+author_email = "yannik.schaelte@gmail.com"
+
+license = BSD-3-Clause
+license_file = LICENSE
+
+[options]
+install_requires =
+    petab >= 0.1.28
+
+python_requires = >= 3.8
+zip_safe = False
+include_package_data = True
+
+packages = find:
+
+[flake8]
+per-file-ignores =
+    */__init__.py:F401
diff --git a/src/python/setup.py b/src/python/setup.py
@@ -0,0 +1,5 @@
+"""Setup.py required for editable install."""
+
+import setuptools
+
+setuptools.setup()
diff --git a/src/python/test/test_base.py b/src/python/test/test_base.py
@@ -0,0 +1,16 @@
+"""Basic tests."""
+
+import benchmark_models_petab as models
+
+
+def test_constants():
+    """Assert that constant values can be evaluated."""
+    assert models.MODELS_DIR
+    assert models.MODELS
+    assert models.MODEL_DIRS
+
+
+def test_get_problem():
+    """Test whether extracting a petab problem works."""
+    problem = models.get_problem(models.MODELS[0])
+    assert problem.measurement_df is not None

Original file line number	Diff line number	Diff line change
`@@ -0,0 +1 @@`
	`1`	`+include benchmark_models_petab/Benchmark-Models//`