[WIP] Moving to pyproject.toml Based Packaging (#280)

* Adding option to disable Numba during tests to run code as pure Python to get coverage information

* Add check for correctly raised warning

* Update to unitest job name

* Fix

* Adding journal test back

Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>

* Install problem fix

* Install problem fix

* Moving to toml based packaging

* Better versioning

* Fix

* Fix

* Fix

* Tweaking action

* Tweaking action

* Tweak

.github/workflows/python-app.yml

@@ -27,7 +27,7 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install flake8 coverage
-        pip install -r requirements.txt
+        pip install -e .
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names

.github/workflows/python-build.yml

@@ -30,11 +30,6 @@ jobs:
       uses: actions/setup-python@v2
       with:
         python-version: '3.7'
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install flake8 wheel twine
-        pip install -r requirements.txt
     - if: runner.os == 'Linux'
       name: Set up GCC
       uses: egor-tensin/setup-gcc@v1
@@ -46,17 +41,23 @@ jobs:
       uses: egor-tensin/setup-mingw@v2
       with:
        platform: x64
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install flake8 wheel twine
     - name: Build package
-      run: python setup.py bdist_wheel
+      run: |
+        pip install -e .
+        pip wheel .
     - if: github.event_name == 'push' || github.event_name == 'pull_request'
       name: Test publish package
       run: |
-        python3 -m twine check dist/*
+        python3 -m twine check exetera-*.whl
 
     - if: github.event_name == 'release'
       name: Publish package on release
       run: |
-        python3 -m twine upload dist/*
-        env:
-          TWINE_USERNAME: __token__
-          TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}
+        python3 -m twine upload exetera-*.whl
+      env:
+        TWINE_USERNAME: __token__
+        TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}

README.md

@@ -23,29 +23,27 @@ format more suited to performing analytics. This is done through `exetera import
 
 
 ### `exetera import`
+
 ```
-exetera import
--s path/to/covid_schema.json \
--i "patients:path/to/patient_data.csv, assessments:path/to/assessmentdata.csv, tests:path/to/covid_test_data.csv, diet:path/to/diet_study_data.csv" \
--o /path/to/output_dataset_name.hdf5
---include "patients:(id,country_code,blood_group), assessments:(id,patient_id,chest_pain)"
---exclude "tests:(country_code)"
+exetera import \
+  -s path/to/covid_schema.json \
+  -i "patients:path/to/patient_data.csv, assessments:path/to/assessmentdata.csv, tests:path/to/covid_test_data.csv, diet:path/to/diet_study_data.csv" \
+  -o /path/to/output_dataset_name.hdf5 \
+  --include "patients:(id,country_code,blood_group), assessments:(id,patient_id,chest_pain)" \
+  --exclude "tests:(country_code)"
 ```
 
 
 #### Arguments
  * `-s/--schema`: The location and name of the schema file
- * `-te/--territories`: If set, this only imports the listed territories. If left unset, all
-   territories are imported
- * `-i/--inputs` : A comma separated list of 'name:file' pairs. This should be put in parentheses if it contains any
-  whitespace. See the example above.
+ * `-te/--territories`: If set, this only imports the listed territories. If left unset, all territories are imported
+ * `-i/--inputs` : A comma separated list of 'name:file' pairs. This should be put in parentheses if it contains any whitespace. See the example above.
  * `-o/--output_hdf5`: The path and name to where the resulting hdf5 dataset should be written
- * `-ts/--timestamp`: An override for the timestamp to be written
-   (defaults to `datetime.now(timezone.utc)`)
+ * `-ts/--timestamp`: An override for the timestamp to be written (defaults to `datetime.now(timezone.utc)`)
  * `-w/--overwrite`: If set, overwrite any existing dataset with the same name; appends to existing dataset otherwise
  * `-n/--include`: If set, filters out all fields apart from those in the list.
  * `-x/--exclude`: If set, filters out the fields in this list.
- 
+
 Expect this script to take about an hour or more to execute on very large datasets.
 
 

exetera/_version.py

@@ -1,2 +1,2 @@
 
-__version__ = '0.6.0b'
+__version__ = '0.6.0b5'

pyproject.toml

@@ -1,9 +1,29 @@
 
 [build-system]
-requires = ["setuptools<61.0.0", "wheel"]
+requires = ["setuptools>=61", "wheel"]
 build-backend = "setuptools.build_meta"
 
 [project]
-name = "ExeTera"
-
+name = "exetera"
+description = "High-volume key-value store and analytics, based on hdf5"
+license = {file = "LICENSE.txt"}
 dependencies = ["numpy", "pandas", "h5py", "numba", "parameterized"]
+requires-python = ">=3.7"
+authors = [{ name = "Ben Murray", email = "benjamin.murray@kcl.ac.uk" }]
+dynamic = ["version", "readme"]
+
+[project.urls]
+homepage = "https://github.com/kcl-bmeis/ExeTera"
+
+[project.scripts]
+exetera = "exetera.bin.exetera:main"
+
+[tool.setuptools.packages.find]
+include = ["exetera*"]
+
+[tool.setuptools.dynamic]
+version = {attr = "exetera._version.__version__"}
+readme = {file = ["README.md"], content-type = "text/markdown"}
+
+[metadata]
+description-file = "README.md"

setup.py

@@ -1,36 +1,5 @@
-from setuptools import setup, find_packages
-from pkg_resources import parse_requirements
-#from Cython.Build import cythonize
 
-from os import path
-this_directory = path.abspath(path.dirname(__file__))
-with open(path.join(this_directory, 'README.md'), encoding='utf-8') as f:
-    long_description = f.read()
+from setuptools import setup
 
-# read the version and other strings from _version.py
-with open(path.join(this_directory, "exetera", "_version.py")) as o:
-    exec(o.read())
-
-# read install requirements from requirements.txt
-with open(path.join(this_directory, "requirements.txt")) as o:
-    requirements = [str(r) for r in parse_requirements(o.read())]
-
-#pyxfiles = ['ops.pyx']
-#pyx_full_path = [path.join(this_directory, 'exetera', '_libs', pyx) for pyx in pyxfiles]
-
-setup(
-    name='exetera',
-    version=__version__,
-    description='High-volume key-value store and analytics, based on hdf5',
-    long_description=long_description,
-    long_description_content_type = "text/markdown",
-    url='https://github.com/kcl-bmeis/ExeTera',
-    author='Ben Murray',
-    author_email='benjamin.murray@kcl.ac.uk',
-    license='http://www.apache.org/licenses/LICENSE-2.0',
-    packages=find_packages(),
-    scripts=['exetera/bin/exetera'],
-    #ext_modules = cythonize(pyx_full_path),
-    python_requires='>=3.7',
-    install_requires=requirements
-)
+if __name__ == "__main__":
+    setup()