fix: restructure package

BenTenmann · Dec 1, 2021 · 1e87d25 · 1e87d25
1 parent 62318e8
commit 1e87d25
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Showing 16 changed files with 11 additions and 9 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -15,7 +15,7 @@ jobs:
           name: install dependencies
           command: |
             python -m pip install -r requirements.txt
-            python -m pip install -e .
+            python -m pip install .
       - save_cache:
           paths:
             - ~/.cache/pip
@@ -24,7 +24,7 @@ jobs:
       - run:
           name: run unit tests
           command: |
-            python -m pytest -v tests --cov=${CIRCLE_REPO_NAME/-/_}
+            python -m pytest -v tests --cov=${CIRCLE_REPONAME/-/_}
 
 workflows:
   version: 2

diff --git a/setup.py b/setup.py
@@ -13,7 +13,7 @@
 import traceback
 from glob import glob
 
-from pybind11.setup_helpers import Pybind11Extension
+from pybind11.setup_helpers import ParallelCompile, Pybind11Extension
 from setuptools import setup, find_packages
 
 logging.basicConfig(
@@ -35,12 +35,14 @@
     logging.warning(f'Unable to get semantic release version. Setting version to {__version__}.')
 
 PROJECT_NAME = 'setriq'
-SOURCE_DIR = 'setriq'
+SOURCE_DIR = 'src'
+
+ParallelCompile("NPY_NUM_BUILD_JOBS").install()
 
 extensions = [
     Pybind11Extension(
         f'{PROJECT_NAME}._C',
-        sources=sorted(glob(f'{SOURCE_DIR}/_C/**/*.cpp', recursive=True)),
+        sources=sorted(glob(f'{SOURCE_DIR}/{PROJECT_NAME}/_C/**/*.cpp', recursive=True)),
         cxx_std=14,
         define_macros=[('VERSION_INFO', __version__)],
         include_dirs=['include/setriq'],
@@ -59,9 +61,9 @@
     url='https://github.com/BenTenmann/setriq',
     ext_modules=extensions,
     license='MIT',
-    requires=[],
     python_requires='>=3.7,<3.10',
-    packages=find_packages(exclude=['tests', 'scripts']),
-    package_data={f'{SOURCE_DIR}': sorted(glob(f'data/*.json'))},
+    package_dir={f'{PROJECT_NAME}': f'{SOURCE_DIR}/{PROJECT_NAME}'},
+    packages=find_packages(where=f'{SOURCE_DIR}', exclude=['tests', 'scripts']),
+    package_data={f'{PROJECT_NAME}': sorted(glob(f'data/*.json'))},
     include_package_data=True
 )
diff --git a/setriq/_C/PairwiseDistanceComputer.cpp → src/setriq/_C/PairwiseDistanceComputer.cpp b/setriq/_C/PairwiseDistanceComputer.cpp → src/setriq/_C/PairwiseDistanceComputer.cpp
diff --git a/setriq/_C/alignment/SmithWaterman.cpp → src/setriq/_C/alignment/SmithWaterman.cpp b/setriq/_C/alignment/SmithWaterman.cpp → src/setriq/_C/alignment/SmithWaterman.cpp
diff --git a/setriq/_C/alignment/SubstitutionMatrix.cpp → ...etriq/_C/alignment/SubstitutionMatrix.cpp b/setriq/_C/alignment/SubstitutionMatrix.cpp → ...etriq/_C/alignment/SubstitutionMatrix.cpp
diff --git a/setriq/_C/metrics/CdrDist.cpp → src/setriq/_C/metrics/CdrDist.cpp b/setriq/_C/metrics/CdrDist.cpp → src/setriq/_C/metrics/CdrDist.cpp
diff --git a/setriq/_C/metrics/TcrDist.cpp → src/setriq/_C/metrics/TcrDist.cpp b/setriq/_C/metrics/TcrDist.cpp → src/setriq/_C/metrics/TcrDist.cpp
diff --git a/setriq/_C/pythonWrapper.cpp → src/setriq/_C/pythonWrapper.cpp b/setriq/_C/pythonWrapper.cpp → src/setriq/_C/pythonWrapper.cpp
diff --git a/setriq/__init__.py → src/setriq/__init__.py b/setriq/__init__.py → src/setriq/__init__.py
diff --git a/setriq/data/blosum-45.json → src/setriq/data/blosum-45.json b/setriq/data/blosum-45.json → src/setriq/data/blosum-45.json
diff --git a/setriq/data/blosum-62.json → src/setriq/data/blosum-62.json b/setriq/data/blosum-62.json → src/setriq/data/blosum-62.json
diff --git a/setriq/data/blosum-90.json → src/setriq/data/blosum-90.json b/setriq/data/blosum-90.json → src/setriq/data/blosum-90.json
diff --git a/setriq/modules/__init__.py → src/setriq/modules/__init__.py b/setriq/modules/__init__.py → src/setriq/modules/__init__.py
diff --git a/setriq/modules/_distances.py → src/setriq/modules/_distances.py b/setriq/modules/_distances.py → src/setriq/modules/_distances.py
diff --git a/setriq/modules/_substitution.py → src/setriq/modules/_substitution.py b/setriq/modules/_substitution.py → src/setriq/modules/_substitution.py
diff --git a/tests/test_setriq.py b/tests/test_setriq.py
@@ -3,7 +3,7 @@
 
 import pytest
 
-import setriq
+from src import setriq
 
 ROUNDING = decimal.Decimal('0.0001')