Add CI script + lint code.

.github/workflows/package.yml

@@ -0,0 +1,128 @@
+name: Python package
+
+on: [push, pull_request]
+
+jobs:
+  code-qc:
+    runs-on: ubuntu-22.04
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: "3.10"
+    - name: Lint with flake8
+      run: |
+        python -m pip install flake8
+	flake8 src/
+  build-sdist:
+    runs-on: ubuntu-22.04
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: "3.10"
+    - name: Set up R ${{ matrix.r-version }}
+      uses: r-lib/actions/setup-r@v2
+      with:
+        r-version: release
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install setuptools build
+    - name: Build sdist
+      run: |
+        python -m build -o dist/ --sdist .
+    - name: Upload source package.
+      uses: actions/upload-artifact@v3
+      with:
+        name: mashing-pumkins-sdist
+        path: dist/mashing-pumpkins-*.tar.gz
+  build-wheel-posix:
+    runs-on: ${{ matrix.os }}
+    permissions:
+      packages: read
+    continue-on-error: true
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - os: ubuntu-latest
+            python: 39
+            platform_id: manylinux2014
+          - os: macos-11
+            python: 310
+            platform_id: macosx_x86_64
+          - os: macos-11
+            python: 310
+            platform_id: macosx_arm64
+          - os: macos-12
+            python: 310
+            platform_id: macosx_arm64
+          - os: macos-13
+            python: 310
+            platform_id: macosx_arm64
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.9'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install setuptools build cibuildwheel
+    - name: Build wheel
+      uses: pypa/[email protected]
+      env:
+          CIBW_SKIP: cp36-* cp37-*
+          CIBW_ARCHS_LINUX: "auto aarch64"
+          CIBW_ARCHS_MACOS: "x86_64 arm64"
+          CIBW_BUILD_VERBOSITY: 1
+      with:
+        output-dir: wheelhouse
+        config-file: pyproject.toml
+    - name: Upload wheels
+      uses: actions/upload-artifact@v3
+      with:
+          name: binary-wheels-${{ matrix.platform_id }}
+          path: wheelhouse/*.whl
+  test:
+    needs: [build-sdist]
+    runs-on: ${{ matrix.os }}
+    continue-on-error: ${{ matrix.experimental }}
+    strategy:
+      max-parallel: 4
+      matrix:
+        python-version: [3.8, 3.9, "3.10", "3.11"]
+        r-version: ['release']
+        os: [ubuntu-latest, ubuntu-20.04, macOS-latest]
+        venv_activate: ["source pyenv_base/bin/activate"]
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Create base virtualenv (non-windows)
+      run: |
+        python -m venv pyenv_base
+        ${{ matrix.venv_activate }}
+        python -m  pip install -U pip wheel
+    - uses: actions/download-artifact@v3
+      with:
+        name: mashing-pumpkins-sdist
+        path: dist/
+    - name: Source package path.
+      shell: bash
+      run: echo "SRC_DIST=$(ls -1 dist/*.tar.gz | tail -n 1)" >> $GITHUB_ENV
+    - name: Install package (non-Windows)
+      run: |
+        ${{ matrix.venv_activate }}
+        pip install $SRC_DIST
+    - name: Test
+      run: |
+        ${{ matrix.venv_activate }}
+        python -m pip install $SRC_DIST'[test_minimal]'
+        pytest src/tests/

src/minhashsketch.py

@@ -70,7 +70,7 @@ def _minmaxhash_add_ngrams(
                 # Replace the maximum value in the heap.
                 heapmap[h] = elt
                 out = heapreplace(heap, elt)
-                del(heapmap[sign * out[0]])
+                del (heapmap[sign * out[0]])
                 # The negative of the hash is needed for MinHash.
                 heaptop = sign * heap[0][0]
                 if anynew is not None:
@@ -172,7 +172,7 @@ def _replace(self, h, elt):
         heapmap = self._heapmap
         heapmap[h] = elt
         out = heapreplace(self._heap, elt)
-        del(heapmap[self._extracthash(out)])
+        del (heapmap[self._extracthash(out)])
         return out
 
     def __add__(self, obj):
@@ -405,7 +405,7 @@ def _replace(self, h, elt):
         heapmap = self._heapmap
         heapmap[h] = elt
         out = heapreplace(self._heap, elt)
-        del(heapmap[self._extracthash(out)])
+        del (heapmap[self._extracthash(out)])
         return out
 
     def _add(self, subs, nsubs, hashbuffer, heaptop,
@@ -541,7 +541,7 @@ class CountTrait(object):
 
     def _replace(self, h, elt):
         out = super()._replace(h, elt)
-        del(self._count[self._extracthash(out)])
+        del (self._count[self._extracthash(out)])
         return out
 
     def _anynew(self, h):

src/parallel.py

@@ -2,21 +2,20 @@
 Parallelization utilities
 """
 
-from functools import reduce
-import multiprocessing
-
 
 class Sketch(object):
 
     @staticmethod
     def initializer(cls, *args):
         """
-        FIXME: use of global not really nice (possible root of mysterious issue for user)
+        FIXME: use of global not really nice (possible root of mysterious
+        issue for user)
         """
         global sketch_constructor
+
         def sketch_constructor():
             return cls(*args)
-    
+
     @staticmethod
     def map_sequence(sequence):
         """
@@ -59,7 +58,8 @@ class SketchList(object):
     @staticmethod
     def initializer(clslist, argslist):
         """
-        FIXME: use of global not really nice (possible root of mysterious issue for user)
+        FIXME: use of global not really nice (possible root of mysterious
+        issue for user)
         """
 
         # Allow automagic expansion of the list of classes
@@ -69,12 +69,15 @@ def initializer(clslist, argslist):
         # Allow automagic expansion of the list of args
         if len(argslist) == 1:
             argslist = tuple(argslist[0] for x in range(len(clslist)))
-        
+
         if len(clslist) != len(argslist):
-            raise ValueError("The arguments argslist and clslist must be sequences of either the "
-                             "same length, or of length 1.")
-
+            raise ValueError(
+                "The arguments argslist and clslist must be sequences of "
+                "either the same length, or of length 1."
+            )
+
         global sketchlist_constructor
+
         def sketchlist_constructor():
             return (cls(*args) for cls, args in zip(clslist, argslist))
 
@@ -111,8 +114,9 @@ def reduce(alist, blist):
         - alist: a sequence of sketches
         - blist: a sequence of sketches
 
-        return alist after each of its elements has been updated to the corresponding element in blist
+        return alist after each of its elements has been updated to the
+        corresponding element in blist
         """
-        for a,b in zip(alist, blist):
+        for a, b in zip(alist, blist):
             a.update(b)
         return alist

src/tests/test__murmurhash3.py

@@ -1,11 +1,9 @@
-import pytest
-
 import array
 from mashingpumpkins import _murmurhash3
 
 
 def test_hasharray():
-    nsize=3
+    nsize = 3
     buffer = array.array('Q', [0, ])
     seed = 42
     _murmurhash3.hasharray(b"ACG", nsize, buffer, seed)
@@ -14,4 +12,3 @@ def test_hasharray():
     seed = 43
     _murmurhash3.hasharray(b"ACG", nsize, buffer, seed)
     assert buffer[0] != 1731421407650554201
-