Merge pull request #56 from biocore/relax-sk-pin

Update pins

.github/workflows/python-package-conda.yml

@@ -4,40 +4,62 @@ on:
   push:
     branches: [ master ]
   pull_request:
+    branches: [ master ]
+
+env:
+  latest_python: "3.12"
+  supported_pythons: '["3.8", "3.9", "3.10", "3.11", "3.12"]'
+  miniforge_version: "22.9.0-2"
+  miniforge_variant: "Mambaforge"
 
 jobs:
-  build-linux:
+  conf:
+    # This job is needed to route the global environment variables into
+    # a context that's available for matrix (and name, but that's unimportant)
+    name: Prepare Test Plan
+    runs-on: "ubuntu-latest"
+    outputs:
+      latest_python: ${{ steps.set-vars.outputs.latest_python }}
+      supported_pythons: ${{ steps.set-vars.outputs.supported_pythons }}
+    steps:
+      - name: Report Plan
+        id: set-vars
+        run: |
+          echo "latest_python=$latest_python" >> $GITHUB_OUTPUT
+          echo "supported_pythons=$supported_pythons" >> $GITHUB_OUTPUT
+  build-lint-test:
+    needs: conf
     strategy:
       max-parallel: 5
+      fail-fast: true
       matrix:
-        python-version: ['3.7', '3.8', '3.9']
-        os: [ubuntu-latest, macos-latest]
+        python_version: ${{ fromJSON(needs.conf.outputs.supported_pythons) }}
+        os: [ubuntu-latest, macos-13, macos-14]
     runs-on: ${{ matrix.os }}
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
       with:
         submodules: true
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+    - uses: conda-incubator/setup-miniconda@v2
       with:
-        python-version: ${{ matrix.python-version }}
-    - name: Add conda to system path
-      run: |
-        # $CONDA is an environment variable pointing to the root of the miniconda directory
-        echo $CONDA/bin >> $GITHUB_PATH
+        auto-update-conda: true
+        python-version: ${{ matrix.python_version }}
+        miniforge-version: ${{ env.miniforge_version }}
+        miniforge-variant: ${{ env.miniforge_variant }}
+        environment-file: ci/conda_host_env.yml
     - name: Install dependencies
+      shell: bash -l {0}
       run: |
-        conda install python=${{ matrix.python-version }} cython scikit-bio numpy
-        pip install versioneer
-        pip install -e .
+        conda install --yes -c conda-forge --file ci/conda_requirements.txt
     - name: Lint with flake8
+      shell: bash -l {0}
       run: |
-        conda install flake8
         # stop the build if there are Python syntax errors or undefined names
         flake8 bp --count --select=E9,F63,F7,F82 --show-source --statistics
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
         flake8 bp --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: Test with pytest
+      shell: bash -l {0}
       run: |
-        conda install pytest
+        pip install --no-deps -e .
         pytest

bp/_conv.pyx

@@ -24,9 +24,9 @@ def to_skbio_treenode(BP bp):
         The tree represented as an skbio.TreeNode
     """
     cdef int i
-
-    nodes = [skbio.TreeNode() for i in range(sum(bp.B))]
-
+    
+    nodes = [skbio.TreeNode() for i in range(bp.B.sum())]
+    
     # skbio.TreeNode.append makes a very expensive call to
     # invalidate_caches. Let's remove that from consideration
     # temporarily while constructing the tree
@@ -41,7 +41,7 @@ def to_skbio_treenode(BP bp):
 
     root = nodes[0]
 
-    for i in range(sum(bp.B)):
+    for i in range(bp.B.sum()):
         node_idx = bp.preorderselect(i)
         nodes[i].name = bp.name(node_idx)
         nodes[i].length = bp.length(node_idx)

ci/conda_host_env.yml

@@ -0,0 +1,6 @@
+# directly adapted from
+# https://github.com/biocore/scikit-bio/blob/31123c6471dc62f45a55bfdff59c61a4850be367/ci/conda_host_env.yml#LL1C1-L9C35
+name: testing
+channels:
+  - conda-forge
+  - defaults

ci/conda_requirements.txt

@@ -1,5 +1,5 @@
-nose
+pytest
 numpy
 flake8
-cython
+cython < 1.0.0
 scikit-bio

setup.py

@@ -101,30 +101,30 @@ def run(self):
 
 if USE_CYTHON:
     from Cython.Build import cythonize
-    extensions = cythonize(extensions)
+    extensions = cythonize(extensions,
+                           language_level=3)
 
 
 setup(name='iow',
       version=versioneer.get_version(),
       description='Balanced parentheses',
       author='Daniel McDonald',
-      author_email='d3mcdonald@eng.ucsd.edu',
+      author_email='damcdonald@ucsd.edu',
       maintainer='Daniel McDonald',
-      maintainer_email='d3mcdonald@eng.ucsd.edu',
+      maintainer_email='damcdonald@ucsd.edu',
       url='https://github.com/biocore/improved-octo-waddle',
       packages=['bp'],
       ext_modules=extensions,
       include_dirs=[np.get_include(), bitarr],
       setup_requires=['numpy >= 1.9.2'],
-      package_data={'bp': ['BitArray/*',
-                           'GPL/*']},
+      package_data={'bp': ['BitArray/*', ]},
       install_requires=[
           'numpy >= 1.9.2',
           'nose >= 1.3.7',
-          'cython >= 0.24.1',
+          'cython >= 0.24.1, < 1.0.0',
           'pandas',
           'click',
-          'scikit-bio >= 0.5.0, < 0.6.0'],
+          'scikit-bio >= 0.5.0'],
       long_description=long_description,
       long_description_content_type='text/markdown',
       cmdclass=versioneer.get_cmdclass({'build_py': BitArrayBuild,