Expand build matrix (#144)

* Expand build matrix

* relax dependency resolution

* bring in hdf5-static

* pin biom

* back to 3.6

* ls hdf5 libs

* fix config

* now do 3.8

* pin hdf5

* re-expand build matrix, remove biom pin

* repin biom

* pin h5py

* unpin biom-format

* BUG: fixed widths were problematic

* change pin

* change pin

* change pin

* or not and

Author: wasade

.github/workflows/main.yml

@@ -29,14 +29,15 @@ jobs:
     needs: lint
     strategy:
       matrix:
+        python-version: ['3.6', '3.7', '3.8', '3.9', '3.10']
         os: [ubuntu-latest, macos-latest]
     runs-on: ${{ matrix.os }}
     steps:
     - uses: actions/checkout@v2
     - uses: conda-incubator/setup-miniconda@v2
       with:        
         auto-update-conda: true
-        python-version: 3.6 
+        python-version: ${{ matrix.python-version }}
     - name: Install 
       shell: bash -l {0}
       run: |
@@ -48,7 +49,7 @@ jobs:
           # the system tools are unusable, hide them
           sudo mv -f /Library/Developer/CommandLineTools /Library/Developer/CommandLineTools.org
         fi
-        conda create --yes -n unifrac -c conda-forge -c bioconda python=3.6
+        conda create --yes -n unifrac -c conda-forge -c bioconda python=${{ matrix.python-version }}
         conda activate unifrac
         conda config --add channels conda-forge
         conda config --add channels bioconda
@@ -57,8 +58,9 @@ jobs:
           conda install --yes -c conda-forge -c bioconda gxx_linux-64
         else
           conda install --yes -c conda-forge -c bioconda clangxx_osx-64
-        fi 
-        conda install --yes -c conda-forge -c bioconda cython "hdf5>=1.8.17" biom-format numpy "h5py>=2.7.0" "scikit-bio>=0.5.1" unifrac-binaries flake8 nose
+        fi
+        conda install --yes -c conda-forge -c bioconda unifrac-binaries
+        conda install --yes -c conda-forge -c bioconda cython "hdf5<1.12.1" biom-format numpy "h5py<3.0.0 | >3.3.0" "scikit-bio>=0.5.1" nose
         echo "$(uname -s)"
         if [[ "$(uname -s)" == "Linux" ]];
         then
@@ -77,8 +79,8 @@ jobs:
       shell: bash -l {0}
       run: |
         conda activate unifrac
+        ls -lrt $CONDA_PREFIX/lib/libhdf5_cpp*
         nosetests
-        flake8 unifrac setup.py
         
     - name: Sanity checks
       shell: bash -l {0}

unifrac/_api.pyx

@@ -447,8 +447,14 @@ cdef support_biom* construct_support_biom(object table):
         np.ndarray[np.int32_t, ndim=1] table_indptr
         np.ndarray[np.double_t, ndim=1] table_data
 
-    table_obs_ids = table.ids(axis='observation')
-    table_samp_ids = table.ids(axis='sample')
+    # it seems that even if we use fixed width upstream, we cannot readily
+    # utilize it within cython. Casting to 'object' now. It likely would be
+    # beneficial to operate directly on fixed width.
+    # https://stackoverflow.com/questions/42543485/cython-specify-numpy-array-of-fixed-length-strings#comment72258848_
+
+    table_obs_ids = table.ids(axis='observation').astype(object)
+    table_samp_ids = table.ids(axis='sample').astype(object)
+
     table_indices = table.matrix_data.indices
     table_indptr = table.matrix_data.indptr
     table_data = table.matrix_data.data