Merge pull request #11 from antgonza/python-3.9

python 3.9

Author: charles-cowart

.github/workflows/qiita-plugin-ci.yml

@@ -19,12 +19,12 @@ jobs:
         uses: conda-incubator/setup-miniconda@v2
         with:
           auto-update-conda: true
-          python-version: 3.6
+          python-version: 3.9
 
       - name: Basic dependencies install
         shell: bash -l {0}
         run: |
-          conda create --yes -n qiita-files python=3.6 h5py pandas scipy numpy
+          conda create --yes -n qiita-files python=3.9 h5py pandas scipy numpy
           conda activate qiita-files
           pip install .
           pip install sphinx sphinx-bootstrap-theme nose-timer codecov Click
@@ -41,7 +41,7 @@ jobs:
     - name: flake8
       uses: actions/setup-python@v2
       with:
-        python-version: 3.6
+        python-version: 3.9
     - name: install dependencies
       run: python -m pip install --upgrade pip
     - name: Check out repository code

qiita_files/demux.py

@@ -596,11 +596,14 @@ def fetch(demux, samples=None, k=None):
         # only yield qual if we have it
         quals = repeat([])
         if demux.attrs['has-qual']:
+            # See https://github.com/h5py/h5py/issues/1847 for indexing below
             if len(indices) == 1:
                 if indices[0]:
-                    quals = demux[pjoin(dset_paths_bytes['qual'])][:]
+                    quals = demux[
+                        pjoin(dset_paths_bytes['qual'])][:, :][:]
             else:
-                quals = demux[pjoin(dset_paths_bytes['qual'])][indices, :]
+                quals = demux[
+                    pjoin(dset_paths_bytes['qual'])][:, :][indices, :]
 
         bc_original = demux[
             pjoin(dset_paths_bytes['barcode_original'])][indices]