Merge branch 'master' of https://github.com/alleninstitute/ecephys_spike_sorting

Author: jsiegle

.travis.yml

@@ -1,64 +1,18 @@
-env:
- global:
-   - PIPENV_VENV_IN_PROJECT=1
-   - PIPENV_IGNORE_VIRTUALENVS=1
-
-matrix:
-  include:
-    - os: linux
-      sudo: required
-      python: 2.7
-      env: TEST_PYTHON_VERSION=2.7
-    - os: linux
-      sudo: required
-      python: 3.5
-      env: TEST_PYTHON_VERSION=3.5
-    - os: linux
-      sudo: required
-      python: 3.6
-      env: TEST_PYTHON_VERSION=3.6
-    - os: osx
-      language: generic
-      env: TEST_PYTHON_VERSION=2.7
-    - os: osx
-      languageL: generic
-      env: TEST_PYTHON_VERSION=3.5
-    - os: osx
-      language: generic
-      env: TEST_PYTHON_VERSION=3.6
+language: python
+python:
+    - '3.7'
+notifications:
+  email: false
+before_install:
+ - python --version
+ - pip install -U cython setuptools pip numpy
 
 install:
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then
-      brew update;
-      if [[ "$TEST_PYTHON_VERSION" == "2.7" ]]; then
-        wget https://repo.continuum.io/miniconda/Miniconda2-latest-MacOSX-x86_64.sh -O miniconda.sh;
-      else
-        wget https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O miniconda.sh;
-      fi
-    else
-      sudo apt-get update;
-      if [[ "$TEST_PYTHON_VERSION" == "2.7" ]]; then
-        wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -O miniconda.sh;
-      else
-        wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
-      fi
-    fi
-  - bash miniconda.sh -b -p $HOME/miniconda
-  - export PATH="$HOME/miniconda/bin:$PATH"
-  - hash -r
-  - conda config --set always_yes yes --set changeps1 no
-  - conda update -q conda
-  - conda create -q -n test-environment python=$TEST_PYTHON_VERSION
-  - source activate test-environment
-  - if [[ "$TRAVIS_OS_NAME" == "osx" && "$TEST_PYTHON_VERSION" == "2.7" ]]; then
-      conda install virtualenv;
-    fi
-  - pip install pipenv
-  - pipenv --update
-  - pipenv --python ${TEST_PYTHON_VERSION}
-  - pipenv install --dev
-  - pipenv run pip install .
-
-script:
-  - pipenv run coverage run --source ecephys_spike_sorting -m pytest
-  - pipenv run codecov
+  - pip install .
+  - pip install pytest-cov
+  - pip install coveralls
+  - pip install codecov
+script: pytest --cov=ecephys_spike_sorting tests/
+after_success:
+  - codecov
+  - coveralls

ecephys_spike_sorting/modules/quality_metrics/metrics.py

@@ -270,7 +270,8 @@ def calculate_pc_metrics_one_cluster(cluster_peak_channels, idx, cluster_id,clus
 
     all_pcs = np.reshape(all_pcs, (all_pcs.shape[0], pc_features.shape[1]*channels_to_use.size))
     if ((all_pcs.shape[0] > 10)
-            and (cluster_id in all_labels)
+            and not (all_labels == cluster_id).all()  # Not all labels are this cluster
+            and (sum(all_labels == cluster_id) > 20)  # No fewer than 20 spikes in this cluster
             and (len(channels_to_use) > 0)):
         isolation_distance, l_ratio = mahalanobis_metrics(all_pcs, all_labels, cluster_id)