diff --git a/REQUIREMENTS-STRICT.txt b/REQUIREMENTS-STRICT.txt index a045c80f6..7e6602079 100644 --- a/REQUIREMENTS-STRICT.txt +++ b/REQUIREMENTS-STRICT.txt @@ -3,9 +3,9 @@ appnope==0.1.0 attrs==19.3.0 backcall==0.1.0 bleach==3.1.0 -boto3==1.10.19 -botocore==1.13.19 -certifi==2019.9.11 +boto3==1.10.29 +botocore==1.13.29 +certifi==2019.11.28 chardet==3.0.4 Click==7.0 cycler==0.10.0 @@ -17,9 +17,9 @@ docutils==0.15.2 entrypoints==0.3 idna==2.8 imageio==2.6.1 -importlib-metadata==0.23 +importlib-metadata==1.1.0 ipykernel==5.1.3 -ipython==7.9.0 +ipython==7.10.1 ipython-genutils==0.2.0 ipywidgets==7.5.1 jedi==0.15.1 @@ -31,9 +31,9 @@ jupyter-client==5.3.4 jupyter-core==4.6.1 kiwisolver==1.1.0 MarkupSafe==1.1.1 -matplotlib==3.1.1 +matplotlib==3.1.2 mistune==0.8.4 -more-itertools==7.2.0 +more-itertools==8.0.0 mpmath==1.1.0 nbconvert==5.6.1 nbformat==4.4.0 @@ -48,11 +48,11 @@ pexpect==4.7.0 pickleshare==0.7.5 Pillow==6.2.1 prometheus-client==0.7.1 -prompt-toolkit==2.0.10 +prompt-toolkit==3.0.2 ptyprocess==0.6.0 -Pygments==2.4.2 +Pygments==2.5.2 pyparsing==2.4.5 -pyrsistent==0.15.5 +pyrsistent==0.15.6 python-dateutil==2.8.0 pytz==2019.3 PyWavelets==1.1.1 @@ -63,8 +63,8 @@ requests==2.22.0 s3transfer==0.2.1 scikit-image==0.15.0 scikit-learn==0.21.3 -scipy==1.3.2 -semantic-version==2.8.2 +scipy==1.3.3 +semantic-version==2.8.3 Send2Trash==1.5.0 showit==1.1.4 six==1.13.0 @@ -73,7 +73,7 @@ sympy==1.4 terminado==0.8.3 testpath==0.4.4 tornado==6.0.3 -tqdm==4.38.0 +tqdm==4.40.0 trackpy==0.4.2 traitlets==4.3.3 urllib3==1.25.7 @@ -81,5 +81,5 @@ validators==0.14.0 wcwidth==0.1.7 webencodings==0.5.1 widgetsnbextension==3.5.1 -xarray==0.14.0 +xarray==0.14.1 zipp==0.6.0 diff --git a/starfish/REQUIREMENTS-STRICT.txt b/starfish/REQUIREMENTS-STRICT.txt index a045c80f6..7e6602079 100644 --- a/starfish/REQUIREMENTS-STRICT.txt +++ b/starfish/REQUIREMENTS-STRICT.txt @@ -3,9 +3,9 @@ appnope==0.1.0 attrs==19.3.0 backcall==0.1.0 bleach==3.1.0 -boto3==1.10.19 -botocore==1.13.19 -certifi==2019.9.11 +boto3==1.10.29 +botocore==1.13.29 +certifi==2019.11.28 chardet==3.0.4 Click==7.0 cycler==0.10.0 @@ -17,9 +17,9 @@ docutils==0.15.2 entrypoints==0.3 idna==2.8 imageio==2.6.1 -importlib-metadata==0.23 +importlib-metadata==1.1.0 ipykernel==5.1.3 -ipython==7.9.0 +ipython==7.10.1 ipython-genutils==0.2.0 ipywidgets==7.5.1 jedi==0.15.1 @@ -31,9 +31,9 @@ jupyter-client==5.3.4 jupyter-core==4.6.1 kiwisolver==1.1.0 MarkupSafe==1.1.1 -matplotlib==3.1.1 +matplotlib==3.1.2 mistune==0.8.4 -more-itertools==7.2.0 +more-itertools==8.0.0 mpmath==1.1.0 nbconvert==5.6.1 nbformat==4.4.0 @@ -48,11 +48,11 @@ pexpect==4.7.0 pickleshare==0.7.5 Pillow==6.2.1 prometheus-client==0.7.1 -prompt-toolkit==2.0.10 +prompt-toolkit==3.0.2 ptyprocess==0.6.0 -Pygments==2.4.2 +Pygments==2.5.2 pyparsing==2.4.5 -pyrsistent==0.15.5 +pyrsistent==0.15.6 python-dateutil==2.8.0 pytz==2019.3 PyWavelets==1.1.1 @@ -63,8 +63,8 @@ requests==2.22.0 s3transfer==0.2.1 scikit-image==0.15.0 scikit-learn==0.21.3 -scipy==1.3.2 -semantic-version==2.8.2 +scipy==1.3.3 +semantic-version==2.8.3 Send2Trash==1.5.0 showit==1.1.4 six==1.13.0 @@ -73,7 +73,7 @@ sympy==1.4 terminado==0.8.3 testpath==0.4.4 tornado==6.0.3 -tqdm==4.38.0 +tqdm==4.40.0 trackpy==0.4.2 traitlets==4.3.3 urllib3==1.25.7 @@ -81,5 +81,5 @@ validators==0.14.0 wcwidth==0.1.7 webencodings==0.5.1 widgetsnbextension==3.5.1 -xarray==0.14.0 +xarray==0.14.1 zipp==0.6.0 diff --git a/starfish/core/spots/DetectPixels/combine_adjacent_features.py b/starfish/core/spots/DetectPixels/combine_adjacent_features.py index 2aba7aefc..7057fb100 100644 --- a/starfish/core/spots/DetectPixels/combine_adjacent_features.py +++ b/starfish/core/spots/DetectPixels/combine_adjacent_features.py @@ -212,7 +212,7 @@ def _calculate_mean_pixel_traces( # the 0th pixel trace corresponds to background. If present, drop it. try: - mean_pixel_traces = mean_pixel_traces.drop(0, dim=Features.AXIS) + mean_pixel_traces = mean_pixel_traces.drop_sel({Features.AXIS: 0}) except KeyError: pass