Merge pull request #81 from HumanCellAtlas/np_gl-1148_update_dependen…

…cies

gl_1148_updating_sctools_dependencies

Dockerfile

@@ -1,8 +1,8 @@
-FROM python:3.6.2
+FROM python:3.7.7
 
 LABEL maintainer="Ambrose J. Carr <acarr@broadinstitute.org>" \
-  software="python 3.6.2" \
-  description="python 3.6.2 with pysam, sctools, requests, and a basic science stack"
+  software="python 3.7.7" \
+  description="python 3.7.7 with pysam, sctools, requests, and a basic science stack"
 
 COPY requirements.txt .
 RUN pip3 install -r requirements.txt

requirements.txt

@@ -1,17 +1,14 @@
-HTSeq==0.11.2
+crimson==0.5.2
+pandas==0.25.3
+pysam==0.16.0.1
+pytest-cov==2.5.1
+pytest==5.1.1
+scipy==1.5.2
 black==19.3b0
-crimson==0.4.0
 flake8==3.7.7
 gffutils==0.9
-matplotlib==3.1.1
 numpy==1.17.5
-pandas==0.25.3
-pre-commit==1.14.4
-pysam==0.13.0
-pytest-cov==2.5.1
-pytest==5.1.1
 requests==2.20.0
-scipy==1.3.1
 setuptools==40.4.3
 setuptools_scm==3.1.0
-tables==3.4.2
+tables==3.4.2

src/sctools/groups.py

@@ -112,7 +112,8 @@ def write_aggregated_qc_metrics(file_names, output_name):
     for file_name in file_names:
         dat = pd.read_csv(file_name, index_col=0)
         print(dat.index)
-        df = pd.concat([df, dat], axis=1, join_axes=[dat.index])
+        print(df.head())
+        df = pd.concat([df, dat], axis=1, join='outer')
     df.to_csv(output_name + '.csv', index=True)