From 62bea7428d5fa73c689c3caed2175719f9d5a2cc Mon Sep 17 00:00:00 2001 From: nikellepetrillo Date: Wed, 26 Aug 2020 08:11:06 -0400 Subject: [PATCH 1/4] updating the requirements.txt, switching tp python 3.7.7, and updated the notation in groups.py --- Dockerfile | 6 +++--- requirements.txt | 17 +++-------------- src/sctools/groups.py | 3 ++- 3 files changed, 8 insertions(+), 18 deletions(-) diff --git a/Dockerfile b/Dockerfile index 25a0db6..ec5bab5 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,8 +1,8 @@ -FROM python:3.6.2 +FROM python:3.7.7 LABEL maintainer="Ambrose J. Carr " \ - 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 diff --git a/requirements.txt b/requirements.txt index f7e5542..0b8220a 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,17 +1,6 @@ -HTSeq==0.11.2 -black==19.3b0 -crimson==0.4.0 -flake8==3.7.7 -gffutils==0.9 -matplotlib==3.1.1 -numpy==1.17.5 +crimson==0.5.2 pandas==0.25.3 -pre-commit==1.14.4 -pysam==0.13.0 +pysam==0.16.0.1 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 +scipy==1.5.2 diff --git a/src/sctools/groups.py b/src/sctools/groups.py index d019945..511bc61 100644 --- a/src/sctools/groups.py +++ b/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) From db52f1f70b50030ac9aa7b39c8a9c037b150e352 Mon Sep 17 00:00:00 2001 From: nikellepetrillo Date: Thu, 27 Aug 2020 08:56:04 -0400 Subject: [PATCH 2/4] adding bLack package to requirements.txt --- requirements.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/requirements.txt b/requirements.txt index 0b8220a..99d1508 100644 --- a/requirements.txt +++ b/requirements.txt @@ -4,3 +4,4 @@ pysam==0.16.0.1 pytest-cov==2.5.1 pytest==5.1.1 scipy==1.5.2 +black==19.3b0 From 21b5ad636fb4f047e72597c32178845d696f4f6d Mon Sep 17 00:00:00 2001 From: nikellepetrillo Date: Thu, 27 Aug 2020 08:58:37 -0400 Subject: [PATCH 3/4] adding flake8 to requirements.txt --- requirements.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/requirements.txt b/requirements.txt index 99d1508..70cf5bc 100644 --- a/requirements.txt +++ b/requirements.txt @@ -5,3 +5,4 @@ pytest-cov==2.5.1 pytest==5.1.1 scipy==1.5.2 black==19.3b0 +flake8==3.7.7 From d12a5179d40e415f8d2fcac682ad70ac7abd98a0 Mon Sep 17 00:00:00 2001 From: nikellepetrillo Date: Thu, 27 Aug 2020 14:31:56 -0400 Subject: [PATCH 4/4] adding some more important packages to requirements.txt --- requirements.txt | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/requirements.txt b/requirements.txt index 70cf5bc..19390fe 100644 --- a/requirements.txt +++ b/requirements.txt @@ -6,3 +6,9 @@ pytest==5.1.1 scipy==1.5.2 black==19.3b0 flake8==3.7.7 +gffutils==0.9 +numpy==1.17.5 +requests==2.20.0 +setuptools==40.4.3 +setuptools_scm==3.1.0 +tables==3.4.2 \ No newline at end of file