From d898dd37c9f16d4101514136755d2319b08b6436 Mon Sep 17 00:00:00 2001 From: Chris Tomkins-Tinch Date: Tue, 25 Sep 2018 11:54:42 -0400 Subject: [PATCH 1/4] update dateutil and paramiko --- conda-environment_py2.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/conda-environment_py2.yaml b/conda-environment_py2.yaml index 3fe9bb3f..6aa94ca6 100644 --- a/conda-environment_py2.yaml +++ b/conda-environment_py2.yaml @@ -13,7 +13,7 @@ dependencies: - htslib=1.3.1=0 - peewee=2.8.0 - pysam=0.9.1 -- python-dateutil=2.3 +- python-dateutil=2.7.3 - samtools=1.3.1 - selscan=1.1.0b - biopython=1.67 @@ -34,7 +34,7 @@ dependencies: - ncurses=5.9 - openssl=1.0.2h - pandas=0.18.1 -- paramiko=1.16.0 +- paramiko=2.4.1 - pip=8.1.2 - pycrypto=2.6.1 - pygments=2.1.3 From 1c07eaeb8b0b69e1737b96f386fd34fa109070c0 Mon Sep 17 00:00:00 2001 From: Chris Tomkins-Tinch Date: Tue, 25 Sep 2018 11:55:39 -0400 Subject: [PATCH 2/4] update dateutil and paramiko for py3 --- conda-environment_py3.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/conda-environment_py3.yaml b/conda-environment_py3.yaml index 71b2513d..7af5a081 100644 --- a/conda-environment_py3.yaml +++ b/conda-environment_py3.yaml @@ -13,7 +13,7 @@ dependencies: - htslib=1.3.1=0 - peewee=2.8.0 - pysam=0.9.1 -- python-dateutil=2.3 +- python-dateutil=2.7.3 - samtools=1.3.1 - selscan=1.1.0b - biopython=1.67 @@ -34,7 +34,7 @@ dependencies: - ncurses=5.9 - openssl=1.0.2h - pandas=0.18.1 -- paramiko=1.16.0 +- paramiko=2.4.1 - pip=8.1.2 - pycrypto=2.6.1 - pygments=2.1.3 From 3920496e1a16abb42beee4b409b1e6de6f652b20 Mon Sep 17 00:00:00 2001 From: Chris Tomkins-Tinch Date: Wed, 26 Sep 2018 10:02:28 -0400 Subject: [PATCH 3/4] remove conda pin --- travis/install-conda.sh | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/travis/install-conda.sh b/travis/install-conda.sh index d31c12c1..cc22a409 100755 --- a/travis/install-conda.sh +++ b/travis/install-conda.sh @@ -44,7 +44,7 @@ else # if it does not exist, we need to install miniconda conda config --add channels bioconda conda config --add channels r conda config --add channels conda-forge - conda install -y -q conda=4.2 # pin to 4.2.* until this is fixed: https://github.com/conda/conda-build/issues/1666 + conda install -y -q conda #=4.2 # pin to 4.2.* until this is fixed: https://github.com/conda/conda-build/issues/1666 conda config --set auto_update_conda false conda install -y java-jdk==8.0.112 conda install -y conda-build # needed to build recipe @@ -52,4 +52,4 @@ else # if it does not exist, we need to install miniconda conda install -y -c conda-forge -f curl # the bioconda curl is broken as of 21 Feb 2017 fi -conda info -a # for debugging \ No newline at end of file +conda info -a # for debugging From 5d3a1e59523cc115db2937cc8e4988230742b43a Mon Sep 17 00:00:00 2001 From: Chris Tomkins-Tinch Date: Wed, 26 Sep 2018 10:03:01 -0400 Subject: [PATCH 4/4] remove paramiko from docs requirements --- requirements-docs.txt | 1 - 1 file changed, 1 deletion(-) diff --git a/requirements-docs.txt b/requirements-docs.txt index db99b81e..465fcab3 100644 --- a/requirements-docs.txt +++ b/requirements-docs.txt @@ -2,7 +2,6 @@ biopython==1.65 pysam==0.8.2.1 numpy==1.8.0 pandas==0.16.0 -paramiko==1.15.2 crypto==1.3.4 boltons==0.6.3 peewee==2.8.0