From 0ee1b740646f6fc33ba0d349050e66f7b6c8d014 Mon Sep 17 00:00:00 2001 From: Joseph Huttner Date: Fri, 14 Apr 2017 16:07:57 +0000 Subject: [PATCH 1/3] Do not install dxfs dependencies, and provide explicit toolkit_version.py --- .gitignore | 1 - src/python/dxpy/toolkit_version.py | 1 + src/python/setup.py | 10 +++++++++- 3 files changed, 10 insertions(+), 2 deletions(-) create mode 100644 src/python/dxpy/toolkit_version.py diff --git a/.gitignore b/.gitignore index e360789f..a75978b2 100644 --- a/.gitignore +++ b/.gitignore @@ -12,7 +12,6 @@ /src/.setup_doc_virtualenv /src/java/target/ /src/java/src/main/java/com/dnanexus/DXToolkitVersion.java -/src/python/dxpy/toolkit_version.py /src/python/coverage-reports/ /src/R/install_dxR_deps.Rout /src/R/dxR*.tar.gz diff --git a/src/python/dxpy/toolkit_version.py b/src/python/dxpy/toolkit_version.py new file mode 100644 index 00000000..2f546186 --- /dev/null +++ b/src/python/dxpy/toolkit_version.py @@ -0,0 +1 @@ +version = '0.218.0' diff --git a/src/python/setup.py b/src/python/setup.py index 4aca1f85..056fffde 100755 --- a/src/python/setup.py +++ b/src/python/setup.py @@ -64,7 +64,15 @@ dependencies.extend(backports_dependencies) # dxfs is not compatible with Windows, and is currently disabled on Python 3 if platform.system() != 'Windows': - dependencies.extend(dxfs_dependencies) + # dependencies.extend(dxfs_dependencies) + print 'Skipping installation of dxfs dependencies!' + print '' + print 'SolveBio deploys on the Alpine Linux distribution, which does ' + print 'not appear to be compatible with the xattrs (extended attributes) ' + print 'package, which dxpy utilizes to provide a virtual filesystem on ' + print 'the guest host. Since SolveBio does not use this functionality of ' + print 'dxpy, it is believed safe to proceed without it.' + print '' if 'DNANEXUS_INSTALL_PYTHON_TEST_DEPS' in os.environ: dependencies.extend(test_dependencies) From 57c49b20a5cfd115c0442455241b28d318c59074 Mon Sep 17 00:00:00 2001 From: Joseph Huttner Date: Fri, 14 Apr 2017 16:46:48 +0000 Subject: [PATCH 2/3] Bump requests version for compatibility with existing code --- src/python/requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/python/requirements.txt b/src/python/requirements.txt index abc63a68..6f5fd6d5 100644 --- a/src/python/requirements.txt +++ b/src/python/requirements.txt @@ -3,4 +3,4 @@ python-dateutil==2.3 python-magic==0.4.6 beautifulsoup4==4.4.1 psutil==3.3.0 -requests==2.7.0 +requests==2.10.0 From 923e14aa32fc23e4e6837d4d2cbfc4661ccbca0c Mon Sep 17 00:00:00 2001 From: Jeff Hull Date: Tue, 14 Aug 2018 19:19:19 -0400 Subject: [PATCH 3/3] upgrade package for libressl compiling --- src/python/requirements.txt | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/src/python/requirements.txt b/src/python/requirements.txt index 4990d351..fd12e9a5 100644 --- a/src/python/requirements.txt +++ b/src/python/requirements.txt @@ -4,4 +4,7 @@ python-magic==0.4.6 beautifulsoup4==4.4.1 psutil>=3.3.0 requests>=2.8.0 -cryptography<=2.2.2 \ No newline at end of file +# cryptography<=2.2.2 +# Needed for compiling against libressl +# https://github.com/pyca/cryptography/blob/master/CHANGELOG.rst#23---2018-07-18 +cryptography<=2.3.1