From 020461708973b4c784abb75521e17db63b8cda72 Mon Sep 17 00:00:00 2001 From: oesteban Date: Tue, 16 Jul 2019 14:45:07 -0700 Subject: [PATCH 1/4] MAINT: Sort dependencies alphabetically --- nipype/info.py | 40 ++++++++++++++++++++-------------------- requirements.txt | 24 ++++++++++++------------ rtd_requirements.txt | 30 +++++++++++++++--------------- 3 files changed, 47 insertions(+), 47 deletions(-) diff --git a/nipype/info.py b/nipype/info.py index d4a5df9cac..0ad54a6682 100644 --- a/nipype/info.py +++ b/nipype/info.py @@ -135,47 +135,47 @@ def get_nipype_gitversion(): VERSION = __version__ PROVIDES = ['nipype'] REQUIRES = [ - 'nibabel>=%s' % NIBABEL_MIN_VERSION, - 'networkx>=%s,<=%s ; python_version < "3.0"' % (NETWORKX_MIN_VERSION, NETWORKX_MAX_VERSION_27), + 'click>=%s' % CLICK_MIN_VERSION, + 'configparser; python_version <= "3.4"', + 'funcsigs', + 'future>=%s' % FUTURE_MIN_VERSION, + 'futures; python_version == "2.7"', 'networkx>=%s ; python_version >= "3.0"' % NETWORKX_MIN_VERSION, - 'numpy>=%s,!=%s ; python_version == "2.7"' % (NUMPY_MIN_VERSION, NUMPY_BAD_VERSION_27), + 'networkx>=%s,<=%s ; python_version < "3.0"' % (NETWORKX_MIN_VERSION, NETWORKX_MAX_VERSION_27), + 'neurdflib', + 'nibabel>=%s' % NIBABEL_MIN_VERSION, 'numpy>=%s ; python_version > "3.0" and python_version < "3.7"' % NUMPY_MIN_VERSION, 'numpy>=%s ; python_version >= "3.7"' % NUMPY_MIN_VERSION_37, + 'numpy>=%s,!=%s ; python_version == "2.7"' % (NUMPY_MIN_VERSION, NUMPY_BAD_VERSION_27), + 'packaging', + 'prov>=%s' % PROV_VERSION, + 'pydot>=%s' % PYDOT_MIN_VERSION, + 'pydotplus', 'python-dateutil>=%s' % DATEUTIL_MIN_VERSION, 'scipy>=%s' % SCIPY_MIN_VERSION, - 'traits>=%s,!=5.0' % TRAITS_MIN_VERSION, - 'future>=%s' % FUTURE_MIN_VERSION, 'simplejson>=%s' % SIMPLEJSON_MIN_VERSION, - 'prov>=%s' % PROV_VERSION, - 'neurdflib', - 'click>=%s' % CLICK_MIN_VERSION, - 'funcsigs', - 'pydotplus', - 'pydot>=%s' % PYDOT_MIN_VERSION, - 'packaging', - 'futures; python_version == "2.7"', - 'configparser; python_version <= "3.4"', + 'traits>=%s,!=5.0' % TRAITS_MIN_VERSION, ] TESTS_REQUIRES = [ + 'codecov', + 'coverage<5', 'mock', 'pytest', 'pytest-cov', - 'codecov', 'pytest-env', - 'coverage<5' ] EXTRA_REQUIRES = { 'doc': ['Sphinx>=1.4', 'numpydoc', 'matplotlib', 'pydotplus', 'pydot>=1.2.3'], - 'tests': TESTS_REQUIRES, - 'specs': ['yapf'], + 'duecredit': ['duecredit'], 'nipy': ['nitime', 'nilearn<0.5.0', 'dipy', 'nipy', 'matplotlib'], 'profiler': ['psutil>=5.0'], - 'duecredit': ['duecredit'], - 'xvfbwrapper': ['xvfbwrapper'], 'pybids': ['pybids>=0.7.0'], + 'specs': ['yapf'], 'ssh': ['paramiko'], + 'tests': TESTS_REQUIRES, + 'xvfbwrapper': ['xvfbwrapper'], # 'mesh': ['mayavi'] # Enable when it works } diff --git a/requirements.txt b/requirements.txt index 0d951f49c0..66d250209c 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,16 +1,16 @@ -numpy>=1.9.0 -scipy>=0.14 +click>=6.6.0 +configparser +funcsigs +future>=0.16.0 networkx>=1.9 -traits>=4.6 -python-dateutil>=2.2 +neurdflib nibabel>=2.1.0 -future>=0.16.0 -simplejson>=3.8.0 +numpy>=1.9.0 +packaging prov>=1.5.2 -neurdflib -click>=6.6.0 -funcsigs -configparser -pydotplus pydot>=1.2.3 -packaging +pydotplus +python-dateutil>=2.2 +scipy>=0.14 +simplejson>=3.8.0 +traits>=4.6 diff --git a/rtd_requirements.txt b/rtd_requirements.txt index 68a366bbdf..8f8295c280 100644 --- a/rtd_requirements.txt +++ b/rtd_requirements.txt @@ -1,19 +1,19 @@ -numpy>=1.9.0 -scipy>=0.14 +configparser +funcsigs +future>=0.16.0 +matplotlib +mock networkx>=1.9 -traits>=4.6 -python-dateutil>=2.2 nibabel>=2.1.0 -future>=0.16.0 -simplejson>=3.8.0 +numpy>=1.9.0 +numpydoc +packaging prov==1.5.0 -funcsigs -configparser -pytest>=3.0 -mock -pydotplus -pydot>=1.2.3 psutil -matplotlib -packaging -numpydoc +pydot>=1.2.3 +pydotplus +pytest>=3.0 +python-dateutil>=2.2 +scipy>=0.14 +simplejson>=3.8.0 +traits>=4.6 From f7de5db865af64f6d5d1acf51744306b6258fafb Mon Sep 17 00:00:00 2001 From: oesteban Date: Tue, 16 Jul 2019 19:09:18 -0700 Subject: [PATCH 2/4] pin(neurodocker): set docker image tagged 0.5.0 with the hope of reenable image building. --- docker/generate_dockerfiles.sh | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docker/generate_dockerfiles.sh b/docker/generate_dockerfiles.sh index 453e6bd232..c31bd1a350 100755 --- a/docker/generate_dockerfiles.sh +++ b/docker/generate_dockerfiles.sh @@ -52,8 +52,8 @@ do esac done -# neurodocker version 0.4.1-22-g7c44e01 -NEURODOCKER_IMAGE="kaczmarj/neurodocker:master@sha256:858632a7533cac100f70932749b4cfc77fc40f667f41fca208f406215cff8a27" +# neurodocker version 0.5.0 +NEURODOCKER_IMAGE="kaczmarj/neurodocker:0.5.0" # neurodebian:stretch-non-free pulled on September 19, 2018 BASE_IMAGE="neurodebian:stretch-non-free@sha256:7cd978427d7ad215834fee221d0536ed7825b3cddebc481eba2d792dfc2f7332" From 0ac149ea91fa3d205606e3a47cb4c11c6a598dcf Mon Sep 17 00:00:00 2001 From: oesteban Date: Tue, 16 Jul 2019 19:11:48 -0700 Subject: [PATCH 3/4] enh: make sure neurdflib comes after prov see https://github.com/nipy/nipype/pull/2961#issuecomment-512035484 --- nipype/info.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/nipype/info.py b/nipype/info.py index 0ad54a6682..268a3763e2 100644 --- a/nipype/info.py +++ b/nipype/info.py @@ -142,7 +142,6 @@ def get_nipype_gitversion(): 'futures; python_version == "2.7"', 'networkx>=%s ; python_version >= "3.0"' % NETWORKX_MIN_VERSION, 'networkx>=%s,<=%s ; python_version < "3.0"' % (NETWORKX_MIN_VERSION, NETWORKX_MAX_VERSION_27), - 'neurdflib', 'nibabel>=%s' % NIBABEL_MIN_VERSION, 'numpy>=%s ; python_version > "3.0" and python_version < "3.7"' % NUMPY_MIN_VERSION, 'numpy>=%s ; python_version >= "3.7"' % NUMPY_MIN_VERSION_37, @@ -157,6 +156,10 @@ def get_nipype_gitversion(): 'traits>=%s,!=5.0' % TRAITS_MIN_VERSION, ] +# neurdflib has to come after prov +# https://github.com/nipy/nipype/pull/2961#issuecomment-512035484 +REQUIRES += ['neurdflib'] + TESTS_REQUIRES = [ 'codecov', 'coverage<5', From 772d0c86d1bd3a796f65313038473a733375c1bf Mon Sep 17 00:00:00 2001 From: Oscar Esteban Date: Wed, 17 Jul 2019 11:50:00 -0700 Subject: [PATCH 4/4] Update rtd_requirements.txt Co-Authored-By: Chris Markiewicz --- rtd_requirements.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/rtd_requirements.txt b/rtd_requirements.txt index a47818f6d7..8cb274347a 100644 --- a/rtd_requirements.txt +++ b/rtd_requirements.txt @@ -9,6 +9,7 @@ numpy>=1.9.0 numpydoc packaging prov>=1.5.2 +neurdflib psutil pydot>=1.2.3 pydotplus