From d584b3fafe97b4b1a52216d0d04872a65746027a Mon Sep 17 00:00:00 2001 From: miykael Date: Tue, 9 Oct 2018 18:51:34 -0400 Subject: [PATCH 1/7] FIX: corrects readthedocs build error --- doc/conf.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/conf.py b/doc/conf.py index 94f3a97b5c..5f8e13e278 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -50,7 +50,7 @@ 'sphinx.ext.autosummary', 'numpydoc', 'matplotlib.sphinxext.plot_directive', - 'matplotlib.sphinxext.only_directives', + #'matplotlib.sphinxext.only_directives', 'nipype.sphinxext.plot_workflow', #'IPython.sphinxext.ipython_directive', #'IPython.sphinxext.ipython_console_highlighting' From 46cbed655a4dcea4109a06b9e73845742a1a8c89 Mon Sep 17 00:00:00 2001 From: miykael Date: Wed, 10 Oct 2018 00:38:50 -0400 Subject: [PATCH 2/7] FIX: update pybids to newest release --- docker/generate_dockerfiles.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docker/generate_dockerfiles.sh b/docker/generate_dockerfiles.sh index bd1fcb637e..2c383df5df 100755 --- a/docker/generate_dockerfiles.sh +++ b/docker/generate_dockerfiles.sh @@ -109,7 +109,7 @@ function generate_main_dockerfile() { --miniconda env_name=neuro \ pip_install="grabbit==0.1.2" \ --run-bash "mkdir -p /src/pybids - && curl -sSL --retry 5 https://github.com/INCF/pybids/tarball/0.5.1 + && curl -sSL --retry 5 https://github.com/INCF/pybids/tarball/0.6.5 | tar -xz -C /src/pybids --strip-components 1 && source activate neuro && pip install --no-cache-dir -e /src/pybids" \ From 7c204a42b6634cb43033d91a1970e758ec6eecfb Mon Sep 17 00:00:00 2001 From: miykael Date: Wed, 10 Oct 2018 02:59:32 -0400 Subject: [PATCH 3/7] ENH: update neurodocker and neurodebian docker image --- docker/generate_dockerfiles.sh | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/docker/generate_dockerfiles.sh b/docker/generate_dockerfiles.sh index 2c383df5df..ae4973b46d 100755 --- a/docker/generate_dockerfiles.sh +++ b/docker/generate_dockerfiles.sh @@ -53,11 +53,11 @@ do done -# neurodocker version 0.3.1-22-gb0ee069 -NEURODOCKER_IMAGE="kaczmarj/neurodocker@sha256:f15ca90803f4b89acfca55cd1c7269bf2ec2dfd95b3de1118b08afa34b87d9d1" +# neurodocker:master pulled on October 9, 2018 +NEURODOCKER_IMAGE="kaczmarj/neurodocker@sha256:c5c10fc11cbd7efe18ac10d2370742b8ecb3588c3aa9b2c15ca7e18363bfa9dc" -# neurodebian:stretch-non-free pulled on November 3, 2017 -BASE_IMAGE="neurodebian@sha256:7590552afd0e7a481a33314724ae27f76ccedd05ffd7ac06ec38638872427b9b" +# neurodebian:stretch-non-free pulled on October 9, 2018 +BASE_IMAGE="neurodebian@sha256:7cd978427d7ad215834fee221d0536ed7825b3cddebc481eba2d792dfc2f7332" NIPYPE_BASE_IMAGE="nipype/nipype:base" PKG_MANAGER="apt" From 0c556341484d9e41feaa570c02750e258fa02a6e Mon Sep 17 00:00:00 2001 From: miykael Date: Wed, 10 Oct 2018 03:02:56 -0400 Subject: [PATCH 4/7] FIX: correct syntax to neurodocker version +0.4.0 --- 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 ae4973b46d..e3cf19a019 100755 --- a/docker/generate_dockerfiles.sh +++ b/docker/generate_dockerfiles.sh @@ -64,7 +64,7 @@ PKG_MANAGER="apt" DIR="$(dirname "$0")" function generate_base_dockerfile() { - docker run --rm "$NEURODOCKER_IMAGE" generate \ + docker run --rm "$NEURODOCKER_IMAGE" generate docker \ --base "$BASE_IMAGE" --pkg-manager "$PKG_MANAGER" \ --label maintainer="The nipype developers https://github.com/nipy/nipype" \ --spm version=12 matlab_version=R2017a \ @@ -81,7 +81,7 @@ function generate_base_dockerfile() { function generate_main_dockerfile() { - docker run --rm "$NEURODOCKER_IMAGE" generate \ + docker run --rm "$NEURODOCKER_IMAGE" generate docker \ --base "$NIPYPE_BASE_IMAGE" --pkg-manager "$PKG_MANAGER" \ --label maintainer="The nipype developers https://github.com/nipy/nipype" \ --env MKL_NUM_THREADS=1 OMP_NUM_THREADS=1 \ From 2213b247ee1be46af31fa3c1eba6d54e29b55f23 Mon Sep 17 00:00:00 2001 From: miykael Date: Wed, 10 Oct 2018 03:11:38 -0400 Subject: [PATCH 5/7] FIX: update spm and miniconda syntax for neurodocker cmd --- docker/generate_dockerfiles.sh | 14 ++++++-------- 1 file changed, 6 insertions(+), 8 deletions(-) diff --git a/docker/generate_dockerfiles.sh b/docker/generate_dockerfiles.sh index e3cf19a019..9f68cb258b 100755 --- a/docker/generate_dockerfiles.sh +++ b/docker/generate_dockerfiles.sh @@ -67,7 +67,7 @@ function generate_base_dockerfile() { docker run --rm "$NEURODOCKER_IMAGE" generate docker \ --base "$BASE_IMAGE" --pkg-manager "$PKG_MANAGER" \ --label maintainer="The nipype developers https://github.com/nipy/nipype" \ - --spm version=12 matlab_version=R2017a \ + --spm12 version=r7219 \ --afni version=latest install_python2=true \ --freesurfer version=6.0.0 min=true \ --run 'echo "cHJpbnRmICJrcnp5c3p0b2YuZ29yZ29sZXdza2lAZ21haWwuY29tXG41MTcyXG4gKkN2dW12RVYzelRmZ1xuRlM1Si8yYzFhZ2c0RVxuIiA+IC9vcHQvZnJlZXN1cmZlci9saWNlbnNlLnR4dAo=" | base64 -d | sh' \ @@ -75,8 +75,7 @@ function generate_base_dockerfile() { fusefat g++ git graphviz make ruby unzip xvfb \ --add-to-entrypoint "source /etc/fsl/fsl.sh" \ --env ANTSPATH='/usr/lib/ants' PATH='/usr/lib/ants:$PATH' \ - --run "gem install fakes3" \ - --no-check-urls > "$DIR/Dockerfile.base" + --run "gem install fakes3" > "$DIR/Dockerfile.base" } @@ -86,7 +85,7 @@ function generate_main_dockerfile() { --label maintainer="The nipype developers https://github.com/nipy/nipype" \ --env MKL_NUM_THREADS=1 OMP_NUM_THREADS=1 \ --user neuro \ - --miniconda env_name=neuro \ + --miniconda create_env=neuro \ activate=true \ --copy docker/files/run_builddocs.sh docker/files/run_examples.sh \ docker/files/run_pytests.sh nipype/external/fsl_imglob.py /usr/bin/ \ @@ -100,13 +99,13 @@ function generate_main_dockerfile() { && chown neuro /work' \ --user neuro \ --arg PYTHON_VERSION_MAJOR=3 PYTHON_VERSION_MINOR=6 BUILD_DATE VCS_REF VERSION \ - --miniconda env_name=neuro \ + --miniconda create_env=neuro \ conda_install='python=${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR} icu=58.1 libxml2 libxslt matplotlib mkl numpy paramiko pandas psutil scikit-learn scipy traits=4.6.0' \ pip_opts="-e" \ pip_install="/src/nipype[all]" \ - --miniconda env_name=neuro \ + --miniconda create_env=neuro \ pip_install="grabbit==0.1.2" \ --run-bash "mkdir -p /src/pybids && curl -sSL --retry 5 https://github.com/INCF/pybids/tarball/0.6.5 @@ -121,8 +120,7 @@ function generate_main_dockerfile() { org.label-schema.vcs-ref='$VCS_REF' \ org.label-schema.vcs-url="https://github.com/nipy/nipype" \ org.label-schema.version='$VERSION' \ - org.label-schema.schema-version="1.0" \ - --no-check-urls + org.label-schema.schema-version="1.0" } From 0856b7b8131df12a9db0999c933a7c8fef5100c2 Mon Sep 17 00:00:00 2001 From: miykael Date: Wed, 10 Oct 2018 03:20:57 -0400 Subject: [PATCH 6/7] FIX: update generate_main_dockerfile to new miniconda specification --- docker/generate_dockerfiles.sh | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/docker/generate_dockerfiles.sh b/docker/generate_dockerfiles.sh index 9f68cb258b..64f55f3e53 100755 --- a/docker/generate_dockerfiles.sh +++ b/docker/generate_dockerfiles.sh @@ -86,6 +86,7 @@ function generate_main_dockerfile() { --env MKL_NUM_THREADS=1 OMP_NUM_THREADS=1 \ --user neuro \ --miniconda create_env=neuro \ + conda_install='python=${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}' \ activate=true \ --copy docker/files/run_builddocs.sh docker/files/run_examples.sh \ docker/files/run_pytests.sh nipype/external/fsl_imglob.py /usr/bin/ \ @@ -99,13 +100,12 @@ function generate_main_dockerfile() { && chown neuro /work' \ --user neuro \ --arg PYTHON_VERSION_MAJOR=3 PYTHON_VERSION_MINOR=6 BUILD_DATE VCS_REF VERSION \ - --miniconda create_env=neuro \ - conda_install='python=${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR} - icu=58.1 libxml2 libxslt matplotlib mkl numpy paramiko + --miniconda use_env=neuro \ + conda_install='icu=58.1 libxml2 libxslt matplotlib mkl numpy paramiko pandas psutil scikit-learn scipy traits=4.6.0' \ pip_opts="-e" \ pip_install="/src/nipype[all]" \ - --miniconda create_env=neuro \ + --miniconda use_env=neuro \ pip_install="grabbit==0.1.2" \ --run-bash "mkdir -p /src/pybids && curl -sSL --retry 5 https://github.com/INCF/pybids/tarball/0.6.5 From 912039e685f5d57b0ae6657df4940e75658a5e73 Mon Sep 17 00:00:00 2001 From: miykael Date: Wed, 10 Oct 2018 09:18:01 -0400 Subject: [PATCH 7/7] FIX: revert changes in generate_dockerfiles.sh --- docker/generate_dockerfiles.sh | 32 +++++++++++++++++--------------- 1 file changed, 17 insertions(+), 15 deletions(-) diff --git a/docker/generate_dockerfiles.sh b/docker/generate_dockerfiles.sh index 64f55f3e53..bd1fcb637e 100755 --- a/docker/generate_dockerfiles.sh +++ b/docker/generate_dockerfiles.sh @@ -53,21 +53,21 @@ do done -# neurodocker:master pulled on October 9, 2018 -NEURODOCKER_IMAGE="kaczmarj/neurodocker@sha256:c5c10fc11cbd7efe18ac10d2370742b8ecb3588c3aa9b2c15ca7e18363bfa9dc" +# neurodocker version 0.3.1-22-gb0ee069 +NEURODOCKER_IMAGE="kaczmarj/neurodocker@sha256:f15ca90803f4b89acfca55cd1c7269bf2ec2dfd95b3de1118b08afa34b87d9d1" -# neurodebian:stretch-non-free pulled on October 9, 2018 -BASE_IMAGE="neurodebian@sha256:7cd978427d7ad215834fee221d0536ed7825b3cddebc481eba2d792dfc2f7332" +# neurodebian:stretch-non-free pulled on November 3, 2017 +BASE_IMAGE="neurodebian@sha256:7590552afd0e7a481a33314724ae27f76ccedd05ffd7ac06ec38638872427b9b" NIPYPE_BASE_IMAGE="nipype/nipype:base" PKG_MANAGER="apt" DIR="$(dirname "$0")" function generate_base_dockerfile() { - docker run --rm "$NEURODOCKER_IMAGE" generate docker \ + docker run --rm "$NEURODOCKER_IMAGE" generate \ --base "$BASE_IMAGE" --pkg-manager "$PKG_MANAGER" \ --label maintainer="The nipype developers https://github.com/nipy/nipype" \ - --spm12 version=r7219 \ + --spm version=12 matlab_version=R2017a \ --afni version=latest install_python2=true \ --freesurfer version=6.0.0 min=true \ --run 'echo "cHJpbnRmICJrcnp5c3p0b2YuZ29yZ29sZXdza2lAZ21haWwuY29tXG41MTcyXG4gKkN2dW12RVYzelRmZ1xuRlM1Si8yYzFhZ2c0RVxuIiA+IC9vcHQvZnJlZXN1cmZlci9saWNlbnNlLnR4dAo=" | base64 -d | sh' \ @@ -75,18 +75,18 @@ function generate_base_dockerfile() { fusefat g++ git graphviz make ruby unzip xvfb \ --add-to-entrypoint "source /etc/fsl/fsl.sh" \ --env ANTSPATH='/usr/lib/ants' PATH='/usr/lib/ants:$PATH' \ - --run "gem install fakes3" > "$DIR/Dockerfile.base" + --run "gem install fakes3" \ + --no-check-urls > "$DIR/Dockerfile.base" } function generate_main_dockerfile() { - docker run --rm "$NEURODOCKER_IMAGE" generate docker \ + docker run --rm "$NEURODOCKER_IMAGE" generate \ --base "$NIPYPE_BASE_IMAGE" --pkg-manager "$PKG_MANAGER" \ --label maintainer="The nipype developers https://github.com/nipy/nipype" \ --env MKL_NUM_THREADS=1 OMP_NUM_THREADS=1 \ --user neuro \ - --miniconda create_env=neuro \ - conda_install='python=${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}' \ + --miniconda env_name=neuro \ activate=true \ --copy docker/files/run_builddocs.sh docker/files/run_examples.sh \ docker/files/run_pytests.sh nipype/external/fsl_imglob.py /usr/bin/ \ @@ -100,15 +100,16 @@ function generate_main_dockerfile() { && chown neuro /work' \ --user neuro \ --arg PYTHON_VERSION_MAJOR=3 PYTHON_VERSION_MINOR=6 BUILD_DATE VCS_REF VERSION \ - --miniconda use_env=neuro \ - conda_install='icu=58.1 libxml2 libxslt matplotlib mkl numpy paramiko + --miniconda env_name=neuro \ + conda_install='python=${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR} + icu=58.1 libxml2 libxslt matplotlib mkl numpy paramiko pandas psutil scikit-learn scipy traits=4.6.0' \ pip_opts="-e" \ pip_install="/src/nipype[all]" \ - --miniconda use_env=neuro \ + --miniconda env_name=neuro \ pip_install="grabbit==0.1.2" \ --run-bash "mkdir -p /src/pybids - && curl -sSL --retry 5 https://github.com/INCF/pybids/tarball/0.6.5 + && curl -sSL --retry 5 https://github.com/INCF/pybids/tarball/0.5.1 | tar -xz -C /src/pybids --strip-components 1 && source activate neuro && pip install --no-cache-dir -e /src/pybids" \ @@ -120,7 +121,8 @@ function generate_main_dockerfile() { org.label-schema.vcs-ref='$VCS_REF' \ org.label-schema.vcs-url="https://github.com/nipy/nipype" \ org.label-schema.version='$VERSION' \ - org.label-schema.schema-version="1.0" + org.label-schema.schema-version="1.0" \ + --no-check-urls }