From 2c25d55e0a8a15912e08e0ff46424ad555d6577b Mon Sep 17 00:00:00 2001 From: mathiasg Date: Tue, 3 Mar 2020 11:01:28 -0500 Subject: [PATCH 1/5] MAINT: Make py37 explicit --- docs/installation.rst | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/docs/installation.rst b/docs/installation.rst index ec6edd571..fcb51b88d 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -6,7 +6,7 @@ Installation There are two ways to get *fMRIPrep* installed: -* within a `Manually Prepared Environment (Python 3.5+)`_, also known as +* within a `Manually Prepared Environment (Python 3.7+)`_, also known as *bare-metal installation*; or * using container technologies (RECOMMENDED), such as :ref:`run_docker` or :ref:`run_singularity`. @@ -55,10 +55,10 @@ You can check your `Docker Engine`_ installation running their ``hello-world`` i $ docker run --rm hello-world If you have a functional installation, then you should obtain the following output. :: - + Hello from Docker! This message shows that your installation appears to be working correctly. - + To generate this message, Docker took the following steps: 1. The Docker client contacted the Docker daemon. 1. The Docker daemon pulled the "hello-world" image from the Docker Hub. @@ -67,19 +67,19 @@ If you have a functional installation, then you should obtain the following outp executable that produces the output you are currently reading. 1. The Docker daemon streamed that output to the Docker client, which sent it to your terminal. - + To try something more ambitious, you can run an Ubuntu container with: $ docker run -it ubuntu bash - + Share images, automate workflows, and more with a free Docker ID: https://hub.docker.com/ - + For more examples and ideas, visit: https://docs.docker.com/get-started/ After checking your Docker Engine is capable of running Docker images, then go ahead and `check out our documentation `_ to run the *fMRIPrep* image. -The list of Docker images ready to use is found at the `Docker Hub`_, +The list of Docker images ready to use is found at the `Docker Hub`_, under the ``poldracklab/fmriprep`` identifier. The ``fmriprep-docker`` wrapper @@ -106,7 +106,7 @@ Please make sure you `follow our tips and tricks to run fMRIPrep's Singularity i `_. -Manually Prepared Environment (Python 3.5+) +Manually Prepared Environment (Python 3.7+) =========================================== .. warning:: @@ -121,7 +121,7 @@ A relatively interpretable description of how your environment can be set-up is found in the `Dockerfile `_. As an additional installation setting, FreeSurfer requires a license file (see :ref:`fs_license`). -On a functional Python 3.5 (or above) environment with ``pip`` installed, +On a functional Python 3.7 (or above) environment with ``pip`` installed, *fMRIPRep* can be installed using the habitual command :: $ python -m pip install fmriprep @@ -134,7 +134,7 @@ Check your installation with the ``--version`` argument :: External Dependencies --------------------- -*fMRIPRep* is written using Python 3.5 (or above), and is based on +*fMRIPRep* is written using Python 3.7 (or above), and is based on nipype_. *fMRIPRep* requires some other neuroimaging software tools that are From 8688aaef2b47c68a2dea565c0f20ebae28059e03 Mon Sep 17 00:00:00 2001 From: mathiasg Date: Tue, 3 Mar 2020 11:01:48 -0500 Subject: [PATCH 2/5] MAINT: Remove py2 test --- .circleci/config.yml | 13 ------------- 1 file changed, 13 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index a710943c5..bf7ee9ea8 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -232,19 +232,6 @@ jobs: --entrypoint="pytest" poldracklab/fmriprep:latest \ /src/fmriprep/fmriprep -svx --doctest-modules - - run: - name: Test fmriprep-wrapper (Python 2) - command: | - export PY2=$(pyenv versions | grep '2\.' | - sed -e 's/.* 2\./2./' -e 's/ .*//') - pyenv local $PY2 - echo -n "Python version: " - python --version - pip install --upgrade pip setuptools - pip install --upgrade wrapper/ - which fmriprep-docker - fmriprep-docker -i poldracklab/fmriprep:latest --help - fmriprep-docker -i poldracklab/fmriprep:latest --version - run: name: Test fmriprep-wrapper (Python 3) command: | From 6e9859a96e65fc4620aaa01df9437d345a07b049 Mon Sep 17 00:00:00 2001 From: mathiasg Date: Tue, 3 Mar 2020 11:08:33 -0500 Subject: [PATCH 3/5] maint: bump license year [skip ci] --- docs/license.rst | 2 +- fmriprep/__about__.py | 2 +- wrapper/fmriprep_docker.py | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/license.rst b/docs/license.rst index 79df780bc..a3c4b1e08 100644 --- a/docs/license.rst +++ b/docs/license.rst @@ -7,5 +7,5 @@ in the *fMRIPrep* distribution. All trademarks referenced herein are property of their respective holders. -Copyright (c) 2015-2019, the *fMRIPrep* developers and the CRN. +Copyright (c) 2015-2020, the *fMRIPrep* developers and the CRN. All rights reserved. diff --git a/fmriprep/__about__.py b/fmriprep/__about__.py index 3948805de..6fc141e3a 100644 --- a/fmriprep/__about__.py +++ b/fmriprep/__about__.py @@ -8,7 +8,7 @@ del get_versions __packagename__ = 'fmriprep' -__copyright__ = 'Copyright 2019, Center for Reproducible Neuroscience, Stanford University' +__copyright__ = 'Copyright 2020, Center for Reproducible Neuroscience, Stanford University' __credits__ = ('Contributors: please check the ``.zenodo.json`` file at the top-level folder' 'of the repository') __url__ = 'https://github.com/poldracklab/fmriprep' diff --git a/wrapper/fmriprep_docker.py b/wrapper/fmriprep_docker.py index ae3e9b168..41388f3b6 100755 --- a/wrapper/fmriprep_docker.py +++ b/wrapper/fmriprep_docker.py @@ -20,7 +20,7 @@ import subprocess __version__ = '99.99.99' -__copyright__ = 'Copyright 2019, Center for Reproducible Neuroscience, Stanford University' +__copyright__ = 'Copyright 2020, Center for Reproducible Neuroscience, Stanford University' __credits__ = ['Craig Moodie', 'Ross Blair', 'Oscar Esteban', 'Chris Gorgolewski', 'Shoshana Berleant', 'Christopher J. Markiewicz', 'Russell A. Poldrack'] __bugreports__ = 'https://github.com/poldracklab/fmriprep/issues' From d4f9ccac00afa4f7fee52e922a742e4c4f8b14de Mon Sep 17 00:00:00 2001 From: mathiasg Date: Tue, 3 Mar 2020 14:07:15 -0500 Subject: [PATCH 4/5] Revert "MAINT: Remove py2 test" This reverts commit 8688aaef2b47c68a2dea565c0f20ebae28059e03. --- .circleci/config.yml | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/.circleci/config.yml b/.circleci/config.yml index bf7ee9ea8..a710943c5 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -232,6 +232,19 @@ jobs: --entrypoint="pytest" poldracklab/fmriprep:latest \ /src/fmriprep/fmriprep -svx --doctest-modules + - run: + name: Test fmriprep-wrapper (Python 2) + command: | + export PY2=$(pyenv versions | grep '2\.' | + sed -e 's/.* 2\./2./' -e 's/ .*//') + pyenv local $PY2 + echo -n "Python version: " + python --version + pip install --upgrade pip setuptools + pip install --upgrade wrapper/ + which fmriprep-docker + fmriprep-docker -i poldracklab/fmriprep:latest --help + fmriprep-docker -i poldracklab/fmriprep:latest --version - run: name: Test fmriprep-wrapper (Python 3) command: | From 4118d909abd1e6e8ba0d50fd144f53828412a983 Mon Sep 17 00:00:00 2001 From: mathiasg Date: Tue, 3 Mar 2020 14:10:14 -0500 Subject: [PATCH 5/5] MAINT: missed python descs [skip ci] --- .travis.yml | 2 +- setup.cfg | 5 ++--- 2 files changed, 3 insertions(+), 4 deletions(-) diff --git a/.travis.yml b/.travis.yml index 465db5d46..adcc549ea 100644 --- a/.travis.yml +++ b/.travis.yml @@ -6,7 +6,7 @@ cache: - $HOME/.cache/pip python: - - 3.6 + - 3.7 before_install: - python -m pip install --upgrade pip diff --git a/setup.cfg b/setup.cfg index 53840b924..36c570162 100644 --- a/setup.cfg +++ b/setup.cfg @@ -13,12 +13,11 @@ classifiers = Intended Audience :: Science/Research Topic :: Scientific/Engineering :: Image Recognition License :: OSI Approved :: BSD License - Programming Language :: Python :: 3.5 - Programming Language :: Python :: 3.6 Programming Language :: Python :: 3.7 + Programming Language :: Python :: 3.8 [options] -python_requires = >=3.5 +python_requires = >=3.7 install_requires = indexed_gzip >= 0.8.8 nibabel >= 3.0.1