diff --git a/README.md b/README.md index b484f6a7..6dfc4434 100644 --- a/README.md +++ b/README.md @@ -21,7 +21,7 @@ _Neurodocker_ is a command-line program that generates custom Dockerfiles and Si Use the _Neurodocker_ Docker image (recommended): ```shell -$ docker run --rm kaczmarj/neurodocker:0.4.0rc1 --help +$ docker run --rm kaczmarj/neurodocker:0.4.0 --help ``` _Note_: Do not use the `-t/--tty` flag with `docker run` or non-printable characters will be a part of the output (see [moby/moby#8513 (comment)](https://github.com/moby/moby/issues/8513#issuecomment-216191236)). @@ -226,7 +226,7 @@ Please see the [examples](examples) directory. ## Canonical examples -The canonical examples install ANTs version 2.2.0 on Ubuntu 18.04. +The canonical examples install ANTs version 2.2.0 on Debian 9 (Stretch). _Note_: Do not use the `-t/--tty` flag with `docker run` or non-printable characters will be a part of the output (see [moby/moby#8513 (comment)](https://github.com/moby/moby/issues/8513#issuecomment-216191236)). @@ -234,21 +234,21 @@ _Note_: Do not use the `-t/--tty` flag with `docker run` or non-printable charac ### Docker ```shell -$ docker run --rm kaczmarj/neurodocker:0.4.0rc1 generate docker \ - --base ubuntu:18.04 --pkg-manager apt --ants version=2.2.0 +$ docker run --rm kaczmarj/neurodocker:0.4.0 generate docker \ + --base debian:stretch --pkg-manager apt --ants version=2.2.0 # Build image by piping Dockerfile to `docker build` -$ docker run --rm kaczmarj/neurodocker:0.4.0rc1 generate docker \ - --base ubuntu:18.04 --pkg-manager apt --ants version=2.2.0 | docker build - +$ docker run --rm kaczmarj/neurodocker:0.4.0 generate docker \ + --base debian:stretch --pkg-manager apt --ants version=2.2.0 | docker build - ``` ### Singularity -Install ANTs on Ubuntu 18.04. +Install ANTs on Debian 9 (Stretch). ```shell -$ docker run --rm kaczmarj/neurodocker:0.4.0rc1 generate singularity \ - --base ubuntu:18.04 --pkg-manager apt --ants version=2.2.0 +$ docker run --rm kaczmarj/neurodocker:0.4.0 generate singularity \ + --base debian:stretch --pkg-manager apt --ants version=2.2.0 ``` diff --git a/neurodocker/neurodocker.py b/neurodocker/neurodocker.py index f582dd19..a8a6edf8 100644 --- a/neurodocker/neurodocker.py +++ b/neurodocker/neurodocker.py @@ -42,7 +42,8 @@ def _list_of_kv(kv): def _add_generate_common_arguments(parser): p = parser - p.add_argument("-b", "--base", help="Base Docker image. Eg, ubuntu:17.04") + p.add_argument( + "-b", "--base", help="Base Docker image. E.g., debian:stretch") p.add_argument( "-p", "--pkg-manager", choices={'apt', 'yum'}, help="Linux package manager.") @@ -127,8 +128,8 @@ def _add_generate_common_arguments(parser): "mrtrix3": "Install MRtrix3. Valid keys are version (required)," " method, and install_path", "neurodebian": "Add NeuroDebian repository. Valid keys are " - "os_codename (eg zesty), server (eg usa-nh), and full" - " (if true, use non-free packages). Valid download" + "os_codename (e.g., zesty), server (e.g., usa-nh), and" + " full (if true, use non-free packages). Valid download" " servers are {}.".format(_ndeb_servers), "spm12": "Install SPM12 and its dependency, Matlab Compiler Runtime." " Valid keys are version and install_path.", @@ -140,8 +141,7 @@ def _add_generate_common_arguments(parser): } pkgs = p.add_argument_group( - title="software package arguments", description=pkgs_help['all'] - ) + title="software package arguments", description=pkgs_help['all']) for pkg in _installation_implementations.keys(): if pkg == '_header': @@ -151,8 +151,7 @@ def _add_generate_common_arguments(parser): nargs = "*" if pkg == "mrtrix3" else "+" pkgs.add_argument( flag, dest=pkg, nargs=nargs, action=OrderedArgs, metavar="", - type=_list_of_kv, help=pkgs_help[pkg] - ) + type=_list_of_kv, help=pkgs_help[pkg]) def _add_generate_docker_arguments(parser): @@ -207,8 +206,7 @@ def create_parser(): """Return command-line argument parser.""" parser = ArgumentParser( - description=__doc__, formatter_class=RawDescriptionHelpFormatter - ) + description=__doc__, formatter_class=RawDescriptionHelpFormatter) verbosity_choices = ('debug', 'info', 'warning', 'error', 'critical') parser.add_argument("-v", "--verbosity", choices=verbosity_choices) @@ -217,10 +215,9 @@ def create_parser(): subparsers = parser.add_subparsers( dest="subparser_name", title="subcommands", - description="valid subcommands" - ) + description="valid subcommands") - # `neurodocker gnerate` parsers. + # `neurodocker generate` parsers. generate_parser = subparsers.add_parser( 'generate', help="generate recipes") generate_subparsers = generate_parser.add_subparsers( diff --git a/neurodocker/version.py b/neurodocker/version.py index fa0e61f9..e16c7b57 100644 --- a/neurodocker/version.py +++ b/neurodocker/version.py @@ -3,7 +3,7 @@ Copied from https://github.com/nipy/nipype/blob/master/nipype/info.py. """ -__version__ = '0.4.0.dev2' +__version__ = '0.4.0' def get_gitversion():