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Oct 10, 2018
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ENH: updates notebooks to newest docs/user version #128

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13 changes: 6 additions & 7 deletions notebooks/basic_debug.ipynb
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Expand Up @@ -21,14 +21,13 @@
" config.enable_debug_mode()\n",
" ```\n",
"\n",
" as the first import of your nipype script. To enable debug logging use:\n",
"\n",
" ```python\n",
" from nipype import logging\n",
" logging.update_logging(config)\n",
" ```\n",
" as the first import of your nipype script.\n",
" \n",
" **Note:**\n",
" - Turning on debug will rerun your workflows and will rerun them after debugging is turned off.\n",
" - Turning on debug mode will also override log levels specified elsewhere, such as in the nipype configuration. \n",
" - `workflow`, `interface` and `utils` loggers will all be set to level `DEBUG`.\n",
" \n",
" **Note:** Turning on debug will rerun your workflows and will rerun them after debugging is turned off.\n",
"\n",
"- There are several configuration options that can help with debugging.\n",
" See [Configuration File](config_file.ipynb) for more details:\n",
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22 changes: 18 additions & 4 deletions notebooks/basic_execution_configuration.ipynb
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Expand Up @@ -276,9 +276,8 @@
"metadata": {},
"outputs": [],
"source": [
"from nipype import config, logging\n",
"config.enable_debug_mode()\n",
"logging.update_logging(config)"
"from nipype import config\n",
"config.enable_debug_mode()"
]
},
{
Expand All @@ -296,8 +295,23 @@
"source": [
"config.set('execution', 'stop_on_first_crash', 'true')\n",
"config.set('execution', 'remove_unnecessary_outputs', 'false')\n",
"config.set('execution', 'keep_inputs', 'true')\n",
"config.set('logging', 'workflow_level', 'DEBUG')\n",
"config.set('logging', 'interface_level', 'DEBUG')"
"config.set('logging', 'interface_level', 'DEBUG')\n",
"config.set('logging', 'utils_level', 'DEBUG')"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"The primary loggers (`workflow`, `interface` and `utils`) are also reset to level `DEBUG`.\n",
"\n",
"You may wish to adjust these manually using:\n",
"```python\n",
"from nipype import logging\n",
"logging.getLogger(<logger>).setLevel(<level>)\n",
"```"
]
},
{
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59 changes: 41 additions & 18 deletions notebooks/introduction_neurodocker.ipynb
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Expand Up @@ -6,13 +6,11 @@
"source": [
"# Neurodocker tutorial\n",
"\n",
"[Neurodocker](https://github.com/kaczmarj/neurodocker) is a brilliant tool to create your own neuroimaging docker container. [Neurodocker](https://github.com/kaczmarj/neurodocker) is a command-line program that enables users to generate [Docker](http://www.docker.io/) containers that include neuroimaging software. These containers can be\n",
"converted to [Singularity](http://singularity.lbl.gov/) containers for use in high-performance computing\n",
"centers.\n",
"This page covers the steps to create containers with [Neurodocker](https://github.com/kaczmarj/neurodocker). [Neurodocker](https://github.com/kaczmarj/neurodocker) is a brilliant tool to create your own neuroimaging docker container. [Neurodocker](https://github.com/kaczmarj/neurodocker) is a command-line program that enables users to generate [Docker](http://www.docker.io/) containers and [Singularity](http://singularity.lbl.gov/) images that include neuroimaging software.\n",
"\n",
"Requirements:\n",
"\n",
"* [Docker](http://www.docker.io/)\n",
"* [Docker](http://www.docker.io/) or [Singularity](http://singularity.lbl.gov/)\n",
"* Internet connection"
]
},
Expand All @@ -24,7 +22,9 @@
"\n",
"To view the Neurodocker help message\n",
"\n",
" docker run --rm kaczmarj/neurodocker:v0.3.2 generate --help\n",
" docker run --rm kaczmarj/neurodocker:v0.4.0 generate [docker|singularity] --help\n",
"\n",
"**Note**: choose between ``docker`` and ``singularity`` in ``[docker|singularity]``.\n",
"\n",
"1. Users must specify a base Docker image and the package manager. Any Docker\n",
" image on DockerHub can be used as your base image. Common base images\n",
Expand All @@ -39,23 +39,26 @@
" machine into the container, and other operations. The list of supported\n",
" neuroimaging software packages is available in the ``neurodocker`` help\n",
" message.\n",
"3. The ``neurodocker`` command will generate a Dockerfile. This Dockerfile can\n",
" be used to build a Docker image with the ``docker build`` command."
"3. The ``neurodocker`` command will generate a Dockerfile or Singularity recipe.\n",
" The Dockerfile can be used with the ``docker build`` command to build a\n",
" Docker image. The Singularity recipe can be used to build a Singularity\n",
" container with the ``singularity build`` command."
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Create a Dockerfile with FSL, Python 3.6, and Nipype\n",
"## Create a Dockerfile or Singularity recipe with FSL, Python 3.6, and Nipype\n",
"\n",
"This command prints a Dockerfile (the specification for a Docker image) to the\n",
"This command prints a Dockerfile (the specification for a Docker image) or a\n",
"Singularity recipe (the specification for a Singularity container) to the\n",
"terminal.\n",
"\n",
" docker run --rm kaczmarj/neurodocker:v0.3.2 generate \\\n",
" docker run --rm kaczmarj/neurodocker:0.4.0 generate [docker|singularity] \\\n",
" --base debian:stretch --pkg-manager apt \\\n",
" --fsl version=5.0.10 \\\n",
" --miniconda env_name=neuro \\\n",
" --miniconda create_env=neuro \\\n",
" conda_install=\"python=3.6 traits\" \\\n",
" pip_install=\"nipype\""
]
Expand All @@ -68,7 +71,7 @@
"\n",
"The Dockerfile can be saved and used to build the Docker image\n",
"\n",
" docker run --rm kaczmarj/neurodocker:v0.3.2 generate \\\n",
" docker run --rm kaczmarj/neurodocker:v0.4.0 generate docker \\\n",
" --base debian:stretch --pkg-manager apt \\\n",
" --fsl version=5.0.10 \\\n",
" --miniconda env_name=neuro \\\n",
Expand All @@ -80,6 +83,24 @@
" docker build --tag my_image - < Dockerfile"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Build the Singularity container\n",
"\n",
"The Singularity recipe can be saved and used to build the Singularity container\n",
"\n",
" docker run --rm kaczmarj/neurodocker:0.4.0 generate singularity \\\n",
" --base debian:stretch --pkg-manager apt \\\n",
" --fsl version=5.0.10 \\\n",
" --miniconda create_env=neuro \\\n",
" conda_install=\"python=3.6 traits\" \\\n",
" pip_install=\"nipype\" > Singularity\n",
"\n",
" singularity build my_nipype.simg Singularity"
]
},
{
"cell_type": "markdown",
"metadata": {},
Expand All @@ -89,7 +110,7 @@
"This example installs AFNI and ANTs from the NeuroDebian repositories. It also\n",
"installs ``git`` and ``vim``.\n",
"\n",
" docker run --rm kaczmarj/neurodocker:v0.3.2 generate \\\n",
" docker run --rm kaczmarj/neurodocker:v0.4.0 generate [docker|singularity] \\\n",
" --base neurodebian:stretch --pkg-manager apt \\\n",
" --install afni ants git vim\n",
"\n",
Expand All @@ -109,19 +130,21 @@
"Miniconda as a non-root user, and activate the Miniconda environment upon\n",
"running the container.\n",
"\n",
" docker run --rm kaczmarj/neurodocker:v0.3.2 generate \\\n",
" docker run --rm kaczmarj/neurodocker:v0.4.0 generate docker \\\n",
" --base centos:7 --pkg-manager yum \\\n",
" --dcm2niix version=master \\\n",
" --dcm2niix version=master method=source \\\n",
" --user neuro \\\n",
" --miniconda env_name=neuro conda_install=\"jupyter traits nipype\" \\\n",
" --miniconda create_env=neuro conda_install=\"jupyter traits nipype\" \\\n",
" > Dockerfile\n",
" docker build --tag my_nipype - < Dockerfile\n",
"\n",
"Copy local files into a container.\n",
"\n",
" docker run --rm kaczmarj/neurodocker:v0.3.2 generate \\\n",
" docker run --rm kaczmarj/neurodocker:v0.4.0 generate [docker|singularity] \\\n",
" --base ubuntu:16.04 --pkg-manager apt \\\n",
" --copy relative/path/to/source.txt /absolute/path/to/destination.txt"
" --copy relative/path/to/source.txt /absolute/path/to/destination.txt\n",
" \n",
"See the [Neurodocker examples page](https://github.com/kaczmarj/neurodocker/tree/master/examples/) for more."
]
}
],
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