Merge pull request #128 from miykael/update_user_doc_notebooks

ENH: updates notebooks to newest docs/user version

Author: miykael

notebooks/basic_debug.ipynb

@@ -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",

notebooks/basic_execution_configuration.ipynb

@@ -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()"
    ]
   },
   {
@@ -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",
+    "```"
    ]
   },
   {

notebooks/introduction_neurodocker.ipynb

@@ -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"
    ]
   },
@@ -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",
@@ -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\""
    ]
@@ -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",
@@ -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": {},
@@ -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",
@@ -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."
    ]
   }
  ],