diff --git a/new-docs/source/examples/real-example.ipynb b/new-docs/source/examples/t1w-preprocess.ipynb similarity index 96% rename from new-docs/source/examples/real-example.ipynb rename to new-docs/source/examples/t1w-preprocess.ipynb index b2aa082a3..3c1271d26 100644 --- a/new-docs/source/examples/real-example.ipynb +++ b/new-docs/source/examples/t1w-preprocess.ipynb @@ -4,7 +4,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Real-world example" + "# T1w MRI preprocessing" ] }, { diff --git a/new-docs/source/explanation/environments.rst b/new-docs/source/explanation/environments.rst new file mode 100644 index 000000000..778b2bc35 --- /dev/null +++ b/new-docs/source/explanation/environments.rst @@ -0,0 +1,4 @@ +Containers and environments +=========================== + +Work in progress... diff --git a/new-docs/source/explanation/provenance.rst b/new-docs/source/explanation/provenance.rst deleted file mode 100644 index 6f97a3ed9..000000000 --- a/new-docs/source/explanation/provenance.rst +++ /dev/null @@ -1,4 +0,0 @@ -Provenance -========== - -Work in progress.... diff --git a/new-docs/source/index.rst b/new-docs/source/index.rst index 17a5b0e52..e95ea081b 100644 --- a/new-docs/source/index.rst +++ b/new-docs/source/index.rst @@ -9,29 +9,38 @@ implement scientific workflows that use a mix of shell commands and Python funct Pydra is developed as an open-source project in the neuroimaging community, but it is designed as a general-purpose dataflow engine to support any scientific domain. -See the :ref:`Design philosophy` for more an explanation of the design -philosophy and goals of Pydra. +See :ref:`Design philosophy` for more an explanation of the design of Pydra. Installation ------------ Pydra itself is a pure-Python package, which has only a handful of dependencies, -therefore, it is straightforward to install via pip +therefore, it is straightforward to install via pip for Python >= 3.11 .. code-block:: bash $ pip install pydra -Of course, if you use Pydra to execute shell-commands tools, you will need to either have -those commands installed on the execution machine, or use software containers -(e.g., Docker or Singularity) to run them. +Pre-designed tasks are available under the `pydra.tasks.*` package namespace. These tasks +are implemented within separate packages that are typically specific to a given shell-command toolkit such as FSL_, AFNI_ or ANTs_, +or a collection of related tasks/workflows (e.g. `niworkflows`_). Pip can be used to +install these packages as well: + + +.. code-block:: bash + + $ pip install pydra-fsl pydra-ants + +Of course, if you use Pydra to execute commands within toolkits, you will need to +either have those commands installed on the execution machine, or use containers +environments (see [Environments](../explanation/environments.html)) to run them. Tutorials --------- * :ref:`Getting started` -* :ref:`Execution options` +* :ref:`Advanced execution` * :ref:`Python-tasks` * :ref:`Shell-tasks` * :ref:`Workflows` @@ -39,7 +48,7 @@ Tutorials Examples -------- -* :ref:`Real-world example` +* :ref:`T1w MRI preprocessing` How-to Guides ------------- @@ -55,6 +64,7 @@ Indices and tables .. toctree:: :maxdepth: 2 + :caption: Execution :hidden: tutorial/getting-started @@ -75,7 +85,7 @@ Indices and tables :caption: Examples :hidden: - examples/real-example + examples/t1w-preprocess .. toctree:: :maxdepth: 2 @@ -92,10 +102,10 @@ Indices and tables explanation/design-approach explanation/splitting-combining + explanation/conditional-lazy explanation/typing explanation/hashing-caching - explanation/conditional-lazy - explanation/provenance + explanation/environments .. toctree:: @@ -104,3 +114,8 @@ Indices and tables :hidden: reference/api + +.. _FSL: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSL +.. _ANTs: http://stnava.github.io/ANTs/ +.. _AFNI: https://afni.nimh.nih.gov/ +.. _niworkflows: https://niworkflows.readthedocs.io/en/latest/ diff --git a/new-docs/source/tutorial/advanced-execution.ipynb b/new-docs/source/tutorial/advanced-execution.ipynb index 59bafe2fd..1105a8f31 100644 --- a/new-docs/source/tutorial/advanced-execution.ipynb +++ b/new-docs/source/tutorial/advanced-execution.ipynb @@ -4,28 +4,39 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Execution options" + "# Advanced execution" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "## Execution plugins" + "## Plugins" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "## Cache locations" + "## Caching results\n", + "\n", + "See [Caching and hashing](../explanation/hashing-caching.html) for more details." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "## Environments" + "## Environments (containers)\n", + "\n", + "See [Containers and Environments](../explanation/environments.rst) for more details." + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Provenance" ] }, {