diff --git a/docs/bids_app/workflow.md b/docs/bids_app/workflow.md index bb456d89..86bd9b27 100644 --- a/docs/bids_app/workflow.md +++ b/docs/bids_app/workflow.md @@ -30,11 +30,11 @@ Snakebids workflow features The [](#snakebids.bids) function generates a properly-formatted BIDS filename with the specified entities, as documented in more detail elsewhere in this documentation. -[](#snakebids.generate_inputs) returns an instance of [](#snakebids.BidsDataset), a special [](#dict) with keys mapping to the {class}`~snakebids.BidsComponents` defined in [the config file](/bids_app/config). Each {class}`~snakebids.BidsComponent` contains a number of attributes to assist processing a BIDS dataset with snakemake. {func}`~snakebids.generate_inputs` should be called at the beginning of the workflow and assigned to a variable called `inputs`. +[](#snakebids.generate_inputs) returns an instance of [](#snakebids.BidsDataset), a special with keys mapping to the {class}`BidsComponents ` defined in [the config file](/bids_app/config). Each {class}`~snakebids.BidsComponent` contains a number of attributes to assist processing a BIDS dataset with snakemake. {func}`~snakebids.generate_inputs` should be called at the beginning of the workflow and assigned to a variable called `inputs`. -The {attr}`~snakebids.BidsComponent.path` member of [](#snakebids.BidsComponent) is generated by snakebids and contains a list of matched files for every input type. Often, the first rule to be invoked will use one or more entries in `inputs.path` as the input file specification. +The {attr}`~snakebids.BidsComponent.path` member of {class}`~snakebids.BidsComponent` is generated by snakebids and contains a list of matched files for every input type. Often, the first rule to be invoked will use one or more entries in `inputs.path` as the input file specification. -The {attr}`~snakebids.BidsComponent.zip_lists` member of [](#snakebids.BidsComponent) is used with [`bids()`](#snakebids.bids) and [`expand()`](#snakefiles_expand) to fill the wildcards with corresponding values from input files. The usage pattern is as follows: +The {attr}`~snakebids.BidsComponent.zip_lists` member of {class}`~snakebids.BidsComponent` is used with [`bids()`](#snakebids.bids) and [`expand()`](#snakefiles_expand) to fill the wildcards with corresponding values from input files. The usage pattern is as follows: ```py expand( @@ -49,9 +49,9 @@ expand( ) ``` -The {attr}`~snakebids.BidsComponent.wildcards` member of {class}`snakebids.BidsComponent` is generated by snakebids and contains a dictionary mapping the wildcards for each input type to snakemake-formatted wildcards, for convenient use in the ``bids`` function. +The {attr}`~snakebids.BidsComponent.wildcards` member of {class}`~snakebids.BidsComponent` is generated by snakebids and contains a dictionary mapping the wildcards for each input type to snakemake-formatted wildcards, for convenient use in the ``bids`` function. ## Accessing the underlying *pybids* dataset -In addition to mapping all of the {class}`~snakebids.BidsComponents` to their names, {class}`~snakebids.BidsDataset` also has a {attr}`~snakebids.BidsDataset.layout` member which gives access to the underlying {class}`BIDSLayout `. This can be used to access advanced pybids features not covered by `snakebids`. Note that if `custom_paths` are specified for every {class}`BidsComponent `, pybids indexing will be skipped and `layout` will be set to `None`. If your workflow relies on accessing this `layout`, you must ensure your users do not provide a `custom_path` for every single component, either in the config file or [via the CLI](/running_snakebids/overview) (``--path_{component}``). +In addition to mapping all of the {class}`BidsComponents ` to their names, {class}`~snakebids.BidsDataset` also has a {attr}`~snakebids.BidsDataset.layout` member which gives access to the underlying {class}`BIDSLayout `. This can be used to access advanced pybids features not covered by `snakebids`. Note that if `custom_paths` are specified for every {class}`BidsComponent `, pybids indexing will be skipped and {attr}`~snakebids.BidsDataset.layout` will be set to `None`. If your workflow relies on accessing this {attr}`~snakebids.BidsDataset.layout`, you must ensure your users do not provide a `custom_path` for every single component, either in the config file or [via the CLI](/running_snakebids/overview) (``--path_{component}``). diff --git a/docs/tutorial/tutorial.md b/docs/tutorial/tutorial.md index eca683cf..a84120af 100644 --- a/docs/tutorial/tutorial.md +++ b/docs/tutorial/tutorial.md @@ -372,11 +372,11 @@ $ snakemake -nq BidsDataset({ "bold": BidsComponent( name="bold", - path="/path/to/bids_bold/sub-{subject}/func/sub-{subject}_task-{task}_run-{run}_bold.nii.gz", + path="/path/to/data/sub-{subject}/func/sub-{subject}_task-{task}_run-{run}_bold.nii.gz", zip_lists={ - "subject": ["1", "2", "2" ], - "task": ["rest", "rest", "rest"], - "run": ["1", "1", "2" ], + "subject": ["001", "001" ], + "task": ["rest", "rest"], + "run": ["1", "2" ], }, ), }) @@ -413,7 +413,7 @@ inputs['bold'].wildcards == { } ``` -This is super useful when combined with {func}`bids() `, as we can use the keyword expansion (`**inputs[].wildcards`{l=python} to set all the wildcard parameters to the {func}`bids() ` function. Thus, we can make our workflow even more general, by replacing this: +This is super useful when combined with {func}`bids() `, as we can use the keyword expansion `**inputs[""].wildcards`{l=python} to set all the wildcard parameters to the {func}`bids() ` function. Thus, we can make our workflow even more general, by replacing this: ```{literalinclude} step6/Snakefile :language: python diff --git a/poetry.lock b/poetry.lock index 493af1c8..7a75c48b 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,3 +1,5 @@ +# This file is automatically @generated by Poetry 1.4.1 and should not be changed by hand. + [[package]] name = "appdirs" version = "1.4.4" @@ -5,6 +7,10 @@ description = "A small Python module for determining appropriate platform-specif category = "main" optional = false python-versions = "*" +files = [ + {file = "appdirs-1.4.4-py2.py3-none-any.whl", hash = "sha256:a841dacd6b99318a741b166adb07e19ee71a274450e68237b4650ca1055ab128"}, + {file = "appdirs-1.4.4.tar.gz", hash = "sha256:7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41"}, +] [[package]] name = "arrow" @@ -13,6 +19,10 @@ description = "Better dates & times for Python" category = "main" optional = false python-versions = ">=3.6" +files = [ + {file = 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