Merge pull request #44 from emu-project/dev-refactor

[ENH] Updated package structure

README.md

@@ -1,16 +1,34 @@
 # func_processing
-Pipeline used to take functional data from DICOMs through group-level analyses. Organization is as follows:
+Pipeline used to take functional data from DICOMs through group-level analyses. 
 
-- cli: **User-level entrypoint.** Contains scripts to start AFNI, ASHS, fMRIprep, FreeSurfer, refacing, and data checking workflows.
-- cron: Outdated. Automate cli. Can be used to schedule/automate cli usage.
-- dockerfiles: Contains Dockerfile and scripts used for generating, running docker.
-- docs: Resources for formal documentation, via sphinx. Instructions in build_docs.txt.
-- logs: Mainly for completed_preprocessing.tsv, other output logs written here.
-- qc: Files/scripts for conducting qc on pipeline workflows for non-default options. Also serves as example of user-specified timing files.
-- resources: Location of modules for AFNI, ASHS, FreeSurfer, fMRIprep, and reports.
-- tests: Scripts for testing resources and workflows.
-- workflow: Manages resources, controlled by cli.
+## Entry Points
+Following `python setup.py install` or `python setup.py develop`, use the following entry points to trigger cli.
 
-See [Wiki](https://github.com/emu-project/func_processing/wiki) for details and description.
+- `check` : print help, run `cli.checks`, used to determine which participants have which preprocessed files.
+- `ashs` : trigger help of `cli.ashs`, for running Automated Hippocampal Subfield Segmentation.
+- `reface` : trigger help of `cli.reface`, for de/refacing participant T1w files.
+- `fmriprep` : trigger help of `cli.fmriprep`, for moving data found in `dset` through FreeSurfer and fMRIPrep.
+- `task_subj` : trigger help of `cli.afni_task_subj`, move task EPI output of `fmriprep` through extra preprocessing, deconvolution.
+- `rs_subj` : trigger help of `cli.afni_resting_subj`, move resting EPI output of `fmriprep` through extra preprocessing, deconvolution.
+- `task_group` : trigger help of `cli.afni_task_group`, conduct group-level task EPI analyses.
+- `rs_group` : trigger help of `cli.afni_resting_group`, conduct group-level resting EPI analyses.
 
-Module documentation [here](https://emu-func-processing.readthedocs.io/en/latest/), assuming sphinx is cooperative.
+## Project organization
+
+Top Level
+
+- dockerfiles : Dockerfile, shell script backup
+- docs : Project documentation, for [ReadTheDocs](https://emu-func-processing.readthedocs.io/en/latest/), assuming sphinx is cooperative. Build instruction found in build_docs.txt. 
+- func_processing : Main package
+
+func_processing
+
+- cli : Contains scripts to start AFNI, ASHS, fMRIprep, FreeSurfer, refacing, and data checking workflows.
+- examples : Contains example scripts and files.
+- logs : Mainly for completed_preprocessing.tsv, other output logs written here.
+- resources : Location of modules for AFNI, ASHS, FreeSurfer, fMRIprep, and reports.
+- tests : Scripts for testing resources and workflows.
+- tools : Location for auxiliary/shell scripts. Currently contains (outdated) cron scripts
+- workflow : Manages resources, controlled by cli.
+
+See [Wiki](https://github.com/emu-project/func_processing/wiki) for details and description, now a little outdated due to refactoring.

docs/_build/html/.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: f9ae069b753a0cb0f4029da6874faed6
+config: a4df39dc9917fefea032fc7212f5a7be
 tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/_build/html/_sources/func_processing.resources.afni.rst.txt

@@ -0,0 +1,69 @@
+func\_processing.resources.afni package
+=======================================
+
+Submodules
+----------
+
+func\_processing.resources.afni.copy module
+-------------------------------------------
+
+.. automodule:: func_processing.resources.afni.copy
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+func\_processing.resources.afni.deconvolve module
+-------------------------------------------------
+
+.. automodule:: func_processing.resources.afni.deconvolve
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+func\_processing.resources.afni.group module
+--------------------------------------------
+
+.. automodule:: func_processing.resources.afni.group
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+func\_processing.resources.afni.masks module
+--------------------------------------------
+
+.. automodule:: func_processing.resources.afni.masks
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+func\_processing.resources.afni.motion module
+---------------------------------------------
+
+.. automodule:: func_processing.resources.afni.motion
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+func\_processing.resources.afni.process module
+----------------------------------------------
+
+.. automodule:: func_processing.resources.afni.process
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+func\_processing.resources.afni.submit module
+---------------------------------------------
+
+.. automodule:: func_processing.resources.afni.submit
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: func_processing.resources.afni
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/_build/html/_sources/func_processing.resources.ashs.rst.txt

@@ -0,0 +1,21 @@
+func\_processing.resources.ashs package
+=======================================
+
+Submodules
+----------
+
+func\_processing.resources.ashs.hipseg module
+---------------------------------------------
+
+.. automodule:: func_processing.resources.ashs.hipseg
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: func_processing.resources.ashs
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/_build/html/_sources/func_processing.resources.fmriprep.rst.txt

@@ -0,0 +1,21 @@
+func\_processing.resources.fmriprep package
+===========================================
+
+Submodules
+----------
+
+func\_processing.resources.fmriprep.preprocess module
+-----------------------------------------------------
+
+.. automodule:: func_processing.resources.fmriprep.preprocess
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: func_processing.resources.fmriprep
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/_build/html/_sources/func_processing.resources.reports.rst.txt

@@ -0,0 +1,21 @@
+func\_processing.resources.reports package
+==========================================
+
+Submodules
+----------
+
+func\_processing.resources.reports.check\_complete module
+---------------------------------------------------------
+
+.. automodule:: func_processing.resources.reports.check_complete
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: func_processing.resources.reports
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/_build/html/_sources/func_processing.resources.rst.txt

@@ -0,0 +1,21 @@
+func\_processing.resources package
+==================================
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   func_processing.resources.afni
+   func_processing.resources.ashs
+   func_processing.resources.fmriprep
+   func_processing.resources.reports
+
+Module contents
+---------------
+
+.. automodule:: func_processing.resources
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/resources.rst → docs/_build/html/_sources/func_processing.rst.txt

@@ -1,21 +1,19 @@
-resources package
-=================
+func\_processing package
+========================
 
 Subpackages
 -----------
 
 .. toctree::
    :maxdepth: 4
 
-   resources.afni
-   resources.ashs
-   resources.fmriprep
-   resources.reports
+   func_processing.resources
+   func_processing.workflow
 
 Module contents
 ---------------
 
-.. automodule:: resources
+.. automodule:: func_processing
    :members:
    :undoc-members:
    :show-inheritance:

docs/_build/html/_sources/func_processing.workflow.rst.txt

@@ -0,0 +1,45 @@
+func\_processing.workflow package
+=================================
+
+Submodules
+----------
+
+func\_processing.workflow.control\_afni module
+----------------------------------------------
+
+.. automodule:: func_processing.workflow.control_afni
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+func\_processing.workflow.control\_ashs module
+----------------------------------------------
+
+.. automodule:: func_processing.workflow.control_ashs
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+func\_processing.workflow.control\_fmriprep module
+--------------------------------------------------
+
+.. automodule:: func_processing.workflow.control_fmriprep
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+func\_processing.workflow.control\_reface module
+------------------------------------------------
+
+.. automodule:: func_processing.workflow.control_reface
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: func_processing.workflow
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/_build/html/_sources/index.rst.txt

@@ -1,18 +1,17 @@
-.. emu-func-processing documentation master file, created by
-   sphinx-quickstart on Fri Mar 25 15:40:39 2022.
+.. func_processing documentation master file, created by
+   sphinx-quickstart on Tue May 17 16:53:05 2022.
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
-Welcome to emu-func-processing's documentation!
-===============================================
+Welcome to func_processing's documentation!
+===========================================
 
 .. toctree::
-   :maxdepth: 2
+   :maxdepth: 3
    :caption: Package Contents:
 
    modules
-   workflow
-   resources
+   func_processing
 
 
 Indices and tables

docs/_build/html/_sources/modules.rst.txt

@@ -4,6 +4,5 @@ func_processing
 .. toctree::
    :maxdepth: 4
 
-   resources
+   func_processing
    setup
-   workflow