Merge branch 'dev-v2.0.0' into BBtemplate

.dryrun_test_all.sh

@@ -1,17 +1,17 @@
 #!/bin/bash
 set -euxo pipefail
 HIPPUNFOLD_CACHE_DIR=`pwd`/test_data/fake_models
-hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w
-hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --hemi R
-hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --hemi L
-hippunfold test_data/bids_multiT2w test_out participant -np --modality T2w
-hippunfold test_data/bids_T1w test_out participant -np --modality T1w
-hippunfold test_data/bids_hippb500 test_out participant -np --modality hippb500
-hippunfold test_data/bids_T1w_longitudinal test_out participant -np --modality T1w
-hippunfold test_data/bids_singleT2w_longitudinal test_out participant -np --modality T2w
-hippunfold test_data/bids_segT2w test_out participant -np --modality segT2w
-hippunfold . test_out participant -np --modality cropseg --path_cropseg test_data/data_cropseg/sub-{subject}_hemi-{hemi}_dseg.nii.gz
-hippunfold . test_out participant -np --modality cropseg --path_cropseg test_data/data_cropseg_1hemi/sub-{subject}_hemi-{hemi}_dseg.nii.gz --hemi L
-hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --t1_reg_template
-hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --output_space T1w
-hippunfold test_data/bids_T1w test_out participant -np --modality T1w --use-template-seg
+hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w 
+hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --hemi R 
+hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --hemi L 
+hippunfold test_data/bids_multiT2w test_out participant -np --modality T2w 
+hippunfold test_data/bids_T1w test_out participant -np --modality T1w 
+hippunfold test_data/bids_hippb500 test_out participant -np --modality hippb500 
+hippunfold test_data/bids_T1w_longitudinal test_out participant -np --modality T1w 
+hippunfold test_data/bids_singleT2w_longitudinal test_out participant -np --modality T2w 
+hippunfold test_data/bids_segT2w test_out participant -np --modality segT2w 
+hippunfold . test_out participant -np --modality cropseg --path_cropseg test_data/data_cropseg/sub-{subject}_hemi-{hemi}_dseg.nii.gz 
+hippunfold . test_out participant -np --modality cropseg --path_cropseg test_data/data_cropseg_1hemi/sub-{subject}_hemi-{hemi}_dseg.nii.gz --hemi L 
+hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --t1_reg_template 
+hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --output_space T1w 
+hippunfold test_data/bids_T1w test_out participant -np --modality T1w --use-template-seg 

.github/workflows/python-testing.yml

@@ -35,7 +35,7 @@ jobs:
     needs: ["quality"]
     strategy:
       matrix:
-        python-version: ["3.7", "3.8", "3.9"]
+        python-version: ["3.8", "3.9"]
 
     steps:
       - name: Install non-python dependencies

.gitignore

@@ -1,3 +1,160 @@
-hippunfold.egg-info
-hippunfold/.snakemake
-hippunfold/__pycache__
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/

Dockerfile

@@ -1,4 +1,4 @@
-FROM khanlab/autotop_deps:v0.4.4-fix
+FROM khanlab/hippunfold_deps:v0.5.1
 
 MAINTAINER [email protected]
 

docs/contributing/contributing.md

@@ -75,6 +75,10 @@ from the `hippunfold` folder that contains the
     cd hippunfold
     snakemake -np
 
+## Wet-run testing your workflow:
+
+Opensource data has been made available for wet-run testing any changes to HippUnfold on OSF [here](https://osf.io/k2nme/). These are real opensource data meant ot span a wide array of HippUnfold use cases with various modalities, resolutions, developmental stages, and species. Please note that some changes to hippUnfold will impact all worflows and should be run and then visually inspected for all these cases. Other changes may impact only one workflow (e.g. adding a new template) and so the recommended run parameters should be adjusted accordingly. 
+
 ## Instructions for Compute Canada
 
 This section provides an example of how to set up a `pip installed` copy