Update snakebids and add conda support

.github/workflows/test.yml

@@ -11,39 +11,50 @@ jobs:
     if: github.event.pull_request.merged == false
     runs-on: ubuntu-latest
     steps:
+      - name: Clone repo
+        uses: actions/checkout@v4
+        with:
+          ref: ${{ github.event.pull_request.head.sha || github.base_ref }}
+
       - name: Setup Python environment
-        uses: khanlab/actions/.github/actions/action-setup_task-installPyProject@v0.3.6
+        uses: prefix-dev/setup-pixi@v0.8.14
         with:
-          python-version: '3.10'
-      - name: yamlfix
-        run: poetry run poe yamlfix-check
-      - name: ruff
-        run: poetry run poe ruff-lint-check
+          environments: >-
+            dev-only
+          activate-environment: dev-only
+
+      - name: isort
+        run: isort scattr/* -c
+
+      - name: Black
+        run: black scattr --check
+
       - name: snakefmt
-        run: poetry run poe snakefmt-check
-  test:
-    runs-on: ubuntu-latest
-    needs: [quality]
-    strategy:
-      matrix:
-        python-version: ['3.8', '3.9', '3.10', '3.11']
-    steps:
-      - name: Setup Python environments
-        uses: khanlab/actions/.github/actions/[email protected]
-        with:
-          python-version: ${{ matrix.python-version }}
-          install-library: true
-      - name: Test minimum inputs
-        run: poetry run poe test_base
-      - name: Test freesurfer input
-        run: poetry run poe test_freesurfer
-      - name: Test responsemean input
-        run: poetry run poe test_responsemean
-      - name: Test dwi input
-        run: poetry run poe test_dwi
-      - name: Test custom labelmerge inputs
-        run: poetry run poe test_labelmerge
-      - name: Test using single atlas (skipping labelmerge)
-        run: poetry run poe test_skip_labelmerge
-      - name: Test sessions
-        run: poetry run poe test_sessions
+        run: snakefmt scattr --check
+
+  # test:
+  #   runs-on: ubuntu-latest
+  #   needs: [quality]
+  #   strategy:
+  #     matrix:
+  #       python-version: ['3.11', '3.12', '3.13']
+  #   steps:
+  #     - name: Setup Python environments
+  #       uses: khanlab/actions/.github/actions/[email protected]
+  #       with:
+  #         python-version: ${{ matrix.python-version }}
+  #         install-library: true
+  #     - name: Test minimum inputs
+  #       run: poetry run poe test_base
+  #     - name: Test freesurfer input
+  #       run: poetry run poe test_freesurfer
+  #     - name: Test responsemean input
+  #       run: poetry run poe test_responsemean
+  #     - name: Test dwi input
+  #       run: poetry run poe test_dwi
+  #     - name: Test custom labelmerge inputs
+  #       run: poetry run poe test_labelmerge
+  #     - name: Test using single atlas (skipping labelmerge)
+  #       run: poetry run poe test_skip_labelmerge
+  #     - name: Test sessions
+  #       run: poetry run poe test_sessions

.gitignore

@@ -19,3 +19,5 @@ __pycache__/
 
 # Ruff
 .ruff_cache
+
+.pixi

.readthedocs.yml

@@ -17,7 +17,7 @@ formats: [pdf]
 build:
   os: ubuntu-20.04
   tools:
-    python: '3.10'
+    python: '3.11'
 python:
   install:
     - requirements: docs/requirements.txt

docs/requirements.txt

@@ -1,5 +1,7 @@
-docutils<0.18
-sphinx-argparse<0.5.0
-sphinx_rtd_theme
-sphinxcontrib-asciinema
-myst-parser
+docutils==0.17
+sphinx-argparse==0.4.0
+sphinx_rtd_theme>=1.0.0
+snakebids>=0.4.0
+myst-parser==1.0.0
+sphinxcontrib.asciinema==0.3.7
+pulp<2.8.0

pyproject.toml

@@ -1,145 +1,63 @@
-[tool.poetry]
+[project]
 name = "scattr"
 version = "0.3.4-pre.1"
 description = "[Snakebids app] Structural connectivity between targeted regions"
-authors = [
-    "Jason Kai <[email protected]>",
-    "Tristan Kuehn",
-    "Ali R. Khan",
-    "Roy A.M. Haast",
-    "Jonathan C. Lau",
-]
 readme = "README.md"
-documentation = "https://scattr.readthedocs.io"
-packages = [{ include = "scattr" }]
-
-[tool.poetry.dependencies]
-python = ">=3.8, <3.12"
-snakebids = "^0.10.2"
-labelmerge = "^0.4.7"
-matplotlib = "^3.7.1"
-nibabel = "^3.2.2"
-nilearn = "^0.10.0"
-niworkflows = "^1.7.9"
-numpy = "^1.22.3"
-pygments = "^2.15.1"
-scipy = "^1.8.0"
-# Required constraint for compatability with snakebids
-pulp = "<2.8.0"
-
-[tool.poetry.group.dev.dependencies]
-pytest-console-scripts = "1.2"
-pytest = "^7.0.1"
-poethepoet = "^0.13.1"
-pre-commit = "^2.17.0"
-snakefmt = "^0.6.1"
-yamlfix = "^1.1.0"
-ruff = "^0.1.14"
-
-[tool.poetry.scripts]
-scattr = 'scattr.run:main'
-
-[build-system]
-requires = ["poetry-core"]
-build-backend = "poetry.core.masonry.api"
-
-[tool.poe.tasks]
+license = "MIT"
+authors = [{name = "Jason Kai, Tristan Kuehn, Roy A.M. Haast & Jonathan C. Lau", email = "[email protected]"}]
+requires-python = ">= 3.11"
+dependencies = []
+scripts = { scattr = "scattr.run:app.run" }
+
+[package.build.backend]
+name = "pixi-build-python"
+version = "==0.4.0"
+
+[tool.pixi.workspace]
+channels = ["conda-forge", "bioconda"]
+platforms = ["linux-64"]
+
+[tool.pixi.feature.runtime.dependencies]
+snakebids = ">=0.14.0,<0.15"
+appdirs   = ">=1.4.4,<2.0.0"
+pyvista   = ">=0.44.2,<0.45.0"
+conda = ">=25.5.0,<26"
+
+[tool.pixi.feature.dev.dependencies]
+flake8 = ">=4.0.1,<5.0.0"
+pytest-console-scripts = ">=1.2.1,<2.0.0"
+pytest = "*"
+black = ">=24.0.0,<25.0.0"
+pylint = ">=2.11.1,<3.0.0"
+isort = ">=5.10.1,<6.0.0"
+poethepoet = ">=0.10.0,<0.11.0"
+snakefmt = ">=0.10.0,<0.11.0"
+pygraphviz = "*"
+Jinja2 = ">=3.0.3,<4.0.0"
+
+[tool.pixi.environments.default]
+features = ["runtime"]
+
+[tool.pixi.environments.dev]
+features = ["runtime", "dev"]
+
+[tool.pixi.environments.dev-only]
+features = ["dev"]
+
+[tool.isort]
+profile = "black"
+multi_line_output = 3
+
+[tool.pixi.pypi-dependencies]
+scattr = { path = ".", editable = true }
+
+[tool.pixi.tasks]
 setup = "pre-commit install"
 ruff-lint = "ruff check --fix scattr"
 ruff-lint-check = "ruff check scattr"
 ruff-format = "ruff format ."
 snakefmt = "snakefmt scattr"
 snakefmt-check = "snakefmt --check scattr"
-quality = ["yamlfix", "ruff-lint", "ruff-format", "snakefmt"]
-quality-check = ["yamlfix-check", "ruff-lint-check", "snakefmt-check"]
-test = [
-    "test_base",
-    "test_freesurfer",
-    "test_responsemean",
-    "test_dwi",
-    "test_labelmerge",
-    "test_skip_labelmerge",
-    "test_sessions",
-]
-
-[tool.poe.tasks.test_base]
-shell = """
-python ./scattr/run.py ./test/data/bids ./test/data/derivatives/ participant \
-    --fs-license ./test/.fs_license -np --force-output
-"""
-
-[tool.poe.tasks.test_freesurfer]
-shell = """
-python ./scattr/run.py ./test/data/bids test/data/derivatives/ participant \
-    --freesurfer_dir ./test/data/derivatives/freesurfer \
-    --fs-license ./test/.fs_license -np --force-output
-"""
-
-[tool.poe.tasks.test_responsemean]
-shell = """
-python ./scattr/run.py ./test/data/bids test/data/derivatives/ participant \
-    --responsemean_dir ./test/data/derivatives/mrtrix/avg \
-    --fs-license ./test/.fs_license -np --force-output
-"""
-
-[tool.poe.tasks.test_dwi]
-shell = """
-python ./scattr/run.py ./test/data/bids_nodwi test/data/derivatives/ \
-    participant --path-dwi \
-    ./test/data/derivatives/prepdwi/sub-{subject}/dwi/sub-{subject}_space-T1w_desc-preproc_dwi.nii.gz \
-    --path-mask \
-    ./test/data/derivatives/prepdwi/sub-{subject}/dwi/sub-{subject}_space-T1w_desc-preproc_mask.nii.gz \
-    --fs-license ./test/.fs_license -np --force-output
-"""
-
-[tool.poe.tasks.test_snakedwi]
-shell = """
-python ./scattr/run.py ./test/data/bids_nodwi test/data/derivatives/ \
-    participant --path-dwi \
-    ./test/data/derivatives/snakedwi/sub-{subject}/dwi/sub-{subject}_space-T1w_desc-eddy_res-orig_dwi.nii.gz \
-    --path-dwi-mask \
-    ./test/data/derivatives/snakedwi/sub-{subject}/dwi/sub-{subject}_space-T1w_desc-eddy_res-orig_mask.nii.gz \
-    --fs-license ./test/.fs_license -np --force-output
-"""
-
-[tool.poe.tasks.test_labelmerge]
-shell = """
-python ./scattr/run.py ./test/data/bids test/data/derivatives/ participant \
-    --labelmerge_base_dir ./base_dir \
-    --labelmerge_overlay_dir ./overlay_dir \
-    --skip_brainstem --skip_thal_seg \
-    --fs-license ./test/.fs_license -np --force-output
-"""
-
-[tool.poe.tasks.test_skip_labelmerge]
-shell = """
-python ./scattr/run.py ./test/data/bids test/data/derivatives/ participant \
-    --skip_labelmerge --skip_brainstem --skip_thal_seg \
-    --fs-license ./test/.fs_license -np --force-output
-"""
-
-[tool.poe.tasks.test_sessions]
-shell = """
-python ./scattr/run.py ./test/data/bids_sessions \
-    test/data/derivatives_sessions/ participant \
-    --fs-license ./test.fs_license -np --force-output
-"""
-
-[tool.poe.tasks.yamlfix]
-shell = """
-find . -type f \\( \
-    -iname \\*.yaml -o -iname \\*.yml ! -iname snakemake* \
-    ! -iname snakebids* \
-\\) -exec yamlfix {} \\;
-"""
-
-[tool.poe.tasks.yamlfix-check]
-shell = """
-find . -type f \\( \
-    -iname \\*.yaml -o -iname \\*.yml ! -iname snakemake* \
-    ! -iname snakebids* \
-\\) -exec yamlfix --check {} \\;
-"""
 
 [tool.ruff]
 select = ["E", "W", "N", "RUF", "I", "UP"]

scattr.egg-info/PKG-INFO

@@ -0,0 +1,71 @@
+Metadata-Version: 2.4
+Name: scattr
+Version: 0.3.4rc1
+Summary: [Snakebids app] Structural connectivity between targeted regions
+Author-email: "Jason Kai, Tristan Kuehn, Roy A.M. Haast & Jonathan C. Lau" <[email protected]>
+License-Expression: MIT
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Dynamic: license-file
+
+# Structural Connectivity Applied To Targeted Regions (SCATTR)
+[![Documentation Status](https://readthedocs.org/projects/scattr/badge/?version=stable)](https://scattr.readthedocs.io/en/stable/?badge=stable)
+![Version](https://img.shields.io/github/v/tag/khanlab/scattr?label=version)
+![Python3](https://img.shields.io/badge/python-3.8_|_3.9_|_3.10_|_3.11-blue.svg)
+[![Tests](https://github.com/khanlab/scattr/actions/workflows/test.yml/badge.svg?branch=main)](https://github.com/khanlab/scattr/actions/workflows/test.yml?query=branch%3Amain)
+![Docker Pulls](https://img.shields.io/docker/pulls/khanlab/scattr)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7636506.svg)](https://doi.org/10.5281/zenodo.7636506)
+
+SCATTR is a BIDS App that performs a tractography processing workflow to 
+identify connections between targetted structures of interest (extracted from
+various atlases) in the brain, using some common neuroimaging tools like 
+`prepdwi`, `Freesurfer`, and `Mrtrix3`.
+
+![Example outputs](https://raw.githubusercontent.com/khanlab/scattr/main/docs/images/ex_output.png)
+
+This is useful for:
+
+* Analyzing structural connections of known brain circuits
+* Examining specific connections of interest
+* Comparison across different groups (e.g. controls vs patients)
+
+
+## Example use of workflow 
+This workflow was used to process and analyze the data from
+[`hcp_subcortical_repo`](https://github.com/kaitj/hcp_subcortical_repro) 
+(see Kai et al., 2022). 
+
+## Workflow 
+A brief summary of the workflow can be found below (see documentation for
+a detailed summary):
+
+_Note: The workflow assumes Freesurfer has already been run on the dataset, as 
+well as diffusion preprocessing (e.g. distortion correction)._
+
+![Workflow example](https://raw.githubusercontent.com/khanlab/scattr/main/docs/images/workflow.png)
+
+1. Merge the segmentations of structures in a standard template space from 
+various sources (if necessary) via 
+[labelmerge](https://zenodo.org/record/7636410) into a combined atlas, which is 
+used downstream to identify targeted connections.
+1. Estimate and apply transformations from standard template space to 
+subject-specific space.
+1. Further process the pre-processed diffusion data to enable tractography
+(e.g. compute response functions, fibre orientation distribution, 
+normalization).
+1. Perform whole-brain tractography from computed files, applying filtering 
+(e.g. SIFT2) to computed tractogram. Once filtered, connections between the 
+merged segmentations (from step 1) are identified, generating a connectome map.
+1. Analysis can then be performed on the map to examine and explore the 
+connectome of interest.
+
+### **Full documentation:** [here](https://scattr.readthedocs.io/en/stable/)
+
+## Relevant Papers
+
+* Kai, J., Khan, A.R., Haast, R.A.M., Lau, J.C. (2022).
+Mapping the subcortical connectome using in vivo diffusion MRI: feasibility
+and reliability. Terra incognita: diving into the human subcortex,
+special issue of NeuroImage. doi: 
+[10.1016/j.neuroimage.2022.119553](https://doi.org/10.1016/j.neuroimage.2022.119553).