replaces setup.py with pyproject.toml and poetry

.github/workflows/bump_version.yml

@@ -35,13 +35,20 @@ jobs:
         run: |
           echo "NEW_BUMP=$(($BUMP_VER + 1))" >> $GITHUB_ENV
 
-      - name: Update version in files
+      - name: Update version in pyproject
         uses: jacobtomlinson/gha-find-replace@master
         with:
           include: 'pyproject.toml'
           find: 'version = "(?:([0-9]+\.[0-9]+\.[0-9]+.+)|([0-9]+\.[0-9]+\.[0-9]+))"'
           replace: 'version = "${{ steps.release-drafter.outputs.name }}-pre.${{ env.NEW_BUMP }}"'
 
+      - name: Update version in pipeline_description
+        uses: jacobtomlinson/gha-find-replace@master
+        with:
+          include: 'hippunfold/pipeline_description.json'
+          find: 'version = "(?:([0-9]+\.[0-9]+\.[0-9]+.+)|([0-9]+\.[0-9]+\.[0-9]+))"'
+          replace: 'version = "${{ steps.release-drafter.outputs.name }}-pre.${{ env.NEW_BUMP }}"'
+
       - name: Commit updates
         env:
           SNAKEBIDS_VERSION: ${{ steps.release-drafter.outputs.name }}-pre.${{ env.NEW_BUMP }}

.github/workflows/deploy.yml

@@ -0,0 +1,100 @@
+name: Deploy workflow
+
+on:
+  workflow_dispatch:
+    inputs:
+      author:
+        description: "Author"
+        required: true
+        default: "github-actions[bot] (user publishing release)"
+      date:
+        description: "Date"
+        required: true
+        default: "YYYY-MM-DD"
+      comments:
+        description: "Comments"
+
+jobs:
+  release_changelog:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Print author
+        run: |
+          echo "Author: ${{ github.event.inputs.author }}"
+          echo "Date: ${{ github.event.inputs.date }}"
+          echo "Comments: ${{ github.event.inputs.comments }}"
+
+      - uses: actions/checkout@master
+        with:
+          ref: refs/heads/master
+
+      - name: Draft change log
+        uses: release-drafter/release-drafter@v5
+        id: release-drafter
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Update version in pyproject
+        uses: jacobtomlinson/gha-find-replace@master
+        with:
+          include: 'pyproject.toml'
+          find: 'version = "(?:([0-9]+\.[0-9]+\.[0-9]+.+)|([0-9]+\.[0-9]+\.[0-9]+))"'
+          replace: 'version = "${{ steps.release-drafter.outputs.name }}-pre.${{ env.NEW_BUMP }}"'
+
+      - name: Update version in pipeline_description
+        uses: jacobtomlinson/gha-find-replace@master
+        with:
+          include: 'hippunfold/pipeline_description.json'
+          find: 'version = "(?:([0-9]+\.[0-9]+\.[0-9]+.+)|([0-9]+\.[0-9]+\.[0-9]+))"'
+          replace: 'version = "${{ steps.release-drafter.outputs.name }}-pre.${{ env.NEW_BUMP }}"'
+
+      - name: Commit updates
+        env:
+          LATEST_VERSION: ${{ steps.release-drafter.outputs.name }}
+        run: |
+          git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com"
+          git config --local user.name "github-actions[bot]"
+          git diff-index --quiet HEAD || git commit -m "Bump version to $LATEST_VERSION" -a
+
+      - name: Push changes
+        uses: ad-m/github-push-action@master
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Publish change log
+        uses: release-drafter/release-drafter@v5
+        with:
+          publish: true
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+  deploy:
+    runs-on: ubuntu-latest
+    needs: [release_changelog]
+
+    steps:
+      - uses: actions/checkout@master
+        with:
+          ref: refs/heads/master
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: '3.9'
+
+      #----------------------------------------------
+      #  -----  install & configure poetry  -----
+      #----------------------------------------------
+      - name: Install Poetry
+        uses: snok/install-poetry@v1
+        with:
+          virtualenvs-create: true
+          virtualenvs-in-project: true
+
+      - name: Build and publish
+        env:
+          POETRY_PYPI_TOKEN_PYPI: ${{ secrets.PYPI_API_TOKEN }}
+        run: |
+          poetry publish --build
+

.github/workflows/python-testing.yml

@@ -32,7 +32,7 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         python -m pip install flake8 pytest pytest-console-scripts
-        python -m pip install -e .
+        python -m pip install .
 #    - name: Lint with flake8
 #      run: |
         # stop the build if there are Python syntax errors or undefined names

docs/getting_started/installation.rst

@@ -74,13 +74,9 @@ Option 2:
 
 This assumes you have created and activated a virtualenv or conda environment first.
 
-#. Clone the repository::
-
-    git clone --recursive http://github.com/khanlab/hippunfold
-
-#. Install hippunfold using pip, with the -e option (for development mode)::
+#. Install hippunfold using pip::
 
-    pip install -e ./hippunfold
+    pip install hippunfold
 
 #. Run the following to download the U-net models::
 
@@ -96,7 +92,6 @@ This assumes you have created and activated a virtualenv or conda environment fi
 
 
 
-
 Additional instructions for Compute Canada 
 ------------------------------------------
 

hippunfold/config/snakebids.yml

@@ -1,7 +1,7 @@
-bids_dir: '/path/to/bids/dir'
-output_dir: '/path/to/output/dir' #don't use '.'
+bids_dir: '../test_data/bids_singleT2w'
+output_dir: 'test_output' #don't use '.'
 
-snakebids_dir: '.' #do not modify this variable -- is used to refer to files needed by the workflow when running with CLI
+snakemake_dir: '/localscratch/hippunfold_warps/hippunfold' #do not modify this variable -- is used to refer to files needed by the workflow when running with CLI
 
 #enable printing debug statements during parsing -- disable if generating dag visualization
 debug: False
@@ -365,6 +365,27 @@ laplace_labels:
       - 0 
 
 
+output_spaces:
+  - cropT1w
+
+participant_label:
+exclude_participant_label:
+hemi:
+  - L
+  - R
+output_density:
+  - 2k
+  - 7k
+
+laminar_coords_method: equivolume
+skip_preproc: False
+nnunet_disable_tta: False
+use_gpu: False
+skip_coreg: False
+keep_work: False
+skip_inject_template_labels: False
+
+
 #---- dwi options below, not used in the default workflow ----
 
 #eddy options only used for experimental dwi workflow

hippunfold/pipeline_description.json

@@ -5,7 +5,7 @@
     "GeneratedBy": [
         {
             "Name": "hippunfold",
-            "Version": "0.6.10",
+            "Version": "0.5.0",
             "CodeURL": "https://github.com/khanlab/hippunfold",
             "Author": "Jordan DeKraker & Ali Khan",
             "AuthorEmail": "ali.khan@uwo.ca"