From 77f881cb8ef36c7d90cf4b33cad46a3524735520 Mon Sep 17 00:00:00 2001
From: Ali Khan <alik@robarts.ca>
Date: Fri, 17 Dec 2021 19:38:59 -0500
Subject: [PATCH 1/3] replaces setup.py with pyproject.toml and poetry

- should fix dependency issues
- still works with pip install
- however for development-mode (pip install -e ) you will need to use:
poetry install (and install poetry beforehand)
- updates documentation to replace pip install -e with pip install from
pypi
---
 docs/getting_started/installation.rst |    9 +-
 poetry.lock                           | 2718 +++++++++++++++++++++++++
 pyproject.toml                        |   64 +
 setup.py                              |   55 -
 4 files changed, 2784 insertions(+), 62 deletions(-)
 create mode 100644 poetry.lock
 create mode 100644 pyproject.toml
 delete mode 100644 setup.py

diff --git a/docs/getting_started/installation.rst b/docs/getting_started/installation.rst
index e1645456..fb14eed3 100644
--- a/docs/getting_started/installation.rst
+++ b/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 
 ------------------------------------------
 
diff --git a/poetry.lock b/poetry.lock
new file mode 100644
index 00000000..ab13d0f9
--- /dev/null
+++ b/poetry.lock
@@ -0,0 +1,2718 @@
+[[package]]
+name = "appdirs"
+version = "1.4.4"
+description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
+category = "main"
+optional = false
+python-versions = "*"
+
+[[package]]
+name = "argparse"
+version = "1.4.0"
+description = "Python command-line parsing library"
+category = "main"
+optional = false
+python-versions = "*"
+
+[[package]]
+name = "arrow"
+version = "1.2.1"
+description = "Better dates & times for Python"
+category = "main"
+optional = false
+python-versions = ">=3.6"
+
+[package.dependencies]
+python-dateutil = ">=2.7.0"
+typing-extensions = {version = "*", markers = "python_version < \"3.8\""}
+
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+description = "Read/rewrite/write Python ASTs"
+category = "main"
+optional = false
+python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,>=2.7"
+
+[[package]]
+name = "astroid"
+version = "2.9.0"
+description = "An abstract syntax tree for Python with inference support."
+category = "dev"
+optional = false
+python-versions = "~=3.6"
+
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+wrapt = ">=1.11,<1.14"
+
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+name = "astropy"
+version = "4.3.1"
+description = "Astronomy and astrophysics core library"
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+docs = ["sphinx (<4)", "sphinx-astropy (>=1.3)", "pytest", "PyYAML (>=3.13)", "scipy (>=1.1)", "matplotlib (>=3.1,!=3.4.0)", "sphinx-changelog (>=1.1.0)", "packaging"]
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+[package.dependencies]
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+
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+[[package]]
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+
+[package.extras]
+pipfile_deprecated_finder = ["pipreqs", "requirementslib"]
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+
+[package.dependencies]
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+
+[package.extras]
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+
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+[package.dependencies]
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+
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+
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+
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+
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+[package.dependencies]
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+[[package]]
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+
+[package.dependencies]
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+]
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 00000000..a1b08841
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,64 @@
+[tool.poetry]
+name = "hippunfold"
+version = "0.6.9"
+description = "BIDS App for Hippocampal AutoTop (automated hippocampal unfolding and subfield segmentation)"
+authors = ["Jordan DeKraker & Ali Khan <alik@robarts.ca>"]
+
+[tool.poetry.dependencies]
+python = ">=3.7.1,<3.10"
+snakemake = ">=6.0.0"
+snakebids = ">=0.4.0"
+batchgenerators = "0.21"
+nnunet-inference-on-cpu-and-gpu = "1.6.6"
+numpy = ">=1.20.2"
+astropy = "^4.0"
+appdirs = "^1.4.4"
+pandas = "^1.2.0"
+nibabel = "^3.2.1"
+scipy = "^1.7.3"
+nilearn = "^0.8.1"
+seaborn = "^0.11.2"
+Jinja2 = "^3.0.3"
+pygraphviz = "^1.7"
+Pygments = "^2.10.0"
+scikit-fmm = "^2021.10.29"
+
+[tool.poetry.dev-dependencies]
+flake8 = "^4.0.1"
+pytest-console-scripts = "^1.2.1"
+pytest = "^6.2.5"
+black = "^21.10b0"
+pylint = "^2.11.1"
+isort = "^5.10.1"
+poethepoet = "^0.10.0"
+snakefmt = "^0.4.4"
+
+[tool.poetry.scripts]
+hippunfold = "hippunfold.run:main"
+
+
+[build-system]
+requires = ["poetry-core>=1.0.0"]
+build-backend = "poetry.core.masonry.api"
+
+[tool.poe.tasks]
+quality_check = { shell = "isort hippunfold -c && black hippunfold --check && flake8 hippunfold && pylint hippunfold && snakefmt . --check" }
+quality_fix = { shell = "isort hippunfold && black hippunfold  && flake8 hippunfold && pylint hippunfold && snakefmt ." }
+test = "pytest"
+
+[tool.isort]
+profile = "black"
+multi_line_output = 3
+
+[tool.pylint.master]
+ignore-patterns = "^[0-9][0-9]+_,^test_"
+
+[tool.pylint.format]
+good-names = "i,j,k,ex,_,x,y,f,d"
+
+[tool.pylint.messages_control]
+disable = """
+    missing-function-docstring,
+    missing-module-docstring,
+    fixme
+"""
diff --git a/setup.py b/setup.py
deleted file mode 100644
index cc854f19..00000000
--- a/setup.py
+++ /dev/null
@@ -1,55 +0,0 @@
-import setuptools
-import json
-
-with open("README.rst", "r") as fh:
-    long_description = fh.read()
-
-with open('hippunfold/pipeline_description.json', 'r') as fh:
-    pipeline = json.load(fh)
-    name = pipeline['GeneratedBy'][0]['Name']
-    description = pipeline['Name']
-    version = pipeline['GeneratedBy'][0]['Version']
-    url = pipeline['GeneratedBy'][0]['CodeURL']
-    author = pipeline['GeneratedBy'][0]['Author']
-    author_email = pipeline['GeneratedBy'][0]['AuthorEmail']
- 
-setuptools.setup(
-    name=name,
-    version=version,
-    author=author,
-    author_email=author_email,
-    description=description,
-    long_description=long_description,
-    long_description_content_type="text/x-rst",
-    url=url,
-    packages=setuptools.find_packages(),
-    include_package_data=True,
-    classifiers=[
-        "Programming Language :: Python :: 3",
-        "License :: OSI Approved :: MIT License",
-        "Operating System :: OS Independent",
-    ],
-    entry_points={'console_scripts': [
-        'hippunfold=hippunfold.run:main',
-        'hippunfold_download_models=hippunfold.download_models:main'
-    ]},
-    install_requires=[
-        "snakebids>=0.3.10",
-        "snakemake>=6.5.2",
-        "batchgenerators==0.21",
-        "nnunet-inference-on-cpu-and-gpu==1.6.6",
-        "numpy>=1.20.2",
-        "astropy",
-        "appdirs",
-        "pandas",
-        "nibabel",
-        "scipy",
-        "nilearn",
-        "seaborn",
-        "jinja2",
-        "pygraphviz",
-        "pygments",
-        "scikit-fmm"
-    ],
-    python_requires='>=3.7'
-)

From e885b82a5ba004e0d92bd3427f2cf9361e33c14e Mon Sep 17 00:00:00 2001
From: Ali Khan <alik@robarts.ca>
Date: Fri, 17 Dec 2021 19:48:30 -0500
Subject: [PATCH 2/3] remove pip install editable from test workflow

---
 .github/workflows/python-testing.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/python-testing.yml b/.github/workflows/python-testing.yml
index 05cbf985..86cd969d 100644
--- a/.github/workflows/python-testing.yml
+++ b/.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

From 8466af1ad534f08e837e21ff436d7685dd9e9459 Mon Sep 17 00:00:00 2001
From: Ali Khan <alik@robarts.ca>
Date: Fri, 17 Dec 2021 20:47:28 -0500
Subject: [PATCH 3/3] fixes for bumpversion, add deploy workflow

- rolls back to 0.5.0 temporarily (since merging this PR will change version to
0.6.0.pre)
- fixes to find/replace version in all files
- add deploy workflow
---
 .github/workflows/bump_version.yml   |   9 ++-
 .github/workflows/deploy.yml         | 100 +++++++++++++++++++++++++++
 hippunfold/config/snakebids.yml      |  27 +++++++-
 hippunfold/pipeline_description.json |   2 +-
 pyproject.toml                       |   2 +-
 5 files changed, 134 insertions(+), 6 deletions(-)
 create mode 100644 .github/workflows/deploy.yml

diff --git a/.github/workflows/bump_version.yml b/.github/workflows/bump_version.yml
index 2a54c996..2b2f82fa 100644
--- a/.github/workflows/bump_version.yml
+++ b/.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 }}
diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml
new file mode 100644
index 00000000..e6814746
--- /dev/null
+++ b/.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
+
diff --git a/hippunfold/config/snakebids.yml b/hippunfold/config/snakebids.yml
index 5a7d6cab..706c545c 100644
--- a/hippunfold/config/snakebids.yml
+++ b/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
diff --git a/hippunfold/pipeline_description.json b/hippunfold/pipeline_description.json
index 1edfd686..dee0aaa4 100644
--- a/hippunfold/pipeline_description.json
+++ b/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"
diff --git a/pyproject.toml b/pyproject.toml
index a1b08841..bc93d225 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "hippunfold"
-version = "0.6.9"
+version = "0.5.0"
 description = "BIDS App for Hippocampal AutoTop (automated hippocampal unfolding and subfield segmentation)"
 authors = ["Jordan DeKraker & Ali Khan <alik@robarts.ca>"]