Merge branch 'dev' into axon_parent_validation_fix

.bumpversion.cfg

@@ -1,6 +1,7 @@
 [bumpversion]
-current_version = 1.1.7
+current_version = 1.2.1
 commit = True
 tag = True
 
 [bumpversion:file:neuron_morphology/VERSION.txt]
+

.github/workflows/publish.yml

@@ -0,0 +1,53 @@
+name: Publish Python Package
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  release-build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.9"
+          cache: 'pip'
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -U twine setuptools wheel
+
+      - name: build release distributions
+        run: |
+          python setup.py sdist
+          python setup.py bdist_wheel
+
+      - name: upload windows dists
+        uses: actions/upload-artifact@v4
+        with:
+          name: release-dists
+          path: dist/
+
+  pypi-publish:
+    runs-on: ubuntu-latest
+    needs:
+      - release-build
+    permissions:
+      id-token: write
+
+    steps:
+      - name: Retrieve release distributions
+        uses: actions/download-artifact@v4
+        with:
+          name: release-dists
+          path: dist/
+
+      - name: Publish release distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/python-package-conda.yml

@@ -0,0 +1,84 @@
+name: Python Package using Conda
+
+on: [push]
+
+jobs:
+  build-windows:
+    runs-on: windows-latest
+    strategy:
+      max-parallel: 5
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.9'
+        cache: 'pip'
+    - name: Install dependencies
+      run: |
+        C:\Miniconda\condabin\conda.bat install tqdm openjpeg ruamel.yaml
+        python -m pip install --upgrade pip 
+        pip install -r test_requirements.txt -U
+        pip install -r requirements.txt -U
+        pip install -e .
+    - name: Test with pytest
+      run: |
+        python -m pytest tests/
+  
+  build-linux:
+    runs-on: ubuntu-latest
+    strategy:
+      max-parallel: 5
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.9'
+        cache: 'pip'
+    - name: Install dependencies
+      run: |
+        conda install tqdm openjpeg ruamel.yaml
+        python -m pip install --upgrade pip
+        pip install -r test_requirements.txt -U
+        pip install -r requirements.txt -U
+        pip install -e .
+    - name: Lint with flake8
+      run: |
+        # flake8 already installed via test_requirements.txt
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test with pytest
+      run: |
+        python -m pytest tests/
+  
+  build-mac:
+    runs-on: macos-latest
+    strategy:
+      max-parallel: 5
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.9'
+        cache: 'pip'
+    - name: Set up Conda
+      uses: conda-incubator/setup-miniconda@v3
+    - name: Install dependencies
+      run: |
+        conda install tqdm openjpeg ruamel.yaml
+        brew install hdf5
+        export HDF5_DIR="$(brew --prefix hdf5)"
+        python -m pip install --upgrade pip
+        pip install -r test_requirements.txt -U --disable-pip-version-check
+        pip install -r requirements.txt -U --disable-pip-version-check
+        pip install -e . --disable-pip-version-check
+    - name: Test with pytest
+      run: |
+        python -m pytest tests/

README.md

@@ -1,5 +1,5 @@
-[![Documentation Status](https://readthedocs.org/projects/neuron-morphology/badge/?version=latest)](https://neuron-morphology.readthedocs.io/en/latest/?badge=latest) [![Allen Institute](https://circleci.com/gh/AllenInstitute/neuron_morphology.svg?style=svg)](https://app.circleci.com/pipelines/github/AllenInstitute/neuron_morphology) [![Build status](https://ci.appveyor.com/api/projects/status/7fekclwnq58p61ax?svg=true)](https://ci.appveyor.com/project/fcollman/neuron-morphology)
-
+[![Documentation Status](https://readthedocs.org/projects/neuron-morphology/badge/?version=latest)](https://neuron-morphology.readthedocs.io/en/latest/?badge=latest)
+![build workflow](https://github.com/alleninstitute/neuron_morphology/actions/workflows/python-package-conda.yml/badge.svg)
 
 neuron_morphology
 =================

neuron_morphology/VERSION.txt

@@ -1,2 +1,2 @@
-1.1.7
+1.2.1
 

neuron_morphology/feature_extractor/mark.py

@@ -72,7 +72,7 @@ class RequiresRelativeSomaDepth(Mark):
 
     @classmethod
     def validate(cls, data: Data) -> bool:
-        return data.morphology.has_type(RELATIVE_SOMA_DEPTH)
+        return data.morphology.has_type(SOMA)
 
 class RequiresSoma(Mark):
     """Indicates that these features require a soma."""

neuron_morphology/features/layer/layer_histogram.py

@@ -43,7 +43,7 @@ def ensure_tuple(
         raise ValueError("if_none must be a tuple or \"raise\"")
 
     if inputs is None:
-        if if_none is "raise":
+        if if_none == "raise":
             raise ValueError("inputs were None")
         else:
             return if_none # type: ignore[]

neuron_morphology/transforms/streamline.py

@@ -2,6 +2,7 @@
 import ufl
 import numpy as np
 import dolfinx.fem as fem
+from dolfinx.fem.petsc import LinearProblem
 from dolfinx.io import gmshio
 from typing import List, Tuple
 from mpi4py import MPI
@@ -14,7 +15,7 @@
 
 def solve_laplace_2d(V: fem.FunctionSpace,
                      domain,
-                     bcs: List[fem.bcs.DirichletBCMetaClass]):
+                     bcs: List[fem.bcs.DirichletBC]):
     """
         Solves the laplace equation with boundary conditions bcs on V
 
@@ -30,7 +31,7 @@ def solve_laplace_2d(V: fem.FunctionSpace,
     a = ufl.dot(ufl.grad(u), ufl.grad(v)) * ufl.dx
     L = f * v * ufl.dx
 
-    problem = fem.petsc.LinearProblem(a, L, bcs=bcs, petsc_options={"ksp_type": "preonly", "pc_type": "lu"})
+    problem = LinearProblem(a, L, bcs=bcs, petsc_options={"ksp_type": "preonly", "pc_type": "lu"})
     uh = problem.solve()
 
     return uh
@@ -47,7 +48,7 @@ def compute_gradient(uh, W, bcs=[]):
     a = ufl.inner(u, v) * dx
     L = ufl.inner(f, v) * dx
 
-    problem = fem.petsc.LinearProblem(a, L, bcs=bcs, petsc_options={"ksp_type": "preonly", "pc_type": "lu"})
+    problem = LinearProblem(a, L, bcs=bcs, petsc_options={"ksp_type": "preonly", "pc_type": "lu"})
     grad_uh = problem.solve()
 
     return grad_uh
@@ -98,6 +99,7 @@ def generate_laplace_field(top_line: List[Tuple],
 
     # Create mesh with gmsh
     gmsh.initialize()
+    gmsh.clear()
 
     # Set up the points
     point_tags = [gmsh.model.geo.addPoint(x, y, 0, meshSize=mesh_res)
@@ -123,7 +125,8 @@ def generate_laplace_field(top_line: List[Tuple],
     # import mesh into dolfinx
     gmsh_model_rank = 0
     mesh_comm = MPI.COMM_WORLD
-    domain, cell_markers, facet_markers = gmshio.model_to_mesh(gmsh.model, mesh_comm, gmsh_model_rank, gdim=gdim)
+    domain, cell_markers, facet_markers = gmshio.model_to_mesh(
+        gmsh.model, mesh_comm, gmsh_model_rank, gdim=gdim)
 
     # Create variational space
     V = fem.FunctionSpace(domain, ("CG", 1))

tests/pipeline/test_post_data_to_s3.py

@@ -2,7 +2,7 @@
 import os
 import boto3
 import zipfile
-from moto import mock_s3
+from moto import mock_aws
 import unittest
 
 from neuron_morphology.pipeline.post_data_to_s3 import post_object_to_s3, zip_files
@@ -35,7 +35,7 @@ def test_zip_files(self):
 
         self.assertListEqual(self.mock_listing, file_list)
 
-@mock_s3
+@mock_aws
 def test_post_data_to_s3(tmpdir_factory):
 
     temp_output_dir = str(tmpdir_factory.mktemp("test"))