swcgeom 0.14.0__tar.gz → 0.16.0__tar.gz

swcgeom-0.16.0/.github/workflows/build.yml

@@ -0,0 +1,38 @@
+name: Build Python Package
+
+on:
+  workflow_call:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v3
+        with:
+          python-version: "3.10"
+
+      - name: Get history and tags for SCM versioning to work
+        run: |
+          git fetch --prune --unshallow
+          git fetch --depth=1 origin +refs/tags/*:refs/tags/*
+          git describe --tags
+          git describe --tags $(git rev-list --tags --max-count=1)
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install build
+
+      - name: Build package
+        run: python -m build
+
+      - name: Archive production artifacts
+        uses: actions/upload-artifact@v3
+        with:
+          name: release
+          path: |
+            dist/
+            swcgeom.egg-info/

swcgeom-0.16.0/.github/workflows/github-publish.yml

@@ -0,0 +1,35 @@
+name: Release to GitHub
+
+on:
+  push:
+    tags:
+      - v*
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+    uses: ./.github/workflows/build.yml
+
+  publish:
+    runs-on: ubuntu-latest
+    needs: build
+    steps:
+      - name: Get version
+        id: get_version
+        run: echo ::set-output name=VERSION::${GITHUB_REF/refs\/tags\//}
+
+      - name: Download release
+        uses: actions/download-artifact@v3
+        with:
+          name: release
+
+      - name: Pack release
+        run: tar czf swcgeom-${{ steps.get_version.outputs.VERSION }}.tgz dist/
+
+      - name: Create release
+        uses: softprops/action-gh-release@v1
+        with:
+          token: ${{ secrets.GH_TOKEN }}
+          files: swcgeom-${{ steps.get_version.outputs.VERSION }}.tgz

{swcgeom-0.14.0 → swcgeom-0.16.0}/.github/workflows/pypi-publish.yml

@@ -6,26 +6,26 @@ name: Release to PyPI
 on:
   push:
     tags:
-    - v*
+      - v*
 
 permissions:
   contents: read
 
 jobs:
-  build: 
+  build:
     uses: ./.github/workflows/build.yml
 
-  release:
+  publish:
     runs-on: ubuntu-latest
     needs: build
     steps:
-    - name: Download release
-      uses: actions/download-artifact@v3
-      with:
-        name: release
+      - name: Download release
+        uses: actions/download-artifact@v3
+        with:
+          name: release
 
-    - name: Publish package
-      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
-      with:
-        user: __token__
-        password: ${{ secrets.PYPI_API_TOKEN }}
+      - name: Publish package
+        uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_API_TOKEN }}

{swcgeom-0.14.0 → swcgeom-0.16.0}/.github/workflows/test.yml

@@ -3,7 +3,7 @@ name: Run tests
 on: [push]
 
 jobs:
-  build:
+  test:
     runs-on: ubuntu-latest
     strategy:
       matrix:

{swcgeom-0.14.0 → swcgeom-0.16.0}/.gitignore

@@ -1,5 +1,6 @@
 # Auto generated
 _version.py
+.DS_Store
 
 # Byte-compiled / optimized / DLL files
 __pycache__/

swcgeom-0.16.0/.vscode/settings.json

@@ -0,0 +1,15 @@
+{
+    "[python]": {
+        "editor.defaultFormatter": "ms-python.black-formatter"
+    },
+    "python.analysis.typeCheckingMode": "basic",
+    "python.testing.pytestArgs": [
+        "tests"
+    ],
+    "python.testing.unittestEnabled": false,
+    "python.testing.pytestEnabled": true,
+    "isort.args": [
+        "--profile",
+        "black"
+    ],
+}

{swcgeom-0.14.0 → swcgeom-0.16.0}/CHANGELOG.md

@@ -1,5 +1,87 @@
 # Changelog
 
+## **0.16.0**&emsp;<sub><sup>2024-03-16 ([bf2bf95...7029483](https://github.com/yzx9/swcgeom/compare/bf2bf95ee9fbfb7eba871db7303292f1dfcc7b8f...70294836643e51ca43d039887bbd71de3a9b561b?diff=split))</sup></sub>
+
+### Features
+
+##### &ensp;`analysis`
+
+- add l\-measure support \(close \#13\) ([15ddc33](https://github.com/yzx9/swcgeom/commit/15ddc333c4cdce42fe99fb2383fa0768bc2e35b2))
+
+##### &ensp;`core`
+
+- \`Tree\` accpet values with custom names ([722f84f](https://github.com/yzx9/swcgeom/commit/722f84fdd71133d07e74b5f90171b3671a4fe4c9))
+- add \`Population\.map\` parallel processing support ([a1ee5bb](https://github.com/yzx9/swcgeom/commit/a1ee5bb6344ad5ab7b6572962f3b84caedf1351f))
+
+##### &ensp;`images`
+
+- add image contrast functions ([85b881e](https://github.com/yzx9/swcgeom/commit/85b881e91e878daf6fb3aa2862b5cd62eaa3488b))
+- stat image stack folder ([ffc5e3a](https://github.com/yzx9/swcgeom/commit/ffc5e3a649a4d8203c2530b6351a7b509b262cf3))
+
+##### &ensp;`transforms`
+
+- add basic neuronlucida asc format support \(close \#12\) ([619a275](https://github.com/yzx9/swcgeom/commit/619a275aaa5a311c66e1a2438e6251ee4b9bd703))
+- add \`SGuoImPreProcess\` ([dab7481](https://github.com/yzx9/swcgeom/commit/dab74818e5ea82d27450758f868bdc633b8992bf))
+- add image stack related transforms ([7029483](https://github.com/yzx9/swcgeom/commit/70294836643e51ca43d039887bbd71de3a9b561b))
+
+##### &ensp;`utils`
+
+- \`Tree\` support array like inputs ([1f228d0](https://github.com/yzx9/swcgeom/commit/1f228d055b99c8545ba51da5af2bca8d7b760f3f))
+- download source swc and log from neuromorpho ([d4fbfb6](https://github.com/yzx9/swcgeom/commit/d4fbfb6f0b89990bf63b481333d6c3c3cb16705c))
+
+### Bug Fixes
+
+##### &ensp;`utils`
+
+- expecting a figure from the axes ([bf2bf95](https://github.com/yzx9/swcgeom/commit/bf2bf95ee9fbfb7eba871db7303292f1dfcc7b8f))
+
+### Performance Improvements
+
+##### &ensp;`core`
+
+- use NamedTuple for SWCNames and SWCTypes ([300bfea](https://github.com/yzx9/swcgeom/commit/300bfeac92b90e09f262a850ecc226257c2af2e5))
+
+
+### BREAKING CHANGES
+
+- `core` \`Tree\` accpet values with custom names ([722f84f](https://github.com/yzx9/swcgeom/commit/722f84fdd71133d07e74b5f90171b3671a4fe4c9))
+- `core` remove deprecated \`Tree\.Node\.get\_branch\` and \`Node\.child\_ids\` method ([1de86af](https://github.com/yzx9/swcgeom/commit/1de86afc21451be4c6bde5084688170d901eb625))
+
+<br>
+
+## **0.15.0**&emsp;<sub><sup>2024-01-28 ([d300b41...8c9e0ab](https://github.com/yzx9/swcgeom/compare/d300b41689ee892fe5a23dad57f92e1054c0f9e9...8c9e0ab45c447d3d8121b0cc4178be5f65d18a56?diff=split))</sup></sub>
+
+### Features
+
+##### `core`
+
+- expose subtree id mapping ([35738a3](https://github.com/yzx9/swcgeom/commit/35738a31b2373a43ab29550335a457c51b7befce))
+
+##### `images`
+
+- add dtype support ([d300b41](https://github.com/yzx9/swcgeom/commit/d300b41689ee892fe5a23dad57f92e1054c0f9e9))
+
+##### `transforms`
+
+- generate image stack patch ([decd3a1](https://github.com/yzx9/swcgeom/commit/decd3a1ee63e1657aafa24ec5dfbf7439d25a551))
+- add \`extra\_repr\` api ([ca19361](https://github.com/yzx9/swcgeom/commit/ca1936146783ebccc2ffe25596799580e89b3432))
+
+### Bug Fixes
+
+##### `core`
+
+- fix classmethod typing annotations ([0123eeb](https://github.com/yzx9/swcgeom/commit/0123eeb46142c3c3a695a5cf2495588a2effe275))
+
+##### `transforms`
+
+- should stack images ([8c9e0ab](https://github.com/yzx9/swcgeom/commit/8c9e0ab45c447d3d8121b0cc4178be5f65d18a56))
+
+
+### BREAKING CHANGES
+- `core` remove assembler module ([414533d](https://github.com/yzx9/swcgeom/commit/414533d17238ed45972dff1909cf025a19b7fa1e))
+<br>
+
+
 ## **0.14.0**&emsp;<sub><sup>2023-12-26 ([b9c95f5...cc22018](https://github.com/yzx9/swcgeom/compare/b9c95f58f725490f3b624233cc0be20b31605e53...cc22018ad79af18ecd812b932812a0ff40a0fe40?diff=split))</sup></sub>
 
 ### Features

{swcgeom-0.14.0/swcgeom.egg-info → swcgeom-0.16.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: swcgeom
-Version: 0.14.0
+Version: 0.16.0
 Summary: Neuron geometry library for swc format
 Author-email: yzx9 <yuan.zx@outlook.com>
 License: Apache-2.0
@@ -19,14 +19,14 @@ Requires-Dist: sdflit>=0.2.1
 Requires-Dist: seaborn>=0.12.0
 Requires-Dist: tifffile>=2022.8.12
 Requires-Dist: typing_extensions>=4.4.0
+Requires-Dist: tqdm>=4.46.1
 Requires-Dist: v3d-py-helper>=0.1.0
 Provides-Extra: all
 Requires-Dist: beautifulsoup4>=4.11.1; extra == "all"
 Requires-Dist: certifi>=2023.5.7; extra == "all"
 Requires-Dist: chardet>=5.2.0; extra == "all"
 Requires-Dist: lmdb>=1.4.1; extra == "all"
-Requires-Dist: pycurl>=7.0.0; extra == "all"
-Requires-Dist: tqdm>=4.46.1; extra == "all"
+Requires-Dist: requests>=2.0.0; extra == "all"
 Requires-Dist: urllib3>=1.26.0; extra == "all"
 
 # SWCGEOM

{swcgeom-0.14.0 → swcgeom-0.16.0}/examples/ImageStack.ipynb

@@ -49,6 +49,12 @@
    "outputs": [],
    "source": [
     "trans = ToImageStack(resolution=[1, 1, 1])\n",
+    "\n",
+    "# load entire image stack into memory, should be avoided for large images\n",
+    "x = trans(tree1)\n",
+    "print(x.dtype, x.shape)\n",
+    "\n",
+    "# save image stack to file\n",
     "trans.transform_and_save(\"test.tif\", tree1)"
    ]
   }
@@ -69,7 +75,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.6"
+   "version": "3.12.1"
   },
   "orig_nbformat": 4,
   "vscode": {

{swcgeom-0.14.0 → swcgeom-0.16.0}/examples/pytorch/branch_dataset.py

@@ -8,7 +8,7 @@ import torch
 import torch.utils.data
 from tree_folder_dataset import TreeFolderDataset
 
-from swcgeom import Branch
+from swcgeom.core import Branch
 from swcgeom.transforms import Identity, Transform
 from swcgeom.utils import numpy_err
 

{swcgeom-0.14.0 → swcgeom-0.16.0}/pyproject.toml

@@ -22,6 +22,7 @@ dependencies = [
     "seaborn>=0.12.0",
     "tifffile>=2022.8.12",
     "typing_extensions>=4.4.0",
+    "tqdm>=4.46.1",
     "v3d-py-helper>=0.1.0",
 ]
 
@@ -31,8 +32,7 @@ all = [
     "certifi>=2023.5.7",
     "chardet>=5.2.0",
     "lmdb>=1.4.1",
-    "pycurl>=7.0.0",
-    "tqdm>=4.46.1",
+    "requests>=2.0.0",
     "urllib3>=1.26.0",
 ]
 

{swcgeom-0.14.0 → swcgeom-0.16.0}/swcgeom/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.14.0'
-__version_tuple__ = version_tuple = (0, 14, 0)
+__version__ = version = '0.16.0'
+__version_tuple__ = version_tuple = (0, 16, 0)