build: Update readme and release to point to GitHub releases (#1115)

Instead of depending on 4DNucleome server, just point to GitHub
artifacts

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit

- **New Features**
- Updated download URLs to point to GitHub releases for easier access to
the latest binaries.

- **Chores**
- Updated VM image in Azure Pipelines to Ubuntu 22.04 for enhanced
compatibility.
  - Improved build script to include versioning and progress indicators.

- **Documentation**
  - Enhanced `pyproject.toml` to dynamically include readme information.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->

---------

Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>

Readme.md

@@ -34,10 +34,10 @@ This application is designed to help biologist with segmentation based on thresh
 
 - From binaries:
 
-  - [Windows](https://4dnucleome.cent.uw.edu.pl/PartSeg/Downloads/PartSeg-lastest-windows.zip) (build on Windows 10)
-  - [Linux](https://4dnucleome.cent.uw.edu.pl/PartSeg/Downloads/PartSeg-lastest-linux.zip) (build on Ubuntu 20.04)
-  - [MacOS](https://4dnucleome.cent.uw.edu.pl/PartSeg/Downloads/PartSeg-lastest-macos.zip) (build on MacOS 11)
-    There are reported problems with permissions systems on macOS. If you have problem with starting application please try to run it from terminal.
+  - [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)
+    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:
 

azure-pipelines.yml

@@ -152,7 +152,7 @@ stages:
     dependsOn: GetTestData
     jobs:
       - job: sdist
-        pool: {vmImage: 'Ubuntu-20.04'}
+        pool: {vmImage: 'Ubuntu-22.04'}
         steps:
           - task: UsePythonVersion@0
           - bash: pip install -r requirements/requirements_dev.txt

build_utils/create_and_pack_executable.py

@@ -6,6 +6,7 @@
 import tarfile
 import zipfile
 
+import tqdm
 from PyInstaller.__main__ import run as pyinstaller_run
 
 import PartSeg
@@ -16,9 +17,12 @@
 SYSTEM_NAME_DICT = {"Linux": "linux", "Windows": "windows", "Darwin": "macos"}
 
 
-def create_archive(working_dir):
+def create_archive(working_dir, with_version=True):
     os.makedirs(os.path.join(working_dir, "dist2"), exist_ok=True)
-    file_name = f"PartSeg-{PartSeg.__version__}-{SYSTEM_NAME_DICT[platform.system()]}"
+    if with_version:
+        file_name = f"PartSeg-{PartSeg.__version__}-{SYSTEM_NAME_DICT[platform.system()]}"
+    else:
+        file_name = f"PartSeg-{SYSTEM_NAME_DICT[platform.system()]}"
     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")
@@ -48,11 +52,13 @@ def create_bundle(spec_path, working_dir):
     pyinstaller_run(pyinstaller_args)
 
 
-def archive_build(working_dir, dir_name):
+def archive_build(working_dir, dir_name, with_version=True):
     base_zip_path = os.path.join(working_dir, "dist")
 
-    with create_archive(working_dir) as arch_file:
-        for root, _dirs, files in os.walk(os.path.join(working_dir, "dist", dir_name), topdown=False, followlinks=True):
+    with create_archive(working_dir, with_version=with_version) as arch_file:
+        for root, _dirs, files in tqdm.tqdm(
+            os.walk(os.path.join(working_dir, "dist", dir_name), topdown=False, followlinks=True)
+        ):
             for file_name in files:
                 arch_file.write(
                     os.path.join(root, file_name), os.path.relpath(os.path.join(root, file_name), base_zip_path)
@@ -74,6 +80,7 @@ def main():
 
     fix_qt_location(args.working_dir, dir_name)
     archive_build(args.working_dir, dir_name)
+    archive_build(args.working_dir, dir_name, with_version=False)
 
 
 if __name__ == "__main__":

pyproject.toml

@@ -77,10 +77,12 @@ dependencies = [
 ]
 dynamic = [
     "version",
+    "readme",
 ]
-[project.readme]
-file = "Readme.md"
-content-type = "text/markdown"
+
+#[project.readme]
+#file = "Readme.md"
+#content-type = "text/markdown"
 
 [project.license]
 text = "BSD-3-Clause"

setup.py

@@ -17,14 +17,15 @@ def read(*parts):
 def readme():
     this_directory = os.path.abspath(os.path.dirname(__file__))
     reg = re.compile(r"(!\[[^]]*\])\((images/[^)]*)\)")
-    reg2 = re.compile(r"PartSeg-lastest")
+    reg2 = re.compile(r"releases/latest/download/PartSeg")
     with open(os.path.join(this_directory, "Readme.md")) 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"PartSeg-{get_version()}", text)
+            text = reg2.sub(f"releases/download/v{get_version()}/PartSeg-{get_version()}", text)
+
     with open(os.path.join(this_directory, "changelog.md")) as f:
         chg = f.read()
         text += "\n\n" + chg.replace("# ", "## ")