Switch from os.path to pathlib

https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html

.gitea/workflows/deploy.yaml

@@ -0,0 +1,53 @@
+name: pyzebra CI/CD pipeline
+
+on:
+  push:
+    branches:
+      - main
+    tags:
+      - '*'
+
+env:
+  CONDA: /opt/miniforge3
+
+jobs:
+  prepare:
+    runs-on: pyzebra
+    steps:
+      - run: $CONDA/bin/conda config --add channels conda-forge
+      - run: $CONDA/bin/conda config --set solver libmamba
+
+  test-env:
+    runs-on: pyzebra
+    needs: prepare
+    if: github.ref == 'refs/heads/main'
+    env:
+      BUILD_DIR: ${{ runner.temp }}/conda_build
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+      - run: $CONDA/bin/conda build --no-anaconda-upload --output-folder $BUILD_DIR ./conda-recipe
+      - run: $CONDA/bin/conda remove --name test --all --keep-env -y
+      - run: $CONDA/bin/conda install --name test --channel $BUILD_DIR python=3.8 pyzebra -y
+      - run: sudo systemctl restart pyzebra-test.service
+
+  prod-env:
+    runs-on: pyzebra
+    needs: prepare
+    if: startsWith(github.ref, 'refs/tags/')
+    env:
+      BUILD_DIR: ${{ runner.temp }}/conda_build
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+      - run: $CONDA/bin/conda build --token ${{ secrets.ANACONDA_TOKEN }} --output-folder $BUILD_DIR ./conda-recipe
+      - run: $CONDA/bin/conda remove --name prod --all --keep-env -y
+      - run: $CONDA/bin/conda install --name prod --channel $BUILD_DIR python=3.8 pyzebra -y
+      - run: sudo systemctl restart pyzebra-prod.service
+
+  cleanup:
+    runs-on: pyzebra
+    needs: [test-env, prod-env]
+    if: always()
+    steps:
+      - run: $CONDA/bin/conda build purge-all

.gitlab-ci.yml

@@ -1,58 +0,0 @@
-stages:
-  - build
-  - deploy
-  - publish
-  - cleanup
-
-workflow:
-  rules:
-    - if: $CI_COMMIT_TAG
-      variables:
-        BUILD_PATH: /home/pyzebra/build-prod
-    - if: $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH
-      variables:
-        BUILD_PATH: /home/pyzebra/build-test
-
-default:
-  before_script:
-    - source /opt/miniconda3/etc/profile.d/conda.sh
-
-build-job:
-  stage: build
-  script:
-    - conda config --add channels conda-forge
-    - conda config --set solver libmamba
-    - conda build --no-anaconda-upload --output-folder $BUILD_PATH ./conda-recipe
-
-deploy-test-job:
-  stage: deploy
-  environment: testing
-  rules:
-    - if: $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH
-  script:
-    - conda activate test
-    - conda install --channel $BUILD_PATH --force-reinstall pyzebra -y
-    - sudo systemctl restart pyzebra-test.service
-
-deploy-prod-job:
-  stage: deploy
-  environment: production
-  rules:
-    - if: $CI_COMMIT_TAG
-  script:
-    - conda activate prod
-    - conda install --channel $BUILD_PATH pyzebra -y
-    - sudo systemctl restart pyzebra-prod.service
-
-publish-job:
-  stage: publish
-  rules:
-    - if: $CI_COMMIT_TAG
-  script:
-    - conda activate base
-    - anaconda --token $ANACONDA_TOKEN upload $(conda build --output-folder $BUILD_PATH ./conda-recipe --output)
-
-cleanup-job:
-  stage: cleanup
-  script:
-    - conda build purge-all

conda-recipe/bld.bat

@@ -1,2 +0,0 @@
-"%PYTHON%" setup.py install --single-version-externally-managed --record=record.txt
-if errorlevel 1 exit 1

conda-recipe/build.sh

@@ -1,2 +0,0 @@
-#!/bin/bash
-$PYTHON setup.py install --single-version-externally-managed --record=record.txt

conda-recipe/meta.yaml

@@ -1,34 +1,36 @@
-{% set data = load_setup_py_data() %}
+{% set version_match = load_file_regex(load_file="pyzebra/__init__.py", regex_pattern='__version__ = "(.+?)"') %}
+{% set version = version_match[1] %}
+{% set pyproject = load_file_data('pyproject.toml') %}
 
 package:
-  name: pyzebra
-  version: {{ data['version'] }}
+  name: {{ pyproject['project']['name'] }}
+  version: {{ version }}
 
 source:
   path: ..
 
 build:
+  script: python -m pip install .
   noarch: python
-  number: 0
   entry_points:
     - pyzebra = pyzebra.app.cli:main
 
 requirements:
-  build:
+  host:
     - python >=3.8
-    - setuptools
+    - hatchling
   run:
     - python >=3.8
-    - numpy
-    - scipy
-    - h5py
-    - bokeh =2.4
-    - numba
-    - lmfit >=1.0.2
+    {% for dep in pyproject['project']['dependencies'] %}
+    - {{ dep }}
+    {% endfor %}
 
 
 about:
-  home: https://gitlab.psi.ch/zebra/pyzebra
-  summary: {{ data['description'] }}
-  license: GNU GPLv3
-  license_file: LICENSE
+  home: {{ pyproject['project']['urls']['Homepage'] }}
+  summary: {{ pyproject['project']['description'] }}
+  license: {{ pyproject['project']['license'] }}
+  license_file:
+    {% for lf in pyproject['project']['license-files'] %}
+    - {{ lf }}
+    {% endfor %}

make_release.py

@@ -4,24 +4,27 @@ import argparse
 import os
 import re
 import subprocess
+from pathlib import Path
 
 
 def main():
+    default_branch = "main"
     branch = subprocess.check_output("git rev-parse --abbrev-ref HEAD", shell=True).decode().strip()
-    if branch != "main":
-        print("Aborting, not on 'main' branch.")
+    if branch != default_branch:
+        print(f"Aborting, not on '{default_branch}' branch.")
         return
 
-    filepath = "pyzebra/__init__.py"
+    project_path = Path(__file__).resolve().parent
+    version_filepath = project_path / project_path.name / "__init__.py"
 
     parser = argparse.ArgumentParser()
     parser.add_argument("level", type=str, choices=["patch", "minor", "major"])
     args = parser.parse_args()
 
-    with open(filepath) as f:
+    with open(version_filepath) as f:
         file_content = f.read()
 
-    version = re.search(r'__version__ = "(.*?)"', file_content).group(1)
+    version = re.search(r'__version__ = "(.+?)"', file_content).group(1)
     major, minor, patch = map(int, version.split(sep="."))
 
     if args.level == "patch":
@@ -36,11 +39,12 @@ def main():
 
     new_version = f"{major}.{minor}.{patch}"
 
-    with open(filepath, "w") as f:
-        f.write(re.sub(r'__version__ = "(.*?)"', f'__version__ = "{new_version}"', file_content))
+    with open(version_filepath, "w") as f:
+        f.write(re.sub(r'__version__ = "(.+?)"', f'__version__ = "{new_version}"', file_content))
 
-    os.system(f"git commit {filepath} -m 'Updating for version {new_version}'")
+    os.system(f"git commit {version_filepath} -m 'Updating for version {new_version}'")
     os.system(f"git tag -a {new_version} -m 'Release {new_version}'")
+    os.system("git push --follow-tags")
 
 
 if __name__ == "__main__":

pyproject.toml

@@ -0,0 +1,35 @@
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[project]
+name = "pyzebra"
+dynamic = ["version"]  # version will be read from __init__.py
+requires-python = ">=3.8"
+dependencies = [
+    "numpy",
+    "scipy",
+    "h5py",
+    "bokeh ~=2.4",
+    "numba",
+    "lmfit >=1.0.2",
+]
+authors = [
+  {name = "Paul Scherrer Institute"}
+]
+maintainers = [
+  {name = "Ivan Usov", email = "ivan.usov@psi.ch"}
+]
+description = "An experimental data analysis library for zebra instrument."
+readme = "README.md"
+license = "GPL-3.0-or-later"
+license-files = ["LICENSE"]
+
+[project.urls]
+Homepage = "https://gitea.psi.ch/zebra/pyzebra"
+
+[tool.hatch.build.targets.wheel]
+include = ["pyzebra"]
+
+[tool.hatch.version]
+path = "pyzebra/__init__.py"

pyzebra/__init__.py

@@ -6,4 +6,4 @@ from pyzebra.sxtal_refgen import *
 from pyzebra.utils import *
 from pyzebra.xtal import *
 
-__version__ = "0.7.10"
+__version__ = "0.7.11"

pyzebra/app/panel_hdf_param_study.py

@@ -364,7 +364,7 @@ def create():
         _update_proj_plots()
 
     proj_auto_checkbox = CheckboxGroup(
-        labels=["Projections Intensity Range:"], active=[0], width=145, margin=[10, 5, 0, 5]
+        labels=["Projections Intensity Range"], active=[0], width=145, margin=[10, 5, 0, 5]
     )
     proj_auto_checkbox.on_change("active", proj_auto_checkbox_callback)
 

pyzebra/app/panel_hdf_viewer.py

@@ -689,7 +689,7 @@ def create():
         _update_image()
 
     main_auto_checkbox = CheckboxGroup(
-        labels=["Frame Intensity Range:"], active=[0], width=145, margin=[10, 5, 0, 5]
+        labels=["Frame Intensity Range"], active=[0], width=145, margin=[10, 5, 0, 5]
     )
     main_auto_checkbox.on_change("active", main_auto_checkbox_callback)
 
@@ -721,7 +721,7 @@ def create():
         _update_proj_plots()
 
     proj_auto_checkbox = CheckboxGroup(
-        labels=["Projections Intensity Range:"], active=[0], width=145, margin=[10, 5, 0, 5]
+        labels=["Projections Intensity Range"], active=[0], width=145, margin=[10, 5, 0, 5]
     )
     proj_auto_checkbox.on_change("active", proj_auto_checkbox_callback)
 

scripts/pyzebra-test.service

@@ -1,11 +0,0 @@
-[Unit]
-Description=pyzebra-test web server
-
-[Service]
-Type=simple
-User=pyzebra
-ExecStart=/bin/bash /usr/local/sbin/pyzebra-test.sh
-Restart=always
-
-[Install]
-WantedBy=multi-user.target

scripts/pyzebra-test.sh

@@ -1,4 +0,0 @@
-source /opt/miniconda3/etc/profile.d/conda.sh
-
-conda activate test
-python /opt/pyzebra/pyzebra/app/cli.py --port=5010 --allow-websocket-origin=pyzebra.psi.ch:5010 --args --spind-path=/opt/spind

scripts/pyzebra.service

@@ -1,10 +0,0 @@
-[Unit]
-Description=pyzebra web server
-
-[Service]
-Type=simple
-ExecStart=/bin/bash /usr/local/sbin/pyzebra.sh
-Restart=always
-
-[Install]
-WantedBy=multi-user.target

scripts/pyzebra.sh

@@ -1,4 +0,0 @@
-source /opt/miniconda3/etc/profile.d/conda.sh
-
-conda activate prod
-pyzebra --port=80 --allow-websocket-origin=pyzebra.psi.ch:80 --args --spind-path=/opt/spind

setup.py

@@ -1,14 +0,0 @@
-import re
-
-from setuptools import find_packages, setup
-
-with open("pyzebra/__init__.py") as f:
-    version = re.search(r'__version__ = "(.*?)"', f.read()).group(1)
-
-setup(
-    name="pyzebra",
-    version=version,
-    description="An experimental data analysis library for zebra instrument.",
-    packages=find_packages(),
-    license="GNU GPLv3",
-)