Merge pull request #10 from s-sajid-ali/cleanup_and_ci

refactor & CI with GithubActions

.github/dependabot.yml

@@ -0,0 +1,11 @@
+# Set update schedule for GitHub Actions
+
+version: 2
+updates:
+
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      # Check for updates to GitHub Actions every week
+      interval: "weekly"
+

.github/workflows/ci.yml

@@ -0,0 +1,23 @@
+name: Python package
+
+on: [push]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11", "3.12"]
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: python -m pip install .[test]
+      - name: Test with pytest
+        run: pytest
+

.gitignore

@@ -1,12 +1,169 @@
-# setuptools
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
 build/
+develop-eggs/
 dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
 *.egg-info/
-__pycache__
-*.pyc
+.installed.cfg
+*.egg
+MANIFEST
 
 # conda
 conda_recipe/linux-64/
 conda_recipe/linux-ppc64le/
 conda_recipe/osx-64/
 conda_recipe/win-64/
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# ruff Python linter
+.ruff_cache/
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at /~https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/

README.md

@@ -1,6 +1,6 @@
 # openPMD Updater
 
-[![Build Status `master`](https://img.shields.io/travis/openPMD/openPMD-updater/master.svg?label=master)](https://travis-ci.com/openPMD/openPMD-updater/branches)
+[![CI:ubuntu](https://github.com/openPMD/openPMD-updater/actions/workflows/ci.yml/badge.svg)](https://github.com/openPMD/openPMD-updater/actions/workflows/ci.yml)
 ![Supported Python Versions](https://img.shields.io/pypi/pyversions/openPMD-updater.svg)
 [![License](https://img.shields.io/badge/license-ISC-blue.svg)](https://opensource.org/licenses/ISC)
 
@@ -43,10 +43,10 @@ git clone /~https://github.com/openPMD/openPMD-updater.git
 cd openPMD-updater
 
 # install dependencies
-pip install -r requirements.txt
+pip install .
 
-# optional: append --user
-python setup.py install
+# with optional dependencies for testing
+pip install .[test]
 ```
 
 ## Usage
@@ -77,26 +77,16 @@ updater.update(target_version="2.0.0", in_place=True)
 
 ### Testing
 
+Additional packages need to be installed for the tests. To install them do:
 ```bash
-export PYTHONPATH=$(pwd):$PYTHONPATH
+pip install .[test]
+```
 
+Then one can run the tests as follows:
+```bash
 # all
-nosetests
+pytest
 
 # specific
-nosetests tests/test_backend_h5.py
-
-# manual
-python tests/test_backend_h5.py
-```
-
-*note*: this changes your `example_files/1_1_0/structure.h5` files in-place.
-`git checkout` it for a reset or do a comparison:
-
-```bash
-h5diff -c example_files/1_1_0/structure.h5.bak example_files/1_1_0/structure.h5
-    attribute: <openPMD of </>> and <openPMD of </>>
-    35 differences found
-    Not comparable: <openPMDextension> is of class H5T_INTEGER and <openPMDextension> is of class H5T_STRING
-    # ...
+pytest tests/test_backend_h5.py
 ```

openpmd_updater/Updater.py

@@ -5,10 +5,16 @@
 Authors: Axel Huebl
 License: ISC
 """
+
 import packaging.version
-from openpmd_updater.backends.HDF5 import HDF5
-from openpmd_updater.transforms.v2_0_0 import \
-    DataOrder, GridUnit, ParticleBoundary, ExtensionString, Version
+from .backends.HDF5 import HDF5
+from .transforms.v2_0_0 import (
+    DataOrder,
+    GridUnit,
+    ParticleBoundary,
+    ExtensionString,
+    Version,
+)
 
 
 class Updater(object):
@@ -18,22 +24,22 @@ class Updater(object):
     (see: openpmd_updater.backend.IBackend) for a given file and applies a set
     of transformations (see: openpmd_updater.transforms.ITransform) on it.
     """
+
     def __init__(self, filename, verbose=False):
-        """Open a file with suiteable file format backend.
-        """
+        """Open a file with suiteable file format backend."""
         # supported file format backends
         self.backends = [HDF5]
 
         # dict of updates with each a list of transforms
         #   keys: "to_version" of targeted openPMD standard version
         #   values: ordered list of transforms
         self.updates = {
-            "2.0.0" : [
+            "2.0.0": [
                 DataOrder.DataOrder,  # must be before move of particleBoundary
                 GridUnit.GridUnit,
                 ParticleBoundary.ParticleBoundary,
                 ExtensionString.ExtensionString,
-                Version.Version  # must be last
+                Version.Version,  # must be last
             ]
         }
 
@@ -44,13 +50,14 @@ def __init__(self, filename, verbose=False):
 
         for b in self.backends:
             if self.verbose:
-                print("[Updater] Trying file format {0}".format(type(b)))
+                print("[Updater] Trying file format {0}".format(b.__name__))
             if b.can_handle(filename):
                 self.fb = b(filename)
                 break
         if self.fb is None:
-            raise RuntimeError("No matching file format backend found for "
-                               "{0}!".format(filename))
+            raise RuntimeError(
+                "No matching file format backend found for " "{0}!".format(filename)
+            )
 
     def update(self, new_version="2.0.0", in_place=True):
         """Perform update to new version of the openPMD standard"""
@@ -60,8 +67,15 @@ def update(self, new_version="2.0.0", in_place=True):
         # check if new version is known by the updater
         update_valid = False
         if new_version not in self.updates.keys():
-            raise RuntimeError("Only updates to openPMD standard(s) '{0}' are "
-                               "supported!".format(" ".join(self.updates.keys())))
+            raise RuntimeError(
+                "Only updates to openPMD standard(s) '{0}' are " "supported!".format(
+                    " ".join(self.updates.keys())
+                )
+            )
+
+        if file_version == packaging.version.parse(new_version):
+            print("[Updater] File is at already at the requested version!")
+            return
 
         # select proper update depending on initial version
         #   note: multiple updates over intermediate openPMD standard releases are possible
@@ -70,18 +84,23 @@ def update(self, new_version="2.0.0", in_place=True):
                 if file_version <= packaging.version.parse("1.1.0"):
                     update_valid = True
                     if self.verbose:
-                        print("[Updater] Performing update from {0} to "
-                              "{1}".format(file_version, new_version))
+                        print(
+                            "[Updater] Performing update from {0} to " "{1}".format(
+                                file_version, new_version
+                            )
+                        )
                     for t in self.updates[new_version]:
                         self.fb.cd(None)
                         next_transform = t(self.fb)
                         if self.verbose:
                             name, desc = t.name
-                            print("[Updater] Transform {0}: "
-                                  "{1}".format(name, desc))
+                            print("[Updater] Transform {0}: " "{1}".format(name, desc))
                         next_transform.transform(in_place)
                     file_version = packaging.version.parse(new_version)
 
             if not update_valid:
-                raise RuntimeError("Unsupported openPMD standard '{0}' in file "
-                                   "'{1}':".format(file_version, self.filename))
+                raise RuntimeError(
+                    "Unsupported openPMD standard '{0}' in file " "'{1}':".format(
+                        file_version, self.filename
+                    )
+                )

openpmd_updater/__init__.py

@@ -0,0 +1,5 @@
+"⏫ Update openPMD files to newer versions of the openPMD standard"
+
+from .Updater import *
+from .backends import *
+from .transforms import *