Initial commit

.editorconfig

+root = true
+
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+ij_visual_guides = none
+ij_wrap_on_typing = false
+
+[{*.bash,*.sh,*.zsh}]
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+ij_shell_binary_ops_start_line = false
+ij_shell_keep_column_alignment_padding = false
+ij_shell_minify_program = false
+ij_shell_redirect_followed_by_space = false
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+ij_shell_use_unix_line_separator = true
+
+[{*.har,*.jsb2,*.jsb3,*.json,.babelrc,.eslintrc,.stylelintrc,bowerrc,jest.config}]
+indent_size = 2
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+[{*.markdown,*.md}]
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.gitignore

+dist/*
+*.egg-info
+*.pyc
+
+.coverage
+coverage.xml
+htmlcov/*
+
+# Setuptools SCM
+attribute_wrapper/_version.py
+
+# IDE configuration
+.vscode
+.idea

.gitlab-ci.yml

+default:
+  image: python:3.10  # use latest for building/linting
+  before_script:
+    - python --version # For debugging
+    - python -m pip install --upgrade pip
+    - pip install --upgrade tox twine
+  cache:
+    paths:
+      - .cache/pip
+      # Do not cache .tox, to recreate virtualenvs for every step
+
+stages:
+  - lint
+  # check if this needs to be a separate step
+  # - build_extensions
+  - test
+  - package
+  - integration
+  - publish # publish instead of deploy
+
+# Caching of dependencies to speed up builds
+variables:
+  PIP_CACHE_DIR: "$CI_PROJECT_DIR/.cache/pip"
+
+run_black:
+  stage: lint
+  script:
+    - tox -e black
+  allow_failure: true
+
+run_flake8:
+  stage: lint
+  script:
+    - tox -e pep8
+  allow_failure: true
+
+run_pylint:
+  stage: lint
+  script:
+    - tox -e pylint
+  allow_failure: true
+
+# build_extensions:
+#   stage: build_extensions
+#   script:
+#     - echo "build fortran/c/cpp extension source code"
+
+run_unit_tests_coverage:
+  stage: test
+  image: python:3.7
+  script:
+   - tox -e coverage
+  artifacts:
+    reports:
+      coverage_report:
+        coverage_format: cobertura
+        path: coverage.xml
+    paths:
+      - htmlcov/*
+
+run_unit_tests:
+  stage: test
+  image: python:3.${PY_VERSION}
+  script:
+    - tox -e py3${PY_VERSION}
+  parallel:
+    matrix: # use the matrix for testing
+      - PY_VERSION: [7, 8, 9, 10]
+
+package_files:
+  stage: package
+  artifacts:
+    expire_in: 1w
+    paths:
+      - dist/*
+  script:
+    - tox -e build
+
+package_docs:
+  stage: package
+  artifacts:
+    expire_in: 1w
+    paths:
+      - docs/* # update path to match the dest dir for documentation
+  script:
+    - echo "build and collect docs"
+
+run_integration_tests:
+  stage: integration
+  needs:
+    - package_files
+  script:
+    - echo "make sure to move out of source dir"
+    - echo "install package from filesystem (or use the artefact)"
+    - echo "run against foreign systems (e.g. databases, cwl etc.)"
+
+publish_on_gitlab:
+  stage: publish
+  environment: gitlab
+  needs:
+    - package_files
+  when: manual
+  rules:
+    - if: $CI_COMMIT_TAG
+  script:
+    - echo "run twine for gitlab"
+    - |
+      TWINE_PASSWORD=${CI_JOB_TOKEN} \
+      TWINE_USERNAME=gitlab-ci-token \
+      python -m twine upload \
+      --repository-url ${CI_API_V4_URL}/projects/${CI_PROJECT_ID}/packages/pypi dist/*
+
+publish_on_test_pypi:
+  stage: publish
+  environment: pypi-test
+  needs:
+    - package_files
+  when: manual
+  rules:
+    - if: $CI_COMMIT_TAG
+  script:
+    - echo "run twine for test pypi"
+    # - |
+    #   TWINE_PASSWORD=${PIPY_TOKEN} \
+    #   TWINE_USERNAME=${PIPY_USERNAME} \
+    # TODO: replace URL with a pipy URL
+    #   python -m twine upload \
+    #   --repository-url ${CI_API_V4_URL}/projects/${CI_PROJECT_ID}/packages/pypi dist/*
+
+publish_on_pypi:
+  stage: publish
+  environment: pypi
+  needs:
+    - package_files
+  when: manual
+  rules:
+    - if: $CI_COMMIT_TAG
+  script:
+    - echo "run twine for pypi"
+    # - |
+    #   TWINE_PASSWORD=${PIPY_TOKEN} \
+    #   TWINE_USERNAME=${PIPY_USERNAME} \
+    # TODO: replace URL with a pipy URL
+    #   python -m twine upload \
+    #   --repository-url ${CI_API_V4_URL}/projects/${CI_PROJECT_ID}/packages/pypi dist/*
+
+publish_to_readthedocs:
+  stage: publish
+  environment: readthedocs
+  needs:
+    - package_docs
+  when: manual
+  rules:
+    - if: $CI_COMMIT_TAG
+  script:
+    - echo "scp docs/* ???"

Attribute_wrapper/__init__.py

+""" My Awesome Package """
+
+try:
+    from importlib import metadata
+except ImportError:  # for Python<3.8
+    import importlib_metadata as metadata
+
+__version__ = metadata.version("AttributeWrapper")

Attribute_wrapper/attribute_wrapper.py

+# Copyright (C) 2022 ASTRON (Netherlands Institute for Radio Astronomy)
+# SPDX-License-Identifier: Apache-2.0
+
+import logging
+from functools import reduce
+from operator import mul
+
+import numpy
+from tango import AttrWriteType, AttReqType
+from tango.server import attribute
+
+logger = logging.getLogger()
+
+__all__ = ["AttributeWrapper"]
+
+def fault_on_error():
+    """
+    Wrapper to catch exceptions. Sets the device in a FAULT state if any occurs.
+    """
+
+    def inner(func):
+        @wraps(func)
+        def error_wrapper(device, *args, **kwargs):
+            try:
+                return func(device, *args, **kwargs)
+            except Exception as e:
+                logger.exception("Function failed.")
+                device.Fault(f"FAULT in {func.__name__}: {e.__class__.__name__}: {e}")
+                raise
+
+        return error_wrapper
+
+    return inner
+
+
+class AttributeIO(object):
+    """Holds the I/O functionality for an attribute for a specific device."""
+
+    def __init__(self, device, attribute_wrapper):
+        # Link to the associated device
+        self.device = device
+
+        # Link to the associated attribute wrapper
+        self.attribute_wrapper = attribute_wrapper
+
+        # Link to last (written) value
+        self.cached_value = None
+
+        # Specific read and write functions for this attribute on this device
+        self.read_function = lambda: None
+        self.write_function = lambda value: None
+
+    def cached_read_function(self):
+        """Return the last (written) value, if available. Otherwise, read
+        from the device."""
+
+        if self.cached_value is not None:
+            return self.cached_value
+
+        self.cached_value = self.read_function()
+        return self.cached_value
+
+    def cached_write_function(self, value):
+        """Writes the given value to the device, and updates the cache."""
+
+        # flexible array sizes are not supported by all clients. make sure we only write arrays of maximum size.
+        if self.attribute_wrapper.shape != ():
+            if isinstance(value, numpy.ndarray):
+                value_shape = value.shape
+            else:
+                if len(value) > 0 and isinstance(value[0], list):
+                    # nested list
+                    value_shape = (len(value), len(value[0]))
+                else:
+                    # straight list
+                    value_shape = (len(value),)
+
+            if value_shape != self.attribute_wrapper.shape:
+                raise ValueError(
+                    f"Tried writing an array of shape {value_shape} into an attribute of shape {self.attribute_wrapper.shape}"
+                )
+
+        self.write_function(value)
+        self.cached_value = value
+
+
+class AttributeWrapper(attribute):
+    """
+    Wraps all the attributes in a wrapper class to manage most of the redundant code behind the scenes
+    """
+
+    def __init__(
+        self,
+        comms_id=None,
+        comms_annotation=None,
+        datatype=None,
+        dims=(1,),
+        access=AttrWriteType.READ,
+        **kwargs,
+    ):
+        """
+        wraps around the tango Attribute class. Provides an easier interface for 1d or 2d arrays. Also provides a way to abstract
+        managing the communications interface.
+
+        comms_id: user-supplied identifier that is attached to this object, to identify which communication class will need to be attached
+        comms_annotation: data passed along to the attribute. can be given any form of data. handling is up to client implementation
+        datatype: any numpy datatype
+        dims: dimensions of the attribute as a tuple, or (1,) for a scalar.
+        init_value: value
+        """
+
+        # ensure the type is a numpy array.
+        # see also https://pytango.readthedocs.io/en/stable/server_api/server.html?highlight=devlong#module-tango.server for
+        # more details about type conversion Python/numpy -> PyTango
+        if "numpy" not in str(datatype) and datatype != str and datatype != bool:
+            raise ValueError(
+                f"Attribute needs to be a Tango-supported numpy, str or bool type, but has type {datatype}"
+            )
+
+        self.comms_id = comms_id  # store data that can be used to identify the comms interface to use. not used by the wrapper itself
+        self.comms_annotation = comms_annotation  # store data that can be used by the comms interface. not used by the wrapper itself
+
+        self.datatype = datatype
+
+        if dims == (1,):
+            # scalar
+            # Tango defines a scalar as having dimensions (1,0), see https://pytango.readthedocs.io/en/stable/server_api/attribute.html
+            max_dim_x = 1
+            max_dim_y = 0
+            dtype = datatype
+            shape = ()
+        elif len(dims) == 1:
+            # spectrum
+            max_dim_x = dims[0]
+            max_dim_y = 0
+            dtype = (datatype,)
+            shape = (max_dim_x,)
+        elif len(dims) == 2:
+            # image
+            max_dim_x = dims[1]
+            max_dim_y = dims[0]
+            dtype = ((datatype,),)
+            shape = (max_dim_y, max_dim_x)
+        else:
+            # higher dimensional
+            # >2D arrays collapse into the X and Y dimensions. The Y (major) dimension mirrors the first dimension given, the
+            # rest collapses into the X (minor) dimension.
+            max_dim_x = reduce(mul, dims[1:])
+            max_dim_y = dims[0]
+            dtype = ((datatype,),)
+            shape = (max_dim_y, max_dim_x)
+
+        # actual shape of the data as it is read/written
+        self.shape = shape
+
+        if access == AttrWriteType.READ_WRITE:
+            """If the attribute is of READ_WRITE type, assign the write and read functions to it"""
+
+            # we return the last written value, as we are the only ones in control,
+            # and the hardware does not necessarily return what we've written
+            # (see L2SDP-725).
+
+            @fault_on_error()
+            def write_func_wrapper(device, value):
+                """
+                write_func_wrapper writes a value to this attribute
+                """
+
+                try:
+                    io = self.get_attribute_io(device)
+
+                    return io.cached_write_function(value)
+                except Exception as e:
+                    raise e.__class__(
+                        f"Could not write attribute {comms_annotation}"
+                    ) from e
+
+            @fault_on_error()
+            def read_func_wrapper(device):
+                """
+                read_func_wrapper reads the attribute value, stores it and returns it"
+                """
+
+                # lofar.read_attribute ignores fisallowed. So check again if we're allowed to read.
+                if not device.is_attribute_access_allowed(AttReqType.READ_REQ):
+                    return None
+
+                try:
+                    io = self.get_attribute_io(device)
+
+                    return io.cached_read_function()
+                except Exception as e:
+                    raise e.__class__(
+                        f"Could not read attribute {comms_annotation}"
+                    ) from e
+
+            self.fset = write_func_wrapper
+            self.fget = read_func_wrapper
+        else:
+            """Assign the read function to the attribute"""
+
+            @fault_on_error()
+            def read_func_wrapper(device):
+                """
+                read_func_wrapper reads the attribute value, stores it and returns it"
+                """
+
+                # lofar.read_attribute ignores fisallowed. So check again if we're allowed to read.
+                if not device.is_attribute_access_allowed(AttReqType.READ_REQ):
+                    return None
+
+                try:
+                    io = self.get_attribute_io(device)
+
+                    return io.read_function()
+                except Exception as e:
+                    raise e.__class__(
+                        f"Could not read attribute {comms_annotation}"
+                    ) from e
+
+            self.fget = read_func_wrapper
+
+        # "fisallowed" is called to ask us whether an attribute can be accessed. If not, the attribute won't be accessed,
+        # and the cache not updated. This forces Tango to also force a read the moment an attribute does become accessible.
+        # The provided function will be used with the call signature "(device: Device, req_type: AttReqType) -> bool".
+        #
+        # NOTE: fisallowed=<callable> does not work: https://gitlab.com/tango-controls/pytango/-/issues/435
+        # So we have to use fisallowed=<str> here, which causes the function device.<str> to be called.
+        super().__init__(
+            dtype=dtype,
+            max_dim_y=max_dim_y,
+            max_dim_x=max_dim_x,
+            access=access,
+            fisallowed="is_attribute_access_allowed",
+            format=str(dims),
+            **kwargs,
+        )
+
+    def get_attribute_io(self, device):
+        """
+        returns the attribute I/O functions from a certain device, or registers it if not present
+        """
+
+        try:
+            return device._attribute_wrapper_io[self]
+        except KeyError:
+            device._attribute_wrapper_io[self] = AttributeIO(device, self)
+            return device._attribute_wrapper_io[self]
+
+    def set_comm_client(self, device, client):
+        """
+        takes a communications client as input arguments This client should be of a class containing a "get_mapping" function
+        and return a read and write function that the wrapper will use to get/set data.
+        """
+        try:
+            read_attr_func, write_attr_func = client.setup_attribute(
+                self.comms_annotation, self
+            )
+
+            io = self.get_attribute_io(device)
+            io.read_function = read_attr_func
+            io.write_function = write_attr_func
+        except Exception as e:
+            raise Exception(
+                f"Exception while setting {client.__class__.__name__} attribute with annotation: '{self.comms_annotation}'"
+            ) from e
+
+    async def async_set_comm_client(self, device, client):
+        """
+        Asynchronous version of set_comm_client.
+        """
+        try:
+            read_attr_func, write_attr_func = await client.setup_attribute(
+                self.comms_annotation, self
+            )
+
+            io = self.get_attribute_io(device)
+            io.read_function = read_attr_func
+            io.write_function = write_attr_func
+        except Exception as e:
+            raise Exception(
+                f"Exception while setting {client.__class__.__name__} attribute with annotation: '{self.comms_annotation}'"
+            ) from e
+
+    def set_pass_func(self, device):
+        logger.debug(
+            "using pass function for attribute with annotation: {}".format(
+                self.comms_annotation
+            )
+        )
+
+        io = self.get_attribute_io(device)
+        io.read_function = lambda: None
+        io.write_function = lambda value: None

Attribute_wrapper/cool_module.py

+""" Cool module containing functions, classes and other useful things """
+
+
+def greeter():
+    """Prints a nice message"""
+    print("Hello World!")

LICENSE

+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
+   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+   1. Definitions.
+
+      "License" shall mean the terms and conditions for use, reproduction,
+      and distribution as defined by Sections 1 through 9 of this document.
+
+      "Licensor" shall mean the copyright owner or entity authorized by
+      the copyright owner that is granting the License.
+
+      "Legal Entity" shall mean the union of the acting entity and all
+      other entities that control, are controlled by, or are under common
+      control with that entity. For the purposes of this definition,
+      "control" means (i) the power, direct or indirect, to cause the
+      direction or management of such entity, whether by contract or
+      otherwise, or (ii) ownership of fifty percent (50%) or more of the
+      outstanding shares, or (iii) beneficial ownership of such entity.
+
+      "You" (or "Your") shall mean an individual or Legal Entity
+      exercising permissions granted by this License.
+
+      "Source" form shall mean the preferred form for making modifications,
+      including but not limited to software source code, documentation
+      source, and configuration files.
+
+      "Object" form shall mean any form resulting from mechanical
+      transformation or translation of a Source form, including but
+      not limited to compiled object code, generated documentation,
+      and conversions to other media types.
+
+      "Work" shall mean the work of authorship, whether in Source or
+      Object form, made available under the License, as indicated by a
+      copyright notice that is included in or attached to the work
+      (an example is provided in the Appendix below).
+
+      "Derivative Works" shall mean any work, whether in Source or Object
+      form, that is based on (or derived from) the Work and for which the
+      editorial revisions, annotations, elaborations, or other modifications
+      represent, as a whole, an original work of authorship. For the purposes
+      of this License, Derivative Works shall not include works that remain
+      separable from, or merely link (or bind by name) to the interfaces of,
+      the Work and Derivative Works thereof.
+
+      "Contribution" shall mean any work of authorship, including
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+   See the License for the specific language governing permissions and
+   limitations under the License.

MANIFEST.in

+include LICENSE
+include README.md
+
+recursive-include docs *
+recursive-exclude tests *

README.md

+# Example Python Package
+
+An example repository of an CI/CD pipeline for building, testing and publishing a python package.
+
+If you find some missing functionality with regards to CI/CD, testing, linting or something else, feel free to make a merge request with the proposed changes.
+
+
+## Example of README.md contents below:
+
+## Installation
+```
+pip install .
+```
+
+## Usage
+```
+from my_awesome_app import cool_module
+
+cool_module.greeter()   # prints "Hello World"
+```
+
+## Contributing
+
+To contribute, please create a feature branch and a "Draft" merge request.
+Upon completion, the merge request should be marked as ready and a reviewer
+should be assigned.
+
+Verify your changes locally and be sure to add tests. Verifying local
+changes is done through `tox`.
+
+```pip install tox```
+
+With tox the same jobs as run on the CI/CD pipeline can be ran. These
+include unit tests and linting.
+
+```tox```
+
+To automatically apply most suggested linting changes execute:
+
+```tox -e format```
+
+## License
+This project is licensed under the Apache License Version 2.0

pyproject.toml

+[build-system]
+requires = [
+    "setuptools>=45",
+    "setuptools_scm[toml]>=6.2",
+    "wheel"
+]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools_scm]
+write_to = "attribute_wrapper/_version.py"
+
+[tool.pylint]
+ignore = "_version.py"

requirements.txt

+numpy >= 1.20.0 # BSD

setup.cfg

+[metadata]
+name = AttributeWrapper
+description = #TODO
+long_description = file: README.md
+long_description_content_type = text/markdown
+url = https://git.astron.nl/templates/python-package
+license = Apache License 2.0
+classifiers =
+    Development Status :: 3 - Alpha
+    Environment :: Web Environment
+    Intended Audience :: Developers
+    Intended Audience :: Science/Research
+    License :: OSI Approved :: Apache Software License
+    Operating System :: OS Independent
+    Programming Language :: Python
+    Programming Language :: Python :: 3
+    Programming Language :: Python :: 3 :: Only
+    Programming Language :: Python :: 3.7
+    Programming Language :: Python :: 3.8
+    Programming Language :: Python :: 3.9
+    Programming Language :: Python :: 3.10
+    Topic :: Internet :: WWW/HTTP
+    Topic :: Internet :: WWW/HTTP :: Dynamic Content
+    Topic :: Scientific/Engineering
+    Topic :: Scientific/Engineering :: Astronomy
+
+[options]
+include_package_data = true
+packages = find:
+python_requires = >=3.7
+install_requires =
+    importlib-metadata>=0.12;python_version<"3.8"
+    numpy
+
+[flake8]
+max-line-length = 88
+extend-ignore = E203

setup.py

+import setuptools
+
+setuptools.setup()

tests/requirements.txt

+autopep8 >= 1.7.0 # MIT
+black >= 22.0.0 # MIT
+build >= 0.8.0 # MIT
+flake8 >= 5.0.0 # MIT
+pylint >= 2.15.0 # GPLv2
+pytest >= 7.0.0 # MIT
+pytest-cov >= 3.0.0 # MIT

tox.ini

+[tox]
+# Generative environment list to test all supported Python versions
+envlist = py3{7,8,9,10},black,pep8,pylint
+minversion = 3.18.0
+# Source distributions are explicitly build using tox -e build
+skipsdist = True
+
+[testenv]
+usedevelop = True
+setenv =
+    LANGUAGE=en_US
+    LC_ALL=en_US.UTF-8
+    PYTHONWARNINGS=default::DeprecationWarning
+deps =
+    -r{toxinidir}/requirements.txt
+    -r{toxinidir}/tests/requirements.txt
+commands =
+    {envpython} --version
+    {envpython} -m pytest
+
+[testenv:coverage]
+commands =
+    {envpython} --version
+    {envpython} -m pytest --cov-report xml --cov-report html --cov=map
+
+# Use generative name and command prefixes to reuse the same virtualenv
+# for all linting jobs.
+[testenv:{pep8,black,pylint,format}]
+usedevelop = False
+envdir = {toxworkdir}/linting
+commands =
+    pep8: {envpython} -m flake8 --version
+    pep8: {envpython} -m flake8 --extend-exclude './.venv/','./venv/'
+    black: {envpython} -m black --version
+    black: {envpython} -m black --check --diff .
+    pylint: {envpython} -m pylint --version
+    pylint: {envpython} -m pylint my_awesome_app tests
+    format: {envpython} -m autopep8 -v -aa --in-place --recursive my_awesome_app
+    format: {envpython} -m autopep8 -v -aa --in-place --recursive tests
+    format: {envpython} -m black -v .
+
+
+[testenv:build]
+usedevelop = False
+commands = {envpython} -m build