Merge pull request #17 from openkim/setup-upgrade

Setup upgrade

.github/workflows/pythonpackage.yml

@@ -7,8 +7,9 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-latest, macos-latest]
-        python-version: [3.7, 3.8, 3.9, '3.10', 3.11, 3.12]
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: [3.8, 3.9, '3.10', 3.11, 3.12]
+
     steps:
     - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
@@ -18,23 +19,25 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install kim-edn
+        pip install kim-edn>1.4.0
         pip install coverage
     - name: Lint with flake8
       run: |
         pip install flake8
         # stop the build if there are Python syntax errors or undefined names
         flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+        flake8 . --count --exit-zero --max-complexity=40 --max-line-length=127 --statistics --exclude external
     - name: Test with unittest
       run: |
         python -m tests
         coverage run -m tests
     - name: Post Coverage
       uses: codecov/codecov-action@v4
-      if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.9'
+      if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.11'
       with:
-        token: ${{ secrets.CODECOV_TOKEN }}
         verbose: true
-
+        fail_ci_if_error: true
+        flags: unittests
+      env:
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/pythonpublish.yml

@@ -9,19 +9,20 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
     - name: Set up Python
       uses: actions/setup-python@v5
       with:
         python-version: '3.x'
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install build
+        pip install --upgrade build
     - name: Build package
       run: python -m build
     - name: Publish package
-      uses: pypa/gh-action-pypi-publish@v1.8.11
+      uses: pypa/gh-action-pypi-publish@release/v1.8
       with:
         user: __token__
         password: ${{ secrets.PYPI_PASSWORD_OPENKIM }}
-

MANIFEST.in

@@ -1,4 +1,2 @@
-include LICENSE
-include versioneer.py
 include kim_property/_version.py
 recursive-include kim_property/properties *

README.md

@@ -1,7 +1,6 @@
 # KIM-PROPERTY utility module
 
 [![Python package](https://github.com/openkim/kim-property/workflows/Python%20package/badge.svg)](https://github.com/openkim/kim-property/actions)
-[![Windows Build status](https://ci.appveyor.com/api/projects/status/5860x3twnmpwwmsa?svg=true)](https://ci.appveyor.com/project/yafshar/kim-property)
 [![codecov](https://codecov.io/gh/openkim/kim-property/branch/master/graph/badge.svg)](https://codecov.io/gh/openkim/kim-property)
 [![Anaconda-Server Badge](https://img.shields.io/conda/vn/conda-forge/kim-property.svg)](https://anaconda.org/conda-forge/kim-property)
 [![PyPI](https://img.shields.io/pypi/v/kim-property.svg)](https://pypi.python.org/pypi/kim-property)
@@ -13,29 +12,32 @@ example a [LAMMPS](https://lammps.sandia.gov/) script) that computes a
 
 This utility module has 5 modes:
 
-1- **[Create](#Create)**\
+1- **[Create](#create)**\
     Take as input the property instance ID and property definition name and
     create initial property instance data structure. It checks and indicates
     whether the property definition exists in [OpenKIM](https://openkim.org/).
 
-2- **[Destroy](#Destroy)**\
+2- **[Destroy](#destroy)**\
     Delete a previously created property instance ID.
 
-3- **[Modify](#Modify)**\
+3- **[Modify](#modify)**\
     Incrementally build the property instance by receiving keys with
     associated arguments. It can "append" and add to a key's existing array
     argument.
 
-4- **[Remove](#Remove)**\
+4- **[Remove](#remove)**\
     Remove a key.
 
-5- **[Dump](#Dump)**\
+5- **[Dump](#dump)**\
     Take as input the generated instance and a filename, validate each
     instance against the property definition and either issues an error or
     writes the instance out to file in edn format. Final validation should
     make sure all keys/arguments are legal and all required keys are
     provided.
 
+To get started, you'll need to install the `kim-property` package. Please refer
+to the [installation instructions](#installing-kim-property).
+
 ## Create
 
 Creating property instances::
@@ -796,30 +798,56 @@ For more information and examples, see the
 
 **conda** is the package management tool for Anaconda Python installations.
 
-Installing `kim-property` from the `conda-forge` channel can be achieved by
-adding `conda-forge` to your channels with:
+Installing `kim-property` from the `conda-forge` channel can be achieved
+by adding `conda-forge` to your channels with:
 
 ```sh
 conda config --add channels conda-forge
+conda config --set channel_priority strict
 ```
 
 Once the `conda-forge` channel has been enabled, `kim-property` can be
-installed with:
+installed with `conda`:
 
 ```sh
 conda install kim-property
 ```
 
+or with `mamba`:
+
+```sh
+mamba install kim-property
+```
+
 It is possible to list all of the versions of `kim-property` available on
-your platform with:
+your platform with `conda`:
 
 ```sh
 conda search kim-property --channel conda-forge
 ```
 
+or with `mamba`:
+
+```sh
+mamba search kim-property --channel conda-forge
+```
+
+Alternatively, `mamba repoquery` may provide more information:
+
+```sh
+# Search all versions available on your platform:
+mamba repoquery search kim-property --channel conda-forge
+
+# List packages depending on `kim-property`:
+mamba repoquery whoneeds kim-property --channel conda-forge
+
+# List dependencies of `kim-property`:
+mamba repoquery depends kim-property --channel conda-forge
+```
+
 ## Copyright
 
-Copyright (c) 2020-2023, Regents of the University of Minnesota.\
+Copyright (c) 2020-2024, Regents of the University of Minnesota.\
 All Rights Reserved
 
 ## Contributing

external/README.md

@@ -52,42 +52,40 @@ git submodule update --remote
 
 Once you cloned the repository with external submodule and fetch all the latest
 changes from
-[`openkim-properties`](https://github.com/openkim/openkim-properties.git). First, if properties have been added or removed, update the lists ``kim_property_names`` and ``kim_property_ids`` in ``kim_property/pickle.py``. Then, in the package main directory,
+[`openkim-properties`](https://github.com/openkim/openkim-properties.git).
+First, if properties have been added or removed, update the lists
+``kim_property_names`` and ``kim_property_ids`` in ``kim_property/ednify.py``.
+Then, in the package main directory,
 
 ```sh
 ├── LICENSE
 ├── MANIFEST.in
 ├── README.md
 ├── external
 ├── kim_property
-├── setup.cfg
+├── pyproject.toml
 ├── setup.py
-├── tests
-└── versioneer.py
+└── tests
 ```
 
 please run python and do as,
 
 ```sh
 python
 >>> import kim_property
->>> kim_property.pickle.pickle_kim_properties()
+>>> kim_property.ednify.ednify_kim_properties()
 ```
 
 Now, you have the latest update from
 [`openkim-properties`](https://github.com/openkim/openkim-properties.git).
 
 **NOTE:**
 
-Suppose you are a developer with write access to the `kim-property` repository
+If you are a developer with a write access to the `kim-property` repository
 and would like to update the property definition with the new updates. In that
 case, you should commit and publish your changes to the repository and make a
 new release. This release will update the binary distribution of the package
 with the latest changes.
 
-Please install the `kim-property` package using pip in the package main
-directory,
-
-```sh
-pip install .
-```
+To get started, you'll need to install the `kim-property` package. Please refer
+to the [installation instructions](../README.md#installing-kim-property).

kim_property/__init__.py

@@ -365,9 +365,7 @@
         }
     ]
 
-"""
-
-from . import _version
+"""  # noqa: E501
 
 from .err import KIMPropertyError
 from .definition import \
@@ -433,5 +431,5 @@
 
 __author__ = 'Yaser Afshar <yafshar@umn.edu>'
 
+from . import _version  # noqa: E402
 __version__ = _version.get_versions()['version']
-

kim_property/_version.py

@@ -51,7 +51,7 @@ def get_config() -> VersioneerConfig:
     cfg = VersioneerConfig()
     cfg.VCS = "git"
     cfg.style = "pep440"
-    cfg.tag_prefix = ""
+    cfg.tag_prefix = "v"
     cfg.parentdir_prefix = "kim_property-"
     cfg.versionfile_source = "kim_property/_version.py"
     cfg.verbose = False

kim_property/create.py

@@ -7,7 +7,7 @@
 from .err import KIMPropertyError
 from .definition import check_property_definition
 from .instance import get_property_id_path, check_instance_id_format
-from .pickle import unpickle_kim_properties
+from .ednify import unednify_kim_properties
 
 __all__ = [
     "get_properties",
@@ -26,14 +26,14 @@
 
 # Get the standard KIM properties
 KIM_PROPERTIES, PROPERTY_NAME_TO_PROPERTY_ID, \
-    PROPERTY_ID_TO_PROPERTY_NAME = unpickle_kim_properties()
+    PROPERTY_ID_TO_PROPERTY_NAME = unednify_kim_properties()
 
 NEW_PROPERTY_IDS = None
 """list: Newly added property IDs """
 
 
 def get_properties():
-    """Get the kim properties object hierarchy from the pickled object.
+    """Get the kim properties object hierarchy from the edn object.
 
     Returns:
         dict -- KIM_PROPERTIES.
@@ -116,7 +116,7 @@ def kim_property_create(instance_id, property_name, property_instances=None):
     Returns:
         string -- serialized KIM-EDN formatted property instances.
 
-    """
+    """  # noqa: E501
     global KIM_PROPERTIES
     global PROPERTY_NAME_TO_PROPERTY_ID
     global PROPERTY_ID_TO_PROPERTY_NAME
@@ -168,13 +168,11 @@ def kim_property_create(instance_id, property_name, property_instances=None):
         # Check to make sure that this property does not exist in OpenKIM
         if _property_id in KIM_PROPERTIES:
             msg = 'the input property_name file contains a property ID:\n'
-            msg += '"{}"\nwhich already '.format(_property_id)
-            msg += 'exists in the KIM Property Definition list.\n'
-            msg += 'Use the KIM Property Definition or update the ID in the'
-            msg += 'property_name file.\n'
-            msg += 'See the KIM Property Definitions at '
-            msg += 'https://openkim.org/properties for more detailed '
-            msg += 'information.'
+            msg += f'"{_property_id}"\nwhich already exists in the KIM '
+            msg += 'Property Definition list.\nUse the KIM Property '
+            msg += 'Definition or update the ID in the property_name '
+            msg += 'file.\nSee the KIM Property Definitions at https://'
+            msg += 'openkim.org/properties for more detailed information.'
             raise KIMPropertyError(msg)
 
         # Add the new property definition to KIM_PROPERTIES
@@ -203,13 +201,10 @@ def kim_property_create(instance_id, property_name, property_instances=None):
         elif property_name in kim_property_ids:
             new_property_instance["property-id"] = property_name
         else:
-            msg = 'the requested "property_name" :\n'
-            msg += '"{}"\n'.format(property_name)
-            msg += 'is not a valid KIM property name nor '
-            msg += 'a path-like object to a file.\n'
-            msg += 'See the KIM Property Definitions at '
-            msg += 'https://openkim.org/properties for more detailed '
-            msg += 'information.'
+            msg = f'the requested "property_name" :\n"{property_name}"\nis not'
+            msg += ' a valid KIM property property name nor a path-like object'
+            msg += ' to a file.\nSee the KIM Property Definitions at https://'
+            msg += 'openkim.org/properties for more detailed information.'
             raise KIMPropertyError(msg)
 
     new_property_instance["instance-id"] = instance_id