Merge pull request #319 from ceteri/fix_unit_tests

Fix unit tests, try to integrate `pyproject.toml`

Pipfile

@@ -26,7 +26,7 @@ python-dateutil = ">=2.8"
 pyvis = ">=0.1.9"
 rdflib = ">=6.1"
 requests = ">=2.27"
-scikit-learn = "==1.1.2"
+scikit-learn = "==1.1.3"
 scipy = ">=1.8.0"
 statsmodels = ">=0.13"
 tqdm = ">=4.63"
@@ -55,17 +55,12 @@ pylint = ">=2.12"
 pymdown-extensions = ">=9.2"
 pytest = ">=7.1"
 responses = ">=0.19"
-scikit-learn = ">=1.0"
+scikit-learn = ">=1.1"
 selenium = ">=4.1"
 twine = ">=3.8"
 types-python-dateutil = ">=2.8"
 types-requests = ">=2.27"
 xmltodict = ">=0.12"
 
 [requires]
-# python_version = "3.11"
-# python_version = "3.10"
-# python_version = "3.9"
-# python_version = "3.8"
-# python_version = "3.7"
-# python_version = "3"
+python_version = "3.7"

README.md

@@ -36,62 +36,59 @@ Morph-KGC, pythonPSL, and many more.
 See the ["Getting Started"](https://derwen.ai/docs/kgl/start/)
 section of the online documentation.
 
-## Useing kglab as a package for your project
 
-### We recommend installing from [PyPi](https://pypi.python.org/pypi/kglab):
+### Using `kglab` as a library for your Python project
 
-#### pip
-```bash
-python3 -m pip install kglab
-```
+We recommend installing from [PyPi](https://pypi.python.org/pypi/kglab) or [conda](https://anaconda.org/anaconda/conda):
 
-#### pipenv
-Kglab supports python 3.7 and above. 
-You will need to specify the python version in your Pipfile or whne creating the pipenv
-If you have specified the python version in your Pipfile, you can install kglab with:
-```bash
-pipenv install kglab
-```
+#### `pip`
 
-If you have not specified the python version in your Pipfile, you can install kglab with:
 ```bash
-pipenv install --python 3.7 kglab
+python3 -m pip install kglab
 ```
 
-#### poetry
-You can install into you existing poetry project with:
+#### `pipenv`
+
 ```bash
-potery add kglab
+pipenv install kglab
 ```
 
-#### conda
+#### `conda`
 ```bash
 conda env create -n kglab
 conda activate kglab
 pip install kglab
 ```
 
 ### Or, install from source:
+
 If you work directly from this Git repo, be sure to install the 
 dependencies:
+
 #### pip
+
 ```bash
 python3 -m pip install -U pip wheel
 python3 -m pip install -r requirements.txt
 ```
 
 #### pipenv
+
 ```bash
 pipenv install --dev
-# NEED TO HAVE a Pipfile
 ```
+
 Alternatively, to install dependencies using `conda`:
+
 ```bash
 conda env create -f environment.yml --force
 conda activate kglab
 ```
 
+### Sample Code
+
 Then to run some simple uses of this library:
+
 ```python
 import kglab
 
@@ -136,12 +133,14 @@ Also, container images for each release are available on DockerHub:
 <https://hub.docker.com/repository/docker/derwenai/kglab>
 
 To build a container image and run it for the tutorials:
+
 ```bash
 docker build --pull --rm -f "docker/Dockerfile" -t kglab:latest .
 docker run -p 8888:8888 -it kglab
 ```
 
 To build and run a container image for testing:
+
 ```bash
 docker build --pull --rm -f "docker/testsuite.Dockerfile" -t kglabtest:latest .
 docker run --rm -it kglabtest

for_poetry/README.md

@@ -0,0 +1,5 @@
+#### `poetry`
+
+```bash
+poetry add kglab
+```

for_poetry/pyproject.toml

@@ -0,0 +1,148 @@
+
+
+[tool.poetry]
+name = "kglab"
+version = "0.6.7"
+description = "a simple abstraction layer in Python for building knowledge graphs"
+license = "MIT"
+authors = ["Paco Nathan"]
+maintainers = ["kglab contributors"]
+repository = "https://github.com/DerwenAI/kglab"
+homepage = "https//derwen.ai/docs/kgl/"
+readme = "README.md"
+documentation = "https://derwen.ai/docs/kgl/"
+keywords = [
+    "controlled vocabulary",
+    "cugraph",
+    "deep learning",
+    "embedding",
+    "gpu",
+    "graph algorithms",
+    "igraph",
+    "inference",
+    "interactive visualization",
+    "json-ld",
+    "knowledge graph",
+    "managing namespaces",
+    "morph-kgc",
+    "n3",
+    "networkx",
+    "owl",
+    "pandas",
+    "parquet",
+    "probabilistic soft logic",
+    "psl",
+    "pyvis",
+    "rapids",
+    "rdf",
+    "rml",
+    "roam research",
+    "serialization",
+    "shacl",
+    "skos",
+    "sparql",
+    "statistical relational learning",
+    "topology",
+    "turtle",
+    "validation"
+    ]
+classifiers = [
+    "Programming Language :: Python",
+    "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",
+    "Operating System :: OS Independent",
+    "License :: OSI Approved :: MIT License",
+    "Development Status :: 5 - Production/Stable",
+    "Intended Audience :: Developers",
+    "Intended Audience :: Education",
+    "Intended Audience :: Information Technology",
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering :: Artificial Intelligence",
+    "Topic :: Scientific/Engineering :: Human Machine Interfaces",
+    "Topic :: Scientific/Engineering :: Information Analysis",
+    "Topic :: Software Development :: Libraries :: Python Modules",
+    "Topic :: Text Processing :: Indexing"
+    ]
+
+
+[tool.poetry.dependencies]
+python = "^3.10"
+aiohttp = "^3.8.1"
+chocolate = "^0.0.2"
+csvwlib = "^0.3.2"
+cryptography = "^38.0.1"
+decorator = "^5.1.1"
+fsspec = {extras = ["gs", "s3"], version = "^2022.8.2"}
+gcsfs = "^2022.8.2"
+icecream = "^2.1.3"
+morph-kgc = "^2.2.0"
+networkx = "^2.8.6"
+numpy = "^1.23.3"
+owlrl = "^6.0.2"
+oxrdflib = "^0.3.2"
+pandas = "^1.4.4"
+pslpython = "^2.3.0"
+pyarrow = "^9.0.0"
+pynvml = "^11.4.1"
+pyshacl = "^0.20.0"
+python-dateutil = "^2.8.2"
+pyvis = "^0.2.1"
+rdflib = "^6.2.0"
+requests = "^2.28.1"
+tqdm = "^4.64.1"
+urlpath = "^1.2.0"
+bandit = "^1.7.4"
+codespell = "^2.2.1"
+coverage = "^6.4.4"
+Flask = "^2.2.2"
+grayskull = "^1.8.3"
+mistune = "^2.0.4"
+mkdocs-git-revision-date-plugin = "^0.3.2"
+mkdocs-material = "^8.5.1"
+pipdeptree = "^2.3.1"
+Pygments = "^2.13.0"
+pymdown-extensions = "^9.5"
+responses = "^0.21.0"
+selenium = "^4.4.3"
+twine = "^4.0.1"
+types-python-dateutil = "^2.8.19"
+types-requests = "^2.28.10"
+wheel = "^0.37.1"
+xmltodict = "^0.13.0"
+
+
+[tool.poetry.group.dev.dependencies]
+pytest = "^7.1.3"
+pre-commit = "^2.20.0"
+mypy = "^0.971"
+black = "^22.8.0"
+flake8 = "^5.0.4"
+mypy = "^0.971"
+pylint = "^2.15.2"
+flake8-pylint = "^0.1.3"
+bandit = "^1.7.4"
+flake8-bandit = "^4.1.1"
+mkdocs-git-revision-date-plugin = "^0.3.2"
+mkdocs-material = "^8.5.1"
+
+
+[tool.poetry.group.tut.dependencies]
+cairocffi = "^1.3"
+gensim = "^3.8"
+igraph = "^0.9"
+jupyterlab = "^3.1.4"
+leidenalg = "^0.8"
+matplotlib = "^3.3.4"
+pylev = "^1.3"
+
+tool.poetry.scripts = [
+    "Makefile = Makefile:main",
+]
+
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"

pyproject.toml

@@ -1,65 +1,11 @@
-[build-system]
-requires = ["flit_core >=3.2,<4"]
-build-backend = "flit_core.buildapi"
-
-[project]
 name = "kglab"
+version = "0.6.7"
 authors = [
-    {name = "Paco Nathan", email = "info@derwen.ai"}
+    {name = "Paco Nathan", email = "paco@derwen.ai"},
 ]
-description = "A simple abstraction layer in Python for building knowledge graphs"
-readme = "README.md"
-license = {file = "LICENSE"}
+description = "a simple abstraction layer in Python for building knowledge graphs"
 requires-python = ">=3.7"
-dependencies = [
-    "aiohttp >= 3.8",
-    "chocolate >= 0.0.2",
-    "csvwlib >= 0.3.2",
-    "cryptography >= 35.0",
-    "decorator >= 5.1",
-    "fsspec[gs,s3] >= 2022.2",
-    "gcsfs >= 2022.2",
-    "icecream >= 2.1",
-    "morph-kgc >= 2.0.0",
-    "networkx >= 2.7",
-    "numpy >= 1.23.0",
-    "owlrl >= 6.0.2",
-    "oxrdflib >= 0.3.1",
-    "pandas >= 1.4",
-    "pslpython >= 2.2.2",
-    "pyarrow >= 7.0",
-    "pynvml >= 11.4",
-    "pyshacl >= 0.18",
-    "python-dateutil >= 2.8",
-    "pyvis >= 0.1.9",
-    "rdflib >= 6.1",
-    "requests >= 2.27",
-    "scikit-learn == 1.1.3",
-    "scipy >= 1.8.0",
-    "statsmodels >= 0.13",
-    "tqdm >= 4.63",
-    "urlpath >= 1.2",
-]
-classifiers = [
-    "Development Status :: 5 - Production/Stable",
-    "Intended Audience :: Developers",
-    "Intended Audience :: Education",
-    "Intended Audience :: Information Technology",
-    "Intended Audience :: Science/Research",
-    "License :: OSI Approved :: MIT License",
-    "Operating System :: OS Independent",
-    "Programming Language :: Python :: 3 :: Only",
-    "Programming Language :: Python :: 3.10",
-    "Programming Language :: Python :: 3.7",
-    "Programming Language :: Python :: 3.8",
-    "Programming Language :: Python :: 3.9",
-    "Programming Language :: Python",
-    "Topic :: Scientific/Engineering :: Artificial Intelligence",
-    "Topic :: Scientific/Engineering :: Human Machine Interfaces",
-    "Topic :: Scientific/Engineering :: Information Analysis",
-    "Topic :: Software Development :: Libraries :: Python Modules",
-    "Topic :: Text Processing :: Indexing",
-]
+license = {text = "MIT"}
 keywords = [
     "controlled vocabulary",
     "cugraph",
@@ -93,18 +39,30 @@ keywords = [
     "statistical relational learning",
     "topology",
     "turtle",
-    "validation",
+    "validation"
 ]
-dynamic = ["version"]
-
-[project.urls]
-Home = "https://derwen.ai/docs/kgl/"
-DOI = "https://doi.org/10.5281/zenodo.6360664"
-Discussions = "https://www.linkedin.com/groups/6725785/"
-DockerHub = "https://hub.docker.com/r/derwenai/kglab"
-Tutorial = "https://derwen.ai/docs/kgl/tutorial/"
-Issues = "https://github.com/DerwenAI/kglab/issues"
-Source = "https://github.com/DerwenAI/kglab"
+classifiers = [
+    "Programming Language :: Python",
+    "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",
+    "Operating System :: OS Independent",
+    "License :: OSI Approved :: MIT License",
+    "Development Status :: 5 - Production/Stable",
+    "Intended Audience :: Developers",
+    "Intended Audience :: Education",
+    "Intended Audience :: Information Technology",
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering :: Artificial Intelligence",
+    "Topic :: Scientific/Engineering :: Human Machine Interfaces",
+    "Topic :: Scientific/Engineering :: Information Analysis",
+    "Topic :: Software Development :: Libraries :: Python Modules",
+    "Topic :: Text Processing :: Indexing"
+]
+dynamic = ["dependencies", "readme"]
 
-[project.entry-points."rdf.plugins.store"]
-kglab = "kglab:PropertyStore"
+[tool.setuptools.dynamic]
+dependencies = {file = ["requirements.txt"]}
+readme = {file = ["README.md"]}