Clean up repository & fix workflows (#5)

Update tripper folder:
Move files around, use imports from "tripper.*" and extend Python
support to include 3.7 and 3.8.

Update files according to pre-commit.

Update tests for better isolation:
Split up tests into separate test functions for better environment
isolation.

Use `tripperpy` as package name.

Use `s`, `p`, and `o` as variable names:
These represent the parts of an RDF Triple: subject, predicate, object.

Co-authored-by: Jesper Friis <jesper-friis@users.noreply.github.com>

.github/workflows/cd_release.yml

@@ -11,14 +11,22 @@ jobs:
     uses: SINTEF/ci-cd/.github/workflows/cd_release.yml@v1
     if: github.repository == 'EMMC-ASBL/tripper' && startsWith(github.ref, 'refs/tags/v')
     with:
+      # General
       git_username: "TEAM 4.0[bot]"
       git_email: "Team4.0@SINTEF.no"
-      package_dirs: tripper
       release_branch: main
       install_extras: "[dev]"
-      python_version: "3.9"
+
+      # Build package
+      python_package: true
+      package_dirs: tripper
+      python_version_build: "3.7"
       build_cmd: "pip install -U flit && flit build"
+      publish_on_pypi: true
+
+      # Build & publish documentation
       update_docs: true
+      python_version_docs: "3.7"
       doc_extras: "[docs]"
       changelog_exclude_labels: "skip_changelog,duplicate,question,invalid,wontfix"
     secrets:

.github/workflows/ci_cd_updated_main.yml

@@ -18,7 +18,7 @@ jobs:
       update_docs: true
       update_python_api_ref: true
       update_docs_landing_page: true
-      python_version: "3.9"
+      python_version: "3.7"
       doc_extras: "[docs]"
     secrets:
       PAT: ${{ secrets.RELEASE_PAT }}

.github/workflows/ci_check_dependencies.yml

@@ -15,7 +15,7 @@ jobs:
       git_username: "TEAM 4.0[bot]"
       git_email: "Team4.0@SINTEF.no"
       permanent_dependencies_branch: "ci/dependency-updates"
-      python_version: "3.9"
+      python_version: "3.7"
       install_extras: "[dev]"
       pr_labels: "CI/CD,skip_changelog"
     secrets:

.github/workflows/ci_tests.yml

@@ -17,26 +17,36 @@ jobs:
 
       # pre-commit
       run_pre-commit: true
-      python_version_pre-commit: "3.9"
+      python_version_pre-commit: "3.8"
       skip_pre-commit_hooks: pylint,pylint-tests
 
       # pylint & safety
-      python_version_pylint_safety: "3.9"
+      python_version_pylint_safety: "3.7"
       run_pylint: true
       pylint_runs: |
         --rcfile=pyproject.toml tripper
         --rcfile=pyproject.toml --disable=import-outside-toplevel,redefined-outer-name tests
       run_safety: true
+      # 48547: RDFLib vulnerability: https://pyup.io/vulnerabilities/PVE-2022-48547/48547/
+      # 44715-44717: NumPy vulnerabilities:
+      #  https://pyup.io/vulnerabilities/CVE-2021-41495/44715/
+      #  https://pyup.io/vulnerabilities/CVE-2021-41496/44716/
+      #  https://pyup.io/vulnerabilities/CVE-2021-34141/44717/
+      safety_options: |
+        --ignore=48547
+        --ignore=44715
+        --ignore=44716
+        --ignore=44717
 
       # Build package
       run_build_package: true
-      python_version_package: "3.9"
+      python_version_package: "3.7"
       build_libs: flit
       build_cmd: flit build
 
       # Build documentation
       run_build_docs: true
-      python_version_docs: "3.9"
+      python_version_docs: "3.7"
       update_python_api_ref: true
       update_docs_landing_page: true
       package_dirs: tripper
@@ -47,7 +57,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10"]
+        python-version: ["3.7", "3.8", "3.9", "3.10"]
 
     steps:
     - name: Checkout tripper

.github/workflows/ci_update_dependencies.yml

@@ -19,7 +19,7 @@ jobs:
       pr_labels: "CI/CD,skip_changelog"
       extra_to_dos: "- [ ] Make sure that the PR is **squash** merged, with a sensible commit message."
       update_pre-commit: true
-      python_version: "3.9"
+      python_version: "3.7"
       install_extras: "[pre-commit]"
       skip_pre-commit_hooks: "pylint,pylint-tests"
     secrets:

.pre-commit-config.yaml

@@ -46,11 +46,11 @@ repos:
         - "pydantic"
 
   - repo: https://github.com/SINTEF/ci-cd
-    rev: b648cea02c07ef2c2a81b60696c0e3eb283fa3d0  # frozen: v1
+    rev: 6a258b3bce2d2db022908c127d0532c8a7591707  # frozen: v1
     hooks:
     - id: docs-api-reference
       args:
-      - --package-dirs=tripper
+      - --package-dir=tripper
     - id: docs-landing-page
 
   - repo: local

README.md

@@ -4,6 +4,14 @@
 
 _The best ride when handling any triplestore._
 
+## Installation
+
+The package can be installed from [PyPI](https://pypi.org/project/tripperpy) using `pip`:
+
+```shell
+pip install tripperpy
+```
+
 ## License and copyright
 
 All files in this repository are licensed under the [MIT license](LICENSE) with copyright © 2022 European Material Modelling Council.

docs/api_reference/.pages

@@ -0,0 +1 @@
+title: "API Reference"

docs/api_reference/backends/.pages

@@ -0,0 +1 @@
+title: "backends"

docs/api_reference/backends/ontopy.md

@@ -0,0 +1,3 @@
+# ontopy
+
+::: tripper.backends.ontopy

docs/api_reference/backends/rdflib.md

@@ -0,0 +1,3 @@
+# rdflib
+
+::: tripper.backends.rdflib

docs/api_reference/interface.md

@@ -0,0 +1,3 @@
+# interface
+
+::: tripper.interface

docs/api_reference/triplestore.md

@@ -0,0 +1,3 @@
+# triplestore
+
+::: tripper.triplestore

docs/index.md

@@ -0,0 +1,17 @@
+# Tripper
+
+**A triplestore wrapper for Python.**
+
+_The best ride when handling any triplestore._
+
+## Installation
+
+The package can be installed from [PyPI](https://pypi.org/project/tripperpy) using `pip`:
+
+```shell
+pip install tripperpy
+```
+
+## License and copyright
+
+All files in this repository are licensed under the [MIT license](LICENSE.md) with copyright © 2022 European Material Modelling Council.

tripper/README.md → docs/overview.md

@@ -1,15 +1,15 @@
-Triplestore
-===========
-> A Python package encapsulating different triplestores using the strategy
-> design pattern.
-
-This package has by itself no dependencies outside the standard library,
-but the triplestore backends may have.
-
-The main class is Triplestore, who's `__init__()` method takes the name of the
-backend to encapsulate as first argument.  Its interface is strongly inspired
-by rdflib.Graph, but simplified when possible to make it easy to use.  Some
-important differences:
+# Overview
+
+<!-- markdownlint-disable MD007 -->
+
+A Python package encapsulating different triplestores using the strategy design pattern.
+
+This package has by itself no dependencies outside the standard library, but the triplestore backends may have.
+
+The main class is Triplestore, who's `__init__()` method takes the name of the backend to encapsulate as first argument.
+Its interface is strongly inspired by rdflib.Graph, but simplified when possible to make it easy to use.
+Some important differences:
+
 - all IRIs are represented by Python strings
 - blank nodes are strings starting with "_:"
 - literals are constructed with `Literal()`
@@ -19,32 +19,30 @@ from triplestore import Triplestore
 ts = Triplestore(backend="rdflib")
 ```
 
-The module already provides a set of pre-defined namespaces that simplifies
-writing IRIs. For example:
+The module already provides a set of pre-defined namespaces that simplifies writing IRIs.
+For example:
 
 ```python
 from triplestore import RDFS, OWL
 RDFS.subClassOf
 # -> 'http://www.w3.org/2000/01/rdf-schema#subClassOf'
 ```
 
-New namespaces can be created using the Namespace class, but are usually
-added with the `bind()` method:
+New namespaces can be created using the Namespace class, but are usually added with the `bind()` method:
 
 ```python
 ONTO = ts.bind("onto", "http://example.com/onto#")
 ONTO.MyConcept
 # -> 'http://example.com/onto#MyConcept'
 ```
 
-Namespace also support access by label and IRI checking.  Both of these features
-requires loading an ontology.  The following example shows how to create an EMMO
-namespace with IRI checking.  The keyword argument `label_annotations=True` enables
-access by `skos:prefLabel`, `rdfs:label` or `skos:altLabel`.  The `check=True`
-enables checking for existing IRIs.  The `triplestore_url=...` is a resolvable URL
-that can be read by the 'rdflib' backend.  It is needed, because the 'rdflib'
-backend is currently not able to load EMMO from the "http://emmo.info/emmo#"
-namespace.
+Namespace also support access by label and IRI checking.
+Both of these features requires loading an ontology.
+The following example shows how to create an EMMO namespace with IRI checking.
+The keyword argument `label_annotations=True` enables access by `skos:prefLabel`, `rdfs:label` or `skos:altLabel`.
+The `check=True` enables checking for existing IRIs.
+The `triplestore_url=...` is a resolvable URL that can be read by the 'rdflib' backend.
+It is needed, because the 'rdflib' backend is currently not able to load EMMO from the `http://emmo.info/emmo#` namespace.
 
 ```python
 EMMO = ts.bind(
@@ -59,8 +57,7 @@ EMMO.invalid_name
 # -> NoSuchIRIError: http://emmo.info/emmo#invalid_name
 ```
 
-New triples can be added either with the `parse()` method (for
-backends that support it) or the `add()` and `add_triples()` methods:
+New triples can be added either with the `parse()` method (for backends that support it) or the `add()` and `add_triples()` methods:
 
 ```python
 # en(msg) is a convenient function for adding english literals.
@@ -73,17 +70,15 @@ ts.add_triples([
 ])
 ```
 
-For backends that support it the triplestore can be serialised using
-`serialize()`:
+For backends that support it the triplestore can be serialised using `serialize()`:
 
 ```python
 ts.serialize("onto2.ttl")
 ```
 
-A set of convenient functions exists for simple queries, including
-`triples()`, `subjects()`, `predicates()`, `objects()`, `subject_predicates()`,
-`subject_objects()`, `predicate_objects()` and `value()`.  Except for `value()`,
-they return the result as generators. For example:
+A set of convenient functions exists for simple queries, including `triples()`, `subjects()`, `predicates()`, `objects()`, `subject_predicates()`, `subject_objects()`, `predicate_objects()` and `value()`.
+Except for `value()`, they return the result as generators.
+For example:
 
 ```python
 ts.objects(subject=ONTO.MyConcept, predicate=RDFS.subClassOf)
@@ -92,31 +87,28 @@ list(ts.objects(subject=ONTO.MyConcept, predicate=RDFS.subClassOf))
 # -> ['http://www.w3.org/2002/07/owl#Thing']
 ```
 
-The `query()` and `update()` methods can be used to query and update the
-triplestore using SPARQL.
+The `query()` and `update()` methods can be used to query and update the triplestore using SPARQL.
 
-Finally Triplestore has two specialised methods `add_mapsTo()` and
-`add_function()` that simplify working with mappings.  `add_mapsTo()` is
-convinient for defining new mappings:
+Finally Triplestore has two specialised methods `add_mapsTo()` and `add_function()` that simplify working with mappings.
+`add_mapsTo()` is convinient for defining new mappings:
 
 ```python
 from triplestore import Namespace
 META = Namespace("http://onto-ns.com/meta/0.1/MyEntity#")
 ts.add_mapsTo(ONTO.MyConcept, META.my_property)
 ```
 
-It can also be used with DLite and SOFT7 data models.  Here we repeat
-the above with DLite:
+It can also be used with DLite and SOFT7 data models.
+Here we repeat the above with DLite:
 
 ```python
 import dlite
 meta = dlite.get_instance("http://onto-ns.com/meta/0.1/MyEntity")
 ts.add_mapsTo(ONTO.MyConcept, meta, "my_property")
 ```
 
-The `add_function()` describes a function and adds mappings for its
-arguments and return value(s).  Currently it only supports the [Function
-Ontology (FnO)](https://fno.io/).
+The `add_function()` describes a function and adds mappings for its arguments and return value(s).
+Currently it only supports the [Function Ontology (FnO)](https://fno.io/).
 
 ```python
 def mean(x, y):
@@ -130,12 +122,11 @@ ts.add_function(
 )
 ```
 
+## Further development
+
+- Update the `query()` method to return the SPARQL result in a backend-independent way.
+- Add additional backends. Candidates include:
 
-Further development
--------------------
-* Update the `query()` method to return the SPARQL result in a backend-
-  independent way.
-* Add additional backends. Candidates include:
     - list of tuples
     - owlready2/EMMOntoPy
     - OntoRec/OntoFlowKB
@@ -145,4 +136,3 @@ Further development
     - Apache Jena Fuseki
     - Allegrograph
     - Wikidata
-* Add ontological validation of physical dimension to Triplestore.mapsTo().

mkdocs.yml

@@ -79,6 +79,7 @@ plugins:
 
 nav:
   - Home: index.md
+  - Overview: overview.md
   - License: LICENSE.md
   - Changelog: CHANGELOG.md
   - ... | api_reference/**