Merge remote-tracking branch 'upstream/develop' into develop

Author: elichad

.github/workflows/testing.yaml

@@ -39,9 +39,9 @@ env:
     FORCE_COLOR: "1"  # Force color output in CI
 
 jobs:
-    # Verifies pep8, pyflakes and circular complexity
-    flake8:
-        name: 🚨 Lint Python Code
+    # Verifies pep8, pyflakes, circular complexity, and spelling
+    lint:
+        name: 🚨 Lint and spellcheck
         runs-on: ubuntu-latest
         steps:
             # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
@@ -53,14 +53,16 @@ jobs:
                   python-version: ${{ env.PYTHON_VERSION }}
             - name: 🔽 Install flake8
               run: pip install flake8
-            - name: ⌛ Run checks
+            - name: ⌛ Lint Python code
               run: flake8 -v rocrate_validator tests
+            - name: ⌛ Spell check code and profiles (covers Python and SHACL)
+              uses: crate-ci/typos@v1.41.0
 
     # Runs the tests
     test:
         name: ⌛ Run tests
         runs-on: ubuntu-latest
-        needs: [flake8]
+        needs: [lint]
         steps:
             - name: ⬇️ Checkout
               uses: actions/checkout@v4

.gitignore

@@ -27,3 +27,7 @@ docs/_build
 **/.coverage
 **/.coverage.*
 **/.report
+
+# ignore IDE files
+.vscode/
+.idea/

CITATION.cff

@@ -0,0 +1,29 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it using these metadata."
+title: "rocrate-validator"
+abstract: "A Python package to validate RO-Crates."
+type: software
+authors:
+  - family-names: "Piras"
+    given-names: "Marco Enrico"
+    orcid: https://orcid.org/0000-0002-5207-0030
+  - family-names: "Leo"
+    given-names: "Simone"
+    orcid: https://orcid.org/0000-0001-8271-5429
+  - family-names: "Pireddu"
+    given-names: "Luca"
+    orcid: https://orcid.org/0000-0002-4663-5613
+  - family-names: Chadwick
+    given-names: Eli
+    orcid: https://orcid.org/0000-0002-0035-6475
+  - family-names: Bauer
+    given-names: Daniel
+    orcid: https://orcid.org/0000-0001-9447-460X
+repository-code: "https://github.com/crs4/rocrate-validator"
+url: "https://github.com/crs4/rocrate-validator"
+keywords:
+  - "RO-Crate"
+  - "validation"
+  - "metadata"
+  - "FAIR"
+license: "Apache-2.0"

poetry.lock

@@ -70,6 +70,7 @@ requests = ">=2.32,<3.0"
 requests-cache = ">=1.2,<2.0"
 inquirerpy = ">=0.3.4,<0.4.0"
 enum-tools = ">=0.12,<0.13"
+typos = "^1.41.0"
 
 [tool.poetry.group.dev.dependencies]
 pyproject-flake8 = "^6.1.0"
@@ -105,3 +106,6 @@ skip_dirs = [".git", ".github", ".vscode"]
 
 [tool.pytest.ini_options]
 testpaths = ["tests"]
+
+[tool.typos.files]
+extend-exclude = ["tests/data","docs/diagrams","*.json","*.html","*__init__.py"]

pyproject.toml

@@ -44,7 +44,7 @@
         # it's in JSON-LD format
         dct:format <https://w3id.org/mediatype/application/ld+json> ;
 
-        # it conforms to JSON-LD, here refered to by its namespace URI as a Profile
+        # it conforms to JSON-LD, here referred to by its namespace URI as a Profile
         dct:conformsTo <https://www.w3.org/TR/json-ld11/> ;
 
         # this profile resource plays the role of "Vocabulary"
@@ -62,7 +62,7 @@
         # it's in HTML format
         dct:format <https://w3id.org/mediatype/text/html> ;
 
-        # it conforms to HTML, here refered to by its namespace URI as a Profile
+        # it conforms to HTML, here referred to by its namespace URI as a Profile
         dct:conformsTo <https://www.w3.org/TR/html/> ;
 
         # this profile resource plays the role of "Specification"

rocrate_validator/profiles/process-run-crate/profile.ttl

@@ -45,7 +45,7 @@
         # it's in JSON-LD format
         dct:format <https://w3id.org/mediatype/application/ld+json> ;
 
-        # it conforms to JSON-LD, here refered to by its namespace URI as a Profile
+        # it conforms to JSON-LD, here referred to by its namespace URI as a Profile
         dct:conformsTo <https://www.w3.org/TR/json-ld11/> ;
 
         # this profile resource plays the role of "Vocabulary"
@@ -63,7 +63,7 @@
         # it's in HTML format
         dct:format <https://w3id.org/mediatype/text/html> ;
 
-        # it conforms to HTML, here refered to by its namespace URI as a Profile
+        # it conforms to HTML, here referred to by its namespace URI as a Profile
         dct:conformsTo <https://www.w3.org/TR/html/> ;
 
         # this profile resource plays the role of "Specification"

rocrate_validator/profiles/provenance-run-crate/profile.ttl

@@ -29,7 +29,7 @@ provenance-run-crate:ProvRCParameterConnectionReferencesRecommended a sh:NodeSha
     sh:description "Recommended references for ParameterConnection entities" ;
     sh:targetClass wfrun:ParameterConnection ;
     sh:property [
-        sh:name "ParamenterConnection references" ;
+        sh:name "ParameterConnection references" ;
         sh:description """References to `ParameterConnection` instances
         SHOULD follow the CWL convention,
         where connections to workflow output parameters are referenced by the workflow

rocrate_validator/profiles/provenance-run-crate/should/5_parameterconnection.ttl

@@ -27,7 +27,7 @@ ro-crate:FileDataEntityWebOptionalProperties a sh:NodeShape ;
     for instance a landing page that describes the file, including persistence identifiers (e.g. DOI),
     resolving to an intermediate HTML page instead of the downloadable file directly.
     These can included for File Data Entities as additional metadata by using the properties:
-    `ìdentifier`, `url`, `subjectOf`and `mainEntityOfPage`""" ;
+    `identifier`, `url`, `subjectOf`and `mainEntityOfPage`""" ;
     sh:targetClass ro-crate:File ;
     # Check if the Web-based Data Entity has a contentSize property
     sh:property [
@@ -87,4 +87,3 @@ ro-crate:DirectoryDataEntityWebOptionalDistribution a sh:NodeShape ;
         sh:severity sh:Info ;
         sh:message """The Directory Data Entity MAY have a `distribution` property to denote the distribution of the files within the directory""" ;
     ] .
-

rocrate_validator/profiles/ro-crate/may/4_data_entity_metadata.ttl

@@ -129,7 +129,7 @@ ro-crate:RootDataEntityRequiredProperties
     ] ;
     sh:property [
         a sh:PropertyShape ;
-        sh:name "Root Data Entity: `licence` property" ;
+        sh:name "Root Data Entity: `license` property" ;
         sh:description """Check if the Root Data Entity includes a `license` property (as specified by schema.org)
         to provide information about the license of the dataset.""" ;
         sh:path schema_org:license;