Development

.readthedocs.yml

@@ -7,6 +7,7 @@ build:
 
 sphinx:
   fail_on_warning: false
+  configuration: docs/source/conf.py
 
 python:
   # Install our python package before building the docs

docs/source/user/api.rst

@@ -9,6 +9,12 @@ Annotator Module
 .. automodule:: spinneret.annotator
    :members:
 
+Benchmark Module
+----------------
+
+.. automodule:: spinneret.benchmark
+   :members:
+
 Datasets Module
 ---------------
 

environment-min.yml

@@ -16,4 +16,6 @@ dependencies:
   - rdflib
   - sphinx
   - sphinx-autoapi
+  - daiquiri
+  - matplotlib
 prefix: /opt/miniconda3/envs/spinneret

environment.yml

@@ -5,96 +5,126 @@ channels:
 dependencies:
   - alabaster=1.0.0
   - annotated-types=0.7.0
-  - anyascii=0.3.2
-  - astroid=3.2.4
-  - black=24.8.0
+  - anyio=4.6.2.post1
+  - babel=2.16.0
+  - backoff=2.2.1
+  - brotli=1.1.0
+  - brotli-bin=1.1.0
   - brotli-python=1.1.0
   - bzip2=1.0.8
-  - ca-certificates=2024.8.30
+  - ca-certificates=2024.12.14
+  - certifi=2024.12.14
   - cffi=1.17.1
-  - charset-normalizer=3.3.2
   - click=8.1.7
   - click-option-group=0.5.6
   - colorama=0.4.6
-  - coverage=7.6.1
-  - dill=0.3.8
+  - contourpy=1.3.1
+  - cycler=0.12.1
   - docutils=0.21.2
   - dotty-dict=1.3.1
   - exceptiongroup=1.2.2
+  - fonttools=4.55.3
+  - freetype=2.12.1
   - gitdb=4.0.11
   - gitpython=3.1.43
+  - gql=3.5.0
+  - graphql-core=3.2.5
   - h2=4.1.0
   - hpack=4.0.0
   - hyperframe=6.0.1
-  - icu=75.1
+  - idna=3.10
   - imagesize=1.4.1
-  - importlib-metadata=8.5.0
+  - importlib-resources=6.4.5
+  - importlib_resources=6.4.5
   - iniconfig=2.0.0
-  - isodate=0.6.1
   - isort=5.13.2
   - jinja2=3.1.4
+  - kiwisolver=1.4.7
+  - lcms2=2.16
+  - lerc=4.0.0
   - libblas=3.9.0
+  - libbrotlicommon=1.1.0
+  - libbrotlidec=1.1.0
+  - libbrotlienc=1.1.0
   - libcblas=3.9.0
-  - libcxx=18.1.8
-  - libexpat=2.6.3
+  - libcxx=19.1.4
+  - libdeflate=1.23
+  - libexpat=2.6.4
   - libffi=3.4.2
   - libgfortran=5.0.0
   - libgfortran5=13.2.0
   - libiconv=1.17
+  - libjpeg-turbo=3.0.0
   - liblapack=3.9.0
-  - libopenblas=0.3.27
-  - libsqlite=3.46.1
-  - libxml2=2.12.7
+  - liblzma=5.6.3
+  - libopenblas=0.3.28
+  - libpng=1.6.44
+  - libsqlite=3.47.0
+  - libtiff=4.7.0
+  - libwebp-base=1.4.0
+  - libxcb=1.17.0
+  - libxml2=2.13.5
   - libxslt=1.1.39
   - libzlib=1.3.1
-  - llvm-openmp=18.1.8
+  - llvm-openmp=19.1.4
   - lxml=5.3.0
   - markdown-it-py=3.0.0
-  - markupsafe=2.1.5
+  - matplotlib=3.10.0
+  - matplotlib-base=3.10.0
   - mccabe=0.7.0
+  - mdit-py-plugins=0.4.2
   - mdurl=0.1.2
+  - multidict=6.1.0
+  - munkres=1.1.4
   - mypy_extensions=1.0.0
   - myst-parser=4.0.0
   - ncurses=6.5
-  - openssl=3.3.2
-  - packaging=24.1
-  - pandas=2.2.2
+  - openjpeg=2.5.3
+  - openssl=3.4.0
   - pathspec=0.12.1
-  - pip=24.2
+  - pillow=11.0.0
+  - pip=24.3.1
+  - platformdirs=4.3.6
   - pluggy=1.5.0
+  - propcache=0.2.0
+  - pthread-stubs=0.4
   - pycparser=2.22
   - pygments=2.18.0
   - pysocks=1.7.1
-  - pytest-cov=5.0.0
+  - pytest=8.3.3
   - pytest-mock=3.14.0
   - python=3.11.10
-  - python-tzdata=2024.1
+  - python-dateutil=2.9.0.post0
+  - python-json-logger=2.0.7
   - python_abi=3.11
   - pyyaml=6.0.2
-  - rdflib=7.0.0
+  - qhull=2020.2
   - readline=8.2
   - requests=2.32.3
   - requests-toolbelt=1.0.0
   - shellingham=1.5.4
   - six=1.16.0
+  - sniffio=1.3.1
   - snowballstemmer=2.2.0
-  - sphinx=8.0.2
   - sphinxcontrib-applehelp=2.0.0
   - sphinxcontrib-devhelp=2.0.0
   - sphinxcontrib-htmlhelp=2.1.0
   - sphinxcontrib-jsmath=1.0.1
   - sphinxcontrib-qthelp=2.0.0
+  - stdlib-list=0.11.0
   - tk=8.6.13
   - toml=0.10.2
-  - tomli=2.0.1
+  - tomli=2.1.0
   - tomlkit=0.13.2
+  - tornado=6.4.2
   - typing-extensions=4.12.2
   - typing_extensions=4.12.2
-  - tzdata=2024a
-  - wheel=0.44.0
+  - unicodedata2=15.1.0
+  - wheel=0.45.1
+  - xorg-libxau=1.0.12
+  - xorg-libxdmcp=1.1.5
   - xz=5.2.6
   - yaml=0.2.5
-  - zipp=3.20.2
   - zstandard=0.23.0
   - zstd=1.5.6
   - pip:
@@ -106,27 +136,30 @@ dependencies:
       - airium==0.2.6
       - aniso8601==9.0.1
       - antlr4-python3-runtime==4.9.3
-      - anyio==4.6.2.post1
       - appdirs==1.4.4
       - arrow==1.3.0
+      - astroid==3.2.4
       - attrs==24.2.0
-      - babel==2.16.0
       - bcp47==0.1.0
       - beautifulsoup4==4.12.3
       - bioc==2.1
+      - black==24.8.0
       - blinker==1.8.2
       - boto3==1.35.54
       - botocore==1.35.54
       - cachier==3.1.2
       - cattrs==24.1.2
-      - certifi==2024.8.30
       - cfgraph==0.2.1
       - chardet==5.2.0
+      - charset-normalizer==3.3.2
       - class-resolver==0.5.2
+      - coverage==7.6.1
       - curies==0.9.0
+      - daiquiri==3.2.5.1
       - defusedxml==0.7.1
       - deprecated==1.2.14
       - deprecation==2.1.0
+      - dill==0.3.8
       - diskcache==5.6.3
       - distro==1.9.0
       - docopt==0.6.2
@@ -143,18 +176,19 @@ dependencies:
       - fsspec==2024.10.0
       - funowl==0.2.3
       - gilda==1.4.0
+      - graphviz==0.20.3
       - h11==0.14.0
       - hbreader==0.9.1
       - html5lib==1.1
       - httpcore==1.0.6
       - httpx==0.27.2
       - huggingface-hub==0.26.2
-      - idna==3.10
       - ijson==3.3.0
-      - importlib-resources==6.4.5
+      - importlib-metadata==8.5.0
       - inflect==7.4.0
       - inflection==0.5.1
       - intervaltree==3.1.0
+      - isodate==0.6.1
       - isoduration==20.11.0
       - itsdangerous==2.2.0
       - jiter==0.7.0
@@ -178,10 +212,9 @@ dependencies:
       - linkml-renderer==0.3.1
       - linkml-runtime==1.8.3
       - litellm==1.51.2
-      - mdit-py-plugins==0.4.2
+      - markupsafe==2.1.5
       - more-click==0.1.2
       - more-itertools==10.5.0
-      - multidict==6.1.0
       - ndex2==3.9.0
       - networkx==3.4.2
       - nltk==3.9.1
@@ -193,16 +226,16 @@ dependencies:
       - openai==1.53.0
       - openpyxl==3.1.5
       - owlrl==6.0.2
+      - packaging==24.1
+      - pandas==2.2.2
       - pansql==0.0.1
       - parse==1.20.2
-      - platformdirs==4.3.6
       - ply==3.11
       - portalocker==2.10.1
       - prefixcommons==0.1.12
       - prefixmaps==0.2.6
       - prettytable==3.11.0
       - pronto==2.5.8
-      - propcache==0.2.0
       - pydantic==2.9.2
       - pydantic-core==2.23.4
       - pyjsg==0.11.10
@@ -214,16 +247,15 @@ dependencies:
       - pyshexc==0.9.1
       - pysolr==3.10.0
       - pystow==0.5.6
-      - pytest==8.3.3
+      - pytest-cov==5.0.0
       - pytest-logging==2015.11.4
-      - python-dateutil==2.9.0.post0
       - python-dotenv==1.0.1
       - python-gitlab==4.11.1
-      - python-graphviz==0.20.3
       - python-semantic-release==9.8.8
       - pytrie==0.4.0
       - pytz==2024.2
       - ratelimit==2.2.1
+      - rdflib==7.0.0
       - rdflib-jsonld==0.6.1
       - rdflib-shim==1.0.3
       - referencing==0.35.1
@@ -242,15 +274,15 @@ dependencies:
       - setuptools==75.3.0
       - shexjsg==0.8.2
       - smmap==5.0.1
-      - sniffio==1.3.1
       - sortedcontainers==2.4.0
       - soso==0.2.0
       - soupsieve==2.6
       - sparqlslurper==0.5.1
       - sparqlwrapper==2.0.0
+      - sphinx==8.0.2
       - sphinx-autoapi==3.3.1
       - sphinxcontrib-serializinghtml==2.0.0
-      - spinneret==0.1.0
+      - spinneret==0.2.0
       - sqlalchemy==2.0.36
       - sqlalchemy-utils==0.38.3
       - sssom==0.4.12
@@ -263,6 +295,7 @@ dependencies:
       - tqdm==4.66.6
       - typeguard==4.4.0
       - types-python-dateutil==2.9.0.20241003
+      - tzdata==2024.1
       - unidecode==1.3.8
       - uri-template==1.3.0
       - url-normalize==1.4.3
@@ -278,4 +311,5 @@ dependencies:
       - wikipedia-api==0.7.1
       - wrapt==1.16.0
       - yarl==1.17.1
+      - zipp==3.20.2
 prefix: /opt/miniconda3/envs/spinneret