fix: update dependencies to resolve doc build failures

Update the 'autoapi.extension' to prevent the exception "'Module' object has no attribute 'doc'" and to enable successful local and Read the Docs documentation builds. Pin project documentation dependencies to address the deprecation of default project dependencies on Read the Docs (see: https://blog.readthedocs.com/newsletter-september-2023/). Update related project dependencies and resolve associated deprecation errors and warnings to maintain a functional code base.
EDIorg · Oct 11, 2023 · f23fc23 · f23fc23
1 parent 6a71eec
commit f23fc23
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Showing 14 changed files with 1,124 additions and 2,226 deletions.
diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -11,5 +11,3 @@ build:
 python:
   install:
     - requirements: docs/requirements.txt
-    - method: pip
-      path: .
diff --git a/docs/conf.py b/docs/conf.py
@@ -16,10 +16,10 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    "myst_nb",
     "autoapi.extension",
     "sphinx.ext.napoleon",
     "sphinx.ext.viewcode",
+    "myst_parser"
 ]
 autoapi_dirs = ["../src"]
 

diff --git a/docs/example.ipynb b/docs/example.ipynb
diff --git a/docs/index.md b/docs/index.md
@@ -5,7 +5,6 @@
 :maxdepth: 1
 :hidden:
 
-example.ipynb
 changelog.md
 contributing.md
 conduct.md

diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -1,3 +1,4 @@
-myst-nb
-sphinx-autoapi
-sphinx-rtd-theme
+sphinx==7.2.6
+myst-parser==2.0.0
+sphinx-autoapi==3.0.0
+sphinx-rtd-theme==1.3.0
diff --git a/environment-min.yml b/environment-min.yml
@@ -3,21 +3,13 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - wheel=0.38.4
-  - python=3.9.15
-  - tk=8.6.12
-  - libsqlite=3.40.0
-  - setuptools=65.5.1
-  - tzdata=2022g
-  - pip=22.3.1
-  - bzip2=1.0.8
-  - xz=5.2.6
-  - libffi=3.4.2
-  - libzlib=1.2.13
-  - openssl
-  - readline=8.1.2
-  - ncurses=6.3
-  - ca-certificates
+  - python=3.9
+  - pandas
+  - pylint
+  - black
+  - sphinx-rtd-theme
+  - sphinx-autoapi
   - pytest-mock
   - lxml
+  - myst-parser
 prefix: /opt/miniconda3/envs/gbif_registrar
diff --git a/environment.yml b/environment.yml
@@ -3,147 +3,115 @@ channels:
   - conda-forge
   - defaults
 dependencies:
+  - alabaster=0.7.13
+  - astroid=3.0.0
+  - babel=2.13.0
+  - black=23.9.1
+  - brotli-python=1.1.0
   - bzip2=1.0.8
   - ca-certificates=2023.7.22
+  - certifi=2023.7.22
+  - charset-normalizer=3.3.0
+  - click=8.1.7
   - colorama=0.4.6
+  - dill=0.3.7
+  - docutils=0.18.1
+  - exceptiongroup=1.1.3
   - icu=73.2
+  - idna=3.4
+  - imagesize=1.4.1
+  - importlib-metadata=6.8.0
+  - iniconfig=2.0.0
+  - isort=5.12.0
+  - jinja2=3.1.2
+  - libblas=3.9.0
+  - libcblas=3.9.0
+  - libcxx=16.0.6
   - libffi=3.4.2
+  - libgfortran=5.0.0
+  - libgfortran5=13.2.0
   - libiconv=1.17
-  - libsqlite=3.40.0
+  - liblapack=3.9.0
+  - libopenblas=0.3.24
+  - libsqlite=3.43.2
   - libxml2=2.11.5
   - libxslt=1.1.37
   - libzlib=1.2.13
+  - llvm-openmp=17.0.2
   - lxml=4.9.3
-  - ncurses=6.3
-  - openssl=3.1.2
-  - pip=22.3.1
+  - markdown-it-py=3.0.0
+  - markupsafe=2.1.3
+  - mccabe=0.7.0
+  - mdit-py-plugins=0.4.0
+  - mypy_extensions=1.0.0
+  - myst-parser=2.0.0
+  - ncurses=6.4
+  - numpy=1.26.0
+  - openssl=3.1.3
+  - packaging=23.2
+  - pandas=2.1.1
+  - pathspec=0.11.2
+  - pip=23.2.1
+  - platformdirs=3.11.0
+  - pluggy=1.3.0
+  - pygments=2.16.1
+  - pylint=3.0.1
+  - pysocks=1.7.1
+  - pytest=7.4.2
   - pytest-mock=3.11.1
-  - python=3.9.15
+  - python=3.9.18
+  - python-dateutil=2.8.2
+  - python-tzdata=2023.3
   - python_abi=3.9
-  - readline=8.1.2
-  - setuptools=65.5.1
-  - tk=8.6.12
+  - pytz=2023.3.post1
+  - pyyaml=6.0.1
+  - readline=8.2
+  - requests=2.31.0
+  - setuptools=68.2.2
+  - six=1.16.0
+  - snowballstemmer=2.2.0
+  - sphinx=7.2.6
+  - sphinx-rtd-theme=1.3.0
+  - sphinx_rtd_theme=1.3.0
+  - sphinxcontrib-applehelp=1.0.7
+  - sphinxcontrib-devhelp=1.0.5
+  - sphinxcontrib-dotnetdomain=0.4
+  - sphinxcontrib-golangdomain=0.2.0.dev0
+  - sphinxcontrib-htmlhelp=2.0.4
+  - sphinxcontrib-jquery=4.1
+  - sphinxcontrib-jsmath=1.0.1
+  - sphinxcontrib-qthelp=1.0.6
+  - sphinxcontrib-serializinghtml=1.1.9
+  - tk=8.6.13
   - tomli=2.0.1
-  - tzdata=2022g
-  - wheel=0.38.4
+  - tomlkit=0.12.1
+  - typing-extensions=4.8.0
+  - typing_extensions=4.8.0
+  - tzdata=2023c
+  - unidecode=1.3.7
+  - urllib3=2.0.6
+  - wheel=0.41.2
   - xz=5.2.6
+  - yaml=0.2.5
+  - zipp=3.17.0
   - pip:
-      - alabaster==0.7.12
-      - appnope==0.1.3
-      - astroid==2.12.13
-      - asttokens==2.2.1
-      - attrs==22.1.0
-      - babel==2.11.0
-      - backcall==0.2.0
-      - black==22.10.0
-      - bleach==5.0.1
-      - certifi==2022.12.7
-      - cffi==1.15.1
-      - charset-normalizer==2.1.1
-      - click==8.1.3
-      - click-log==0.4.0
-      - comm==0.1.1
-      - coverage==6.5.0
-      - debugpy==1.6.4
-      - decorator==5.1.1
-      - dill==0.3.6
-      - docutils==0.17.1
+      - annotated-types==0.6.0
+      - anyascii==0.3.2
+      - coverage==7.3.2
       - dotty-dict==1.3.1
-      - entrypoints==0.4
-      - exceptiongroup==1.0.4
-      - executing==1.2.0
-      - fastjsonschema==2.16.2
       - gbif-registrar==0.1.1
       - gitdb==4.0.10
-      - gitpython==3.1.29
-      - greenlet==2.0.1
-      - idna==3.4
-      - imagesize==1.4.1
-      - importlib-metadata==5.1.0
-      - iniconfig==1.1.1
-      - invoke==1.7.3
-      - ipykernel==6.19.0
-      - ipython==8.7.0
-      - isort==5.10.1
-      - jaraco-classes==3.2.3
-      - jedi==0.18.2
-      - jinja2==3.1.2
-      - jsonschema==4.17.3
-      - jupyter-cache==0.5.0
-      - jupyter-client==7.4.8
-      - jupyter-core==5.1.0
-      - keyring==23.11.0
-      - lazy-object-proxy==1.8.0
-      - markdown-it-py==2.1.0
-      - markupsafe==2.1.1
-      - matplotlib-inline==0.1.6
-      - mccabe==0.7.0
-      - mdit-py-plugins==0.3.3
+      - gitpython==3.1.37
+      - importlib-resources==5.13.0
       - mdurl==0.1.2
-      - more-itertools==9.0.0
-      - mypy-extensions==0.4.3
-      - myst-nb==0.17.1
-      - myst-parser==0.18.1
-      - nbclient==0.5.13
-      - nbformat==5.7.0
-      - nest-asyncio==1.5.6
-      - numpy==1.23.5
-      - packaging==22.0
-      - pandas==1.5.2
-      - parso==0.8.3
-      - pathspec==0.10.2
-      - pexpect==4.8.0
-      - pickleshare==0.7.5
-      - pkginfo==1.9.2
-      - platformdirs==2.6.0
-      - pluggy==1.0.0
-      - prompt-toolkit==3.0.36
-      - psutil==5.9.4
-      - ptyprocess==0.7.0
-      - pure-eval==0.2.2
-      - pycparser==2.21
-      - pygments==2.13.0
-      - pylint==2.15.8
-      - pyparsing==3.0.9
-      - pyrsistent==0.19.2
-      - pytest==7.2.0
-      - pytest-cov==4.0.0
-      - python-dateutil==2.8.2
-      - python-gitlab==3.12.0
-      - python-semantic-release==7.32.2
-      - pytz==2022.6
-      - pyyaml==6.0
-      - pyzmq==24.0.1
-      - readme-renderer==37.3
-      - requests==2.28.1
-      - requests-toolbelt==0.10.1
-      - rfc3986==2.0.0
-      - semver==2.13.0
-      - six==1.16.0
-      - smmap==5.0.0
-      - snowballstemmer==2.2.0
-      - sphinx==5.3.0
-      - sphinx-autoapi==2.0.0
-      - sphinx-rtd-theme==1.1.1
-      - sphinxcontrib-applehelp==1.0.2
-      - sphinxcontrib-devhelp==1.0.2
-      - sphinxcontrib-htmlhelp==2.0.0
-      - sphinxcontrib-jsmath==1.0.1
-      - sphinxcontrib-qthelp==1.0.3
-      - sphinxcontrib-serializinghtml==1.1.5
-      - sqlalchemy==1.4.44
-      - stack-data==0.6.2
-      - tabulate==0.9.0
-      - tomlkit==0.11.6
-      - tornado==6.2
-      - tqdm==4.64.1
-      - traitlets==5.6.0
-      - twine==3.8.0
-      - typing-extensions==4.4.0
-      - unidecode==1.3.6
-      - urllib3==1.26.13
-      - wcwidth==0.2.5
-      - webencodings==0.5.1
-      - wrapt==1.14.1
-      - zipp==3.11.0
+      - pydantic==2.4.2
+      - pydantic-core==2.10.1
+      - pytest-cov==4.1.0
+      - python-gitlab==3.15.0
+      - python-semantic-release==8.1.1
+      - requests-toolbelt==1.0.0
+      - rich==13.6.0
+      - shellingham==1.5.3
+      - smmap==5.0.1
+      - sphinx-autoapi==3.0.0
 prefix: /opt/miniconda3/envs/gbif_registrar