From a5c332dbb50e3a21ebe6251ee788cedce219450d Mon Sep 17 00:00:00 2001 From: Doug Latornell Date: Tue, 19 Nov 2024 13:56:41 -0800 Subject: [PATCH 1/9] Update ReadTheDocs build config Upgraded the OS to Ubuntu 24.04 and updated the Python toolchain to mambaforge-23.11 in the .readthedocs.yaml file. This ensures compatibility with the latest environment settings available on readthedocs. --- .readthedocs.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index b98d0ca..22ad41a 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -1,9 +1,9 @@ version: 2 build: - os: ubuntu-20.04 + os: ubuntu-22.04 tools: - python: "mambaforge-4.10" + python: "mambaforge-23.11" conda: environment: envs/environment-rtd.yaml From 60455f9cab05396036bd987661a14e055a536be1 Mon Sep 17 00:00:00 2001 From: Doug Latornell Date: Tue, 19 Nov 2024 14:00:25 -0800 Subject: [PATCH 2/9] Update Sphinx & optional dependencies version pin Updated Sphinx and optional dependencies packages pinned versions in `environment-dev.yaml`, `environment-test.yaml`, and `environment-rtd.yaml` in preparation for Python 3.13 environment. --- envs/environment-dev.yaml | 12 +-- envs/environment-rtd.yaml | 13 ++- envs/environment-test.yaml | 8 +- envs/requirements.txt | 203 ++++++++++++++++++------------------- 4 files changed, 119 insertions(+), 117 deletions(-) diff --git a/envs/environment-dev.yaml b/envs/environment-dev.yaml index 80b9946..e330f1f 100644 --- a/envs/environment-dev.yaml +++ b/envs/environment-dev.yaml @@ -6,7 +6,7 @@ # # $ conda env create -f MoaceanParcels/envs/environment-dev.yaml # $ conda activate moacean-parcels -# (moacean-parcels)$ python3 -m pip install --editable MoaceanParcels +# (moacean-parcels)$ python -m pip install --editable MoaceanParcels # # See the envs/requirements.txt file for an exhaustive list of all of the # packages installed in the environment and their versions used in @@ -21,7 +21,7 @@ channels: dependencies: - parcels - pip - - python=3.10 + - python=3.13 # To speed up numpy and xarray - bottleneck @@ -48,10 +48,10 @@ dependencies: - tomli # For documentation - - nbsphinx - - sphinx - - sphinx_rtd_theme - - sphinx-notfound-page + - nbsphinx==0.9.5 + - sphinx==8.1.3 + - sphinx-notfound-page==1.0.4 + - sphinx-rtd-theme==3.0.0 - pip: # For unit tests diff --git a/envs/environment-rtd.yaml b/envs/environment-rtd.yaml index 63a5670..52c80d1 100644 --- a/envs/environment-rtd.yaml +++ b/envs/environment-rtd.yaml @@ -19,14 +19,17 @@ dependencies: - pytest - python=3.10 - # readthedocs packages + # Sphinx and extensions + - nbsphinx==0.9.5 + - sphinx==8.1.3 + - sphinx-notfound-page==1.0.4 + - sphinx-rtd-theme==3.0.0 + + # readthedocs build system packages - mock - pillow - - sphinx - - sphinx_rtd_theme - - sphinx-notfound-page - - pip: + - commonmark - recommonmark - readthedocs-sphinx-ext diff --git a/envs/environment-test.yaml b/envs/environment-test.yaml index cde0e35..34ecc29 100644 --- a/envs/environment-test.yaml +++ b/envs/environment-test.yaml @@ -23,10 +23,10 @@ dependencies: - tomli # For documentation links checking - - nbsphinx - - sphinx - - sphinx_rtd_theme - - sphinx-notfound-page + - nbsphinx==0.9.5 + - sphinx==8.1.3 + - sphinx-notfound-page==1.0.4 + - sphinx-rtd-theme==3.0.0 - pip: # For unit tests diff --git a/envs/requirements.txt b/envs/requirements.txt index 9b949d0..074a893 100644 --- a/envs/requirements.txt +++ b/envs/requirements.txt @@ -3,201 +3,200 @@ # Create/update this file with: # (moacean-parcels)$ python -m pip list --format=freeze >> envs/requirements.txt -alabaster==0.7.16 -anyio==4.4.0 +alabaster==1.0.0 +anyio==4.6.2.post1 argon2-cffi==23.1.0 argon2-cffi-bindings==21.2.0 arrow==1.3.0 asciitree==0.3.3 asttokens==2.4.1 async-lru==2.0.4 -attrs==23.2.0 -Babel==2.14.0 +attrs==24.2.0 +babel==2.16.0 beautifulsoup4==4.12.3 -black==24.4.2 -bleach==6.1.0 -bokeh==3.4.1 -Bottleneck==1.3.8 +black==24.10.0 +bleach==6.2.0 +bokeh==3.6.1 +Bottleneck==1.4.2 Brotli==1.1.0 cached-property==1.5.2 -Cartopy==0.23.0 -certifi==2024.7.4 -cf_xarray==0.9.1 -cffi==1.16.0 +Cartopy==0.24.0 +certifi==2024.8.30 +cf_xarray==0.10.0 +cffi==1.17.1 cfgv==3.3.1 cftime==1.6.4 cgen==2020.1 -charset-normalizer==3.3.2 +charset-normalizer==3.4.0 click==8.1.7 -cloudpickle==3.0.0 +cloudpickle==3.1.0 cmocean==4.0.3 colorama==0.4.6 colorspacious==1.1.2 comm==0.2.2 -contourpy==1.2.1 -coverage==7.5.3 +contourpy==1.3.1 +coverage==7.6.7 cycler==0.12.1 -cytoolz==0.12.3 -dask==2024.6.0 -dask-expr==1.1.3 -debugpy==1.8.1 +cytoolz==1.0.0 +dask==2024.11.2 +dask-expr==1.1.19 +debugpy==1.8.8 decorator==5.1.1 defusedxml==0.7.1 -distlib==0.3.8 -distributed==2024.6.0 -docutils==0.20.1 +distlib==0.3.9 +distributed==2024.11.2 +docutils==0.21.2 entrypoints==0.4 -exceptiongroup==1.2.0 -executing==2.0.1 +exceptiongroup==1.2.2 +executing==2.1.0 fasteners==0.17.3 fastjsonschema==2.20.0 ffmpeg==1.4 -filelock==3.15.1 -fonttools==4.53.0 +filelock==3.16.1 +fonttools==4.55.0 fqdn==1.5.1 -fsspec==2024.6.0 +fsspec==2024.10.0 h11==0.14.0 h2==4.1.0 hpack==4.0.0 -httpcore==1.0.5 -httpx==0.27.0 +httpcore==1.0.7 +httpx==0.27.2 hyperframe==6.0.1 -identify==2.5.36 -idna==3.7 +identify==2.6.2 +idna==3.10 imagesize==1.4.1 -importlib_metadata==7.1.0 -importlib_resources==6.4.0 +importlib_metadata==8.5.0 +importlib_resources==6.4.5 iniconfig==2.0.0 -ipykernel==6.29.4 -ipython==8.25.0 +ipykernel==6.29.5 +ipython==8.29.0 isoduration==20.11.0 -jedi==0.19.1 +jedi==0.19.2 Jinja2==3.1.4 -json5==0.9.25 +json5==0.9.28 jsonpointer==3.0.0 -jsonschema==4.22.0 -jsonschema-specifications==2023.12.1 -jupyter_client==8.6.2 +jsonschema==4.23.0 +jsonschema-specifications==2024.10.1 +jupyter_client==8.6.3 jupyter_core==5.7.2 jupyter-events==0.10.0 jupyter-lsp==2.2.5 -jupyter_server==2.14.1 +jupyter_server==2.14.2 jupyter_server_terminals==0.5.3 -jupyterlab==4.2.5 +jupyterlab==4.3.1 jupyterlab_pygments==0.3.0 -jupyterlab_server==2.27.2 -kiwisolver==1.4.5 +jupyterlab_server==2.27.3 +kiwisolver==1.4.7 locket==1.0.0 lz4==4.3.3 -MarkupSafe==2.1.5 -matplotlib==3.8.4 +MarkupSafe==3.0.2 +matplotlib==3.9.2 matplotlib-inline==0.1.7 mistune==3.0.2 MoaceanParcels==22.1.dev0 -msgpack==1.0.8 +msgpack==1.1.0 munkres==1.1.4 mypy-extensions==1.0.0 nbclient==0.10.0 nbconvert==7.16.4 nbformat==5.10.4 -nbsphinx==0.9.4 +nbsphinx==0.9.5 nest_asyncio==1.6.0 -netCDF4==1.6.5 +netCDF4==1.7.2 nodeenv==1.9.1 notebook_shim==0.2.4 -numcodecs==0.12.1 -numpy==1.26.4 +numcodecs==0.14.0 +numpy==2.1.3 overrides==7.7.0 -packaging==24.1 -pandas==2.2.2 +packaging==24.2 +pandas==2.2.3 pandocfilters==1.5.0 -parcels==3.0.3 +parcels==3.1.0 parso==0.8.4 partd==1.4.2 pathspec==0.12.1 pexpect==4.9.0 pickleshare==0.7.5 -pillow==10.3.0 -pip==24.0 +pillow==11.0.0 +pip==24.3.1 pkgutil_resolve_name==1.3.10 -platformdirs==4.2.2 +platformdirs==4.3.6 pluggy==1.5.0 -pre_commit==3.7.1 -prometheus_client==0.20.0 -prompt_toolkit==3.0.47 -psutil==5.9.8 +pre_commit==4.0.1 +prometheus_client==0.21.0 +prompt_toolkit==3.0.48 +psutil==6.1.0 ptyprocess==0.7.0 -pure-eval==0.2.2 -pyarrow==16.1.0 -pyarrow-hotfix==0.6 +pure_eval==0.2.3 +pyarrow==18.0.0 pycparser==2.22 Pygments==2.18.0 pymbolic==2022.2 -pyparsing==3.1.2 -pyproj==3.6.1 +pyparsing==3.2.0 +pyproj==3.7.0 pyshp==2.3.1 PySocks==1.7.1 -pytest==8.2.2 -pytest-cov==5.0.0 -pytest-randomly==3.15.0 -python-dateutil==2.9.0 +pytest==8.3.3 +pytest-cov==6.0.0 +pytest-randomly==3.16.0 +python-dateutil==2.9.0.post0 python-json-logger==2.0.7 -pytools==2024.1.5 +pytools==2024.1.15 pytz==2024.1 -PyYAML==6.0.1 -pyzmq==26.0.3 +PyYAML==6.0.2 +pyzmq==26.2.0 referencing==0.35.1 requests==2.32.3 rfc3339-validator==0.1.4 rfc3986-validator==0.1.1 -roaring-landmask==0.7.1 -rpds-py==0.18.1 -scipy==1.13.1 +roaring-landmask==0.9.1 +rpds-py==0.21.0 +scipy==1.14.1 Send2Trash==1.8.3 -setuptools==70.0.0 -shapely==2.0.4 +setuptools==75.5.0 +shapely==2.0.6 +siphash24==1.7 six==1.16.0 sniffio==1.3.1 snowballstemmer==2.2.0 sortedcontainers==2.4.0 soupsieve==2.5 -Sphinx==7.3.7 -sphinx-notfound-page==1.0.2 -sphinx-rtd-theme==2.0.0 -sphinxcontrib-applehelp==1.0.8 -sphinxcontrib-devhelp==1.0.6 -sphinxcontrib-htmlhelp==2.0.5 +Sphinx==8.1.3 +sphinx-notfound-page==1.0.4 +sphinx_rtd_theme==3.0.0 +sphinxcontrib-applehelp==2.0.0 +sphinxcontrib-devhelp==2.0.0 +sphinxcontrib-htmlhelp==2.1.0 sphinxcontrib-jquery==4.1 sphinxcontrib-jsmath==1.0.1 -sphinxcontrib-qthelp==1.0.7 +sphinxcontrib-qthelp==2.0.0 sphinxcontrib-serializinghtml==1.1.10 stack-data==0.6.2 tblib==3.0.0 terminado==0.18.1 -tinycss2==1.3.0 +tinycss2==1.4.0 toml==0.10.2 -tomli==2.0.1 -toolz==0.12.1 +tomli==2.1.0 +toolz==1.0.0 tornado==6.4.1 -tqdm==4.66.4 +tqdm==4.67.0 traitlets==5.14.3 -trajan==0.6.1 -types-python-dateutil==2.9.0.20240316 +trajan==0.7.0 +types-python-dateutil==2.9.0.20241003 typing_extensions==4.12.2 typing-utils==0.1.0 -tzdata==2024.1 +tzdata==2024.2 ukkonen==1.0.1 -unicodedata2==15.1.0 uri-template==1.3.0 -urllib3==2.2.2 -virtualenv==20.26.2 +urllib3==2.2.3 +virtualenv==20.27.1 wcwidth==0.2.13 -webcolors==24.6.0 +webcolors==24.8.0 webencodings==0.5.1 websocket-client==1.8.0 -wheel==0.43.0 -xarray==2024.6.0 -xyzservices==2024.6.0 -zarr==2.18.2 +xarray==2024.10.0 +xyzservices==2024.9.0 +zarr==2.18.3 zict==3.0.0 -zipp==3.19.2 +zipp==3.21.0 +zstandard==0.23.0 From a03e6411ee9fd7de9f33427f6264196adcbf88ee Mon Sep 17 00:00:00 2001 From: Doug Latornell Date: Tue, 19 Nov 2024 14:28:26 -0800 Subject: [PATCH 3/9] Upgrade blacken-docs dependency in pre-commit config Updated the black formatter for blacken-docs from version 21.10b0 to 24.10.0. This change ensures compatibility with the latest version of black and avoids a version conflict problem during setup of the the pre-commit virtualenv. --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 2bb056a..6d79f28 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -26,5 +26,5 @@ repos: rev: 1.19.1 hooks: - id: blacken-docs - additional_dependencies: [black==21.10b0] + additional_dependencies: [black==24.10.0] args: [--skip-errors] From b3f7c31de4bd6adf0eccc21cae882ab7a562d382 Mon Sep 17 00:00:00 2001 From: Doug Latornell Date: Tue, 19 Nov 2024 14:29:11 -0800 Subject: [PATCH 4/9] Update OceanParcels doc URL in Sphinx configuration Change the intersphinx mapping for OceanParcels to its new documentation URL. This ensures references to OceanParcels documentation are correctly resolved during the build process. --- docs/conf.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/conf.py b/docs/conf.py index 3fc8561..766b385 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -52,7 +52,7 @@ intersphinx_mapping = { "moaddocs": ("https://ubc-moad-docs.readthedocs.io/en/latest/", None), "numpy": ("https://numpy.org/doc/stable/", None), - "oceanparcels": ("https://oceanparcels.org/gh-pages/html/", None), + "oceanparcels": ("https://docs.oceanparcels.org/en/latest/", None), } # Add any paths that contain templates here, relative to this directory. From ac18aa1f428ce855479ab87a14deaec599e345e2 Mon Sep 17 00:00:00 2001 From: Doug Latornell Date: Tue, 19 Nov 2024 14:38:47 -0800 Subject: [PATCH 5/9] Fix xref link in Stokes_drift kernel docstring Changed the documentation reference link in the Stokes_drift kernel to point to the correct section in the example notebooks. This ensures users can find more detailed usage examples without any confusion. --- moacean_parcels/kernels/Stokes_drift.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/moacean_parcels/kernels/Stokes_drift.py b/moacean_parcels/kernels/Stokes_drift.py index 04b011f..e62d305 100644 --- a/moacean_parcels/kernels/Stokes_drift.py +++ b/moacean_parcels/kernels/Stokes_drift.py @@ -40,7 +40,7 @@ def Stokes_drift(particle, fieldset, time): For a more detailed usage example, please see the example notebook for this kernel in the - :ref:`particle_behaviour_kernels` section. + :ref:`ParticleBehaviourKernelExampleNotebooks` section. :param particle: Particle to add behaviour. :type particle: :py:class:`parcels.particle.JITParticle` or From 1973f767c0a6104b15e005660576f3dcfb751b49 Mon Sep 17 00:00:00 2001 From: Doug Latornell Date: Tue, 19 Nov 2024 14:40:05 -0800 Subject: [PATCH 6/9] Fix xref link in Stokes_drift kernel docstring Changed the documentation reference link in the Stokes_drift kernel to point to the correct section in the example notebooks. This ensures users can find more detailed usage examples without any confusion. --- moacean_parcels/kernels/Stokes_drift.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/moacean_parcels/kernels/Stokes_drift.py b/moacean_parcels/kernels/Stokes_drift.py index e62d305..0b75f27 100644 --- a/moacean_parcels/kernels/Stokes_drift.py +++ b/moacean_parcels/kernels/Stokes_drift.py @@ -14,8 +14,6 @@ # SPDX-License-Identifier: Apache-2.0 -# SPDX-License-Identifier: Apache-2.0 - def Stokes_drift(particle, fieldset, time): """Include the effect of Stokes drift to your particles From d3482a3461d9896a288e6f66df12111fda8ee613 Mon Sep 17 00:00:00 2001 From: Doug Latornell Date: Tue, 19 Nov 2024 14:54:23 -0800 Subject: [PATCH 7/9] Update redirected docs links found by linkcheck Changed outdated Conda links in `docs/pkg_development.rst` and `docs/installation.rst` to their current URLs. This ensures users are directed to the most accurate and up-to-date documentation. --- docs/installation.rst | 2 +- docs/pkg_development.rst | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/installation.rst b/docs/installation.rst index db4b746..eced1e6 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -76,7 +76,7 @@ will have all of the Python packages necessary for development, testing, and building the documentation for the package with the commands below. -.. _Conda: https://conda.io/en/latest/ +.. _Conda: https://docs.conda.io/en/latest/ .. _Miniconda3: https://docs.conda.io/en/latest/miniconda.html .. code-block:: bash diff --git a/docs/pkg_development.rst b/docs/pkg_development.rst index 5d39790..aa59de3 100644 --- a/docs/pkg_development.rst +++ b/docs/pkg_development.rst @@ -111,7 +111,7 @@ will have all of the Python packages necessary for development, testing, and building the documentation with the commands below. -.. _Conda: https://conda.io/en/latest/ +.. _Conda: https://docs.conda.io/en/latest/ .. _Miniconda3: https://docs.conda.io/en/latest/miniconda.html .. code-block:: bash From b057ea2ddb903e1d1cd2444a3e8e6edff008ea78 Mon Sep 17 00:00:00 2001 From: Doug Latornell Date: Tue, 19 Nov 2024 14:58:26 -0800 Subject: [PATCH 8/9] Fix duplicated link definition in install docs --- docs/installation.rst | 2 -- 1 file changed, 2 deletions(-) diff --git a/docs/installation.rst b/docs/installation.rst index eced1e6..eb8dff6 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -45,8 +45,6 @@ Getting the Code Clone the code and documentation `repository`_ from GitHub with: -.. _repository: https://github.com/UBC-MOAD/MoaceanParcels - .. code-block:: bash $ git clone git@github.com:UBC-MOAD/MoaceanParcels.git From de3415d47a1e94f62da4e7dababa792f9f519342 Mon Sep 17 00:00:00 2001 From: Doug Latornell Date: Tue, 19 Nov 2024 14:59:15 -0800 Subject: [PATCH 9/9] Update docs example output from Sphinx Updated Sphinx build and linkcheck commands example outputs. --- docs/pkg_development.rst | 123 +++++++++++++++++++++++++-------------- 1 file changed, 79 insertions(+), 44 deletions(-) diff --git a/docs/pkg_development.rst b/docs/pkg_development.rst index aa59de3..0eb14b1 100644 --- a/docs/pkg_development.rst +++ b/docs/pkg_development.rst @@ -197,27 +197,39 @@ The output looks something like: .. code-block:: text Removing everything under '_build'... - Running Sphinx v4.3.1 + Running Sphinx v8.1.3 + loading translations [en]... done making output directory... done - loading intersphinx inventory from https://ubc-moad-docs.readthedocs.io/en/latest/objects.inv... - loading intersphinx inventory from https://numpy.org/doc/stable/objects.inv... - loading intersphinx inventory from https://oceanparcels.org/gh-pages/html/objects.inv... + Writing evaluated template result to /media/doug/warehouse/MOAD/MoaceanParcels/docs/_build/html/_static/nbsphinx-code-cells.css + loading intersphinx inventory 'moaddocs' from https://ubc-moad-docs.readthedocs.io/en/latest/objects.inv ... + loading intersphinx inventory 'numpy' from https://numpy.org/doc/stable/objects.inv ... + loading intersphinx inventory 'oceanparcels' from https://docs.oceanparcels.org/en/latest/objects.inv ... building [mo]: targets for 0 po files that are out of date - building [html]: targets for 9 source files that are out of date - updating environment: [new config] 9 added, 0 changed, 0 removed + writing output... + building [html]: targets for 11 source files that are out of date + updating environment: [new config] 11 added, 0 changed, 0 removed reading sources... [100%] pkg_development looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done + copying assets... + copying static files... + Writing evaluated template result to /media/doug/warehouse/MOAD/MoaceanParcels/docs/_build/html/_static/language_data.js + Writing evaluated template result to /media/doug/warehouse/MOAD/MoaceanParcels/docs/_build/html/_static/documentation_options.js + Writing evaluated template result to /media/doug/warehouse/MOAD/MoaceanParcels/docs/_build/html/_static/basic.css + Writing evaluated template result to /media/doug/warehouse/MOAD/MoaceanParcels/docs/_build/html/_static/js/versions.js + copying static files: done + copying extra files... + copying extra files: done + copying assets: done writing output... [100%] pkg_development generating indices... genindex py-modindex done + copying linked files... copying notebooks ... [100%] kernels/kernel_example_notebooks/recovery_kernels/DeleteParticle-example.ipynb - highlighting module code... [100%] moacean_parcels.kernels.DeleteParticle + highlighting module code... [100%] moacean_parcels.kernels.Stokes_drift writing additional pages... search done copying images... [100%] _build/doctrees/nbsphinx/kernels_kernel_example_notebooks_recovery_kernels_DeleteParticle-example_13_0.png - copying static files... done - copying extra files... done dumping search index in English (code: en)... done dumping object inventory... done build succeeded. @@ -263,49 +275,72 @@ The output looks something like: .. code-block:: text - Running Sphinx v4.2.0 - loading pickled environment... done + Removing everything under '_build'... + Running Sphinx v8.1.3 + loading translations [en]... done + making output directory... done + loading intersphinx inventory 'moaddocs' from https://ubc-moad-docs.readthedocs.io/en/latest/objects.inv ... + loading intersphinx inventory 'numpy' from https://numpy.org/doc/stable/objects.inv ... + loading intersphinx inventory 'oceanparcels' from https://docs.oceanparcels.org/en/latest/objects.inv ... building [mo]: targets for 0 po files that are out of date - building [linkcheck]: targets for 2 source files that are out of date - updating environment: 0 added, 1 changed, 0 removed + writing output... + building [linkcheck]: targets for 11 source files that are out of date + updating environment: [new config] 11 added, 0 changed, 0 removed reading sources... [100%] pkg_development looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done + copying assets... + copying assets: done writing output... [100%] pkg_development - ( pkg_development: line 20) ok https://black.readthedocs.io/en/stable/ - ( pkg_development: line 261) ok https://coverage.readthedocs.io/en/latest/ - ( pkg_development: line 20) ok https://docs.python.org/3.10/ - ( pkg_development: line 62) ok https://docs.python.org/3/reference/lexical_analysis.html#f-strings - ( pkg_development: line 241) ok https://docs.pytest.org/en/latest/ - ( pkg_development: line 298) ok https://git-scm.com/ - ( pkg_development: line 106) ok https://conda.io/en/latest/ - ( pkg_development: line 106) ok https://docs.conda.io/en/latest/miniconda.html - ( pkg_development: line 93) ok https://docs.github.com/en/authentication/connecting-to-github-with-ssh - ( pkg_development: line 20) ok https://img.shields.io/badge/code%20style-black-000000.svg - ( index: line 36) ok https://img.shields.io/badge/license-Apache%202-cb2533.svg - ( pkg_development: line 20) ok https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white - ( pkg_development: line 20) ok https://img.shields.io/badge/python-3.10-blue.svg - ( pkg_development: line 20) ok https://img.shields.io/badge/version%20control-git-blue.svg?logo=github - ( pkg_development: line 231) ok https://github.com/UBC-MOAD/MoaceanParcels/actions?query=workflow=sphinx-linkcheck - ( pkg_development: line 20) ok https://github.com/UBC-MOAD/MoaceanParcels/issues - ( pkg_development: line 20) ok https://moaceanparcels.readthedocs.io/en/latest/ - ( pkg_development: line 261) ok https://pytest-cov.readthedocs.io/en/latest/ - ( pkg_development: line 307) ok https://img.shields.io/github/issues/MIDOSS/WWatch3-Cmd?logo=github - ( pkg_development: line 20) ok https://github.com/pre-commit/pre-commit - ( pkg_development: line 20) ok https://readthedocs.org/projects/MoaceanParcels/badge/?version=latest - ( pkg_development: line 20) ok https://github.com/UBC-MOAD/MoaceanParcels - ( pkg_development: line 93) ok https://ubc-moad-docs.readthedocs.io/en/latest/ssh_access.html#copyyourpublicsshkeytogithub - ( index: line 36) ok https://www.apache.org/licenses/LICENSE-2.0 - ( pkg_development: line 58) ok https://www.python.org/ - ( pkg_development: line 143) ok https://www.python.org/dev/peps/pep-0008/ - ( pkg_development: line 93) ok https://ubc-moad-docs.readthedocs.io/en/latest/ssh_access.html#secureremoteaccess - ( pkg_development: line 177) ok https://www.sphinx-doc.org/en/master/ - ( pkg_development: line 177) ok https://www.sphinx-doc.org/en/master/usage/restructuredtext/basics.html - ( pkg_development: line 20) ok https://img.shields.io/github/issues/UBC-MOAD/MoaceanParcels?logo=github - ( pkg_development: line 171) ok https://readthedocs.org/projects/moaceanparcels/badge/?version=latest + ( pkg_development: line 355) ok https://coverage.readthedocs.io/en/latest/ + ( installation: line 71) ok https://docs.conda.io/en/latest/ + ( installation: line 27) ok https://docs.conda.io/projects/conda/en/latest/ + ( installation: line 60) ok https://docs.github.com/en/authentication/connecting-to-github-with-ssh + ( installation: line 71) ok https://docs.conda.io/en/latest/miniconda.html + ( pkg_development: line 22) ok https://black.readthedocs.io/en/stable/ + ( pkg_development: line 335) ok https://docs.pytest.org/en/latest/ + (kernels/kernel_functions: line 44) ok https://docs.oceanparcels.org/en/latest/reference/particles.html#parcels.particle.JITParticle + (kernels/add_kernel_howto: line 147) ok https://docs.oceanparcels.org/en/latest/examples/tutorial_jit_vs_scipy.html + ( pkg_development: line 22) ok https://docs.python.org/3.10/ + (kernels/kernel_functions: line 44) ok https://docs.oceanparcels.org/en/latest/reference/fields.html#parcels.fieldset.FieldSet + ( pkg_development: line 392) ok https://git-scm.com/ + (kernels/kernel_functions: line 56) ok https://docs.oceanparcels.org/en/latest/reference/misc.html#module-parcels.tools.statuscodes + ( pkg_development: line 46) ok https://github.com/UBC-MOAD/MoaceanParcels/actions/workflows/codeql-analysis.yaml/badge.svg + ( pkg_development: line 22) ok https://github.com/UBC-MOAD/MoaceanParcels/actions?query=workflow%3Acodeql-analysis + ( installation: line 23) ok https://github.com/UBC-MOAD/MoaceanParcels + ( pkg_development: line 22) ok https://github.com/UBC-MOAD/MoaceanParcels/issues + ( pkg_development: line 43) ok https://github.com/UBC-MOAD/MoaceanParcels/workflows/sphinx-linkcheck/badge.svg + ( pkg_development: line 37) ok https://img.shields.io/badge/code%20style-black-000000.svg + ( index: line 46) ok https://img.shields.io/badge/license-Apache%202-cb2533.svg + ( pkg_development: line 34) ok https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white + ( installation: line 42) ok https://img.shields.io/badge/version%20control-git-blue.svg?logo=github + ( pkg_development: line 403) ok https://img.shields.io/github/issues/MIDOSS/WWatch3-Cmd?logo=github + ( pkg_development: line 28) ok https://img.shields.io/badge/Python-3.10-blue?logo=python&label=Python&logoColor=gold + ( pkg_development: line 49) ok https://img.shields.io/github/issues/UBC-MOAD/MoaceanParcels?logo=github + (kernels/add_kernel_howto: line 388) ok https://moaceanparcels.readthedocs.io/en/latest/ + (kernels/add_kernel_howto: line 405) ok https://nbsphinx.readthedocs.io/en/latest/ + ( pkg_development: line 325) ok https://github.com/UBC-MOAD/MoaceanParcels/actions?query=workflow=sphinx-linkcheck + ( pkg_development: line 22) ok https://github.com/pre-commit/pre-commit + (kernels/kernel_functions: line 44) ok https://numpy.org/doc/stable/reference/arrays.scalars.html#numpy.float64 + ( index: line 21) ok https://oceanparcels.org/ + ( pkg_development: line 22) ok https://github.com/UBC-MOAD/MoaceanParcels/actions?query=workflow:sphinx-linkcheck + (kernels/add_kernel_howto: line 78) ok https://peps.python.org/pep-0008/ + ( pkg_development: line 355) ok https://pytest-cov.readthedocs.io/en/latest/ + ( installation: line 129) ok https://pip.pypa.io/en/stable/topics/local-project-installs/#editable-installs + ( installation: line 31) ok https://pip.pypa.io/en/stable/cli/pip_install/#editable-installs + ( installation: line 60) ok https://ubc-moad-docs.readthedocs.io/en/latest/ssh_access.html#copyyourpublicsshkeytogithub + ( installation: line 60) ok https://ubc-moad-docs.readthedocs.io/en/latest/ssh_access.html#secureremoteaccess + ( index: line 44) ok https://www.apache.org/licenses/LICENSE-2.0 + ( pkg_development: line 66) ok https://www.python.org/ + ( pkg_development: line 40) ok https://readthedocs.org/projects/MoaceanParcels/badge/?version=latest + ( pkg_development: line 149) ok https://pre-commit.com/ + ( pkg_development: line 175) ok https://readthedocs.org/projects/moaceanparcels/badge/?version=latest + ( pkg_development: line 179) ok https://www.sphinx-doc.org/en/master/usage/restructuredtext/basics.html + ( pkg_development: line 179) ok https://www.sphinx-doc.org/en/master/ + (kernels/add_kernel_howto: line 360) ok https://www.sphinx-doc.org/en/master/usage/extensions/autodoc.html build succeeded. Look for any errors in the above output or in _build/linkcheck/output.txt