add dependabot updates and linkcheck

[ocefpaf]

Should help keep links updated. I also added dependabot for GHA updates and change to hashes instead of the unsafe versioned ones.

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[ocefpaf]

It is not worth fixing them all in this PR but here is a list of the broken links in our docs:

(ohw22/tutorials/02-Wed/01-data-visualization-in-python/tutorial/04_Basic_Plotting: line 130006) broken    http://datashader.org/user_guide/1_Plotting_Pitfalls.html#1.-Overplotting - 404 Client Error: Not Found for url: https://datashader.org/user_guide/1_Plotting_Pitfalls.html
(ohw22/tutorials/02-Wed/01-data-visualization-in-python/tutorial/exercises/Overview: line 70004) broken    http://graphics.wsj.com/infectious-diseases-and-vaccines/#b02g20t20w15 - Anchor 'b02g20t20w15' not found
(ohw22/tutorials/02-Wed/01-data-visualization-in-python/tutorial/01_Overview: line 110020) broken    http://geo.holoviews.org - HTTPConnectionPool(host='geo.holoviews.org', port=80): Max retries exceeded with url: / (Caused by NameResolutionError("<urllib3.connection.HTTPConnection object at 0x7f766de8cb50>: Failed to resolve 'geo.holoviews.org' ([Errno -2] Name or service not known)"))
(ohw22/tutorials/02-Wed/01-data-visualization-in-python/tutorial/00_Setup: line 30006) broken    http://holoviz.org/installation.html - 404 Client Error: Not Found for url: https://holoviz.org/installation.html
(ohw23/tutorials/03-Thu/OHW_omics_lesson: line 500004) broken    http://scikit-bio.org/docs/0.4.2/generated/skbio.stats.composition.html#module-skbio.stats.composition - 404 Client Error: Not Found for url: http://scikit-bio.org/docs/0.4.2/generated/skbio.stats.composition.html
(ohw22/tutorials/02-Wed/01-data-visualization-in-python/tutorial/01_Overview: line 120014) broken    http://xarray - HTTPConnectionPool(host='xarray', port=80): Max retries exceeded with url: / (Caused by NameResolutionError("<urllib3.connection.HTTPConnection object at 0x7f766e3df610>: Failed to resolve 'xarray' ([Errno -3] Temporary failure in name resolution)"))
(ohw23/tutorials/01-Tue/Data_access_methods_Python: line 170003) broken    http://tds.marine.rutgers.edu/thredds/dodsC/roms/doppio/2017_da/avg/Averages_Best.html - 404 Client Error:  for url: https://tds.marine.rutgers.edu/thredds/dodsC/roms/doppio/2017_da/avg/Averages_Best.html
(ohw24/tutorials-index/index: line   22) broken    https://apl.uw.edu/people/profile.php?last_name=Sarason&first_name=Christian - HTTPSConnectionPool(host='apl.uw.edu', port=443): Max retries exceeded with url: /people/profile.php?last_name=Sarason&first_name=Christian (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1149)')))
(ohw23/tutorials/01-Tue/Data_access_methods_Python: line 180004) broken    http://www.opengeospatial.org/standards/wfs - 403 Client Error: Forbidden for url: https://www.ogc.org/standards/wfs
(ohw23/tutorials/01-Tue/Data_access_methods_Python: line 180004) broken    http://www.opengeospatial.org/ - 403 Client Error: Forbidden for url: https://www.ogc.org/
(ohw23/tutorials/01-Tue/Data_access_methods_Python: line 220002) broken    https://catalogue-imos.aodn.org.au/geonetwork/srv/eng/catalog.search#/metadata/7b901002-b1dc-46c3-89f2-b4951cedca48 - Anchor '/metadata/7b901002-b1dc-46c3-89f2-b4951cedca48' not found
(ohw23/tutorials/01-Tue/Data_access_methods_Python: line 140002) broken    https://catalogue-imos.aodn.org.au/geonetwork/srv/eng/catalog.search#/metadata/279a50e3-21a5-4590-85a0-71f963efab82 - Anchor '/metadata/279a50e3-21a5-4590-85a0-71f963efab82' not found
(ohw23/tutorials/01-Tue/Data_access_methods_Python: line 340004) broken    https://catalogue-imos.aodn.org.au/geonetwork/srv/eng/catalog.search#/metadata/a4170ca8-0942-4d13-bdb8-ad4718ce14bb - Anchor '/metadata/a4170ca8-0942-4d13-bdb8-ad4718ce14bb' not found
(ohw23/tutorials/02-Wed/ai_assisted_programming_ohw: line 50004) broken    https://chat.openai.com/ - 403 Client Error: Forbidden for url: https://chatgpt.com/
(ohw22/tutorials/optional/espanol/datos-espaciales-tidy/slides/espaciales: line 240027) broken    https://cds.climate.copernicus.eu/cdsapp#!/home - 404 Client Error: Not Found for url: https://cds.climate.copernicus.eu/cdsapp
(ohw22/seattle/index: line   67) broken    https://docs.google.com/presentation/d/17h4m6gTG8mRfWaQR3nOn6LPR3hQdCgWzH2hPzpCtyFU/edit#slide=id.p1 - Anchor 'slide=id.p1' not found
(ohw24/projects/projects_thisyear: line   56) broken    https://docs.google.com/presentation/d/1MG32LTh15YH1vHQdv_7U-SAyclAFcNLs-xWWvf0eZ8g/edit#slide=id.g2f660589f1f_13_0 - Anchor 'slide=id.g2f660589f1f_13_0' not found
(ohw24/projects/projects_thisyear: line   41) broken    https://docs.google.com/presentation/d/1MG32LTh15YH1vHQdv_7U-SAyclAFcNLs-xWWvf0eZ8g/edit#slide=id.g2f660589f1f_18_0 - Anchor 'slide=id.g2f660589f1f_18_0' not found
(ohw24/projects/projects_thisyear: line   27) broken    https://docs.google.com/presentation/d/1MG32LTh15YH1vHQdv_7U-SAyclAFcNLs-xWWvf0eZ8g/edit#slide=id.g2f660589f1f_3_5 - Anchor 'slide=id.g2f660589f1f_3_5' not found
(ohw24/projects/projects_thisyear: line   34) broken    https://docs.google.com/presentation/d/1MG32LTh15YH1vHQdv_7U-SAyclAFcNLs-xWWvf0eZ8g/edit#slide=id.g2f660589f1f_28_0 - Anchor 'slide=id.g2f660589f1f_28_0' not found
(ohw24/projects/projects_thisyear: line   20) broken    https://docs.google.com/presentation/d/1MG32LTh15YH1vHQdv_7U-SAyclAFcNLs-xWWvf0eZ8g/edit#slide=id.g2f660589f1f_42_0 - Anchor 'slide=id.g2f660589f1f_42_0' not found
(ohw24/projects/projects_thisyear: line   49) broken    https://docs.google.com/presentation/d/1MG32LTh15YH1vHQdv_7U-SAyclAFcNLs-xWWvf0eZ8g/edit#slide=id.g2f660589f1f_4_0 - Anchor 'slide=id.g2f660589f1f_4_0' not found
(ohw23/projects/projects_thisyear: line   56) broken    https://docs.google.com/presentation/d/1uUAIsuj9bxOFMVeIG_h5Bs-ZGDrRodldlz2FHfj4TbE/edit#slide=id.p - 410 Client Error: Gone for url: https://docs.google.com/presentation/d/1uUAIsuj9bxOFMVeIG_h5Bs-ZGDrRodldlz2FHfj4TbE/edit
(ohw23/projects/index: line    5) broken    https://docs.google.com/presentation/d/1eQKSdFHNGMDqGJMY4d-yGnNm4UrUj5kIS2mLQGPMZC8/edit#slide=id.p - Anchor 'slide=id.p' not found
(ohw23/projects/projects_thisyear: line   20) broken    https://docs.google.com/presentation/d/1eQKSdFHNGMDqGJMY4d-yGnNm4UrUj5kIS2mLQGPMZC8/edit#slide=id.g25f8e87bf15_11_0 - Anchor 'slide=id.g25f8e87bf15_11_0' not found
(     about/index: line   37) broken    https://doi.org/10.1073/pnas.1717196115 - 403 Client Error: Forbidden for url: https://pnas.org/doi/full/10.1073/pnas.1717196115
(ohw22/tutorials/02-Wed/01-data-visualization-in-python/tutorial/exercises/Overview: line 520002) broken    https://github.com/andrix/python-snappy#dependencies - Anchor 'dependencies' not found
(ohw23/tutorials/01-Tue/Data_access_methods_Python: line 540002) broken    https://github.com/aodn/rimrep-examples/blob/main/Python_based_scripts/Extracting_Water_Temperature_at_Site.ipynb - 404 Client Error: Not Found for url: https://github.com/gbr-dms/rimrep-examples/blob/main/Python_based_scripts/Extracting_Water_Temperature_at_Site.ipynb
(ohw23/tutorials/01-Tue/Data_access_methods_Python: line 610012) broken    https://github.com/aodn/rimrep-examples/blob/main/Python_based_scripts/ogccoverages.ipynb - 404 Client Error: Not Found for url: https://github.com/gbr-dms/rimrep-examples/blob/main/Python_based_scripts/ogccoverages.ipynb
(ohw23/tutorials/01-Tue/Data_access_methods_Python: line 610011) broken    https://github.com/aodn/rimrep-examples/blob/main/Python_based_scripts/ogcfeatures.ipynb - 404 Client Error: Not Found for url: https://github.com/gbr-dms/rimrep-examples/blob/main/Python_based_scripts/ogcfeatures.ipynb
(resources/prep/conda: line   24) broken    https://github.com/oceanhackweek/jupyter-image/blob/main/py-base/environment.yml - 404 Client Error: Not Found for url: https://github.com/oceanhackweek/jupyter-image/blob/main/py-base/environment.yml
(ohw24/tutorials-index/index: line   49) broken    https://github.com/oceanhackweek/ohw-tutorials/tree/OHW24/us/00-Mon#reproducible-research - Anchor 'reproducible-research' not found
(ohw24/tutorials-index/index: line   22) broken    https://github.com/oceanhackweek/ohw-tutorials/tree/OHW24/us/00-Mon#packagesjupyterlabhub - Anchor 'packagesjupyterlabhub' not found
(ohw24/tutorials-index/index: line   33) broken    https://github.com/oceanhackweek/ohw-tutorials/tree/OHW24/us/01-Tue#assessing-weather-model-skill-during-extreme-events-noaa-gfs-vs-sofar-spotter-buoy-observations-of-hurricane-henri - Anchor 'assessing-weather-model-skill-during-extreme-events-noaa-gfs-vs-sofar-spotter-buoy-observations-of-hurricane-henri' not found
(ohw24/tutorials-index/index: line   31) broken    https://github.com/oceanhackweek/ohw-tutorials/tree/OHW24/us/01-Tue#xarray - Anchor 'xarray' not found
(ohw24/tutorials-index/index: line   29) broken    https://github.com/oceanhackweek/ohw-tutorials/tree/OHW24/us/01-Tue#data-access-in-python - Anchor 'data-access-in-python' not found
(ohw24/tutorials-index/index: line   27) broken    https://github.com/oceanhackweek/ohw-tutorials/tree/OHW24/us/01-Tue#git--github-primer - Anchor 'git--github-primer' not found
(ohw24/tutorials-index/index: line   39) broken    https://github.com/oceanhackweek/ohw-tutorials/tree/OHW24/us/02-Wed#deep-learning-introduction-to-transformers - Anchor 'deep-learning-introduction-to-transformers' not found
(ohw24/tutorials-index/index: line   37) broken    https://github.com/oceanhackweek/ohw-tutorials/tree/OHW24/us/02-Wed#ai-assisted-programming - Anchor 'ai-assisted-programming' not found
(ohw22/tutorials/02-Wed/01-data-visualization-in-python/tutorial/01_Overview: line 150010) broken    https://holoviz.org/installation - 404 Client Error: Not Found for url: https://holoviz.org/installation
(ohw23/tutorials/00-Mon/README: line   12) broken    https://hackmd.io/@iKjr9f0pTj6CZO1DZOjJyw/BkqeRfYjh#/ - Anchor '/' not found
(about/steering_committee: line   13) broken    https://imos.org.au/fileadmin/_processed_/b/c/csm_DSC_8209_f513b959ad.jpg - 404 Client Error: Not Found for url: https://imos.org.au/fileadmin/_processed_/b/c/csm_DSC_8209_f513b959ad.jpg
(resources/prep/jupyterhub: line   77) broken    https://jupyterhub.github.io/nbgitpuller/#when-to-use-nbgitpuller - Anchor 'when-to-use-nbgitpuller' not found
(resources/prep/jupyterhub: line   71) broken    https://jupyterhub.github.io/nbgitpuller/topic/automatic-merging.html#topic-automatic-merging - Anchor 'topic-automatic-merging' not found
(resources/prep/git: line  255) broken    https://lab.github.com/ - HTTPSConnectionPool(host='lab.github.com', port=443): Max retries exceeded with url: / (Caused by NameResolutionError("<urllib3.connection.HTTPSConnection object at 0x7f766deffe20>: Failed to resolve 'lab.github.com' ([Errno -5] No address associated with hostname)"))
(ohw22/logistics/index: line   21) broken    https://oceanhackweek.2i2c.cloud - HTTPSConnectionPool(host='oceanhackweek.2i2c.cloud', port=443): Max retries exceeded with url: / (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: self-signed certificate (_ssl.c:1149)')))
(resources/prep/jupyterhub: line  124) broken    https://oceanhackweek.2i2c.cloud/hub/home - HTTPSConnectionPool(host='oceanhackweek.2i2c.cloud', port=443): Max retries exceeded with url: /hub/home (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: self-signed certificate (_ssl.c:1149)')))
(ohw22/tutorials_getting_started: line   24) broken    https://oceanhackweek.2i2c.cloud/hub/user-redirect/git-pull?repo=https%3A%2F%2Fgithub.com%2Foceanhackweek%2Fohw-tutorials&urlpath=lab%2Ftree%2Fohw-tutorials%2F&branch=OHW22 - HTTPSConnectionPool(host='oceanhackweek.2i2c.cloud', port=443): Max retries exceeded with url: /hub/user-redirect/git-pull?repo=https%3A%2F%2Fgithub.com%2Foceanhackweek%2Fohw-tutorials&urlpath=lab%2Ftree%2Fohw-tutorials%2F&branch=OHW22 (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: self-signed certificate (_ssl.c:1149)')))
(ohw23/tutorials_getting_started: line   24) broken    https://oceanhackweek.2i2c.cloud/hub/user-redirect/git-pull?repo=https%3A%2F%2Fgithub.com%2Foceanhackweek%2Fohw-tutorials&urlpath=lab%2Ftree%2Fohw-tutorials%2F&branch=OHW23 - HTTPSConnectionPool(host='oceanhackweek.2i2c.cloud', port=443): Max retries exceeded with url: /hub/user-redirect/git-pull?repo=https%3A%2F%2Fgithub.com%2Foceanhackweek%2Fohw-tutorials&urlpath=lab%2Ftree%2Fohw-tutorials%2F&branch=OHW23 (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: self-signed certificate (_ssl.c:1149)')))
(ohw22/tutorials_getting_started: line   30) broken    https://oceanhackweek.2i2c.cloud/hub/user-redirect/git-pull?repo=https%3A%2F%2Fgithub.com%2Foceanhackweek%2Fohw-tutorials&urlpath=rstudio%2F&branch=OHW22 - HTTPSConnectionPool(host='oceanhackweek.2i2c.cloud', port=443): Max retries exceeded with url: /hub/user-redirect/git-pull?repo=https%3A%2F%2Fgithub.com%2Foceanhackweek%2Fohw-tutorials&urlpath=rstudio%2F&branch=OHW22 (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: self-signed certificate (_ssl.c:1149)')))
(ohw24/tutorials_getting_started: line   24) broken    https://oceanhackweek.2i2c.cloud/hub/user-redirect/git-pull?repo=https%3A%2F%2Fgithub.com%2Foceanhackweek%2Fohw-tutorials&urlpath=lab%2Ftree%2Fohw-tutorials%2F&branch=OHW24 - HTTPSConnectionPool(host='oceanhackweek.2i2c.cloud', port=443): Max retries exceeded with url: /hub/user-redirect/git-pull?repo=https%3A%2F%2Fgithub.com%2Foceanhackweek%2Fohw-tutorials&urlpath=lab%2Ftree%2Fohw-tutorials%2F&branch=OHW24 (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: self-signed certificate (_ssl.c:1149)')))
(ohw23/tutorials_getting_started: line   30) broken    https://oceanhackweek.2i2c.cloud/hub/user-redirect/git-pull?repo=https%3A%2F%2Fgithub.com%2Foceanhackweek%2Fohw-tutorials&urlpath=rstudio%2F&branch=OHW23 - HTTPSConnectionPool(host='oceanhackweek.2i2c.cloud', port=443): Max retries exceeded with url: /hub/user-redirect/git-pull?repo=https%3A%2F%2Fgithub.com%2Foceanhackweek%2Fohw-tutorials&urlpath=rstudio%2F&branch=OHW23 (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: self-signed certificate (_ssl.c:1149)')))
(ohw24/tutorials_getting_started: line   30) broken    https://oceanhackweek.2i2c.cloud/hub/user-redirect/git-pull?repo=https%3A%2F%2Fgithub.com%2Foceanhackweek%2Fohw-tutorials&urlpath=rstudio%2F&branch=OHW24 - HTTPSConnectionPool(host='oceanhackweek.2i2c.cloud', port=443): Max retries exceeded with url: /hub/user-redirect/git-pull?repo=https%3A%2F%2Fgithub.com%2Foceanhackweek%2Fohw-tutorials&urlpath=rstudio%2F&branch=OHW24 (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: self-signed certificate (_ssl.c:1149)')))
(     about/index: line   23) broken    https://osm2022.secure-platform.com/a/gallery/rounds/3/details/8367 - 403 Client Error: Forbidden for url: https://osm2022.secure-platform.com/a/gallery/rounds/3/details/8367
(resources/prep/git: line  251) broken    https://swcarpentry.github.io/git-novice/02-setup/index.html - 404 Client Error: Not Found for url: https://swcarpentry.github.io/git-novice/02-setup/index.html
(   about/contact: line    9) broken    https://twitter.com/oceanhackweek - 400 Client Error: Bad Request for url: https://x.com/oceanhackweek
(ohw22/espanol/index.es: line   14) broken    https://udelar.edu.uy/directorio/lugares/centro-universitario-regional-del-este-cure-sede-rocha-1/ - HTTPSConnectionPool(host='udelar.edu.uy', port=443): Max retries exceeded with url: /directorio/lugares/centro-universitario-regional-del-este-cure-sede-rocha-1/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1149)')))
(ohw22/espanol/index.en: line   42) broken    https://www.maren.cure.edu.uy/wp-content/uploads/2014/08/angel.jpg - 404 Client Error: Not Found for url: https://www.maren.cure.edu.uy/wp-content/uploads/2014/08/angel.jpg
(ohw23/tutorials-index/index: line   30) broken    https://www.vanderbilt.edu/datascience/data-science-team/ - 404 Client Error: Not Found for url: https://www.vanderbilt.edu/datascience/data-science-team/
( resources/numpy: line   13) broken    https://hub-binder.mybinder.ovh/user/uwescience-hack-inary-tutorials-e704wqfz/notebooks/notebooks/numpy-intro.ipynb - HTTPSConnectionPool(host='hub-binder.mybinder.ovh', port=443): Max retries exceeded with url: /user/uwescience-hack-inary-tutorials-e704wqfz/notebooks/notebooks/numpy-intro.ipynb (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f766de65670>: Failed to establish a new connection: [Errno 110] Connection timed out'))
(resources/pandas: line    9) broken    https://hub-binder.mybinder.ovh/user/uwescience-hack-inary-tutorials-e704wqfz/notebooks/notebooks/pandas-intro.ipynb - HTTPSConnectionPool(host='hub-binder.mybinder.ovh', port=443): Max retries exceeded with url: /user/uwescience-hack-inary-tutorials-e704wqfz/notebooks/notebooks/pandas-intro.ipynb (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f766de5c4c0>: Failed to establish a new connection: [Errno 110] Connection timed out'))

[valentina-s]

@ocefpaf I can copy them to another issue and we merge this one? Could later go through them and see what can be fixed.

[ocefpaf]

@ocefpaf I can copy them to another issue and we merge this one?

Yes please!

Could later go through them and see what can be fixed.

+1

[valentina-s]

@ocefpaf I saw that some of the links with anchors are actually valid but listed as errors: to disable those seems one needs to set linkcheck_anchors = False in the conf.py file.

I added the list to #341.

I do not have merging power but LGTM.

[ocefpaf]

I do not have merging power but LGTM.

We should fix that!