Update some easy to fix links in documentation (#4256)

Author: katjaweigel

doc/sphinx/source/changelog.rst

@@ -712,7 +712,7 @@ Highlights
    <https://doi.org/10.1175/JCLI-D-22-0181.1>`__.
    See :ref:`recipe documentation <recipes_clouds>` about added recipes.
 -  Addition of a set of recipes for extreme events, regional and impact
-   evaluation as used in `Weigel et al. (2021), J. Climate
+   evaluation as used in `Weigel et al. (2021), GMD
    <https://doi.org/10.5194/gmd-14-3159-2021>`__ and in IPCC AR5.
    See :ref:`recipe documentation <recipes_ipccwg1ar5ch9>` about added recipes.
 
@@ -909,7 +909,7 @@ v2.7.0
 Highlights
 ~~~~~~~~~~
 
--  This release has seen the inclusion of the code for figures 3.3, 3.4, 3.5, 3,13 and 3.15 of the IPCC AR6 WG1 report, see them in the `new documentation <https://esmvaltool--2533.org.readthedocs.build/en/2533/recipes/recipe_ipccwg1ar6ch3.html>`__
+-  This release has seen the inclusion of the code for figures 3.3, 3.4, 3.5, 3,13 and 3.15 of the IPCC AR6 WG1 report, see them in the `new documentation <https://docs.esmvaltool.org/en/latest/recipes/recipe_ipccwg1ar6ch3.html>`__
 -  We have also included new diagnostics and recipe necessary to produce the plots and tables for the journal article "Climate model projections from the Scenario Model Intercomparison Project (ScenarioMIP) of CMIP6" by `Tebaldi et al. in ESD 2020-68 <https://doi.org/10.5194/esd-2020-68>`__ from 2021; also see the `recipe entry <https://docs.esmvaltool.org/en/latest/recipes/recipe_tebaldi21esd.html>`__
 -  We have also extended the support for MERRA2 observational dataset, by adding support for a large number of variables, including 3D variables, see the `table of supported obs datasets <https://docs.esmvaltool.org/en/latest/input.html#supported-datasets-for-which-a-cmorizer-script-is-available>`__
 
@@ -1308,7 +1308,7 @@ Documentation
 -  Add titles to ocean recipes (maintainer Lovato) (:pull:`2375`) :user:`tomaslovato`
 -  Add titles for three c3s-magic recipes (:pull:`2378`) :user:`zklaus`
 -  Add title for recipe maintained by Ruth Lorenz (:pull:`2379`) :user:`zklaus`
--  Fix toymodel recipe (:pull:`2381`) `Javier Vegas-Regidor <https://github.com/jvegasbsc>`__
+-  Fix toymodel recipe (:pull:`2381`) Javier Vegas-Regidor
 -  Added titles for recipes of maintainer `schlund_manuel` (:pull:`2377`) :user:`schlunma`
 -  Write_plots and titles for deangelis15nat, li17natcc, martin18grl, pv_capacity_factor (:pull:`2382`) :user:`katjaweigel`
 -  Add titles for some recipes (:pull:`2383`) :user:`zklaus`
@@ -1446,7 +1446,7 @@ Automatic testing
 Installation
 ~~~~~~~~~~~~
 
--  Fix conda build by skipping documentation test (:pull:`2058`) `Javier Vegas-Regidor <https://github.com/jvegasbsc>`__
+-  Fix conda build by skipping documentation test (:pull:`2058`) Javier Vegas-Regidor
 -  Update pin on esmvalcore pick up esmvalcore=2.3.0 (:pull:`2200`) :user:`valeriupredoi`
 -  Pin Python to 3.9 for development installation (:pull:`2208`) :user:`bouweandela`
 
@@ -1459,7 +1459,7 @@ Improvements
 -  Update use of fx vars to new syntax  (:pull:`2145`) :user:`sloosvel`
 -  Add recipe for climate impact research (:pull:`2072`) :user:`Peter9192`
 -  Update references "master" to "main" (:pull:`2172`) :user:`axel-lauer`
--  Force git to ignore VSCode workspace files (:pull:`2186`) `Javier Vegas-Regidor <https://github.com/jvegasbsc>`__
+-  Force git to ignore VSCode workspace files (:pull:`2186`) Javier Vegas-Regidor
 -  Update to new ESMValTool logo (:pull:`2168`) :user:`axel-lauer`
 -  Python cmorizers for CDR1 and CDR2 ESACCI H2O (TCWV=prw) data. (:pull:`2152`) :user:`katjaweigel`
 -  Remove obsolete conda package (closes #2100) (:pull:`2103`) :user:`zklaus`
@@ -1492,7 +1492,7 @@ Bug fixes
 -  Fix logging import in cmorize_obs again since last merge was nulled by pre-commit hooks (:pull:`2022`) :user:`valeriupredoi`
 -  Refactor the functions in derive_evspsblpot due to new iris (:pull:`2023`) :user:`SarahAlidoost`
 -  Avoid importing private ESMValCore functions in CMORizer (:pull:`2027`) :user:`bouweandela`
--  Fix extract_seasons in validation recipe  (:pull:`2054`) `Javier Vegas-Regidor <https://github.com/jvegasbsc>`__
+-  Fix extract_seasons in validation recipe  (:pull:`2054`) Javier Vegas-Regidor
 
 Deprecations
 ~~~~~~~~~~~~
@@ -1524,8 +1524,8 @@ Documentation
 -  List Remi Kazeroni as a code owner and sole merger of CMORizers (:pull:`2017`) :user:`bouweandela`
 -  Install documentation: mention that we build conda package with python>=3.7 (:pull:`2030`) :user:`valeriupredoi`
 -  Recipe and documentation update for ERA5-Land. (:pull:`1906`) :user:`katjaweigel`
--  Update changelog and changelog tool for v2.2.0 (:pull:`2043`) `Javier Vegas-Regidor <https://github.com/jvegasbsc>`__
--  Final update to the changelog for v2.2.0 (:pull:`2056`) `Javier Vegas-Regidor <https://github.com/jvegasbsc>`__
+-  Update changelog and changelog tool for v2.2.0 (:pull:`2043`) Javier Vegas-Regidor
+-  Final update to the changelog for v2.2.0 (:pull:`2056`) Javier Vegas-Regidor
 
 Diagnostics
 ~~~~~~~~~~~
@@ -1586,7 +1586,7 @@ Improvements
 -  Align ESMValTool to ESMValCore=2.2.0 (adopt iris3, fix environment for new Core release) (:pull:`1874`) :user:`stefsmeets`
 -  Make it possible to use write_plots and write_netcdf from recipe instead of config-user.yml (:pull:`2018`) :user:`bouweandela`
 -  Revise lisflood and hype recipes (:pull:`2035`) :user:`SarahAlidoost`
--  Set version to 2.2.0 (:pull:`2042`) `Javier Vegas-Regidor <https://github.com/jvegasbsc>`__
+-  Set version to 2.2.0 (:pull:`2042`) Javier Vegas-Regidor
 
 .. _changelog-v2-1-1:
 
@@ -1644,15 +1644,15 @@ Documentation
 Improvements
 ~~~~~~~~~~~~
 
--  Fix R installation in WSL (:pull:`1789`) `Javier Vegas-Regidor <https://github.com/jvegasbsc>`__
+-  Fix R installation in WSL (:pull:`1789`) Javier Vegas-Regidor
 -  Add pre-commit for linting/formatting (:pull:`1796`) :user:`stefsmeets`
 -  Speed up tests on CircleCI and use pytest to run them (:pull:`1804`) :user:`bouweandela`
 -  Move pre-commit excludes to top-level and correct order of lintr and styler (:pull:`1805`) :user:`stefsmeets`
 -  Remove isort setup to fix formatting conflict with yapf (:pull:`1815`) :user:`stefsmeets`
 -  GitHub Actions (:pull:`1806`) :user:`valeriupredoi`
 -  Fix yapf-isort import formatting conflict (:pull:`1822`) :user:`stefsmeets`
 -  Replace vmprof with vprof as the default profiler (:pull:`1829`) :user:`bouweandela`
--  Update ESMValCore v2.1.0 requirement (:pull:`1839`) `Javier Vegas-Regidor <https://github.com/jvegasbsc>`__
+-  Update ESMValCore v2.1.0 requirement (:pull:`1839`) Javier Vegas-Regidor
 -  Pin iris to version 2 (:pull:`1881`) :user:`bouweandela`
 -  Pin eccodes to not use eccodes=2.19.0 for cdo to work fine (:pull:`1869`) :user:`valeriupredoi`
 -  Increase version to 2.1.0 and add release notes (:pull:`1868`) :user:`valeriupredoi`
@@ -1680,17 +1680,17 @@ Bug fixes
 -  Fix small errors in the arctic_ocean diagnostic (:pull:`1722`) :user:`koldunovn`
 -  Flatten ancestor lists for diag_spei.R and diag_spi.R. (:pull:`1745`) :user:`katjaweigel`
 -  Fix for recipe_ocean_ice_extent.yml (:pull:`1744`) :user:`mattiarighi`
--  Fix recipe_combined_indices.yml provenance (:pull:`1746`) `Javier Vegas-Regidor <https://github.com/jvegasbsc>`__
--  Fix provenance in recipe_multimodel_products (:pull:`1747`) `Javier Vegas-Regidor <https://github.com/jvegasbsc>`__
+-  Fix recipe_combined_indices.yml provenance (:pull:`1746`) Javier Vegas-Regidor
+-  Fix provenance in recipe_multimodel_products (:pull:`1747`) Javier Vegas-Regidor
 -  Exclude FGOALS-g2 due to ESMValCore issue #728 (:pull:`1749`) :user:`mattiarighi`
--  Fix recipe_modes_of_variability (:pull:`1753`) `Javier Vegas-Regidor <https://github.com/jvegasbsc>`__
+-  Fix recipe_modes_of_variability (:pull:`1753`) Javier Vegas-Regidor
 -  Flatten lists for ancestors for hyint to prevent nested lists. (:pull:`1752`) :user:`katjaweigel`
 -  Fix bug in cmorize_obs_eppley_vgpm_modis.py (#1729) (:pull:`1759`) :user:`tomaslovato`
 -  Correct mip for clltkisccp in example derive preprocessor recipe (:pull:`1768`) :user:`bouweandela`
 -  Update date conversion in recipe_hype.yml (:pull:`1769`) :user:`bouweandela`
 -  Fix recipe_correlation.yml (:pull:`1767`) :user:`bouweandela`
 -  Add attribute positive: down to plev coordinate in ERA-Interim CMORizer (:pull:`1771`) :user:`bouweandela`
--  Fix sispeed in recipe_preprocessor_derive_test (:pull:`1772`) `Javier Vegas-Regidor <https://github.com/jvegasbsc>`__
+-  Fix sispeed in recipe_preprocessor_derive_test (:pull:`1772`) Javier Vegas-Regidor
 -  Fix extreme events and extreme index ancestors (:pull:`1774`) :user:`katjaweigel`
 -  Correct date in output filenames of ERA5 CMORizer recipe (:pull:`1773`) :user:`bouweandela`
 -  Exclude WOA from multi-model stats in recipe_ocean_bgc (:pull:`1778`) :user:`mattiarighi`
@@ -1717,7 +1717,7 @@ Diagnostics
 -  Add mask albedolandcover (:pull:`1673`) :user:`bascrezee`
 -  IPCC AR5 fig. 9.3 (seasonality) (:pull:`1726`) :user:`axel-lauer`
 -  Added additional emergent constraints on ECS (:pull:`1585`) :user:`schlunma`
--  A diagnostic to evaluate the turnover times of land ecosystem carbon (:pull:`1395`) `koir-su <https://github.com/koir-su>`__
+-  A diagnostic to evaluate the turnover times of land ecosystem carbon (:pull:`1395`) koir-su
 -  Removed multi_model_statistics step in recipe_oceans_example.yml as a workaround (:pull:`1779`) :user:`valeriupredoi`
 
 Documentation
@@ -1745,17 +1745,17 @@ Improvements
 -  Remove curly brackets around issue number in pull request template (:pull:`1637`) :user:`bouweandela`
 -  Fix style issue in test (:pull:`1639`) :user:`bouweandela`
 -  Update Codacy badges (:pull:`1662`) :user:`bouweandela`
--  Support extra installation methods in R (:pull:`1360`) `Javier Vegas-Regidor <https://github.com/jvegasbsc>`__
+-  Support extra installation methods in R (:pull:`1360`) Javier Vegas-Regidor
 -  Add ncdf4.helpers package as a dependency again (:pull:`1678`) :user:`bouweandela`
 -  Speed up conda installation (:pull:`1677`) :user:`bouweandela`
 -  Update CMORizers and recipes for ESMValCore v2.0.0 (:pull:`1699`) :user:`SarahAlidoost`
 -  Update setup.py for PyPI package (:pull:`1700`) :user:`bouweandela`
 -  Cleanup recipe headers before the release (:pull:`1740`) :user:`mattiarighi`
--    Add colortables as esmvaltool subcommand (:pull:`1666`) `Javier Vegas-Regidor <https://github.com/jvegasbsc>`__
+-    Add colortables as esmvaltool subcommand (:pull:`1666`) Javier Vegas-Regidor
 -  Increase version to v2.0.0 (:pull:`1756`) :user:`bouweandela`
 -  Update job script (:pull:`1757`) :user:`mattiarighi`
 -  Read authors and description from .zenodo.json (:pull:`1758`) :user:`bouweandela`
--  Update docker recipe to install from source (:pull:`1651`) `Javier Vegas-Regidor <https://github.com/jvegasbsc>`__
+-  Update docker recipe to install from source (:pull:`1651`) Javier Vegas-Regidor
 
 Observational and re-analysis dataset support
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -1790,7 +1790,7 @@ Bug fixes
 Diagnostics
 ~~~~~~~~~~~
 
--  Applicate sea ice negative feedback (:pull:`1299`) `Javier Vegas-Regidor <https://github.com/jvegasbsc>`__
+-  Applicate sea ice negative feedback (:pull:`1299`) Javier Vegas-Regidor
 -  Add Russell18jgr ocean diagnostics (:pull:`1592`) :user:`bouweandela`
 -  Refactor marrmot recipe and diagnostic to use ERA5 daily data made by new cmorizer (:pull:`1600`) :user:`SarahAlidoost`
 -  In recipe_wflow, use daily ERA5 data from the new cmorizer. (:pull:`1599`) :user:`Peter9192`

doc/sphinx/source/community/code_documentation.rst

@@ -312,7 +312,7 @@ There are two main ways of adding documentation:
 #. As written text in the directory
    `doc/sphinx/source <https://github.com/ESMValGroup/ESMValTool/tree/main/doc/sphinx/source>`__.
    When writing
-   `reStructuredText <https://www.sphinx-doc.org/en/main/usage/restructuredtext/basics.html>`_
+   `reStructuredText <https://www.sphinx-doc.org/en/master/usage/restructuredtext/basics.html>`_
    (``.rst``) files, please try to limit the line length to 80 characters and
    always start a sentence on a new line.
    This makes it easier to review changes to documentation on GitHub.
@@ -391,7 +391,7 @@ Successful checks have a green ✓ in front, a ❌ means the test job failed.
 
 Integration with the ESMValCore documentation
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-The `ESMValCore documentation <https://docs.esmvaltool.org/projects/esmvalcore>`_
+The `ESMValCore documentation <https://docs.esmvaltool.org/projects/ESMValCore/en/latest/index.html>`_
 is hosted as a
 `subproject <https://docs.readthedocs.io/en/stable/subprojects.html>`_
 of the ESMValTool documentation on readthedocs.
@@ -484,9 +484,9 @@ We follow the guidelines set out in `SPEC-0 <https://scientific-python.org/specs
 regarding the supported Python versions and dependencies.
 
 Before considering adding a new dependency, carefully check that the
-`license <https://the-turing-way.netlify.app/reproducible-research/licensing/licensing-software.html>`__
+`license <https://book.the-turing-way.org/reproducible-research/licensing/>`__
 of the dependency you want to add and any of its dependencies are
-`compatible <https://the-turing-way.netlify.app/reproducible-research/licensing/licensing-compatibility.html>`__
+`compatible <https://book.the-turing-way.org/reproducible-research/licensing/licensing-compatibility/>`__
 with the
 `Apache 2.0 <https://github.com/ESMValGroup/ESMValTool/blob/main/LICENSE/>`_
 license that applies to the ESMValTool.

doc/sphinx/source/community/private_repository.rst

@@ -56,7 +56,7 @@ and push your branch to the public repository
 
 6. Make a pull request in the public repository
 ===============================================
-Go to https://github.com/esmalgroup/esmvaltool/pulls and click the 'New pull request button'.
+Go to https://github.com/ESMValGroup/ESMValCore/pulls and click the 'New pull request button'.
 Process reviewer comments and get it merged as described in :ref:`reviewing`.
 
 7. Obtain a DOI for your code and add it to your paper

doc/sphinx/source/community/release_strategy/detailed_release_procedure.rst

@@ -140,7 +140,7 @@ Recipe output can be copied by doing from the VM:
 
 By copying the debug.html and index.html files into /shared/esmvaltool/v2.x.x/, the output
 becomes available online, see for `example
-<https://esmvaltool.dkrz.de/shared/esmvaltool/v2.7.0>`_.
+<https://esmvaltool.dkrz.de/shared/esmvaltool/stable_release/>`_.
 Before copying the recipe output to the VM, you may want to clean up your directory containing
 the results by removing any large ``preproc`` directories of failed runs and only keeping the last run for each recipe.
 This will help generating a clearer overview webpage.

doc/sphinx/source/community/upgrading.rst

@@ -6,7 +6,7 @@ Upgrading a namelist (recipe) or diagnostic to ESMValTool v2
 
 This guide summarizes the main steps to be taken in order to port an ESMValTool namelist (now called **recipe**) and the corresponding diagnostic(s) from v1.0 to v2.0, hereafter also referred as the *"old"* and the *"new version"*, respectively. The new ESMValTool version is being developed in the public git branch ``main``. An identical version of this branch is maintained in the private repository as well and kept synchronized on an hourly basis.
 
-In the following, it is assumed that the user has successfully installed ESMValTool v2 and has a rough overview of its structure (see `Technical Overview <http://www.esmvaltool.org/download/Righi_ESMValTool2-TechnicalOverview.pdf>`_).
+In the following, it is assumed that the user has successfully installed ESMValTool v2 and has a rough overview of its structure (see `Technical Overview <https://doi.org/10.5194/gmd-13-1179-2020>`_).
 
 Create a github issue
 =====================

doc/sphinx/source/develop/dataset.rst

@@ -97,7 +97,7 @@ from source and store the data in the appropriate tier subdirectory of the
 folder ``RAWOBS`` automatically.
 There are many downloading scripts available in
 `/esmvaltool/cmorizers/data/downloaders/datasets/
-<https://github.com/ESMValGroup/ESMValTool/blob/main/esmvaltool/data/downloaders/datasets/>`_
+<https://github.com/ESMValGroup/ESMValTool/tree/main/esmvaltool/cmorizers/data/downloaders/datasets>`_
 where several data download mechanisms are provided:
 
 - A `wget` get based downloader for http(s) downloads, with a specific derivation for NASA datasets.

doc/sphinx/source/input.rst

@@ -5,9 +5,9 @@ Obtaining input data
 ********************
 
 ESMValTool supports input data from climate models participating in
-`CMIP6 <https://www.wcrp-climate.org/wgcm-cmip/wgcm-cmip6>`__,
-`CMIP5 <https://www.wcrp-climate.org/wgcm-cmip/wgcm-cmip5>`__,
-`CMIP3 <https://www.wcrp-climate.org/wgcm-cmip/wgcm-cmip3>`__, and
+`CMIP6 <https://wcrp-cmip.org/cmip-phases/cmip6/>`__,
+`CMIP5 <https://wcrp-cmip.org/cmip-phases/cmip5/>`__,
+`CMIP3 <https://wcrp-cmip.org/cmip-phases/cmip3/>`__, and
 `CORDEX <https://cordex.org/>`__
 as well as observations, reanalysis, and any other data, provided that it
 adheres to the
@@ -22,7 +22,7 @@ as used in the various
 .. note::
 
     CORDEX support is still
-    `work in progress <https://github.com/orgs/ESMValGroup/projects/11>`__.
+    work in progress.
     Contributions, in the form of
     :ref:`pull request reviews <reviewing>` or
     :ref:`pull requests <esmvalcore:contributing>`
@@ -44,9 +44,7 @@ but many more exist around the world.
 
 If you do not have access to such a facility through your institute or the
 project you are working on, you can request access by applying for the
-`ENES Climate Analytics Service <https://portal.enes.org/data/data-metadata-service/climate-analytics-service>`__
-or, if you need longer term access or more computational resources, the
-`IS-ENES3 Trans-national Access call <https://portal.enes.org/data/data-metadata-service/analysis-platforms>`__.
+`ENES Climate Analytics Service <https://is.enes.org/sdm-climate-analytics-data/>`.
 
 If the options above are not available to you, ESMValTool also offers a feature
 to make it easy to download CMIP6, CMIP5, CMIP3, CORDEX, and obs4MIPs from ESGF.
@@ -82,8 +80,8 @@ See :ref:`esmvalcore:config-esgf` for a more in depth explanation and the
 available configuration options.
 
 Alternatively, you can use an external tool called
-`Synda <http://prodiguer.github.io/synda/index.html>`__
-to maintain your own collection of ESGF data.
+`esgpull <https://github.com/ESGF/esgf-download>`__
+to download and store files from ESGF.
 
 
 .. _inputdata_observations:

doc/sphinx/source/quickstart/installation.rst

@@ -58,7 +58,7 @@ for your conda environments instead of
 much faster, see `move-to-mamba`_ for more information.
 
 For a minimal mamba installation (recommended) go to
-https://mamba.readthedocs.io/en/latest/installation.html.
+https://mamba.readthedocs.io/en/latest/installation/micromamba-installation.html.
 
 .. note::
     It is recommended that you always use the latest version of mamba, as

doc/sphinx/source/recipes/legacy/recipe_schlund20jgr.rst

@@ -69,13 +69,12 @@ Observations and reformat scripts
 
 * CRU_ (*pr*, *tas*)
 * ERA-Interim_ (*rsds*)
-* LAI3g_ (*lai*)
+* LAI3g (*lai*)
 * MTE_ (*gpp*, *gppStderr*)
 * Scripps-CO2-KUM_ (*co2s*)
 
 .. _CRU: https://crudata.uea.ac.uk/cru/data/hrg/cru_ts_4.02/cruts.1811131722.v4.02/
-.. _ERA-Interim: http://apps.ecmwf.int/datasets/data/interim-full-moda/
-.. _LAI3g: http://cliveg.bu.edu/modismisr/lai3g-fpar3g.html
+.. _ERA-Interim: https://cds.climate.copernicus.eu/stac-browser/collections/reanalysis-era-interim?.language=en
 .. _MTE: http://www.bgc-jena.mpg.de/geodb/BGI/Home
 .. _Scripps-CO2-KUM: https://scrippsco2.ucsd.edu/data/atmospheric_co2/kum.html
 

doc/sphinx/source/recipes/recipe_autoassess_landsurface_permafrost.rst

@@ -112,7 +112,7 @@ None
 References
 ----------
 
-* Observed permafrost extent is from http://nsidc.org/data/ggd318.html: Brown, J.,
+* Observed permafrost extent is from https://nsidc.org/data/ggd318/versions/2: Brown, J.,
   O. Ferrians, J. A. Heginbottom, and E. Melnikov. 2002. Circum-Arctic Map of
   Permafrost and Ground-Ice Conditions, Version 2. Boulder, Colorado USA. NSIDC:
   National Snow and Ice Data Center.  When calculating the global area of