From 5bae64ebec4433d21d76a0d336a8dbe00d36e915 Mon Sep 17 00:00:00 2001 From: "Navid C. Constantinou" Date: Sun, 15 Jun 2025 17:36:34 +1000 Subject: [PATCH 01/21] try subcategory --- Recipes/{ => regional}/regional-mom6-forced-by-access-om2.ipynb | 0 docs/index.rst | 1 + 2 files changed, 1 insertion(+) rename Recipes/{ => regional}/regional-mom6-forced-by-access-om2.ipynb (100%) diff --git a/Recipes/regional-mom6-forced-by-access-om2.ipynb b/Recipes/regional/regional-mom6-forced-by-access-om2.ipynb similarity index 100% rename from Recipes/regional-mom6-forced-by-access-om2.ipynb rename to Recipes/regional/regional-mom6-forced-by-access-om2.ipynb diff --git a/docs/index.rst b/docs/index.rst index 82d0f12e..b164c036 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -30,6 +30,7 @@ The `COSIMA Cookbook tutorial`_ is perhaps the best place to start. tutorials recipes + recipes/regional guidelines contributing GitHub Repository From 5ab1302d50c28b0689f8e2e9807454bc8e6435e7 Mon Sep 17 00:00:00 2001 From: "Navid C. Constantinou" Date: Sun, 15 Jun 2025 17:40:31 +1000 Subject: [PATCH 02/21] depth=2 --- docs/index.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/index.rst b/docs/index.rst index b164c036..be11aabf 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -25,7 +25,7 @@ The `COSIMA Cookbook tutorial`_ is perhaps the best place to start. .. _COSIMA Cookbook tutorial: https://cosima-recipes.readthedocs.io/en/latest/Tutorials/COSIMA_CookBook_Tutorial.html .. toctree:: - :maxdepth: 1 + :maxdepth: 2 :caption: Contents: tutorials From 616a1b64874d04a355080b7867f98d32ec158009 Mon Sep 17 00:00:00 2001 From: "Navid C. Constantinou" Date: Sun, 15 Jun 2025 17:59:30 +1000 Subject: [PATCH 03/21] Update index.rst --- docs/index.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/index.rst b/docs/index.rst index be11aabf..b164c036 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -25,7 +25,7 @@ The `COSIMA Cookbook tutorial`_ is perhaps the best place to start. .. _COSIMA Cookbook tutorial: https://cosima-recipes.readthedocs.io/en/latest/Tutorials/COSIMA_CookBook_Tutorial.html .. toctree:: - :maxdepth: 2 + :maxdepth: 1 :caption: Contents: tutorials From 5875aef118d45a8f8176590c7aa6f46c9558de24 Mon Sep 17 00:00:00 2001 From: Angus Gibson Date: Mon, 16 Jun 2025 10:51:49 +1000 Subject: [PATCH 04/21] Use subheadings on index page? --- docs/index.rst | 1 - docs/recipes.rst | 14 ++++++++++++++ 2 files changed, 14 insertions(+), 1 deletion(-) diff --git a/docs/index.rst b/docs/index.rst index b164c036..82d0f12e 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -30,7 +30,6 @@ The `COSIMA Cookbook tutorial`_ is perhaps the best place to start. tutorials recipes - recipes/regional guidelines contributing GitHub Repository diff --git a/docs/recipes.rst b/docs/recipes.rst index f115aefc..1f2d7197 100644 --- a/docs/recipes.rst +++ b/docs/recipes.rst @@ -1,6 +1,9 @@ Recipes ======= +General +------- + .. nbgallery:: :caption: Recipes :name: recipe-gallery @@ -8,3 +11,14 @@ Recipes :hidden: Recipes/* + +Regional MOM6 +------------- + +.. nbgallery:: + :caption: Regional MOM6 + :name: recipe-gallery + :glob: + :hidden: + + Recipes/regional/* From 4f777a0c7e191f3515ea15e0870d3990a38320ca Mon Sep 17 00:00:00 2001 From: Angus Gibson Date: Mon, 16 Jun 2025 11:13:31 +1000 Subject: [PATCH 05/21] Working subcategory implementation --- docs/conf.py | 4 ++++ docs/index.rst | 5 +++-- docs/recipes.rst | 24 ------------------------ docs/recipes/general.rst | 10 ++++++++++ docs/recipes/index.rst | 9 +++++++++ docs/recipes/regional.rst | 10 ++++++++++ 6 files changed, 36 insertions(+), 26 deletions(-) delete mode 100644 docs/recipes.rst create mode 100644 docs/recipes/general.rst create mode 100644 docs/recipes/index.rst create mode 100644 docs/recipes/regional.rst diff --git a/docs/conf.py b/docs/conf.py index 992710cd..ca907282 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -55,6 +55,10 @@ # a list of builtin themes. # # html_theme = 'default' +html_theme_options = { + "sidebar_collapse": False, + "sidebar_includehidden": False, +} # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, diff --git a/docs/index.rst b/docs/index.rst index 82d0f12e..4ebdf28f 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -3,6 +3,7 @@ You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. + COSIMA Cookbook =============== @@ -25,11 +26,11 @@ The `COSIMA Cookbook tutorial`_ is perhaps the best place to start. .. _COSIMA Cookbook tutorial: https://cosima-recipes.readthedocs.io/en/latest/Tutorials/COSIMA_CookBook_Tutorial.html .. toctree:: - :maxdepth: 1 + :maxdepth: 2 :caption: Contents: tutorials - recipes + recipes/index guidelines contributing GitHub Repository diff --git a/docs/recipes.rst b/docs/recipes.rst deleted file mode 100644 index 1f2d7197..00000000 --- a/docs/recipes.rst +++ /dev/null @@ -1,24 +0,0 @@ -Recipes -======= - -General -------- - -.. nbgallery:: - :caption: Recipes - :name: recipe-gallery - :glob: - :hidden: - - Recipes/* - -Regional MOM6 -------------- - -.. nbgallery:: - :caption: Regional MOM6 - :name: recipe-gallery - :glob: - :hidden: - - Recipes/regional/* diff --git a/docs/recipes/general.rst b/docs/recipes/general.rst new file mode 100644 index 00000000..4c2ad971 --- /dev/null +++ b/docs/recipes/general.rst @@ -0,0 +1,10 @@ +General +======= + +.. nbgallery:: + :caption: Recipes + :name: recipe-gallery-general + :glob: + :hidden: + + ../Recipes/* diff --git a/docs/recipes/index.rst b/docs/recipes/index.rst new file mode 100644 index 00000000..d560a46a --- /dev/null +++ b/docs/recipes/index.rst @@ -0,0 +1,9 @@ +Recipes +======= + +.. toctree:: + :maxdepth: 1 + :caption: Recipes: + + general + regional diff --git a/docs/recipes/regional.rst b/docs/recipes/regional.rst new file mode 100644 index 00000000..43313db5 --- /dev/null +++ b/docs/recipes/regional.rst @@ -0,0 +1,10 @@ +Regional MOM6 +============= + +.. nbgallery:: + :caption: Regional MOM6 + :name: recipe-gallery-regional + :glob: + :hidden: + + ../Recipes/regional/* From 075232b372c78149766e6bda2dfd5a200850850b Mon Sep 17 00:00:00 2001 From: "Navid C. Constantinou" Date: Mon, 16 Jun 2025 13:49:13 +1000 Subject: [PATCH 06/21] categorise --- ...tic_IndoPacific_Basin_Overturning_Circulation.ipynb | 0 .../Barotropic_Streamfunction.ipynb | 0 .../{ => appetisers-easy}/Compare_SSH_model_obs.ipynb | 0 .../Compare_SST_SSS_TemperatureSalinity_to_WOA13.ipynb | 0 .../Hovmoller_Temperature_Depth.ipynb | 0 .../Meridional_Overturning_Circulation.ipynb | 0 .../Model_Resolution_Comparison.ipynb | 0 ...r_Quantities_and_Annually_Averaged_Timeseries.ipynb | 0 Recipes/{ => appetisers-easy}/Relative_Vorticity.ipynb | 0 .../Transport_Through_Straits.ipynb | 0 Recipes/{ => appetisers-easy}/True_Zonal_Mean.ipynb | 0 .../regional-mom6-forced-by-access-om2.ipynb | 0 .../{ => mains-advanced}/Along-slope-velocities.ipynb | 0 .../{ => mains-advanced}/Along_Isobath_Average.ipynb | 0 .../{ => mains-advanced}/Cross-contour_transport.ipynb | 0 Recipes/{ => mains-advanced}/Cross-slope_section.ipynb | 0 .../Eddy-Mean_Kinetic_Energy_Decomposition.ipynb | 0 ...uatorial_thermal_and_zonal_velocity_structure.ipynb | 0 .../Extract_Variables_at_Ocean_Bottom.ipynb | 0 .../Geostrophic_Velocities_from_Sea_Level.ipynb | 0 .../{ => mains-advanced}/Horizontal_Regridding.ipynb | 0 .../Meridional_heat_transport.ipynb | 0 .../Nearest_Neighbour_Distance.ipynb | 0 Recipes/{ => mains-advanced}/Neutral_density.ipynb | 0 .../Particle_tracking_with_Parcels.ipynb | 0 .../Sea_Ice_Area_Concentration_Volume_with_Obs.ipynb | 0 Recipes/{ => mains-advanced}/Sea_Ice_Coordinates.ipynb | 0 .../Sea_Ice_Seasonality_Statistics.ipynb | 0 .../Surface_Water_Mass_Transformation.ipynb | 0 .../Temperature_Salinity_Diagram.ipynb | 0 ...ransformation_from_Depth_to_Potential_Density.ipynb | 0 docs/guidelines.rst | 3 +-- docs/recipes/{general.rst => appetisers.rst} | 6 +++--- docs/recipes/index.rst | 5 +++-- docs/recipes/local-dishes.rst | 10 ++++++++++ docs/recipes/mains.rst | 10 ++++++++++ docs/recipes/regional.rst | 10 ---------- 37 files changed, 27 insertions(+), 17 deletions(-) rename Recipes/{ => appetisers-easy}/Atlantic_IndoPacific_Basin_Overturning_Circulation.ipynb (100%) rename Recipes/{ => appetisers-easy}/Barotropic_Streamfunction.ipynb (100%) rename Recipes/{ => appetisers-easy}/Compare_SSH_model_obs.ipynb (100%) rename Recipes/{ => appetisers-easy}/Compare_SST_SSS_TemperatureSalinity_to_WOA13.ipynb (100%) rename Recipes/{ => appetisers-easy}/Hovmoller_Temperature_Depth.ipynb (100%) rename Recipes/{ => appetisers-easy}/Meridional_Overturning_Circulation.ipynb (100%) rename Recipes/{ => appetisers-easy}/Model_Resolution_Comparison.ipynb (100%) rename Recipes/{ => appetisers-easy}/Querying_Scalar_Quantities_and_Annually_Averaged_Timeseries.ipynb (100%) rename Recipes/{ => appetisers-easy}/Relative_Vorticity.ipynb (100%) rename Recipes/{ => appetisers-easy}/Transport_Through_Straits.ipynb (100%) rename Recipes/{ => appetisers-easy}/True_Zonal_Mean.ipynb (100%) rename Recipes/{regional => local-dishes-regional}/regional-mom6-forced-by-access-om2.ipynb (100%) rename Recipes/{ => mains-advanced}/Along-slope-velocities.ipynb (100%) rename Recipes/{ => mains-advanced}/Along_Isobath_Average.ipynb (100%) rename Recipes/{ => mains-advanced}/Cross-contour_transport.ipynb (100%) rename Recipes/{ => mains-advanced}/Cross-slope_section.ipynb (100%) rename Recipes/{ => mains-advanced}/Eddy-Mean_Kinetic_Energy_Decomposition.ipynb (100%) rename Recipes/{ => mains-advanced}/Equatorial_thermal_and_zonal_velocity_structure.ipynb (100%) rename Recipes/{ => mains-advanced}/Extract_Variables_at_Ocean_Bottom.ipynb (100%) rename Recipes/{ => mains-advanced}/Geostrophic_Velocities_from_Sea_Level.ipynb (100%) rename Recipes/{ => mains-advanced}/Horizontal_Regridding.ipynb (100%) rename Recipes/{ => mains-advanced}/Meridional_heat_transport.ipynb (100%) rename Recipes/{ => mains-advanced}/Nearest_Neighbour_Distance.ipynb (100%) rename Recipes/{ => mains-advanced}/Neutral_density.ipynb (100%) rename Recipes/{ => mains-advanced}/Particle_tracking_with_Parcels.ipynb (100%) rename Recipes/{ => mains-advanced}/Sea_Ice_Area_Concentration_Volume_with_Obs.ipynb (100%) rename Recipes/{ => mains-advanced}/Sea_Ice_Coordinates.ipynb (100%) rename Recipes/{ => mains-advanced}/Sea_Ice_Seasonality_Statistics.ipynb (100%) rename Recipes/{ => mains-advanced}/Surface_Water_Mass_Transformation.ipynb (100%) rename Recipes/{ => mains-advanced}/Temperature_Salinity_Diagram.ipynb (100%) rename Recipes/{ => mains-advanced}/Transformation_from_Depth_to_Potential_Density.ipynb (100%) rename docs/recipes/{general.rst => appetisers.rst} (57%) create mode 100644 docs/recipes/local-dishes.rst create mode 100644 docs/recipes/mains.rst delete mode 100644 docs/recipes/regional.rst diff --git a/Recipes/Atlantic_IndoPacific_Basin_Overturning_Circulation.ipynb b/Recipes/appetisers-easy/Atlantic_IndoPacific_Basin_Overturning_Circulation.ipynb similarity index 100% rename from Recipes/Atlantic_IndoPacific_Basin_Overturning_Circulation.ipynb rename to Recipes/appetisers-easy/Atlantic_IndoPacific_Basin_Overturning_Circulation.ipynb diff --git a/Recipes/Barotropic_Streamfunction.ipynb b/Recipes/appetisers-easy/Barotropic_Streamfunction.ipynb similarity index 100% rename from Recipes/Barotropic_Streamfunction.ipynb rename to Recipes/appetisers-easy/Barotropic_Streamfunction.ipynb diff --git a/Recipes/Compare_SSH_model_obs.ipynb b/Recipes/appetisers-easy/Compare_SSH_model_obs.ipynb similarity index 100% rename from Recipes/Compare_SSH_model_obs.ipynb rename to Recipes/appetisers-easy/Compare_SSH_model_obs.ipynb diff --git a/Recipes/Compare_SST_SSS_TemperatureSalinity_to_WOA13.ipynb b/Recipes/appetisers-easy/Compare_SST_SSS_TemperatureSalinity_to_WOA13.ipynb similarity index 100% rename from Recipes/Compare_SST_SSS_TemperatureSalinity_to_WOA13.ipynb rename to Recipes/appetisers-easy/Compare_SST_SSS_TemperatureSalinity_to_WOA13.ipynb diff --git a/Recipes/Hovmoller_Temperature_Depth.ipynb b/Recipes/appetisers-easy/Hovmoller_Temperature_Depth.ipynb similarity index 100% rename from Recipes/Hovmoller_Temperature_Depth.ipynb rename to Recipes/appetisers-easy/Hovmoller_Temperature_Depth.ipynb diff --git a/Recipes/Meridional_Overturning_Circulation.ipynb b/Recipes/appetisers-easy/Meridional_Overturning_Circulation.ipynb similarity index 100% rename from Recipes/Meridional_Overturning_Circulation.ipynb rename to Recipes/appetisers-easy/Meridional_Overturning_Circulation.ipynb diff --git a/Recipes/Model_Resolution_Comparison.ipynb b/Recipes/appetisers-easy/Model_Resolution_Comparison.ipynb similarity index 100% rename from Recipes/Model_Resolution_Comparison.ipynb rename to Recipes/appetisers-easy/Model_Resolution_Comparison.ipynb diff --git a/Recipes/Querying_Scalar_Quantities_and_Annually_Averaged_Timeseries.ipynb b/Recipes/appetisers-easy/Querying_Scalar_Quantities_and_Annually_Averaged_Timeseries.ipynb similarity index 100% rename from Recipes/Querying_Scalar_Quantities_and_Annually_Averaged_Timeseries.ipynb rename to Recipes/appetisers-easy/Querying_Scalar_Quantities_and_Annually_Averaged_Timeseries.ipynb diff --git a/Recipes/Relative_Vorticity.ipynb b/Recipes/appetisers-easy/Relative_Vorticity.ipynb similarity index 100% rename from Recipes/Relative_Vorticity.ipynb rename to Recipes/appetisers-easy/Relative_Vorticity.ipynb diff --git a/Recipes/Transport_Through_Straits.ipynb b/Recipes/appetisers-easy/Transport_Through_Straits.ipynb similarity index 100% rename from Recipes/Transport_Through_Straits.ipynb rename to Recipes/appetisers-easy/Transport_Through_Straits.ipynb diff --git a/Recipes/True_Zonal_Mean.ipynb b/Recipes/appetisers-easy/True_Zonal_Mean.ipynb similarity index 100% rename from Recipes/True_Zonal_Mean.ipynb rename to Recipes/appetisers-easy/True_Zonal_Mean.ipynb diff --git a/Recipes/regional/regional-mom6-forced-by-access-om2.ipynb b/Recipes/local-dishes-regional/regional-mom6-forced-by-access-om2.ipynb similarity index 100% rename from Recipes/regional/regional-mom6-forced-by-access-om2.ipynb rename to Recipes/local-dishes-regional/regional-mom6-forced-by-access-om2.ipynb diff --git a/Recipes/Along-slope-velocities.ipynb b/Recipes/mains-advanced/Along-slope-velocities.ipynb similarity index 100% rename from Recipes/Along-slope-velocities.ipynb rename to Recipes/mains-advanced/Along-slope-velocities.ipynb diff --git a/Recipes/Along_Isobath_Average.ipynb b/Recipes/mains-advanced/Along_Isobath_Average.ipynb similarity index 100% rename from Recipes/Along_Isobath_Average.ipynb rename to Recipes/mains-advanced/Along_Isobath_Average.ipynb diff --git a/Recipes/Cross-contour_transport.ipynb b/Recipes/mains-advanced/Cross-contour_transport.ipynb similarity index 100% rename from Recipes/Cross-contour_transport.ipynb rename to Recipes/mains-advanced/Cross-contour_transport.ipynb diff --git a/Recipes/Cross-slope_section.ipynb b/Recipes/mains-advanced/Cross-slope_section.ipynb similarity index 100% rename from Recipes/Cross-slope_section.ipynb rename to Recipes/mains-advanced/Cross-slope_section.ipynb diff --git a/Recipes/Eddy-Mean_Kinetic_Energy_Decomposition.ipynb b/Recipes/mains-advanced/Eddy-Mean_Kinetic_Energy_Decomposition.ipynb similarity index 100% rename from Recipes/Eddy-Mean_Kinetic_Energy_Decomposition.ipynb rename to Recipes/mains-advanced/Eddy-Mean_Kinetic_Energy_Decomposition.ipynb diff --git a/Recipes/Equatorial_thermal_and_zonal_velocity_structure.ipynb b/Recipes/mains-advanced/Equatorial_thermal_and_zonal_velocity_structure.ipynb similarity index 100% rename from Recipes/Equatorial_thermal_and_zonal_velocity_structure.ipynb rename to Recipes/mains-advanced/Equatorial_thermal_and_zonal_velocity_structure.ipynb diff --git a/Recipes/Extract_Variables_at_Ocean_Bottom.ipynb b/Recipes/mains-advanced/Extract_Variables_at_Ocean_Bottom.ipynb similarity index 100% rename from Recipes/Extract_Variables_at_Ocean_Bottom.ipynb rename to Recipes/mains-advanced/Extract_Variables_at_Ocean_Bottom.ipynb diff --git a/Recipes/Geostrophic_Velocities_from_Sea_Level.ipynb b/Recipes/mains-advanced/Geostrophic_Velocities_from_Sea_Level.ipynb similarity index 100% rename from Recipes/Geostrophic_Velocities_from_Sea_Level.ipynb rename to Recipes/mains-advanced/Geostrophic_Velocities_from_Sea_Level.ipynb diff --git a/Recipes/Horizontal_Regridding.ipynb b/Recipes/mains-advanced/Horizontal_Regridding.ipynb similarity index 100% rename from Recipes/Horizontal_Regridding.ipynb rename to Recipes/mains-advanced/Horizontal_Regridding.ipynb diff --git a/Recipes/Meridional_heat_transport.ipynb b/Recipes/mains-advanced/Meridional_heat_transport.ipynb similarity index 100% rename from Recipes/Meridional_heat_transport.ipynb rename to Recipes/mains-advanced/Meridional_heat_transport.ipynb diff --git a/Recipes/Nearest_Neighbour_Distance.ipynb b/Recipes/mains-advanced/Nearest_Neighbour_Distance.ipynb similarity index 100% rename from Recipes/Nearest_Neighbour_Distance.ipynb rename to Recipes/mains-advanced/Nearest_Neighbour_Distance.ipynb diff --git a/Recipes/Neutral_density.ipynb b/Recipes/mains-advanced/Neutral_density.ipynb similarity index 100% rename from Recipes/Neutral_density.ipynb rename to Recipes/mains-advanced/Neutral_density.ipynb diff --git a/Recipes/Particle_tracking_with_Parcels.ipynb b/Recipes/mains-advanced/Particle_tracking_with_Parcels.ipynb similarity index 100% rename from Recipes/Particle_tracking_with_Parcels.ipynb rename to Recipes/mains-advanced/Particle_tracking_with_Parcels.ipynb diff --git a/Recipes/Sea_Ice_Area_Concentration_Volume_with_Obs.ipynb b/Recipes/mains-advanced/Sea_Ice_Area_Concentration_Volume_with_Obs.ipynb similarity index 100% rename from Recipes/Sea_Ice_Area_Concentration_Volume_with_Obs.ipynb rename to Recipes/mains-advanced/Sea_Ice_Area_Concentration_Volume_with_Obs.ipynb diff --git a/Recipes/Sea_Ice_Coordinates.ipynb b/Recipes/mains-advanced/Sea_Ice_Coordinates.ipynb similarity index 100% rename from Recipes/Sea_Ice_Coordinates.ipynb rename to Recipes/mains-advanced/Sea_Ice_Coordinates.ipynb diff --git a/Recipes/Sea_Ice_Seasonality_Statistics.ipynb b/Recipes/mains-advanced/Sea_Ice_Seasonality_Statistics.ipynb similarity index 100% rename from Recipes/Sea_Ice_Seasonality_Statistics.ipynb rename to Recipes/mains-advanced/Sea_Ice_Seasonality_Statistics.ipynb diff --git a/Recipes/Surface_Water_Mass_Transformation.ipynb b/Recipes/mains-advanced/Surface_Water_Mass_Transformation.ipynb similarity index 100% rename from Recipes/Surface_Water_Mass_Transformation.ipynb rename to Recipes/mains-advanced/Surface_Water_Mass_Transformation.ipynb diff --git a/Recipes/Temperature_Salinity_Diagram.ipynb b/Recipes/mains-advanced/Temperature_Salinity_Diagram.ipynb similarity index 100% rename from Recipes/Temperature_Salinity_Diagram.ipynb rename to Recipes/mains-advanced/Temperature_Salinity_Diagram.ipynb diff --git a/Recipes/Transformation_from_Depth_to_Potential_Density.ipynb b/Recipes/mains-advanced/Transformation_from_Depth_to_Potential_Density.ipynb similarity index 100% rename from Recipes/Transformation_from_Depth_to_Potential_Density.ipynb rename to Recipes/mains-advanced/Transformation_from_Depth_to_Potential_Density.ipynb diff --git a/docs/guidelines.rst b/docs/guidelines.rst index d83b4aae..b2cc50ef 100644 --- a/docs/guidelines.rst +++ b/docs/guidelines.rst @@ -44,8 +44,7 @@ format for the other entries already in there. Images in notebooks ------------------- -If including external images (i.e. not plots generated in the code) in +If including external images (i.e., not plots tgenerated in the code) in notebooks, place them in the ``images/`` directory next to the notebook. Use the syntax ``![image caption](images/image.png)`` to include the image in the notebook. - diff --git a/docs/recipes/general.rst b/docs/recipes/appetisers.rst similarity index 57% rename from docs/recipes/general.rst rename to docs/recipes/appetisers.rst index 4c2ad971..04d788a0 100644 --- a/docs/recipes/general.rst +++ b/docs/recipes/appetisers.rst @@ -1,5 +1,5 @@ -General -======= +Appetisers (easy) +================= .. nbgallery:: :caption: Recipes @@ -7,4 +7,4 @@ General :glob: :hidden: - ../Recipes/* + ../Recipes/appetisers-easy/* diff --git a/docs/recipes/index.rst b/docs/recipes/index.rst index d560a46a..c200ab6c 100644 --- a/docs/recipes/index.rst +++ b/docs/recipes/index.rst @@ -5,5 +5,6 @@ Recipes :maxdepth: 1 :caption: Recipes: - general - regional + appetisers + mains + local-dishes diff --git a/docs/recipes/local-dishes.rst b/docs/recipes/local-dishes.rst new file mode 100644 index 00000000..a704aab5 --- /dev/null +++ b/docs/recipes/local-dishes.rst @@ -0,0 +1,10 @@ +Local dishes (Regional configurations) +====================================== + +.. nbgallery:: + :caption: Local dishes (Regional configurations) + :name: recipe-gallery-regional + :glob: + :hidden: + + ../Recipes/local-dishes-regional/* diff --git a/docs/recipes/mains.rst b/docs/recipes/mains.rst new file mode 100644 index 00000000..da32c7b8 --- /dev/null +++ b/docs/recipes/mains.rst @@ -0,0 +1,10 @@ +Main dishes (advanced) +====================== + +.. nbgallery:: + :caption: Recipes + :name: recipe-gallery-general + :glob: + :hidden: + + ../Recipes/mains-advanced/* diff --git a/docs/recipes/regional.rst b/docs/recipes/regional.rst deleted file mode 100644 index 43313db5..00000000 --- a/docs/recipes/regional.rst +++ /dev/null @@ -1,10 +0,0 @@ -Regional MOM6 -============= - -.. nbgallery:: - :caption: Regional MOM6 - :name: recipe-gallery-regional - :glob: - :hidden: - - ../Recipes/regional/* From 08f8aff568aedc13395ccec454ec817de15139b5 Mon Sep 17 00:00:00 2001 From: "Navid C. Constantinou" Date: Mon, 16 Jun 2025 13:57:49 +1000 Subject: [PATCH 07/21] add explainer --- docs/recipes/index.rst | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/docs/recipes/index.rst b/docs/recipes/index.rst index c200ab6c..669717b6 100644 --- a/docs/recipes/index.rst +++ b/docs/recipes/index.rst @@ -1,6 +1,14 @@ Recipes ======= +The recipes are split into Appetisers_ (i.e., easier/simpler recipes -- a good place +to start after you've been through the tutorials), Mains_ (i.e. elaborate/advanced recipes) +and :ref:`Local Dishes ` (i.e. recipes for regional configurations). + +.. _Appetisers: appetisers.html +.. _Mains: mains.html +.. _local-dishes: local-dishes.html + .. toctree:: :maxdepth: 1 :caption: Recipes: From 60cc21c2d364f55100a82298aad3a164f1ac2fb0 Mon Sep 17 00:00:00 2001 From: "Navid C. Constantinou" Date: Mon, 16 Jun 2025 14:04:21 +1000 Subject: [PATCH 08/21] add explainer for recipes categorisation --- docs/recipes/index.rst | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/recipes/index.rst b/docs/recipes/index.rst index 669717b6..74a4c08f 100644 --- a/docs/recipes/index.rst +++ b/docs/recipes/index.rst @@ -2,16 +2,16 @@ Recipes ======= The recipes are split into Appetisers_ (i.e., easier/simpler recipes -- a good place -to start after you've been through the tutorials), Mains_ (i.e. elaborate/advanced recipes) -and :ref:`Local Dishes ` (i.e. recipes for regional configurations). +to start after you've been through the tutorials_), Mains_ (i.e. elaborate/advanced recipes) +and `Local Dishes`_ (i.e. recipes for regional configurations). +.. _tutorials: ../tutorials.html .. _Appetisers: appetisers.html .. _Mains: mains.html -.. _local-dishes: local-dishes.html +.. _Local Dishes: local-dishes.html .. toctree:: :maxdepth: 1 - :caption: Recipes: appetisers mains From 9d09d07655685adecfdf1396ead482663683de90 Mon Sep 17 00:00:00 2001 From: "Navid C. Constantinou" Date: Mon, 16 Jun 2025 14:11:37 +1000 Subject: [PATCH 09/21] remove duplicate titles --- docs/recipes/appetisers.rst | 1 - docs/recipes/local-dishes.rst | 1 - docs/recipes/mains.rst | 1 - 3 files changed, 3 deletions(-) diff --git a/docs/recipes/appetisers.rst b/docs/recipes/appetisers.rst index 04d788a0..a9ce2009 100644 --- a/docs/recipes/appetisers.rst +++ b/docs/recipes/appetisers.rst @@ -2,7 +2,6 @@ Appetisers (easy) ================= .. nbgallery:: - :caption: Recipes :name: recipe-gallery-general :glob: :hidden: diff --git a/docs/recipes/local-dishes.rst b/docs/recipes/local-dishes.rst index a704aab5..296cb644 100644 --- a/docs/recipes/local-dishes.rst +++ b/docs/recipes/local-dishes.rst @@ -2,7 +2,6 @@ Local dishes (Regional configurations) ====================================== .. nbgallery:: - :caption: Local dishes (Regional configurations) :name: recipe-gallery-regional :glob: :hidden: diff --git a/docs/recipes/mains.rst b/docs/recipes/mains.rst index da32c7b8..6e55402f 100644 --- a/docs/recipes/mains.rst +++ b/docs/recipes/mains.rst @@ -2,7 +2,6 @@ Main dishes (advanced) ====================== .. nbgallery:: - :caption: Recipes :name: recipe-gallery-general :glob: :hidden: From 480e67825d6b642f5dd37f657769074f7629a3b0 Mon Sep 17 00:00:00 2001 From: "Navid C. Constantinou" Date: Mon, 16 Jun 2025 16:08:54 +1000 Subject: [PATCH 10/21] Update docs/guidelines.rst Co-authored-by: Angus Gibson --- docs/guidelines.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/guidelines.rst b/docs/guidelines.rst index b2cc50ef..51071080 100644 --- a/docs/guidelines.rst +++ b/docs/guidelines.rst @@ -44,7 +44,7 @@ format for the other entries already in there. Images in notebooks ------------------- -If including external images (i.e., not plots tgenerated in the code) in +If including external images (i.e., not plots generated in the code) in notebooks, place them in the ``images/`` directory next to the notebook. Use the syntax ``![image caption](images/image.png)`` to include the image in the notebook. From b262d67d4ab7e371a7a572f9baa3cbab3cc2178c Mon Sep 17 00:00:00 2001 From: "Navid C. Constantinou" Date: Mon, 16 Jun 2025 16:12:28 +1000 Subject: [PATCH 11/21] resolve conflicts --- Recipes/mains-advanced/Along-slope-velocities.ipynb | 2 +- .../Geostrophic_Velocities_from_Sea_Level.ipynb | 4 ++-- Recipes/mains-advanced/Nearest_Neighbour_Distance.ipynb | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/Recipes/mains-advanced/Along-slope-velocities.ipynb b/Recipes/mains-advanced/Along-slope-velocities.ipynb index 6856e6b4..e9ef7c2b 100644 --- a/Recipes/mains-advanced/Along-slope-velocities.ipynb +++ b/Recipes/mains-advanced/Along-slope-velocities.ipynb @@ -5543,7 +5543,7 @@ "metadata": {}, "source": [ "### Map of along-slope velocity with bathymetry contours. \n", - "#### On a Large ARE Instance, this should take ~45 seconds" + "**On a Large ARE Instance, this should take ~45 seconds**" ] }, { diff --git a/Recipes/mains-advanced/Geostrophic_Velocities_from_Sea_Level.ipynb b/Recipes/mains-advanced/Geostrophic_Velocities_from_Sea_Level.ipynb index 420e68b7..8ec0fcfd 100644 --- a/Recipes/mains-advanced/Geostrophic_Velocities_from_Sea_Level.ipynb +++ b/Recipes/mains-advanced/Geostrophic_Velocities_from_Sea_Level.ipynb @@ -1678,10 +1678,10 @@ "id": "d4520ed1-f69e-460e-8a7c-0abb0589387f", "metadata": {}, "source": [ - "\\begin{eqnarray}\n", + "$$\n", " u_{g,s} = -\\frac{g}{f}\\frac{\\partial \\eta}{\\partial y} \\quad \\textrm{and} \\quad\n", " v_{g,s} = \\frac{g}{f}\\frac{\\partial \\eta}{\\partial x}\n", - "\\end{eqnarray}" + "$$" ] }, { diff --git a/Recipes/mains-advanced/Nearest_Neighbour_Distance.ipynb b/Recipes/mains-advanced/Nearest_Neighbour_Distance.ipynb index 2fb7ecee..0f82cfe0 100644 --- a/Recipes/mains-advanced/Nearest_Neighbour_Distance.ipynb +++ b/Recipes/mains-advanced/Nearest_Neighbour_Distance.ipynb @@ -1432,7 +1432,7 @@ "id": "ce17902e-7eae-4a71-aa8a-94703a1bb4ad", "metadata": {}, "source": [ - "The sea ice outputs need some processing before we can start our calculations. You can check this [example](IcePlottingExample.ipynb) for a guide on how to load and plot sea ice data. \n", + "The sea ice outputs need some processing before we can start our calculations. You can check this [example](Sea_Ice_Coordinates.ipynb) for a guide on how to load and plot sea ice data. \n", " \n", "We will follow these processing steps:\n", "1. Correct time dimension values by subtracting 12 hours,\n", From 256f802bc778e4523c349a34b4fafebbc89dd474 Mon Sep 17 00:00:00 2001 From: "Navid C. Constantinou" Date: Mon, 16 Jun 2025 16:13:51 +1000 Subject: [PATCH 12/21] try without .html --- docs/recipes/index.rst | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/recipes/index.rst b/docs/recipes/index.rst index 74a4c08f..0cb2cf94 100644 --- a/docs/recipes/index.rst +++ b/docs/recipes/index.rst @@ -5,10 +5,10 @@ The recipes are split into Appetisers_ (i.e., easier/simpler recipes -- a good p to start after you've been through the tutorials_), Mains_ (i.e. elaborate/advanced recipes) and `Local Dishes`_ (i.e. recipes for regional configurations). -.. _tutorials: ../tutorials.html -.. _Appetisers: appetisers.html -.. _Mains: mains.html -.. _Local Dishes: local-dishes.html +.. _tutorials: ../tutorials +.. _Appetisers: appetisers +.. _Mains: mains +.. _Local Dishes: local-dishes .. toctree:: :maxdepth: 1 From 9dbb647a17d47714ce28b6a563f278f5cdcd80eb Mon Sep 17 00:00:00 2001 From: "Navid C. Constantinou" Date: Mon, 16 Jun 2025 16:15:01 +1000 Subject: [PATCH 13/21] different gallery names --- docs/recipes/appetisers.rst | 2 +- docs/recipes/mains.rst | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/recipes/appetisers.rst b/docs/recipes/appetisers.rst index a9ce2009..5f9d35a4 100644 --- a/docs/recipes/appetisers.rst +++ b/docs/recipes/appetisers.rst @@ -2,7 +2,7 @@ Appetisers (easy) ================= .. nbgallery:: - :name: recipe-gallery-general + :name: recipe-gallery-appetisers :glob: :hidden: diff --git a/docs/recipes/mains.rst b/docs/recipes/mains.rst index 6e55402f..b8434367 100644 --- a/docs/recipes/mains.rst +++ b/docs/recipes/mains.rst @@ -2,7 +2,7 @@ Main dishes (advanced) ====================== .. nbgallery:: - :name: recipe-gallery-general + :name: recipe-gallery-mains :glob: :hidden: From a0d849a6ff431ae6fafac0cc09d4fdadfad7b4bc Mon Sep 17 00:00:00 2001 From: Angus Gibson Date: Mon, 16 Jun 2025 16:22:41 +1000 Subject: [PATCH 14/21] Use doc role for links --- docs/recipes/index.rst | 11 +++-------- 1 file changed, 3 insertions(+), 8 deletions(-) diff --git a/docs/recipes/index.rst b/docs/recipes/index.rst index 0cb2cf94..3c32c24e 100644 --- a/docs/recipes/index.rst +++ b/docs/recipes/index.rst @@ -1,14 +1,9 @@ Recipes ======= -The recipes are split into Appetisers_ (i.e., easier/simpler recipes -- a good place -to start after you've been through the tutorials_), Mains_ (i.e. elaborate/advanced recipes) -and `Local Dishes`_ (i.e. recipes for regional configurations). - -.. _tutorials: ../tutorials -.. _Appetisers: appetisers -.. _Mains: mains -.. _Local Dishes: local-dishes +The recipes are split into :doc:`appetisers` (i.e., easier/simpler recipes -- a good place +to start after you've been through the :doc:`../tutorials`), :doc:`mains` (i.e. elaborate/advanced recipes) +and :doc:`local-dishes` (i.e. recipes for regional configurations). .. toctree:: :maxdepth: 1 From b027eb510350773a9a1a39fb7c130cbf445815d3 Mon Sep 17 00:00:00 2001 From: "Navid C. Constantinou" Date: Tue, 17 Jun 2025 08:40:23 +1000 Subject: [PATCH 15/21] Tutorials -> Cooking Lessons --- docs/index.rst | 7 ++++--- docs/tutorials.rst | 5 ++--- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/docs/index.rst b/docs/index.rst index 4ebdf28f..7b54721e 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -17,12 +17,13 @@ All the recipes combined form a cookbook 📒! Happy cooking! 😉 🥙 🍱 🍲 -To get started have a look at the tutorials_ and then browse through the +To get started you should first take the `Cooking Lessons 101`_ (that is, look at our Tutorials). +After you've gone through them and feel comfortable, browse through the available recipes_ to find something the better suits your 'taste' (i.e., your needs)! The `COSIMA Cookbook tutorial`_ is perhaps the best place to start. -.. _tutorials: tutorials.html -.. _recipes: recipes.html +.. _Cooking Lessons 101: tutorials +.. _recipes: recipes .. _COSIMA Cookbook tutorial: https://cosima-recipes.readthedocs.io/en/latest/Tutorials/COSIMA_CookBook_Tutorial.html .. toctree:: diff --git a/docs/tutorials.rst b/docs/tutorials.rst index 71c60f97..cf463418 100644 --- a/docs/tutorials.rst +++ b/docs/tutorials.rst @@ -1,8 +1,7 @@ -Tutorials -========= +Cooking lessons 101 (Tutorials) +=============================== .. nbgallery:: - :caption: Tutorials :name: tutorial-gallery :glob: :hidden: From 4cd4457ce292a07b49430588a87d3e8acba78c39 Mon Sep 17 00:00:00 2001 From: "Navid C. Constantinou" Date: Tue, 17 Jun 2025 08:46:34 +1000 Subject: [PATCH 16/21] fix links --- docs/index.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/index.rst b/docs/index.rst index 7b54721e..6b79c09c 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -24,7 +24,7 @@ The `COSIMA Cookbook tutorial`_ is perhaps the best place to start. .. _Cooking Lessons 101: tutorials .. _recipes: recipes -.. _COSIMA Cookbook tutorial: https://cosima-recipes.readthedocs.io/en/latest/Tutorials/COSIMA_CookBook_Tutorial.html +.. _COSIMA Cookbook tutorial: tutorials/COSIMA_CookBook_Tutorial .. toctree:: :maxdepth: 2 From bebd85ec61750fce1b6836763849e59b31181368 Mon Sep 17 00:00:00 2001 From: "Navid C. Constantinou" Date: Tue, 17 Jun 2025 08:51:59 +1000 Subject: [PATCH 17/21] fix links --- docs/index.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/index.rst b/docs/index.rst index 6b79c09c..ada4f78b 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -22,9 +22,9 @@ After you've gone through them and feel comfortable, browse through the available recipes_ to find something the better suits your 'taste' (i.e., your needs)! The `COSIMA Cookbook tutorial`_ is perhaps the best place to start. -.. _Cooking Lessons 101: tutorials +.. _Cooking Lessons 101: tutorials.html .. _recipes: recipes -.. _COSIMA Cookbook tutorial: tutorials/COSIMA_CookBook_Tutorial +.. _COSIMA Cookbook tutorial: tutorials/COSIMA_CookBook_Tutorial.html .. toctree:: :maxdepth: 2 From 2ddc218783cb2c92dc05a767b03c91d256ae8ca8 Mon Sep 17 00:00:00 2001 From: "Navid C. Constantinou" Date: Tue, 17 Jun 2025 08:51:59 +1000 Subject: [PATCH 18/21] update readme --- README.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 7ff3d17c..4b23bac1 100644 --- a/README.md +++ b/README.md @@ -12,11 +12,11 @@ # COSIMA Cookbook This repository is a Cookbook of Recipes 👩🏽‍🍳 👨🏻‍🍳. -A collection of recipes and tutorials for analysing ocean and sea ice model output produced by the [Consortium for Ocean-Sea Ice Modelling in Australia (COSIMA)](http://cosima.org.au/). +A collection of cooking lessons and recipes for analysing ocean and sea ice model output produced by the [Consortium for Ocean-Sea Ice Modelling in Australia (COSIMA)](http://cosima.org.au/). -We explain: a "recipe" here is an example of an analysis of some ocean-sea ice model output or some ocean-related observational datasets. -Each "recipe" comes in a self-contained and well-documented Jupyter notebook. -All the recipes combined form a cookbook 📒! +We explain: a "cooking lesson" here is a tutorial that teaches you something generic (e.g. about plotting or loading data); a "recipe" is an example of an analysis of some ocean-sea ice model output or some ocean-related observational datasets. +Both "cooking lessons" and "recipes" come in self-contained and well-documented Jupyter notebooks. +All the lessons and the recipes combined form a cookbook 📒! Most recipes use output from the [ACCESS-OM2 model](https://doi.org/10.5194/gmd-13-401-2020), while some also use results from configurations of the [Modular Ocean Model 6 (MOM6)](https://github.com/mom-ocean/MOM6) and remote sensing observations. From 339c677d093bbad0a9a7b3d432599e4a4889ea91 Mon Sep 17 00:00:00 2001 From: "Navid C. Constantinou" Date: Tue, 17 Jun 2025 08:54:19 +1000 Subject: [PATCH 19/21] fix links --- docs/index.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/index.rst b/docs/index.rst index ada4f78b..635a8dfd 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -24,7 +24,7 @@ The `COSIMA Cookbook tutorial`_ is perhaps the best place to start. .. _Cooking Lessons 101: tutorials.html .. _recipes: recipes -.. _COSIMA Cookbook tutorial: tutorials/COSIMA_CookBook_Tutorial.html +.. _COSIMA Cookbook tutorial: Tutorials/COSIMA_CookBook_Tutorial.html .. toctree:: :maxdepth: 2 From f7f2ba29758a61b6dd6f05bd1cbd470139339fc2 Mon Sep 17 00:00:00 2001 From: "Navid C. Constantinou" Date: Tue, 17 Jun 2025 08:55:23 +1000 Subject: [PATCH 20/21] homogenise language --- docs/index.rst | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/docs/index.rst b/docs/index.rst index 635a8dfd..51aa0f31 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -17,9 +17,10 @@ All the recipes combined form a cookbook 📒! Happy cooking! 😉 🥙 🍱 🍲 -To get started you should first take the `Cooking Lessons 101`_ (that is, look at our Tutorials). +To get started you should first take the `Cooking Lessons 101`_ (i.e., our Tutorials). After you've gone through them and feel comfortable, browse through the -available recipes_ to find something the better suits your 'taste' (i.e., your needs)! +available recipes_ (i.e., examples) to find something the better suits your 'taste' (i.e., your needs)! + The `COSIMA Cookbook tutorial`_ is perhaps the best place to start. .. _Cooking Lessons 101: tutorials.html From 61b32c650dcb9f19b9960356a5451c4b8bd2b08b Mon Sep 17 00:00:00 2001 From: Angus Gibson Date: Tue, 17 Jun 2025 09:13:08 +1000 Subject: [PATCH 21/21] Use doc role on index page links --- docs/index.rst | 10 +++------- 1 file changed, 3 insertions(+), 7 deletions(-) diff --git a/docs/index.rst b/docs/index.rst index 51aa0f31..a45861b7 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -17,15 +17,11 @@ All the recipes combined form a cookbook 📒! Happy cooking! 😉 🥙 🍱 🍲 -To get started you should first take the `Cooking Lessons 101`_ (i.e., our Tutorials). +To get started you should first take the :doc:`Cooking Lessons 101 ` (i.e., our Tutorials). After you've gone through them and feel comfortable, browse through the -available recipes_ (i.e., examples) to find something the better suits your 'taste' (i.e., your needs)! +available :doc:`recipes/index` (i.e., examples) to find something the better suits your 'taste' (i.e., your needs)! -The `COSIMA Cookbook tutorial`_ is perhaps the best place to start. - -.. _Cooking Lessons 101: tutorials.html -.. _recipes: recipes -.. _COSIMA Cookbook tutorial: Tutorials/COSIMA_CookBook_Tutorial.html +The :doc:`COSIMA Cookbook tutorial ` is perhaps the best place to start. .. toctree:: :maxdepth: 2