Store images directly in repository, managed by git LFS

billsacks · fritzt · commit 231924824ee3 · 2021-05-19T13:02:07.000-04:00
Get rid of the images external. Instead, put the images directly in the
users guide / tech note source. These images will be managed by git LFS.
diff --git a/.gitignore b/.gitignore
@@ -5,7 +5,6 @@ manage_externals.log
 /tools/PTCLM/
 /cime/
 /components/
-/doc/images/
 
 # ignore svn directories
 **/.svn/**
diff --git a/Externals_CLM.cfg b/Externals_CLM.cfg
@@ -12,13 +12,6 @@ repo_url = https://github.com/ESCOMP/PTCLM
 tag = PTCLM2_20200121
 required = True
 
-[doc-images]
-local_path = doc/images
-protocol = git
-repo_url = https://github.com/ESCOMP/CTSM-doc-images.git
-hash = 476c694359e76c5054958e1397b8fa18aa0ff3e0
-required = False
-
 [externals_description]
 schema_version = 1.0.0
 
diff --git a/doc/source/tech_note/CN_Pools/CLM50_Tech_Note_CN_Pools.rst b/doc/source/tech_note/CN_Pools/CLM50_Tech_Note_CN_Pools.rst
@@ -35,7 +35,7 @@ variables for vegetation carbon, and 22 for vegetation nitrogen.
 
 .. _Figure Vegetation fluxes and pools:
 
-.. figure:: ../../../images/tech_note/CN_Pools/CLMCN_pool_structure_v2_lores.png
+.. figure:: CLMCN_pool_structure_v2_lores.png
     :width: 753px
     :height: 513px
 
diff --git a/doc/source/tech_note/CN_Pools/CLMCN_pool_structure_v2_lores.png b/doc/source/tech_note/CN_Pools/CLMCN_pool_structure_v2_lores.png
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diff --git a/doc/source/tech_note/Decomposition/CLM4_vertsoil_soilstruct_drawing.png b/doc/source/tech_note/Decomposition/CLM4_vertsoil_soilstruct_drawing.png
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diff --git a/doc/source/tech_note/Decomposition/CLM50_Tech_Note_Decomposition.rst b/doc/source/tech_note/Decomposition/CLM50_Tech_Note_Decomposition.rst
@@ -20,7 +20,7 @@ calculations (see Section  :numref:`Soil Layers` for soil layering).
 
 .. _Figure Schematic of decomposition model in CLM:
 
-.. figure:: ../../../images/tech_note/Decomposition/CLM4_vertsoil_soilstruct_drawing.png
+.. figure:: CLM4_vertsoil_soilstruct_drawing.png
 
  Schematic of decomposition model in CLM.
 
@@ -65,7 +65,7 @@ structures is in :ref:`Koven et al. (2013) <Kovenetal2013>`.
 
 .. _Figure Pool structure:
 
-.. figure:: ../../../images/tech_note/Decomposition/soil_C_pools_CN_century.png
+.. figure:: soil_C_pools_CN_century.png
 
  Pool structure, transitions, respired fractions (numbers at 
  end of arrows), and turnover times (numbers in boxes) for the 2
diff --git a/doc/source/tech_note/Decomposition/soil_C_pools_CN_century.png b/doc/source/tech_note/Decomposition/soil_C_pools_CN_century.png
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diff --git a/doc/source/tech_note/Ecosystem/CLM50_Tech_Note_Ecosystem.rst b/doc/source/tech_note/Ecosystem/CLM50_Tech_Note_Ecosystem.rst
@@ -53,7 +53,7 @@ classes.
 
 .. _Figure CLM subgrid hierarchy:
 
-.. Figure:: ../../../images/tech_note/Ecosystem/image1.png
+.. Figure:: image1.png
 
   Configuration of the CLM subgrid hierarchy.  Box in upper right shows hypothetical subgrid distribution for a single grid cell.  Note that the Crop land unit is only used when the model is run with the crop model active. Abbreviations: TBD – Tall Building District; HD – High Density; MD – Medium Density, G – Glacier, L – Lake, U – Urban, C – Crop, V – Vegetated, PFT – Plant Functional Type, Irr – Irrigated, UIrr – Unirrigated.  Red arrows indicate allowed land unit transitions.  Purple arrows indicate allowed patch-level transitions.  
 
diff --git a/doc/source/tech_note/Ecosystem/image1.png b/doc/source/tech_note/Ecosystem/image1.png
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diff --git a/doc/source/tech_note/External_Nitrogen_Cycle/CLM50_Tech_Note_External_Nitrogen_Cycle.rst b/doc/source/tech_note/External_Nitrogen_Cycle/CLM50_Tech_Note_External_Nitrogen_Cycle.rst
@@ -118,7 +118,7 @@ Where :math:`{NF}_{nfix,sminn}` (gN m\ :sup:`-2` s\ :sup:`-1`) is the rate of fr
 
 .. _Figure Biological nitrogen fixation:
 
-.. figure:: ../../../images/tech_note/External_Nitrogen_Cycle/image1.png
+.. figure:: image1.png
 
  Free-living nitrogen fixation as a function of annual evapotranspiration. Results here show annual N inputs from free-living N fixations, but the model actually calculates inputs on a per second basis.
 
diff --git a/doc/source/tech_note/External_Nitrogen_Cycle/image1.png b/doc/source/tech_note/External_Nitrogen_Cycle/image1.png
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diff --git a/doc/source/tech_note/Fluxes/CLM50_Tech_Note_Fluxes.rst b/doc/source/tech_note/Fluxes/CLM50_Tech_Note_Fluxes.rst
@@ -961,14 +961,14 @@ height :math:`z_{0h} ^{{'} }`  and the canopy air at height
 
 .. _Figure Schematic diagram of sensible heat fluxes:
 
-.. figure:: ../../../images/tech_note/Fluxes/image1.png
+.. figure:: image1.png
 
  Figure Schematic diagram of sensible heat fluxes for (a)
  non-vegetated surfaces and (b) vegetated surfaces.
 
 .. _Figure Schematic diagram of latent heat fluxes:
 
-.. figure:: ../../../images/tech_note/Fluxes/image2.png
+.. figure:: image2.png
 
  Figure Schematic diagram of water vapor fluxes for (a)
  non-vegetated surfaces and (b) vegetated surfaces.
diff --git a/doc/source/tech_note/Fluxes/image1.png b/doc/source/tech_note/Fluxes/image1.png
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diff --git a/doc/source/tech_note/Fluxes/image2.png b/doc/source/tech_note/Fluxes/image2.png
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diff --git a/doc/source/tech_note/Hydrology/CLM50_Tech_Note_Hydrology.rst b/doc/source/tech_note/Hydrology/CLM50_Tech_Note_Hydrology.rst
@@ -38,7 +38,7 @@ al. 2008) <Lawrenceetal2008>` and :math:`\Delta t` is the time step (s).
 
 .. _Figure Hydrologic processes:
 
-.. Figure:: ../../../images/tech_note/Hydrology/hydrologic.processes.png
+.. Figure:: hydrologic.processes.png
 
  Hydrologic processes represented in CLM.
 
@@ -798,7 +798,7 @@ the effective root fraction :math:`r_{e,\, i}`
 
 .. _Figure Water flux schematic:
 
-.. Figure:: ../../../images/tech_note/Hydrology/image2.png
+.. Figure:: image2.png
 
  Schematic diagram of numerical scheme used to solve for soil water fluxes.
 
diff --git a/doc/source/tech_note/Hydrology/hydrologic.processes.png b/doc/source/tech_note/Hydrology/hydrologic.processes.png
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diff --git a/doc/source/tech_note/Hydrology/image1.png b/doc/source/tech_note/Hydrology/image1.png
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diff --git a/doc/source/tech_note/Introduction/CLM50_Tech_Note_Introduction.rst b/doc/source/tech_note/Introduction/CLM50_Tech_Note_Introduction.rst
@@ -627,6 +627,6 @@ processes simulated include (:numref:`Figure Land processes`):
 
 .. _Figure Land processes:
 
-.. figure:: ../../../images/tech_note/Introduction/image1.png
+.. figure:: image1.png
 
  Land biogeophysical, biogeochemical, and landscape processes simulated by CLM (adapted from :ref:`Lawrence et al. (2011)<Lawrenceetal2011>` for CLM5.0).
diff --git a/doc/source/tech_note/Introduction/image1.png b/doc/source/tech_note/Introduction/image1.png
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diff --git a/doc/source/tech_note/Isotopes/image1.png b/doc/source/tech_note/Isotopes/image1.png
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diff --git a/doc/source/tech_note/MOSART/CLM50_Tech_Note_MOSART.rst b/doc/source/tech_note/MOSART/CLM50_Tech_Note_MOSART.rst
@@ -47,7 +47,7 @@ and discharges the water to its downstream spatial unit or the ocean.
 
 .. _Figure MOSART conceptual diagram:
 
-.. figure:: ../../../images/tech_note/MOSART/mosart_diagram.png
+.. figure:: mosart_diagram.png
     :width: 800px
     :height: 400px
 
diff --git a/doc/source/tech_note/MOSART/mosart_diagram.png b/doc/source/tech_note/MOSART/mosart_diagram.png
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diff --git a/doc/source/tech_note/Methane/CLM50_Tech_Note_Methane.rst b/doc/source/tech_note/Methane/CLM50_Tech_Note_Methane.rst
@@ -89,7 +89,7 @@ into the inundated concentration when the inundated fraction increases.
 
 .. _Figure Methane Schematic:
 
-.. figure:: ../../../images/tech_note/Methane/image1.png
+.. figure:: image1.png
 
  Schematic representation of biological and physical
  processes integrated in CLM that affect the net CH\ :sub:`4`
diff --git a/doc/source/tech_note/Methane/image1.png b/doc/source/tech_note/Methane/image1.png
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diff --git a/doc/source/tech_note/Plant_Hydraulics/CLM50_Tech_Note_Plant_Hydraulics.rst b/doc/source/tech_note/Plant_Hydraulics/CLM50_Tech_Note_Plant_Hydraulics.rst
@@ -159,7 +159,7 @@ on leaf water potential.
 
 .. _Figure Plant hydraulic circuit:
 
-.. figure:: ../../../images/tech_note/Plant_Hydraulics/circuit.jpg
+.. figure:: circuit.jpg
 
  Circuit diagram of plant hydraulics scheme
 
@@ -714,6 +714,6 @@ The outermost level of iteration works towards convergence of leaf temperature,
 
 .. _Figure PHS Flow Diagram:
 
-.. figure:: ../../../images/tech_note/Plant_Hydraulics/phs_iteration_schematic.svg
+.. figure:: phs_iteration_schematic.svg
 
  Flow diagram of leaf flux calculations
diff --git a/doc/source/tech_note/Plant_Hydraulics/circuit.jpg b/doc/source/tech_note/Plant_Hydraulics/circuit.jpg
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diff --git a/doc/source/tech_note/Plant_Respiration/image1.png b/doc/source/tech_note/Plant_Respiration/image1.png
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diff --git a/doc/source/tech_note/Radiative_Fluxes/CLM50_Tech_Note_Radiative_Fluxes.rst b/doc/source/tech_note/Radiative_Fluxes/CLM50_Tech_Note_Radiative_Fluxes.rst
@@ -36,7 +36,7 @@ depth of direct beam per unit leaf and stem area (section :numref:`Canopy Radiat
 
 .. _Figure Radiation Schematic:
 
-.. figure:: ../../../images/tech_note/Radiative_Fluxes/image1.png
+.. figure:: image1.png
 
  Schematic diagram of (a) direct beam radiation, (b) diffuse
  solar radiation, and (c) longwave radiation absorbed, transmitted, and
diff --git a/doc/source/tech_note/Radiative_Fluxes/image1.png b/doc/source/tech_note/Radiative_Fluxes/image1.png
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diff --git a/doc/source/tech_note/Snow_Hydrology/CLM50_Tech_Note_Snow_Hydrology.rst b/doc/source/tech_note/Snow_Hydrology/CLM50_Tech_Note_Snow_Hydrology.rst
@@ -18,7 +18,7 @@ snow pack.
 
 .. _Figure three layer snow pack:
 
-.. Figure:: ../../../images/tech_note/Snow_Hydrology/image1.png
+.. Figure:: image1.png
 
  Example of three layer snow pack (:math:`snl=-3`).
 
diff --git a/doc/source/tech_note/Snow_Hydrology/image1.png b/doc/source/tech_note/Snow_Hydrology/image1.png
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diff --git a/doc/source/tech_note/Soil_Snow_Temperatures/CLM50_Tech_Note_Soil_Snow_Temperatures.rst b/doc/source/tech_note/Soil_Snow_Temperatures/CLM50_Tech_Note_Soil_Snow_Temperatures.rst
@@ -223,7 +223,7 @@ interface of two layers
 
 .. _Figure Soil Temperature Schematic:
 
-.. figure:: ../../../images/tech_note/Soil_Snow_Temperatures/image1.png
+.. figure:: image1.png
 
  Schematic diagram of numerical scheme used to solve for soil temperature.
 
diff --git a/doc/source/tech_note/Soil_Snow_Temperatures/image1.png b/doc/source/tech_note/Soil_Snow_Temperatures/image1.png
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diff --git a/doc/source/tech_note/Transient_Landcover/CLM50_Tech_Note_Transient_Landcover.rst b/doc/source/tech_note/Transient_Landcover/CLM50_Tech_Note_Transient_Landcover.rst
@@ -347,18 +347,18 @@ data files in the mksurfdata_map tool.
 
 .. _Figure Schematic of land cover change:
 
-.. figure:: ../../../images/tech_note/Transient_Landcover/image1.png
+.. figure:: image1.png
 
  Schematic of land cover change impacts on CLM carbon pools and fluxes.
 
 .. _Figure Schematic of translation of annual LUH2 land units:
 
-.. figure:: ../../../images/tech_note/Transient_Landcover/image2.png
+.. figure:: image2.png
 
  Schematic of translation of annual LUH2 land units to CLM5 plant and crop functional types.
  
 .. _Figure Workflow of CLM5 Land Use Data Tool and Mksurfdata_map Tool:
 
-.. figure:: ../../../images/tech_note/Transient_Landcover/image3.png
+.. figure:: image3.png
 
  Workflow of CLM5 Land Use Data Tool and Mksurfdata_map Tool
diff --git a/doc/source/tech_note/Transient_Landcover/image1.png b/doc/source/tech_note/Transient_Landcover/image1.png
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diff --git a/doc/source/tech_note/Urban/CLM50_Tech_Note_Urban.rst b/doc/source/tech_note/Urban/CLM50_Tech_Note_Urban.rst
@@ -128,7 +128,7 @@ interior building temperature at yearly time resolution.
 
 .. _Figure schematic representation of the urban landunit:
 
-.. figure:: ../../../images/tech_note/Urban/image1.png
+.. figure:: image1.png
 
  Schematic representation of the urban land unit. See the text for description of notation. Incident, reflected, and net solar and longwave radiation are calculated for each individual surface but are not shown for clarity.
 
@@ -137,15 +137,15 @@ interior building temperature at yearly time resolution.
 
 .. _Figure schematic of urban and atmospheric model coupling:
 
-.. Figure:: ../../../images/tech_note/Urban/image2.png
+.. Figure:: image2.png
 
  Schematic of urban and atmospheric model coupling.  The urban model is forced by the atmospheric model wind (:math:`u_{atm}` ), temperature (:math:`T_{atm}` ), specific humidity (:math:`q_{atm}` ), precipitation (:math:`P_{atm}` ), solar (:math:`S_{atm} \, \downarrow` ) and longwave (:math:`L_{atm} \, \downarrow` ) radiation at reference height :math:`z'_{atm}`  (section :numref:`Atmospheric Coupling`). Fluxes from the urban landunit to the atmosphere are turbulent sensible (:math:`H`) and latent heat (:math:`\lambda E`), momentum (:math:`\tau` ), albedo (:math:`I\uparrow` ), emitted longwave (:math:`L\uparrow` ), and absorbed shortwave (:math:`\vec{S}`) radiation. Air temperature (:math:`T_{ac}` ), specific humidity (:math:`q_{ac}` ), and wind speed (:math:`u_{c}` ) within the urban canopy layer are diagnosed by the urban model. :math:`H` is the average building height.
 
 .. Figure 12.3. Schematic of THESIS urban properties tool
 
 .. _Figure schematic of THESIS urban properties tool:
 
-.. Figure:: ../../../images/tech_note/Urban/image3.png
+.. Figure:: image3.png
 
  Schematic of THESIS urban properties tool.  Executable scripts are in orange, input files are blue, and output files are green.  Items within the black box outline are either read in as input, executed, or output by the driver script (urban_prop.csh).  
 
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diff --git a/doc/source/tech_note/Vegetation_Phenology_Turnover/CLM50_Tech_Note_Vegetation_Phenology_Turnover.rst b/doc/source/tech_note/Vegetation_Phenology_Turnover/CLM50_Tech_Note_Vegetation_Phenology_Turnover.rst
@@ -33,7 +33,7 @@ storage over the course of a single growing season.
 
 .. _Figure annual phenology cycle:
 
-.. figure:: ../../../images/tech_note/Vegetation_Phenology_Turnover/image1.png
+.. figure:: image1.png
 
  Example of annual phenology cycle for seasonal deciduous.
 
diff --git a/doc/source/tech_note/Vegetation_Phenology_Turnover/image1.png b/doc/source/tech_note/Vegetation_Phenology_Turnover/image1.png
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diff --git a/doc/source/users_guide/running-special-cases/Spinning-up-the-Satellite-Phenology-Model-CLMSP-spinup.rst b/doc/source/users_guide/running-special-cases/Spinning-up-the-Satellite-Phenology-Model-CLMSP-spinup.rst
@@ -19,7 +19,7 @@ a specified equilibrium state (denoted by the dotted lines) due to the different
 
 .. _Figure SP spinup plot for 1850:
 
-.. figure:: ../../../images/users_guide/running-special-cases/image1.png
+.. figure:: image1.png
 
  SP spinup plot for year 1850. Variables examined are FSH (sensible heat flux), EFLX_LH_TOT (latent heat flux), GPP (photosynthesis), TWS (total water storage), H2OSOI (volumetric soil water in layer 8) and TSOI (soil temperature in layer 10). Generated using .../tools/contrib/SpinupStability_SP.ncl.
 
@@ -28,6 +28,6 @@ Again, it takes about 10 years to reach equilibrium.
 
 .. _Figure SP spinup plot for 2000 CO2:
 
-.. figure:: ../../../images/users_guide/running-special-cases/image2.png
+.. figure:: image2.png
 
  SP spinup plot for year 2000 CO2. Variables examined are FSH (sensible heat flux), EFLX_LH_TOT (latent heat flux), GPP (photosynthesis), TWS (total water storage), H2OSOI (volumetric soil water in layer 8) and TSOI (soil temperature in layer 10). Generated using .../tools/contrib/SpinupStability_SP.ncl.
diff --git a/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst b/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst
@@ -12,7 +12,7 @@ total ecosystem carbon disequilibrium takes the longest to satisfy due to slow s
 
 .. _Figure BGC AD spinup plot for 1850 GSWP3:
 
-.. figure:: ../../../images/users_guide/running-special-cases/image3.png
+.. figure:: image3.png
 
  BGC AD spinup plot for a year 1850 case with GSWP3 atmospheric forcing. Variables examined are TOTECOSYSC (total ecosystem carbon), TOTSOMC (total soil organic matter carbon), TOTVEGC (total vegetation carbon), TLAI (total leaf area index), GPP (gross primary production) and TWS (total water storage). Generated using .../tools/contrib/SpinupStability.ncl.
 
@@ -24,7 +24,7 @@ criteria depending on their application.
 
 .. _Figure BGC pAD spinup plot for 1850 GSWP3:
 
-.. figure:: ../../../images/users_guide/running-special-cases/image4.png
+.. figure:: image4.png
 
  BGC pAD spinup plot for a year 1850 case with GSWP3 atmospheric forcing and initialization from the end of the BGC AD spinup case. Variables examined are TOTECOSYSC (total ecosystem carbon), TOTSOMC (total soil organic matter carbon), TOTVEGC (total vegetation carbon), TLAI (total leaf area index), GPP (gross primary production) and TWS (total water storage). Generated using .../tools/contrib/SpinupStability.ncl.
 
@@ -35,7 +35,7 @@ such as TLAI (total leaf area index), GPP (gross primary production), and TWS (t
 
 .. _Figure BGC initialized spinup plot for 1850:
 
-.. figure:: ../../../images/users_guide/running-special-cases/image5.png
+.. figure:: image5.png
 
  BGC initialized spinup plot for year 1850. Variables examined are TOTECOSYSC (total ecosystem carbon), TOTSOMC (total soil organic matter carbon), TOTVEGC (total vegetation carbon), TLAI (total leaf area index), GPP (gross primary production) and TWS (total water storage). Generated using .../tools/contrib/SpinupStability.ncl.
 
@@ -44,7 +44,7 @@ Again, it takes about 10 years to reach equilibrium for TLAI, GPP, and TWS.
 
 .. _Figure BGC initialized spinup plot for 2000 CO2:
 
-.. figure:: ../../../images/users_guide/running-special-cases/image6.png
+.. figure:: image6.png
 
  BGC initialized spinup plot for year 2000 CO2.  Variables examined are TOTECOSYSC (total ecosystem carbon), TOTSOMC (total soil organic matter carbon), TOTVEGC (total vegetation carbon), TLAI (total leaf area index), GPP (gross primary production) and TWS (total water storage). Generated using .../tools/contrib/SpinupStability.ncl.
 
diff --git a/doc/source/users_guide/running-special-cases/image1.png b/doc/source/users_guide/running-special-cases/image1.png
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diff --git a/doc/source/users_guide/running-special-cases/image5.png b/doc/source/users_guide/running-special-cases/image5.png
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