From ec78cac5f2e9e660653b44c48c668694712cfc43 Mon Sep 17 00:00:00 2001 From: Edward Hartnett Date: Sat, 5 Oct 2024 18:57:23 -0600 Subject: [PATCH 01/32] adding API rst files --- doc/source/HWP_tools.rst | 7 ++ doc/source/UFS_plot_domains.rst | 7 ++ doc/source/blending_fv3.rst | 7 ++ doc/source/chgres_cold2fv3.rst | 7 ++ doc/source/create_diag_table_file.rst | 7 ++ doc/source/create_model_configure_file.rst | 7 ++ doc/source/create_ufs_configure_file.rst | 7 ++ doc/source/enspost_config.rst | 7 ++ doc/source/fill_jinja_template.rst | 7 ++ doc/source/fire_emiss_tools.rst | 7 ++ doc/source/fvcom_remap.rst | 7 ++ doc/source/generate_fire_emissions.rst | 7 ++ doc/source/get_crontab_contents.rst | 7 ++ doc/source/interp_tools.rst | 7 ++ doc/source/log_change.rst | 7 ++ doc/source/modules.rst | 24 +++++ doc/source/python_utils.rst | 117 +++++++++++++++++++++ doc/source/rrfsfw_domain.rst | 7 ++ doc/source/set_namelist.rst | 7 ++ 19 files changed, 260 insertions(+) create mode 100644 doc/source/HWP_tools.rst create mode 100644 doc/source/UFS_plot_domains.rst create mode 100644 doc/source/blending_fv3.rst create mode 100644 doc/source/chgres_cold2fv3.rst create mode 100644 doc/source/create_diag_table_file.rst create mode 100644 doc/source/create_model_configure_file.rst create mode 100644 doc/source/create_ufs_configure_file.rst create mode 100644 doc/source/enspost_config.rst create mode 100644 doc/source/fill_jinja_template.rst create mode 100644 doc/source/fire_emiss_tools.rst create mode 100644 doc/source/fvcom_remap.rst create mode 100644 doc/source/generate_fire_emissions.rst create mode 100644 doc/source/get_crontab_contents.rst create mode 100644 doc/source/interp_tools.rst create mode 100644 doc/source/log_change.rst create mode 100644 doc/source/modules.rst create mode 100644 doc/source/python_utils.rst create mode 100644 doc/source/rrfsfw_domain.rst create mode 100644 doc/source/set_namelist.rst diff --git a/doc/source/HWP_tools.rst b/doc/source/HWP_tools.rst new file mode 100644 index 00000000..b72c398d --- /dev/null +++ b/doc/source/HWP_tools.rst @@ -0,0 +1,7 @@ +HWP\_tools module +================= + +.. automodule:: HWP_tools + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/UFS_plot_domains.rst b/doc/source/UFS_plot_domains.rst new file mode 100644 index 00000000..bd1b4231 --- /dev/null +++ b/doc/source/UFS_plot_domains.rst @@ -0,0 +1,7 @@ +UFS\_plot\_domains module +========================= + +.. automodule:: UFS_plot_domains + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/blending_fv3.rst b/doc/source/blending_fv3.rst new file mode 100644 index 00000000..c5a8d924 --- /dev/null +++ b/doc/source/blending_fv3.rst @@ -0,0 +1,7 @@ +blending\_fv3 module +==================== + +.. automodule:: blending_fv3 + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/chgres_cold2fv3.rst b/doc/source/chgres_cold2fv3.rst new file mode 100644 index 00000000..71ed3276 --- /dev/null +++ b/doc/source/chgres_cold2fv3.rst @@ -0,0 +1,7 @@ +chgres\_cold2fv3 module +======================= + +.. automodule:: chgres_cold2fv3 + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/create_diag_table_file.rst b/doc/source/create_diag_table_file.rst new file mode 100644 index 00000000..5a317526 --- /dev/null +++ b/doc/source/create_diag_table_file.rst @@ -0,0 +1,7 @@ +create\_diag\_table\_file module +================================ + +.. automodule:: create_diag_table_file + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/create_model_configure_file.rst b/doc/source/create_model_configure_file.rst new file mode 100644 index 00000000..7a8dd0cd --- /dev/null +++ b/doc/source/create_model_configure_file.rst @@ -0,0 +1,7 @@ +create\_model\_configure\_file module +===================================== + +.. automodule:: create_model_configure_file + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/create_ufs_configure_file.rst b/doc/source/create_ufs_configure_file.rst new file mode 100644 index 00000000..56c17689 --- /dev/null +++ b/doc/source/create_ufs_configure_file.rst @@ -0,0 +1,7 @@ +create\_ufs\_configure\_file module +=================================== + +.. automodule:: create_ufs_configure_file + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/enspost_config.rst b/doc/source/enspost_config.rst new file mode 100644 index 00000000..35891abd --- /dev/null +++ b/doc/source/enspost_config.rst @@ -0,0 +1,7 @@ +enspost\_config module +====================== + +.. automodule:: enspost_config + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/fill_jinja_template.rst b/doc/source/fill_jinja_template.rst new file mode 100644 index 00000000..0c1c9e34 --- /dev/null +++ b/doc/source/fill_jinja_template.rst @@ -0,0 +1,7 @@ +fill\_jinja\_template module +============================ + +.. automodule:: fill_jinja_template + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/fire_emiss_tools.rst b/doc/source/fire_emiss_tools.rst new file mode 100644 index 00000000..373d868c --- /dev/null +++ b/doc/source/fire_emiss_tools.rst @@ -0,0 +1,7 @@ +fire\_emiss\_tools module +========================= + +.. automodule:: fire_emiss_tools + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/fvcom_remap.rst b/doc/source/fvcom_remap.rst new file mode 100644 index 00000000..d104fab6 --- /dev/null +++ b/doc/source/fvcom_remap.rst @@ -0,0 +1,7 @@ +fvcom\_remap module +=================== + +.. automodule:: fvcom_remap + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/generate_fire_emissions.rst b/doc/source/generate_fire_emissions.rst new file mode 100644 index 00000000..f30ce48c --- /dev/null +++ b/doc/source/generate_fire_emissions.rst @@ -0,0 +1,7 @@ +generate\_fire\_emissions module +================================ + +.. automodule:: generate_fire_emissions + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/get_crontab_contents.rst b/doc/source/get_crontab_contents.rst new file mode 100644 index 00000000..8e62d5a2 --- /dev/null +++ b/doc/source/get_crontab_contents.rst @@ -0,0 +1,7 @@ +get\_crontab\_contents module +============================= + +.. automodule:: get_crontab_contents + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/interp_tools.rst b/doc/source/interp_tools.rst new file mode 100644 index 00000000..15a83551 --- /dev/null +++ b/doc/source/interp_tools.rst @@ -0,0 +1,7 @@ +interp\_tools module +==================== + +.. automodule:: interp_tools + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/log_change.rst b/doc/source/log_change.rst new file mode 100644 index 00000000..34d44581 --- /dev/null +++ b/doc/source/log_change.rst @@ -0,0 +1,7 @@ +log\_change module +================== + +.. automodule:: log_change + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/modules.rst b/doc/source/modules.rst new file mode 100644 index 00000000..56715f65 --- /dev/null +++ b/doc/source/modules.rst @@ -0,0 +1,24 @@ +ush +=== + +.. toctree:: + :maxdepth: 4 + + HWP_tools + UFS_plot_domains + blending_fv3 + chgres_cold2fv3 + create_diag_table_file + create_model_configure_file + create_ufs_configure_file + enspost_config + fill_jinja_template + fire_emiss_tools + fvcom_remap + generate_fire_emissions + get_crontab_contents + interp_tools + log_change + python_utils + rrfsfw_domain + set_namelist diff --git a/doc/source/python_utils.rst b/doc/source/python_utils.rst new file mode 100644 index 00000000..3b6d8fdd --- /dev/null +++ b/doc/source/python_utils.rst @@ -0,0 +1,117 @@ +python\_utils package +===================== + +Submodules +---------- + +python\_utils.check\_for\_preexist\_dir\_file module +---------------------------------------------------- + +.. automodule:: python_utils.check_for_preexist_dir_file + :members: + :undoc-members: + :show-inheritance: + +python\_utils.check\_var\_valid\_value module +--------------------------------------------- + +.. automodule:: python_utils.check_var_valid_value + :members: + :undoc-members: + :show-inheritance: + +python\_utils.config\_parser module +----------------------------------- + +.. automodule:: python_utils.config_parser + :members: + :undoc-members: + :show-inheritance: + +python\_utils.create\_symlink\_to\_file module +---------------------------------------------- + +.. automodule:: python_utils.create_symlink_to_file + :members: + :undoc-members: + :show-inheritance: + +python\_utils.define\_macos\_utilities module +--------------------------------------------- + +.. automodule:: python_utils.define_macos_utilities + :members: + :undoc-members: + :show-inheritance: + +python\_utils.environment module +-------------------------------- + +.. automodule:: python_utils.environment + :members: + :undoc-members: + :show-inheritance: + +python\_utils.filesys\_cmds\_vrfy module +---------------------------------------- + +.. automodule:: python_utils.filesys_cmds_vrfy + :members: + :undoc-members: + :show-inheritance: + +python\_utils.fv3write\_parms\_lambert module +--------------------------------------------- + +.. automodule:: python_utils.fv3write_parms_lambert + :members: + :undoc-members: + :show-inheritance: + +python\_utils.misc module +------------------------- + +.. automodule:: python_utils.misc + :members: + :undoc-members: + :show-inheritance: + +python\_utils.print\_input\_args module +--------------------------------------- + +.. automodule:: python_utils.print_input_args + :members: + :undoc-members: + :show-inheritance: + +python\_utils.print\_msg module +------------------------------- + +.. automodule:: python_utils.print_msg + :members: + :undoc-members: + :show-inheritance: + +python\_utils.run\_command module +--------------------------------- + +.. automodule:: python_utils.run_command + :members: + :undoc-members: + :show-inheritance: + +python\_utils.xml\_parser module +-------------------------------- + +.. automodule:: python_utils.xml_parser + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: python_utils + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/rrfsfw_domain.rst b/doc/source/rrfsfw_domain.rst new file mode 100644 index 00000000..6ada6a27 --- /dev/null +++ b/doc/source/rrfsfw_domain.rst @@ -0,0 +1,7 @@ +rrfsfw\_domain module +===================== + +.. automodule:: rrfsfw_domain + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/set_namelist.rst b/doc/source/set_namelist.rst new file mode 100644 index 00000000..1245a45b --- /dev/null +++ b/doc/source/set_namelist.rst @@ -0,0 +1,7 @@ +set\_namelist module +==================== + +.. automodule:: set_namelist + :members: + :undoc-members: + :show-inheritance: From 8b437eb2f590767f6d66266ccd0636274ec371c0 Mon Sep 17 00:00:00 2001 From: Edward Hartnett Date: Sun, 6 Oct 2024 06:26:52 -0600 Subject: [PATCH 02/32] moved files --- doc/{source => UsersGuide}/HWP_tools.rst | 0 doc/{source => UsersGuide}/UFS_plot_domains.rst | 0 doc/{source => UsersGuide}/blending_fv3.rst | 0 doc/{source => UsersGuide}/chgres_cold2fv3.rst | 0 doc/{source => UsersGuide}/create_diag_table_file.rst | 0 doc/{source => UsersGuide}/create_model_configure_file.rst | 0 doc/{source => UsersGuide}/create_ufs_configure_file.rst | 0 doc/{source => UsersGuide}/enspost_config.rst | 0 doc/{source => UsersGuide}/fill_jinja_template.rst | 0 doc/{source => UsersGuide}/fire_emiss_tools.rst | 0 doc/{source => UsersGuide}/fvcom_remap.rst | 0 doc/{source => UsersGuide}/generate_fire_emissions.rst | 0 doc/{source => UsersGuide}/get_crontab_contents.rst | 0 doc/{source => UsersGuide}/interp_tools.rst | 0 doc/{source => UsersGuide}/log_change.rst | 0 doc/{source => UsersGuide}/modules.rst | 0 doc/{source => UsersGuide}/python_utils.rst | 0 doc/{source => UsersGuide}/rrfsfw_domain.rst | 0 doc/{source => UsersGuide}/set_namelist.rst | 0 19 files changed, 0 insertions(+), 0 deletions(-) rename doc/{source => UsersGuide}/HWP_tools.rst (100%) rename doc/{source => UsersGuide}/UFS_plot_domains.rst (100%) rename doc/{source => UsersGuide}/blending_fv3.rst (100%) rename doc/{source => UsersGuide}/chgres_cold2fv3.rst (100%) rename doc/{source => UsersGuide}/create_diag_table_file.rst (100%) rename doc/{source => UsersGuide}/create_model_configure_file.rst (100%) rename doc/{source => UsersGuide}/create_ufs_configure_file.rst (100%) rename doc/{source => UsersGuide}/enspost_config.rst (100%) rename doc/{source => UsersGuide}/fill_jinja_template.rst (100%) rename doc/{source => UsersGuide}/fire_emiss_tools.rst (100%) rename doc/{source => UsersGuide}/fvcom_remap.rst (100%) rename doc/{source => UsersGuide}/generate_fire_emissions.rst (100%) rename doc/{source => UsersGuide}/get_crontab_contents.rst (100%) rename doc/{source => UsersGuide}/interp_tools.rst (100%) rename doc/{source => UsersGuide}/log_change.rst (100%) rename doc/{source => UsersGuide}/modules.rst (100%) rename doc/{source => UsersGuide}/python_utils.rst (100%) rename doc/{source => UsersGuide}/rrfsfw_domain.rst (100%) rename doc/{source => UsersGuide}/set_namelist.rst (100%) diff --git a/doc/source/HWP_tools.rst b/doc/UsersGuide/HWP_tools.rst similarity index 100% rename from doc/source/HWP_tools.rst rename to doc/UsersGuide/HWP_tools.rst diff --git a/doc/source/UFS_plot_domains.rst b/doc/UsersGuide/UFS_plot_domains.rst similarity index 100% rename from doc/source/UFS_plot_domains.rst rename to doc/UsersGuide/UFS_plot_domains.rst diff --git a/doc/source/blending_fv3.rst b/doc/UsersGuide/blending_fv3.rst similarity index 100% rename from doc/source/blending_fv3.rst rename to doc/UsersGuide/blending_fv3.rst diff --git a/doc/source/chgres_cold2fv3.rst b/doc/UsersGuide/chgres_cold2fv3.rst similarity index 100% rename from doc/source/chgres_cold2fv3.rst rename to doc/UsersGuide/chgres_cold2fv3.rst diff --git a/doc/source/create_diag_table_file.rst b/doc/UsersGuide/create_diag_table_file.rst similarity index 100% rename from doc/source/create_diag_table_file.rst rename to doc/UsersGuide/create_diag_table_file.rst diff --git a/doc/source/create_model_configure_file.rst b/doc/UsersGuide/create_model_configure_file.rst similarity index 100% rename from doc/source/create_model_configure_file.rst rename to doc/UsersGuide/create_model_configure_file.rst diff --git a/doc/source/create_ufs_configure_file.rst b/doc/UsersGuide/create_ufs_configure_file.rst similarity index 100% rename from doc/source/create_ufs_configure_file.rst rename to doc/UsersGuide/create_ufs_configure_file.rst diff --git a/doc/source/enspost_config.rst b/doc/UsersGuide/enspost_config.rst similarity index 100% rename from doc/source/enspost_config.rst rename to doc/UsersGuide/enspost_config.rst diff --git a/doc/source/fill_jinja_template.rst b/doc/UsersGuide/fill_jinja_template.rst similarity index 100% rename from doc/source/fill_jinja_template.rst rename to doc/UsersGuide/fill_jinja_template.rst diff --git a/doc/source/fire_emiss_tools.rst b/doc/UsersGuide/fire_emiss_tools.rst similarity index 100% rename from doc/source/fire_emiss_tools.rst rename to doc/UsersGuide/fire_emiss_tools.rst diff --git a/doc/source/fvcom_remap.rst b/doc/UsersGuide/fvcom_remap.rst similarity index 100% rename from doc/source/fvcom_remap.rst rename to doc/UsersGuide/fvcom_remap.rst diff --git a/doc/source/generate_fire_emissions.rst b/doc/UsersGuide/generate_fire_emissions.rst similarity index 100% rename from doc/source/generate_fire_emissions.rst rename to doc/UsersGuide/generate_fire_emissions.rst diff --git a/doc/source/get_crontab_contents.rst b/doc/UsersGuide/get_crontab_contents.rst similarity index 100% rename from doc/source/get_crontab_contents.rst rename to doc/UsersGuide/get_crontab_contents.rst diff --git a/doc/source/interp_tools.rst b/doc/UsersGuide/interp_tools.rst similarity index 100% rename from doc/source/interp_tools.rst rename to doc/UsersGuide/interp_tools.rst diff --git a/doc/source/log_change.rst b/doc/UsersGuide/log_change.rst similarity index 100% rename from doc/source/log_change.rst rename to doc/UsersGuide/log_change.rst diff --git a/doc/source/modules.rst b/doc/UsersGuide/modules.rst similarity index 100% rename from doc/source/modules.rst rename to doc/UsersGuide/modules.rst diff --git a/doc/source/python_utils.rst b/doc/UsersGuide/python_utils.rst similarity index 100% rename from doc/source/python_utils.rst rename to doc/UsersGuide/python_utils.rst diff --git a/doc/source/rrfsfw_domain.rst b/doc/UsersGuide/rrfsfw_domain.rst similarity index 100% rename from doc/source/rrfsfw_domain.rst rename to doc/UsersGuide/rrfsfw_domain.rst diff --git a/doc/source/set_namelist.rst b/doc/UsersGuide/set_namelist.rst similarity index 100% rename from doc/source/set_namelist.rst rename to doc/UsersGuide/set_namelist.rst From 5a393e2884535773ffeb5ba086e11025d2ce249f Mon Sep 17 00:00:00 2001 From: Edward Hartnett Date: Sun, 6 Oct 2024 06:50:15 -0600 Subject: [PATCH 03/32] more docs work --- doc/UsersGuide/HWP_tools.rst | 7 -- doc/UsersGuide/UFS_plot_domains.rst | 7 -- doc/UsersGuide/blending_fv3.rst | 7 -- doc/UsersGuide/chgres_cold2fv3.rst | 7 -- doc/UsersGuide/create_diag_table_file.rst | 7 -- .../create_model_configure_file.rst | 7 -- doc/UsersGuide/create_ufs_configure_file.rst | 7 -- doc/UsersGuide/enspost_config.rst | 7 -- doc/UsersGuide/fill_jinja_template.rst | 7 -- doc/UsersGuide/fire_emiss_tools.rst | 7 -- doc/UsersGuide/fvcom_remap.rst | 7 -- doc/UsersGuide/generate_fire_emissions.rst | 7 -- doc/UsersGuide/get_crontab_contents.rst | 7 -- doc/UsersGuide/interp_tools.rst | 7 -- doc/UsersGuide/log_change.rst | 7 -- doc/UsersGuide/modules.rst | 24 ---- doc/UsersGuide/python_utils.rst | 117 ------------------ doc/UsersGuide/rrfsfw_domain.rst | 7 -- doc/UsersGuide/set_namelist.rst | 7 -- doc/UsersGuide/source/index.rst | 2 +- 20 files changed, 1 insertion(+), 261 deletions(-) delete mode 100644 doc/UsersGuide/HWP_tools.rst delete mode 100644 doc/UsersGuide/UFS_plot_domains.rst delete mode 100644 doc/UsersGuide/blending_fv3.rst delete mode 100644 doc/UsersGuide/chgres_cold2fv3.rst delete mode 100644 doc/UsersGuide/create_diag_table_file.rst delete mode 100644 doc/UsersGuide/create_model_configure_file.rst delete mode 100644 doc/UsersGuide/create_ufs_configure_file.rst delete mode 100644 doc/UsersGuide/enspost_config.rst delete mode 100644 doc/UsersGuide/fill_jinja_template.rst delete mode 100644 doc/UsersGuide/fire_emiss_tools.rst delete mode 100644 doc/UsersGuide/fvcom_remap.rst delete mode 100644 doc/UsersGuide/generate_fire_emissions.rst delete mode 100644 doc/UsersGuide/get_crontab_contents.rst delete mode 100644 doc/UsersGuide/interp_tools.rst delete mode 100644 doc/UsersGuide/log_change.rst delete mode 100644 doc/UsersGuide/modules.rst delete mode 100644 doc/UsersGuide/python_utils.rst delete mode 100644 doc/UsersGuide/rrfsfw_domain.rst delete mode 100644 doc/UsersGuide/set_namelist.rst diff --git a/doc/UsersGuide/HWP_tools.rst b/doc/UsersGuide/HWP_tools.rst deleted file mode 100644 index b72c398d..00000000 --- a/doc/UsersGuide/HWP_tools.rst +++ /dev/null @@ -1,7 +0,0 @@ -HWP\_tools module -================= - -.. automodule:: HWP_tools - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/UsersGuide/UFS_plot_domains.rst b/doc/UsersGuide/UFS_plot_domains.rst deleted file mode 100644 index bd1b4231..00000000 --- a/doc/UsersGuide/UFS_plot_domains.rst +++ /dev/null @@ -1,7 +0,0 @@ -UFS\_plot\_domains module -========================= - -.. automodule:: UFS_plot_domains - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/UsersGuide/blending_fv3.rst b/doc/UsersGuide/blending_fv3.rst deleted file mode 100644 index c5a8d924..00000000 --- a/doc/UsersGuide/blending_fv3.rst +++ /dev/null @@ -1,7 +0,0 @@ -blending\_fv3 module -==================== - -.. automodule:: blending_fv3 - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/UsersGuide/chgres_cold2fv3.rst b/doc/UsersGuide/chgres_cold2fv3.rst deleted file mode 100644 index 71ed3276..00000000 --- a/doc/UsersGuide/chgres_cold2fv3.rst +++ /dev/null @@ -1,7 +0,0 @@ -chgres\_cold2fv3 module -======================= - -.. automodule:: chgres_cold2fv3 - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/UsersGuide/create_diag_table_file.rst b/doc/UsersGuide/create_diag_table_file.rst deleted file mode 100644 index 5a317526..00000000 --- a/doc/UsersGuide/create_diag_table_file.rst +++ /dev/null @@ -1,7 +0,0 @@ -create\_diag\_table\_file module -================================ - -.. automodule:: create_diag_table_file - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/UsersGuide/create_model_configure_file.rst b/doc/UsersGuide/create_model_configure_file.rst deleted file mode 100644 index 7a8dd0cd..00000000 --- a/doc/UsersGuide/create_model_configure_file.rst +++ /dev/null @@ -1,7 +0,0 @@ -create\_model\_configure\_file module -===================================== - -.. automodule:: create_model_configure_file - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/UsersGuide/create_ufs_configure_file.rst b/doc/UsersGuide/create_ufs_configure_file.rst deleted file mode 100644 index 56c17689..00000000 --- a/doc/UsersGuide/create_ufs_configure_file.rst +++ /dev/null @@ -1,7 +0,0 @@ -create\_ufs\_configure\_file module -=================================== - -.. automodule:: create_ufs_configure_file - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/UsersGuide/enspost_config.rst b/doc/UsersGuide/enspost_config.rst deleted file mode 100644 index 35891abd..00000000 --- a/doc/UsersGuide/enspost_config.rst +++ /dev/null @@ -1,7 +0,0 @@ -enspost\_config module -====================== - -.. automodule:: enspost_config - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/UsersGuide/fill_jinja_template.rst b/doc/UsersGuide/fill_jinja_template.rst deleted file mode 100644 index 0c1c9e34..00000000 --- a/doc/UsersGuide/fill_jinja_template.rst +++ /dev/null @@ -1,7 +0,0 @@ -fill\_jinja\_template module -============================ - -.. automodule:: fill_jinja_template - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/UsersGuide/fire_emiss_tools.rst b/doc/UsersGuide/fire_emiss_tools.rst deleted file mode 100644 index 373d868c..00000000 --- a/doc/UsersGuide/fire_emiss_tools.rst +++ /dev/null @@ -1,7 +0,0 @@ -fire\_emiss\_tools module -========================= - -.. automodule:: fire_emiss_tools - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/UsersGuide/fvcom_remap.rst b/doc/UsersGuide/fvcom_remap.rst deleted file mode 100644 index d104fab6..00000000 --- a/doc/UsersGuide/fvcom_remap.rst +++ /dev/null @@ -1,7 +0,0 @@ -fvcom\_remap module -=================== - -.. automodule:: fvcom_remap - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/UsersGuide/generate_fire_emissions.rst b/doc/UsersGuide/generate_fire_emissions.rst deleted file mode 100644 index f30ce48c..00000000 --- a/doc/UsersGuide/generate_fire_emissions.rst +++ /dev/null @@ -1,7 +0,0 @@ -generate\_fire\_emissions module -================================ - -.. automodule:: generate_fire_emissions - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/UsersGuide/get_crontab_contents.rst b/doc/UsersGuide/get_crontab_contents.rst deleted file mode 100644 index 8e62d5a2..00000000 --- a/doc/UsersGuide/get_crontab_contents.rst +++ /dev/null @@ -1,7 +0,0 @@ -get\_crontab\_contents module -============================= - -.. automodule:: get_crontab_contents - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/UsersGuide/interp_tools.rst b/doc/UsersGuide/interp_tools.rst deleted file mode 100644 index 15a83551..00000000 --- a/doc/UsersGuide/interp_tools.rst +++ /dev/null @@ -1,7 +0,0 @@ -interp\_tools module -==================== - -.. automodule:: interp_tools - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/UsersGuide/log_change.rst b/doc/UsersGuide/log_change.rst deleted file mode 100644 index 34d44581..00000000 --- a/doc/UsersGuide/log_change.rst +++ /dev/null @@ -1,7 +0,0 @@ -log\_change module -================== - -.. automodule:: log_change - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/UsersGuide/modules.rst b/doc/UsersGuide/modules.rst deleted file mode 100644 index 56715f65..00000000 --- a/doc/UsersGuide/modules.rst +++ /dev/null @@ -1,24 +0,0 @@ -ush -=== - -.. toctree:: - :maxdepth: 4 - - HWP_tools - UFS_plot_domains - blending_fv3 - chgres_cold2fv3 - create_diag_table_file - create_model_configure_file - create_ufs_configure_file - enspost_config - fill_jinja_template - fire_emiss_tools - fvcom_remap - generate_fire_emissions - get_crontab_contents - interp_tools - log_change - python_utils - rrfsfw_domain - set_namelist diff --git a/doc/UsersGuide/python_utils.rst b/doc/UsersGuide/python_utils.rst deleted file mode 100644 index 3b6d8fdd..00000000 --- a/doc/UsersGuide/python_utils.rst +++ /dev/null @@ -1,117 +0,0 @@ -python\_utils package -===================== - -Submodules ----------- - -python\_utils.check\_for\_preexist\_dir\_file module ----------------------------------------------------- - -.. automodule:: python_utils.check_for_preexist_dir_file - :members: - :undoc-members: - :show-inheritance: - -python\_utils.check\_var\_valid\_value module ---------------------------------------------- - -.. automodule:: python_utils.check_var_valid_value - :members: - :undoc-members: - :show-inheritance: - -python\_utils.config\_parser module ------------------------------------ - -.. automodule:: python_utils.config_parser - :members: - :undoc-members: - :show-inheritance: - -python\_utils.create\_symlink\_to\_file module ----------------------------------------------- - -.. automodule:: python_utils.create_symlink_to_file - :members: - :undoc-members: - :show-inheritance: - -python\_utils.define\_macos\_utilities module ---------------------------------------------- - -.. automodule:: python_utils.define_macos_utilities - :members: - :undoc-members: - :show-inheritance: - -python\_utils.environment module --------------------------------- - -.. automodule:: python_utils.environment - :members: - :undoc-members: - :show-inheritance: - -python\_utils.filesys\_cmds\_vrfy module ----------------------------------------- - -.. automodule:: python_utils.filesys_cmds_vrfy - :members: - :undoc-members: - :show-inheritance: - -python\_utils.fv3write\_parms\_lambert module ---------------------------------------------- - -.. automodule:: python_utils.fv3write_parms_lambert - :members: - :undoc-members: - :show-inheritance: - -python\_utils.misc module -------------------------- - -.. automodule:: python_utils.misc - :members: - :undoc-members: - :show-inheritance: - -python\_utils.print\_input\_args module ---------------------------------------- - -.. automodule:: python_utils.print_input_args - :members: - :undoc-members: - :show-inheritance: - -python\_utils.print\_msg module -------------------------------- - -.. automodule:: python_utils.print_msg - :members: - :undoc-members: - :show-inheritance: - -python\_utils.run\_command module ---------------------------------- - -.. automodule:: python_utils.run_command - :members: - :undoc-members: - :show-inheritance: - -python\_utils.xml\_parser module --------------------------------- - -.. automodule:: python_utils.xml_parser - :members: - :undoc-members: - :show-inheritance: - -Module contents ---------------- - -.. automodule:: python_utils - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/UsersGuide/rrfsfw_domain.rst b/doc/UsersGuide/rrfsfw_domain.rst deleted file mode 100644 index 6ada6a27..00000000 --- a/doc/UsersGuide/rrfsfw_domain.rst +++ /dev/null @@ -1,7 +0,0 @@ -rrfsfw\_domain module -===================== - -.. automodule:: rrfsfw_domain - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/UsersGuide/set_namelist.rst b/doc/UsersGuide/set_namelist.rst deleted file mode 100644 index 1245a45b..00000000 --- a/doc/UsersGuide/set_namelist.rst +++ /dev/null @@ -1,7 +0,0 @@ -set\_namelist module -==================== - -.. automodule:: set_namelist - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/UsersGuide/source/index.rst b/doc/UsersGuide/source/index.rst index 276f0499..adf6cd36 100644 --- a/doc/UsersGuide/source/index.rst +++ b/doc/UsersGuide/source/index.rst @@ -2,7 +2,7 @@ You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. -RRFS-WORKFLOW Users Guide +RRFS-WORKFLOW Users Guide 1 ======================================= .. toctree:: From 5e185f305e93115efcd6a70fe168c9921754b4d6 Mon Sep 17 00:00:00 2001 From: Edward Hartnett Date: Sun, 6 Oct 2024 06:53:38 -0600 Subject: [PATCH 04/32] more docs work --- doc/UsersGuide/source/index.rst | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/doc/UsersGuide/source/index.rst b/doc/UsersGuide/source/index.rst index adf6cd36..e167fe26 100644 --- a/doc/UsersGuide/source/index.rst +++ b/doc/UsersGuide/source/index.rst @@ -2,7 +2,7 @@ You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. -RRFS-WORKFLOW Users Guide 1 +RRFS-WORKFLOW Users Guide ======================================= .. toctree:: @@ -10,5 +10,6 @@ RRFS-WORKFLOW Users Guide 1 :maxdepth: 3 + modules Quickstart modules From 5cb7f8dad919d46c9a6980a31f34f7b04fe9bdaa Mon Sep 17 00:00:00 2001 From: Edward Hartnett Date: Sun, 6 Oct 2024 06:54:44 -0600 Subject: [PATCH 05/32] more docs work --- doc/UsersGuide/source/index.rst | 2 -- 1 file changed, 2 deletions(-) diff --git a/doc/UsersGuide/source/index.rst b/doc/UsersGuide/source/index.rst index e167fe26..c250ff1b 100644 --- a/doc/UsersGuide/source/index.rst +++ b/doc/UsersGuide/source/index.rst @@ -11,5 +11,3 @@ RRFS-WORKFLOW Users Guide modules - Quickstart - modules From b86dce165109e71aca8615da0093d9b05b6dea85 Mon Sep 17 00:00:00 2001 From: Edward Hartnett Date: Sun, 6 Oct 2024 06:56:32 -0600 Subject: [PATCH 06/32] more docs work --- doc/UsersGuide/source/index.rst | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/doc/UsersGuide/source/index.rst b/doc/UsersGuide/source/index.rst index c250ff1b..adf6cd36 100644 --- a/doc/UsersGuide/source/index.rst +++ b/doc/UsersGuide/source/index.rst @@ -2,7 +2,7 @@ You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. -RRFS-WORKFLOW Users Guide +RRFS-WORKFLOW Users Guide 1 ======================================= .. toctree:: @@ -10,4 +10,5 @@ RRFS-WORKFLOW Users Guide :maxdepth: 3 - modules + Quickstart + modules From 60843d505bd7477226218bca9df220ea432756ce Mon Sep 17 00:00:00 2001 From: Edward Hartnett Date: Sun, 6 Oct 2024 06:58:32 -0600 Subject: [PATCH 07/32] more docs work --- doc/UsersGuide/source/Q2.rst | 221 ++++++++++++++++++++++++++++++++ doc/UsersGuide/source/index.rst | 1 + 2 files changed, 222 insertions(+) create mode 100644 doc/UsersGuide/source/Q2.rst diff --git a/doc/UsersGuide/source/Q2.rst b/doc/UsersGuide/source/Q2.rst new file mode 100644 index 00000000..39b45bdd --- /dev/null +++ b/doc/UsersGuide/source/Q2.rst @@ -0,0 +1,221 @@ +.. _NCQuickstart: + +==================== +Quick Start Guide +==================== + +This chapter provides a brief summary of how to build and run the RRFS-Workflow. + + +.. _QuickBuildRun: + +Building RRFS workflow +=============================================== + + #. Clone the ``main`` branch of the RRFS-Workflow from GitHub: + + .. code-block:: console + + git clone https://github.com/NOAA-EMC/rrfs-workflow.git + + #. Check out the external components: + + .. code-block:: console + + cd rrfs-workflow/sorc + ./manage_externals/checkout_externals + + #. Set up the build environment and build the executables: + + .. code-block:: console + + ./app_build.sh + + Alternatively, the above command can be followed by the platform (machine) name as follows: + + .. code-block:: console + + ./app_build.sh --platform= + + where ```` is ``wcoss2``, ``hera``, ``jet``, ``orion``, or ``hercules``. + + #. Move to the home directory (rrfs-workflow): + + .. code-block:: console + + cd .. + +Engineering Test: Non-DA +=============================================== + + #. Load the python environment: + + * On WCOSS2: + + .. code-block:: console + + source versions/run.ver + module use modulefiles + module load wflow_wcoss2 + + * On Hera | Jet | Orion | Hercules: + + .. code-block:: console + + module use modulefiles + module load wflow_ + conda activate workflow_tools + + where ```` is ``hera``, ``jet``, ``orion``, or ``hercules``. + + #. Copy the pre-defined configuration file: + + .. code-block:: console + + cd ush + cp sample_configs/non-DA_eng/config.nonDA...sh config.sh + + where ```` is ``grib2`` or ``netcdf``, and ```` is ``wcoss2``, ``hera``, ``jet``, ``orion``, or ``hercules``. Note that you may need to change ``ACCOUNT``, ``STMP``, or ``PTMP`` in the configuration file ``config.sh``. + + #. Generate the experiment workflow: + + .. code-block:: console + + ./generate_FV3LAM_wflow.sh + + #. Launch the workflow: + + .. code-block:: console + + cd ../../expt_dirs/test_nonDA + ./launch_FV3LAM_wflow.sh + + .. note:: + The workflow tasks will be submitted every three minutes by ``cron`` until the log output includes a ``Workflow status: SUCCESS`` message if you did not modify the following parameters in the configuration file: + + .. code-block:: console + + USE_CRON_TO_RELAUNCH="TRUE" + CRON_RELAUNCH_INTVL_MNTS="03" + + +Engineering Test: DA +=============================================== + + #. Load the python environment: + + * On WCOSS2: + + .. code-block:: console + + source versions/run.ver + module use modulefiles + module load wflow_wcoss2 + + * On Hera | Jet | Orion | Hercules : + + .. code-block:: console + + module use modulefiles + module load wflow_ + conda activate workflow_tools + + where ```` is ``hera``, ``jet``, ``orion``, or ``hercules``. + + #. Copy the pre-defined configuration file: + + .. code-block:: console + + cd ush + cp sample_configs/DA_eng/config.DA...sh config.sh + + where ```` is ``para`` with ```` is ``wcoss2``, or ```` is ``retro`` or ``ens`` with ```` is ``hera``. Note that you may need to change ``ACCOUNT`` in the configuration file ``config.sh``. + + .. note:: + For the real-time (``para``) test run on WCOSS2, you should replace ``DATE_FIRST_CYCL``, ``DATE_LAST_CYCL``, ``CYCLEMONTH``, and ``CYCLEDAY`` with those of Today's date. + + #. Generate the experiment workflow: + + .. code-block:: console + + ./generate_FV3LAM_wflow.sh + + #. Launch the workflow: + + .. code-block:: console + + cd ../../expt_dirs/rrfs_test_da + ./run_rocoto.sh + + #. Launch the following tasks as needed: + + * On WCOSS2: with ``config.DA.para.wcoss2.sh`` (in case of today=20230726) + + .. code-block:: console + + rocotoboot -w FV3LAM_wflow.xml -d FV3LAM_wflow.db -v 10 -c 202307260000 -t get_extrn_lbcs + rocotoboot -w FV3LAM_wflow.xml -d FV3LAM_wflow.db -v 10 -c 202307260600 -t get_extrn_lbcs + rocotoboot -w FV3LAM_wflow.xml -d FV3LAM_wflow.db -v 10 -c 202307261200 -t get_extrn_lbcs + rocotoboot -w FV3LAM_wflow.xml -d FV3LAM_wflow.db -v 10 -c 202307261800 -t get_extrn_lbcs (only when data is available) + rocotoboot -w FV3LAM_wflow.xml -d FV3LAM_wflow.db -v 10 -c 202307260300 -t get_extrn_ics + rocotoboot -w FV3LAM_wflow.xml -d FV3LAM_wflow.db -v 10 -c 202307261500 -t get_extrn_ics (only when data is available) + + Note that you may need to run ``rocotoboot`` for the task ``prep_cyc_spinup`` at 04z sequentially only if it is not launched: + + .. code-block:: console + + rocotoboot -w FV3LAM_wflow.xml -d FV3LAM_wflow.db -v 10 -c 202307260400 -t prep_cyc_spinup + + * On Hera: with ``config.DA.retro.hera.sh`` (in case of cycle_date=20230611) + + If you want to run beyond ``11z``, you should launch the ``get_extrn_lbcs`` tasks for ``12z`` and ``18z`` and the ``get_extrn_ics`` task for ``15z`` manually: + + .. code-block:: console + + rocotoboot -w FV3LAM_wflow.xml -d FV3LAM_wflow.db -v 10 -c 202306111200 -t get_extrn_lbcs + rocotoboot -w FV3LAM_wflow.xml -d FV3LAM_wflow.db -v 10 -c 202306111800 -t get_extrn_lbcs + rocotoboot -w FV3LAM_wflow.xml -d FV3LAM_wflow.db -v 10 -c 202306111500 -t get_extrn_ics + + Once both ``make_lbcs`` and ``make_ics`` tasks are complete, launch the ``prep_cyc_spinup`` task for ``03z`` manually: + + .. code-block:: console + + rocotoboot -w FV3LAM_wflow.xml -d FV3LAM_wflow.db -v 10 -c 202306110300 -t prep_cyc_spinup + + Keep monitoring and launching the workflow if ``USE_CRON_TO_RELAUNCH`` was NOT set to ``TRUE`` in ``config.sh``. If ``USE_CRON_TO_RELAUNCH`` was set to ``TRUE``, you should remove the crontab line manually once all tasks are complete. + + .. code-block:: console + + ./run_rocoto.sh + + * On Hera: with ``config.DA.ens.hera.sh`` (in case of cycle_date=20230610) + + Once the ``save_restart_ensinit_mem000X`` tasks are complete, launch the following tasks for ``06z`` manually: + + .. code-block:: console + + rocotoboot -w FV3LAM_wflow.xml -d FV3LAM_wflow.db -v 10 -c 202306100600 -t prep_cyc_spinup_ensinit_mem0001 + rocotoboot -w FV3LAM_wflow.xml -d FV3LAM_wflow.db -v 10 -c 202306100600 -t prep_cyc_spinup_ensinit_mem0002 + rocotoboot -w FV3LAM_wflow.xml -d FV3LAM_wflow.db -v 10 -c 202306100600 -t prep_cyc_spinup_ensinit_mem0003 + + Once the above three tasks are complete, launch the ``run_recenter_spinup`` task for ``06z`` manually: + + .. code-block:: console + + rocotoboot -w FV3LAM_wflow.xml -d FV3LAM_wflow.db -v 10 -c 202306100600 -t run_recenter_spinup + + Keep monitoring and launching the workflow if ``USE_CRON_TO_RELAUNCH`` was NOT set to ``TRUE`` in ``config.sh``: + + .. code-block:: console + + ./run_rocoto.sh + + .. note:: + You should manually launch the above tasks for ``18z`` as well (due to the incorrect path to the dependency ``nonvarcldana_complete.txt``). + + #. Check the status of your run with ``rocotostat``: + + .. code-block:: console + + rocotostat -w FV3LAM_wflow.xml -d FV3LAM_wflow.db -v 10 > test.log + diff --git a/doc/UsersGuide/source/index.rst b/doc/UsersGuide/source/index.rst index adf6cd36..cfd0ee79 100644 --- a/doc/UsersGuide/source/index.rst +++ b/doc/UsersGuide/source/index.rst @@ -11,4 +11,5 @@ RRFS-WORKFLOW Users Guide 1 Quickstart + Q2 modules From 5b8e85277a70d2d93fa189b92caa256032b195a9 Mon Sep 17 00:00:00 2001 From: Edward Hartnett Date: Sun, 6 Oct 2024 07:29:53 -0600 Subject: [PATCH 08/32] more docs work --- doc/UsersGuide/source/Q2.rst | 3 --- 1 file changed, 3 deletions(-) diff --git a/doc/UsersGuide/source/Q2.rst b/doc/UsersGuide/source/Q2.rst index 39b45bdd..4e622788 100644 --- a/doc/UsersGuide/source/Q2.rst +++ b/doc/UsersGuide/source/Q2.rst @@ -1,6 +1,3 @@ -.. _NCQuickstart: - -==================== Quick Start Guide ==================== From 7bb62e4ea2a8db9459f37c3270ea9cbf5c9fa7dc Mon Sep 17 00:00:00 2001 From: Edward Hartnett Date: Sun, 6 Oct 2024 07:30:53 -0600 Subject: [PATCH 09/32] more docs work --- doc/UsersGuide/source/Q2.rst | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/doc/UsersGuide/source/Q2.rst b/doc/UsersGuide/source/Q2.rst index 4e622788..030a3140 100644 --- a/doc/UsersGuide/source/Q2.rst +++ b/doc/UsersGuide/source/Q2.rst @@ -1,3 +1,28 @@ +ush +=== + +.. toctree:: + :maxdepth: 4 + + HWP_tools + UFS_plot_domains + blending_fv3 + chgres_cold2fv3 + create_diag_table_file + create_model_configure_file + create_ufs_configure_file + enspost_config + fill_jinja_template + fire_emiss_tools + fvcom_remap + generate_fire_emissions + get_crontab_contents + interp_tools + log_change + python_utils + rrfsfw_domain + set_namelist + Quick Start Guide ==================== From e7575cea2ead279a9148a626f74bdddd5aa217b7 Mon Sep 17 00:00:00 2001 From: Edward Hartnett Date: Sun, 6 Oct 2024 07:31:59 -0600 Subject: [PATCH 10/32] more docs work --- doc/UsersGuide/source/Q2.rst | 218 ----------------------------------- 1 file changed, 218 deletions(-) diff --git a/doc/UsersGuide/source/Q2.rst b/doc/UsersGuide/source/Q2.rst index 030a3140..45e89b0d 100644 --- a/doc/UsersGuide/source/Q2.rst +++ b/doc/UsersGuide/source/Q2.rst @@ -23,221 +23,3 @@ ush rrfsfw_domain set_namelist -Quick Start Guide -==================== - -This chapter provides a brief summary of how to build and run the RRFS-Workflow. - - -.. _QuickBuildRun: - -Building RRFS workflow -=============================================== - - #. Clone the ``main`` branch of the RRFS-Workflow from GitHub: - - .. code-block:: console - - git clone https://github.com/NOAA-EMC/rrfs-workflow.git - - #. Check out the external components: - - .. code-block:: console - - cd rrfs-workflow/sorc - ./manage_externals/checkout_externals - - #. Set up the build environment and build the executables: - - .. code-block:: console - - ./app_build.sh - - Alternatively, the above command can be followed by the platform (machine) name as follows: - - .. code-block:: console - - ./app_build.sh --platform= - - where ```` is ``wcoss2``, ``hera``, ``jet``, ``orion``, or ``hercules``. - - #. Move to the home directory (rrfs-workflow): - - .. code-block:: console - - cd .. - -Engineering Test: Non-DA -=============================================== - - #. Load the python environment: - - * On WCOSS2: - - .. code-block:: console - - source versions/run.ver - module use modulefiles - module load wflow_wcoss2 - - * On Hera | Jet | Orion | Hercules: - - .. code-block:: console - - module use modulefiles - module load wflow_ - conda activate workflow_tools - - where ```` is ``hera``, ``jet``, ``orion``, or ``hercules``. - - #. Copy the pre-defined configuration file: - - .. code-block:: console - - cd ush - cp sample_configs/non-DA_eng/config.nonDA...sh config.sh - - where ```` is ``grib2`` or ``netcdf``, and ```` is ``wcoss2``, ``hera``, ``jet``, ``orion``, or ``hercules``. Note that you may need to change ``ACCOUNT``, ``STMP``, or ``PTMP`` in the configuration file ``config.sh``. - - #. Generate the experiment workflow: - - .. code-block:: console - - ./generate_FV3LAM_wflow.sh - - #. Launch the workflow: - - .. code-block:: console - - cd ../../expt_dirs/test_nonDA - ./launch_FV3LAM_wflow.sh - - .. note:: - The workflow tasks will be submitted every three minutes by ``cron`` until the log output includes a ``Workflow status: SUCCESS`` message if you did not modify the following parameters in the configuration file: - - .. code-block:: console - - USE_CRON_TO_RELAUNCH="TRUE" - CRON_RELAUNCH_INTVL_MNTS="03" - - -Engineering Test: DA -=============================================== - - #. Load the python environment: - - * On WCOSS2: - - .. code-block:: console - - source versions/run.ver - module use modulefiles - module load wflow_wcoss2 - - * On Hera | Jet | Orion | Hercules : - - .. code-block:: console - - module use modulefiles - module load wflow_ - conda activate workflow_tools - - where ```` is ``hera``, ``jet``, ``orion``, or ``hercules``. - - #. Copy the pre-defined configuration file: - - .. code-block:: console - - cd ush - cp sample_configs/DA_eng/config.DA...sh config.sh - - where ```` is ``para`` with ```` is ``wcoss2``, or ```` is ``retro`` or ``ens`` with ```` is ``hera``. Note that you may need to change ``ACCOUNT`` in the configuration file ``config.sh``. - - .. note:: - For the real-time (``para``) test run on WCOSS2, you should replace ``DATE_FIRST_CYCL``, ``DATE_LAST_CYCL``, ``CYCLEMONTH``, and ``CYCLEDAY`` with those of Today's date. - - #. Generate the experiment workflow: - - .. code-block:: console - - ./generate_FV3LAM_wflow.sh - - #. Launch the workflow: - - .. code-block:: console - - cd ../../expt_dirs/rrfs_test_da - ./run_rocoto.sh - - #. Launch the following tasks as needed: - - * On WCOSS2: with ``config.DA.para.wcoss2.sh`` (in case of today=20230726) - - .. code-block:: console - - rocotoboot -w FV3LAM_wflow.xml -d FV3LAM_wflow.db -v 10 -c 202307260000 -t get_extrn_lbcs - rocotoboot -w FV3LAM_wflow.xml -d FV3LAM_wflow.db -v 10 -c 202307260600 -t get_extrn_lbcs - rocotoboot -w FV3LAM_wflow.xml -d FV3LAM_wflow.db -v 10 -c 202307261200 -t get_extrn_lbcs - rocotoboot -w FV3LAM_wflow.xml -d FV3LAM_wflow.db -v 10 -c 202307261800 -t get_extrn_lbcs (only when data is available) - rocotoboot -w FV3LAM_wflow.xml -d FV3LAM_wflow.db -v 10 -c 202307260300 -t get_extrn_ics - rocotoboot -w FV3LAM_wflow.xml -d FV3LAM_wflow.db -v 10 -c 202307261500 -t get_extrn_ics (only when data is available) - - Note that you may need to run ``rocotoboot`` for the task ``prep_cyc_spinup`` at 04z sequentially only if it is not launched: - - .. code-block:: console - - rocotoboot -w FV3LAM_wflow.xml -d FV3LAM_wflow.db -v 10 -c 202307260400 -t prep_cyc_spinup - - * On Hera: with ``config.DA.retro.hera.sh`` (in case of cycle_date=20230611) - - If you want to run beyond ``11z``, you should launch the ``get_extrn_lbcs`` tasks for ``12z`` and ``18z`` and the ``get_extrn_ics`` task for ``15z`` manually: - - .. code-block:: console - - rocotoboot -w FV3LAM_wflow.xml -d FV3LAM_wflow.db -v 10 -c 202306111200 -t get_extrn_lbcs - rocotoboot -w FV3LAM_wflow.xml -d FV3LAM_wflow.db -v 10 -c 202306111800 -t get_extrn_lbcs - rocotoboot -w FV3LAM_wflow.xml -d FV3LAM_wflow.db -v 10 -c 202306111500 -t get_extrn_ics - - Once both ``make_lbcs`` and ``make_ics`` tasks are complete, launch the ``prep_cyc_spinup`` task for ``03z`` manually: - - .. code-block:: console - - rocotoboot -w FV3LAM_wflow.xml -d FV3LAM_wflow.db -v 10 -c 202306110300 -t prep_cyc_spinup - - Keep monitoring and launching the workflow if ``USE_CRON_TO_RELAUNCH`` was NOT set to ``TRUE`` in ``config.sh``. If ``USE_CRON_TO_RELAUNCH`` was set to ``TRUE``, you should remove the crontab line manually once all tasks are complete. - - .. code-block:: console - - ./run_rocoto.sh - - * On Hera: with ``config.DA.ens.hera.sh`` (in case of cycle_date=20230610) - - Once the ``save_restart_ensinit_mem000X`` tasks are complete, launch the following tasks for ``06z`` manually: - - .. code-block:: console - - rocotoboot -w FV3LAM_wflow.xml -d FV3LAM_wflow.db -v 10 -c 202306100600 -t prep_cyc_spinup_ensinit_mem0001 - rocotoboot -w FV3LAM_wflow.xml -d FV3LAM_wflow.db -v 10 -c 202306100600 -t prep_cyc_spinup_ensinit_mem0002 - rocotoboot -w FV3LAM_wflow.xml -d FV3LAM_wflow.db -v 10 -c 202306100600 -t prep_cyc_spinup_ensinit_mem0003 - - Once the above three tasks are complete, launch the ``run_recenter_spinup`` task for ``06z`` manually: - - .. code-block:: console - - rocotoboot -w FV3LAM_wflow.xml -d FV3LAM_wflow.db -v 10 -c 202306100600 -t run_recenter_spinup - - Keep monitoring and launching the workflow if ``USE_CRON_TO_RELAUNCH`` was NOT set to ``TRUE`` in ``config.sh``: - - .. code-block:: console - - ./run_rocoto.sh - - .. note:: - You should manually launch the above tasks for ``18z`` as well (due to the incorrect path to the dependency ``nonvarcldana_complete.txt``). - - #. Check the status of your run with ``rocotostat``: - - .. code-block:: console - - rocotostat -w FV3LAM_wflow.xml -d FV3LAM_wflow.db -v 10 > test.log - From 3c4d4ad3c4099c6c27174a7822065e66101073bc Mon Sep 17 00:00:00 2001 From: Edward Hartnett Date: Sun, 6 Oct 2024 07:32:56 -0600 Subject: [PATCH 11/32] more docs work --- doc/UsersGuide/source/index.rst | 1 - 1 file changed, 1 deletion(-) diff --git a/doc/UsersGuide/source/index.rst b/doc/UsersGuide/source/index.rst index cfd0ee79..005bc87f 100644 --- a/doc/UsersGuide/source/index.rst +++ b/doc/UsersGuide/source/index.rst @@ -12,4 +12,3 @@ RRFS-WORKFLOW Users Guide 1 Quickstart Q2 - modules From 1e37abce46e9fd633a1d8680785bf321045f48e7 Mon Sep 17 00:00:00 2001 From: Edward Hartnett Date: Sun, 6 Oct 2024 07:34:19 -0600 Subject: [PATCH 12/32] more docs work --- doc/UsersGuide/source/{Q2.rst => Qmodules.rst} | 0 doc/UsersGuide/source/index.rst | 2 +- 2 files changed, 1 insertion(+), 1 deletion(-) rename doc/UsersGuide/source/{Q2.rst => Qmodules.rst} (100%) diff --git a/doc/UsersGuide/source/Q2.rst b/doc/UsersGuide/source/Qmodules.rst similarity index 100% rename from doc/UsersGuide/source/Q2.rst rename to doc/UsersGuide/source/Qmodules.rst diff --git a/doc/UsersGuide/source/index.rst b/doc/UsersGuide/source/index.rst index 005bc87f..d80e6707 100644 --- a/doc/UsersGuide/source/index.rst +++ b/doc/UsersGuide/source/index.rst @@ -11,4 +11,4 @@ RRFS-WORKFLOW Users Guide 1 Quickstart - Q2 + Qmodules From 11df1de7cc2b64a74485e9aae2e80a58ef4cd866 Mon Sep 17 00:00:00 2001 From: Edward Hartnett Date: Sun, 6 Oct 2024 07:39:45 -0600 Subject: [PATCH 13/32] more --- doc/UsersGuide/source/Qmodules.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/UsersGuide/source/Qmodules.rst b/doc/UsersGuide/source/Qmodules.rst index 45e89b0d..5d0dd454 100644 --- a/doc/UsersGuide/source/Qmodules.rst +++ b/doc/UsersGuide/source/Qmodules.rst @@ -2,7 +2,7 @@ ush === .. toctree:: - :maxdepth: 4 + :maxdepth: 2 HWP_tools UFS_plot_domains From dd745b75047714183cd27c1b2fa9e8f3effc6984 Mon Sep 17 00:00:00 2001 From: Edward Hartnett Date: Sun, 6 Oct 2024 08:11:48 -0600 Subject: [PATCH 14/32] adding files --- doc/UsersGuide/source/HWP_tools.rst | 7 ++ doc/UsersGuide/source/UFS_plot_domains.rst | 7 ++ doc/UsersGuide/source/blending_fv3.rst | 7 ++ doc/UsersGuide/source/chgres_cold2fv3.rst | 7 ++ .../source/create_diag_table_file.rst | 7 ++ .../source/create_model_configure_file.rst | 7 ++ .../source/create_ufs_configure_file.rst | 7 ++ doc/UsersGuide/source/enspost_config.rst | 7 ++ doc/UsersGuide/source/fill_jinja_template.rst | 7 ++ doc/UsersGuide/source/fire_emiss_tools.rst | 7 ++ doc/UsersGuide/source/fvcom_remap.rst | 7 ++ .../source/generate_fire_emissions.rst | 7 ++ .../source/get_crontab_contents.rst | 7 ++ doc/UsersGuide/source/interp_tools.rst | 7 ++ doc/UsersGuide/source/log_change.rst | 7 ++ doc/UsersGuide/source/modules.rst | 24 ++++ doc/UsersGuide/source/python_utils.rst | 117 ++++++++++++++++++ doc/UsersGuide/source/rrfsfw_domain.rst | 7 ++ doc/UsersGuide/source/set_namelist.rst | 7 ++ 19 files changed, 260 insertions(+) create mode 100644 doc/UsersGuide/source/HWP_tools.rst create mode 100644 doc/UsersGuide/source/UFS_plot_domains.rst create mode 100644 doc/UsersGuide/source/blending_fv3.rst create mode 100644 doc/UsersGuide/source/chgres_cold2fv3.rst create mode 100644 doc/UsersGuide/source/create_diag_table_file.rst create mode 100644 doc/UsersGuide/source/create_model_configure_file.rst create mode 100644 doc/UsersGuide/source/create_ufs_configure_file.rst create mode 100644 doc/UsersGuide/source/enspost_config.rst create mode 100644 doc/UsersGuide/source/fill_jinja_template.rst create mode 100644 doc/UsersGuide/source/fire_emiss_tools.rst create mode 100644 doc/UsersGuide/source/fvcom_remap.rst create mode 100644 doc/UsersGuide/source/generate_fire_emissions.rst create mode 100644 doc/UsersGuide/source/get_crontab_contents.rst create mode 100644 doc/UsersGuide/source/interp_tools.rst create mode 100644 doc/UsersGuide/source/log_change.rst create mode 100644 doc/UsersGuide/source/modules.rst create mode 100644 doc/UsersGuide/source/python_utils.rst create mode 100644 doc/UsersGuide/source/rrfsfw_domain.rst create mode 100644 doc/UsersGuide/source/set_namelist.rst diff --git a/doc/UsersGuide/source/HWP_tools.rst b/doc/UsersGuide/source/HWP_tools.rst new file mode 100644 index 00000000..b72c398d --- /dev/null +++ b/doc/UsersGuide/source/HWP_tools.rst @@ -0,0 +1,7 @@ +HWP\_tools module +================= + +.. automodule:: HWP_tools + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/UsersGuide/source/UFS_plot_domains.rst b/doc/UsersGuide/source/UFS_plot_domains.rst new file mode 100644 index 00000000..bd1b4231 --- /dev/null +++ b/doc/UsersGuide/source/UFS_plot_domains.rst @@ -0,0 +1,7 @@ +UFS\_plot\_domains module +========================= + +.. automodule:: UFS_plot_domains + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/UsersGuide/source/blending_fv3.rst b/doc/UsersGuide/source/blending_fv3.rst new file mode 100644 index 00000000..c5a8d924 --- /dev/null +++ b/doc/UsersGuide/source/blending_fv3.rst @@ -0,0 +1,7 @@ +blending\_fv3 module +==================== + +.. automodule:: blending_fv3 + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/UsersGuide/source/chgres_cold2fv3.rst b/doc/UsersGuide/source/chgres_cold2fv3.rst new file mode 100644 index 00000000..71ed3276 --- /dev/null +++ b/doc/UsersGuide/source/chgres_cold2fv3.rst @@ -0,0 +1,7 @@ +chgres\_cold2fv3 module +======================= + +.. automodule:: chgres_cold2fv3 + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/UsersGuide/source/create_diag_table_file.rst b/doc/UsersGuide/source/create_diag_table_file.rst new file mode 100644 index 00000000..5a317526 --- /dev/null +++ b/doc/UsersGuide/source/create_diag_table_file.rst @@ -0,0 +1,7 @@ +create\_diag\_table\_file module +================================ + +.. automodule:: create_diag_table_file + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/UsersGuide/source/create_model_configure_file.rst b/doc/UsersGuide/source/create_model_configure_file.rst new file mode 100644 index 00000000..7a8dd0cd --- /dev/null +++ b/doc/UsersGuide/source/create_model_configure_file.rst @@ -0,0 +1,7 @@ +create\_model\_configure\_file module +===================================== + +.. automodule:: create_model_configure_file + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/UsersGuide/source/create_ufs_configure_file.rst b/doc/UsersGuide/source/create_ufs_configure_file.rst new file mode 100644 index 00000000..56c17689 --- /dev/null +++ b/doc/UsersGuide/source/create_ufs_configure_file.rst @@ -0,0 +1,7 @@ +create\_ufs\_configure\_file module +=================================== + +.. automodule:: create_ufs_configure_file + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/UsersGuide/source/enspost_config.rst b/doc/UsersGuide/source/enspost_config.rst new file mode 100644 index 00000000..35891abd --- /dev/null +++ b/doc/UsersGuide/source/enspost_config.rst @@ -0,0 +1,7 @@ +enspost\_config module +====================== + +.. automodule:: enspost_config + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/UsersGuide/source/fill_jinja_template.rst b/doc/UsersGuide/source/fill_jinja_template.rst new file mode 100644 index 00000000..0c1c9e34 --- /dev/null +++ b/doc/UsersGuide/source/fill_jinja_template.rst @@ -0,0 +1,7 @@ +fill\_jinja\_template module +============================ + +.. automodule:: fill_jinja_template + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/UsersGuide/source/fire_emiss_tools.rst b/doc/UsersGuide/source/fire_emiss_tools.rst new file mode 100644 index 00000000..373d868c --- /dev/null +++ b/doc/UsersGuide/source/fire_emiss_tools.rst @@ -0,0 +1,7 @@ +fire\_emiss\_tools module +========================= + +.. automodule:: fire_emiss_tools + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/UsersGuide/source/fvcom_remap.rst b/doc/UsersGuide/source/fvcom_remap.rst new file mode 100644 index 00000000..d104fab6 --- /dev/null +++ b/doc/UsersGuide/source/fvcom_remap.rst @@ -0,0 +1,7 @@ +fvcom\_remap module +=================== + +.. automodule:: fvcom_remap + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/UsersGuide/source/generate_fire_emissions.rst b/doc/UsersGuide/source/generate_fire_emissions.rst new file mode 100644 index 00000000..f30ce48c --- /dev/null +++ b/doc/UsersGuide/source/generate_fire_emissions.rst @@ -0,0 +1,7 @@ +generate\_fire\_emissions module +================================ + +.. automodule:: generate_fire_emissions + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/UsersGuide/source/get_crontab_contents.rst b/doc/UsersGuide/source/get_crontab_contents.rst new file mode 100644 index 00000000..8e62d5a2 --- /dev/null +++ b/doc/UsersGuide/source/get_crontab_contents.rst @@ -0,0 +1,7 @@ +get\_crontab\_contents module +============================= + +.. automodule:: get_crontab_contents + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/UsersGuide/source/interp_tools.rst b/doc/UsersGuide/source/interp_tools.rst new file mode 100644 index 00000000..15a83551 --- /dev/null +++ b/doc/UsersGuide/source/interp_tools.rst @@ -0,0 +1,7 @@ +interp\_tools module +==================== + +.. automodule:: interp_tools + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/UsersGuide/source/log_change.rst b/doc/UsersGuide/source/log_change.rst new file mode 100644 index 00000000..34d44581 --- /dev/null +++ b/doc/UsersGuide/source/log_change.rst @@ -0,0 +1,7 @@ +log\_change module +================== + +.. automodule:: log_change + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/UsersGuide/source/modules.rst b/doc/UsersGuide/source/modules.rst new file mode 100644 index 00000000..56715f65 --- /dev/null +++ b/doc/UsersGuide/source/modules.rst @@ -0,0 +1,24 @@ +ush +=== + +.. toctree:: + :maxdepth: 4 + + HWP_tools + UFS_plot_domains + blending_fv3 + chgres_cold2fv3 + create_diag_table_file + create_model_configure_file + create_ufs_configure_file + enspost_config + fill_jinja_template + fire_emiss_tools + fvcom_remap + generate_fire_emissions + get_crontab_contents + interp_tools + log_change + python_utils + rrfsfw_domain + set_namelist diff --git a/doc/UsersGuide/source/python_utils.rst b/doc/UsersGuide/source/python_utils.rst new file mode 100644 index 00000000..3b6d8fdd --- /dev/null +++ b/doc/UsersGuide/source/python_utils.rst @@ -0,0 +1,117 @@ +python\_utils package +===================== + +Submodules +---------- + +python\_utils.check\_for\_preexist\_dir\_file module +---------------------------------------------------- + +.. automodule:: python_utils.check_for_preexist_dir_file + :members: + :undoc-members: + :show-inheritance: + +python\_utils.check\_var\_valid\_value module +--------------------------------------------- + +.. automodule:: python_utils.check_var_valid_value + :members: + :undoc-members: + :show-inheritance: + +python\_utils.config\_parser module +----------------------------------- + +.. automodule:: python_utils.config_parser + :members: + :undoc-members: + :show-inheritance: + +python\_utils.create\_symlink\_to\_file module +---------------------------------------------- + +.. automodule:: python_utils.create_symlink_to_file + :members: + :undoc-members: + :show-inheritance: + +python\_utils.define\_macos\_utilities module +--------------------------------------------- + +.. automodule:: python_utils.define_macos_utilities + :members: + :undoc-members: + :show-inheritance: + +python\_utils.environment module +-------------------------------- + +.. automodule:: python_utils.environment + :members: + :undoc-members: + :show-inheritance: + +python\_utils.filesys\_cmds\_vrfy module +---------------------------------------- + +.. automodule:: python_utils.filesys_cmds_vrfy + :members: + :undoc-members: + :show-inheritance: + +python\_utils.fv3write\_parms\_lambert module +--------------------------------------------- + +.. automodule:: python_utils.fv3write_parms_lambert + :members: + :undoc-members: + :show-inheritance: + +python\_utils.misc module +------------------------- + +.. automodule:: python_utils.misc + :members: + :undoc-members: + :show-inheritance: + +python\_utils.print\_input\_args module +--------------------------------------- + +.. automodule:: python_utils.print_input_args + :members: + :undoc-members: + :show-inheritance: + +python\_utils.print\_msg module +------------------------------- + +.. automodule:: python_utils.print_msg + :members: + :undoc-members: + :show-inheritance: + +python\_utils.run\_command module +--------------------------------- + +.. automodule:: python_utils.run_command + :members: + :undoc-members: + :show-inheritance: + +python\_utils.xml\_parser module +-------------------------------- + +.. automodule:: python_utils.xml_parser + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: python_utils + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/UsersGuide/source/rrfsfw_domain.rst b/doc/UsersGuide/source/rrfsfw_domain.rst new file mode 100644 index 00000000..6ada6a27 --- /dev/null +++ b/doc/UsersGuide/source/rrfsfw_domain.rst @@ -0,0 +1,7 @@ +rrfsfw\_domain module +===================== + +.. automodule:: rrfsfw_domain + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/UsersGuide/source/set_namelist.rst b/doc/UsersGuide/source/set_namelist.rst new file mode 100644 index 00000000..1245a45b --- /dev/null +++ b/doc/UsersGuide/source/set_namelist.rst @@ -0,0 +1,7 @@ +set\_namelist module +==================== + +.. automodule:: set_namelist + :members: + :undoc-members: + :show-inheritance: From 51afbcb80a8f8e109da0423c09dd95ae78f068fd Mon Sep 17 00:00:00 2001 From: Edward Hartnett Date: Mon, 7 Oct 2024 03:54:15 -0600 Subject: [PATCH 15/32] more work --- doc/UsersGuide/source/index.rst | 2 +- doc/UsersGuide/source/modules.rst | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/doc/UsersGuide/source/index.rst b/doc/UsersGuide/source/index.rst index d80e6707..adf6cd36 100644 --- a/doc/UsersGuide/source/index.rst +++ b/doc/UsersGuide/source/index.rst @@ -11,4 +11,4 @@ RRFS-WORKFLOW Users Guide 1 Quickstart - Qmodules + modules diff --git a/doc/UsersGuide/source/modules.rst b/doc/UsersGuide/source/modules.rst index 56715f65..5d0dd454 100644 --- a/doc/UsersGuide/source/modules.rst +++ b/doc/UsersGuide/source/modules.rst @@ -2,7 +2,7 @@ ush === .. toctree:: - :maxdepth: 4 + :maxdepth: 2 HWP_tools UFS_plot_domains @@ -22,3 +22,4 @@ ush python_utils rrfsfw_domain set_namelist + From 9d1abe3984fcb73cf221d5d942bf4664a6bb9803 Mon Sep 17 00:00:00 2001 From: Edward Hartnett Date: Mon, 7 Oct 2024 03:56:56 -0600 Subject: [PATCH 16/32] more work --- doc/UsersGuide/source/modules.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/UsersGuide/source/modules.rst b/doc/UsersGuide/source/modules.rst index 5d0dd454..bae37d64 100644 --- a/doc/UsersGuide/source/modules.rst +++ b/doc/UsersGuide/source/modules.rst @@ -1,5 +1,5 @@ -ush -=== +Utility Scripts +=============== .. toctree:: :maxdepth: 2 From 4dcb01d3b26e944f9da1505a82da5876d5ceb17d Mon Sep 17 00:00:00 2001 From: Edward Hartnett Date: Mon, 7 Oct 2024 04:01:38 -0600 Subject: [PATCH 17/32] more work --- doc/UsersGuide/source/index.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/UsersGuide/source/index.rst b/doc/UsersGuide/source/index.rst index adf6cd36..276f0499 100644 --- a/doc/UsersGuide/source/index.rst +++ b/doc/UsersGuide/source/index.rst @@ -2,7 +2,7 @@ You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. -RRFS-WORKFLOW Users Guide 1 +RRFS-WORKFLOW Users Guide ======================================= .. toctree:: From 2bb5cc6f26f289d3256ab4f6e251cc0db08a6b3d Mon Sep 17 00:00:00 2001 From: Edward Hartnett Date: Mon, 7 Oct 2024 04:04:15 -0600 Subject: [PATCH 18/32] renamed directory --- .readthedocs.yaml | 4 ++-- {doc => docs}/README.xml_templating.md | 0 {doc => docs}/Setup-RRFS.md | 0 {doc => docs}/Setup-RTMA.md | 0 {doc => docs}/UsersGuide/Makefile | 0 {doc => docs}/UsersGuide/README | 0 {doc => docs}/UsersGuide/make.bat | 0 {doc => docs}/UsersGuide/requirements.txt | 0 {doc => docs}/UsersGuide/source/HWP_tools.rst | 0 {doc => docs}/UsersGuide/source/Qmodules.rst | 0 {doc => docs}/UsersGuide/source/Quickstart.rst | 0 .../UsersGuide/source/UFS_plot_domains.rst | 0 {doc => docs}/UsersGuide/source/_static/custom.css | 0 .../UsersGuide/source/_static/theme_overrides.css | 0 .../UsersGuide/source/_templates/.gitignore | 0 {doc => docs}/UsersGuide/source/blending_fv3.rst | 0 {doc => docs}/UsersGuide/source/chgres_cold2fv3.rst | 0 {doc => docs}/UsersGuide/source/conf.py | 0 .../UsersGuide/source/create_diag_table_file.rst | 0 .../source/create_model_configure_file.rst | 0 .../UsersGuide/source/create_ufs_configure_file.rst | 0 {doc => docs}/UsersGuide/source/enspost_config.rst | 0 .../UsersGuide/source/fill_jinja_template.rst | 0 .../UsersGuide/source/fire_emiss_tools.rst | 0 {doc => docs}/UsersGuide/source/fvcom_remap.rst | 0 .../UsersGuide/source/generate_fire_emissions.rst | 0 .../UsersGuide/source/get_crontab_contents.rst | 0 {doc => docs}/UsersGuide/source/index.rst | 0 {doc => docs}/UsersGuide/source/interp_tools.rst | 0 {doc => docs}/UsersGuide/source/log_change.rst | 0 {doc => docs}/UsersGuide/source/modules.rst | 0 {doc => docs}/UsersGuide/source/python_utils.rst | 0 {doc => docs}/UsersGuide/source/references.bib | 0 {doc => docs}/UsersGuide/source/rrfsfw_domain.rst | 0 {doc => docs}/UsersGuide/source/set_namelist.rst | 0 {doc => docs}/UsersGuide/source/tables/.DS_Store | Bin 36 files changed, 2 insertions(+), 2 deletions(-) rename {doc => docs}/README.xml_templating.md (100%) rename {doc => docs}/Setup-RRFS.md (100%) rename {doc => docs}/Setup-RTMA.md (100%) rename {doc => docs}/UsersGuide/Makefile (100%) rename {doc => docs}/UsersGuide/README (100%) rename {doc => docs}/UsersGuide/make.bat (100%) rename {doc => docs}/UsersGuide/requirements.txt (100%) rename {doc => docs}/UsersGuide/source/HWP_tools.rst (100%) rename {doc => docs}/UsersGuide/source/Qmodules.rst (100%) rename {doc => docs}/UsersGuide/source/Quickstart.rst (100%) rename {doc => docs}/UsersGuide/source/UFS_plot_domains.rst (100%) rename {doc => docs}/UsersGuide/source/_static/custom.css (100%) rename {doc => docs}/UsersGuide/source/_static/theme_overrides.css (100%) rename {doc => docs}/UsersGuide/source/_templates/.gitignore (100%) rename {doc => docs}/UsersGuide/source/blending_fv3.rst (100%) rename {doc => docs}/UsersGuide/source/chgres_cold2fv3.rst (100%) rename {doc => docs}/UsersGuide/source/conf.py (100%) rename {doc => docs}/UsersGuide/source/create_diag_table_file.rst (100%) rename {doc => docs}/UsersGuide/source/create_model_configure_file.rst (100%) rename {doc => docs}/UsersGuide/source/create_ufs_configure_file.rst (100%) rename {doc => docs}/UsersGuide/source/enspost_config.rst (100%) rename {doc => docs}/UsersGuide/source/fill_jinja_template.rst (100%) rename {doc => docs}/UsersGuide/source/fire_emiss_tools.rst (100%) rename {doc => docs}/UsersGuide/source/fvcom_remap.rst (100%) rename {doc => docs}/UsersGuide/source/generate_fire_emissions.rst (100%) rename {doc => docs}/UsersGuide/source/get_crontab_contents.rst (100%) rename {doc => docs}/UsersGuide/source/index.rst (100%) rename {doc => docs}/UsersGuide/source/interp_tools.rst (100%) rename {doc => docs}/UsersGuide/source/log_change.rst (100%) rename {doc => docs}/UsersGuide/source/modules.rst (100%) rename {doc => docs}/UsersGuide/source/python_utils.rst (100%) rename {doc => docs}/UsersGuide/source/references.bib (100%) rename {doc => docs}/UsersGuide/source/rrfsfw_domain.rst (100%) rename {doc => docs}/UsersGuide/source/set_namelist.rst (100%) rename {doc => docs}/UsersGuide/source/tables/.DS_Store (100%) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 60d4d66a..544fad0e 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -17,7 +17,7 @@ build: # Build documentation in the docs/ directory with Sphinx sphinx: - configuration: doc/UsersGuide/source/conf.py + configuration: docs/UsersGuide/source/conf.py # If using Sphinx, optionally build your docs in additional formats such as PDF # formats: @@ -26,7 +26,7 @@ sphinx: # Optionally declare the Python requirements required to build your docs python: install: - - requirements: doc/UsersGuide/requirements.txt + - requirements: docs/UsersGuide/requirements.txt submodules: include: diff --git a/doc/README.xml_templating.md b/docs/README.xml_templating.md similarity index 100% rename from doc/README.xml_templating.md rename to docs/README.xml_templating.md diff --git a/doc/Setup-RRFS.md b/docs/Setup-RRFS.md similarity index 100% rename from doc/Setup-RRFS.md rename to docs/Setup-RRFS.md diff --git a/doc/Setup-RTMA.md b/docs/Setup-RTMA.md similarity index 100% rename from doc/Setup-RTMA.md rename to docs/Setup-RTMA.md diff --git a/doc/UsersGuide/Makefile b/docs/UsersGuide/Makefile similarity index 100% rename from doc/UsersGuide/Makefile rename to docs/UsersGuide/Makefile diff --git a/doc/UsersGuide/README b/docs/UsersGuide/README similarity index 100% rename from doc/UsersGuide/README rename to docs/UsersGuide/README diff --git a/doc/UsersGuide/make.bat b/docs/UsersGuide/make.bat similarity index 100% rename from doc/UsersGuide/make.bat rename to docs/UsersGuide/make.bat diff --git a/doc/UsersGuide/requirements.txt b/docs/UsersGuide/requirements.txt similarity index 100% rename from doc/UsersGuide/requirements.txt rename to docs/UsersGuide/requirements.txt diff --git a/doc/UsersGuide/source/HWP_tools.rst b/docs/UsersGuide/source/HWP_tools.rst similarity index 100% rename from doc/UsersGuide/source/HWP_tools.rst rename to docs/UsersGuide/source/HWP_tools.rst diff --git a/doc/UsersGuide/source/Qmodules.rst b/docs/UsersGuide/source/Qmodules.rst similarity index 100% rename from doc/UsersGuide/source/Qmodules.rst rename to docs/UsersGuide/source/Qmodules.rst diff --git a/doc/UsersGuide/source/Quickstart.rst b/docs/UsersGuide/source/Quickstart.rst similarity index 100% rename from doc/UsersGuide/source/Quickstart.rst rename to docs/UsersGuide/source/Quickstart.rst diff --git a/doc/UsersGuide/source/UFS_plot_domains.rst b/docs/UsersGuide/source/UFS_plot_domains.rst similarity index 100% rename from doc/UsersGuide/source/UFS_plot_domains.rst rename to docs/UsersGuide/source/UFS_plot_domains.rst diff --git a/doc/UsersGuide/source/_static/custom.css b/docs/UsersGuide/source/_static/custom.css similarity index 100% rename from doc/UsersGuide/source/_static/custom.css rename to docs/UsersGuide/source/_static/custom.css diff --git a/doc/UsersGuide/source/_static/theme_overrides.css b/docs/UsersGuide/source/_static/theme_overrides.css similarity index 100% rename from doc/UsersGuide/source/_static/theme_overrides.css rename to docs/UsersGuide/source/_static/theme_overrides.css diff --git a/doc/UsersGuide/source/_templates/.gitignore b/docs/UsersGuide/source/_templates/.gitignore similarity index 100% rename from doc/UsersGuide/source/_templates/.gitignore rename to docs/UsersGuide/source/_templates/.gitignore diff --git a/doc/UsersGuide/source/blending_fv3.rst b/docs/UsersGuide/source/blending_fv3.rst similarity index 100% rename from doc/UsersGuide/source/blending_fv3.rst rename to docs/UsersGuide/source/blending_fv3.rst diff --git a/doc/UsersGuide/source/chgres_cold2fv3.rst b/docs/UsersGuide/source/chgres_cold2fv3.rst similarity index 100% rename from doc/UsersGuide/source/chgres_cold2fv3.rst rename to docs/UsersGuide/source/chgres_cold2fv3.rst diff --git a/doc/UsersGuide/source/conf.py b/docs/UsersGuide/source/conf.py similarity index 100% rename from doc/UsersGuide/source/conf.py rename to docs/UsersGuide/source/conf.py diff --git a/doc/UsersGuide/source/create_diag_table_file.rst b/docs/UsersGuide/source/create_diag_table_file.rst similarity index 100% rename from doc/UsersGuide/source/create_diag_table_file.rst rename to docs/UsersGuide/source/create_diag_table_file.rst diff --git a/doc/UsersGuide/source/create_model_configure_file.rst b/docs/UsersGuide/source/create_model_configure_file.rst similarity index 100% rename from doc/UsersGuide/source/create_model_configure_file.rst rename to docs/UsersGuide/source/create_model_configure_file.rst diff --git a/doc/UsersGuide/source/create_ufs_configure_file.rst b/docs/UsersGuide/source/create_ufs_configure_file.rst similarity index 100% rename from doc/UsersGuide/source/create_ufs_configure_file.rst rename to docs/UsersGuide/source/create_ufs_configure_file.rst diff --git a/doc/UsersGuide/source/enspost_config.rst b/docs/UsersGuide/source/enspost_config.rst similarity index 100% rename from doc/UsersGuide/source/enspost_config.rst rename to docs/UsersGuide/source/enspost_config.rst diff --git a/doc/UsersGuide/source/fill_jinja_template.rst b/docs/UsersGuide/source/fill_jinja_template.rst similarity index 100% rename from doc/UsersGuide/source/fill_jinja_template.rst rename to docs/UsersGuide/source/fill_jinja_template.rst diff --git a/doc/UsersGuide/source/fire_emiss_tools.rst b/docs/UsersGuide/source/fire_emiss_tools.rst similarity index 100% rename from doc/UsersGuide/source/fire_emiss_tools.rst rename to docs/UsersGuide/source/fire_emiss_tools.rst diff --git a/doc/UsersGuide/source/fvcom_remap.rst b/docs/UsersGuide/source/fvcom_remap.rst similarity index 100% rename from doc/UsersGuide/source/fvcom_remap.rst rename to docs/UsersGuide/source/fvcom_remap.rst diff --git a/doc/UsersGuide/source/generate_fire_emissions.rst b/docs/UsersGuide/source/generate_fire_emissions.rst similarity index 100% rename from doc/UsersGuide/source/generate_fire_emissions.rst rename to docs/UsersGuide/source/generate_fire_emissions.rst diff --git a/doc/UsersGuide/source/get_crontab_contents.rst b/docs/UsersGuide/source/get_crontab_contents.rst similarity index 100% rename from doc/UsersGuide/source/get_crontab_contents.rst rename to docs/UsersGuide/source/get_crontab_contents.rst diff --git a/doc/UsersGuide/source/index.rst b/docs/UsersGuide/source/index.rst similarity index 100% rename from doc/UsersGuide/source/index.rst rename to docs/UsersGuide/source/index.rst diff --git a/doc/UsersGuide/source/interp_tools.rst b/docs/UsersGuide/source/interp_tools.rst similarity index 100% rename from doc/UsersGuide/source/interp_tools.rst rename to docs/UsersGuide/source/interp_tools.rst diff --git a/doc/UsersGuide/source/log_change.rst b/docs/UsersGuide/source/log_change.rst similarity index 100% rename from doc/UsersGuide/source/log_change.rst rename to docs/UsersGuide/source/log_change.rst diff --git a/doc/UsersGuide/source/modules.rst b/docs/UsersGuide/source/modules.rst similarity index 100% rename from doc/UsersGuide/source/modules.rst rename to docs/UsersGuide/source/modules.rst diff --git a/doc/UsersGuide/source/python_utils.rst b/docs/UsersGuide/source/python_utils.rst similarity index 100% rename from doc/UsersGuide/source/python_utils.rst rename to docs/UsersGuide/source/python_utils.rst diff --git a/doc/UsersGuide/source/references.bib b/docs/UsersGuide/source/references.bib similarity index 100% rename from doc/UsersGuide/source/references.bib rename to docs/UsersGuide/source/references.bib diff --git a/doc/UsersGuide/source/rrfsfw_domain.rst b/docs/UsersGuide/source/rrfsfw_domain.rst similarity index 100% rename from doc/UsersGuide/source/rrfsfw_domain.rst rename to docs/UsersGuide/source/rrfsfw_domain.rst diff --git a/doc/UsersGuide/source/set_namelist.rst b/docs/UsersGuide/source/set_namelist.rst similarity index 100% rename from doc/UsersGuide/source/set_namelist.rst rename to docs/UsersGuide/source/set_namelist.rst diff --git a/doc/UsersGuide/source/tables/.DS_Store b/docs/UsersGuide/source/tables/.DS_Store similarity index 100% rename from doc/UsersGuide/source/tables/.DS_Store rename to docs/UsersGuide/source/tables/.DS_Store From cc014c0615b9897b0997fb348cbc43a2272d9adc Mon Sep 17 00:00:00 2001 From: Edward Hartnett Date: Mon, 7 Oct 2024 04:09:59 -0600 Subject: [PATCH 19/32] moving stuff --- .readthedocs.yaml | 2 +- docs/{UsersGuide => }/requirements.txt | 0 2 files changed, 1 insertion(+), 1 deletion(-) rename docs/{UsersGuide => }/requirements.txt (100%) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 544fad0e..9370f9e7 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -26,7 +26,7 @@ sphinx: # Optionally declare the Python requirements required to build your docs python: install: - - requirements: docs/UsersGuide/requirements.txt + - requirements: docs/requirements.txt submodules: include: diff --git a/docs/UsersGuide/requirements.txt b/docs/requirements.txt similarity index 100% rename from docs/UsersGuide/requirements.txt rename to docs/requirements.txt From fc587ecb7e5de32ed7138bd83f7f28406dcd4f6f Mon Sep 17 00:00:00 2001 From: Edward Hartnett Date: Mon, 7 Oct 2024 04:16:18 -0600 Subject: [PATCH 20/32] more moving --- .readthedocs.yaml | 2 +- docs/{UsersGuide => }/source/HWP_tools.rst | 0 docs/{UsersGuide => }/source/Qmodules.rst | 0 docs/{UsersGuide => }/source/Quickstart.rst | 0 docs/{UsersGuide => }/source/UFS_plot_domains.rst | 0 docs/{UsersGuide => }/source/_static/custom.css | 0 docs/{UsersGuide => }/source/_static/theme_overrides.css | 0 docs/{UsersGuide => }/source/blending_fv3.rst | 0 docs/{UsersGuide => }/source/chgres_cold2fv3.rst | 0 docs/{UsersGuide => }/source/conf.py | 0 docs/{UsersGuide => }/source/create_diag_table_file.rst | 0 docs/{UsersGuide => }/source/create_model_configure_file.rst | 0 docs/{UsersGuide => }/source/create_ufs_configure_file.rst | 0 docs/{UsersGuide => }/source/enspost_config.rst | 0 docs/{UsersGuide => }/source/fill_jinja_template.rst | 0 docs/{UsersGuide => }/source/fire_emiss_tools.rst | 0 docs/{UsersGuide => }/source/fvcom_remap.rst | 0 docs/{UsersGuide => }/source/generate_fire_emissions.rst | 0 docs/{UsersGuide => }/source/get_crontab_contents.rst | 0 docs/{UsersGuide => }/source/index.rst | 0 docs/{UsersGuide => }/source/interp_tools.rst | 0 docs/{UsersGuide => }/source/log_change.rst | 0 docs/{UsersGuide => }/source/modules.rst | 0 docs/{UsersGuide => }/source/python_utils.rst | 0 docs/{UsersGuide => }/source/references.bib | 0 docs/{UsersGuide => }/source/rrfsfw_domain.rst | 0 docs/{UsersGuide => }/source/set_namelist.rst | 0 27 files changed, 1 insertion(+), 1 deletion(-) rename docs/{UsersGuide => }/source/HWP_tools.rst (100%) rename docs/{UsersGuide => }/source/Qmodules.rst (100%) rename docs/{UsersGuide => }/source/Quickstart.rst (100%) rename docs/{UsersGuide => }/source/UFS_plot_domains.rst (100%) rename docs/{UsersGuide => }/source/_static/custom.css (100%) rename docs/{UsersGuide => }/source/_static/theme_overrides.css (100%) rename docs/{UsersGuide => }/source/blending_fv3.rst (100%) rename docs/{UsersGuide => }/source/chgres_cold2fv3.rst (100%) rename docs/{UsersGuide => }/source/conf.py (100%) rename docs/{UsersGuide => }/source/create_diag_table_file.rst (100%) rename docs/{UsersGuide => }/source/create_model_configure_file.rst (100%) rename docs/{UsersGuide => }/source/create_ufs_configure_file.rst (100%) rename docs/{UsersGuide => }/source/enspost_config.rst (100%) rename docs/{UsersGuide => }/source/fill_jinja_template.rst (100%) rename docs/{UsersGuide => }/source/fire_emiss_tools.rst (100%) rename docs/{UsersGuide => }/source/fvcom_remap.rst (100%) rename docs/{UsersGuide => }/source/generate_fire_emissions.rst (100%) rename docs/{UsersGuide => }/source/get_crontab_contents.rst (100%) rename docs/{UsersGuide => }/source/index.rst (100%) rename docs/{UsersGuide => }/source/interp_tools.rst (100%) rename docs/{UsersGuide => }/source/log_change.rst (100%) rename docs/{UsersGuide => }/source/modules.rst (100%) rename docs/{UsersGuide => }/source/python_utils.rst (100%) rename docs/{UsersGuide => }/source/references.bib (100%) rename docs/{UsersGuide => }/source/rrfsfw_domain.rst (100%) rename docs/{UsersGuide => }/source/set_namelist.rst (100%) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 9370f9e7..cdeeb1b7 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -17,7 +17,7 @@ build: # Build documentation in the docs/ directory with Sphinx sphinx: - configuration: docs/UsersGuide/source/conf.py + configuration: docs/source/conf.py # If using Sphinx, optionally build your docs in additional formats such as PDF # formats: diff --git a/docs/UsersGuide/source/HWP_tools.rst b/docs/source/HWP_tools.rst similarity index 100% rename from docs/UsersGuide/source/HWP_tools.rst rename to docs/source/HWP_tools.rst diff --git a/docs/UsersGuide/source/Qmodules.rst b/docs/source/Qmodules.rst similarity index 100% rename from docs/UsersGuide/source/Qmodules.rst rename to docs/source/Qmodules.rst diff --git a/docs/UsersGuide/source/Quickstart.rst b/docs/source/Quickstart.rst similarity index 100% rename from docs/UsersGuide/source/Quickstart.rst rename to docs/source/Quickstart.rst diff --git a/docs/UsersGuide/source/UFS_plot_domains.rst b/docs/source/UFS_plot_domains.rst similarity index 100% rename from docs/UsersGuide/source/UFS_plot_domains.rst rename to docs/source/UFS_plot_domains.rst diff --git a/docs/UsersGuide/source/_static/custom.css b/docs/source/_static/custom.css similarity index 100% rename from docs/UsersGuide/source/_static/custom.css rename to docs/source/_static/custom.css diff --git a/docs/UsersGuide/source/_static/theme_overrides.css b/docs/source/_static/theme_overrides.css similarity index 100% rename from docs/UsersGuide/source/_static/theme_overrides.css rename to docs/source/_static/theme_overrides.css diff --git a/docs/UsersGuide/source/blending_fv3.rst b/docs/source/blending_fv3.rst similarity index 100% rename from docs/UsersGuide/source/blending_fv3.rst rename to docs/source/blending_fv3.rst diff --git a/docs/UsersGuide/source/chgres_cold2fv3.rst b/docs/source/chgres_cold2fv3.rst similarity index 100% rename from docs/UsersGuide/source/chgres_cold2fv3.rst rename to docs/source/chgres_cold2fv3.rst diff --git a/docs/UsersGuide/source/conf.py b/docs/source/conf.py similarity index 100% rename from docs/UsersGuide/source/conf.py rename to docs/source/conf.py diff --git a/docs/UsersGuide/source/create_diag_table_file.rst b/docs/source/create_diag_table_file.rst similarity index 100% rename from docs/UsersGuide/source/create_diag_table_file.rst rename to docs/source/create_diag_table_file.rst diff --git a/docs/UsersGuide/source/create_model_configure_file.rst b/docs/source/create_model_configure_file.rst similarity index 100% rename from docs/UsersGuide/source/create_model_configure_file.rst rename to docs/source/create_model_configure_file.rst diff --git a/docs/UsersGuide/source/create_ufs_configure_file.rst b/docs/source/create_ufs_configure_file.rst similarity index 100% rename from docs/UsersGuide/source/create_ufs_configure_file.rst rename to docs/source/create_ufs_configure_file.rst diff --git a/docs/UsersGuide/source/enspost_config.rst b/docs/source/enspost_config.rst similarity index 100% rename from docs/UsersGuide/source/enspost_config.rst rename to docs/source/enspost_config.rst diff --git a/docs/UsersGuide/source/fill_jinja_template.rst b/docs/source/fill_jinja_template.rst similarity index 100% rename from docs/UsersGuide/source/fill_jinja_template.rst rename to docs/source/fill_jinja_template.rst diff --git a/docs/UsersGuide/source/fire_emiss_tools.rst b/docs/source/fire_emiss_tools.rst similarity index 100% rename from docs/UsersGuide/source/fire_emiss_tools.rst rename to docs/source/fire_emiss_tools.rst diff --git a/docs/UsersGuide/source/fvcom_remap.rst b/docs/source/fvcom_remap.rst similarity index 100% rename from docs/UsersGuide/source/fvcom_remap.rst rename to docs/source/fvcom_remap.rst diff --git a/docs/UsersGuide/source/generate_fire_emissions.rst b/docs/source/generate_fire_emissions.rst similarity index 100% rename from docs/UsersGuide/source/generate_fire_emissions.rst rename to docs/source/generate_fire_emissions.rst diff --git a/docs/UsersGuide/source/get_crontab_contents.rst b/docs/source/get_crontab_contents.rst similarity index 100% rename from docs/UsersGuide/source/get_crontab_contents.rst rename to docs/source/get_crontab_contents.rst diff --git a/docs/UsersGuide/source/index.rst b/docs/source/index.rst similarity index 100% rename from docs/UsersGuide/source/index.rst rename to docs/source/index.rst diff --git a/docs/UsersGuide/source/interp_tools.rst b/docs/source/interp_tools.rst similarity index 100% rename from docs/UsersGuide/source/interp_tools.rst rename to docs/source/interp_tools.rst diff --git a/docs/UsersGuide/source/log_change.rst b/docs/source/log_change.rst similarity index 100% rename from docs/UsersGuide/source/log_change.rst rename to docs/source/log_change.rst diff --git a/docs/UsersGuide/source/modules.rst b/docs/source/modules.rst similarity index 100% rename from docs/UsersGuide/source/modules.rst rename to docs/source/modules.rst diff --git a/docs/UsersGuide/source/python_utils.rst b/docs/source/python_utils.rst similarity index 100% rename from docs/UsersGuide/source/python_utils.rst rename to docs/source/python_utils.rst diff --git a/docs/UsersGuide/source/references.bib b/docs/source/references.bib similarity index 100% rename from docs/UsersGuide/source/references.bib rename to docs/source/references.bib diff --git a/docs/UsersGuide/source/rrfsfw_domain.rst b/docs/source/rrfsfw_domain.rst similarity index 100% rename from docs/UsersGuide/source/rrfsfw_domain.rst rename to docs/source/rrfsfw_domain.rst diff --git a/docs/UsersGuide/source/set_namelist.rst b/docs/source/set_namelist.rst similarity index 100% rename from docs/UsersGuide/source/set_namelist.rst rename to docs/source/set_namelist.rst From 9e4051c28a6a0184e26a6d437fee7fb93fb06c15 Mon Sep 17 00:00:00 2001 From: Edward Hartnett Date: Mon, 7 Oct 2024 04:18:09 -0600 Subject: [PATCH 21/32] more moving --- docs/source/conf.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/conf.py b/docs/source/conf.py index f7b71492..79adf640 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -15,7 +15,7 @@ import os import sys sys.path.insert(0, os.path.abspath('.')) -sys.path.insert(0, os.path.abspath('../../../ush')) +sys.path.insert(0, os.path.abspath('../../ush')) # -- Project information ----------------------------------------------------- From 016153f7aa99681cc5aacd3b26362cc1773b2438 Mon Sep 17 00:00:00 2001 From: Edward Hartnett Date: Mon, 7 Oct 2024 04:49:14 -0600 Subject: [PATCH 22/32] more work simplifing build --- docs/{UsersGuide => }/Makefile | 0 docs/{UsersGuide => }/README | 0 docs/UsersGuide/source/_templates/.gitignore | 4 ---- docs/UsersGuide/source/tables/.DS_Store | Bin 6148 -> 0 bytes docs/{UsersGuide => }/make.bat | 0 5 files changed, 4 deletions(-) rename docs/{UsersGuide => }/Makefile (100%) rename docs/{UsersGuide => }/README (100%) delete mode 100644 docs/UsersGuide/source/_templates/.gitignore delete mode 100644 docs/UsersGuide/source/tables/.DS_Store rename docs/{UsersGuide => }/make.bat (100%) diff --git a/docs/UsersGuide/Makefile b/docs/Makefile similarity index 100% rename from docs/UsersGuide/Makefile rename to docs/Makefile diff --git a/docs/UsersGuide/README b/docs/README similarity index 100% rename from docs/UsersGuide/README rename to docs/README diff --git a/docs/UsersGuide/source/_templates/.gitignore b/docs/UsersGuide/source/_templates/.gitignore deleted file mode 100644 index 5e7d2734..00000000 --- a/docs/UsersGuide/source/_templates/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/docs/UsersGuide/source/tables/.DS_Store b/docs/UsersGuide/source/tables/.DS_Store deleted file mode 100644 index c478f9e8ab8ca699042953931ba6347205dab9d8..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 6148 zcmeHK%}N6?5dKDcsCux12QR`tLBTgzYkLqxiuLDM?T;WVRBRQGd-olD1)so^PvuF! znFQIjTM!Q-Iu49j1mtS%JPSL~-rkL$#li?tn4A_&$ggg^p-b`#U8@R+3?$I~Q zxbyqS=wW1a2JAAfS;(-79*%IvxI?xb;{Y9;vNq#MGGMMT^9-5qt~?VweIrlRinbT# z>2hAZug*svzLBSDKChqhtdNtj@u|N_6%)$nV}a3fM8z1!T`__QT>cpYyt7s6YXRLl z1I~am@WFtd4+&K3q@>n=1;6UBn{}+8E^*53@nFgL+}62;`e_!$ZO7kGw`PvkXpOf zZgENRZk=14-n9w!oT{Sz@_-gX6R%?{=vBN$HDOz#1!5X84@eKi{|FcjZk&N1W#Ap5 ChK<_* diff --git a/docs/UsersGuide/make.bat b/docs/make.bat similarity index 100% rename from docs/UsersGuide/make.bat rename to docs/make.bat From 4867639448658fec655816959064ddf50f189a98 Mon Sep 17 00:00:00 2001 From: Edward Hartnett Date: Mon, 7 Oct 2024 04:52:05 -0600 Subject: [PATCH 23/32] changed workflow --- .github/workflows/docs.yml | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 494b3864..37e93505 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -32,16 +32,15 @@ jobs: - name: Install dependencies run: | python -m pip install --upgrade pip - pip install sphinx sphinxcontrib-bibtex sphinx-rtd-theme numpy matplotlib pandas cartopy pandas cartopy f90nml netCDF4 xarray scipy + pip install sphinx sphinxcontrib-bibtex sphinx-rtd-theme - name: Build docs run: | - cd rrfs-workflow/doc/UsersGuide - sphinx-apidoc -o source/ ../../ush/ + cd rrfs-workflow/doc #sphinx-build -W --keep-going source build sphinx-build source build - uses: actions/upload-artifact@v4 with: name: rrfs-workflow docs path: | - rrfs-workflow/doc/UsersGuide/build + rrfs-workflow/doc/build From 1803e53d467b2af4c78df266c55dbd893aa2518e Mon Sep 17 00:00:00 2001 From: Edward Hartnett Date: Mon, 7 Oct 2024 04:52:59 -0600 Subject: [PATCH 24/32] changed workflow --- .github/workflows/docs.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 37e93505..443de9f2 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -35,12 +35,12 @@ jobs: pip install sphinx sphinxcontrib-bibtex sphinx-rtd-theme - name: Build docs run: | - cd rrfs-workflow/doc + cd rrfs-workflow/docs #sphinx-build -W --keep-going source build sphinx-build source build - uses: actions/upload-artifact@v4 with: name: rrfs-workflow docs path: | - rrfs-workflow/doc/build + rrfs-workflow/docs/build From c6a688202b1af86306c8d7317421dd3495a40047 Mon Sep 17 00:00:00 2001 From: Edward Hartnett Date: Mon, 7 Oct 2024 05:44:29 -0600 Subject: [PATCH 25/32] added some docs --- ush/HWP_tools.py | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) diff --git a/ush/HWP_tools.py b/ush/HWP_tools.py index 39aaa4d8..bd7280a9 100755 --- a/ush/HWP_tools.py +++ b/ush/HWP_tools.py @@ -1,3 +1,8 @@ +""" +This file provides HWP tools. + +""" + import numpy as np import os import datetime as dt @@ -7,6 +12,14 @@ import fnmatch def check_restart_files(hourly_hwpdir, fcst_dates): + """Check the restart files. + + Args: + hourly_hwpdir: Hourly ??? directory + fcst_dates: Forecast dates + Returns: + list of hwp_avail_hours, hwp_non_avail_hours + """ hwp_avail_hours = [] hwp_non_avail_hours = [] @@ -25,6 +38,15 @@ def check_restart_files(hourly_hwpdir, fcst_dates): return(hwp_avail_hours, hwp_non_avail_hours) def copy_missing_restart(nwges_dir, hwp_non_avail_hours, hourly_hwpdir): + """Check the restart files. + + Args: + nwges_dir: directory + hwp_non_avail_hours: ??? + hourly_hwpdir: ??? + Returns: + list of (restart_avail_hours, restart_nonavail_hours_test) + """ restart_avail_hours = [] restart_nonavail_hours_test = [] @@ -79,6 +101,18 @@ def copy_missing_restart(nwges_dir, hwp_non_avail_hours, hourly_hwpdir): return(restart_avail_hours, restart_nonavail_hours_test) def process_hwp(fcst_dates, hourly_hwpdir, cols, rows, intp_dir, rave_to_intp): + """Check the restart files. + + Args: + fcst_dates: Forecast dates + hourly_hwpdir: ??? + cols: number of columns + rows: number of rowa + intp_dir: directory + rave_to_intp: ??? + Returns: + list of (hwp_ave_arr, xarr_hwp, totprcp_ave_arr, xarr_totprcp) + """ hwp_ave = [] totprcp = np.zeros((cols*rows)) var1, var2 = 'rrfs_hwp_ave', 'totprcp_ave' From 3a91031c802e99ee7d10fef3dc5ec60f11a8228e Mon Sep 17 00:00:00 2001 From: Edward Hartnett Date: Mon, 7 Oct 2024 05:55:08 -0600 Subject: [PATCH 26/32] added some docs --- docs/requirements.txt | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/docs/requirements.txt b/docs/requirements.txt index 7be32f52..9e2013a3 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -1,3 +1,4 @@ sphinxcontrib-bibtex sphinx_rtd_theme -docutils==0.16 \ No newline at end of file +docutils==0.16 +numpy From 2afd5b8c9739e076e72163c24395db58919ac175 Mon Sep 17 00:00:00 2001 From: Edward Hartnett Date: Mon, 7 Oct 2024 05:56:50 -0600 Subject: [PATCH 27/32] added some docs --- docs/requirements.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/requirements.txt b/docs/requirements.txt index 9e2013a3..a804fd2c 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -2,3 +2,4 @@ sphinxcontrib-bibtex sphinx_rtd_theme docutils==0.16 numpy +xarray From b100b6873c724fdcf2b32255072787928f50c0fd Mon Sep 17 00:00:00 2001 From: Edward Hartnett Date: Mon, 7 Oct 2024 05:58:57 -0600 Subject: [PATCH 28/32] added some docs --- docs/requirements.txt | 3 +++ 1 file changed, 3 insertions(+) diff --git a/docs/requirements.txt b/docs/requirements.txt index a804fd2c..bd02f999 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -3,3 +3,6 @@ sphinx_rtd_theme docutils==0.16 numpy xarray +matplotlib +netCDF4 + From 813047d20b2e7ae3f15b72dc7e39544cb5f40da2 Mon Sep 17 00:00:00 2001 From: Edward Hartnett Date: Mon, 7 Oct 2024 06:03:28 -0600 Subject: [PATCH 29/32] added some docs --- docs/requirements.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/requirements.txt b/docs/requirements.txt index bd02f999..e5668fc8 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -5,4 +5,5 @@ numpy xarray matplotlib netCDF4 +matplotlib From 0edb0af78861ba9aa6c611850f13a9abf89708d3 Mon Sep 17 00:00:00 2001 From: Ed Date: Tue, 8 Oct 2024 10:25:27 -0600 Subject: [PATCH 30/32] more docs --- ush/HWP_tools.py | 15 +++++++++++---- 1 file changed, 11 insertions(+), 4 deletions(-) diff --git a/ush/HWP_tools.py b/ush/HWP_tools.py index bd7280a9..be39a303 100755 --- a/ush/HWP_tools.py +++ b/ush/HWP_tools.py @@ -1,5 +1,5 @@ """ -This file provides HWP tools. +This file provides Hourly Wildfire Potential (HWP) tools. """ @@ -15,7 +15,7 @@ def check_restart_files(hourly_hwpdir, fcst_dates): """Check the restart files. Args: - hourly_hwpdir: Hourly ??? directory + hourly_hwpdir: the directory where the RESTART data is copied (nwges/HOURLY_HWP) fcst_dates: Forecast dates Returns: list of hwp_avail_hours, hwp_non_avail_hours @@ -41,11 +41,18 @@ def copy_missing_restart(nwges_dir, hwp_non_avail_hours, hourly_hwpdir): """Check the restart files. Args: - nwges_dir: directory - hwp_non_avail_hours: ??? + nwges_dir: holds the boundary, INPUT, and RESTART files (e.g, + described here: + [ufs-community/ufs-srweather-app#654](https://github.com/ufs-community/ufs-srweather-app/issues/654)) + The use of NWGES is a bit of a legacy variable name in + production. It is often used to define a directory holding + DA-relevant files (such as first guess and analysis files) + outside of the main COM output directory. + hwp_non_avail_hours: a list of hours without available RESTART files hourly_hwpdir: ??? Returns: list of (restart_avail_hours, restart_nonavail_hours_test) + """ restart_avail_hours = [] restart_nonavail_hours_test = [] From 2ebb0b1f56a1c91b35b35f67a1052519127cc84b Mon Sep 17 00:00:00 2001 From: Ed Date: Tue, 8 Oct 2024 10:34:57 -0600 Subject: [PATCH 31/32] more docs --- ush/HWP_tools.py | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/ush/HWP_tools.py b/ush/HWP_tools.py index be39a303..3fdc1b66 100755 --- a/ush/HWP_tools.py +++ b/ush/HWP_tools.py @@ -49,7 +49,7 @@ def copy_missing_restart(nwges_dir, hwp_non_avail_hours, hourly_hwpdir): DA-relevant files (such as first guess and analysis files) outside of the main COM output directory. hwp_non_avail_hours: a list of hours without available RESTART files - hourly_hwpdir: ??? + hourly_hwpdir: the directory where the RESTART data is copied (nwges/HOURLY_HWP) Returns: list of (restart_avail_hours, restart_nonavail_hours_test) @@ -111,12 +111,12 @@ def process_hwp(fcst_dates, hourly_hwpdir, cols, rows, intp_dir, rave_to_intp): """Check the restart files. Args: - fcst_dates: Forecast dates - hourly_hwpdir: ??? - cols: number of columns - rows: number of rowa - intp_dir: directory - rave_to_intp: ??? + fcst_dates: a list of forecasts (for production/ops/ebb=2, it is {current_day - 25 hours: current_day-1hours}, for ebb=1, it is current_day:current_day+24 hours) + hourly_hwpdir: the directory where the RESTART data is copied (nwges/HOURLY_HWP) + cols: hard coded dimension for the RRFS_NA_3km and RRFS_CONUS_3km domains:: cols = 2700 if predef_grid == 'RRFS_NA_3km' else 1092 + rows: hard coded dimension for the RRFS_NA_3km and RRFS_CONUS_3km domains:: rows = 3950 if predef_grid == 'RRFS_NA_3km' else 1820 + intp_dir: the working directory for smoke processing (${CYCLE_DIR}/process_smoke) + rave_to_intp: a string based on the grid name:: rave_to_intp = predef_grid+"intp" Returns: list of (hwp_ave_arr, xarr_hwp, totprcp_ave_arr, xarr_totprcp) """ From d6289af1b0896986107fed4a86818026a7345313 Mon Sep 17 00:00:00 2001 From: Ed Date: Tue, 8 Oct 2024 11:22:39 -0600 Subject: [PATCH 32/32] more docs --- ush/HWP_tools.py | 17 ++++++++++++++--- 1 file changed, 14 insertions(+), 3 deletions(-) diff --git a/ush/HWP_tools.py b/ush/HWP_tools.py index 3fdc1b66..21bedc72 100755 --- a/ush/HWP_tools.py +++ b/ush/HWP_tools.py @@ -18,7 +18,7 @@ def check_restart_files(hourly_hwpdir, fcst_dates): hourly_hwpdir: the directory where the RESTART data is copied (nwges/HOURLY_HWP) fcst_dates: Forecast dates Returns: - list of hwp_avail_hours, hwp_non_avail_hours + lists of hours with and without available RESTART files """ hwp_avail_hours = [] hwp_non_avail_hours = [] @@ -40,6 +40,11 @@ def check_restart_files(hourly_hwpdir, fcst_dates): def copy_missing_restart(nwges_dir, hwp_non_avail_hours, hourly_hwpdir): """Check the restart files. + The script loops through hwp_non_avail_hours (missing files in + nwges/HOURLY_HWP) and determines if an alternative RESTART file in + nwges/fcst_fv3lam/RESTART is available instead. If so, it is + appended to restart_avail_hours. + Args: nwges_dir: holds the boundary, INPUT, and RESTART files (e.g, described here: @@ -51,7 +56,9 @@ def copy_missing_restart(nwges_dir, hwp_non_avail_hours, hourly_hwpdir): hwp_non_avail_hours: a list of hours without available RESTART files hourly_hwpdir: the directory where the RESTART data is copied (nwges/HOURLY_HWP) Returns: - list of (restart_avail_hours, restart_nonavail_hours_test) + list of:: + - restart_avail_hours + - restart_nonavail_hours_test which is a subset of hwp_non_avail_hours. """ restart_avail_hours = [] @@ -118,7 +125,11 @@ def process_hwp(fcst_dates, hourly_hwpdir, cols, rows, intp_dir, rave_to_intp): intp_dir: the working directory for smoke processing (${CYCLE_DIR}/process_smoke) rave_to_intp: a string based on the grid name:: rave_to_intp = predef_grid+"intp" Returns: - list of (hwp_ave_arr, xarr_hwp, totprcp_ave_arr, xarr_totprcp) + list of:: + - average (through time) of HWP_AVE in the available RESTART files + - hwp_ave_arr converted to an xarray DataArray + - the total precipitation vector (totprcp) reshaped to the 2D grid + - totprcp_ave_arr converted to an xarray DataArray """ hwp_ave = [] totprcp = np.zeros((cols*rows))