From 34ccd3d43b2fe90c52c357f2e24b50f09524155e Mon Sep 17 00:00:00 2001 From: Brandon Selbig <156852197+selbigmtnwx23@users.noreply.github.com> Date: Wed, 28 Jan 2026 13:11:31 -0700 Subject: [PATCH 01/25] Update InputsOutputs.rst for AQM inputs Based off of aqm.rc --- doc/UsersGuide/source/InputsOutputs.rst | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/doc/UsersGuide/source/InputsOutputs.rst b/doc/UsersGuide/source/InputsOutputs.rst index 858c783237..0382bc42e0 100644 --- a/doc/UsersGuide/source/InputsOutputs.rst +++ b/doc/UsersGuide/source/InputsOutputs.rst @@ -1110,21 +1110,21 @@ AQM inputs defined in ``aqm.rc`` are listed and described in :numref:`Table %s < * - Filename - Description - * - AE_cb6r3_ae6_aq.nml + * - AE_cb6r5_ae7_aq.nml - AE Matrix NML - * - GC_cb6r3_ae6_aq.nml + * - GC_cb6r5_ae7_aq.nml - GC Matrix NML - * - NR_cb6r3_ae6_aq.nml + * - NR_cb6r5_ae7_aq.nml - NR Matrix NML * - Species_Table_TR_0.nml - TR Matrix NML - * - CSQY_DATA_cb6r3_ae6_aq + * - CSQY_DATA_cb6r5_ae7_aq - CSQY Data * - PHOT_OPTICS.dat - Optics Data * - omi_cmaq_2015_361X179.dat - OMI data - * - NEXUS/NEXUS_Expt.nc + * - INPUT/NEXUS_Expt.nc - Emissions File * - BEIS_RRFScmaq_C775.ncf - Biogenic File @@ -1133,6 +1133,7 @@ AQM inputs defined in ``aqm.rc`` are listed and described in :numref:`Table %s < * - Hourly_Emissions_regrid_rrfs_13km_20190801_t12z_h72.nc - File Emissions File + .. _lnd-in: -------------- From 3660627083e2f8022e460e252a0c06563a8ec04d Mon Sep 17 00:00:00 2001 From: Brandon Selbig <156852197+selbigmtnwx23@users.noreply.github.com> Date: Thu, 5 Feb 2026 10:27:59 -0700 Subject: [PATCH 02/25] Update InputsOutputs.rst Change instances of 'CMAQ' to UFS AQM --- doc/UsersGuide/source/InputsOutputs.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/UsersGuide/source/InputsOutputs.rst b/doc/UsersGuide/source/InputsOutputs.rst index 0382bc42e0..74870b779f 100644 --- a/doc/UsersGuide/source/InputsOutputs.rst +++ b/doc/UsersGuide/source/InputsOutputs.rst @@ -28,7 +28,7 @@ mediator). Currently, supported configurations include: * - ATMAERO - :term:`ATM` coupled to :term:`GOCART` * - ATMAQ - - :term:`ATM` coupled to :term:`CMAQ` + - :term:`ATM` coupled to :term:`AQM` * - ATML - :term:`ATM` coupled to :term:`NOAHMP` * - ATMF @@ -1078,7 +1078,7 @@ The aerosol initial input currently read by GOCART is the same format as the UFS .. _aqm-in: -------------- -AQM (CMAQ) +UFS AQM -------------- .. _aqm-fix-files: From 9c8938259df905493213c79b6f2a3a0945013ac4 Mon Sep 17 00:00:00 2001 From: Brandon Selbig <156852197+selbigmtnwx23@users.noreply.github.com> Date: Mon, 9 Feb 2026 13:30:04 -0700 Subject: [PATCH 03/25] Update InputsOutputs.rst Defining of abbreviated data files --- doc/UsersGuide/source/InputsOutputs.rst | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/doc/UsersGuide/source/InputsOutputs.rst b/doc/UsersGuide/source/InputsOutputs.rst index 74870b779f..7667995993 100644 --- a/doc/UsersGuide/source/InputsOutputs.rst +++ b/doc/UsersGuide/source/InputsOutputs.rst @@ -1111,19 +1111,19 @@ AQM inputs defined in ``aqm.rc`` are listed and described in :numref:`Table %s < * - Filename - Description * - AE_cb6r5_ae7_aq.nml - - AE Matrix NML + - AE Matrix NML - Specifies chemical species, emissions mapping, and related settings for CMAQ's CB6r5 (Revision 5 of the Carbon Bond 6 Mechanism) chemical mechanism. * - GC_cb6r5_ae7_aq.nml - - GC Matrix NML + - GC Matrix NML - Configures CMAQ's gas-phase chemistry controls. * - NR_cb6r5_ae7_aq.nml - - NR Matrix NML + - NR Matrix NML - Non-reactive, gas-phase chemical species configuration for CMAQ. * - Species_Table_TR_0.nml - - TR Matrix NML + - TR Matrix NML - CMAQ species transport definitions. Empty in the UFS as CMAQ is used as a column model with tracer transport using FV3. * - CSQY_DATA_cb6r5_ae7_aq - - CSQY Data + - CSQY Data - CMAQ's chemical stoichiometric yield data table used by the solver for numerical calculations. * - PHOT_OPTICS.dat - Optics Data * - omi_cmaq_2015_361X179.dat - - OMI data + - OMI data - Ozone Monitoring Instrument (OMI) profile mappings used in establishing CAMQ boundary conditions. * - INPUT/NEXUS_Expt.nc - Emissions File * - BEIS_RRFScmaq_C775.ncf From 74ee027da0ccecc8a0c3bf66dfec5ee38a1bb3fa Mon Sep 17 00:00:00 2001 From: Brandon Selbig <156852197+selbigmtnwx23@users.noreply.github.com> Date: Mon, 9 Feb 2026 14:33:02 -0700 Subject: [PATCH 04/25] Update InputsOutputs.rst Add in info for S3 bucket and the input files --- doc/UsersGuide/source/InputsOutputs.rst | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/doc/UsersGuide/source/InputsOutputs.rst b/doc/UsersGuide/source/InputsOutputs.rst index 7667995993..50090f178b 100644 --- a/doc/UsersGuide/source/InputsOutputs.rst +++ b/doc/UsersGuide/source/InputsOutputs.rst @@ -1134,6 +1134,16 @@ AQM inputs defined in ``aqm.rc`` are listed and described in :numref:`Table %s < - File Emissions File +The most recent AQM input data files are in input-data-202XXXXX/AQM directory which can be found in the Weather Models S3 bucket (https://noaa-ufs-regtests-pds.s3.amazonaws.com/index.html). Below are the different data directories that exist in "AQM" + + * - fix files + - Fix files are static, climatological, and topographical datasets required for model initialization and running. These files include terrain, land use, vegetation, and soil data. + * - NEXUS files + - "NEXUS" (NOAA Emission and eXchange Unified System) files are specialized input files used for air quality modeling within the SRW App to incorporate pollutant emissions data. + * - INPUT files + - This directory contains pre-processing, initial conditions, grid-dependent, and namelist files. + + .. _lnd-in: -------------- From 78d1568d2aa23f8a034c9f9ad9aa1843d20d9afb Mon Sep 17 00:00:00 2001 From: Gillian Petro Date: Tue, 10 Feb 2026 09:06:38 -0500 Subject: [PATCH 05/25] update requirements files --- doc/UsersGuide/requirements.in | 6 +++--- doc/UsersGuide/requirements.txt | 4 ++-- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/doc/UsersGuide/requirements.in b/doc/UsersGuide/requirements.in index d4a3c97475..669d528404 100644 --- a/doc/UsersGuide/requirements.in +++ b/doc/UsersGuide/requirements.in @@ -1,4 +1,4 @@ -sphinx==7.4.7 -sphinx_rtd_theme +sphinx>=8.0.0 +sphinx_rtd_theme>=3.0.0 sphinxcontrib-bibtex -requests==2.32.2 +requests>=2.32.2 diff --git a/doc/UsersGuide/requirements.txt b/doc/UsersGuide/requirements.txt index b0c4c19e68..b909d288cb 100644 --- a/doc/UsersGuide/requirements.txt +++ b/doc/UsersGuide/requirements.txt @@ -50,13 +50,13 @@ six==1.16.0 # pybtex snowballstemmer==2.2.0 # via sphinx -sphinx==7.4.7 +sphinx==8.0.2 # via # -r requirements.in # sphinx-rtd-theme # sphinxcontrib-bibtex # sphinxcontrib-jquery -sphinx-rtd-theme==2.0.0 +sphinx-rtd-theme==3.1.0 # via -r requirements.in sphinxcontrib-applehelp==1.0.8 # via sphinx From 37f5be7fc3650344bdcf638e74e0ba2262d16686 Mon Sep 17 00:00:00 2001 From: Gillian Petro Date: Tue, 10 Feb 2026 10:45:22 -0500 Subject: [PATCH 06/25] upgrade python requirement --- .readthedocs.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 37ba7c6ff0..7dbad0bce6 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -7,7 +7,7 @@ version: 2 build: os: ubuntu-20.04 tools: - python: "3.9" + python: "3.12" # Build documentation in the docs/ directory with Sphinx sphinx: From b96db79bedec70d4c4c24eeddb3b3a3099d9d096 Mon Sep 17 00:00:00 2001 From: Gillian Petro Date: Tue, 10 Feb 2026 10:56:42 -0500 Subject: [PATCH 07/25] upgrade ubuntuin rtd.yaml --- .readthedocs.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 7dbad0bce6..c83fce5dfb 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -5,7 +5,7 @@ # Required version: 2 build: - os: ubuntu-20.04 + os: ubuntu-22.04 tools: python: "3.12" From afb8970bae2be9a98c99ee8359f578e513cae02b Mon Sep 17 00:00:00 2001 From: Gillian Petro Date: Tue, 10 Feb 2026 11:03:25 -0500 Subject: [PATCH 08/25] require setuptools in rtd.yaml --- .readthedocs.yaml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index c83fce5dfb..c82a3ce8b1 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -8,6 +8,10 @@ build: os: ubuntu-22.04 tools: python: "3.12" + jobs: + post_create_environment: + - pip install --upgrade pip + - pip install setuptools # Build documentation in the docs/ directory with Sphinx sphinx: From 134d754882db1a08514f863fbc81e4100d69653f Mon Sep 17 00:00:00 2001 From: Brandon Selbig <156852197+selbigmtnwx23@users.noreply.github.com> Date: Tue, 10 Feb 2026 09:43:22 -0700 Subject: [PATCH 09/25] Update doc/UsersGuide/source/InputsOutputs.rst Co-authored-by: Gillian Petro <96886803+gspetro-NOAA@users.noreply.github.com> --- doc/UsersGuide/source/InputsOutputs.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/UsersGuide/source/InputsOutputs.rst b/doc/UsersGuide/source/InputsOutputs.rst index 50090f178b..ca293e19eb 100644 --- a/doc/UsersGuide/source/InputsOutputs.rst +++ b/doc/UsersGuide/source/InputsOutputs.rst @@ -1123,7 +1123,7 @@ AQM inputs defined in ``aqm.rc`` are listed and described in :numref:`Table %s < * - PHOT_OPTICS.dat - Optics Data * - omi_cmaq_2015_361X179.dat - - OMI data - Ozone Monitoring Instrument (OMI) profile mappings used in establishing CAMQ boundary conditions. + - OMI data - Ozone Monitoring Instrument (OMI) profile mappings used in establishing CMAQ boundary conditions. * - INPUT/NEXUS_Expt.nc - Emissions File * - BEIS_RRFScmaq_C775.ncf From efc871355e13929b660331c13c9c45f574bd5dec Mon Sep 17 00:00:00 2001 From: Brandon Selbig <156852197+selbigmtnwx23@users.noreply.github.com> Date: Tue, 10 Feb 2026 09:43:44 -0700 Subject: [PATCH 10/25] Update doc/UsersGuide/source/InputsOutputs.rst Co-authored-by: Gillian Petro <96886803+gspetro-NOAA@users.noreply.github.com> --- doc/UsersGuide/source/InputsOutputs.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/UsersGuide/source/InputsOutputs.rst b/doc/UsersGuide/source/InputsOutputs.rst index ca293e19eb..fae4079436 100644 --- a/doc/UsersGuide/source/InputsOutputs.rst +++ b/doc/UsersGuide/source/InputsOutputs.rst @@ -1134,7 +1134,7 @@ AQM inputs defined in ``aqm.rc`` are listed and described in :numref:`Table %s < - File Emissions File -The most recent AQM input data files are in input-data-202XXXXX/AQM directory which can be found in the Weather Models S3 bucket (https://noaa-ufs-regtests-pds.s3.amazonaws.com/index.html). Below are the different data directories that exist in "AQM" +The most recent AQM input data files can be found in the `Weather Model S3 bucket `_ in the input-data-202XXXXX/AQM directory for the most recent date. Below are the data subdirectories that exist in ``input-data-202XXXXX/AQM``. * - fix files - Fix files are static, climatological, and topographical datasets required for model initialization and running. These files include terrain, land use, vegetation, and soil data. From e531c0ab2a64c27b23817dca9da4971250010922 Mon Sep 17 00:00:00 2001 From: Brandon Selbig <156852197+selbigmtnwx23@users.noreply.github.com> Date: Tue, 10 Feb 2026 09:43:58 -0700 Subject: [PATCH 11/25] Update doc/UsersGuide/source/InputsOutputs.rst Co-authored-by: Gillian Petro <96886803+gspetro-NOAA@users.noreply.github.com> --- doc/UsersGuide/source/InputsOutputs.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/UsersGuide/source/InputsOutputs.rst b/doc/UsersGuide/source/InputsOutputs.rst index fae4079436..42a75dc9ba 100644 --- a/doc/UsersGuide/source/InputsOutputs.rst +++ b/doc/UsersGuide/source/InputsOutputs.rst @@ -1136,7 +1136,7 @@ AQM inputs defined in ``aqm.rc`` are listed and described in :numref:`Table %s < The most recent AQM input data files can be found in the `Weather Model S3 bucket `_ in the input-data-202XXXXX/AQM directory for the most recent date. Below are the data subdirectories that exist in ``input-data-202XXXXX/AQM``. - * - fix files + * - ``fix`` - Fix files are static, climatological, and topographical datasets required for model initialization and running. These files include terrain, land use, vegetation, and soil data. * - NEXUS files - "NEXUS" (NOAA Emission and eXchange Unified System) files are specialized input files used for air quality modeling within the SRW App to incorporate pollutant emissions data. From d14d872527a4e2bbdfe364f8d11d85fb8b89c72f Mon Sep 17 00:00:00 2001 From: Brandon Selbig <156852197+selbigmtnwx23@users.noreply.github.com> Date: Tue, 10 Feb 2026 09:44:18 -0700 Subject: [PATCH 12/25] Update doc/UsersGuide/source/InputsOutputs.rst Co-authored-by: Gillian Petro <96886803+gspetro-NOAA@users.noreply.github.com> --- doc/UsersGuide/source/InputsOutputs.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/UsersGuide/source/InputsOutputs.rst b/doc/UsersGuide/source/InputsOutputs.rst index 42a75dc9ba..eee496685a 100644 --- a/doc/UsersGuide/source/InputsOutputs.rst +++ b/doc/UsersGuide/source/InputsOutputs.rst @@ -1138,7 +1138,7 @@ The most recent AQM input data files can be found in the `Weather Model S3 bucke * - ``fix`` - Fix files are static, climatological, and topographical datasets required for model initialization and running. These files include terrain, land use, vegetation, and soil data. - * - NEXUS files + * - ``NEXUS`` - "NEXUS" (NOAA Emission and eXchange Unified System) files are specialized input files used for air quality modeling within the SRW App to incorporate pollutant emissions data. * - INPUT files - This directory contains pre-processing, initial conditions, grid-dependent, and namelist files. From bb4dd8a84524c6c98785c5a930e1f56167ca5f46 Mon Sep 17 00:00:00 2001 From: Brandon Selbig <156852197+selbigmtnwx23@users.noreply.github.com> Date: Tue, 10 Feb 2026 09:44:36 -0700 Subject: [PATCH 13/25] Update doc/UsersGuide/source/InputsOutputs.rst Co-authored-by: Gillian Petro <96886803+gspetro-NOAA@users.noreply.github.com> --- doc/UsersGuide/source/InputsOutputs.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/UsersGuide/source/InputsOutputs.rst b/doc/UsersGuide/source/InputsOutputs.rst index eee496685a..4754f729c7 100644 --- a/doc/UsersGuide/source/InputsOutputs.rst +++ b/doc/UsersGuide/source/InputsOutputs.rst @@ -1140,7 +1140,7 @@ The most recent AQM input data files can be found in the `Weather Model S3 bucke - Fix files are static, climatological, and topographical datasets required for model initialization and running. These files include terrain, land use, vegetation, and soil data. * - ``NEXUS`` - "NEXUS" (NOAA Emission and eXchange Unified System) files are specialized input files used for air quality modeling within the SRW App to incorporate pollutant emissions data. - * - INPUT files + * - ``INPUT`` - This directory contains pre-processing, initial conditions, grid-dependent, and namelist files. From 09b2800cda2256d8de46427521ad34dec2924ef3 Mon Sep 17 00:00:00 2001 From: Brandon Selbig <156852197+selbigmtnwx23@users.noreply.github.com> Date: Tue, 10 Feb 2026 09:44:53 -0700 Subject: [PATCH 14/25] Update doc/UsersGuide/source/InputsOutputs.rst Co-authored-by: Gillian Petro <96886803+gspetro-NOAA@users.noreply.github.com> --- doc/UsersGuide/source/InputsOutputs.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/UsersGuide/source/InputsOutputs.rst b/doc/UsersGuide/source/InputsOutputs.rst index 4754f729c7..8ebd7c513a 100644 --- a/doc/UsersGuide/source/InputsOutputs.rst +++ b/doc/UsersGuide/source/InputsOutputs.rst @@ -1139,7 +1139,7 @@ The most recent AQM input data files can be found in the `Weather Model S3 bucke * - ``fix`` - Fix files are static, climatological, and topographical datasets required for model initialization and running. These files include terrain, land use, vegetation, and soil data. * - ``NEXUS`` - - "NEXUS" (NOAA Emission and eXchange Unified System) files are specialized input files used for air quality modeling within the SRW App to incorporate pollutant emissions data. + - "NEXUS" (NOAA Emission and eXchange Unified System) files are specialized input files used for air quality modeling to incorporate pollutant emissions data. * - ``INPUT`` - This directory contains pre-processing, initial conditions, grid-dependent, and namelist files. From 113c727017dc4718af192642ad1b0d8d0183f171 Mon Sep 17 00:00:00 2001 From: Brandon Selbig <156852197+selbigmtnwx23@users.noreply.github.com> Date: Tue, 10 Feb 2026 11:54:42 -0700 Subject: [PATCH 15/25] Update doc/UsersGuide/source/InputsOutputs.rst Co-authored-by: Gillian Petro <96886803+gspetro-NOAA@users.noreply.github.com> --- doc/UsersGuide/source/InputsOutputs.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/UsersGuide/source/InputsOutputs.rst b/doc/UsersGuide/source/InputsOutputs.rst index 8ebd7c513a..75d84d75ea 100644 --- a/doc/UsersGuide/source/InputsOutputs.rst +++ b/doc/UsersGuide/source/InputsOutputs.rst @@ -1124,7 +1124,7 @@ AQM inputs defined in ``aqm.rc`` are listed and described in :numref:`Table %s < - Optics Data * - omi_cmaq_2015_361X179.dat - OMI data - Ozone Monitoring Instrument (OMI) profile mappings used in establishing CMAQ boundary conditions. - * - INPUT/NEXUS_Expt.nc + * - NEXUS/NEXUS_Expt.nc - Emissions File * - BEIS_RRFScmaq_C775.ncf - Biogenic File From 2e0b75cd541d4164a4c26791a2658146ae9f313a Mon Sep 17 00:00:00 2001 From: Brandon Selbig <156852197+selbigmtnwx23@users.noreply.github.com> Date: Tue, 10 Feb 2026 12:05:13 -0700 Subject: [PATCH 16/25] Update doc/UsersGuide/source/InputsOutputs.rst Co-authored-by: Gillian Petro <96886803+gspetro-NOAA@users.noreply.github.com> --- doc/UsersGuide/source/InputsOutputs.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/UsersGuide/source/InputsOutputs.rst b/doc/UsersGuide/source/InputsOutputs.rst index 75d84d75ea..9ea50f1def 100644 --- a/doc/UsersGuide/source/InputsOutputs.rst +++ b/doc/UsersGuide/source/InputsOutputs.rst @@ -1134,7 +1134,7 @@ AQM inputs defined in ``aqm.rc`` are listed and described in :numref:`Table %s < - File Emissions File -The most recent AQM input data files can be found in the `Weather Model S3 bucket `_ in the input-data-202XXXXX/AQM directory for the most recent date. Below are the data subdirectories that exist in ``input-data-202XXXXX/AQM``. +The most recent AQM input data files can be found in the `Weather Model S3 bucket `_ in the input-data-202XXXXX/AQM directory for the most recent date. Below are the data subdirectories that exist in ``input-data-202XXXXX/AQM/v8``. * - ``fix`` - Fix files are static, climatological, and topographical datasets required for model initialization and running. These files include terrain, land use, vegetation, and soil data. From c2365dd297c514e82e35c975d19b6a6234e32e32 Mon Sep 17 00:00:00 2001 From: Gillian Petro Date: Tue, 10 Feb 2026 14:50:42 -0500 Subject: [PATCH 17/25] update sphinxcontrib.bibtex --- doc/UsersGuide/requirements.in | 2 +- doc/UsersGuide/requirements.txt | 5 +++-- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/doc/UsersGuide/requirements.in b/doc/UsersGuide/requirements.in index 669d528404..74690b980a 100644 --- a/doc/UsersGuide/requirements.in +++ b/doc/UsersGuide/requirements.in @@ -1,4 +1,4 @@ sphinx>=8.0.0 sphinx_rtd_theme>=3.0.0 -sphinxcontrib-bibtex +sphinxcontrib-bibtex>=2.6.4 requests>=2.32.2 diff --git a/doc/UsersGuide/requirements.txt b/doc/UsersGuide/requirements.txt index b909d288cb..6be84297d2 100644 --- a/doc/UsersGuide/requirements.txt +++ b/doc/UsersGuide/requirements.txt @@ -2,7 +2,7 @@ # This file is autogenerated by pip-compile with Python 3.13 # by the following command: # -# pip-compile requirements.in +# pip-compile --strip-extras requirements.in # alabaster==0.7.16 # via sphinx @@ -60,7 +60,7 @@ sphinx-rtd-theme==3.1.0 # via -r requirements.in sphinxcontrib-applehelp==1.0.8 # via sphinx -sphinxcontrib-bibtex==2.6.2 +sphinxcontrib-bibtex==2.6.4 # via -r requirements.in sphinxcontrib-devhelp==1.0.6 # via sphinx @@ -76,3 +76,4 @@ sphinxcontrib-serializinghtml==1.1.10 # via sphinx urllib3==2.2.2 # via requests + From 60f211a66a22fa907217e43d2f4a2c49e590f9f6 Mon Sep 17 00:00:00 2001 From: Gillian Petro Date: Tue, 10 Feb 2026 15:43:20 -0500 Subject: [PATCH 18/25] require setuptools --- doc/UsersGuide/requirements.txt | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/doc/UsersGuide/requirements.txt b/doc/UsersGuide/requirements.txt index 6be84297d2..485ed579d4 100644 --- a/doc/UsersGuide/requirements.txt +++ b/doc/UsersGuide/requirements.txt @@ -2,7 +2,7 @@ # This file is autogenerated by pip-compile with Python 3.13 # by the following command: # -# pip-compile --strip-extras requirements.in +# pip-compile --allow-unsafe --strip-extras requirements.in # alabaster==0.7.16 # via sphinx @@ -77,3 +77,6 @@ sphinxcontrib-serializinghtml==1.1.10 urllib3==2.2.2 # via requests +# The following packages are considered to be unsafe in a requirements file: +setuptools==82.0.0 + # via sphinxcontrib-bibtex From 291139558f5b11e3e92e2e15e2051cb0e26d64ef Mon Sep 17 00:00:00 2001 From: Joshua Kublnick Date: Wed, 11 Feb 2026 12:01:00 -0500 Subject: [PATCH 19/25] installing setuptools in docs environment --- .readthedocs.yaml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index c82a3ce8b1..452cd5a502 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -10,8 +10,7 @@ build: python: "3.12" jobs: post_create_environment: - - pip install --upgrade pip - - pip install setuptools + - python -m pip install --upgrade pip setuptools # Build documentation in the docs/ directory with Sphinx sphinx: From 82092fdf0fdbbd522be2f9df3be9fc0f673dac2f Mon Sep 17 00:00:00 2001 From: Joshua Kublnick Date: Wed, 11 Feb 2026 12:21:09 -0500 Subject: [PATCH 20/25] Update build to use Python 3.13 --- .readthedocs.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 452cd5a502..20bdefabd4 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -4,10 +4,10 @@ # Required version: 2 -build: +build: os: ubuntu-22.04 - tools: - python: "3.12" + tools: + python: "3.13" jobs: post_create_environment: - python -m pip install --upgrade pip setuptools From 6cd95b78aec7e7709001c8fcaf122b5e61945c01 Mon Sep 17 00:00:00 2001 From: Joshua Kublnick Date: Wed, 11 Feb 2026 12:24:40 -0500 Subject: [PATCH 21/25] Update build to use Python 3.11 --- .readthedocs.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 20bdefabd4..b6fe2222ee 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -7,7 +7,7 @@ version: 2 build: os: ubuntu-22.04 tools: - python: "3.13" + python: "3.11" jobs: post_create_environment: - python -m pip install --upgrade pip setuptools From 2cb262c97193b38bc8067d8256a020031b09516c Mon Sep 17 00:00:00 2001 From: Joshua Kublnick Date: Wed, 11 Feb 2026 12:31:55 -0500 Subject: [PATCH 22/25] Fix doc builds by pinning setuptools<81 to restore pkg_resources --- .readthedocs.yaml | 4 ++-- doc/UsersGuide/requirements.txt | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index b6fe2222ee..47013894e6 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -7,10 +7,10 @@ version: 2 build: os: ubuntu-22.04 tools: - python: "3.11" + python: "3.12" jobs: post_create_environment: - - python -m pip install --upgrade pip setuptools + - python -m pip install --upgrade "pip" "setuptools<81" # Build documentation in the docs/ directory with Sphinx sphinx: diff --git a/doc/UsersGuide/requirements.txt b/doc/UsersGuide/requirements.txt index 485ed579d4..000156ef54 100644 --- a/doc/UsersGuide/requirements.txt +++ b/doc/UsersGuide/requirements.txt @@ -78,5 +78,5 @@ urllib3==2.2.2 # via requests # The following packages are considered to be unsafe in a requirements file: -setuptools==82.0.0 +setuptools==80.9.0 # via sphinxcontrib-bibtex From a3a66a6b186205691f8ce4ac8464dbc6c8a3349e Mon Sep 17 00:00:00 2001 From: Brandon Selbig <156852197+selbigmtnwx23@users.noreply.github.com> Date: Wed, 11 Feb 2026 11:45:14 -0700 Subject: [PATCH 23/25] Update Glossary.rst Updated link for CCPP site --- doc/UsersGuide/source/Glossary.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/UsersGuide/source/Glossary.rst b/doc/UsersGuide/source/Glossary.rst index 3cb92477db..25ea9fe4e1 100644 --- a/doc/UsersGuide/source/Glossary.rst +++ b/doc/UsersGuide/source/Glossary.rst @@ -22,7 +22,7 @@ Glossary The `Air Quality Model `_ (AQM) is a UFS Application that dynamically couples the Community Multiscale Air Quality (:term:`CMAQ`) model with the UFS Weather Model through the :term:`NUOPC` Layer to simulate temporal and spatial variations of atmospheric compositions (e.g., ozone and aerosol compositions). The CMAQ, treated as a column chemistry model, updates concentrations of chemical species (e.g., ozone and aerosol compositions) at each integration time step. The transport terms (e.g., :term:`advection` and diffusion) of all chemical species are handled by the UFS Weather Model as :term:`tracers`. CCPP - The `Common Community Physics Package `_ is a forecast-model agnostic, vetted collection of code containing atmospheric physical parameterizations and suites of parameterizations for use in Numerical Weather Prediction (:term:`NWP`) along with a framework that connects the physics to the host forecast model. + The `Common Community Physics Package `_ is a forecast-model agnostic, vetted collection of code containing atmospheric physical parameterizations and suites of parameterizations for use in Numerical Weather Prediction (:term:`NWP`) along with a framework that connects the physics to the host forecast model. CCPP-Framework The infrastructure that connects physics schemes with a host model; also refers to a software From 3b08495da846b62a4fa8068c52a520feae1c0034 Mon Sep 17 00:00:00 2001 From: Gillian Petro Date: Wed, 11 Feb 2026 14:11:57 -0500 Subject: [PATCH 24/25] update requirements files w/setuptools --- doc/UsersGuide/requirements.in | 1 + doc/UsersGuide/requirements.txt | 6 ++++-- 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/doc/UsersGuide/requirements.in b/doc/UsersGuide/requirements.in index 74690b980a..b126389fbb 100644 --- a/doc/UsersGuide/requirements.in +++ b/doc/UsersGuide/requirements.in @@ -2,3 +2,4 @@ sphinx>=8.0.0 sphinx_rtd_theme>=3.0.0 sphinxcontrib-bibtex>=2.6.4 requests>=2.32.2 +setuptools<81.0.0 diff --git a/doc/UsersGuide/requirements.txt b/doc/UsersGuide/requirements.txt index 000156ef54..2e01e7545f 100644 --- a/doc/UsersGuide/requirements.txt +++ b/doc/UsersGuide/requirements.txt @@ -78,5 +78,7 @@ urllib3==2.2.2 # via requests # The following packages are considered to be unsafe in a requirements file: -setuptools==80.9.0 - # via sphinxcontrib-bibtex +setuptools==80.10.2 + # via + # -r requirements.in + # sphinxcontrib-bibtex From 648f21d42326459125c242159dfd0cf9f32266e1 Mon Sep 17 00:00:00 2001 From: Brandon Selbig <156852197+selbigmtnwx23@users.noreply.github.com> Date: Fri, 13 Feb 2026 11:36:36 -0700 Subject: [PATCH 25/25] Update InputsOutputs.rst Update link for GSWP3 data --- doc/UsersGuide/source/InputsOutputs.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/UsersGuide/source/InputsOutputs.rst b/doc/UsersGuide/source/InputsOutputs.rst index 9ea50f1def..16651c6444 100644 --- a/doc/UsersGuide/source/InputsOutputs.rst +++ b/doc/UsersGuide/source/InputsOutputs.rst @@ -907,7 +907,7 @@ The input files containing grid information and the time-varying forcing files f .. note:: - Users can find atmospheric forcing files for use with the Noah-MP land component (LND) in the `Land Data Assimilation (DA) data bucket `_. These files provide atmospheric forcing data related to precipitation, solar radiation, longwave radiation, temperature, pressure, winds, humidity, topography, and mesh data. Forcing files for the land component configuration come from the Global Soil Wetness Project Phase 3 (`GSWP3 `_) dataset. + Users can find atmospheric forcing files for use with the Noah-MP land component (LND) in the `Land Data Assimilation (DA) data bucket `_. These files provide atmospheric forcing data related to precipitation, solar radiation, longwave radiation, temperature, pressure, winds, humidity, topography, and mesh data. Forcing files for the land component configuration come from the Global Soil Wetness Project Phase 3 (`GSWP3 `_) dataset. .. code-block:: console