PecanProject · infotroph · Dec 12, 2025 · Dec 11, 2025 · Dec 11, 2025 · Dec 11, 2025
diff --git a/base/all/DESCRIPTION b/base/all/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: PEcAn.all
 Type: Package
 Title: PEcAn Functions Used for Ecological Forecasts and Reanalysis
-Version: 1.9.0.9000
+Version: 1.10.0
 Authors@R: c(person("Mike", "Dietze", role = c("aut"),
                      email = "dietze@bu.edu"),
              person("David", "LeBauer", role = c("aut", "cre"),

diff --git a/base/all/NEWS.md b/base/all/NEWS.md
@@ -1,3 +1,8 @@
+# PEcAn.all 1.10.10
+
+* Added keywords and bug reporting URL to DESCRIPTION.
+* Updated `pecan_version_history` and `pecan_releases` to report the package versions used in PEcAn v1.10.0.
+
 # PEcAn.all 1.9.0
 
 ## License change

diff --git a/base/all/data/pecan_releases.csv b/base/all/data/pecan_releases.csv
@@ -33,3 +33,4 @@
 "v1.7.2",2021-10-08,1.7.2
 "v1.8.0",2024-07-12,1.8.0
 "v1.9.0",2025-05-25,1.9.0
+"v1.10.0",2025-12-12,1.10.0
diff --git a/base/all/data/pecan_version_history.csv b/base/all/data/pecan_version_history.csv
diff --git a/base/db/DESCRIPTION b/base/db/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: PEcAn.DB
 Type: Package
 Title: PEcAn Functions Used for Ecological Forecasts and Reanalysis
-Version: 1.8.1.9000
+Version: 1.8.2
 Authors@R: c(person("David", "LeBauer", role = c("aut", "cre"),
                      email = "dlebauer@email.arizona.edu"),
              person("Mike", "Dietze", role = c("aut"),

diff --git a/base/db/NEWS.md b/base/db/NEWS.md
@@ -1,3 +1,10 @@
+# PEcAn.DB 1.8.2
+
+* Refactored `convert.input()` internals into smaller, and hopefully more testable, chunks. No user-visible changes expected.
+* Roxygen cleanup.
+
+
+
 # PEcAn.DB 1.8.1
 
 ## License change

diff --git a/base/logger/NEWS.md b/base/logger/NEWS.md
@@ -1,28 +1,38 @@
-# PEcAn.logger 1.8.4 (unreleased)
+# PEcAn.logger 1.8.4
 
 - All `logger.set*` functions now invisibly return the previously set value. This can be handy for restoring settings after a temporary change.
 - Multipart logger messages passed in `...` now get a more robust conversion to string before concatenating, hopefully giving nicer results for nontext objects such as dates and lists.
 
+
+
 # PEcAn.logger 1.8.3
 
 - Maintenance release with no user-visible changes.
 
+
+
 # PEcAn.logger 1.8.2
 
 - `PEcAn.logger::setLevel()` now invisibly returns the previously set logger level
 
+
+
 # PEcAn.logger 1.8.1
 
 ## Re-licensing
 
 * PEcAn.logger is now distributed as BSD-3 license. Prior to this the package was released under the NCSA Opensource license from 2009-2021.
 
+
+
 # PEcAn.logger 1.8.0
 
 ## Fixed
 
 * Logger calls no longer create a stray `dump.log` object in the global environment
 
+
+
 # PEcAn.logger 1.7.1
 
 * All changes in 1.7.1 and earlier were recorded in a single file for all of the PEcAn packages; please see 

diff --git a/base/qaqc/DESCRIPTION b/base/qaqc/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: PEcAn.qaqc
 Type: Package
 Title: QAQC
-Version: 1.7.4.9000
+Version: 1.7.5
 Authors@R: c(person("David", "LeBauer", role = c("aut", "cre"),
                      email = "dlebauer@email.arizona.edu"),
              person("Tess", "McCabe", role = c("aut"),

diff --git a/base/qaqc/NEWS.md b/base/qaqc/NEWS.md
@@ -1,9 +1,16 @@
+# PEcAn.qaqc 1.7.5
+
+* Added keywords and bug reporting URL to DESCRIPTION. No code changes in this release.
+
+
+
 # PEcAn.qaqc 1.7.4
 
 ## License change
 * PEcAn.qaqc is now distributed under the BSD three-clause license instead of the NCSA Open Source license.
 
 
+
 # PEcAn.qaqc 1.7.1
 
 * All changes in 1.7.1 and earlier were recorded in a single file for all of the PEcAn packages; please see 

diff --git a/base/remote/DESCRIPTION b/base/remote/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: PEcAn.remote
 Type: Package
 Title: PEcAn Model Execution Utilities
-Version: 1.9.0.9000
+Version: 1.9.1
 Authors@R: c(person("David", "LeBauer", role = c("aut"),
                      email = "dlebauer@email.arizona.edu"),
              person("Rob", "Kooper", role = c("aut", "cre"),

diff --git a/base/remote/NEWS.md b/base/remote/NEWS.md
@@ -1,3 +1,9 @@
+# PEcAn.remote 1.9.1
+
+* Added keywords and bug reporting URL to DESCRIPTION. No code changes in this release.
+
+
+
 # PEcAn.remote 1.9.0
 
 * PEcAn.remote is now distributed under the BSD 3-clause license instead of the NCSA Open Source license.

diff --git a/base/settings/NEWS.md b/base/settings/NEWS.md
@@ -2,13 +2,14 @@
 
 ## Fixed
 
-* listToXml.MultiSettings now produces valid XML from a MultiSettings with length 1.
-* setEnsemblePaths no longer wraps single paths in a list, giving `<path>/your/file.here</path>` instead of the previous `<path><path1>/your/file.here</path1></path>`.
+* listToXml.MultiSettings now produces valid XML from a MultiSettings with length 1 (#3546) .
+* setEnsemblePaths no longer wraps single paths in a list, giving `<path>/your/file.here</path>` instead of the previous `<path><path1>/your/file.here</path1></path>` (#3561).
 
 ## Changed
 
-* The `tag` argument to `listToXml()` is now optional and will default to "pecan" if not specified. This sets the name of the root tag of the resulting XML object.
-* The first argument of `listToXml.MultiSettings()` has been renamed from `item` to `x`, and it now accepts but ignores `...`, both for consistency with the generic.
+* The `tag` argument to `listToXml()` is now optional and will default to "pecan" if not specified. This sets the name of the root tag of the resulting XML object (#3558).
+* The first argument of `listToXml.MultiSettings()` has been renamed from `item` to `x`, and it now accepts but ignores `...`, both for consistency with the generic (#3558).
+* `setEnsemblePaths()` no longer restricts the set of values accepted for `input_type` (#3633)
 
 
 # PEcAn.settings 1.9.0
@@ -33,11 +34,13 @@
 * Internal helper function `getRunSettings` is no longer exported. As the documentation has long noted, it was not intended to be called directly.
 
 
+
 # PEcAn.settings 1.8.0
 
 * Bug fixes for ensemble runs.
 
 
+
 # PEcAn.settings 1.7.1
 
 * All changes in 1.7.1 and earlier were recorded in a single file for all of the

diff --git a/base/utils/NEWS.md b/base/utils/NEWS.md
@@ -2,7 +2,11 @@
 
 ## Added
 
-* New function `nc_write_varfiles()` creates text summaries of the variables in all netCDF files in an output directory, writing either one file named `nc_vars.txt` if `output_mode = "combined"` or a separate `[filename].nc.var` alongside each netCDF if `output_mode = "paired"`.
+* New function `nc_write_varfiles()` creates text summaries of the variables in all netCDF files in an output directory, writing either one file named `nc_vars.txt` if `output_mode = "combined"` or a separate `[filename].nc.var` alongside each netCDF if `output_mode = "paired"` (#3611).
+* New function `nc_merge_all_sites_by_year()` combines many netCDFs into one file per year (#3620)
+* New function `extract_nc_sda`() extracts data from a multi-site netCDF created by `nc_merge_all_sites_by_year` (#3620).
+* Added CH4 and N2O variables to `standard_vars`
+
 
 
 # PEcAn.utils 1.8.1
@@ -13,7 +17,7 @@
 ## Changed
 * utility function `zero.bounded.density` is now exported.
 * Roxygen fixes
-* Add CH4 and N2O to standard_vars
+
 
 
 # PEcAn.utils 1.8.0

diff --git a/base/visualization/DESCRIPTION b/base/visualization/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: PEcAn.visualization
 Type: Package
 Title: PEcAn visualization functions
-Version: 1.8.1.9000
+Version: 1.8.2
 Authors@R: c(person("Mike", "Dietze", role = c("aut"),
                      email = "dietze@bu.edu"),
              person("David", "LeBauer", role = c("aut", "cre"),

diff --git a/base/visualization/NEWS.md b/base/visualization/NEWS.md
@@ -1,3 +1,9 @@
+# PEcAn.visualization 1.8.2
+
+Added keywords and bug reporting URL to DESCRIPTION. No code changes in this release.
+
+
+
 # PEcAn.visualization 1.8.1
 
 ## License change

diff --git a/base/workflow/DESCRIPTION b/base/workflow/DESCRIPTION
@@ -2,7 +2,7 @@ Package: PEcAn.workflow
 Type: Package
 Title: PEcAn Functions Used for Ecological Forecasts and
     Reanalysis
-Version: 1.9.0.9000
+Version: 1.10.0
 Authors@R: c(person("Mike", "Dietze", role = c("aut"),
                      email = "dietze@bu.edu"),
              person("David", "LeBauer", role = c("aut", "cre"),

diff --git a/base/workflow/NEWS.md b/base/workflow/NEWS.md
@@ -1,12 +1,11 @@
-### Joint Ensemble Sampling Implementation
-- **Behavior Change**: Ensemble runs now use shared input samples across all sites instead of independent sampling per site
-- **Affected Components**: 
-  - `get.parameter.samples.R` 
-  - `runModule.run.write.configs.R`
-  - `run.write.configs.R` 
-  - `ensemble.R`
-- **New Default**: The sampling method default has changed from "uniform" to "random"
-- **Impact**: This ensures consistency across sites in ensemble runs but may produce different results compared to previous versions
+# PEcAn.workflow 1.10.0
+
+## Changed
+
+Breaking: Ensemble runs now use shared input samples across all sites instead of independent sampling per site.
+
+* `run.write.configs()` now has two new required args `ensemble.size` and `input_design`, and removes `ens.sample.method` (#3535, #3612).
+* `runModule.run.write.configs()` has new arg `input_design`, with default NULL meaning to generate one internally (#3535).
 
 
 # PEcAn.workflow 1.9.0

diff --git a/modules/allometry/NEWS.md b/modules/allometry/NEWS.md
@@ -1,3 +1,9 @@
+# PEcAn.allometry 1.7.5
+
+* Added keywords and bug reporting URL to DESCRIPTION.
+* No code changes in this release.
+
+
 # PEcAn.allometry 1.7.4
 
 ## License change

diff --git a/modules/assim.batch/DESCRIPTION b/modules/assim.batch/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: PEcAn.assim.batch
 Type: Package
 Title: PEcAn Functions Used for Ecological Forecasts and Reanalysis
-Version: 1.9.0.9000
+Version: 1.9.1
 Authors@R: c(person("Mike", "Dietze", role = c("aut"),
                      email = "dietze@bu.edu"),
              person("Istem", "Fer", role = c("aut", "cre"),

diff --git a/modules/assim.batch/NEWS.md b/modules/assim.batch/NEWS.md
@@ -1,3 +1,9 @@
+# PEcAn.assim.batch 1.9.1
+
+* Added keywords and bug reporting URL to DESCRIPTION.
+* No code changes in this release.
+
+
 # PEcAn.assim.batch 1.9.0
 
 ## License change

diff --git a/modules/assim.sequential/DESCRIPTION b/modules/assim.sequential/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: PEcAnAssimSequential
 Type: Package
 Title: PEcAn Functions Used for Ecological Forecasts and Reanalysis
-Version: 1.9.0.9000
+Version: 1.10.0
 Author: Mike Dietze
 Maintainer: Mike Dietze <dietze@bu.edu>
 Description: The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific

diff --git a/modules/assim.sequential/NEWS.md b/modules/assim.sequential/NEWS.md
@@ -1,3 +1,16 @@
+# PEcAnAssimSequential 1.10.0
+
+## Added
+
+* New function `stack_covariates_2_geotiff` stacks data layers from various GeoTIFFs (with different extents, CRS, and resolutions) to a single map (#3450)
+* New functions `qsub_sda()`, `downscale_qsub_main()`, `qsub_sda()`, `qsub_sda_batch()`, `sda.enkf_local()` for submitting SDA batch jobs by splitting a large number of sites into multiple small groups of sites and spreading their computation across all cores of multiple HPC nodes (#3634, #3450, #3544).
+
+## Changed
+
+* The entire SDA workflow has been overhauled to support parallel computation throughout.
+
+
+
 # PEcAnAssimSequential 1.9.0
 
 ## Added
@@ -11,6 +24,7 @@
 * Documentation improvements
 
 
+
 # PEcAnAssimSequential 1.8.0
 
 

diff --git a/modules/benchmark/DESCRIPTION b/modules/benchmark/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: PEcAn.benchmark
 Type: Package
 Title: PEcAn Functions Used for Benchmarking
-Version: 1.7.4.9000
+Version: 1.7.5
 Authors@R: c(person("Mike", "Dietze", role = c("aut", "cre"),
                      email = "dietze@bu.edu"),
              person("Betsy", "Cowdery", role = c("aut"),

diff --git a/modules/benchmark/NEWS.md b/modules/benchmark/NEWS.md
@@ -1,3 +1,9 @@
+# PEcAn.benchmark 1.7.5
+
+* Added keywords and bug reporting URL to DESCRIPTION.
+* No code changes in this release.
+
+
 # PEcAn.benchmark 1.7.4
 
 * Removed Browndog support

diff --git a/modules/data.atmosphere/NEWS.md b/modules/data.atmosphere/NEWS.md
@@ -1,16 +1,24 @@
 # PEcAn.data.atmosphere 1.9.1
 
-* `ERA5_met_process()` can now process ensemble data efficiently in parallel using new option `n_cores`
+## Added
+* New function `sat_vapor_pressure()` computes saturation vapor pressure from temperature (#3597).
+* New function `AmeriFlux_met_ensemble()` generates weather ensembles from Ameriflux data with ERA5 fallback for missing radiation and soil moisture (#3586).
+* `ERA5_met_process()` gains option `n_cores` to process ensemble data efficiently in parallel (#3563).
+* `download.ERA5_cds` gains options `time`, `dataset`, `product_type`, all defaulting to the values previously hard-coded (#3547).
+
+## Fixed
+* Updated `download.NOAA_GEFS` to work with the current (v12.3) release of GEFS (#3349).
+
+## Changed
 * Dependency `ggplot2` is now suggested rather than required. It is used in two vignettes and for optional diagnostic plots from `debias_met_regression`.
-* `download.ERA5_cds` now uses the R package ecmwfr (replacing python dependency of cdsapi via reticulate), enabling direct NetCDF downloads; and made flexible for both reanalysis and ensemble data product.
-* New function `sat_vapor_pressure()` added for computing saturation vapor pressure from temperature using various methods.
-* Added `AmeriFlux_met_ensemble()` function with ERA5 fallback for AmeriFlux meteorological data processing and ensemble generation
-* `extract.nc.ERA5()` and `met2CF.ERA5` now supports both ensemble and reanalysis data processing .
-* added support for soil temperature, relative humidity, soil moisture, and PPFD downscaling to `met_temporal_downscale.Gaussian_ensemble`
-* `download.NOAA_GEFS` is updated to work again with GEFS v12.3,
-	the current release as of this writing in July 2024 (#3349).
+* `download.ERA5_cds` now downloads NetCDF directly (replacing internal conversion from grib) using the R package ecmwfr (replacing python dependency on cdsapi via reticulate) (#3547).
+* `download.ERA5.cds()` now requires a valid Copernicus CDS API key, replacing the previous `.netrc` authentication. See the [ecmwfr package documentation](https://bluegreen-labs.github.io/ecmwfr/) for details.
+* `extract.nc.ERA5()` and `met2CF.ERA5` now support both ensemble and single-member data products (#3584).
+* added support for soil temperature, relative humidity, soil moisture, and PPFD downscaling to `met_temporal_downscale.Gaussian_ensemble` (#3586).
 * Removed `sitename` and `username` from the formal arguments of `download.NOAA_GEFS`.
-	Before they were silently ignored, now they're treated as part of `...` (which is also ignored!).
+	Before they were silently ignored, now they're treated as part of `...` (which is also ignored!) (#3349).
+
+
 
 # PEcAn.data.atmosphere 1.9.0
 

diff --git a/modules/data.land/DESCRIPTION b/modules/data.land/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: PEcAn.data.land
 Type: Package
 Title: PEcAn Functions Used for Ecological Forecasts and Reanalysis
-Version: 1.8.2
+Version: 1.9.0
 Authors@R: c(person("Mike", "Dietze", role = c("aut", "cre"),
                      email = "dietze@bu.edu"),
              person("David", "LeBauer", role = c("aut"),