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Merge pull request #1791 from PecanProject/release/v1.5.2
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Release/v1.5.2
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mdietze committed Dec 8, 2017
2 parents b3c3982 + 0d7e67b commit 9026e20
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12 changes: 12 additions & 0 deletions .dockerignore
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.git

.install

tests
contrib

modules/rtm/src/RTM/*.o
modules/rtm/src/RTM/*/*.o
modules/rtm/src/RTM/*/*/*.o
modules/rtm/src/*.mod
modules/rtm/src/*.so
131 changes: 131 additions & 0 deletions .zenodo.json
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{
"creators": [
{
"affiliation": "University of Illinois at Urbana-Champaign",
"name": "David LeBauer",
"orcid": "0000-0001-7228-053X"
},
{
"affiliation": "Boston University",
"name": "Michael Dietze",
"orcid": "0000-0002-2324-2518"
},
{
"affiliation": "National Center for Supercomputing Applications",
"name": "Rob Kooper",
"orcid": "0000-0002-5781-7287"
},
{
"affiliation": "Boston University",
"name": "Alexey Shiklomanov",
"orcid": "0000-0003-4022-5979"
},
{
"affiliation": "Boston University",
"name": "Betsy Cowdery",
"orcid": "0000-0002-6538-6296"
},
{
"affiliation": "Boston Univeristy",
"name": "Istem Fer",
"orcid": "0000-0001-8236-303X"
},
{
"affiliation": "Boston Univeristy",
"name": "Anthony Gardella"
},
{
"affiliation": "Pacific Northwest National Laboratory / University of Maryland",
"name": "Ben Bond-Lamberty",
"orcid": "0000-0001-9525-4633"
},
{
"affiliation": "Brookhaven National Laboratory",
"name": "Shawn P. Serbin",
"orcid": "0000-0003-4136-8971"
},
{
"affiliation": "University of Notre Dame",
"name": "Ann Raiho"
},
{
"affiliation": "Brigham Young University",
"name": "Anne Thomas"
},
{
"affiliation": "Pennsylvania State University",
"name": "Chris Black",
"orcid": "0000-0001-8382-298X"
},
{
"affiliation": "University of Wisconsin-Madison",
"name": "James Simkins"
},
{
"affiliation": "University of Wisconsin-Madison",
"name": "Ankur Desai",
"orcid": "0000-0002-5226-6041"
},
{
"affiliation": "Worchester Academy",
"name": "Joshua Mantooth"
},
{
"name": "Aman Kumar"
},
{
"affiliation": "Boston University",
"name": "Liam Burke"
},
{
"affiliation": "Boston University",
"name": "Afshin Pourmokhtarian"
},
{
"affiliation": "Morton Arboretum",
"name": "Christy Rollinson"
},
{
"name": "Shubham Agarwal"
},
{
"affiliation": "Purdue University",
"name": "Brady Hardiman"
},
{
"affiliation": "University of New South Wales",
"name": "Martin De Kauwe",
"orcid": "0000-0002-3399-9098"
},
{
"name": "Eugene"
},
{
"affiliation": "Boston University",
"name": "Tess McCabe"
},
{
"affiliation": "Boston University",
"name": "Katie Ragosta"
},
{
"name": "Tony Cohen"
},
{
"name": "zhangwenx"
},
{
"affiliation": "Finnish Meteorological Institute",
"name": "Tony Viskari",
"oricid": "0000-0002-3357-1374"
},
{
"name": "Yan Zhao"
},
{
"affiliation": "University of Illinois at Urbana-Champaign",
"name": "Jing Xia"
}
],
"access_right": "open",
}
20 changes: 19 additions & 1 deletion CHANGELOG.md
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Expand Up @@ -9,18 +9,36 @@ For more information about this file see also [Keep a Changelog](http://keepacha
## [Unreleased]

### Fixes

### Added

### Removed

### Changed

## [1.5.2] - 2017-12-07

### Fixes
- Updated models/ed/data/pftmapping.csv to include two new BETYdb PFTs
- Simple fix to models/ed/R/write.configs.ed.R to properly align pss and css file prefix
- Fixed issue #1752 by updating the site.lst() function to include `site.id=site$id` instead of site.id=site, as site is an object not just the id
- Update to PEcAn.ED2::met2model.ED2 to fix issue with rhdf5::h5write. Bug fix to #1742
- Fixed write.config.xml.ED2 parsing of data/history* files
- `PEcAn.utils` now lazy-loads data for faster execution of functions that consult lookup tables, especially `to_ncvar`.
- Fixed incorrect `PEcAn.BIOCRO` daily and yearly results: Was calculating every row from whole simulation instead of that day (#1738)

### Added
- New Dockerfile to create PEcAN specific container for SIPNET.

### Removed
- Removed `PEcAn.utils::model2netcdf`, which has been deprecated since PEcAn 1.3.7. Use `model2netcdf.<YOURMODEL>` in the appropriate model package instead.

### Changed
- Major namespace cleanup in the `PEcAn.utils` package. It now loads more quietly and is much less likely to mask functions in a package you loaded earlier.
- Moved many functions from `PEcAn.utils` into other PEcAn packages. The `PEcAn.utils` versions still work with a deprecation warning, but will be removed in a future release.
- Moved many functions from `PEcAn.utils` into other PEcAn packages. The `PEcAn.utils` versions still work with a deprecation warning, but will be removed in next release.
- `listToXml` and `SafeList` moved to `PEcAn.settings`
- `fqdn` moved to `PEcAn.remote`
- PEcAnRTM: Removed effective sample size normalization from likelihood calculation. It was giving weird results.

## [1.5.1] - 2017-10-05

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82 changes: 46 additions & 36 deletions Makefile
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Expand Up @@ -44,48 +44,62 @@ install: $(ALL_PKGS_I) .install/base/all
check: $(ALL_PKGS_C) .check/base/all
test: $(ALL_PKGS_T) .test/base/all

### Dependencies
.doc/base/all: $(ALL_PKGS_D)
.install/base/all: $(ALL_PKGS_I)
.check/base/all: $(ALL_PKGS_C)
.test/base/all: $(ALL_PKGS_T)
depends = .doc/$(1) .install/$(1) .check/$(1) .test/$(1)

$(subst .doc/models/template,,$(MODELS_D)): .install/models/template # for models that import Roxygen docs from template
$(subst .install/base/logger,,$(ALL_PKGS_I)): .install/base/logger
# Make the timestamp directories if they don't exist yet
.doc .install .check .test $(call depends,base) $(call depends,models) $(call depends,modules):
mkdir -p $@

depends = .doc/$(1) .install/$(1) .check/$(1) .test/$(1)
### Dependencies

$(call depends,base/utils): .install/base/remote
$(call depends,base/db): .install/base/utils
$(call depends,base/settings): .install/base/utils .install/base/db
$(call depends,base/visualization): .install/base/db
$(call depends,modules/data.atmosphere): .install/base/utils .install/base/remote
$(call depends,modules/data.land): .install/base/db .install/base/utils .install/base/remote
$(call depends,modules/meta.analysis): .install/base/utils .install/base/db .install/base/remote
$(call depends,modules/priors): .install/base/utils .install/base/remote
$(call depends,modules/assim.batch): .install/base/utils .install/base/db .install/modules/meta.analysis .install/base/remote
$(call depends,modules/rtm): .install/modules/assim.batch .install/base/remote
$(call depends,modules/uncertainty): .install/base/utils .install/modules/priors .install/base/remote
$(call depends,models/template): .install/base/utils .install/base/remote
$(call depends,models/biocro): .install/base/utils .install/base/settings .install/base/db .install/modules/data.atmosphere .install/modules/data.land .install/base/remote
# models import Roxygen docs from *installed* version of template,
# so changes in template mean the models need to be redocumented
$(subst .doc/models/template,,$(MODELS_D)): .install/models/template

### Order-only dependencies
# (i.e. prerequisites must exist before building target, but
# target need not be rebuilt when a prerequisite changes)

.doc/base/all: | $(ALL_PKGS_D)
.install/base/all: | $(ALL_PKGS_I)
.check/base/all: | $(ALL_PKGS_C)
.test/base/all: | $(ALL_PKGS_T)

$(subst .install/base/logger,,$(ALL_PKGS_I)): | .install/base/logger
$(subst .doc/base/logger,,$(ALL_PKGS_D)): | .install/base/logger

$(call depends,base/utils): | .install/base/remote
$(call depends,base/db): | .install/base/utils
$(call depends,base/settings): | .install/base/utils .install/base/db
$(call depends,base/visualization): | .install/base/db
$(call depends,modules/data.atmosphere): | .install/base/utils .install/base/remote
$(call depends,modules/data.land): | .install/base/db .install/base/utils .install/base/remote
$(call depends,modules/meta.analysis): | .install/base/utils .install/base/db .install/base/remote
$(call depends,modules/priors): | .install/base/utils .install/base/remote
$(call depends,modules/assim.batch): | .install/base/utils .install/base/db .install/modules/meta.analysis .install/base/remote
$(call depends,modules/rtm): | .install/modules/assim.batch .install/base/remote
$(call depends,modules/uncertainty): | .install/base/utils .install/modules/priors .install/base/remote
$(call depends,models/template): | .install/base/utils .install/base/remote
$(call depends,models/biocro): | .install/mockery .install/base/utils .install/base/settings .install/base/db .install/modules/data.atmosphere .install/modules/data.land .install/base/remote

clean:
rm -rf .install .check .test .doc
find modules/rtm/src \( -name \*.mod -o -name \*.o -o -name \*.so \) -delete

.install/devtools:
.install/devtools: | .install
Rscript -e "if(!require('devtools')) install.packages('devtools', repos = 'http://cran.rstudio.com', Ncpus = ${NCPUS})"
mkdir -p $(@D)
echo `date` > $@

.install/roxygen2:
.install/roxygen2: | .install
Rscript -e "if(!require('roxygen2')) install.packages('roxygen2', repos = 'http://cran.rstudio.com', Ncpus = ${NCPUS})"
mkdir -p $(@D)
echo `date` > $@

.install/testthat:
.install/testthat: | .install
Rscript -e "if(!require('testthat')) install.packages('testthat', repos = 'http://cran.rstudio.com', Ncpus = ${NCPUS})"
mkdir -p $(@D)
echo `date` > $@

.install/mockery: | .install
Rscript -e "if(!require('mockery')) install.packages('mockery', repos = 'http://cran.rstudio.com', Ncpus = ${NCPUS})"
echo `date` > $@

depends_R_pkg = Rscript -e "devtools::install_deps('$(strip $(1))', threads = ${NCPUS});"
Expand All @@ -94,27 +108,23 @@ check_R_pkg = Rscript scripts/check_with_errors.R $(strip $(1))
test_R_pkg = Rscript -e "devtools::test('"$(strip $(1))"', reporter = 'stop')"
doc_R_pkg = Rscript -e "devtools::document('"$(strip $(1))"')"

$(ALL_PKGS_I) $(ALL_PKGS_C) $(ALL_PKGS_T) $(ALL_PKGS_D): .install/devtools .install/roxygen2 .install/testthat
$(ALL_PKGS_I) $(ALL_PKGS_C) $(ALL_PKGS_T) $(ALL_PKGS_D): | .install/devtools .install/roxygen2 .install/testthat

.SECONDEXPANSION:
.doc/%: $$(wildcard %/**/*) $$(wildcard %/*)
.doc/%: $$(wildcard %/**/*) $$(wildcard %/*) | $$(@D)
$(call depends_R_pkg, $(subst .doc/,,$@))
$(call doc_R_pkg, $(subst .doc/,,$@))
mkdir -p $(@D)
echo `date` > $@

.install/%: $$(wildcard %/**/*) $$(wildcard %/*) .doc/%
.install/%: $$(wildcard %/**/*) $$(wildcard %/*) .doc/% | $$(@D)
$(call install_R_pkg, $(subst .install/,,$@))
mkdir -p $(@D)
echo `date` > $@

.check/%: $$(wildcard %/**/*) $$(wildcard %/*)
.check/%: $$(wildcard %/**/*) $$(wildcard %/*) | $$(@D)
$(call check_R_pkg, $(subst .check/,,$@))
mkdir -p $(@D)
echo `date` > $@

.test/%: $$(wildcard %/**/*) $$(wildcard %/*)
.test/%: $$(wildcard %/**/*) $$(wildcard %/*) | $$(@D)
$(call test_R_pkg, $(subst .test/,,$@))
mkdir -p $(@D)
echo `date` > $@

4 changes: 2 additions & 2 deletions base/all/DESCRIPTION
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Expand Up @@ -2,8 +2,8 @@ Package: PEcAn.all
Type: Package
Title: PEcAn functions used for ecological forecasts and
reanalysis
Version: 1.5.1
Date: 2017-09-25
Version: 1.5.2
Date: 2017-12-04
Author: David LeBauer, Mike Dietze, Xiaohui Feng, Dan Wang,
Mike Dietze, Carl Davidson, Rob Kooper, Shawn Serbin
Maintainer: David LeBauer <dlebauer@illinois.edu>
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4 changes: 2 additions & 2 deletions base/db/DESCRIPTION
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@@ -1,8 +1,8 @@
Package: PEcAn.DB
Type: Package
Title: PEcAn functions used for ecological forecasts and reanalysis
Version: 1.5.1
Date: 2017-09-25
Version: 1.5.2
Date: 2017-12-04
Author: David LeBauer, Mike Dietze, Xiaohui Feng, Dan Wang, Carl
Davidson, Rob Kooper, Shawn Serbin
Maintainer: David LeBauer <dlebauer@illinois.edu>
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1 change: 1 addition & 0 deletions base/db/NAMESPACE
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Expand Up @@ -2,6 +2,7 @@

export(append.covariate)
export(assign.treatments)
export(bety2pecan)
export(betyConnect)
export(db.close)
export(db.exists)
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2 changes: 1 addition & 1 deletion base/db/R/query.file.path.R
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Expand Up @@ -7,7 +7,7 @@
##'
##' @author Betsy Cowdery
query.file.path <- function(input.id, host_name, con){
machine.host <- default_hostname(host_name)
machine.host <- PEcAn.DB::default_hostname(host_name)
machine <- db.query(query = paste0("SELECT * from machines where hostname = '",machine.host,"'"), con = con)
dbfile <- db.query(
query = paste(
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