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Update production server to Where To Work v1.0.0 PR #385
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DanWismer authored Oct 2, 2024
1 parent 316b256 commit 3715122
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4 changes: 2 additions & 2 deletions .github/workflows/R-CMD-check-ubuntu.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,7 @@ jobs:
fail-fast: false
matrix:
config:
- {os: ubuntu-20.04, r: '4.1.2'}
- {os: ubuntu-20.04, r: '4.4.1'}

env:
_R_REMOTES_NO_ERRORS_FROM_WARNINGS_: true
Expand All @@ -51,7 +51,7 @@ jobs:
- name: Install dependencies
run: |
options(install.packages.compile.from.source = "never")
install.packages(c("renv", "remotes"))
install.packages(c("renv", "remotes", "testthat", "rvest"))
renv::restore()
remotes::install_cran("rcmdcheck")
remotes::install_cran("covr")
Expand Down
13 changes: 2 additions & 11 deletions .github/workflows/R-CMD-check-windows.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,7 @@ jobs:
fail-fast: false
matrix:
config:
- {os: windows-latest, r: '4.1.2'}
- {os: windows-latest, r: '4.4.1'}

env:
_R_REMOTES_NO_ERRORS_FROM_WARNINGS_: true
Expand All @@ -44,20 +44,11 @@ jobs:

- uses: r-lib/actions/setup-pandoc@v2

- name: Install system dependencies
run: |
pacman -Sy mingw-w64-x86_64-gmp --noconfirm
pacman -Sy mingw-w64-x86_64-glpk --noconfirm
pacman -Sy mingw-w64-x86_64-libxml2 --noconfirm
shell: bash

- name: Install dependencies
run: |
options(install.packages.compile.from.source = "always")
options(pkgType = "source")
Sys.setenv(LIB_XML = "$(MINGW_PREFIX)")
Sys.setenv(GLPK_HOME = "$(MINGW_PREFIX)")
install.packages(c("renv", "remotes"))
install.packages(c("renv", "remotes", "testthat", "rvest"))
renv::restore()
remotes::install_cran("rcmdcheck")
remotes::install_cran("covr")
Expand Down
135 changes: 67 additions & 68 deletions DESCRIPTION
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
Package: wheretowork
Title: Interactive Systematic Conservation Planning Application
Version: 0.0.0.9000
Version: 1.0.0
Description:
Launch an interactive web application for systematic conservation planning.
Data can be accessed using projects available on disk, uploaded using
Expand All @@ -24,83 +24,81 @@ Authors@R: c(
email='[email protected]', role = c('ctb'))
)
Imports:
utils,
stats,
methods,
assertthat (>= 0.2.0),
rlang (>= 0.4.11),
cachem (>= 1.0.5),
cli (>= 3.0.0),
markdown (>= 1.1),
digest (>= 0.6.27),
stringi (>= 1.7.3),
tools (>= 4.0.5),
Matrix (>= 1.3-3),
pryr (>= 0.1.4),
uuid (>= 0.1.4),
scales (>= 1.1.1),
units (>= 0.7.2),
R.utils (>= 2.10.1),
yaml (>= 2.2.1),
config (>= 0.3.1),
openxlsx (>= 4.2.3),
future (>= 1.21.0),
igraph (>= 1.2.6),
RColorBrewer (>= 1.1.2),
viridisLite (>= 0.4.0),
tibble (>= 3.1.1),
withr (>= 2.4.2),
readxl (>= 1.3.1),
data.table (>= 1.14.0),
plyr (>= 1.8.6),
dplyr (>= 1.0.6),
prioritizr (>= 7.1.1),
fasterize (>= 1.0.3),
stats,
utils,
assertthat (>= 0.2.1),
cachem (>= 1.1.0),
cli (>= 3.6.3),
colourpicker (>= 1.3.0),
config (>= 0.3.2),
DT (>= 0.33),
data.table (>= 1.15.4),
digest (>= 0.6.37),
dplyr (>= 1.1.4),
fields (>= 16.2),
future (>= 1.34.0),
golem (>= 0.5.1),
htmltools (>= 0.5.8.1),
htmlwidgets (>= 1.6.4),
igraph (>= 2.0.3),
ipc (>= 0.1.4),
leaflet (>= 2.2.2.9001),
leaflet.extras2 (>= 1.1.0.9000),
lobstr (>= 1.1.2),
markdown (>= 1.13),
Matrix (>= 1.7-0),
openxlsx (>= 4.2.6.1),
pkgload (>= 1.4.0),
plyr (>= 1.8.9),
prioritizr (>= 8.0.4),
purrr (>= 1.0.2),
R.utils (>= 2.12.3),
rcbc (>= 0.1.0.9001),
shiny (>= 1.6.0),
ipc (>= 0.1.3),
golem (>= 0.3.1),
pkgload (>= 1.2.1),
htmlwidgets (>= 1.5.3),
htmltools (>= 0.5.1.1),
shinyjs (>= 2.0.0),
shinyFeedback (>= 0.3.0),
shinyWidgets (>= 0.6.0),
shinybusy (>= 0.2.2),
shinyalert (>= 2.0.0),
leaflet (>= 2.0.3.9000),
leaflet.extras2 (>= 1.1.0),
colourpicker (>= 1.1.0),
DT (>= 0.18),
fields (>= 0.14.1),
terra (>= 1.7.29),
readxl (>= 1.4.3),
rlang (>= 1.1.4),
RColorBrewer (>= 1.1-3),
scales (>= 1.3.0),
shiny (>= 1.9.1),
shinyalert (>= 3.1.0),
shinybusy (>= 0.3.3),
shinyFeedback (>= 0.4.0),
shinyjs (>= 2.1.0),
shinyWidgets (>= 0.8.6),
stringi (>= 1.8.4),
terra (>= 1.7-78),
tibble (>= 3.2.1),
tools (>= 4.0.5),
units (>= 0.8-5),
uuid (>= 1.2-1),
viridisLite (>= 0.4.2),
withr (>= 3.0.1),
yaml (>= 2.3.10)
Suggests:
testthat (>= 2.0.1),
knitr (>= 1.2.0),
roxygen2 (>= 6.1.1),
rmarkdown (>= 1.10),
rvest (>= 1.0.0),
xml2 (>= 1.3.2),
processx (>= 3.5.2),
rsconnect (>= 0.8.18),
devtools (>= 2.4.2),
whereami (>= 0.1.9),
pkgdown (>= 1.6.1.9001),
testthat (>= 3.2.1.1),
knitr (>= 1.48),
roxygen2 (>= 7.3.2),
rmarkdown (>= 2.28),
rvest (>= 1.0.4),
xml2 (>= 1.3.6),
processx (>= 3.8.4),
devtools (>= 2.4.5),
whereami (>= 0.2.0),
pkgdown (>= 2.1.0),
gurobi (>= 10.0-2),
Depends:
R (>= 4.0.0),
shinyBS (>= 0.6.1),
promises (>= 1.2.0.1),
R6 (>= 2.5.0),
raster (>= 3.6.20),
sf (>= 0.9.8),
R (>= 4.4.0),
promises (>= 1.3.0),
R6 (>= 2.5.1),
sf (>= 1.0-16),
shinyBS (>= 0.61.1),
License: GPL-3
Encoding: UTF-8
Language: en-US
URL: https://NCC-CNC.github.io/wheretowork/
BugReports: https://github.com/NCC-CNC/wheretowork/issues
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.1
RoxygenNote: 7.3.2
Collate:
'app_config.R'
'app_global.R'
Expand Down Expand Up @@ -173,6 +171,7 @@ Collate:
'ui_solutionResultsSidebarPane.R'
'utils-tidy-eval.R'
'utils_acknowledge_packages.R'
'utils_blank_raster.R'
'utils_color_palette.R'
'utils_error_misc.R'
'utils_extract_data_matrix.R'
Expand All @@ -196,5 +195,5 @@ Collate:
Remotes:
r-lib/pkgdown,
NCC-CNC/leaflet.extras2,
NCC-CNC/leaflet@pane-extra,
NCC-CNC/leaflet-ncc@pane-extra,
dirkschumacher/rcbc
2 changes: 1 addition & 1 deletion Dockerfile
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
# base image
FROM rocker/shiny:4.1.0 AS base
FROM rocker/shiny:4.4.0 AS base

## remove example apps
RUN rm -rf /srv/shiny-server/*
Expand Down
101 changes: 24 additions & 77 deletions LICENSE.note
Original file line number Diff line number Diff line change
@@ -1,96 +1,43 @@
The wheretowork package as a whole is distributed under GPL-3
(GNU GENERAL PUBLIC LICENSE version 3).
TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION

The wheretowork package includes other open source software components. The
following is a list of these components (full copies of the license agreements used by these components are included below):
1. Definitions.

- d3: https://github.com/d3/d3
- el-checkbox: https://github.com/EvanLiu2968/el-checkbox
- noUiSlider: https://github.com/leongersen/noUiSlider
- Sortable: https://github.com/SortableJS/Sortable
- wNumb: https://github.com/leongersen/wNumb
"License" shall mean the terms and conditions for use, reproduction, and distribution as defined by Sections 1 through 7 of this document.

d3 license
----------------------------------------------------------------------
"Licensor" shall mean the copyright owner or entity authorized by the copyright owner that is granting the License.

Copyright 2010-2021 Mike Bostock
"You" (or "Your") shall mean an individual or entity exercising permissions granted by this License.

Permission to use, copy, modify, and/or distribute this software for any purpose
with or without fee is hereby granted, provided that the above copyright notice
and this permission notice appear in all copies.
"Source" form shall mean the preferred form for making modifications, including but not limited to software source code, documentation source, and configuration files.

THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH
REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND
FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT,
INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER
TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF
THIS SOFTWARE.
"Object" form shall mean any form resulting from mechanical transformation or translation of a Source form, including but not limited to compiled object code, generated documentation, and conversions to other media types.

el-checkbox license
----------------------------------------------------------------------
"Work" shall mean the work of authorship, whether in Source or Object form, made available under the License, as indicated by a copyright notice that is included in or attached to the work.

Copyright (c) 2017 EvanLiu
"Derivative Works" shall mean any work. that is based on (or derived from) the Work and for which the editorial revisions, annotations, elaborations, or other modifications represent, as a whole, an original work of authorship.

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
2. Permission. Subject to the terms and conditions of this License, You are hereby granted a permission to use, copy, modify, merge, publish, or distribute, for non-commercial academic and research purposes only, the Work or any Derivative Works, provided that the appropriate copyright notice(s) and permission notice(s), including but not limited to those provided below, appear in all copies of and/or any materials describing the Work, including websites and other media. In addition, the [https://ncc.carleton.ca/login ] landing page, and all logo(s) shown on the landing page, must be presented in any Work or Derivative Work in their original form.

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
4. Redistribution. You may reproduce and distribute copies of the Work or Derivative Works thereof in any medium, with or without modifications, and in Source or Object form, provided that You meet the following conditions:
a. You must give any other recipients of the Work or Derivative Works a copy of this License; and
b. You must cause any modified files to carry prominent notices stating that You changed the files; and
c. You must retain, in the Source form of any Derivative Works that You distribute, all copyright, patent, trademark, and attribution notices from the Source form of the Work, excluding those notices that do not pertain to any part of the Derivative Works; and
d. If the Work includes a "NOTICE" text file as part of its distribution, then any Derivative Works that You distribute must include a readable copy of the attribution notices contained within such NOTICE file, excluding those notices that do not pertain to any part of the Derivative Works, in at least one of the following places: within a NOTICE text file distributed as part of the Derivative Works; within the Source form or documentation, if provided along with the Derivative Works; or, within a display generated by the Derivative Works, if and wherever such third-party notices normally appear. The contents of the NOTICE file are for informational purposes only and do not modify the License. You may add Your own attribution notices within Derivative Works that You distribute, alongside or as an addendum to the NOTICE text from the Work, provided that such additional attribution notices cannot be construed as modifying the License.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
You may add Your own copyright statement to Your modifications and may provide additional or different license terms and conditions for use, reproduction, or distribution of Your modifications, or for any such Derivative Works as a whole, provided Your use, reproduction, and distribution of the Work otherwise complies with the conditions stated in this License.

noUiSlider license
----------------------------------------------------------------------
5. Trademarks. This License does not grant permission to use the trade names, trademarks, service marks, logos, or product names of the Licensor, except as required for reasonable and customary use in describing the origin of the Work and reproducing the content of the NOTICE file.

Copyright (c) 2019 Léon Gersen
6. Disclaimer of Warranty. THE WORK OR DERIVATIVE WORKS IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN ANACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH, THE WORK OR DERIVATIVE WORKS, OR THE USE OR OTHER DEALINGS IN THE WORK OR DERIVATIVE WORKS.

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
END OF TERMS AND CONDITIONS

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
COPYRIGHT NOTICE:

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
Copyright © 2022 J Hanson, R Shuster, J Bennett, J Vincent, D Wismer, M Edwards

Sortable license
----------------------------------------------------------------------
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to use, copy, modify, merge, publish, or distribute, for non-commercial academic and research purposes only, copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

Copyright (c) 2019 All contributors to Sortable
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software, as well as all materials, including but not limited to websites, portals or documentation, describing or relating to the Software. In addition, the [https://ncc.carleton.ca/login] landing page, and all logo(s) shown on the landing page, must be presented in any Work or Derivative Work in their original form.

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.

wNumb license
----------------------------------------------------------------------

Copyright (c) 2019 Léon Gersen

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
14 changes: 9 additions & 5 deletions NAMESPACE
Original file line number Diff line number Diff line change
@@ -1,12 +1,11 @@
# Generated by roxygen2: do not edit by hand

S3method(simulate_data,Raster)
S3method(simulate_data,SpatRaster)
S3method(simulate_data,sf)
S3method(spatial_data_statistics,Raster)
S3method(spatial_data_statistics,SpatRaster)
S3method(spatial_data_statistics,data.frame)
S3method(spatial_data_statistics,sf)
S3method(spatial_data_type,Raster)
S3method(spatial_data_type,SpatRaster)
S3method(spatial_data_type,data.frame)
S3method(spatial_data_type,sf)
export(":=")
Expand Down Expand Up @@ -93,7 +92,6 @@ export(new_variable_from_metadata)
export(new_weight)
export(new_weight_results)
export(prepare_fileInput)
export(readNamedRaster)
export(read_project)
export(read_spatial_data)
export(removeMapPane)
Expand Down Expand Up @@ -137,13 +135,17 @@ export(write_project)
export(write_spatial_data)
import(R6)
import(promises)
import(raster)
import(sf)
import(shinyBS)
importFrom(R.utils,gzip)
importFrom(future,future)
importFrom(golem,activate_js)
importFrom(golem,add_resource_path)
importFrom(golem,bundle_resources)
importFrom(golem,favicon)
importFrom(ipc,stopMulticoreFuture)
importFrom(plyr,rbind.fill)
importFrom(rcbc,cbc_solve)
importFrom(rlang,":=")
importFrom(rlang,.data)
importFrom(rlang,as_label)
Expand All @@ -153,3 +155,5 @@ importFrom(rlang,enquos)
importFrom(rlang,expr)
importFrom(rlang,sym)
importFrom(rlang,syms)
importFrom(shinyalert,shinyalert)
importFrom(withr,with_dir)
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