Merge branch 'release/0.1.2'

.github/workflows/pkgdown.yaml

@@ -50,6 +50,18 @@ jobs:
           echo "TEMP_DIR=$(mktemp -d)" >> $GITHUB_ENV
           echo "WORK_DIR=$(pwd)" >> $GITHUB_ENV
 
+      - name: Build data and configuration archive for AMAP/external
+        run: |
+          mkdir -p $TEMP_DIR/external
+          cp -R data/example_external_data $TEMP_DIR/external/
+          mv $TEMP_DIR/external/example_external_data $TEMP_DIR/external/data
+          cp -R information/AMAP $TEMP_DIR/external/
+          mv $TEMP_DIR/external/AMAP $TEMP_DIR/external/information
+          cd $TEMP_DIR
+          zip -r $WORK_DIR/docs/external.zip external
+          cd $WORK_DIR
+        continue-on-error: true
+
       - name: Build data and configuration archive for OSPAR 2022
         run: |
           mkdir -p $TEMP_DIR/ospar

CHANGES.md

@@ -1,5 +1,10 @@
 ## Change log
 
+### Version 0.1.2
+
+- Fixed issues when packaged; see #326, #328
+- Updated AMAP data and packaging; see #329
+
 ### Version 0.1.1
 
 - Fixed issue with auxiliary variables: see #289

CONTRIBUTING.md

@@ -1,47 +1,5 @@
 # Contributor's Guide
 
-This document will help you set up access to the main repository for
-the `harsat` code, and help you contribute to the code.
-
-## Summary
-
-* Main repository on Github: https://github.com/osparcomm/HARSAT
-* Repository is currently *private* -- for access permissions, contact 
-  [Chris Moulton](https://github.com/moultonc) or the OSPAR team, as they
-  are the ones who administer the repository on Github. You will need this access to 
-  both read the code and to contribute.
-* Web documentation on Github Pages: https://osparcomm.github.io/HARSAT/
-
-
-## Packaging
-
-Our aim is to make the `harsat` code work as an R package. It is not
-going to be distributed on CRAN for the near future at least. Instead,
-it can be installed directly from Github. 
-
-To install the latest **development** version, use the `remotes` package:
-
-```
-library(remotes)
-remotes::install_github("osparcomm/harsat", auth_token = 'XXXX')
-```
-
-Installing the latest stable version is similar, but is less likely to
-change or break. The web documentation reflects the stable version, not
-the development version.
-
-```
-library(remotes)
-remotes::install_github("osparcomm/harsat@main", auth_token = 'XXXX')
-```
-
-This should install all the `harsat` code with all its dependencies.
-
-> Note: during development the repository is marked as private on GitHub, so you
-> will need a GitHub Personal Access Token (or PAT) to access it. Put it in the
-> call above as the 'XXXX' string.
-
-
 ## Contributing
 
 ### Issues
@@ -66,22 +24,19 @@ them into the issue directly.
 ### Pull requests
 
 We welcome pull requests. The easiest way to do this is to fork the repository
-on Github, make the changes you want in your fork, push them to Github, and create 
-a pull request using its web interface. At that point it will show up on the
-main repository and we can collaborate with you to integrate it into the 
-code.
-
-Please note that we are particularly keen to improve the code quality. 
+on Github, make the changes you want in your fork, push them to Github, and create
+a pull request using its web interface. This will then be sent to the
+[CODEOWNERS](link to: CODEOWNERS) for review and the pull request
+approved/rejected as appropriate.
 
 
 ## Documentation
 
 All documentation is held within the Github repository. We use the following
 flow.
 
-1. `roxygen2` is used for source-code documentation. We particularly welcome
-   pull requests to improve this documentation. 
-2. We have several vignettes in the `vignettes` directory. Some actually run `harsat` code (the ones 
+1. `roxygen2` is used for source-code documentation. 
+2. We have several vignettes in the `vignettes` directory. Some run `harsat` code (the ones
    matching `*.Rmd.orig`) and are therefore *precompiled*, because they can take 15-20 minutes
    to run. That turns `*.Rmd.orig` into corresponding `*.Rmd` files. Then, the 
    normal documentation building for vignettes on installation will deploy these

DESCRIPTION

@@ -1,22 +1,17 @@
 Package: harsat
 Title: Harmonized Regional Seas Assessment Tool
-Version: 0.1.1
+Version: 0.1.2
 Authors@R: c(
-    person(given = "Rob", family = "Fryer", email = "[email protected]", role = c("aut")),
-    person(given = "Leszek", family = "Kaliciak", email = "[email protected]", role = c("aut")),
-    person(given = "Scottish Government", email = "[email protected]", role = c("fnd", "aut")),
-    person(given = "AmbieSense Ltd", email = "[email protected]", role = c("cph", "cre", "aut")),
-    person(given = "Helsinki Commission (HELCOM)", email = "[email protected]", role = c("cph", "fnd", "ctb")),
-    person(given = "Arctic Monitoring and Assessment Programme (AMAP)", email = "[email protected]", role = c("cph", "fnd", "ctb")),
-    person(given = "OSPAR Commission (OSPAR)", email = "[email protected]", role = c("cph", "fnd", "ctb")),
-    person(given = "International Council for the Exploration of the Sea (ICES)", email = "[email protected]", role = c("cph", "aut"))
+    person(given = "Arctic Monitoring and Assessment Programme (AMAP)", email = "[email protected]", role = c("cph", "fnd", "aut")),
+    person(given = "Helsinki Commission (HELCOM)", email = "[email protected]", role = c("cph", "fnd", "aut")),
+    person(given = "OSPAR Commission (OSPAR)", email = "[email protected]", role = c("cph", "fnd", "cre", "aut")),
+    person(given = "International Council for the Exploration of the Sea (ICES)", email = "[email protected]", role = c("cph", "aut")),
+    person(given = "AmbieSense Ltd", email = "[email protected]", role = c("cph", "aut"))
   )
-Description: Assessment of concentrations of hazardous substances and their
-  biological effects in the marine environment. The code supports periodic
-  international assessments by OSPAR, HELCOM and AMAP and also assessments
-  by individual users. Includes tools for pre-processing data, statistical
-  trend analysis and comparison with threshold values, and post-processing
-  for archiving and reporting.
+Description: Tools for the assessment of data concerning contaminants (hazardous
+  substances) and their effects in the marine environment. The code includes
+  tools for pre-processing data, statistical trend analysis and comparison with
+  threshold values, and post-processing for archiving and reporting.
 License: file LICENSE
 Encoding: UTF-8
 URL: https://github.com/osparcomm/HARSAT, https://osparcomm.github.io/HARSAT/
@@ -43,7 +38,7 @@ Imports:
   tidyr,
   sf
 Suggests: 
-    knitr,
-    rmarkdown,
-    testthat (>= 3.0.0)
+  knitr,
+  rmarkdown,
+  testthat (>= 3.0.0)
 Config/testthat/edition: 3

LICENSE

@@ -1,18 +1,21 @@
 The Copyright to all software developed in the HARSAT project is Shared by 
 the following Parties:
 
-1. The Secretariat of the Arctic Monitoring and Assessment Programme (AMAP)
-2. The Secretariat of the Helsinki Commission (HELCOM)
-3. The Secretariat of the OSPAR Commission (OSPAR)
-4. The Secretariat for the International Council for the Exploration of the Sea (ICES)
-5. AmbieSense Ltd (AMB)
+* The Secretariat of the Arctic Monitoring and Assessment Programme (AMAP)
+* The Secretariat of the Helsinki Commission (HELCOM)
+* The Secretariat of the OSPAR Commission (OSPAR)
+* The Secretariat for the International Council for the Exploration of the Sea (ICES)
+* AmbieSense Ltd (AMB)
+
+HARSAT - Harmonised Regional Seas Assessment Tool code is subject to
+a GNU GPL >= 3.0 license. 
 
-The HARSAT project software will be released as open source, subject to a 
-GNU GPL >= 3.0 license for third parties to use. 
+HARSAT - Harmonised Regional Seas Assessment Tool – User Documentation is
+subject to a Creative Commons Attributional licence - CC-BY-4.0
 
-Additional documentation, as well as test datasets produced and made available 
-by the HARSAT project, is subject to a Creative Common licence (CC-BY-4.0), 
-unless otherwise covered by the rights of original information and/or data 
-originators.
-
-The HARSAT code is based on code originally developed by the Scottish Government.
+HARSAT – Example data provided under the "data" folder are subject to a 
+Creative Common Attributional licence - CC-BY-4.0; unless otherwise covered
+by the rights of original information and/or data originators.
+ 
+The HARSAT code is based on code originally developed by the Scottish Government
+as Contaminant Time Series Analysis (COTSA), for work under OSPAR.

NAMESPACE

@@ -29,6 +29,7 @@ export(ctsm_uncrt_plot_data)
 export(ctsm_uncrt_plot_estimates)
 export(ctsm_uncrt_workup)
 export(get_AC)
+export(get_AC_biota_OSPAR)
 export(get_basis_biota_OSPAR)
 export(get_basis_default)
 export(get_basis_most_common)