diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index afb078d..17d90db 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -3,8 +3,6 @@ on: push: pull_request: - schedule: - - cron: "0 0 * * *" name: R-CMD-check @@ -14,22 +12,23 @@ jobs: name: ${{ matrix.config.os }} (${{ matrix.config.r }}) + if: "contains(github.event.head_commit.message, '[run ci]') || (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/develop') || github.event.pull_request" + strategy: fail-fast: false matrix: config: - - {os: macOS-latest, r: 'release'} + - {os: macos-latest, r: 'release'} - {os: windows-latest, r: 'release'} - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'} - {os: ubuntu-latest, r: 'release'} - - {os: ubuntu-latest, r: 'oldrel-1'} env: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} R_KEEP_PKG_SOURCE: yes steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 - uses: r-lib/actions/setup-pandoc@v2 @@ -41,14 +40,9 @@ jobs: - uses: r-lib/actions/setup-r-dependencies@v2 with: - extra-packages: any::rcmdcheck + extra-packages: any::rcmdcheck, doMC=?ignore needs: check - uses: r-lib/actions/check-r-package@v2 with: upload-snapshots: true - - - name: Show testthat output - if: always() - run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true - shell: bash diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml index a869e0d..ddaeb21 100644 --- a/.github/workflows/test-coverage.yaml +++ b/.github/workflows/test-coverage.yaml @@ -1,28 +1,50 @@ +# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples +# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help on: push: pull_request: - schedule: - - cron: "0 0 * * *" name: test-coverage jobs: test-coverage: runs-on: ubuntu-latest + if: "contains(github.event.head_commit.message, '[run ci]') || (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/develop') || github.event.pull_request" + env: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 - - uses: r-lib/actions/setup-r@v1 + - uses: r-lib/actions/setup-r@v2 with: use-public-rspm: true - - uses: r-lib/actions/setup-r-dependencies@v1 + - uses: r-lib/actions/setup-r-dependencies@v2 with: - extra-packages: covr + extra-packages: any::covr + needs: coverage - name: Test coverage - run: covr::codecov() + run: | + covr::codecov( + quiet = FALSE, + clean = FALSE, + install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package") + ) shell: Rscript {0} + + - name: Show testthat output + if: always() + run: | + ## -------------------------------------------------------------------- + find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true + shell: bash + + - name: Upload test results + if: failure() + uses: actions/upload-artifact@v3 + with: + name: coverage-test-failures + path: ${{ runner.temp }}/package diff --git a/.zenodo.json b/.zenodo.json index fc82104..4a901c7 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -19,6 +19,11 @@ "orcid": "0000-0003-1107-7049", "affiliation": "Uppsala University", "name": "Bilderbeek, Rich\u00e8l J. C." + }, + { + "orcid": "0000-0003-2142-7612", + "affiliation": "University of Groningen", + "name": "Etienne, Rampal S." } ], diff --git a/DESCRIPTION b/DESCRIPTION index 7fa546f..4f0fa2b 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: DAISIEutils Title: Utility Functions for the DAISIE Package -Date: 2022-07-11 -Version: 1.4.0.9000 +Date: 2023-03-01 +Version: 1.5.0 Authors@R: c( person(given = "Pedro", family = "Santos Neves", @@ -23,7 +23,7 @@ Authors@R: c( email = "richel@richelbilderbeek.nl", role = c("aut"), comment = c(ORCID = "0000-0003-1107-7049")), - person(given = "Rampal S.", + person(given = "Rampal S.", family = "Etienne", email = "r.s.etienne@rug.nl", role = c("aut"), @@ -47,6 +47,8 @@ Config/testthat/edition: 3 Imports: sessioninfo, testit, - DAISIE (>= 4.2.1), + DAISIE (>= 4.3.1), ggplot2, cowplot +Remotes: + rsetienne/DAISIE@v4.3.1 diff --git a/NEWS.md b/NEWS.md index 67a27c0..854c30e 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,20 @@ -# DAISIEutils (development version) +# DAISIEutils 1.5.0 + +* Allow relaxed-rate DAISIE ML models. + * This requires new a argument for `run_daisie_ml()` and `setup_model()`: + `par_upper_bound`, which sets the upper limit of the integration of a relaxed + parameter. This defaults to `Inf` in the R function and shell scripts, which + is no upper bound of integration for the relaxed-rate DAISIE model. This + parameter is ignored when using the standard constant-rate case + (i.e., not relaxed-rate). +* Allow 2 type DAISIE ML analyses, handled by `run_daisie_2type_ml()` and +adjacent function `setup_2type_model()`. Similarly add required R +`run_daisie_2type_ml.R` script and shell scripts `submit_run_daisie_2type_ml.sh` +and `submit_run_daisie_2type_ml_long.sh` to run said analyses in an HPCC. +* Package depends on CRAN DAISIE release instead of GitHub repository. Now +requires DAISIE >= v4.3.1 to ensure latest ML related bugfixes are used. +* Add new tests covering new cases. +* Add Rampal Etienne's details to zenodo release. # DAISIEutils 1.4.0