Merge pull request #26 from tece-lab/develop

DAISIEutils v1.5.0

.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

.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

.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."
       }
     ],
 

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 = "[email protected]",
            role = c("aut"),
            comment = c(ORCID = "0000-0003-1107-7049")),
-               person(given = "Rampal S.",
+    person(given = "Rampal S.",
            family = "Etienne",
            email = "[email protected]",
            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/[email protected]

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