1
0
mirror of https://github.com/msberends/AMR.git synced 2024-12-25 06:46:11 +01:00

(v1.1.0.9003) CI fix

This commit is contained in:
dr. M.S. (Matthijs) Berends 2020-05-01 09:14:32 +02:00
parent 77d8f97e0c
commit 9fce546901
12 changed files with 30 additions and 37 deletions

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@ -64,10 +64,9 @@ R-release-test-only:
- Rscript -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE, install_pkgdown = TRUE, install_lintr = TRUE)'
- Rscript -e 'devtools::test(stop_on_failure = FALSE)'
cache:
key: release_4_0
key: release
paths:
- installed_deps/
policy: pull # no uploading after run
R-release:
stage: check
@ -91,7 +90,7 @@ R-release:
- '*.Rcheck/*'
expire_in: '1 month'
cache:
key: release_4_0
key: release
paths:
- installed_deps/
@ -118,7 +117,7 @@ R-devel:
- '*.Rcheck/*'
expire_in: '1 month'
cache:
key: devel_4_1
key: devel
paths:
- installed_deps/
@ -126,17 +125,17 @@ lintr:
stage: lint
allow_failure: true
when: always
cache:
key: release_4_0
paths:
- installed_deps/
policy: pull # no uploading after run
only:
- premaster
- master
script:
# check all syntax with lintr
- Rscript -e 'lintr::lint_package()'
cache:
key: release
paths:
- installed_deps/
policy: pull # no uploading after run
pages:
stage: website
@ -154,11 +153,6 @@ codecovr:
stage: coverage
allow_failure: true
when: always
cache:
key: release_4_0
paths:
- installed_deps/
policy: pull # no uploading after run
only:
- premaster
- master
@ -168,3 +162,8 @@ codecovr:
# Sys.setenv(NOT_CRAN = 'true'), because otherwise skip_on_cran() will be applied on Covr too, resulting in extremely low coverage percentages
- Rscript -e "Sys.setenv(NOT_CRAN = 'true'); cc <- covr::package_coverage(line_exclusions = list('R/atc_online.R', 'R/mo_history.R', 'R/mo_source.R', 'R/resistance_predict.R')); covr::codecov(coverage = cc, token = '$codecov'); cat('Code coverage:', covr::percent_coverage(cc))"
coverage: '/Code coverage: \d+\.\d+/'
cache:
key: release
paths:
- installed_deps/
policy: pull # no uploading after run

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@ -1,6 +1,6 @@
Package: AMR
Version: 1.1.0.9002
Date: 2020-04-30
Version: 1.1.0.9003
Date: 2020-05-01
Title: Antimicrobial Resistance Analysis
Authors@R: c(
person(role = c("aut", "cre"),

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@ -1,5 +1,5 @@
# AMR 1.1.0.9002
## <small>Last updated: 30-Apr-2020</small>
# AMR 1.1.0.9003
## <small>Last updated: 01-May-2020</small>
### Changed
* Small fix for some text input that could not be coerced as valid MIC values

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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9002</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9003</span>
</span>
</div>

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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9002</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9003</span>
</span>
</div>

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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9002</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9003</span>
</span>
</div>

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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9002</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9003</span>
</span>
</div>

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@ -43,7 +43,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9002</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9003</span>
</span>
</div>

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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9002</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9003</span>
</span>
</div>
@ -229,13 +229,13 @@
<small>Source: <a href='https://gitlab.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="amr-1-1-0-9002" class="section level1">
<h1 class="page-header" data-toc-text="1.1.0.9002">
<a href="#amr-1-1-0-9002" class="anchor"></a>AMR 1.1.0.9002<small> Unreleased </small>
<div id="amr-1-1-0-9003" class="section level1">
<h1 class="page-header" data-toc-text="1.1.0.9003">
<a href="#amr-1-1-0-9003" class="anchor"></a>AMR 1.1.0.9003<small> Unreleased </small>
</h1>
<div id="last-updated-30-apr-2020" class="section level2">
<div id="last-updated-01-may-2020" class="section level2">
<h2 class="hasAnchor">
<a href="#last-updated-30-apr-2020" class="anchor"></a><small>Last updated: 30-Apr-2020</small>
<a href="#last-updated-01-may-2020" class="anchor"></a><small>Last updated: 01-May-2020</small>
</h2>
<div id="changed" class="section level3">
<h3 class="hasAnchor">

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@ -10,7 +10,7 @@ articles:
WHONET: WHONET.html
benchmarks: benchmarks.html
resistance_predict: resistance_predict.html
last_built: 2020-04-30T16:46Z
last_built: 2020-05-01T07:13Z
urls:
reference: https://msberends.gitlab.io/AMR/reference
article: https://msberends.gitlab.io/AMR/articles

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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9002</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9003</span>
</span>
</div>

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@ -288,10 +288,4 @@ test_that("as.mo works", {
expect_warning(x[[1]] <- "invalid code")
expect_warning(c(x[1], "test"))
# joining on mo class
expect_identical(class(bind_rows(example_isolates,
example_isolates,
example_isolates)$mo),
"mo")
})