From 7410d5d87deb09cf1a9d2bd44d82ee1d967ea9d3 Mon Sep 17 00:00:00 2001
From: Astre Benjamin <benjamin.astre@inrae.fr>
Date: Tue, 4 Oct 2022 15:44:06 +0200
Subject: [PATCH 01/29] Add a TODO related to warning catched management...
---
templates/templates-r.yml | 1 +
1 file changed, 1 insertion(+)
diff --git a/templates/templates-r.yml b/templates/templates-r.yml
index b4c58e0..c190190 100644
--- a/templates/templates-r.yml
+++ b/templates/templates-r.yml
@@ -37,6 +37,7 @@
warn = 2);
allMessages <- vector("character");
errorOccurs <- FALSE;
+ # TODO Attention le catch warning arrête le code sous-jacent !
tryCatch(
{
con <- textConnection(object = "allMessages",
--
GitLab
From a67e3140c11919fc8d2cad4bf84b88dd2cecdf6f Mon Sep 17 00:00:00 2001
From: Astre Benjamin <benjamin.astre@inrae.fr>
Date: Tue, 4 Oct 2022 15:50:21 +0200
Subject: [PATCH 02/29] Rearrange tests related data
---
.gitlab-ci.yml | 10 +++++-----
.../.gitlab-ci-checkers-tests.yml | 20 +++++++++----------
.../.gitlab-ci-docker-tests.yml | 16 +++++++--------
...itlab-ci-gitlab-package-registry-tests.yml | 0
.../.gitlab-ci-r-tests.yml | 8 ++++----
.../.gitlab-ci-runner-tests.yml | 0
{test => tests}/Checkers-find-test-bad.txt | 0
{test => tests}/Checkers-find-test-good.txt | 0
{test => tests}/Dockerfile-test-linux | 0
{test => tests}/Dockerfile-test-windows | 0
{test => tests}/DummyFile | 0
.../r-package-bad-deps/.Rbuildignore | 0
{test => tests}/r-package-bad-deps/.gitignore | 0
.../r-package-bad-deps/DESCRIPTION | 0
{test => tests}/r-package-bad-deps/LICENSE.md | 0
{test => tests}/r-package-bad-deps/NEWS.md | 0
{test => tests}/r-package-bad-deps/R/dummy.R | 0
{test => tests}/r-package-bad-deps/README.Rmd | 0
.../r-package-bad-deps/tests/spelling.R | 0
.../r-package-bad-deps/tests/testthat.R | 0
.../tests/testthat/test-dummy.R | 0
{test => tests}/r-package/.Rbuildignore | 0
{test => tests}/r-package/.gitignore | 0
{test => tests}/r-package/DESCRIPTION | 0
{test => tests}/r-package/LICENSE.md | 0
{test => tests}/r-package/NEWS.md | 0
{test => tests}/r-package/R/dummy.R | 0
{test => tests}/r-package/README.Rmd | 0
{test => tests}/r-package/tests/spelling.R | 0
{test => tests}/r-package/tests/testthat.R | 0
.../r-package/tests/testthat/test-dummy.R | 0
31 files changed, 27 insertions(+), 27 deletions(-)
rename .gitlab-ci-checkers-tests.yml => tests/.gitlab-ci-checkers-tests.yml (86%)
rename .gitlab-ci-docker-tests.yml => tests/.gitlab-ci-docker-tests.yml (90%)
rename .gitlab-ci-gitlab-package-registry-tests.yml => tests/.gitlab-ci-gitlab-package-registry-tests.yml (100%)
rename .gitlab-ci-r-tests.yml => tests/.gitlab-ci-r-tests.yml (88%)
rename .gitlab-ci-runner-tests.yml => tests/.gitlab-ci-runner-tests.yml (100%)
rename {test => tests}/Checkers-find-test-bad.txt (100%)
rename {test => tests}/Checkers-find-test-good.txt (100%)
rename {test => tests}/Dockerfile-test-linux (100%)
rename {test => tests}/Dockerfile-test-windows (100%)
rename {test => tests}/DummyFile (100%)
rename {test => tests}/r-package-bad-deps/.Rbuildignore (100%)
rename {test => tests}/r-package-bad-deps/.gitignore (100%)
rename {test => tests}/r-package-bad-deps/DESCRIPTION (100%)
rename {test => tests}/r-package-bad-deps/LICENSE.md (100%)
rename {test => tests}/r-package-bad-deps/NEWS.md (100%)
rename {test => tests}/r-package-bad-deps/R/dummy.R (100%)
rename {test => tests}/r-package-bad-deps/README.Rmd (100%)
rename {test => tests}/r-package-bad-deps/tests/spelling.R (100%)
rename {test => tests}/r-package-bad-deps/tests/testthat.R (100%)
rename {test => tests}/r-package-bad-deps/tests/testthat/test-dummy.R (100%)
rename {test => tests}/r-package/.Rbuildignore (100%)
rename {test => tests}/r-package/.gitignore (100%)
rename {test => tests}/r-package/DESCRIPTION (100%)
rename {test => tests}/r-package/LICENSE.md (100%)
rename {test => tests}/r-package/NEWS.md (100%)
rename {test => tests}/r-package/R/dummy.R (100%)
rename {test => tests}/r-package/README.Rmd (100%)
rename {test => tests}/r-package/tests/spelling.R (100%)
rename {test => tests}/r-package/tests/testthat.R (100%)
rename {test => tests}/r-package/tests/testthat/test-dummy.R (100%)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index cc7cef5..6317a23 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -1,6 +1,6 @@
include:
- - local: '/.gitlab-ci-runner-tests.yml'
- - local: '/.gitlab-ci-docker-tests.yml'
- - local: '/.gitlab-ci-checkers-tests.yml'
- - local: '/.gitlab-ci-gitlab-package-registry-tests.yml'
- - local: '/.gitlab-ci-r-tests.yml'
+ - local: '/tests/.gitlab-ci-runner-tests.yml'
+ - local: '/tests/.gitlab-ci-docker-tests.yml'
+ - local: '/tests/.gitlab-ci-checkers-tests.yml'
+ - local: '/tests/.gitlab-ci-gitlab-package-registry-tests.yml'
+ - local: '/tests/.gitlab-ci-r-tests.yml'
diff --git a/.gitlab-ci-checkers-tests.yml b/tests/.gitlab-ci-checkers-tests.yml
similarity index 86%
rename from .gitlab-ci-checkers-tests.yml
rename to tests/.gitlab-ci-checkers-tests.yml
index 2f0db76..e1d4ae1 100644
--- a/.gitlab-ci-checkers-tests.yml
+++ b/tests/.gitlab-ci-checkers-tests.yml
@@ -5,7 +5,7 @@ include:
Test check-find-linux Bad:
variables:
- SEARCH_FILES: test/Checkers-find-test-bad.txt
+ SEARCH_FILES: tests/Checkers-find-test-bad.txt
FOUND_RETURN_CODE: 0
NOTFOUND_RETURN_CODE: 1
extends:
@@ -15,12 +15,12 @@ Test check-find-linux Bad:
- .gitlab-ci.yml
- .gitlab-ci-checkers-tests.yml
- templates/templates-checkers.yml
- - test/Checkers-find-test-bad.txt
+ - tests/Checkers-find-test-bad.txt
allow_failure: false
Test check-find-windows Bad:
variables:
- SEARCH_FILE: test/Checkers-find-test-bad.txt
+ SEARCH_FILE: tests/Checkers-find-test-bad.txt
FOUND_RETURN_CODE: 0
NOTFOUND_RETURN_CODE: 1
extends:
@@ -30,12 +30,12 @@ Test check-find-windows Bad:
- .gitlab-ci.yml
- .gitlab-ci-checkers-tests.yml
- templates/templates-checkers.yml
- - test/Checkers-find-test-bad.txt
+ - tests/Checkers-find-test-bad.txt
allow_failure: false
Test check-find-linux Good:
variables:
- SEARCH_FILES: test/Checkers-find-test-good.txt
+ SEARCH_FILES: tests/Checkers-find-test-good.txt
extends:
- .check-find-bad-keyworkds-in-files-linux
rules:
@@ -43,12 +43,12 @@ Test check-find-linux Good:
- .gitlab-ci.yml
- .gitlab-ci-checkers-tests.yml
- templates/templates-checkers.yml
- - test/Checkers-find-test-good.txt
+ - tests/Checkers-find-test-good.txt
allow_failure: false
Test check-find-windows Good:
variables:
- SEARCH_FILE: test/Checkers-find-test-good.txt
+ SEARCH_FILE: tests/Checkers-find-test-good.txt
extends:
- .check-find-bad-keyworkds-in-file-windows
rules:
@@ -56,7 +56,7 @@ Test check-find-windows Good:
- .gitlab-ci.yml
- .gitlab-ci-checkers-tests.yml
- templates/templates-checkers.yml
- - test/Checkers-find-test-good.txt
+ - tests/Checkers-find-test-good.txt
allow_failure: false
Test check-git-uncommitted-changes No:
@@ -86,10 +86,10 @@ Before test change versioned file:
- .gitlab-ci-checkers-tests.yml
- templates/templates-checkers.yml
script:
- - echo "Hello, world." > test/DummyFile
+ - echo "Hello, world." > tests/DummyFile
artifacts:
paths:
- - test/DummyFile
+ - tests/DummyFile
Before test add a file:
rules:
diff --git a/.gitlab-ci-docker-tests.yml b/tests/.gitlab-ci-docker-tests.yml
similarity index 90%
rename from .gitlab-ci-docker-tests.yml
rename to tests/.gitlab-ci-docker-tests.yml
index 6e673f0..cd8eaa6 100644
--- a/.gitlab-ci-docker-tests.yml
+++ b/tests/.gitlab-ci-docker-tests.yml
@@ -11,7 +11,7 @@ Test Docker Build and Push Linux:
tags:
- docker
variables:
- DOCKERFILE_PATH: test/Dockerfile-test-linux
+ DOCKERFILE_PATH: tests/Dockerfile-test-linux
extends:
- .gitlab-docker-registry-login-dind-vars
- .gitlab-docker-registry-login-linux
@@ -22,13 +22,13 @@ Test Docker Build and Push Linux:
- .gitlab-ci-docker-tests.yml
- templates/templates-gitlab-docker-registry.yml
- templates/templates-docker.yml
- - test/Dockerfile-test-linux
+ - tests/Dockerfile-test-linux
Test Docker Build and Push Windows:
tags:
- windows-shell
variables:
- DOCKERFILE_PATH: test/Dockerfile-test-windows
+ DOCKERFILE_PATH: tests/Dockerfile-test-windows
CONTAINER_TAG: ${BASE_CONTAINER_TAG}-windows
extends:
- .gitlab-docker-registry-login-windows
@@ -39,7 +39,7 @@ Test Docker Build and Push Windows:
- .gitlab-ci-docker-tests.yml
- templates/templates-gitlab-docker-registry.yml
- templates/templates-docker.yml
- - test/Dockerfile-test-windows
+ - tests/Dockerfile-test-windows
Test Docker Push latest Linux:
image: docker:20
@@ -58,7 +58,7 @@ Test Docker Push latest Linux:
- .gitlab-ci-docker-tests.yml
- templates/templates-gitlab-docker-registry.yml
- templates/templates-docker.yml
- - test/Dockerfile-test-linux
+ - tests/Dockerfile-test-linux
Test Docker Push latest Windows:
tags:
@@ -76,7 +76,7 @@ Test Docker Push latest Windows:
- .gitlab-ci-docker-tests.yml
- templates/templates-gitlab-docker-registry.yml
- templates/templates-docker.yml
- - test/Dockerfile-test-windows
+ - tests/Dockerfile-test-windows
Test Docker Push tag Linux:
image: docker:20
@@ -95,7 +95,7 @@ Test Docker Push tag Linux:
- .gitlab-ci-docker-tests.yml
- templates/templates-gitlab-docker-registry.yml
- templates/templates-docker.yml
- - test/Dockerfile-test-linux
+ - tests/Dockerfile-test-linux
Test Docker Push tag Windows:
tags:
@@ -113,7 +113,7 @@ Test Docker Push tag Windows:
- .gitlab-ci-docker-tests.yml
- templates/templates-gitlab-docker-registry.yml
- templates/templates-docker.yml
- - test/Dockerfile-test-windows
+ - tests/Dockerfile-test-windows
# Cleanup for generated image in the registry is done by the project cleanup policy
# (see https://forgemia.inra.fr/urep/dev_utils/gitlab-ci-templates/-/settings/packages_and_registries).
diff --git a/.gitlab-ci-gitlab-package-registry-tests.yml b/tests/.gitlab-ci-gitlab-package-registry-tests.yml
similarity index 100%
rename from .gitlab-ci-gitlab-package-registry-tests.yml
rename to tests/.gitlab-ci-gitlab-package-registry-tests.yml
diff --git a/.gitlab-ci-r-tests.yml b/tests/.gitlab-ci-r-tests.yml
similarity index 88%
rename from .gitlab-ci-r-tests.yml
rename to tests/.gitlab-ci-r-tests.yml
index 2352bf6..0bdc9db 100644
--- a/.gitlab-ci-r-tests.yml
+++ b/tests/.gitlab-ci-r-tests.yml
@@ -11,11 +11,11 @@ Test R-install-package-dependencies-withCache Good:
- .gitlab-ci.yml
- .gitlab-ci-r-tests.yml
- templates/templates-r.yml
- - test/r-package
+ - tests/r-package
variables:
TEST_ERROR: 0
script:
- - cd test/r-package
+ - cd tests/r-package
- !reference [.R-install-package-dependencies-withCache, script]
Test R-install-package-dependencies-withCache Bad:
@@ -26,9 +26,9 @@ Test R-install-package-dependencies-withCache Bad:
- .gitlab-ci.yml
- .gitlab-ci-r-tests.yml
- templates/templates-r.yml
- - test/r-package
+ - tests/r-package
variables:
TEST_ERROR: 1
script:
- - cd test/r-package-bad-deps
+ - cd tests/r-package-bad-deps
- !reference [.R-install-package-dependencies-withCache, script]
diff --git a/.gitlab-ci-runner-tests.yml b/tests/.gitlab-ci-runner-tests.yml
similarity index 100%
rename from .gitlab-ci-runner-tests.yml
rename to tests/.gitlab-ci-runner-tests.yml
diff --git a/test/Checkers-find-test-bad.txt b/tests/Checkers-find-test-bad.txt
similarity index 100%
rename from test/Checkers-find-test-bad.txt
rename to tests/Checkers-find-test-bad.txt
diff --git a/test/Checkers-find-test-good.txt b/tests/Checkers-find-test-good.txt
similarity index 100%
rename from test/Checkers-find-test-good.txt
rename to tests/Checkers-find-test-good.txt
diff --git a/test/Dockerfile-test-linux b/tests/Dockerfile-test-linux
similarity index 100%
rename from test/Dockerfile-test-linux
rename to tests/Dockerfile-test-linux
diff --git a/test/Dockerfile-test-windows b/tests/Dockerfile-test-windows
similarity index 100%
rename from test/Dockerfile-test-windows
rename to tests/Dockerfile-test-windows
diff --git a/test/DummyFile b/tests/DummyFile
similarity index 100%
rename from test/DummyFile
rename to tests/DummyFile
diff --git a/test/r-package-bad-deps/.Rbuildignore b/tests/r-package-bad-deps/.Rbuildignore
similarity index 100%
rename from test/r-package-bad-deps/.Rbuildignore
rename to tests/r-package-bad-deps/.Rbuildignore
diff --git a/test/r-package-bad-deps/.gitignore b/tests/r-package-bad-deps/.gitignore
similarity index 100%
rename from test/r-package-bad-deps/.gitignore
rename to tests/r-package-bad-deps/.gitignore
diff --git a/test/r-package-bad-deps/DESCRIPTION b/tests/r-package-bad-deps/DESCRIPTION
similarity index 100%
rename from test/r-package-bad-deps/DESCRIPTION
rename to tests/r-package-bad-deps/DESCRIPTION
diff --git a/test/r-package-bad-deps/LICENSE.md b/tests/r-package-bad-deps/LICENSE.md
similarity index 100%
rename from test/r-package-bad-deps/LICENSE.md
rename to tests/r-package-bad-deps/LICENSE.md
diff --git a/test/r-package-bad-deps/NEWS.md b/tests/r-package-bad-deps/NEWS.md
similarity index 100%
rename from test/r-package-bad-deps/NEWS.md
rename to tests/r-package-bad-deps/NEWS.md
diff --git a/test/r-package-bad-deps/R/dummy.R b/tests/r-package-bad-deps/R/dummy.R
similarity index 100%
rename from test/r-package-bad-deps/R/dummy.R
rename to tests/r-package-bad-deps/R/dummy.R
diff --git a/test/r-package-bad-deps/README.Rmd b/tests/r-package-bad-deps/README.Rmd
similarity index 100%
rename from test/r-package-bad-deps/README.Rmd
rename to tests/r-package-bad-deps/README.Rmd
diff --git a/test/r-package-bad-deps/tests/spelling.R b/tests/r-package-bad-deps/tests/spelling.R
similarity index 100%
rename from test/r-package-bad-deps/tests/spelling.R
rename to tests/r-package-bad-deps/tests/spelling.R
diff --git a/test/r-package-bad-deps/tests/testthat.R b/tests/r-package-bad-deps/tests/testthat.R
similarity index 100%
rename from test/r-package-bad-deps/tests/testthat.R
rename to tests/r-package-bad-deps/tests/testthat.R
diff --git a/test/r-package-bad-deps/tests/testthat/test-dummy.R b/tests/r-package-bad-deps/tests/testthat/test-dummy.R
similarity index 100%
rename from test/r-package-bad-deps/tests/testthat/test-dummy.R
rename to tests/r-package-bad-deps/tests/testthat/test-dummy.R
diff --git a/test/r-package/.Rbuildignore b/tests/r-package/.Rbuildignore
similarity index 100%
rename from test/r-package/.Rbuildignore
rename to tests/r-package/.Rbuildignore
diff --git a/test/r-package/.gitignore b/tests/r-package/.gitignore
similarity index 100%
rename from test/r-package/.gitignore
rename to tests/r-package/.gitignore
diff --git a/test/r-package/DESCRIPTION b/tests/r-package/DESCRIPTION
similarity index 100%
rename from test/r-package/DESCRIPTION
rename to tests/r-package/DESCRIPTION
diff --git a/test/r-package/LICENSE.md b/tests/r-package/LICENSE.md
similarity index 100%
rename from test/r-package/LICENSE.md
rename to tests/r-package/LICENSE.md
diff --git a/test/r-package/NEWS.md b/tests/r-package/NEWS.md
similarity index 100%
rename from test/r-package/NEWS.md
rename to tests/r-package/NEWS.md
diff --git a/test/r-package/R/dummy.R b/tests/r-package/R/dummy.R
similarity index 100%
rename from test/r-package/R/dummy.R
rename to tests/r-package/R/dummy.R
diff --git a/test/r-package/README.Rmd b/tests/r-package/README.Rmd
similarity index 100%
rename from test/r-package/README.Rmd
rename to tests/r-package/README.Rmd
diff --git a/test/r-package/tests/spelling.R b/tests/r-package/tests/spelling.R
similarity index 100%
rename from test/r-package/tests/spelling.R
rename to tests/r-package/tests/spelling.R
diff --git a/test/r-package/tests/testthat.R b/tests/r-package/tests/testthat.R
similarity index 100%
rename from test/r-package/tests/testthat.R
rename to tests/r-package/tests/testthat.R
diff --git a/test/r-package/tests/testthat/test-dummy.R b/tests/r-package/tests/testthat/test-dummy.R
similarity index 100%
rename from test/r-package/tests/testthat/test-dummy.R
rename to tests/r-package/tests/testthat/test-dummy.R
--
GitLab
From 28e7a1eadaa6825eb0de1593ed872a428685a1a2 Mon Sep 17 00:00:00 2001
From: Astre Benjamin <benjamin.astre@inrae.fr>
Date: Tue, 4 Oct 2022 18:25:52 +0200
Subject: [PATCH 03/29] Reorganize code
---
.lintr | 7 ++
R/installDepsWithErrManagement.R | 108 +++++++++++++++++++++++++++++++
R/optionsForCi.R | 15 +++++
templates/templates-r.yml | 66 +++++++------------
4 files changed, 154 insertions(+), 42 deletions(-)
create mode 100644 .lintr
create mode 100644 R/installDepsWithErrManagement.R
create mode 100644 R/optionsForCi.R
diff --git a/.lintr b/.lintr
new file mode 100644
index 0000000..feae1da
--- /dev/null
+++ b/.lintr
@@ -0,0 +1,7 @@
+linters: linters_with_defaults(
+ line_length_linter = line_length_linter(100L),
+ object_name_linter = object_name_linter(styles = c("snake_case",
+ "CamelCase",
+ "camelCase")),
+ cyclocomp_linter = NULL
+ )
diff --git a/R/installDepsWithErrManagement.R b/R/installDepsWithErrManagement.R
new file mode 100644
index 0000000..965fc6f
--- /dev/null
+++ b/R/installDepsWithErrManagement.R
@@ -0,0 +1,108 @@
+#' @title devtools::install_dev_deps with error management
+#' @description Add an error and warning management around
+#' devtools::install_dev_deps call.
+#' Useful for any R CI.
+#' @param warningsAsErrors Boolean,
+#' TRUE to manage warnings and errors as errors.
+#' FALSE to manage only errors as errors.
+#' @param printAllMessages Boolean, TRUE to print all messages
+#' printed by devtools::install_dev_deps
+#' @return A list with:
+#' - errorOccurs: a boolean at TRUE if an error or a warning occurs
+#' - allMessages: a vector containing all messages
+#' generated by devtools::install_dev_deps
+#' @examples
+#' installDepsWithErrManagement(warningsAsErrors = TRUE, printAllMessages = TRUE)
+installDepsWithErrManagement <- function(warningsAsErrors = FALSE,
+ printAllMessages = TRUE) {
+ allMessages <- vector("character")
+ errorOccurs <- FALSE
+
+ # Call devtools::install_dev_deps and catch error and/or warnings
+ # All generated messages are catched by textConnection con and sink command
+ if (warningsAsErrors) {
+ errorOccurs <- tryCatch(
+ expr = {
+ con <- textConnection(
+ object = "allMessages",
+ open = "wr",
+ local = TRUE)
+ sink(file = con, type = "output")
+ sink(file = con, type = "message")
+
+ repo <- "https://cloud.r-project.org"
+ update.packages(ask = FALSE, repos = repo)
+
+ # Install devtools and stringi packages which are used here
+ install.packages(pkgs = "devtools", repos = repo)
+ install.packages(pkgs = "stringi", repos = repo)
+
+ devtools::install_dev_deps(dependencies = TRUE,
+ upgrade = "always")
+ FALSE
+ },
+ error = function(e) {
+ return(TRUE)
+ },
+ warning = function(w) {
+ return(TRUE)
+ },
+ finally = {
+ sink(type = "output")
+ sink(type = "message")
+ close(con)
+ })
+ } else {
+ errorOccurs <- tryCatch(
+ expr = {
+ con <- textConnection(
+ object = "allMessages",
+ open = "wr",
+ local = TRUE)
+ sink(file = con, type = "output")
+ sink(file = con, type = "message")
+
+ repo <- "https://cloud.r-project.org"
+ update.packages(ask = FALSE, repos = repo)
+
+ # Install devtools and stringi packages which are used here
+ install.packages(pkgs = "devtools", repos = repo)
+ install.packages(pkgs = "stringi", repos = repo)
+
+ devtools::install_dev_deps(dependencies = TRUE)
+ FALSE
+ },
+ error = function(e) {
+ return(TRUE)
+ },
+ finally = {
+ sink(type = "output")
+ sink(type = "message")
+ close(con)
+ })
+ }
+
+ # Print all messages to console
+ if (printAllMessages) {
+ print(allMessages)
+ }
+
+ # Check for other problems:
+ # - Check for unavailable packages
+ pbs <- stringi::stri_detect_regex(
+ str = allMessages,
+ pattern = "Skipping \\d* packages not available:",
+ case_insensitive = FALSE)
+ if (any(pbs)) {
+ message <- "Some packages have not been installed"
+ warning(message)
+ allMessages <- paste0(allMessages, message)
+ errorOccurs <- TRUE
+ }
+
+ if (errorOccurs) {
+ warning("Some error occurs in devtools::install_dev_deps call")
+ }
+
+ return(list(errorOccurs = errorOccurs, allMessages = allMessages))
+}
diff --git a/R/optionsForCi.R b/R/optionsForCi.R
new file mode 100644
index 0000000..dab79d3
--- /dev/null
+++ b/R/optionsForCi.R
@@ -0,0 +1,15 @@
+#' @title Set options for R CI
+#' @description Set some options useful for CI
+#' @return A backup of options before this function call
+#' @examples
+#' beforeOptions <- setOptionsForCi()
+#' # Restor options
+#' options(beforeOptions)
+setOptionsForCi <- function() {
+ optionsBackup <- options()
+ options(showWarnCalls = TRUE, # Show a call stack for warnings
+ showErrorCalls = TRUE, # Show a call stack for errors
+ show.error.messages = TRUE, # Show error message with try or error handler
+ warn = 2) # Warnings turned as errors
+ return(optionsBackup)
+}
diff --git a/templates/templates-r.yml b/templates/templates-r.yml
index c190190..2236d91 100644
--- a/templates/templates-r.yml
+++ b/templates/templates-r.yml
@@ -29,52 +29,34 @@
# For tests purposes
TEST_ERROR: 0
script:
+ # Files other than yml must be download because Gitlab include keyworkd doesn't get it
+ - mkdir temp_gitlabTemplates
+ - curl https://forgemia.inra.fr/api/v4/projects/6031/repository/files/R/optionsForCi.R?ref=main --output "temp_gitlabTemplates/optionsForCi.R"
+ - curl https://forgemia.inra.fr/api/v4/projects/6031/repository/files/R/installDepsWithErrManagement.R?ref=main --output "temp_gitlabTemplates/installDepsWithErrManagement.R"
- >
R -q -e '
- options(showWarnCalls = TRUE,
- showErrorCalls = TRUE,
- show.error.messages = TRUE,
- warn = 2);
- allMessages <- vector("character");
- errorOccurs <- FALSE;
- # TODO Attention le catch warning arrête le code sous-jacent !
- tryCatch(
- {
- con <- textConnection(object = "allMessages",
- open = "wr",
- local = TRUE);
- sink(file = con, type = "output");
- sink(file = con, type = "message");
- devtools::install_dev_deps(dependencies = TRUE)
- },
- error = function(e) {errorOccurs <- TRUE},
- warning = function(w) {errorOccurs <- TRUE},
- finally = {
- sink(type = "output");
- sink(type = "message");
- close(con)
- });
- print(allMessages);
- if (errorOccurs) {
- if (Sys.getenv("TEST_ERROR") == 1) {
- message("Some error occurs in devtools::install_dev_deps call");
- errorOccurs <- TRUE
- } else {
- stop("Some error occurs in devtools::install_dev_deps call")
- }
- };
- pbs <- stringi::stri_detect_regex(
- str = allMessages,
- pattern = "Skipping \\d* packages not available:",
- case_insensitive = FALSE);
- if (any(pbs)) {
+ source("temp_gitlabTemplates/optionsForCi.R");
+ source("temp_gitlabTemplates/installDepsWithErrManagement.R");
+
+ optionsBackup <- setOptionsForCi();
+
+ resList <- installDepsWithErrManagement(warningsAsErrors = TRUE,
+ printAllMessages = TRUE);
+
+ if (resList[["errorOccurs"]]) {
+ message <- "Some error occurs in devtools::install_dev_deps call";
if (Sys.getenv("TEST_ERROR") == 1) {
- message("Some packages have not been installed");
- errorOccurs <- TRUE
+ message(message)
} else {
- stop("Some packages have not been installed")
+ stop(message)
}
- };
+ }
+
if (errorOccurs == FALSE && Sys.getenv("TEST_ERROR") == 1) {
stop("An error is expected but none occurs")
- }'
+ }
+
+ # Restore options
+ options(optionsBackup)
+ '
+ - rm -rf temp_gitlabTemplates
--
GitLab
From 64be1c20fb11e508cc10ff41f229add59f114744 Mon Sep 17 00:00:00 2001
From: Astre Benjamin <benjamin.astre@inrae.fr>
Date: Tue, 4 Oct 2022 18:32:57 +0200
Subject: [PATCH 04/29] Change link to dev branch + install curl in CI when
needed
---
templates/templates-r.yml | 6 ++++--
1 file changed, 4 insertions(+), 2 deletions(-)
diff --git a/templates/templates-r.yml b/templates/templates-r.yml
index 2236d91..bd644b6 100644
--- a/templates/templates-r.yml
+++ b/templates/templates-r.yml
@@ -30,9 +30,11 @@
TEST_ERROR: 0
script:
# Files other than yml must be download because Gitlab include keyworkd doesn't get it
+ - apt update
+ - apt install curl
- mkdir temp_gitlabTemplates
- - curl https://forgemia.inra.fr/api/v4/projects/6031/repository/files/R/optionsForCi.R?ref=main --output "temp_gitlabTemplates/optionsForCi.R"
- - curl https://forgemia.inra.fr/api/v4/projects/6031/repository/files/R/installDepsWithErrManagement.R?ref=main --output "temp_gitlabTemplates/installDepsWithErrManagement.R"
+ - curl https://forgemia.inra.fr/api/v4/projects/6031/repository/files/R/optionsForCi.R?ref=dev --output "temp_gitlabTemplates/optionsForCi.R"
+ - curl https://forgemia.inra.fr/api/v4/projects/6031/repository/files/R/installDepsWithErrManagement.R?ref=dev --output "temp_gitlabTemplates/installDepsWithErrManagement.R"
- >
R -q -e '
source("temp_gitlabTemplates/optionsForCi.R");
--
GitLab
From 8dedba65c25b0ae675ad6b25c82d8637d2a8879d Mon Sep 17 00:00:00 2001
From: Astre Benjamin <benjamin.astre@inrae.fr>
Date: Tue, 4 Oct 2022 18:35:24 +0200
Subject: [PATCH 05/29] Add a getwd() to help debug
---
templates/templates-r.yml | 1 +
1 file changed, 1 insertion(+)
diff --git a/templates/templates-r.yml b/templates/templates-r.yml
index bd644b6..d43a6ff 100644
--- a/templates/templates-r.yml
+++ b/templates/templates-r.yml
@@ -37,6 +37,7 @@
- curl https://forgemia.inra.fr/api/v4/projects/6031/repository/files/R/installDepsWithErrManagement.R?ref=dev --output "temp_gitlabTemplates/installDepsWithErrManagement.R"
- >
R -q -e '
+ getwd()
source("temp_gitlabTemplates/optionsForCi.R");
source("temp_gitlabTemplates/installDepsWithErrManagement.R");
--
GitLab
From af1931cd8b6ad9f5ef48c33080ee8eca532d5f57 Mon Sep 17 00:00:00 2001
From: Astre Benjamin <benjamin.astre@inrae.fr>
Date: Tue, 4 Oct 2022 18:42:06 +0200
Subject: [PATCH 06/29] Try correct paths...
---
templates/templates-r.yml | 11 ++++++-----
1 file changed, 6 insertions(+), 5 deletions(-)
diff --git a/templates/templates-r.yml b/templates/templates-r.yml
index d43a6ff..c8e260f 100644
--- a/templates/templates-r.yml
+++ b/templates/templates-r.yml
@@ -32,14 +32,15 @@
# Files other than yml must be download because Gitlab include keyworkd doesn't get it
- apt update
- apt install curl
- - mkdir temp_gitlabTemplates
- - curl https://forgemia.inra.fr/api/v4/projects/6031/repository/files/R/optionsForCi.R?ref=dev --output "temp_gitlabTemplates/optionsForCi.R"
- - curl https://forgemia.inra.fr/api/v4/projects/6031/repository/files/R/installDepsWithErrManagement.R?ref=dev --output "temp_gitlabTemplates/installDepsWithErrManagement.R"
+ - mkdir $CI_PROJECT_DIR/temp_gitlabTemplates
+ - curl https://forgemia.inra.fr/api/v4/projects/6031/repository/files/R/optionsForCi.R?ref=dev --output "$CI_PROJECT_DIR/temp_gitlabTemplates/optionsForCi.R"
+ - curl https://forgemia.inra.fr/api/v4/projects/6031/repository/files/R/installDepsWithErrManagement.R?ref=dev --output "$CI_PROJECT_DIR/temp_gitlabTemplates/installDepsWithErrManagement.R"
- >
R -q -e '
getwd()
- source("temp_gitlabTemplates/optionsForCi.R");
- source("temp_gitlabTemplates/installDepsWithErrManagement.R");
+ projDir <- Sys.getenv("CI_PROJECT_DIR")
+ source(file.path(projDir, "temp_gitlabTemplates/optionsForCi.R"));
+ source(file.path(projDir, "temp_gitlabTemplates/installDepsWithErrManagement.R"));
optionsBackup <- setOptionsForCi();
--
GitLab
From ec07bd3c060ee7719acd7c5d0a44ae2b165674a1 Mon Sep 17 00:00:00 2001
From: Astre Benjamin <benjamin.astre@inrae.fr>
Date: Tue, 4 Oct 2022 18:45:16 +0200
Subject: [PATCH 07/29] Try force always artifacts for debug
---
templates/templates-r.yml | 4 ++++
1 file changed, 4 insertions(+)
diff --git a/templates/templates-r.yml b/templates/templates-r.yml
index c8e260f..ef5c877 100644
--- a/templates/templates-r.yml
+++ b/templates/templates-r.yml
@@ -64,3 +64,7 @@
options(optionsBackup)
'
- rm -rf temp_gitlabTemplates
+ artifacts:
+ paths:
+ - .
+ when: always
--
GitLab
From cf76b4806ed713d70a644922bd4993d3bd8e2395 Mon Sep 17 00:00:00 2001
From: Astre Benjamin <benjamin.astre@inrae.fr>
Date: Tue, 4 Oct 2022 18:47:56 +0200
Subject: [PATCH 08/29] Another try...
---
templates/templates-r.yml | 2 --
1 file changed, 2 deletions(-)
diff --git a/templates/templates-r.yml b/templates/templates-r.yml
index ef5c877..3333b08 100644
--- a/templates/templates-r.yml
+++ b/templates/templates-r.yml
@@ -65,6 +65,4 @@
'
- rm -rf temp_gitlabTemplates
artifacts:
- paths:
- - .
when: always
--
GitLab
From f70df1b99f01b7298a4a5c3755fcc3205ffb2862 Mon Sep 17 00:00:00 2001
From: Astre Benjamin <benjamin.astre@inrae.fr>
Date: Tue, 4 Oct 2022 18:50:22 +0200
Subject: [PATCH 09/29] Another try...
---
templates/templates-r.yml | 3 +++
1 file changed, 3 insertions(+)
diff --git a/templates/templates-r.yml b/templates/templates-r.yml
index 3333b08..77dc0b0 100644
--- a/templates/templates-r.yml
+++ b/templates/templates-r.yml
@@ -39,6 +39,7 @@
R -q -e '
getwd()
projDir <- Sys.getenv("CI_PROJECT_DIR")
+ print(projDir)
source(file.path(projDir, "temp_gitlabTemplates/optionsForCi.R"));
source(file.path(projDir, "temp_gitlabTemplates/installDepsWithErrManagement.R"));
@@ -65,4 +66,6 @@
'
- rm -rf temp_gitlabTemplates
artifacts:
+ paths:
+ - temp_gitlabTemplates/
when: always
--
GitLab
From 9928bcf4ca66b8ccca6c81be4bd348cb95039b40 Mon Sep 17 00:00:00 2001
From: Astre Benjamin <benjamin.astre@inrae.fr>
Date: Wed, 5 Oct 2022 10:22:00 +0200
Subject: [PATCH 10/29] Adjust paths
---
templates/templates-r.yml | 16 ++++++++--------
1 file changed, 8 insertions(+), 8 deletions(-)
diff --git a/templates/templates-r.yml b/templates/templates-r.yml
index 77dc0b0..4312763 100644
--- a/templates/templates-r.yml
+++ b/templates/templates-r.yml
@@ -32,16 +32,16 @@
# Files other than yml must be download because Gitlab include keyworkd doesn't get it
- apt update
- apt install curl
- - mkdir $CI_PROJECT_DIR/temp_gitlabTemplates
- - curl https://forgemia.inra.fr/api/v4/projects/6031/repository/files/R/optionsForCi.R?ref=dev --output "$CI_PROJECT_DIR/temp_gitlabTemplates/optionsForCi.R"
- - curl https://forgemia.inra.fr/api/v4/projects/6031/repository/files/R/installDepsWithErrManagement.R?ref=dev --output "$CI_PROJECT_DIR/temp_gitlabTemplates/installDepsWithErrManagement.R"
+ - mkdir temp_gitlabTemplates
+ - cd temp_gitlabTemplates
+ - curl https://forgemia.inra.fr/api/v4/projects/6031/repository/files/R/optionsForCi.R?ref=dev
+ - curl https://forgemia.inra.fr/api/v4/projects/6031/repository/files/R/installDepsWithErrManagement.R?ref=dev
+ - cd ..
- >
R -q -e '
getwd()
- projDir <- Sys.getenv("CI_PROJECT_DIR")
- print(projDir)
- source(file.path(projDir, "temp_gitlabTemplates/optionsForCi.R"));
- source(file.path(projDir, "temp_gitlabTemplates/installDepsWithErrManagement.R"));
+ source("temp_gitlabTemplates/optionsForCi.R");
+ source("temp_gitlabTemplates/installDepsWithErrManagement.R");
optionsBackup <- setOptionsForCi();
@@ -67,5 +67,5 @@
- rm -rf temp_gitlabTemplates
artifacts:
paths:
- - temp_gitlabTemplates/
+ - tests/
when: always
--
GitLab
From 9dfd84270f8490395d8f41e058a359708db136b6 Mon Sep 17 00:00:00 2001
From: Astre Benjamin <benjamin.astre@inrae.fr>
Date: Wed, 5 Oct 2022 10:29:38 +0200
Subject: [PATCH 11/29] Try wget instead of curl (curl is bad for CI because it
doesn't return an error code)
---
templates/templates-r.yml | 10 ++++++----
1 file changed, 6 insertions(+), 4 deletions(-)
diff --git a/templates/templates-r.yml b/templates/templates-r.yml
index 4312763..f50768c 100644
--- a/templates/templates-r.yml
+++ b/templates/templates-r.yml
@@ -30,12 +30,14 @@
TEST_ERROR: 0
script:
# Files other than yml must be download because Gitlab include keyworkd doesn't get it
- - apt update
- - apt install curl
+ #- apt update
+ #- apt install curl
- mkdir temp_gitlabTemplates
- cd temp_gitlabTemplates
- - curl https://forgemia.inra.fr/api/v4/projects/6031/repository/files/R/optionsForCi.R?ref=dev
- - curl https://forgemia.inra.fr/api/v4/projects/6031/repository/files/R/installDepsWithErrManagement.R?ref=dev
+ #- curl https://forgemia.inra.fr/api/v4/projects/6031/repository/files/R/optionsForCi.R?ref=dev
+ #- curl https://forgemia.inra.fr/api/v4/projects/6031/repository/files/R/installDepsWithErrManagement.R?ref=dev
+ - wget https://forgemia.inra.fr/api/v4/projects/6031/repository/files/R/optionsForCi.R?ref=dev
+ - wget https://forgemia.inra.fr/api/v4/projects/6031/repository/files/R/installDepsWithErrManagement.R?ref=dev
- cd ..
- >
R -q -e '
--
GitLab
From e975e676ff9c4e35030a808b1f479fc03bed71a2 Mon Sep 17 00:00:00 2001
From: Astre Benjamin <benjamin.astre@inrae.fr>
Date: Wed, 5 Oct 2022 10:33:35 +0200
Subject: [PATCH 12/29] Correct web paths
---
templates/templates-r.yml | 8 ++------
1 file changed, 2 insertions(+), 6 deletions(-)
diff --git a/templates/templates-r.yml b/templates/templates-r.yml
index f50768c..f6c3a4c 100644
--- a/templates/templates-r.yml
+++ b/templates/templates-r.yml
@@ -30,14 +30,10 @@
TEST_ERROR: 0
script:
# Files other than yml must be download because Gitlab include keyworkd doesn't get it
- #- apt update
- #- apt install curl
- mkdir temp_gitlabTemplates
- cd temp_gitlabTemplates
- #- curl https://forgemia.inra.fr/api/v4/projects/6031/repository/files/R/optionsForCi.R?ref=dev
- #- curl https://forgemia.inra.fr/api/v4/projects/6031/repository/files/R/installDepsWithErrManagement.R?ref=dev
- - wget https://forgemia.inra.fr/api/v4/projects/6031/repository/files/R/optionsForCi.R?ref=dev
- - wget https://forgemia.inra.fr/api/v4/projects/6031/repository/files/R/installDepsWithErrManagement.R?ref=dev
+ - wget https://forgemia.inra.fr/api/v4/projects/6031/repository/files/R%2FoptionsForCi.R?ref=dev
+ - wget https://forgemia.inra.fr/api/v4/projects/6031/repository/files/R%2FinstallDepsWithErrManagement.R?ref=dev
- cd ..
- >
R -q -e '
--
GitLab
From 48a95f0f787e9122fb20a871dee5ec0592a07cff Mon Sep 17 00:00:00 2001
From: Astre Benjamin <benjamin.astre@inrae.fr>
Date: Wed, 5 Oct 2022 10:38:38 +0200
Subject: [PATCH 13/29] Correct again paths!
---
templates/templates-r.yml | 6 ++----
1 file changed, 2 insertions(+), 4 deletions(-)
diff --git a/templates/templates-r.yml b/templates/templates-r.yml
index f6c3a4c..73a4ec8 100644
--- a/templates/templates-r.yml
+++ b/templates/templates-r.yml
@@ -31,10 +31,8 @@
script:
# Files other than yml must be download because Gitlab include keyworkd doesn't get it
- mkdir temp_gitlabTemplates
- - cd temp_gitlabTemplates
- - wget https://forgemia.inra.fr/api/v4/projects/6031/repository/files/R%2FoptionsForCi.R?ref=dev
- - wget https://forgemia.inra.fr/api/v4/projects/6031/repository/files/R%2FinstallDepsWithErrManagement.R?ref=dev
- - cd ..
+ - wget https://forgemia.inra.fr/api/v4/projects/6031/repository/files/R%2FoptionsForCi.R?ref=dev --output-document=temp_gitlabTemplates/optionsForCi.R
+ - wget https://forgemia.inra.fr/api/v4/projects/6031/repository/files/R%2FinstallDepsWithErrManagement.R?ref=dev --output-document=temp_gitlabTemplates/installDepsWithErrManagement.R
- >
R -q -e '
getwd()
--
GitLab
From c393b0b8bc7d51e0e3937410423c756f2c110250 Mon Sep 17 00:00:00 2001
From: Astre Benjamin <benjamin.astre@inrae.fr>
Date: Wed, 5 Oct 2022 10:44:43 +0200
Subject: [PATCH 14/29] Retry with curl
---
templates/templates-r.yml | 11 +++++++++--
1 file changed, 9 insertions(+), 2 deletions(-)
diff --git a/templates/templates-r.yml b/templates/templates-r.yml
index 73a4ec8..e05a285 100644
--- a/templates/templates-r.yml
+++ b/templates/templates-r.yml
@@ -30,9 +30,16 @@
TEST_ERROR: 0
script:
# Files other than yml must be download because Gitlab include keyworkd doesn't get it
+ - apt update
+ - apt install curl
- mkdir temp_gitlabTemplates
- - wget https://forgemia.inra.fr/api/v4/projects/6031/repository/files/R%2FoptionsForCi.R?ref=dev --output-document=temp_gitlabTemplates/optionsForCi.R
- - wget https://forgemia.inra.fr/api/v4/projects/6031/repository/files/R%2FinstallDepsWithErrManagement.R?ref=dev --output-document=temp_gitlabTemplates/installDepsWithErrManagement.R
+ - cd temp_gitlabTemplates
+ - curl --fail https://forgemia.inra.fr/api/v4/projects/6031/repository/files/R/optionsForCi.R?ref=dev
+ - curl --fail https://forgemia.inra.fr/api/v4/projects/6031/repository/files/R/installDepsWithErrManagement.R?ref=dev
+ - cd ..
+ #- mkdir temp_gitlabTemplates
+ #- wget https://forgemia.inra.fr/api/v4/projects/6031/repository/files/R%2FoptionsForCi.R?ref=dev --output-document=temp_gitlabTemplates/optionsForCi.R
+ #- wget https://forgemia.inra.fr/api/v4/projects/6031/repository/files/R%2FinstallDepsWithErrManagement.R?ref=dev --output-document=temp_gitlabTemplates/installDepsWithErrManagement.R
- >
R -q -e '
getwd()
--
GitLab
From e2e628b1b7bd5e9a25693921e26057e13e8d0ebe Mon Sep 17 00:00:00 2001
From: Astre Benjamin <benjamin.astre@inrae.fr>
Date: Wed, 5 Oct 2022 10:45:38 +0200
Subject: [PATCH 15/29] Retry with curl
---
templates/templates-r.yml | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/templates/templates-r.yml b/templates/templates-r.yml
index e05a285..9874188 100644
--- a/templates/templates-r.yml
+++ b/templates/templates-r.yml
@@ -34,8 +34,8 @@
- apt install curl
- mkdir temp_gitlabTemplates
- cd temp_gitlabTemplates
- - curl --fail https://forgemia.inra.fr/api/v4/projects/6031/repository/files/R/optionsForCi.R?ref=dev
- - curl --fail https://forgemia.inra.fr/api/v4/projects/6031/repository/files/R/installDepsWithErrManagement.R?ref=dev
+ - curl --fail https://forgemia.inra.fr/api/v4/projects/6031/repository/files/R%2FoptionsForCi.R?ref=dev
+ - curl --fail https://forgemia.inra.fr/api/v4/projects/6031/repository/files/R%2FinstallDepsWithErrManagement.R?ref=dev
- cd ..
#- mkdir temp_gitlabTemplates
#- wget https://forgemia.inra.fr/api/v4/projects/6031/repository/files/R%2FoptionsForCi.R?ref=dev --output-document=temp_gitlabTemplates/optionsForCi.R
--
GitLab
From 137e4fb6f1d988ac6083c9433a03a9647edeffef Mon Sep 17 00:00:00 2001
From: Astre Benjamin <benjamin.astre@inrae.fr>
Date: Wed, 5 Oct 2022 11:13:03 +0200
Subject: [PATCH 16/29] Another try with wget, new web address to download
files (not using bad Gitlab API !!!)
---
templates/templates-r.yml | 15 ++++++++-------
1 file changed, 8 insertions(+), 7 deletions(-)
diff --git a/templates/templates-r.yml b/templates/templates-r.yml
index 9874188..e29ea82 100644
--- a/templates/templates-r.yml
+++ b/templates/templates-r.yml
@@ -30,16 +30,17 @@
TEST_ERROR: 0
script:
# Files other than yml must be download because Gitlab include keyworkd doesn't get it
- - apt update
- - apt install curl
+ #- apt update
+ #- apt install curl
- mkdir temp_gitlabTemplates
- - cd temp_gitlabTemplates
- - curl --fail https://forgemia.inra.fr/api/v4/projects/6031/repository/files/R%2FoptionsForCi.R?ref=dev
- - curl --fail https://forgemia.inra.fr/api/v4/projects/6031/repository/files/R%2FinstallDepsWithErrManagement.R?ref=dev
- - cd ..
- #- mkdir temp_gitlabTemplates
+ #- cd temp_gitlabTemplates
+ #- curl --fail https://forgemia.inra.fr/api/v4/projects/6031/repository/files/R%2FoptionsForCi.R?ref=dev --output temp_gitlabTemplates/optionsForCi.R
+ #- curl --fail https://forgemia.inra.fr/api/v4/projects/6031/repository/files/R%2FinstallDepsWithErrManagement.R?ref=dev --output temp_gitlabTemplates/installDepsWithErrManagement.R
+ #- cd ..
#- wget https://forgemia.inra.fr/api/v4/projects/6031/repository/files/R%2FoptionsForCi.R?ref=dev --output-document=temp_gitlabTemplates/optionsForCi.R
#- wget https://forgemia.inra.fr/api/v4/projects/6031/repository/files/R%2FinstallDepsWithErrManagement.R?ref=dev --output-document=temp_gitlabTemplates/installDepsWithErrManagement.R
+ - wget https://forgemia.inra.fr/urep/dev_utils/gitlab-ci-templates/-/raw/dev/R/optionsForCi.R?inline=false --output-document=temp_gitlabTemplates/optionsForCi.R
+ - wget https://forgemia.inra.fr/urep/dev_utils/gitlab-ci-templates/-/raw/dev/R/installDepsWithErrManagement.R?inline=false --output-document=temp_gitlabTemplates/installDepsWithErrManagement.R
- >
R -q -e '
getwd()
--
GitLab
From bb0c68499d7bc3a7e6084a62829a8c012b4118bd Mon Sep 17 00:00:00 2001
From: Astre Benjamin <benjamin.astre@inrae.fr>
Date: Wed, 5 Oct 2022 11:17:20 +0200
Subject: [PATCH 17/29] Use install_deps instead of install_dev_deps
install_dev_deps seems to install "source" versions of packages and not the
packages useful for dev!
---
R/installDepsWithErrManagement.R | 4 ++--
templates/templates-r.yml | 8 --------
2 files changed, 2 insertions(+), 10 deletions(-)
diff --git a/R/installDepsWithErrManagement.R b/R/installDepsWithErrManagement.R
index 965fc6f..9690f51 100644
--- a/R/installDepsWithErrManagement.R
+++ b/R/installDepsWithErrManagement.R
@@ -37,8 +37,8 @@ installDepsWithErrManagement <- function(warningsAsErrors = FALSE,
install.packages(pkgs = "devtools", repos = repo)
install.packages(pkgs = "stringi", repos = repo)
- devtools::install_dev_deps(dependencies = TRUE,
- upgrade = "always")
+ devtools::install_deps(dependencies = TRUE,
+ upgrade = "always")
FALSE
},
error = function(e) {
diff --git a/templates/templates-r.yml b/templates/templates-r.yml
index e29ea82..2430560 100644
--- a/templates/templates-r.yml
+++ b/templates/templates-r.yml
@@ -30,15 +30,7 @@
TEST_ERROR: 0
script:
# Files other than yml must be download because Gitlab include keyworkd doesn't get it
- #- apt update
- #- apt install curl
- mkdir temp_gitlabTemplates
- #- cd temp_gitlabTemplates
- #- curl --fail https://forgemia.inra.fr/api/v4/projects/6031/repository/files/R%2FoptionsForCi.R?ref=dev --output temp_gitlabTemplates/optionsForCi.R
- #- curl --fail https://forgemia.inra.fr/api/v4/projects/6031/repository/files/R%2FinstallDepsWithErrManagement.R?ref=dev --output temp_gitlabTemplates/installDepsWithErrManagement.R
- #- cd ..
- #- wget https://forgemia.inra.fr/api/v4/projects/6031/repository/files/R%2FoptionsForCi.R?ref=dev --output-document=temp_gitlabTemplates/optionsForCi.R
- #- wget https://forgemia.inra.fr/api/v4/projects/6031/repository/files/R%2FinstallDepsWithErrManagement.R?ref=dev --output-document=temp_gitlabTemplates/installDepsWithErrManagement.R
- wget https://forgemia.inra.fr/urep/dev_utils/gitlab-ci-templates/-/raw/dev/R/optionsForCi.R?inline=false --output-document=temp_gitlabTemplates/optionsForCi.R
- wget https://forgemia.inra.fr/urep/dev_utils/gitlab-ci-templates/-/raw/dev/R/installDepsWithErrManagement.R?inline=false --output-document=temp_gitlabTemplates/installDepsWithErrManagement.R
- >
--
GitLab
From 27ccd14e5b402151a2e055fc48545eae0aaa392b Mon Sep 17 00:00:00 2001
From: Astre Benjamin <benjamin.astre@inrae.fr>
Date: Wed, 5 Oct 2022 11:50:49 +0200
Subject: [PATCH 18/29] Revert previous commit + correct code error
---
R/installDepsWithErrManagement.R | 4 ++--
templates/templates-r.yml | 6 +-----
2 files changed, 3 insertions(+), 7 deletions(-)
diff --git a/R/installDepsWithErrManagement.R b/R/installDepsWithErrManagement.R
index 9690f51..965fc6f 100644
--- a/R/installDepsWithErrManagement.R
+++ b/R/installDepsWithErrManagement.R
@@ -37,8 +37,8 @@ installDepsWithErrManagement <- function(warningsAsErrors = FALSE,
install.packages(pkgs = "devtools", repos = repo)
install.packages(pkgs = "stringi", repos = repo)
- devtools::install_deps(dependencies = TRUE,
- upgrade = "always")
+ devtools::install_dev_deps(dependencies = TRUE,
+ upgrade = "always")
FALSE
},
error = function(e) {
diff --git a/templates/templates-r.yml b/templates/templates-r.yml
index 2430560..0bc1fe0 100644
--- a/templates/templates-r.yml
+++ b/templates/templates-r.yml
@@ -53,7 +53,7 @@
}
}
- if (errorOccurs == FALSE && Sys.getenv("TEST_ERROR") == 1) {
+ if (resList[["errorOccurs"]] == FALSE && Sys.getenv("TEST_ERROR") == 1) {
stop("An error is expected but none occurs")
}
@@ -61,7 +61,3 @@
options(optionsBackup)
'
- rm -rf temp_gitlabTemplates
- artifacts:
- paths:
- - tests/
- when: always
--
GitLab
From 2be8e30956222035f507f4d68e0fe5f28cd23a45 Mon Sep 17 00:00:00 2001
From: Astre Benjamin <benjamin.astre@inrae.fr>
Date: Wed, 5 Oct 2022 12:18:37 +0200
Subject: [PATCH 19/29] Remove warnings (which will be converted to errors and
then stop execution, which is not expected)
---
R/installDepsWithErrManagement.R | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/R/installDepsWithErrManagement.R b/R/installDepsWithErrManagement.R
index 965fc6f..20cd8d8 100644
--- a/R/installDepsWithErrManagement.R
+++ b/R/installDepsWithErrManagement.R
@@ -95,13 +95,13 @@ installDepsWithErrManagement <- function(warningsAsErrors = FALSE,
case_insensitive = FALSE)
if (any(pbs)) {
message <- "Some packages have not been installed"
- warning(message)
+ message(message)
allMessages <- paste0(allMessages, message)
errorOccurs <- TRUE
}
if (errorOccurs) {
- warning("Some error occurs in devtools::install_dev_deps call")
+ message("Some error occurs in devtools::install_dev_deps call")
}
return(list(errorOccurs = errorOccurs, allMessages = allMessages))
--
GitLab
From 21c158126d5d971c2df45d5bf82bc8736b85c9e8 Mon Sep 17 00:00:00 2001
From: Astre Benjamin <benjamin.astre@inrae.fr>
Date: Wed, 5 Oct 2022 13:27:43 +0200
Subject: [PATCH 20/29] Forgot some jobs' rules
---
tests/.gitlab-ci-r-tests.yml | 2 ++
1 file changed, 2 insertions(+)
diff --git a/tests/.gitlab-ci-r-tests.yml b/tests/.gitlab-ci-r-tests.yml
index 0bdc9db..e15ea7b 100644
--- a/tests/.gitlab-ci-r-tests.yml
+++ b/tests/.gitlab-ci-r-tests.yml
@@ -12,6 +12,7 @@ Test R-install-package-dependencies-withCache Good:
- .gitlab-ci-r-tests.yml
- templates/templates-r.yml
- tests/r-package
+ - R
variables:
TEST_ERROR: 0
script:
@@ -27,6 +28,7 @@ Test R-install-package-dependencies-withCache Bad:
- .gitlab-ci-r-tests.yml
- templates/templates-r.yml
- tests/r-package
+ - R
variables:
TEST_ERROR: 1
script:
--
GitLab
From 3f9da6a66dd8f8ede6ae0263d1010025570c4863 Mon Sep 17 00:00:00 2001
From: Astre Benjamin <benjamin.astre@inrae.fr>
Date: Wed, 5 Oct 2022 13:32:38 +0200
Subject: [PATCH 21/29] Forgot change of some paths after moved tests files in
subfolder
---
tests/.gitlab-ci-checkers-tests.yml | 20 +++++++++----------
tests/.gitlab-ci-docker-tests.yml | 12 +++++------
...itlab-ci-gitlab-package-registry-tests.yml | 6 +++---
tests/.gitlab-ci-r-tests.yml | 4 ++--
tests/.gitlab-ci-runner-tests.yml | 10 +++++-----
5 files changed, 26 insertions(+), 26 deletions(-)
diff --git a/tests/.gitlab-ci-checkers-tests.yml b/tests/.gitlab-ci-checkers-tests.yml
index e1d4ae1..1dcf10b 100644
--- a/tests/.gitlab-ci-checkers-tests.yml
+++ b/tests/.gitlab-ci-checkers-tests.yml
@@ -13,7 +13,7 @@ Test check-find-linux Bad:
rules:
- changes:
- .gitlab-ci.yml
- - .gitlab-ci-checkers-tests.yml
+ - tests/.gitlab-ci-checkers-tests.yml
- templates/templates-checkers.yml
- tests/Checkers-find-test-bad.txt
allow_failure: false
@@ -28,7 +28,7 @@ Test check-find-windows Bad:
rules:
- changes:
- .gitlab-ci.yml
- - .gitlab-ci-checkers-tests.yml
+ - tests/.gitlab-ci-checkers-tests.yml
- templates/templates-checkers.yml
- tests/Checkers-find-test-bad.txt
allow_failure: false
@@ -41,7 +41,7 @@ Test check-find-linux Good:
rules:
- changes:
- .gitlab-ci.yml
- - .gitlab-ci-checkers-tests.yml
+ - tests/.gitlab-ci-checkers-tests.yml
- templates/templates-checkers.yml
- tests/Checkers-find-test-good.txt
allow_failure: false
@@ -54,7 +54,7 @@ Test check-find-windows Good:
rules:
- changes:
- .gitlab-ci.yml
- - .gitlab-ci-checkers-tests.yml
+ - tests/.gitlab-ci-checkers-tests.yml
- templates/templates-checkers.yml
- tests/Checkers-find-test-good.txt
allow_failure: false
@@ -65,7 +65,7 @@ Test check-git-uncommitted-changes No:
rules:
- changes:
- .gitlab-ci.yml
- - .gitlab-ci-checkers-tests.yml
+ - tests/.gitlab-ci-checkers-tests.yml
- templates/templates-checkers.yml
allow_failure: false
@@ -75,7 +75,7 @@ Test check-git-notmanaged-changes No:
rules:
- changes:
- .gitlab-ci.yml
- - .gitlab-ci-checkers-tests.yml
+ - tests/.gitlab-ci-checkers-tests.yml
- templates/templates-checkers.yml
allow_failure: false
@@ -83,7 +83,7 @@ Before test change versioned file:
rules:
- changes:
- .gitlab-ci.yml
- - .gitlab-ci-checkers-tests.yml
+ - tests/.gitlab-ci-checkers-tests.yml
- templates/templates-checkers.yml
script:
- echo "Hello, world." > tests/DummyFile
@@ -95,7 +95,7 @@ Before test add a file:
rules:
- changes:
- .gitlab-ci.yml
- - .gitlab-ci-checkers-tests.yml
+ - tests/.gitlab-ci-checkers-tests.yml
- templates/templates-checkers.yml
script:
- mkdir temp
@@ -112,7 +112,7 @@ Test check-git-uncommitted-changes Yes:
rules:
- changes:
- .gitlab-ci.yml
- - .gitlab-ci-checkers-tests.yml
+ - tests/.gitlab-ci-checkers-tests.yml
- templates/templates-checkers.yml
variables:
EMPTY_RETURN_CODE: 1
@@ -127,7 +127,7 @@ Test check-git-notmanaged-changes Yes:
rules:
- changes:
- .gitlab-ci.yml
- - .gitlab-ci-checkers-tests.yml
+ - tests/.gitlab-ci-checkers-tests.yml
- templates/templates-checkers.yml
variables:
EMPTY_RETURN_CODE: 1
diff --git a/tests/.gitlab-ci-docker-tests.yml b/tests/.gitlab-ci-docker-tests.yml
index cd8eaa6..d068374 100644
--- a/tests/.gitlab-ci-docker-tests.yml
+++ b/tests/.gitlab-ci-docker-tests.yml
@@ -19,7 +19,7 @@ Test Docker Build and Push Linux:
rules:
- changes:
- .gitlab-ci.yml
- - .gitlab-ci-docker-tests.yml
+ - tests/.gitlab-ci-docker-tests.yml
- templates/templates-gitlab-docker-registry.yml
- templates/templates-docker.yml
- tests/Dockerfile-test-linux
@@ -36,7 +36,7 @@ Test Docker Build and Push Windows:
rules:
- changes:
- .gitlab-ci.yml
- - .gitlab-ci-docker-tests.yml
+ - tests/.gitlab-ci-docker-tests.yml
- templates/templates-gitlab-docker-registry.yml
- templates/templates-docker.yml
- tests/Dockerfile-test-windows
@@ -55,7 +55,7 @@ Test Docker Push latest Linux:
rules:
- changes:
- .gitlab-ci.yml
- - .gitlab-ci-docker-tests.yml
+ - tests/.gitlab-ci-docker-tests.yml
- templates/templates-gitlab-docker-registry.yml
- templates/templates-docker.yml
- tests/Dockerfile-test-linux
@@ -73,7 +73,7 @@ Test Docker Push latest Windows:
rules:
- changes:
- .gitlab-ci.yml
- - .gitlab-ci-docker-tests.yml
+ - tests/.gitlab-ci-docker-tests.yml
- templates/templates-gitlab-docker-registry.yml
- templates/templates-docker.yml
- tests/Dockerfile-test-windows
@@ -92,7 +92,7 @@ Test Docker Push tag Linux:
rules:
- changes:
- .gitlab-ci.yml
- - .gitlab-ci-docker-tests.yml
+ - tests/.gitlab-ci-docker-tests.yml
- templates/templates-gitlab-docker-registry.yml
- templates/templates-docker.yml
- tests/Dockerfile-test-linux
@@ -110,7 +110,7 @@ Test Docker Push tag Windows:
rules:
- changes:
- .gitlab-ci.yml
- - .gitlab-ci-docker-tests.yml
+ - tests/.gitlab-ci-docker-tests.yml
- templates/templates-gitlab-docker-registry.yml
- templates/templates-docker.yml
- tests/Dockerfile-test-windows
diff --git a/tests/.gitlab-ci-gitlab-package-registry-tests.yml b/tests/.gitlab-ci-gitlab-package-registry-tests.yml
index 87ca1ec..a6c0685 100644
--- a/tests/.gitlab-ci-gitlab-package-registry-tests.yml
+++ b/tests/.gitlab-ci-gitlab-package-registry-tests.yml
@@ -9,7 +9,7 @@ Test Package Upload:
rules:
- changes:
- .gitlab-ci.yml
- - .gitlab-ci-gitlab-package-registry-tests.yml
+ - tests/.gitlab-ci-gitlab-package-registry-tests.yml
- templates/templates-gitlab-package-registry.yml
variables:
PACKAGE_NAME: 'CiTests'
@@ -25,7 +25,7 @@ Test Package Download:
rules:
- changes:
- .gitlab-ci.yml
- - .gitlab-ci-gitlab-package-registry-tests.yml
+ - tests/.gitlab-ci-gitlab-package-registry-tests.yml
- templates/templates-gitlab-package-registry.yml
variables:
PACKAGE_NAME: 'CiTests'
@@ -41,7 +41,7 @@ Test Package Download:
# rules:
# - changes:
# - .gitlab-ci.yml
-# - .gitlab-ci-gitlab-package-registry-tests.yml
+# - tests/.gitlab-ci-gitlab-package-registry-tests.yml
# - templates/templates-gitlab-package-registry.yml
# when: always
# variables:
diff --git a/tests/.gitlab-ci-r-tests.yml b/tests/.gitlab-ci-r-tests.yml
index e15ea7b..1251607 100644
--- a/tests/.gitlab-ci-r-tests.yml
+++ b/tests/.gitlab-ci-r-tests.yml
@@ -9,7 +9,7 @@ Test R-install-package-dependencies-withCache Good:
rules:
- changes:
- .gitlab-ci.yml
- - .gitlab-ci-r-tests.yml
+ - tests/.gitlab-ci-r-tests.yml
- templates/templates-r.yml
- tests/r-package
- R
@@ -25,7 +25,7 @@ Test R-install-package-dependencies-withCache Bad:
rules:
- changes:
- .gitlab-ci.yml
- - .gitlab-ci-r-tests.yml
+ - tests/.gitlab-ci-r-tests.yml
- templates/templates-r.yml
- tests/r-package
- R
diff --git a/tests/.gitlab-ci-runner-tests.yml b/tests/.gitlab-ci-runner-tests.yml
index 6cc5f92..05d002e 100644
--- a/tests/.gitlab-ci-runner-tests.yml
+++ b/tests/.gitlab-ci-runner-tests.yml
@@ -10,7 +10,7 @@ Test Linux Docker Runner:
rules:
- changes:
- .gitlab-ci.yml
- - .gitlab-ci-runner-tests.yml
+ - tests/.gitlab-ci-runner-tests.yml
# dind stand for "Docker-in-Docker"
Test Linux Docker Runner with dind:
@@ -24,7 +24,7 @@ Test Linux Docker Runner with dind:
rules:
- changes:
- .gitlab-ci.yml
- - .gitlab-ci-runner-tests.yml
+ - tests/.gitlab-ci-runner-tests.yml
Test Windows Shell Runner:
tags:
@@ -34,7 +34,7 @@ Test Windows Shell Runner:
rules:
- changes:
- .gitlab-ci.yml
- - .gitlab-ci-runner-tests.yml
+ - tests/.gitlab-ci-runner-tests.yml
# Disabled because not working, see issue #1
# Test Windows Docker Runner:
@@ -46,7 +46,7 @@ Test Windows Shell Runner:
# rules:
# - changes:
# - .gitlab-ci.yml
-# - .gitlab-ci-runner-tests.yml
+# - tests/.gitlab-ci-runner-tests.yml
# Disabled because not working, see issue #1
# dind stand for "Docker-in-Docker"
@@ -61,4 +61,4 @@ Test Windows Shell Runner:
# rules:
# - changes:
# - .gitlab-ci.yml
-# - .gitlab-ci-runner-tests.yml
+# - tests/.gitlab-ci-runner-tests.yml
--
GitLab
From 2450d6388d1f76b74d5d5f72d188f46562c28c2d Mon Sep 17 00:00:00 2001
From: Astre Benjamin <benjamin.astre@inrae.fr>
Date: Wed, 5 Oct 2022 14:26:28 +0200
Subject: [PATCH 22/29] Adjust some runner tags (tags have changed on my
Windows runners)
---
tests/.gitlab-ci-docker-tests.yml | 6 +++---
tests/.gitlab-ci-runner-tests.yml | 2 +-
2 files changed, 4 insertions(+), 4 deletions(-)
diff --git a/tests/.gitlab-ci-docker-tests.yml b/tests/.gitlab-ci-docker-tests.yml
index d068374..cc40e74 100644
--- a/tests/.gitlab-ci-docker-tests.yml
+++ b/tests/.gitlab-ci-docker-tests.yml
@@ -26,7 +26,7 @@ Test Docker Build and Push Linux:
Test Docker Build and Push Windows:
tags:
- - windows-shell
+ - windows-cmd-shell
variables:
DOCKERFILE_PATH: tests/Dockerfile-test-windows
CONTAINER_TAG: ${BASE_CONTAINER_TAG}-windows
@@ -62,7 +62,7 @@ Test Docker Push latest Linux:
Test Docker Push latest Windows:
tags:
- - windows-shell
+ - windows-cmd-shell
needs: ["Test Docker Build and Push Windows"]
extends:
- .gitlab-docker-registry-login-windows
@@ -99,7 +99,7 @@ Test Docker Push tag Linux:
Test Docker Push tag Windows:
tags:
- - windows-shell
+ - windows-cmd-shell
needs: ["Test Docker Build and Push Windows"]
extends:
- .gitlab-docker-registry-login-windows
diff --git a/tests/.gitlab-ci-runner-tests.yml b/tests/.gitlab-ci-runner-tests.yml
index 05d002e..ec20c70 100644
--- a/tests/.gitlab-ci-runner-tests.yml
+++ b/tests/.gitlab-ci-runner-tests.yml
@@ -28,7 +28,7 @@ Test Linux Docker Runner with dind:
Test Windows Shell Runner:
tags:
- - windows-shell
+ - windows-cmd-shell
script:
- dir
rules:
--
GitLab
From c2738935fc596697e439722b9c1a7a08d3107fa1 Mon Sep 17 00:00:00 2001
From: Astre Benjamin <benjamin.astre@inrae.fr>
Date: Wed, 5 Oct 2022 15:10:41 +0200
Subject: [PATCH 23/29] Change runners for windows-powershell (instead of
windows-cmd-shell)
---
tests/.gitlab-ci-docker-tests.yml | 6 +++---
tests/.gitlab-ci-runner-tests.yml | 2 +-
2 files changed, 4 insertions(+), 4 deletions(-)
diff --git a/tests/.gitlab-ci-docker-tests.yml b/tests/.gitlab-ci-docker-tests.yml
index cc40e74..c828beb 100644
--- a/tests/.gitlab-ci-docker-tests.yml
+++ b/tests/.gitlab-ci-docker-tests.yml
@@ -26,7 +26,7 @@ Test Docker Build and Push Linux:
Test Docker Build and Push Windows:
tags:
- - windows-cmd-shell
+ - windows-powershell
variables:
DOCKERFILE_PATH: tests/Dockerfile-test-windows
CONTAINER_TAG: ${BASE_CONTAINER_TAG}-windows
@@ -62,7 +62,7 @@ Test Docker Push latest Linux:
Test Docker Push latest Windows:
tags:
- - windows-cmd-shell
+ - windows-powershell
needs: ["Test Docker Build and Push Windows"]
extends:
- .gitlab-docker-registry-login-windows
@@ -99,7 +99,7 @@ Test Docker Push tag Linux:
Test Docker Push tag Windows:
tags:
- - windows-cmd-shell
+ - windows-powershell
needs: ["Test Docker Build and Push Windows"]
extends:
- .gitlab-docker-registry-login-windows
diff --git a/tests/.gitlab-ci-runner-tests.yml b/tests/.gitlab-ci-runner-tests.yml
index ec20c70..172d64a 100644
--- a/tests/.gitlab-ci-runner-tests.yml
+++ b/tests/.gitlab-ci-runner-tests.yml
@@ -28,7 +28,7 @@ Test Linux Docker Runner with dind:
Test Windows Shell Runner:
tags:
- - windows-cmd-shell
+ - windows-powershell
script:
- dir
rules:
--
GitLab
From 8ebfecc28c5d51170fa596f95d6e6b6dbcc28425 Mon Sep 17 00:00:00 2001
From: Astre Benjamin <benjamin.astre@inrae.fr>
Date: Wed, 5 Oct 2022 16:20:34 +0200
Subject: [PATCH 24/29] Update README
---
README.md | 14 ++++++++------
1 file changed, 8 insertions(+), 6 deletions(-)
diff --git a/README.md b/README.md
index 3b30f92..9dae1a2 100644
--- a/README.md
+++ b/README.md
@@ -2,7 +2,7 @@
[](https://forgemia.inra.fr/urep/dev_utils/gitlab-ci-templates/-/commits/main "main branch CI pipeline status!")
-This repository collect useful Gitlab CI templates files.
+This repository contains useful Gitlab CI templates files.
## Template files descriptions
@@ -11,6 +11,8 @@ This repository collect useful Gitlab CI templates files.
| [templates-docker.yml](/templates/templates-docker.yml) | Templates for build and push docker images |
| [templates-gitlab-docker-registry.yml](/templates/templates-gitlab-docker-registry.yml) | Templates for connection to the project Gitlab Docker Registry |
| [templates-gitlab-package-registry.yml](/templates/templates-gitlab-package-registry.yml) | Templates for download/upload to the project Gitlab Package Registry |
+| [templates-checkers.yml](/templates/templates-checkers.yml) | Templates for checking some job results, for examples: checking keywords presence in logs (errors in compile log, etc.), checking uncommitted git changes, etc. |
+| [templates-r.yml](/templates/templates-r.yml) | Templates around R language |
## Use the templates
@@ -18,17 +20,17 @@ This repository collect useful Gitlab CI templates files.
```yaml
include:
- project:
- - project: 'urep/dev_utils/gitlab-ci-templates'
- file: '/templates/templates-<name>.yml'
+ project:
+ - project: 'urep/dev_utils/gitlab-ci-templates'
+ file: '/templates/templates-<name>.yml'
```
2. Use template jobs in an **extends** keyword field in your .gitlab-ci.yml (or subfile) file:
```yaml
jobname:
- extends:
- - .<template job name>
+ extends:
+ - .<template job name>
```
## Tests
--
GitLab
From bc8fc52942dc56d6ef7f696861e529af68894cd4 Mon Sep 17 00:00:00 2001
From: Astre Benjamin <benjamin.astre@inrae.fr>
Date: Wed, 5 Oct 2022 17:38:43 +0200
Subject: [PATCH 25/29] Add some detailed documentation
---
README.md | 2 +
docs/Descriptions.md | 94 +++++++++++++++++++
templates/templates-checkers.yml | 14 +--
.../templates-gitlab-package-registry.yml | 2 +-
templates/templates-r.yml | 1 -
tests/.gitlab-ci-checkers-tests.yml | 8 +-
6 files changed, 108 insertions(+), 13 deletions(-)
create mode 100644 docs/Descriptions.md
diff --git a/README.md b/README.md
index 9dae1a2..bd1feed 100644
--- a/README.md
+++ b/README.md
@@ -14,6 +14,8 @@ This repository contains useful Gitlab CI templates files.
| [templates-checkers.yml](/templates/templates-checkers.yml) | Templates for checking some job results, for examples: checking keywords presence in logs (errors in compile log, etc.), checking uncommitted git changes, etc. |
| [templates-r.yml](/templates/templates-r.yml) | Templates around R language |
+See detailed descriptions of each template job [here](/docs/Descriptions.md).
+
## Use the templates
1. Include the template file you want to use in you .gitlab-ci.yml (or subfile):
diff --git a/docs/Descriptions.md b/docs/Descriptions.md
new file mode 100644
index 0000000..f2045ea
--- /dev/null
+++ b/docs/Descriptions.md
@@ -0,0 +1,94 @@
+# Templates detailed descriptions
+
+## Docker
+
+*([templates-docker.yml](/templates/templates-docker.yml))*
+
+- **.docker-build-and-push**
+ Builds a Docker image from a Dockerfile and push it to the Gitlab Registry.
+ Required variables:
+ - `DOCKERFILE_PATH`: Path to the Dockerfile to build. Defaulted to "Dockerfile".
+ - `CONTAINER_TAG`: The chosen docker tag for the new image. A default value is defined here: `$CI_REGISTRY_IMAGE:$CI_COMMIT_SHORT_SHA`.
+ Optional variable:
+ - `USE_CACHE`: Empty this variable to use cache.
+- **.docker-push-latest**
+ Tags the Docker image for "main" branch as "latest".
+- **.docker-push-tag**
+ Tags the Docker image for any Git tag.
+ GitLab will start a new pipeline everytime a Git tag is created, which is pretty awesome.
+
+## Gitlab Docker Registry
+
+*([templates-gitlab-docker-registry.yml](/templates/templates-gitlab-docker-registry.yml))*
+
+- **.gitlab-docker-registry-login-linux**
+ Connects to the project registry for linux runners.
+- **.gitlab-docker-registry-login-windows**
+ Connects to the project registry for Windows runners (powershell).
+
+## Gitlab Package Registry
+
+*([templates-gitlab-package-registry.yml](/templates/templates-gitlab-package-registry.yml))*
+
+- **.gitlab-generic-package-upload**
+ Allows uploading a new package to the "package registry" of the current Gitlab project.
+ The variables `PACKAGE_NAME` and `FILENAME` must be redined. The package is stored in registry in this path: `${PACKAGE_NAME}/${GITLAB_PACKAGE_VERSION}/${FILENAME}`.
+ By default `GITLAB_PACKAGE_VERSION` is the commit SHA tag.
+ Optionaliy, variables `GITLAB_PACKAGE_VERSION` and `PATH_IN_PACKAGE_REGISTRY` cand be redefined if default are not what is expected.
+- **.gitlab-generic-package-download**
+ Allows downloading an existing package from the "package registry" of the current Gitlab project.
+ Same variables rules as **.gitlab-generic-package-upload** apply to this template.
+- **.gitlab-generic-package-delete**
+ > :warning: template commented, see issue #2
+
+## Checkers
+
+*([templates-checkers.yml](/templates/templates-checkers.yml))*
+
+- **.check-find-bad-keywords-in-files-linux**
+ Checks in files given in variable `SEARCH_FILES` if keywords given in variable `KEYWORDS` occurs (default keywords: "error ", "warning ", "remark ").
+ If some are found then return an error but not critical for pipeline (warning).
+ The lines found are printed to console.
+ This template is for linux runners.
+ > This has been primarily developped to checkers warnings in compile logs.
+- **.check-find-bad-keywords-in-file-windows**
+ This is a version for Windows runners of the previous template.
+- **.check-git-uncommitted-changes**
+ This job checks if the local git clone has some uncommitted changes.
+ > This is useful to ensure no versionned files have been changed by CI.
+- **.check-git-notmanaged-changes**
+ This job checks if the local git clone has some unversioned files not ignored nor uncommitted changes.
+ > This is useful to ensure there are no files which must be ignored.
+
+## R language
+
+*([templates-r.yml](/templates/templates-r.yml))*
+
+- **.R-package-cache**
+ This template define the useful paths to the local packages libraries in an order which allow a cache creation. The path cached must be within the working project directory, so default ones doesn't work.
+ So this template define a cache with the key `R-installed-packages-cache`.
+ It is recommended to extend this template for all R CI jobs, because this allow some performance gain.
+ > Note: each runner has a dedicated cache, so the running job use only data in the cache of the runner is running on!
+- **optionsForCi.R**
+ This is not a template, but an R function can be call before other R command in order to set some options useful for CI. These options force CI to stop on warnings and force showing additionnal call stack infos and errors messages.
+ To use this, first you need to download it in the script sectionand then the function could be called in an R command (and previous options restored at the end):
+
+ ```yaml
+ - script:
+ - mkdir temp_gitlabTemplates
+ - wget https://forgemia.inra.fr/urep/dev_utils/gitlab-ci-templates/-/raw/dev/R/optionsForCi.R?inline=false --output-document=temp_gitlabTemplates/optionsForCi.R
+ - >
+ R -q -e '
+ source("temp_gitlabTemplates/optionsForCi.R");
+
+ <other R commands>
+
+ options(optionsBackup)
+ '
+ - rm -rf temp_gitlabTemplates
+ ```
+
+- **.R-install-package-dependencies-withCache**
+ This template install all required and suggest packages of a package sources project.
+ > The default behavior of devtools functions is not to raise errors, so if an install fails this doesn't stop the CI. This template purpose is to correct that.
+ > This template use the `R-installed-packages-cache` cache.
diff --git a/templates/templates-checkers.yml b/templates/templates-checkers.yml
index dd38f78..3778939 100644
--- a/templates/templates-checkers.yml
+++ b/templates/templates-checkers.yml
@@ -1,7 +1,7 @@
# This job search in given files for keywords.
# If some are found then return an error but not critical for pipeline (warning)
-# The line found are printed to console
-.check-find-bad-keyworkds-in-files-linux:
+# The lines found are printed to console
+.check-find-bad-keywords-in-files-linux:
tags:
- docker
image: alpine:3.16
@@ -21,8 +21,8 @@
# This job search in given file for keywords.
# If some are found then return an error but not critical for pipeline (warning)
-# The line found are printed to console
-.check-find-bad-keyworkds-in-file-windows:
+# The lines found are printed to console
+.check-find-bad-keywords-in-file-windows:
tags:
- windows-powershell
variables:
@@ -44,7 +44,7 @@
- if ($hints) { exit ${FOUND_RETURN_CODE} } else { exit ${NOTFOUND_RETURN_CODE} }
allow_failure: true
-# This job check if the local git clone has some uncommitted changes
+# This job checks if the local git clone has some uncommitted changes
# This is useful to ensure no versionned files have been changed by CI
.check-git-uncommitted-changes:
tags:
@@ -60,8 +60,8 @@
- if [[ -z "$(git status --untracked-files=no --porcelain=v1)" ]]; then exit ${EMPTY_RETURN_CODE}; exit ${NOTEMPTY_RETURN_CODE}; fi
allow_failure: true
-# This job check if the local git clone has some unversioned files not ignored
-# or uncommitted changes.
+# This job checks if the local git clone has some unversioned files not ignored
+# nor uncommitted changes.
# This is useful to ensure no files which must be ignored
.check-git-notmanaged-changes:
tags:
diff --git a/templates/templates-gitlab-package-registry.yml b/templates/templates-gitlab-package-registry.yml
index 7e5a843..d301bf8 100644
--- a/templates/templates-gitlab-package-registry.yml
+++ b/templates/templates-gitlab-package-registry.yml
@@ -40,7 +40,7 @@
${CI_API_V4_URL}/projects/${TARGET_PROJECT_ID}/packages/generic/${PATH_IN_PACKAGE_REGISTRY}'
- if ! test -f ${FILENAME}; then exit 1; fi
-# Doesn't work! The API seems to require some ids for package, but how to get them automatically?
+# Doesn't work! The API seems to require some ids for package, but how to get them automatically? (see issue #2)
# .gitlab-generic-package-delete:
# image: curlimages/curl:7.83.1
# tags:
diff --git a/templates/templates-r.yml b/templates/templates-r.yml
index 0bc1fe0..f769c17 100644
--- a/templates/templates-r.yml
+++ b/templates/templates-r.yml
@@ -57,7 +57,6 @@
stop("An error is expected but none occurs")
}
- # Restore options
options(optionsBackup)
'
- rm -rf temp_gitlabTemplates
diff --git a/tests/.gitlab-ci-checkers-tests.yml b/tests/.gitlab-ci-checkers-tests.yml
index 1dcf10b..37ab058 100644
--- a/tests/.gitlab-ci-checkers-tests.yml
+++ b/tests/.gitlab-ci-checkers-tests.yml
@@ -9,7 +9,7 @@ Test check-find-linux Bad:
FOUND_RETURN_CODE: 0
NOTFOUND_RETURN_CODE: 1
extends:
- - .check-find-bad-keyworkds-in-files-linux
+ - .check-find-bad-keywords-in-files-linux
rules:
- changes:
- .gitlab-ci.yml
@@ -24,7 +24,7 @@ Test check-find-windows Bad:
FOUND_RETURN_CODE: 0
NOTFOUND_RETURN_CODE: 1
extends:
- - .check-find-bad-keyworkds-in-file-windows
+ - .check-find-bad-keywords-in-file-windows
rules:
- changes:
- .gitlab-ci.yml
@@ -37,7 +37,7 @@ Test check-find-linux Good:
variables:
SEARCH_FILES: tests/Checkers-find-test-good.txt
extends:
- - .check-find-bad-keyworkds-in-files-linux
+ - .check-find-bad-keywords-in-files-linux
rules:
- changes:
- .gitlab-ci.yml
@@ -50,7 +50,7 @@ Test check-find-windows Good:
variables:
SEARCH_FILE: tests/Checkers-find-test-good.txt
extends:
- - .check-find-bad-keyworkds-in-file-windows
+ - .check-find-bad-keywords-in-file-windows
rules:
- changes:
- .gitlab-ci.yml
--
GitLab
From 0e687f2a955edb82af974e3122d7a410053d2949 Mon Sep 17 00:00:00 2001
From: Astre Benjamin <benjamin.astre@inrae.fr>
Date: Wed, 5 Oct 2022 18:14:47 +0200
Subject: [PATCH 26/29] test...
---
R/installDepsWithErrManagement.R | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/R/installDepsWithErrManagement.R b/R/installDepsWithErrManagement.R
index 20cd8d8..1229646 100644
--- a/R/installDepsWithErrManagement.R
+++ b/R/installDepsWithErrManagement.R
@@ -32,6 +32,7 @@ installDepsWithErrManagement <- function(warningsAsErrors = FALSE,
repo <- "https://cloud.r-project.org"
update.packages(ask = FALSE, repos = repo)
+ stop("essai pour voir...")
# Install devtools and stringi packages which are used here
install.packages(pkgs = "devtools", repos = repo)
@@ -69,7 +70,8 @@ installDepsWithErrManagement <- function(warningsAsErrors = FALSE,
install.packages(pkgs = "devtools", repos = repo)
install.packages(pkgs = "stringi", repos = repo)
- devtools::install_dev_deps(dependencies = TRUE)
+ devtools::install_dev_deps(dependencies = TRUE,
+ upgrade = "always")
FALSE
},
error = function(e) {
--
GitLab
From 7be26b92a5ad9169abf7830cfd69657051818ee7 Mon Sep 17 00:00:00 2001
From: Astre Benjamin <benjamin.astre@inrae.fr>
Date: Wed, 5 Oct 2022 18:18:59 +0200
Subject: [PATCH 27/29] Correct R tests rules
---
tests/.gitlab-ci-r-tests.yml | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/tests/.gitlab-ci-r-tests.yml b/tests/.gitlab-ci-r-tests.yml
index 1251607..1597e44 100644
--- a/tests/.gitlab-ci-r-tests.yml
+++ b/tests/.gitlab-ci-r-tests.yml
@@ -11,8 +11,8 @@ Test R-install-package-dependencies-withCache Good:
- .gitlab-ci.yml
- tests/.gitlab-ci-r-tests.yml
- templates/templates-r.yml
- - tests/r-package
- - R
+ - tests/r-package/*
+ - R/*
variables:
TEST_ERROR: 0
script:
@@ -27,8 +27,8 @@ Test R-install-package-dependencies-withCache Bad:
- .gitlab-ci.yml
- tests/.gitlab-ci-r-tests.yml
- templates/templates-r.yml
- - tests/r-package
- - R
+ - tests/r-package/*
+ - R/*
variables:
TEST_ERROR: 1
script:
--
GitLab
From 5ea60923c00db7c84bb6bcbedc498803f21adb6a Mon Sep 17 00:00:00 2001
From: Astre Benjamin <benjamin.astre@inrae.fr>
Date: Wed, 5 Oct 2022 18:28:26 +0200
Subject: [PATCH 28/29] test...
---
R/installDepsWithErrManagement.R | 5 ++---
1 file changed, 2 insertions(+), 3 deletions(-)
diff --git a/R/installDepsWithErrManagement.R b/R/installDepsWithErrManagement.R
index 1229646..ae8786d 100644
--- a/R/installDepsWithErrManagement.R
+++ b/R/installDepsWithErrManagement.R
@@ -31,8 +31,7 @@ installDepsWithErrManagement <- function(warningsAsErrors = FALSE,
sink(file = con, type = "message")
repo <- "https://cloud.r-project.org"
- update.packages(ask = FALSE, repos = repo)
- stop("essai pour voir...")
+ #update.packages(ask = FALSE, repos = repo)
# Install devtools and stringi packages which are used here
install.packages(pkgs = "devtools", repos = repo)
@@ -64,7 +63,7 @@ installDepsWithErrManagement <- function(warningsAsErrors = FALSE,
sink(file = con, type = "message")
repo <- "https://cloud.r-project.org"
- update.packages(ask = FALSE, repos = repo)
+ #update.packages(ask = FALSE, repos = repo)
# Install devtools and stringi packages which are used here
install.packages(pkgs = "devtools", repos = repo)
--
GitLab
From 16a4a72f725a74458949d1838ff529c291e44aee Mon Sep 17 00:00:00 2001
From: Astre Benjamin <benjamin.astre@inrae.fr>
Date: Wed, 5 Oct 2022 18:32:36 +0200
Subject: [PATCH 29/29] Remove force update of R packages Because this cost too
many time with no current reason
---
R/installDepsWithErrManagement.R | 2 --
1 file changed, 2 deletions(-)
diff --git a/R/installDepsWithErrManagement.R b/R/installDepsWithErrManagement.R
index ae8786d..71ca165 100644
--- a/R/installDepsWithErrManagement.R
+++ b/R/installDepsWithErrManagement.R
@@ -31,7 +31,6 @@ installDepsWithErrManagement <- function(warningsAsErrors = FALSE,
sink(file = con, type = "message")
repo <- "https://cloud.r-project.org"
- #update.packages(ask = FALSE, repos = repo)
# Install devtools and stringi packages which are used here
install.packages(pkgs = "devtools", repos = repo)
@@ -63,7 +62,6 @@ installDepsWithErrManagement <- function(warningsAsErrors = FALSE,
sink(file = con, type = "message")
repo <- "https://cloud.r-project.org"
- #update.packages(ask = FALSE, repos = repo)
# Install devtools and stringi packages which are used here
install.packages(pkgs = "devtools", repos = repo)
--
GitLab