Fix GH Actions (#490)

* Add missing title to .onLoad * Remove use of cached packages and explicitly add shinyBS * Style and fix example typo * Add boto3 and pandas to requirements * Add and remove ", where needed * Add newline at end of pkgdown.yaml * Try reticulate::py_discover_config() * Wrap login attempt in case credentials not provided Print error message if not logged in. This is due to challenges printing the credentials in the Windows CI environment. Hopefully we can just skip tests for now.
Sage-Bionetworks · Jun 16, 2021 · 27f0de2 · 27f0de2
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commit 27f0de2
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diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -71,10 +71,10 @@ jobs:
       - name: Install dependencies
         run: |
           library(remotes)
-          deps <- readRDS("depends.Rds")
-          deps[["installed"]] <- vapply(deps[["package"]], remotes:::local_sha, character(1))
+          deps <- readRDS('depends.Rds')
+          deps[['installed']] <- vapply(deps[['package']], remotes:::local_sha, character(1))
           update(deps)
-          remotes::install_cran("rcmdcheck")
+          remotes::install_cran('rcmdcheck')
         shell: Rscript {0}
 
       - name: Install Miniconda
@@ -88,9 +88,8 @@ jobs:
 
       - name: Install Python deps
         run: |
-          Rscript -e "reticulate::conda_create('r-reticulate', packages = c('python==3.7.0'))"
-          Rscript -e "remotes::install_local()"
-          Rscript -e "reticulate::py_install(c('pandas', 'numpy','boto3', 'synapseclient'), pip = TRUE)
+          Rscript -e "reticulate::py_discover_config()"
+          Rscript -e "reticulate::py_install(c('pandas', 'numpy', 'boto3', 'synapseclient'), pip = TRUE)"
 
       - name: Setup Synapse config file for testing
         if: runner.os != 'Windows'

diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -24,27 +24,22 @@ jobs:
           saveRDS(remotes::dev_package_deps(dependencies = TRUE), "depends.Rds", version = 2)
         shell: Rscript {0}
 
-      - name: Cache R packages
-        uses: actions/cache@v1
-        with:
-          path: ${{ env.R_LIBS_USER }}
-          key: macOS-r-3.6-${{ hashFiles('depends.Rds') }}
-          restore-keys: macOS-r-3.6-
-
       - name: Install system dependencies
         run: |
           brew install harfbuzz fribidi
 
       - name: Install dependencies
         run: |
-          install.packages("remotes")
-          remotes::install_deps(dependencies = TRUE)
-          install.packages("pkgdown", type = "binary")
+          library(remotes)
+          deps <- readRDS("depends.Rds")
+          deps[["installed"]] <- vapply(deps[["package"]], remotes:::local_sha, character(1))
+          update(deps)
+          install.packages(c("pkgdown", "shinyBS"), type = "binary")
         shell: Rscript {0}
 
       - name: Install package
         run: R CMD INSTALL .
 
       - name: Deploy package
         run: pkgdown::deploy_to_branch(new_process = FALSE)
-        shell: Rscript {0}
+        shell: Rscript {0}
diff --git a/R/metadata-template-dictionary.R b/R/metadata-template-dictionary.R
@@ -146,7 +146,7 @@ verify_dictionary_structure <- function(dictionary) {
 
   return(check_pass(
     msg = "All keys had a single description and columnType",
-    behavior = "All keys should have a single descrioption and columnType"
+    behavior = "All keys should have a single description and columnType"
   ))
 }
 
@@ -255,8 +255,8 @@ add_dictionary_sheets <- function(template_xlsx_path, annotations) {
 #'     "A person's family name",
 #'     "A person's family name"
 #'   )
-#' generate_key_description(annots)
 #' )
+#' generate_key_description(annots)
 #' }
 generate_key_description <- function(annots) {
   if (!(all(c("key", "description") %in% colnames(annots)))) {

diff --git a/R/mod-synapse-oauth.R b/R/mod-synapse-oauth.R
@@ -7,7 +7,7 @@ app_url <- NULL
 claims_param <- NULL
 authorization_url <- NULL
 
-#' @title
+#' @title Set up Synapse and OAuth variables
 #'
 #' @description Bring in the Synapse Python Client and set up global variables
 #' for OAuth at startup. Requires global variables initialized to NULL: synapse,
@@ -31,7 +31,7 @@ authorization_url <- NULL
 #' @title Synapse Oauth Module
 #'
 #' @description Create the Synapse OAuth component of a Shiny app.
-#' 
+#'
 #' If this is
 #' the first time signing in, will need to do OAuth the process. The OAuth
 #' process will redirect back here and an authorization code
@@ -41,7 +41,7 @@ authorization_url <- NULL
 #' (i.e. the function specified in the `ui` parameter here
 #' `shinyApp(ui = app_ui, server = app_server)`), which receives the `request`
 #' object and can pass it along.
-#' 
+#'
 #' IMPORTANT: this module assumes the following
 #' global variables are available and valid: app, api, authorization_url,
 #' app_url, claims_params, scope. See \code{\link{setup_global_oauth_vars}}.
@@ -58,16 +58,16 @@ authorization_url <- NULL
 #' \dontrun{
 #' library("dccvalidator")
 #' app_ui <- function(request) {
-#' mod_synapse_oauth_ui(id = "oauth", request = request)
+#'   mod_synapse_oauth_ui(id = "oauth", request = request)
 #' }
 #' app_server <- function(input, output, session) {
-#' synapse <- reticulate::import("synapseclient")
-#' syn <- synapse$Synapse()
-#' syn <- mod_synapse_oauth_server(
-#' id = "oauth",
-#' syn = syn
-#' )
-#' shiny::req(inherits(syn, "synapseclient.client.Synapse"), logged_in(syn))
+#'   synapse <- reticulate::import("synapseclient")
+#'   syn <- synapse$Synapse()
+#'   syn <- mod_synapse_oauth_server(
+#'     id = "oauth",
+#'     syn = syn
+#'   )
+#'   shiny::req(inherits(syn, "synapseclient.client.Synapse"), logged_in(syn))
 #' }
 #' run_app()
 #' }

diff --git a/man/dot-onLoad.Rd b/man/dot-onLoad.Rd
diff --git a/man/mod_synapse_oauth_ui.Rd b/man/mod_synapse_oauth_ui.Rd
diff --git a/requirements.txt b/requirements.txt
@@ -1,11 +1,13 @@
 backports.csv==1.0.7
+boto3==1.17.95
 certifi==2019.9.11
 chardet==3.0.4
 Deprecated==1.2.4
 entrypoints==0.3
 future==0.18.2
 idna==2.8
 keyring==12.0.2
+pandas==1.2.4
 requests==2.22.0
 six==1.13.0
 synapseclient==1.9.4

diff --git a/tests/testthat/test-check-all.R b/tests/testthat/test-check-all.R
@@ -2,7 +2,12 @@ context("test-check-all.R")
 
 library("tibble")
 syn <- attempt_instantiate()
-attempt_login(syn)
+tryCatch(
+  attempt_login(syn),
+  error = function(e) {
+    print(glue::glue("Did not log into Synapse: {e$message}"))
+  }
+)
 annots <- tribble(
   ~key, ~value, ~columnType,
   "assay", "rnaSeq", "STRING",

diff --git a/tests/testthat/test-check-annotation-keys.R b/tests/testthat/test-check-annotation-keys.R
@@ -2,7 +2,12 @@ context("test-check-annotation-keys.R")
 
 library("tibble")
 syn <- attempt_instantiate()
-attempt_login(syn = syn)
+tryCatch(
+  attempt_login(syn),
+  error = function(e) {
+    print(glue::glue("Did not log into Synapse: {e$message}"))
+  }
+)
 Sys.setenv(R_CONFIG_ACTIVE = "testing")
 
 annots <- tribble(

diff --git a/tests/testthat/test-check-annotation-values.R b/tests/testthat/test-check-annotation-values.R
@@ -2,7 +2,12 @@ context("test-check-annotation-values.R")
 
 library("tibble")
 syn <- attempt_instantiate()
-attempt_login(syn)
+tryCatch(
+  attempt_login(syn),
+  error = function(e) {
+    print(glue::glue("Did not log into Synapse: {e$message}"))
+  }
+)
 Sys.setenv(R_CONFIG_ACTIVE = "testing")
 annots <- tribble(
   ~key, ~value, ~columnType,

diff --git a/tests/testthat/test-check-certified-user.R b/tests/testthat/test-check-certified-user.R
@@ -1,7 +1,12 @@
 context("test-chec-certified-user.R")
 
 syn <- attempt_instantiate()
-attempt_login(syn)
+tryCatch(
+  attempt_login(syn),
+  error = function(e) {
+    print(glue::glue("Did not log into Synapse: {e$message}"))
+  }
+)
 Sys.setenv(R_CONFIG_ACTIVE = "testing")
 
 test_that("check_certified_user returns check_pass if certified", {

diff --git a/tests/testthat/test-check-col-names.R b/tests/testthat/test-check-col-names.R
@@ -1,7 +1,12 @@
 context("test-check-col-names.R")
 
 syn <- attempt_instantiate()
-attempt_login(syn)
+tryCatch(
+  attempt_login(syn),
+  error = function(e) {
+    print(glue::glue("Did not log into Synapse: {e$message}"))
+  }
+)
 Sys.setenv(R_CONFIG_ACTIVE = "testing")
 
 test_that("check_col_names returns condition object when check passes", {
@@ -37,7 +42,12 @@ test_that("get_template fails when not logged in to Synapse", {
   )
 })
 
-attempt_login(syn)
+tryCatch(
+  attempt_login(syn),
+  error = function(e) {
+    print(glue::glue("Did not log into Synapse: {e$message}"))
+  }
+)
 
 test_that("check_cols_individual works for individual columns", {
   skip_if_not(logged_in(syn = syn))

diff --git a/tests/testthat/test-check-team-membership.R b/tests/testthat/test-check-team-membership.R
@@ -1,7 +1,12 @@
 context("test-check-team-membership.R")
 
 syn <- attempt_instantiate()
-attempt_login(syn)
+tryCatch(
+  attempt_login(syn),
+  error = function(e) {
+    print(glue::glue("Did not log into Synapse: {e$message}"))
+  }
+)
 Sys.setenv(R_CONFIG_ACTIVE = "testing")
 
 test_that("check_team_membership() returns check_pass if user is in the team", {

diff --git a/tests/testthat/test-create-folder.R b/tests/testthat/test-create-folder.R
@@ -1,7 +1,12 @@
 context("test-create-folder.R")
 
 syn <- attempt_instantiate()
-attempt_login(syn)
+tryCatch(
+  attempt_login(syn),
+  error = function(e) {
+    print(glue::glue("Did not log into Synapse: {e$message}"))
+  }
+)
 Sys.setenv(R_CONFIG_ACTIVE = "testing")
 
 test_that("create_folder() creates a folder", {

diff --git a/tests/testthat/test-get-synapse-annotations.R b/tests/testthat/test-get-synapse-annotations.R
@@ -1,7 +1,12 @@
 context("test-get-synapse-annotations.R")
 
 syn <- attempt_instantiate()
-attempt_login(syn = syn)
+tryCatch(
+  attempt_login(syn),
+  error = function(e) {
+    print(glue::glue("Did not log into Synapse: {e$message}"))
+  }
+)
 Sys.setenv(R_CONFIG_ACTIVE = "testing")
 
 test_that("get_synapse_table returns a data frame", {

diff --git a/tests/testthat/test-get-user-teams.R b/tests/testthat/test-get-user-teams.R
@@ -1,7 +1,12 @@
 context("test-get-user-teams.R")
 
 syn <- attempt_instantiate()
-attempt_login(syn)
+tryCatch(
+  attempt_login(syn),
+  error = function(e) {
+    print(glue::glue("Did not log into Synapse: {e$message}"))
+  }
+)
 Sys.setenv(R_CONFIG_ACTIVE = "testing")
 
 test_that("get_user_teams gets team memberships", {

diff --git a/tests/testthat/test-metadata-template-dictionary.R b/tests/testthat/test-metadata-template-dictionary.R
@@ -2,7 +2,12 @@ context("metadata-template-dictionary.R")
 
 # update_template_dictionaries ------------------------------------------------
 syn <- attempt_instantiate()
-attempt_login(syn)
+tryCatch(
+  attempt_login(syn),
+  error = function(e) {
+    print(glue::glue("Did not log into Synapse: {e$message}"))
+  }
+)
 Sys.setenv(R_CONFIG_ACTIVE = "testing")
 
 test_that("update_template_dictionaries returns updated Synapse file list", {

diff --git a/tests/testthat/test-python-helpers.R b/tests/testthat/test-python-helpers.R
@@ -1,7 +1,12 @@
 context("test-python-helpers.R")
 
 syn <- attempt_instantiate()
-attempt_login(syn)
+tryCatch(
+  attempt_login(syn),
+  error = function(e) {
+    print(glue::glue("Did not log into Synapse: {e$message}"))
+  }
+)
 Sys.setenv(R_CONFIG_ACTIVE = "testing")
 
 test_that("dict_to_list converts annotations", {