[ci] add linting and autoformatting for shell scripts (#227)

.ci/install.sh

@@ -1,10 +1,10 @@
 #!/bin/bash
 
 # failure is a natural part of life
-set -e
+set -e -u -o pipefail
 
 if [[ "$TASK" == "rpkg" ]]; then
-  R CMD INSTALL \
-    --clean \
-    $(pwd)/r-pkg
+    R CMD INSTALL \
+        --clean \
+        ./r-pkg
 fi

.ci/report_to_covr.sh

@@ -1,10 +1,10 @@
 #!/bin/bash
 
 # failure is a natural part of life
-set -e
+set -e -u -o pipefail
 
 if [[ "$TASK" == "rpkg" ]]; then
-  Rscript -e " \
+    Rscript -e " \
     Sys.setenv(NOT_CRAN = 'true'); \
     covr::codecov('r-pkg/') \
     "

.ci/setup.sh

@@ -1,26 +1,26 @@
+#!/bin/bash
+
 # failure is a natural part of life
-set -e
+set -e -u -o pipefail
 
 # If language: r,
 # install these testing packages we need
-if [[ "$TASK" == "rpkg" ]];
-then
+if [[ "$TASK" == "rpkg" ]]; then
 
     # `devscripts` is required for 'checkbashisms' (https://github.com/r-lib/actions/issues/111)
     sudo apt-get update
     sudo apt-get install \
         --no-install-recommends \
         -y \
         --allow-downgrades \
-            libcurl4-openssl-dev \
-            curl \
-            devscripts \
-            texinfo \
-            texlive-latex-recommended \
-            texlive-fonts-recommended \
-            texlive-fonts-extra \
-            qpdf \
-        || exit -1
+        libcurl4-openssl-dev \
+        curl \
+        devscripts \
+        texinfo \
+        texlive-latex-recommended \
+        texlive-fonts-recommended \
+        texlive-fonts-extra \
+        qpdf
 
     Rscript -e "install.packages(c('assertthat', 'covr', 'data.table', 'futile.logger', 'httr', 'jsonlite', 'knitr', 'lintr', 'purrr', 'rmarkdown', 'stringr', 'testthat', 'uuid'), repos = 'https://cran.r-project.org', Ncpus = parallel::detectCores())"
     cp test-data/* r-pkg/inst/testdata/

.ci/test.sh

@@ -1,13 +1,13 @@
 #!/bin/bash
 
 # failure is a natural part of life
-set -e
+set -e -u -o pipefail
 
 if [[ "$TASK" == "rpkg" ]]; then
-  Rscript .ci/lint_r_code.R $(pwd)
-  R CMD build $(pwd)/r-pkg
-  export _R_CHECK_CRAN_INCOMING_=false
-  R CMD check \
-    --as-cran \
-    *.tar.gz
+    Rscript .ci/lint_r_code.R "$(pwd)"
+    R CMD build ./r-pkg
+    export _R_CHECK_CRAN_INCOMING_=false
+    R CMD check \
+        --as-cran \
+        ./*.tar.gz
 fi

.pre-commit-config.yaml

@@ -0,0 +1,22 @@
+---
+exclude: |
+    (?x)^(
+        test-data/.*
+    )$
+repos:
+  - repo: https://github.com/maxwinterstein/shfmt-py
+    rev: v3.7.0.1
+    hooks:
+      - id: shfmt
+        args: ["--indent=4", "--space-redirects", "--write"]
+  - repo: https://github.com/shellcheck-py/shellcheck-py
+    rev: v0.10.0.1
+    hooks:
+      - id: shellcheck
+        args: ["--exclude=SC2002"]
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.3.0
+    hooks:
+      - id: codespell
+        # additional_dependencies: [tomli]
+        # args: ["--toml", "pyproject.toml"]

cleanup_local.sh

@@ -1,13 +1,13 @@
 #!/bin/bash
 
-set -e 
+set -e -u -o pipefail
 
 # Remove testing directory
 echo "removing testing directory"
-rm -r $(pwd)/sandbox
+rm -r ./sandbox
 
 # Kill the running container
 echo "killing running container"
-docker kill $(docker ps -ql)
+docker kill "$(docker ps -ql)"
 
 echo "done cleaning up test environment"

cran-comments.md

@@ -14,7 +14,7 @@
 * One NOTE from `checking CRAN incoming feasibility ...` can be safely ignored since it's a note that notifies CRAN that this is a new maintainer/submission. 
 
 ### CRAN Response
-* Automatic checking upon CRAN submission yielded two notes. One was the "incoming feasbility..." item we mentioned above, which is not an issue. 
+* Automatic checking upon CRAN submission yielded two notes. One was the "incoming feasibility..." item we mentioned above, which is not an issue. 
 * The other note said that `Author field differs from that derived from Authors@R`. This did not arise when running `R CMD check --as-cran` locally, but it looks like "fnd" is not a supported tag for an author. Removed that tag.
 
 ## v0.0.2 - Submission 2 - (July 17, 2017)
@@ -127,7 +127,7 @@ In this submission, we changed maintainer from `[email protected]` to `jayla
 ## v0.4.0 - Submission 1 - (September 11, 2019)
 
 ### `R CMD check` results
-* No isses
+* No issues
 
 ### CRAN Response
 * No issues. v0.4.0 released to CRAN!

r-pkg/R/es_search.R

@@ -641,7 +641,7 @@ es_search <- function(es_host
     log_info(sprintf("uptasticsearch thinks you are running Elasticsearch %s", version))
 
     # Parse out just the major version. We can adjust this if we find
-    # API differences that occured at the minor version level
+    # API differences that occurred at the minor version level
     major_version <- .major_version(version)
     return(major_version)
 }

r-pkg/tests/testthat/test-integration.R

@@ -166,7 +166,7 @@ futile.logger::flog.threshold(0)
             , ignore.order = TRUE
         )
 
-        # ther stuff we might as well test
+        # the stuff we might as well test
         expect_true(data.table::is.data.table(outDT))
         expect_true(is.numeric(outDT[, doc_count]))
         expect_true(is.character(outDT[, name_i_picked]))
@@ -200,7 +200,7 @@ futile.logger::flog.threshold(0)
 
         # Decided to check that it's coercible to an integer instead of
         # hard-coding known Elasticsearch versions so this test won't require
-        # attention or break builds if/when Elasticsearch 7 or whatever the next major verison
+        # attention or break builds if/when Elasticsearch 7 or whatever the next major version
         # is comes out
         expect_true(!is.na(as.integer(ver)), info = paste0("returned version: ", ver))
     })