Only check warning message for deprecated features

bailey-lab · Jul 31, 2022 · c6a6605 · c6a6605
1 parent b392ca4
commit c6a6605
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diff --git a/tests/testthat/_snaps/read-deprecated.md b/tests/testthat/_snaps/read-deprecated.md
@@ -1,65 +1,7 @@
-# chrom and gene are deprecated
+# read() is deprecated
 
-    Code
-      read("small.csv", "small.csv", "small.csv", chrom = "13")
-    Condition
-      Warning:
-      `read()` was deprecated in miplicorn 0.2.0.
-      Please use `read_tbl_ref_alt_cov()` instead.
-      Warning:
-      The `chrom` argument of `read()` is deprecated as of miplicorn 0.1.0.
-      Please use the `...` argument instead to filter data.
-    Message
-      Joining, by = "gene_id"
-      Joining, by = "gene_id"
-      Joining, by = "gene_id"
-    Output
-      # A ref alt cov table: 0 x 10
-      # ... with 10 variables: sample <chr>, gene_id <chr>, gene <chr>,
-      #   mutation <chr>, func <chr>, aa_chng <chr>, target <chr>,
-      #   ref_umi_count <dbl>, alt_umi_count <dbl>, coverage <dbl>
-      # i Use `colnames()` to see all variable names
-
----
-
-    Code
-      read("small.csv", "small.csv", "small.csv", chrom = "atp")
-    Condition
-      Warning:
-      `read()` was deprecated in miplicorn 0.2.0.
-      Please use `read_tbl_ref_alt_cov()` instead.
-      Warning:
-      The `chrom` argument of `read()` is deprecated as of miplicorn 0.1.0.
-      Please use the `...` argument instead to filter data.
-    Message
-      Joining, by = "gene_id"
-      Joining, by = "gene_id"
-      Joining, by = "gene_id"
-    Output
-      # A ref alt cov table: 0 x 10
-      # ... with 10 variables: sample <chr>, gene_id <chr>, gene <chr>,
-      #   mutation <chr>, func <chr>, aa_chng <chr>, target <chr>,
-      #   ref_umi_count <dbl>, alt_umi_count <dbl>, coverage <dbl>
-      # i Use `colnames()` to see all variable names
-
----
-
-    Code
-      read("small.csv", "small.csv", "small.csv", chrom = "13", gene = "atp")
-    Condition
-      Warning:
-      `read()` was deprecated in miplicorn 0.2.0.
-      Please use `read_tbl_ref_alt_cov()` instead.
-      Warning:
-      The `chrom` argument of `read()` is deprecated as of miplicorn 0.1.0.
-      Please use the `...` argument instead to filter data.
-      Warning:
-      The `gene` argument of `read()` is deprecated as of miplicorn 0.1.0.
-      Please use the `...` argument instead to filter data.
-      Error in `read_tbl_ref_alt_cov()`:
-      ! Multiple filtering criteria selected.
-      x Cannot filter on both `chrom` and `gene`.
-      i Select only one piece of information to filter on.
+    `read()` was deprecated in miplicorn 0.2.0.
+    Please use `read_tbl_ref_alt_cov()` instead.
 
 # read_file() is deprecated
 

diff --git a/tests/testthat/_snaps/read-tbl.md b/tests/testthat/_snaps/read-tbl.md
@@ -33,44 +33,13 @@
 
 # chrom and gene are deprecated
 
-    Code
-      read_tbl_ref_alt_cov(.tbl_ref = "small.csv", .tbl_alt = "small.csv", .tbl_cov = "small.csv",
-        chrom = "13")
-    Condition
-      Warning:
-      The `chrom` argument of `read()` is deprecated as of miplicorn 0.1.0.
-      Please use the `...` argument instead to filter data.
-    Message
-      Joining, by = "gene_id"
-      Joining, by = "gene_id"
-      Joining, by = "gene_id"
-    Output
-      # A ref alt cov table: 0 x 10
-      # ... with 10 variables: sample <chr>, gene_id <chr>, gene <chr>,
-      #   mutation <chr>, func <chr>, aa_chng <chr>, target <chr>,
-      #   ref_umi_count <dbl>, alt_umi_count <dbl>, coverage <dbl>
-      # i Use `colnames()` to see all variable names
+    The `chrom` argument of `read()` is deprecated as of miplicorn 0.1.0.
+    Please use the `...` argument instead to filter data.
 
 ---
 
-    Code
-      read_tbl_ref_alt_cov(.tbl_ref = "small.csv", .tbl_alt = "small.csv", .tbl_cov = "small.csv",
-        gene = "atp")
-    Condition
-      Warning:
-      The `gene` argument of `read()` is deprecated as of miplicorn 0.1.0.
-      Please use the `...` argument instead to filter data.
-    Message
-      Joining, by = "gene"
-      Joining, by = "gene"
-      Joining, by = "gene"
-    Output
-      # A ref alt cov table: 2 x 9
-        sample gene  mutation   func     aa_chng target ref_umi_count alt_um~1 cover~2
-        <chr>  <chr> <chr>      <chr>    <chr>   <chr>          <dbl>    <dbl>   <dbl>
-      1 S1     atp6  atp6-A623E missense A623E   Yes                0        0       0
-      2 S2     atp6  atp6-A623E missense A623E   Yes                0        0       0
-      # ... with abbreviated variable names 1: alt_umi_count, 2: coverage
+    The `gene` argument of `read()` is deprecated as of miplicorn 0.1.0.
+    Please use the `...` argument instead to filter data.
 
 ---
 

diff --git a/tests/testthat/test-read-deprecated.R b/tests/testthat/test-read-deprecated.R
@@ -1,10 +1,5 @@
-test_that("chrom and gene are deprecated", {
-  expect_snapshot(read("small.csv", "small.csv", "small.csv", chrom = "13"))
-  expect_snapshot(read("small.csv", "small.csv", "small.csv", chrom = "atp"))
-  expect_snapshot(
-    error = TRUE,
-    read("small.csv", "small.csv", "small.csv", chrom = "13", gene = "atp")
-  )
+test_that("read() is deprecated", {
+  expect_snapshot_warning(read("small.csv", "small.csv", "small.csv"))
 })
 
 test_that("read_file() is deprecated", {

diff --git a/tests/testthat/test-read-tbl.R b/tests/testthat/test-read-tbl.R
@@ -135,14 +135,14 @@ test_that("can filter rows", {
 
 # Test read_tbl_ref_alt_cov() --------------------------------------------------
 test_that("chrom and gene are deprecated", {
-  expect_snapshot(read_tbl_ref_alt_cov(
+  expect_snapshot_warning(read_tbl_ref_alt_cov(
     .tbl_ref = "small.csv",
     .tbl_alt = "small.csv",
     .tbl_cov = "small.csv",
     chrom = "13"
   ))
 
-  expect_snapshot(read_tbl_ref_alt_cov(
+  expect_snapshot_warning(read_tbl_ref_alt_cov(
     .tbl_ref = "small.csv",
     .tbl_alt = "small.csv",
     .tbl_cov = "small.csv",