tests: Update unit tests: remove use of obsoleted functions.

3 files changed, 33 insertions, 8 deletions

diff --git a/README.org b/README.org
index 9e0324a..20a4de7 100644
--- a/README.org
+++ b/README.org
@@ -217,11 +217,20 @@ To check for correct type usage in the application, run:
 
 Run unit tests with:
 #+BEGIN_SRC shell
-  pytest -k unit_test
+  $ export QCAPP_CONF=</path/to/configuration/file.py>
+  $ pytest -k unit_test
+#+END_SRC
+
+To run ALL tests (not just unit tests):
+#+BEGIN_SRC shell
+  $ export QCAPP_CONF=</path/to/configuration/file.py>
+  $ pytest
 #+END_SRC
 
 ** Deploying/Installing QC
 
+**NOTE**: All tests should pass before you deploy the uploader!
+
 *** CLI: Docker
 
 Generate the docker image file with
diff --git a/tests/r_qtl/test_r_qtl2_geno.py b/tests/r_qtl/test_r_qtl2_geno.py
index d3c77e6..a1e69b7 100644
--- a/tests/r_qtl/test_r_qtl2_geno.py
+++ b/tests/r_qtl/test_r_qtl2_geno.py
@@ -273,12 +273,23 @@ def test_parse_founder_geno_files(relpath, expected):
 
 @pytest.mark.unit_test
 @pytest.mark.parametrize(
-    "filepath,expected",
+    "filepath,member,transposed,expected",
     (("tests/r_qtl/test_files/test_geno.zip",
+      "test_geno.csv",
+      False,
       ("1", "2", "3", "4", "5", "6", "7", "8", "9", "10")),
      ("tests/r_qtl/test_files/test_geno_transposed.zip",
+      "test_geno_transposed.csv",
+      True,
       ("1", "2", "3", "4", "5", "6", "7", "8", "9", "10")),
      ("tests/r_qtl/test_files/test_geno_multiple.zip",
-      ("1", "2", "3", "4", "5", "6", "7", "8", "9", "10"))))
-def test_load_geno_samples(filepath, expected):
-    assert sorted(rqtl2.load_geno_samples(filepath)) == sorted(expected)
+      "test_geno_multiple01.csv",
+      False,
+      ("1", "2", "3", "4", "5")),
+     ("tests/r_qtl/test_files/test_geno_multiple.zip",
+      "test_geno_multiple02.csv",
+      False,
+      ("6", "7", "8", "9", "10"))))
+def test_load_geno_samples(filepath, member, transposed, expected):
+    assert sorted(rqtl2.load_samples(
+        filepath, member, transposed)) == sorted(expected)
diff --git a/tests/r_qtl/test_r_qtl2_pheno.py b/tests/r_qtl/test_r_qtl2_pheno.py
index d31ad54..54244fc 100644
--- a/tests/r_qtl/test_r_qtl2_pheno.py
+++ b/tests/r_qtl/test_r_qtl2_pheno.py
@@ -61,10 +61,15 @@ def test_parse_phenocovar_files(filepath, expected):
 
 @pytest.mark.unit_test
 @pytest.mark.parametrize(
-    "filepath,expected",
+    "filepath,member,transposed,expected",
     (("tests/r_qtl/test_files/test_pheno.zip",
+      "test_pheno.csv",
+      False,
       ("1", "2", "3", "4", "5")),
      ("tests/r_qtl/test_files/test_pheno_transposed.zip",
+      "test_pheno_transposed.csv",
+      True,
       ("1", "2", "3", "4", "5"))))
-def test_load_geno_samples(filepath, expected):
-    assert sorted(rqtl2.load_pheno_samples(filepath)) == sorted(expected)
+def test_load_geno_samples(filepath, member, transposed, expected):
+    assert sorted(rqtl2.load_samples(
+        filepath, member, transposed)) == sorted(expected)