test: update tests with new functions from ccbr_tools

CCBR · Aug 13, 2024 · 295e334 · 295e334
1 parent 58d3d10
commit 295e334
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Showing 3 changed files with 19 additions and 15 deletions.
diff --git a/tests/test_cache.py b/tests/test_cache.py
@@ -3,7 +3,7 @@
 import os.path
 import subprocess
 
-from renee.src.renee.cache import get_sif_cache_dir, get_singularity_cachedir
+from ccbr_tools.pipeline.cache import get_sif_cache_dir, get_singularity_cachedir
 
 renee_run = (
     "./bin/renee run "

diff --git a/tests/test_run.py b/tests/test_run.py
@@ -3,25 +3,26 @@
 import os
 import tempfile
 
-from renee.src.renee.util import (
+from ccbr_tools.pipeline.util import (
     get_tmp_dir,
     get_shared_resources_dir,
     renee_base,
+    get_hpcname,
 )
-from renee.src.renee.cache import get_sif_cache_dir
-from renee.src.renee.run import run, run_in_context
-from renee.src.renee.util import get_hpcname
+from ccbr_tools.pipeline.cache import get_sif_cache_dir
+from ccbr_tools.shell import exec_in_context
+
+from renee.src.renee.util import renee_base
+from renee.src.renee.run import run
 
 
 def test_dryrun():
     if get_hpcname() == "biowulf":
         with tempfile.TemporaryDirectory() as tmp_dir:
             run_args = argparse.Namespace(
-                input=list(glob.glob(os.path.join(renee_base(".tests"), "*.fastq.gz"))),
+                input=list(glob.glob(renee_base(".tests", "*.fastq.gz"))),
                 output=tmp_dir,
-                genome=os.path.join(
-                    renee_base("config"), "genomes", "biowulf", "hg38_36.json"
-                ),
+                genome=renee_base("config", "genomes", "biowulf", "hg38_36.json"),
                 mode="slurm",
                 runmode="run",
                 dry_run=True,
@@ -36,7 +37,7 @@ def test_dryrun():
                 threads=2,
             )
             # execute dry run and capture stdout/stderr
-            allout = run_in_context(run_args)
+            allout = exec_in_context(run, run_args)
         assert (
             "This was a dry-run (flag -n). The order of jobs does not reflect the order of execution."
             in allout

diff --git a/tests/test_util.py b/tests/test_util.py
@@ -6,13 +6,14 @@
 import tempfile
 import warnings
 
-from renee.src.renee.util import (
-    renee_base,
+from ccbr_tools.pipeline.util import (
     _cp_r_safe_,
     get_genomes_dict,
     get_genomes_list,
 )
 
+from renee.src.renee.util import renee_base
+
 
 def test_renee_base():
     renee_bin = renee_base(os.path.join("bin", "renee"))
@@ -52,7 +53,7 @@ def test_cp_unsafe():
 
 def test_get_genomes_warnings():
     with warnings.catch_warnings(record=True) as raised_warnings:
-        genomes = get_genomes_list(hpcname="notAnOption")
+        genomes = get_genomes_list(repo_base=renee_base, hpcname="notAnOption")
         assertions = [
             "len(genomes) == 0",
             "len(raised_warnings) == 2",
@@ -68,10 +69,12 @@ def test_get_genomes_warnings():
 
 def test_get_genomes_error():
     with pytest.raises(UserWarning) as exception_info:
-        get_genomes_list(hpcname="notAnOption", error_on_warnings=True)
+        get_genomes_list(
+            repo_base=renee_base, hpcname="notAnOption", error_on_warnings=True
+        )
         assert "Folder does not exist" in str(exception_info.value)
 
 
 def test_get_genomes_biowulf():
-    genomes_dict = get_genomes_dict(hpcname="biowulf")
+    genomes_dict = get_genomes_dict(repo_base=renee_base, hpcname="biowulf")
     assert len(genomes_dict) > 10