added requirement test to cli

bedboss/bedboss.py

@@ -8,6 +8,7 @@
 import peppy
 from eido import validate_project
 import bbconf
+import subprocess
 
 import pephubclient
 from pephubclient import PEPHubClient
@@ -113,6 +114,18 @@ def load_to_s3(
     pm.run(cmd=command, lock_name="s3_sync_bedstat")
 
 
+def requirements_check() -> None:
+    """
+    Check if all requirements are installed
+
+    :return: None
+    """
+    _LOGGER.info("Checking requirements...")
+    subprocess.run(
+        ["bash", f"{os.path.dirname(os.path.abspath(__file__))}/requirements_test.sh"]
+    )
+
+
 def run_all(
     sample_name: str,
     input_file: str,
@@ -433,13 +446,13 @@ def main(test_args: dict = None) -> NoReturn:
         or "test_outfolder",
     )
     pm_out_folder = os.path.join(os.path.abspath(pm_out_folder[0]), "pipeline_manager")
-
     pm = pypiper.PipelineManager(
         name="bedboss-pipeline",
         outfolder=pm_out_folder,
         version=__version__,
-        args=args,
+        # args=args,
         multi=args_dict.get("multy", False),
+        recover=True,
     )
     if args_dict["command"] == "all":
         run_all(pm=pm, **args_dict)
@@ -455,6 +468,8 @@ def main(test_args: dict = None) -> NoReturn:
         run_bedbuncher(pm=pm, **args_dict)
     elif args_dict["command"] == "index":
         add_to_qdrant(pm=pm, **args_dict)
+    elif args_dict["command"] == "requirements-check":
+        requirements_check()
     else:
         parser.print_help()
         # raise Exception("Incorrect pipeline name.")

bedboss/bedbuncher/bedbuncher.py

@@ -317,8 +317,8 @@ def run_bedbuncher(
     return None
 
 
-if __name__ == "__main__":
-    run_bedbuncher(
-        "/media/alex/Extreme SSD/databio/repos/bedbase_all/bedhost/bedbase_configuration_compose.yaml",
-        "databio/excluderanges:id3",
-    )
+# if __name__ == "__main__":
+#     run_bedbuncher(
+#         "/media/alex/Extreme SSD/databio/repos/bedbase_all/bedhost/bedbase_configuration_compose.yaml",
+#         "databio/excluderanges:id3",
+#     )

bedboss/cli.py

@@ -51,6 +51,10 @@ def build_argparser() -> ArgumentParser:
         "index", help="Index not indexed bed files and add them to the qdrant database "
     )
 
+    subparser.add_parser(
+        "requirements-check", help="Check if all requirements are installed"
+    )
+
     sub_all.add_argument(
         "--outfolder",
         required=True,

docs/changelog.md

@@ -2,6 +2,6 @@
 
 This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html) and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) format.
 
-## [0.1.0a1] - 2023-08-02
+## [0.1.0] - 2024-01-26
 ### Added
 - Initial alpha release

test/test_bedboss.py

@@ -1,4 +1,5 @@
 from bedboss.bedboss import main
+import bedboss
 import os
 import warnings
 import subprocess
@@ -13,7 +14,9 @@
 )
 
 BEDBASE_CONFIG = os.path.join(FILE_DIR, "test_dependencies", "bedbase_config_test.yaml")
-DEPENDENCIES_TEST_SCRIPT = f"{FILE_DIR}/bash_requirements_test.sh"
+DEPENDENCIES_TEST_SCRIPT = (
+    f"{os.path.dirname(os.path.abspath(bedboss.__file__))}/requirements_test.sh"
+)
 
 pytest_db_skip_reason = "Database is not set up... To run this test, set up the database. Go to test/README.md for more information."
 
@@ -23,16 +26,17 @@ def check_dependencies_installed() -> bool:
     print("Testing dependencies...")
     # key = "PATH"
     # value = os.getenv(key)
-    test_dep_return_code = subprocess.run([DEPENDENCIES_TEST_SCRIPT], shell=True)
-    if not (1 > test_dep_return_code.returncode):
+    test_dep_return_code = subprocess.run(["bash", DEPENDENCIES_TEST_SCRIPT])
+    if test_dep_return_code.returncode == 127:
+        raise Exception(f"test script '{DEPENDENCIES_TEST_SCRIPT}' doesn't exist.")
+    elif not (1 > test_dep_return_code.returncode):
         warnings.warn(UserWarning(f"{pytest_db_skip_reason}"))
         return False
     return True
     # return 1 > test_dep_return_code.returncode
 
 
-# dependencies_installed = check_dependencies_installed()
-dependencies_installed = True
+dependencies_installed = check_dependencies_installed()
 
 
 def db_setup():
@@ -45,8 +49,8 @@ def db_setup():
     return True
 
 
-# def test_dependencies():
-#     assert dependencies_installed
+def test_dependencies():
+    assert dependencies_installed
 
 
 @pytest.mark.parametrize(