Test pr (#5)

* Removed some text from the tester. Checking testing works.

* removed pycache, as well as unused bad db example from removed test.

* updated channel defaults for testing env.

* Update testing environment to include hmmer.

* update env

* Update error reporting.

* Update error reporting.

* remove dbs

* Reupload dbs

* Updated assert error for when database fails to run to print the whole log to console. Rather than fail printing too large of a assert text.

* Update readme for DB release instructions.

---------

Co-authored-by: Michael Barnett <ToMichaelBarnett@gmail.com>

Author: MichaelBarnett

README.md

@@ -37,9 +37,13 @@ conda activate commec-dev
 From here, you should have an interactive version of the package installed via (`pip -e .`) as well
 as the necessary shell dependencies.
 
-Database Release Pipeline
-=========================
-Explicit Instructions here.
+Database Release and Update
+===========================
+Updating the databases will entail the following steps:
+- Ensure git lfs is installed.
+- Create a Pull Request for changes into main, triggering unit tests on new database files.
+- On successful PR, merge into main.
+- Create a Release, which will automatically package commec-dbs lfs into a release zip.
 
 About
 =====
@@ -48,4 +52,4 @@ Biosafety Initiative for Science. From 2021-2023, the software and databases wer
 team of technical consultants working with the Nuclear Threat Initiative, led by Dr. Nicole Wheeler
 of the University of Birmingham, and including contributions from Brittany Rife Magalis of the
 University of Louisville and Jennifer Lu of the Center for Computational Biology at Johns Hopkins
-University. In 2024, IBBIS became the home of the project.
+University. In 2024, IBBIS became the home of the project.

tests/environment.yaml

@@ -4,6 +4,6 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - python >=3.8
+  - python >=3.10
   - commec
   - pytest

tests/test_dbs.py

@@ -41,7 +41,14 @@ def test_databases_can_run(input_database, tmp_path):
     output_file = tmp_path / "db.out"
 
     screener = handler_class(db_path, fasta_file, str(output_file), force=True)
-    screener.search()
+    try:
+        screener.search()
+    except RuntimeError:
+        with open(str(output_file)+".log.tmp",'r', encoding = 'utf-8') as f:
+            output_text = str(f.read())
+            print("Error text for database run: ", output_text)
+            assert False, "Failed to run subprocess: Temporary log output."
+
 
     with open(output_file,'r', encoding = 'utf-8') as f:
         output_text = str(f.read())