Feature clean path (#44)

* fix history check in blastn function

* rename main directory variable

* path job cleaned up

* path refactoring in blaster

* refactor blaster module file name

* clean config dict blaster assets

* test cases quality assessment

* path fix and type output for asset

* refactor status file names

* refactor file names viewer asset

* remove all use of pyspark

* update readme to remove openjdk dependency

* fix paths and typo

* attempt to test temp dir

* change flake flag for complexity

* ran flake and black

.github/workflows/ci.yml

@@ -24,7 +24,7 @@ jobs:
         coverage run -m pytest test/unit
         coverage xml -o coverage.xml
       env:
-        PHAGY_DIRECTORY: ${{ env.PHAGY_DIRECTORY }}
+        DATA_DIR: ${{ env.DATA_DIR }}
         FILE_SYSTEM: ${{ env.FILE_SYSTEM }}
         EMAIL: ${{ secrets.EMAIL }}
         API_KEY: ${{ secrets.API_KEY }}

Makefile

@@ -11,6 +11,7 @@ clean: # Remove workspace files
 	@rm -rf ./dist
 	@rm -rf test/fixtures/assets_testing_folder/ncbi_download/fetch
 	@rm -rf test/fixtures/assets_testing_folder/sequence_quality/genbank
+	@rm -rf test/fixtures/assets_testing_folder/sequence_quality_with_history/genbank
 	@rm -rf test/fixtures/assets_testing_folder/blasting/gene_identity
 	@rm -rf test/fixtures/assets_testing_folder/blasting_with_history/gene_identity
 	@rm -rf test/fixtures/assets_testing_folder/synteny/synteny
@@ -25,7 +26,7 @@ black: # Format code
 	@black test
 
 flake: # Lint code
-	@flake8 --ignore=E501,W503,E731,E722 --max-cognitive-complexity=30 synphage
+	@flake8 --ignore=E501,W503,E731,E722 --max-complexity=30 synphage
 	@python -c "print('Linting: 👌')"
 
 radon:

README.md

@@ -40,9 +40,12 @@ docker pull vestalisvirginis/synphage:latest
 
 ### Additional dependencies
 
-Synphage relies on two non-python dependencies that need to be manually installed when Synphage is installed with pip:
+Synphage relies on one non-python dependency that need to be manually installed when Synphage is installed with pip:
 - [Blast+](https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/) >= 2.12.0   
-- [OpenJDK](https://openjdk.org/projects/jdk/17/) == 17  
+```bash
+apt update
+apt install -y ncbi-blast+
+```
 
 
 ## Usage
@@ -61,7 +64,7 @@ Synphage requires:
 #### Path setup
 
 ```bash
-export PHAGY_DIRECTORY=<path_to_data_folder>
+export DATA_DIR=<path_to_data_folder>
 ```
 
 **Note:** For docker users, this path is defaulted to `/data`.

conftest.py

@@ -1,75 +1,59 @@
-# import os
-# import warnings
 import pytest
-# from pyspark.sql import SparkSession
-#import logging
-
-#logger = logging.getLogger(__name__)
 
 
 @pytest.fixture
 def mock_env_ncbi_connect(monkeypatch):
     monkeypatch.setenv("EMAIL", "[email protected]")
     monkeypatch.setenv("API_KEY", "jhd6hdz778ahjeahj8889")
 
-
 @pytest.fixture
 def mock_env_ncbi_download_pos(monkeypatch):
-    monkeypatch.setenv("PHAGY_DIRECTORY", "test/fixtures/ncbi_download/positive")
-
+    monkeypatch.setenv("DATA_DIR", "test/fixtures/ncbi_download/positive")
 
 @pytest.fixture
 def mock_env_ncbi_download_neg(monkeypatch):
-    monkeypatch.setenv("PHAGY_DIRECTORY", "test/fixtures/ncbi_download/negative")
-
+    monkeypatch.setenv("DATA_DIR", "test/fixtures/ncbi_download/negative")
 
 @pytest.fixture
 def mock_env_ncbi_count(monkeypatch):
     monkeypatch.setenv("DATABASE", "nuccore")
     monkeypatch.setenv("KEYWORD", "Bacillus subtilis strain P9_B1")
 
-
 @pytest.fixture
 def mock_env_ncbi_fetch(monkeypatch):
-    monkeypatch.setenv("PHAGY_DIRECTORY", "test/fixtures/ncbi_download/fetch")
-
+    monkeypatch.setenv("DATA_DIR", "test/fixtures/ncbi_download/fetch")
 
 @pytest.fixture
 def mock_env_sequence_check(monkeypatch):
-    monkeypatch.setenv("PHAGY_DIRECTORY", "test/fixtures/assets_testing_folder/sequence_quality")
+    monkeypatch.setenv("DATA_DIR", "test/fixtures/assets_testing_folder/sequence_quality")
 
+@pytest.fixture
+def mock_env_sequence_check_with_history(monkeypatch):
+    monkeypatch.setenv("DATA_DIR", "test/fixtures/assets_testing_folder/sequence_quality_with_history")
 
 @pytest.fixture
 def mock_env_phagy_dir_blasting(monkeypatch):
-    monkeypatch.setenv("PHAGY_DIRECTORY", "test/fixtures/assets_testing_folder/blasting")
+    monkeypatch.setenv("DATA_DIR", "test/fixtures/assets_testing_folder/blasting")
 
 @pytest.fixture
 def mock_env_phagy_dir_blasting_with_history(monkeypatch):
-    monkeypatch.setenv("PHAGY_DIRECTORY", "test/fixtures/assets_testing_folder/blasting_with_history")
+    monkeypatch.setenv("DATA_DIR", "test/fixtures/assets_testing_folder/blasting_with_history")
 
 @pytest.fixture
 def mock_env_phagy_dir_transform(monkeypatch):
-    monkeypatch.setenv("PHAGY_DIRECTORY", "test/fixtures/assets_testing_folder/transform")
+    monkeypatch.setenv("DATA_DIR", "test/fixtures/assets_testing_folder/transform")
     monkeypatch.setenv("FILE_SYSTEM", "fs")
 
 @pytest.fixture
 def mock_env_phagy_dir_transform_step3(monkeypatch):
-    monkeypatch.setenv("PHAGY_DIRECTORY", "test/fixtures/assets_testing_folder/transform_3")
+    monkeypatch.setenv("DATA_DIR", "test/fixtures/assets_testing_folder/transform_3")
 
 @pytest.fixture
 def mock_env_phagy_dir_synteny(monkeypatch):
-    monkeypatch.setenv("PHAGY_DIRECTORY", "test/fixtures/assets_testing_folder/synteny")
+    monkeypatch.setenv("DATA_DIR", "test/fixtures/assets_testing_folder/synteny")
     monkeypatch.setenv("SEQUENCE_FILE", "sequences.csv")
-# @pytest.fixture(scope="session")
-# def spark():
-#     try:
-#         #logger = logging.getLogger("py4j")
-#         #ogger.setLevel(logging.ERROR)
-#         spark_session = SparkSession.builder.config(
-#             "spark.driver.memory", "2g"
-#         ).getOrCreate()
-#         yield spark_session
-#     except:
-#         pass
-#     finally:
-#         spark_session.stop()
+
+@pytest.fixture
+def mock_env_phagy_dir_none(monkeypatch):
+    monkeypatch.delenv("DATA_DIR", raising=False)
+

pyproject.toml

@@ -22,7 +22,6 @@ dependencies = [
     "biopython >= 1.81",
     "reportlab >= 3.6.12",
     "rlPyCairo >= 0.3.0",
-    "pyspark >= 2.15.1",
     "cuallee >= 0.6.0",
     "duckdb >= 0.9.1",
     "polars >= 0.19.11",