minor bug fixes and code improvements

README.md

@@ -339,3 +339,7 @@ by Abolfazl (Abe) Arab ([@abearab](https://github.com/abearab)) as a Research As
 If you use ScreenPro2 in your research, please cite the following paper.
 
   Coming soon...
+
+## Development
+### Testing
+Tests can be easily run using the `pytest` framework.

environment.yml

@@ -29,3 +29,4 @@ dependencies:
       - simple_colors
       - adjustText
       - watermark
+      - pytest

pyproject.toml

@@ -0,0 +1,30 @@
+[tool.poetry]
+name = "ScreenPro2"
+version = "0.5.0"
+description = "Flexible analysis of high-content CRISPR screening"
+authors = [
+    "Abe Arab <abea@arcinstitute.org>"
+]
+license = "MIT"
+readme = "README.md"
+homepage = "https://github.com/ArcInstitute/ScreenPro2"
+repository = "https://github.com/ArcInstitute/ScreenPro2"
+keywords = ["CRISPR", "screening", "bioinformatics"]
+packages = [
+	{ include = "screenpro" },
+	{ include = "pyproject.toml" },
+]
+
+[tool.poetry.dependencies]
+python = ">=3.9"
+
+[tool.poetry.scripts]
+screenpro = "screenpro.main:main"
+
+[tool.poetry.group.test.dependencies]
+pytest = "*"
+tomli = "*"
+
+[build-system]
+requires = ["poetry-core>=1.0.0", "poetry-dynamic-versioning>=1.0.0,<2.0.0"]
+build-backend = "poetry_dynamic_versioning.backend"

screenpro/__init__.py

@@ -29,8 +29,3 @@
 from .ngs import GuideCounter
 from .assays import PooledScreens, GImaps
 from .dashboard import DrugScreenDashboard
-
-
-__version__ = "0.4.18"
-__author__ = "Abe Arab"
-__email__ = 'abea@arcinstitute.org' # "abarbiology@gmail.com"

screenpro/assays/__init__.py

@@ -262,7 +262,7 @@ def calculateDrugScreen(self, score_level: Literal["compare_reps", "compare_guid
                     n_reps=self.n_reps,
                     test=self.test, score_level=score_level,
                     count_filter_threshold=count_filter_threshold,
-                    count_filter_type=count_filter_type
+                    count_filter_type=count_filter_type,
                     **kwargs
                 )
                 self._add_phenotype_results(run_name, f'tau:{tau_name}', tau)

screenpro/dashboard/__init__.py

@@ -220,13 +220,15 @@ def RhoVolcanoPlot(
         hit_label_col='rho_label',
         x_min=-2.5, x_max=2.5, y_min=0, y_max='auto',
         return_html=True,
+        **kwargs
         ):
         p = self._plot_scatter(
             x_source, y_source,
             xaxis_label, yaxis_label,
             up_hit, down_hit,
             hit_label_col,
             x_min, x_max, y_min, y_max,
+            **kwargs
         )
 
         if return_html:
@@ -245,13 +247,15 @@ def GammaVolcanoPlot(
         hit_label_col='gamma_label',
         x_min=-2.5, x_max=2.5, y_min=0, y_max='auto',
         return_html=True,
+        **kwargs
         ):
         p = self._plot_scatter(
             x_source, y_source,
             xaxis_label, yaxis_label,
             up_hit, down_hit,
             hit_label_col,
             x_min, x_max, y_min, y_max,
+            **kwargs
         )
 
         if return_html:
@@ -268,15 +272,17 @@ def RhoGammaScatter(
         yaxis_label='gamma score',
         up_hit='resistance_hit', down_hit='sensitivity_hit',
         hit_label_col='rho_label',
-        return_html=True,
         x_min=-2.5, x_max=2.5, y_min=-2.5, y_max=2.5,
+        return_html=True,
+        **kwargs
         ):
         p = self._plot_scatter(
             x_source, y_source,
             xaxis_label, yaxis_label,
             up_hit, down_hit,
             hit_label_col,
             x_min, x_max, y_min, y_max,
+            **kwargs
         )
 
         if return_html: