Merge pull request #29 from ArcInstitute/master

release v0.2.5

.github/workflows/python-publish.yml

@@ -36,4 +36,4 @@ jobs:
       uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
       with:
         user: __token__
-        password: ${{ secrets.PYPI_API_TOKEN }}
+        password: ${{ secrets.PYPI_TOKEN }}

README.md

@@ -88,8 +88,11 @@ Here is an example for running the workflow on a [CRISPRi-dual-sgRNA-screens](#c
 ```python
 # Run the ScreenPro2 workflow for CRISPRi-dual-sgRNA-screens
 screen.calculateDrugScreen(
-  t0='T0', untreated='DMSO', treated='Drug', 
-  growth_rate=1, # can be replaced by the growth values (population doublings/doubling differences)
+  t0='T0',
+  untreated='DMSO',  # replace with the label for untreated condition
+  treated='Drug',    # replace with the label for treated condition
+  db_untreated=1,    # replace with doubling rate of untreated condition
+  db_treated=1,      # replace with doubling rate of treated condition
   score_level='compare_reps'
 )
 ```
@@ -129,4 +132,4 @@ ScreenPro2 is licensed under the terms of the MIT license (see [LICENSE](LICENSE
 by Abolfazl (Abe) Arab ([@abearab](https://github.com/abearab)), a Research Associate in the Gilbert lab at UCSF and Arc Institute.  
 
 ## Citation
-If you use ScreenPro2 in your research, please cite the following paper.
+If you use ScreenPro2 in your research, please cite the following paper.

screenpro/__init__.py

@@ -60,8 +60,9 @@ def calculateDrugScreen(self, t0, untreated, treated, db_untreated, db_treated,
             n_reps=self.n_reps,
             math=self.math, test=self.test, score_level=score_level
         )
+        # TO-DO: warning / error if db_untreated and db_treated are too close, i.e. growth_rate ~= 0.
         rho_name, rho = ps.runPhenoScore(
-            self.adata, cond1=untreated, cond2=treated, growth_rate=np.abs(db_untreated - (1 - db_treated)),
+            self.adata, cond1=untreated, cond2=treated, growth_rate=np.abs(db_untreated - db_treated),
             n_reps=self.n_reps,
             math=self.math, test=self.test, score_level=score_level
         )