add comments, changes

.gitignore

@@ -130,3 +130,5 @@ dmypy.json
 
 .vscode
 output
+
+.DS_Store

bicytok/MBmodel.py

@@ -23,8 +23,6 @@ def cytBindingModel(
     Return:
         output: amount of receptor bound of each kind of receptor
     """
-    print(recCount)
-    print()
     Kx = getKxStar()
     ligandConc = dose / (vals[0][0] * 1e9)
 

bicytok/figures/common.py

@@ -31,6 +31,9 @@
 matplotlib.rcParams["legend.borderpad"] = 0.35
 
 
+# Armaan: When declaring constants at the top of a file, it is good practice to
+# choose a descriptive name, use ALL CAPS (e.g. DOSE_MAT), and possibly add a
+# brief comment. Also, this particular variable isn't used anywhere.
 dosemat = np.array(
     [
         84,
@@ -90,6 +93,10 @@ def genFigure():
 
     exec("from bicytok.figures." + nameOut + " import makeFigure", globals())
     ff = makeFigure()  # noqa: F821
+
+    # Armaan: add function argument here to toggle the commented code if it's
+    # needed else delete the comment.
+
     # for non cluster maps:
     # ff.savefig(fdir + nameOut + ".svg", dpi=ff.dpi, bbox_inches="tight", pad_inches=0)
     # for cluster maps:
@@ -98,6 +105,7 @@ def genFigure():
     print(f"Figure {sys.argv[1]} is done after {time.time() - start} seconds.\n")
 
 
+# Armaan: resolve this (delete the function or the comment)
 # NOTE: CHECK IF WE NEED THIS
 def subplotLabel(axs: list[Axes]):
     """Place subplot labels on figure."""
@@ -119,9 +127,11 @@ def subplotLabel(axs: list[Axes]):
     "CD8": (6200, 7500),
     "NK": (4000, 5000),
 }
+# Armaan: Unused variable
 ratioSTATlimDict = {"Treg/NK": (0, 4000), "Treg/CD8": (0, 1500)}
 
 
+# Armaan: resolve this
 # NOTE: CHECK IF WE NEED THIS
 def plotBispecific(ax: Axes, df, cellType: str, val=False):
     """Plots all experimental vs. Predicted Values"""

bicytok/figures/figure1.py

@@ -65,7 +65,6 @@ def makeFigure():
     df = pd.DataFrame(columns=["Dose", "Selectivity", "Target Bound", "Ligand"])
 
     for targetPairs in allTargets:
-        print(targetPairs)
         prevOptAffs = [8.0]
         valencies = [signal[1]]
         targets = []
@@ -105,8 +104,6 @@ def makeFigure():
             )
             df = pd.concat([df, df_temp], ignore_index=True)
 
-    print(df)
-
     sns.lineplot(data=df, x="Dose", y="Selectivity", hue="Ligand", ax=ax[0])
     sns.lineplot(data=df, x="Dose", y="Target Bound", hue="Ligand", ax=ax[1])
     ax[0].set(xscale="log")

bicytok/imports.py

@@ -13,6 +13,13 @@
 path_here = os.path.dirname(os.path.dirname(__file__))
 
 
+# Armaan: don't use lru_cache if function returns mutable value. See my
+# explanation here: https://github.com/meyer-lab/tensordata/pull/26.
+# Will you be calling this function multiple times throughout a single program?
+# I would just recommend calling it once, and then using `deepcopy` to create
+# copies which you can change if you need to. You may consider passing the data
+# as a function argument if this is called in separate spots throughout the
+# codebase.
 @lru_cache(maxsize=None)
 def getBindDict():
     """Gets binding to pSTAT fluorescent conversion dictionary"""
@@ -23,9 +30,25 @@ def getBindDict():
     return bindingDF
 
 
+# Armaan: lru_cache mutable return value
 @lru_cache(maxsize=None)
 def importReceptors():
     """Makes Complete receptor expression Dict"""
+    # Armaan: it is bad practice to hard-code path separators into strings,
+    # because path separators differ by OS. Instead use os.path.join or, even
+    # better, use pathlib.Path. I would highly recommend replacing all uses of
+    # os.path.join with the pathlib.Path equivalent. This is also gradually
+    # becoming standard practice.
+    """
+    # Usage of pathlib.Path:
+
+    from pathlib import Path
+
+    THIS_DIR = Path(__file__).parent
+    recDF = THIS_DIR / "bicytok" / "data" / "RecQuantitation.csv" #  You can use
+    slashes outside of the string, as the pathlib.Path object has overloaded the
+    `/` operator to automatically generate the correct path separator.
+    """
     recDF = pd.read_csv(join(path_here, "bicytok/data/RecQuantitation.csv"))
     recDFbin = pd.read_csv(join(path_here, "bicytok/data/BinnedReceptorData.csv"))
     recDFbin = recDFbin.loc[recDFbin["Bin"].isin([1, 3])]
@@ -35,6 +58,7 @@ def importReceptors():
     return recDF
 
 
+# Armaan: lru_cache mutable return value
 @lru_cache(maxsize=None)
 def makeCITEdf():
     """Makes cite surface epitope csv for given cell type, DON'T USE THIS UNLESS DATA NEEDS RESTRUCTURING"""
@@ -154,6 +178,8 @@ def makeTregSC():
     return
 
 
+# Armaan: Move this to the top of the file (and add a brief comment) or into
+# the function `makeTregSC`.
 SC_Stims = [
     "control",
     "IL2_100pM",

bicytok/selectivityFuncs.py

@@ -125,7 +125,6 @@ def optimizeDesign(
     targRecs, offTRecs = get_rec_vecs(
         selectedDF, targCell, offTCells, signal, targets, cellCat
     )
-    print("Optimize")
     optimized = minimize(
         minSelecFunc,
         X0,
@@ -140,7 +139,6 @@ def optimizeDesign(
         ),
         jac="3-point",
     )
-    print("Done")
     optSelectivity = optimized.fun
     optAffs = optimized.x
 

general_comments.md

@@ -1,4 +1,16 @@
 1. File naming should be consistent. The convention for python files is lower
-case letters with '_' to separate words. E.g., `BindingMod.py` ->
+case letters with `_` to separate words. E.g., `BindingMod.py` ->
 `binding_mod.py`. 
-2. Sort imports with Ruff (I did this for you)
+2. Sort imports with Ruff (I did this for you)
+3. Run `ruff check` again with the rules I declared in `pyproject.toml`. There
+are a few small issues outlined in the output.
+4. When possible, use `snake_case` for variable and function naming. Officially,
+the PEP8 convention specifies that variable names should only include lower case
+letters, but it makes sense for us to ignore that part of the convention
+sometimes, particularly when we're implementing mathematical functions which
+were described in a math paper elsewhere, where uppercase variable names were
+used (e.g. binding model paper uses R_eq).
+5. I believe `bicytok/data/epitopeSelectivityList.csv`,
+`bicytok/data/MonomericMutSingleCellData.csv`,
+`bicytok/data/WTDimericMutSingleCellData.csv`, `bicytok/data/WTmutAffData.csv`
+are unused.

pyproject.toml

@@ -43,5 +43,7 @@ select = [
     "SIM",
     # isort
     "I",
+    # Unused arguments
+    "ARG",
 ]