From 992521f3d360a626e15632a3c17732860ea5f152 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?V=C3=ADt=20Ku=C4=8Dera?= <vit.kucera@cern.ch>
Date: Mon, 10 Feb 2025 17:16:42 +0100
Subject: [PATCH 01/13] Plot inclusive jets

---
 .../plotting/plot_jetsubstructure_run3.py     | 40 ++++++++++++-------
 1 file changed, 25 insertions(+), 15 deletions(-)

diff --git a/machine_learning_hep/plotting/plot_jetsubstructure_run3.py b/machine_learning_hep/plotting/plot_jetsubstructure_run3.py
index 7dbba6acfd..9cfb2534c8 100644
--- a/machine_learning_hep/plotting/plot_jetsubstructure_run3.py
+++ b/machine_learning_hep/plotting/plot_jetsubstructure_run3.py
@@ -694,9 +694,13 @@ def plot(self):
 
             if self.species == "D0":
                 # list_iptjet = [0, 1, 2, 3]  # indices of jet pt bins to process
-                list_iptjet = [2, 3]  # indices of jet pt bins to process
+                # list_iptjet = [0, 1, 2, 3, 4, 5, 6, 7]  # indices of jet pt bins to process
+                list_iptjet = [0, 2, 4, 6]  # indices of jet pt bins to process
+                # list_iptjet = [2, 3]  # indices of jet pt bins to process
             if self.species == "Lc":
                 list_iptjet = [1]  # indices of jet pt bins to process
+            if self.species == "incl":
+                list_iptjet = [2]
             plot_lc_vs_d0 = True
             list_stat_all = []
             list_syst_all = []
@@ -794,10 +798,11 @@ def plot(self):
 
                 # Results
                 self.logger.info("Plotting results")
-                plot_run2_data = True
+                plot_run2_data = False
+                # self.list_latex = [
+                # self.text_alice,
                 self.list_latex = [
-                    self.text_alice,
-                    # self.list_latex = [f"{self.text_alice}, {self.text_run3}",
+                    f"{self.text_alice}, {self.text_run3}",
                     self.text_jets,
                     f"{self.get_text_range_ptjet(iptjet)}, {self.text_etajet}",
                     self.get_text_range_pthf(-1, iptjet),
@@ -846,24 +851,24 @@ def plot(self):
                 self.title_full = self.title_full_default
 
                 # Plot additional stuff.
-                plot_run2_lc_ff_data = True
+                plot_run2_lc_ff_data = False
                 plot_run2_lc_ff_sim = False
 
-                plot_run2_d0_ff_data = True
+                plot_run2_d0_ff_data = False
 
-                plot_run2_d0_sd = True
-                plot_run2_d0_sd_hf_data = True
+                plot_run2_d0_sd = False
+                plot_run2_d0_sd_hf_data = False
                 plot_run2_d0_sd_hf_sim = False
                 plot_run2_d0_sd_incl_data = False
                 plot_run2_d0_sd_incl_sim = False
 
                 plot_run3_sim = False
-                plot_run3_d0_sd_hf_sim = True
-                plot_run3_d0_sd_incl_sim = True
+                plot_run3_d0_sd_hf_sim = False
+                plot_run3_d0_sd_incl_sim = False
 
                 plot_data = True
-                plot_sim = True
-                plot_incl = True
+                plot_sim = False
+                plot_incl = False
 
                 # Plot Run 2, Lc, FF, data, 5-7, 7-15, 15-35 GeV/c
                 if (
@@ -1168,7 +1173,7 @@ def plot(self):
             self.plot_errors_x = False
             self.list_latex = [
                 self.text_alice,
-                f"{self.text_tagged} {self.text_jets}",
+                self.text_jets,
                 f"{self.get_text_range_pthf(-1, iptjet)}, {self.text_etajet}",
             ]
             if not plot_run2_data:
@@ -1184,7 +1189,12 @@ def plot(self):
             self.list_markers = list_markers_all * (1 + int(bool(list_syst_all)))
             if plot_run2_data:
                 h_run2, g_run2 = None, None
-                if plot_run2_d0_sd and self.species == "D0" and self.var in ("zg", "rg", "nsd"):
+                if (
+                    plot_run2_d0_sd
+                    and self.species == "D0"
+                    and self.var in ("zg", "rg", "nsd")
+                    and string_ptjet == string_range_ptjet((15, 30))
+                ):  # FIXME
                     h_run2 = run2_d0_sd[self.var]["hf"]["data"]["stat"]
                     g_run2 = run2_d0_sd[self.var]["hf"]["data"]["syst"]
                     if self.var == "nsd":
@@ -1218,7 +1228,7 @@ def plot(self):
             self.labels_obj = []
             self.list_latex = []
             self.y_margin_up = 0.06  # to fix cropped number on the axis
-            self.title_full = f";{self.latex_obs};ratio to    "
+            self.title_full = f";{self.latex_obs};ratio to  "
             can, new = self.make_plot(
                 name_can, can=can, pad=2, scale=pad_heights[1], colours=self.list_colours, markers=self.list_markers
             )

From 407739309853f7d9e4ab834dd280106f2a0e12dc Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?V=C3=ADt=20Ku=C4=8Dera?= <vit.kucera@cern.ch>
Date: Wed, 12 Feb 2025 15:10:52 +0100
Subject: [PATCH 02/13] Fix colour indices. Crop systematics outside x range.

---
 .../analysis/do_systematics.py                | 40 +++++++++----------
 1 file changed, 20 insertions(+), 20 deletions(-)

diff --git a/machine_learning_hep/analysis/do_systematics.py b/machine_learning_hep/analysis/do_systematics.py
index cea89469e2..4e9f28458b 100644
--- a/machine_learning_hep/analysis/do_systematics.py
+++ b/machine_learning_hep/analysis/do_systematics.py
@@ -351,7 +351,7 @@ def do_jet_systematics(self, var: str):
             input_histograms_default.append(input_file_default.Get(name_his))
             if not input_histograms_default[iptjet]:
                 self.logger.critical(make_message_notfound(name_his, path_def))
-            # self.crop_histogram(input_histograms_default[iptjet], var)
+            self.crop_histogram(input_histograms_default[iptjet], var)
             print(f"Default histogram ({range_ptjet[0]} to {range_ptjet[1]})")
             print_histogram(input_histograms_default[iptjet], self.verbose)
             # name_eff = f"h_ptjet-pthf_effnew_pr_{string_range_ptjet(range_ptjet)}"
@@ -419,7 +419,7 @@ def do_jet_systematics(self, var: str):
                     path_eff_file = path_eff.replace(self.string_default, string_catvar)
                     if not sys_var_histo_eff:
                         self.logger.critical(make_message_notfound(name_eff, path_eff_file))
-                    # self.crop_histogram(sys_var_histo, var)
+                    self.crop_histogram(sys_var_histo, var)
                     input_histograms_syscatvar.append(sys_var_histo)
                     input_histograms_eff.append(sys_var_histo_eff)
                     print_histogram(sys_var_histo_eff, self.verbose)
@@ -515,7 +515,7 @@ def do_jet_systematics(self, var: str):
                             )
                         )
                     )
-                    setup_histogram(input_histograms_sys[iptjet][sys_cat][sys_var], get_colour(nsys + 1))
+                    setup_histogram(input_histograms_sys[iptjet][sys_cat][sys_var], get_colour(nsys))
                     input_histograms_sys[iptjet][sys_cat][sys_var].Draw("same")
                     nsys = nsys + 1
 
@@ -562,7 +562,7 @@ def do_jet_systematics(self, var: str):
                         input_histograms_sys[iptjet][sys_cat][sys_var], self.systematic_varlabels[sys_cat][sys_var], "P"
                     )
                     setup_histogram(
-                        input_histograms_sys[iptjet][sys_cat][sys_var], get_colour(nsys + 1), get_marker(nsys + 1)
+                        input_histograms_sys[iptjet][sys_cat][sys_var], get_colour(nsys), get_marker(nsys)
                     )
                     input_histograms_sys[iptjet][sys_cat][sys_var].Draw("same")
                     nsys = nsys + 1
@@ -628,7 +628,7 @@ def do_jet_systematics(self, var: str):
                         histo_ratio[sys_var].SetYTitle("variation/default")
                         histo_ratio[sys_var].Draw()
                     leg_sysvar_ratio.AddEntry(histo_ratio[sys_var], self.systematic_varlabels[sys_cat][sys_var], "P")
-                    setup_histogram(histo_ratio[sys_var], get_colour(nsys + 1), get_marker(nsys + 1))
+                    setup_histogram(histo_ratio[sys_var], get_colour(nsys), get_marker(nsys))
                     histo_ratio[sys_var].Draw("same")
                     nsys = nsys + 1
                 latex = TLatex(
@@ -703,8 +703,8 @@ def do_jet_systematics(self, var: str):
                     )
                     setup_histogram(
                         input_histograms_sys_eff[iptjet][sys_cat][sys_var],
-                        get_colour(nsys + 1),
-                        get_marker(nsys + 1),
+                        get_colour(nsys),
+                        get_marker(nsys),
                     )
                     input_histograms_sys_eff[iptjet][sys_cat][sys_var].Draw("same")
                     nsys = nsys + 1
@@ -754,7 +754,7 @@ def do_jet_systematics(self, var: str):
                     leg_sysvar_eff_ratio.AddEntry(
                         histo_ratio[sys_var], self.systematic_varlabels[sys_cat][sys_var], "P"
                     )
-                    setup_histogram(histo_ratio[sys_var], get_colour(nsys + 1), get_marker(nsys + 1))
+                    setup_histogram(histo_ratio[sys_var], get_colour(nsys), get_marker(nsys))
                     histo_ratio[sys_var].Draw("same")
                     nsys = nsys + 1
                 # line = TLine(obs_rec_min, 1, obs_rec_max, 1)
@@ -1048,9 +1048,9 @@ def do_jet_systematics(self, var: str):
             leg_finalwsys = TLegend(0.7, 0.78, 0.85, 0.88)
             setup_legend(leg_finalwsys)
             leg_finalwsys.AddEntry(input_histograms_default[iptjet], "data", "P")
-            # self.crop_histogram(input_histograms_default[iptjet], var)
-            # self.crop_graph(tgsys[iptjet], var)
-            setup_histogram(input_histograms_default[iptjet], get_colour(0, 0))
+            self.crop_histogram(input_histograms_default[iptjet], var)
+            self.crop_graph(tgsys[iptjet], var)
+            setup_histogram(input_histograms_default[iptjet], get_colour(-1))
             y_min_g, y_max_g = get_y_window_gr([tgsys[iptjet]])
             y_min_h, y_max_h = get_y_window_his([input_histograms_default[iptjet]])
             y_min = min(y_min_g, y_min_h)
@@ -1071,7 +1071,7 @@ def do_jet_systematics(self, var: str):
             input_histograms_default[iptjet].SetYTitle(latex_y)
             input_histograms_default[iptjet].Draw("AXIS")
             # input_histograms_default[iptjet].Draw("")
-            setup_tgraph(tgsys[iptjet], get_colour(7, 0))
+            setup_tgraph(tgsys[iptjet], get_colour(-1, 2))
             tgsys[iptjet].Draw("5")
             input_histograms_default[iptjet].Draw("SAME")
             leg_finalwsys.AddEntry(tgsys[iptjet], "syst. unc.", "F")
@@ -1122,9 +1122,9 @@ def do_jet_systematics(self, var: str):
             crelativesys.SetRightMargin(0.25)
             leg_relativesys = TLegend(0.77, 0.2, 0.95, 0.85)
             setup_legend(leg_relativesys, textsize=self.fontsize)
-            # for g in tgsys_cat[iptjet]:
-            #     self.crop_graph(g, var)
-            # self.crop_histogram(h_default_stat_err[iptjet], var)
+            for g in tgsys_cat[iptjet]:
+                self.crop_graph(g, var)
+            self.crop_histogram(h_default_stat_err[iptjet], var)
             y_min_g, y_max_g = get_y_window_gr(tgsys_cat[iptjet])
             y_min_h, y_max_h = get_y_window_his([h_default_stat_err[iptjet]])
             y_min = min(y_min_g, y_min_h)
@@ -1137,7 +1137,7 @@ def do_jet_systematics(self, var: str):
             h_default_stat_err[iptjet].SetMarkerSize(0)
             leg_relativesys.AddEntry(h_default_stat_err[iptjet], "stat. unc.", "E")
             for sys_cat in range(self.n_sys_cat):
-                setup_tgraph(tgsys_cat[iptjet][sys_cat], get_colour(sys_cat + 1, 0))
+                setup_tgraph(tgsys_cat[iptjet][sys_cat], get_colour(sys_cat, 0))
                 tgsys_cat[iptjet][sys_cat].SetTitle("")
                 tgsys_cat[iptjet][sys_cat].SetLineWidth(3)
                 tgsys_cat[iptjet][sys_cat].SetFillStyle(0)
@@ -1229,9 +1229,9 @@ def do_jet_systematics(self, var: str):
             # leg_relativesys_gr = TLegend(.77, .2, 0.95, .85)
             leg_relativesys_gr = TLegend(0.77 * 9 / 10, 0.5, 0.95, 0.85)  # scale for width 900 -> 1000
             setup_legend(leg_relativesys_gr, textsize=self.fontsize)
-            # for g in tgsys_gr[iptjet]:
-            #     self.crop_graph(g, var)
-            # self.crop_histogram(h_default_stat_err[iptjet], var)
+            for g in tgsys_gr[iptjet]:
+                self.crop_graph(g, var)
+            self.crop_histogram(h_default_stat_err[iptjet], var)
             y_min_g, y_max_g = get_y_window_gr(tgsys_gr[iptjet])
             y_min_h, y_max_h = get_y_window_his([h_default_stat_err[iptjet]])
             y_min = min(y_min_g, y_min_h)
@@ -1244,7 +1244,7 @@ def do_jet_systematics(self, var: str):
             h_default_stat_err[iptjet].SetMarkerSize(0)
             leg_relativesys_gr.AddEntry(h_default_stat_err[iptjet], "stat. unc.", "E")
             for sys_gr, gr in enumerate(self.systematic_catgroups_list):
-                setup_tgraph(tgsys_gr[iptjet][sys_gr], get_colour(sys_gr + 1, 0))
+                setup_tgraph(tgsys_gr[iptjet][sys_gr], get_colour(sys_gr, 0))
                 tgsys_gr[iptjet][sys_gr].SetTitle("")
                 tgsys_gr[iptjet][sys_gr].SetLineWidth(3)
                 tgsys_gr[iptjet][sys_gr].SetFillStyle(0)

From 4a0846b633dc4e1da7dcf1baae410da43570b059 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?V=C3=ADt=20Ku=C4=8Dera?= <vit.kucera@cern.ch>
Date: Wed, 12 Feb 2025 15:21:19 +0100
Subject: [PATCH 03/13] Add number magnitude helper function

---
 machine_learning_hep/utilities.py | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/machine_learning_hep/utilities.py b/machine_learning_hep/utilities.py
index f70a02b26d..b4fa43ddab 100644
--- a/machine_learning_hep/utilities.py
+++ b/machine_learning_hep/utilities.py
@@ -1308,18 +1308,23 @@ def format_number_prec(num, prec):
     return f"{round(num, prec):.{max(0, prec)}f}"
 
 
+def magnitude(num):
+    """Decimal magnitude of a number."""
+    return math.floor(math.log10(abs(num)))
+
+
 def format_value_with_unc(y, e_stat=None, e_syst_plus=None, e_syst_minus=None, n_sig=2):  # pylint: disable=invalid-name
     """Format a value with uncertainties so that the main value is reported with a decimal precision
     given by the number of significant figures of the smallest uncertainty."""
-    mag_y = math.floor(math.log10(y))
+    mag_y = magnitude(y)
     mag_e_stat = mag_y
     mag_e_syst = mag_y
     if e_stat:
-        mag_e_stat = math.floor(math.log10(e_stat))
+        mag_e_stat = magnitude(e_stat)
     if e_syst_plus:
         if not e_syst_minus:
             e_syst_minus = e_syst_plus
-        mag_e_syst = math.floor(math.log10(min(e_syst_plus, e_syst_minus)))
+        mag_e_syst = magnitude(min(e_syst_plus, e_syst_minus))
     mag_y = min(mag_y, mag_e_stat, mag_e_syst)
     # print(f"Mag stat {mag_e_stat}, sys {mag_e_syst}")
     prec_y = n_sig - 1 - mag_y

From 24daf5e891ede9f64ff313bdfdf1e3937e759ddd Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?V=C3=ADt=20Ku=C4=8Dera?= <vit.kucera@cern.ch>
Date: Wed, 12 Feb 2025 15:23:28 +0100
Subject: [PATCH 04/13] Set default scale_title=1. in plotting utils

---
 machine_learning_hep/utilities.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/machine_learning_hep/utilities.py b/machine_learning_hep/utilities.py
index b4fa43ddab..7d0720d599 100644
--- a/machine_learning_hep/utilities.py
+++ b/machine_learning_hep/utilities.py
@@ -641,7 +641,7 @@ def get_markersize(marker: int, size_def=1.5):
     return size_def
 
 
-def setup_histogram(hist, colour=1, markerstyle=kOpenCircle, size=1.5, textsize=0.05, scale_title=1.3):
+def setup_histogram(hist, colour=1, markerstyle=kOpenCircle, size=1.5, textsize=0.05, scale_title=1.0):
     hist.SetStats(0)
     hist.GetXaxis().SetLabelSize(textsize)
     hist.GetYaxis().SetLabelSize(textsize)
@@ -658,7 +658,7 @@ def setup_histogram(hist, colour=1, markerstyle=kOpenCircle, size=1.5, textsize=
 
 
 def setup_tgraph(
-    tg_, colour=1, markerstyle=kOpenCircle, size=1.5, alphastyle=0.8, fillstyle=1001, textsize=0.05, scale_title=1.3
+    tg_, colour=1, markerstyle=kOpenCircle, size=1.5, alphastyle=0.8, fillstyle=1001, textsize=0.05, scale_title=1.0
 ):
     tg_.GetXaxis().SetLabelSize(textsize)
     tg_.GetYaxis().SetLabelSize(textsize)

From bc2cbe5639fcd4380d74b5ba8f10ccf0496719e4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?V=C3=ADt=20Ku=C4=8Dera?= <vit.kucera@cern.ch>
Date: Wed, 12 Feb 2025 15:27:22 +0100
Subject: [PATCH 05/13] Set scale_title=1.3 in make_plot

---
 machine_learning_hep/utilities.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/machine_learning_hep/utilities.py b/machine_learning_hep/utilities.py
index 7d0720d599..6db18f23c2 100644
--- a/machine_learning_hep/utilities.py
+++ b/machine_learning_hep/utilities.py
@@ -840,7 +840,7 @@ def get_my_size(i: int):
 
     def plot_graph(graph):
         setup_tgraph(
-            graph, get_my_colour(i_obj), get_my_marker(i_obj), get_my_size(i_obj), textsize=(font_size / scale)
+            graph, get_my_colour(i_obj), get_my_marker(i_obj), get_my_size(i_obj), textsize=(font_size / scale), scale_title=1.3
         )
         graph.SetTitle(title)
         graph.GetXaxis().SetLimits(x_min_plot, x_max_plot)
@@ -861,7 +861,7 @@ def plot_histogram(histogram):
         # If nothing has been plotted yet, plot an empty graph to set the exact ranges.
         if counter_plot_obj == 0:
             gr = TGraph(histogram)
-            setup_tgraph(gr, textsize=font_size / scale)
+            setup_tgraph(gr, textsize=(font_size / scale), scale_title=1.3)
             gr.SetMarkerSize(0)
             gr.SetTitle(title)
             gr.GetXaxis().SetLimits(x_min_plot, x_max_plot)
@@ -877,7 +877,7 @@ def plot_histogram(histogram):
             gr.DrawClone("AP")
             list_new.append(gr)
         setup_histogram(
-            histogram, get_my_colour(i_obj), get_my_marker(i_obj), get_my_size(i_obj), textsize=(font_size / scale)
+            histogram, get_my_colour(i_obj), get_my_marker(i_obj), get_my_size(i_obj), textsize=(font_size / scale), scale_title=1.3
         )
         histogram.GetXaxis().SetLimits(x_min_plot, x_max_plot)
         histogram.GetXaxis().SetRangeUser(x_min_plot, x_max_plot)

From db1f25ccf19d2e58c67909a6926a65532992ca83 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?V=C3=ADt=20Ku=C4=8Dera?= <vit.kucera@cern.ch>
Date: Thu, 13 Feb 2025 10:35:50 +0100
Subject: [PATCH 06/13] Plot more pt bins

---
 machine_learning_hep/plotting/plot_jetsubstructure_run3.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/machine_learning_hep/plotting/plot_jetsubstructure_run3.py b/machine_learning_hep/plotting/plot_jetsubstructure_run3.py
index 9cfb2534c8..12e3c83bb3 100644
--- a/machine_learning_hep/plotting/plot_jetsubstructure_run3.py
+++ b/machine_learning_hep/plotting/plot_jetsubstructure_run3.py
@@ -695,10 +695,10 @@ def plot(self):
             if self.species == "D0":
                 # list_iptjet = [0, 1, 2, 3]  # indices of jet pt bins to process
                 # list_iptjet = [0, 1, 2, 3, 4, 5, 6, 7]  # indices of jet pt bins to process
-                list_iptjet = [0, 2, 4, 6]  # indices of jet pt bins to process
+                list_iptjet = [2, 3, 4, 5, 6]  # indices of jet pt bins to process
                 # list_iptjet = [2, 3]  # indices of jet pt bins to process
             if self.species == "Lc":
-                list_iptjet = [1]  # indices of jet pt bins to process
+                list_iptjet = [1, 2]  # indices of jet pt bins to process
             if self.species == "incl":
                 list_iptjet = [2]
             plot_lc_vs_d0 = True
@@ -1228,7 +1228,7 @@ def plot(self):
             self.labels_obj = []
             self.list_latex = []
             self.y_margin_up = 0.06  # to fix cropped number on the axis
-            self.title_full = f";{self.latex_obs};ratio to  "
+            self.title_full = f";{self.latex_obs};ratio to    "
             can, new = self.make_plot(
                 name_can, can=can, pad=2, scale=pad_heights[1], colours=self.list_colours, markers=self.list_markers
             )

From 4188f00325907c9ab2ff59877cefc5187f605379 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?V=C3=ADt=20Ku=C4=8Dera?= <vit.kucera@cern.ch>
Date: Thu, 13 Feb 2025 13:52:13 +0100
Subject: [PATCH 07/13] Adjust spacing in ratio to

---
 machine_learning_hep/plotting/plot_jetsubstructure_run3.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/machine_learning_hep/plotting/plot_jetsubstructure_run3.py b/machine_learning_hep/plotting/plot_jetsubstructure_run3.py
index 12e3c83bb3..46f6f137e8 100644
--- a/machine_learning_hep/plotting/plot_jetsubstructure_run3.py
+++ b/machine_learning_hep/plotting/plot_jetsubstructure_run3.py
@@ -1228,7 +1228,7 @@ def plot(self):
             self.labels_obj = []
             self.list_latex = []
             self.y_margin_up = 0.06  # to fix cropped number on the axis
-            self.title_full = f";{self.latex_obs};ratio to    "
+            self.title_full = f";{self.latex_obs};ratio to  "
             can, new = self.make_plot(
                 name_can, can=can, pad=2, scale=pad_heights[1], colours=self.list_colours, markers=self.list_markers
             )

From d7fa0dce0184f4773554cdd49869f80e2f691919 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?V=C3=ADt=20Ku=C4=8Dera?= <vit.kucera@cern.ch>
Date: Tue, 11 Mar 2025 13:29:46 +0100
Subject: [PATCH 08/13] Add protection

---
 machine_learning_hep/plotting/plot_jetsubstructure_run3.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/machine_learning_hep/plotting/plot_jetsubstructure_run3.py b/machine_learning_hep/plotting/plot_jetsubstructure_run3.py
index 46f6f137e8..1fceca4d4a 100644
--- a/machine_learning_hep/plotting/plot_jetsubstructure_run3.py
+++ b/machine_learning_hep/plotting/plot_jetsubstructure_run3.py
@@ -99,8 +99,10 @@ def __init__(self, path_input_file: str, path_database_analysis: str, typean: st
         self.species = None
         if "D0Jet" in path_database_analysis:
             self.species = "D0"
-        if "LcJet" in path_database_analysis:
+        elif "LcJet" in path_database_analysis:
             self.species = "Lc"
+        else:
+            self.logger.critical("Jet species could not be determined.")
 
         with open(path_database_analysis, encoding="utf-8") as file_db:
             db_analysis = yaml.safe_load(file_db)

From fe17125a0a23c5af3953597885d3322779ede329 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?V=C3=ADt=20Ku=C4=8Dera?= <vit.kucera@cern.ch>
Date: Fri, 14 Mar 2025 23:51:44 +0100
Subject: [PATCH 09/13] Fixes

---
 .../plotting/plot_jetsubstructure_run3.py       | 17 +++++++++--------
 1 file changed, 9 insertions(+), 8 deletions(-)

diff --git a/machine_learning_hep/plotting/plot_jetsubstructure_run3.py b/machine_learning_hep/plotting/plot_jetsubstructure_run3.py
index 1fceca4d4a..d45c634351 100644
--- a/machine_learning_hep/plotting/plot_jetsubstructure_run3.py
+++ b/machine_learning_hep/plotting/plot_jetsubstructure_run3.py
@@ -143,7 +143,7 @@ def __init__(self, path_input_file: str, path_database_analysis: str, typean: st
         # LaTeX string
         self.latex_hadron = self.db_typean["latexnamehadron"]
         self.latex_ptjet = "#it{p}_{T}^{jet ch}"
-        self.latex_pthf = "#it{p}_{T}^{%s} (GeV/#it{c})" % self.latex_hadron
+        self.latex_pthf = f"#it{{p}}_{{T}}^{{{self.latex_hadron}}} (GeV/#it{{c}})"
         self.latex_obs = self.db_typean["observables"][self.var]["label"]
         self.latex_y = self.db_typean["observables"][self.var]["label_y"]
 
@@ -255,7 +255,7 @@ def __init__(self, path_input_file: str, path_database_analysis: str, typean: st
         # text
         self.text_alice = "ALICE Preliminary, pp"  # preliminaries
         # self.text_alice = "#bf{ALICE}, pp, #sqrt{#it{s}} = 13.6 TeV"  # paper
-        self.text_tagged = "%s-tagged" % self.latex_hadron
+        self.text_tagged = f"{self.latex_hadron}-tagged"
         # self.text_jets = "charged-particle jets, anti-#it{k}_{T}, #it{R} = 0.4"
         self.text_jets = self.text_tagged + " " + "charged-particle jets, anti-#it{k}_{T}, #it{R} = 0.4"
         self.text_ptjet = "%g #leq %s (GeV/#it{c}) < %g"
@@ -329,7 +329,9 @@ def crop_graph(self, graph, var: str):
     def get_object(self, name: str, file=None):
         if file is None:
             file = self.file_results
-        if not (obj := file.Get(name)):
+        if file is None:
+            self.logger.critical("No result file set")
+        if not (obj := file.Get(name)):  # type: ignore
             self.logger.fatal(make_message_notfound(name))
         if isinstance(obj, TH1):
             obj.SetDirectory(0)  # Decouple the object from the file.
@@ -694,15 +696,14 @@ def plot(self):
 
             # Results
 
+            list_iptjet = []
             if self.species == "D0":
                 # list_iptjet = [0, 1, 2, 3]  # indices of jet pt bins to process
                 # list_iptjet = [0, 1, 2, 3, 4, 5, 6, 7]  # indices of jet pt bins to process
                 list_iptjet = [2, 3, 4, 5, 6]  # indices of jet pt bins to process
                 # list_iptjet = [2, 3]  # indices of jet pt bins to process
-            if self.species == "Lc":
+            elif self.species == "Lc":
                 list_iptjet = [1, 2]  # indices of jet pt bins to process
-            if self.species == "incl":
-                list_iptjet = [2]
             plot_lc_vs_d0 = True
             list_stat_all = []
             list_syst_all = []
@@ -1176,7 +1177,7 @@ def plot(self):
             self.list_latex = [
                 self.text_alice,
                 self.text_jets,
-                f"{self.get_text_range_pthf(-1, iptjet)}, {self.text_etajet}",
+                f"{self.get_text_range_pthf(-1, -1)}, {self.text_etajet}",
             ]
             if not plot_run2_data:
                 self.list_latex[0] = f"{self.text_alice}, {self.text_run3}"
@@ -1267,7 +1268,7 @@ def plot(self):
                 self.list_latex = [
                     self.text_alice,
                     self.text_jets,
-                    f"{self.get_text_range_pthf(-1, iptjet)}, {self.text_etajet}",
+                    f"{self.get_text_range_pthf(-1, -1)}, {self.text_etajet}",
                 ]
                 if self.var in ("zg", "rg", "nsd"):
                     self.list_latex.append(self.text_sd)

From d9e9595ca30a3de1e29d0caaefa7ff32bc5e7ef0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?V=C3=ADt=20Ku=C4=8Dera?= <vit.kucera@cern.ch>
Date: Fri, 14 Mar 2025 23:52:13 +0100
Subject: [PATCH 10/13] Add type annotations

---
 machine_learning_hep/utilities.py | 86 +++++++++++++++++--------------
 1 file changed, 48 insertions(+), 38 deletions(-)

diff --git a/machine_learning_hep/utilities.py b/machine_learning_hep/utilities.py
index 6db18f23c2..1ae2d90d3c 100644
--- a/machine_learning_hep/utilities.py
+++ b/machine_learning_hep/utilities.py
@@ -439,7 +439,7 @@ def folding(h_input, response_matrix, h_output):
     return h_output
 
 
-def get_plot_range(val_min, val_max, margin_min, margin_max, logscale=False):
+def get_plot_range(val_min, val_max, margin_min, margin_max, logscale=False) -> tuple[float, float] | tuple[None, None]:
     """Return the minimum and maximum of the plotting range so that there are margins
     expressed as fractions of the plotting range."""
     k = 1 - margin_min - margin_max
@@ -461,7 +461,7 @@ def get_plot_range(val_min, val_max, margin_min, margin_max, logscale=False):
     return val_min_plot, val_max_plot
 
 
-def get_x_window_gr(l_gr: list, with_errors=True):
+def get_x_window_gr(l_gr: list, with_errors=True) -> tuple[float, float]:
     """Return the minimum and maximum x value so that all the points of the graphs in the list
     fit in the range (by default including the error bars)."""
 
@@ -482,7 +482,7 @@ def err_high(graph):
     return x_min, x_max
 
 
-def get_x_window_his(l_his: list):
+def get_x_window_his(l_his: list) -> tuple[float, float]:
     """Return the minimum and maximum x value so that all the bins of the histograms in the list
     fit in the range."""
     if not isinstance(l_his, list):
@@ -495,7 +495,7 @@ def get_x_window_his(l_his: list):
     return x_min, x_max
 
 
-def get_y_window_gr(l_gr: list, with_errors=True, range_x=None):
+def get_y_window_gr(l_gr: list, with_errors=True, range_x: list[float] | None = None) -> tuple[float, float]:
     """Return the minimum and maximum y value so that all the points of the graphs in the list
     fit in the range (by default including the error bars).
     Consider only points within range_x if provided."""
@@ -521,7 +521,7 @@ def err_high(graph):
     return y_min, y_max
 
 
-def get_y_window_his(l_his: list, with_errors=True, range_x=None):
+def get_y_window_his(l_his: list, with_errors=True, range_x: list[float] | None = None) -> tuple[float, float]:
     """Return the minimum and maximum y value so that all the points of the histograms in the list
     fit in the range (by default including the error bars).
     Consider only bins within range_x if provided."""
@@ -745,36 +745,36 @@ def count_graphs(l_obj: list) -> int:
     return sum(is_graph(o) for o in l_obj)
 
 
-def make_plot(  # pylint: disable=too-many-arguments, too-many-branches, too-many-statements, too-many-locals
-    name,
-    can=None,
-    pad=0,
-    path=None,
-    suffix="eps",
-    title="",
-    size=None,
-    margins_c=None,
-    list_obj=None,
-    labels_obj=None,
-    leg_pos=None,
-    opt_leg_h="P",
-    opt_leg_g="P",
-    opt_plot_h="",
-    opt_plot_g="P0",
-    offsets_xy=None,
-    maxdigits=3,
-    colours=None,
-    markers=None,
-    sizes=None,
-    range_x=None,
-    range_y=None,
-    margins_y=None,
-    with_errors="xy",
-    logscale=None,
-    font_size=0.032,
-    scale=1.0,
-    plot_order=None,
-):
+def make_plot(
+    name: str,
+    can: TCanvas | None = None,
+    pad: int = 0,
+    path: str | None = None,
+    suffix: str = "eps",
+    title: str = "",
+    size: list[int] | None = None,
+    margins_c: list[float] | None = None,
+    list_obj: list | None = None,
+    labels_obj: list[str] | None = None,
+    leg_pos: list[float] | None = None,
+    opt_leg_h: list[str] | str = "P",
+    opt_leg_g: list[str] | str = "P",
+    opt_plot_h: list[str] | str = "",
+    opt_plot_g: list[str] | str = "P0",
+    offsets_xy: list[float] | None = None,
+    maxdigits: int = 3,
+    colours: list[int] | None = None,
+    markers: list[int] | None = None,
+    sizes: list[int] | None = None,
+    range_x: list[float] | None = None,
+    range_y: list[float] | None = None,
+    margins_y: list[float] | None = None,
+    with_errors: str = "xy",
+    logscale: str | None = None,
+    font_size: float = 0.032,
+    scale: float = 1.0,
+    plot_order: list[int] | None = None,
+) -> tuple[TCanvas, list]:
     """
     Make a plot with objects from a list (list_obj).
     Returns a TCanvas and a list of other created ROOT objects.
@@ -840,7 +840,12 @@ def get_my_size(i: int):
 
     def plot_graph(graph):
         setup_tgraph(
-            graph, get_my_colour(i_obj), get_my_marker(i_obj), get_my_size(i_obj), textsize=(font_size / scale), scale_title=1.3
+            graph,
+            get_my_colour(i_obj),
+            get_my_marker(i_obj),
+            get_my_size(i_obj),
+            textsize=(font_size / scale),
+            scale_title=1.3,
         )
         graph.SetTitle(title)
         graph.GetXaxis().SetLimits(x_min_plot, x_max_plot)
@@ -877,7 +882,12 @@ def plot_histogram(histogram):
             gr.DrawClone("AP")
             list_new.append(gr)
         setup_histogram(
-            histogram, get_my_colour(i_obj), get_my_marker(i_obj), get_my_size(i_obj), textsize=(font_size / scale), scale_title=1.3
+            histogram,
+            get_my_colour(i_obj),
+            get_my_marker(i_obj),
+            get_my_size(i_obj),
+            textsize=(font_size / scale),
+            scale_title=1.3,
         )
         histogram.GetXaxis().SetLimits(x_min_plot, x_max_plot)
         histogram.GetXaxis().SetRangeUser(x_min_plot, x_max_plot)
@@ -893,7 +903,7 @@ def plot_latex(latex):
 
     if not (isinstance(list_obj, list) and len(list_obj) > 0):
         print("Error: Empty list of objects")
-        return None, None
+        return None, []
 
     list_new = []  # list of created objects that need to exist outside the function
     if not (isinstance(offsets_xy, list) and len(offsets_xy) == 2):

From 03dc3f5de14ebf11ce428a04a9a47cc744701df0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?V=C3=ADt=20Ku=C4=8Dera?= <vit.kucera@cern.ch>
Date: Sat, 15 Mar 2025 00:07:49 +0100
Subject: [PATCH 11/13] Convert to f-strings

---
 .../analysis/do_systematics.py                | 93 +++++--------------
 1 file changed, 25 insertions(+), 68 deletions(-)

diff --git a/machine_learning_hep/analysis/do_systematics.py b/machine_learning_hep/analysis/do_systematics.py
index 4e9f28458b..0bcb9e0f14 100644
--- a/machine_learning_hep/analysis/do_systematics.py
+++ b/machine_learning_hep/analysis/do_systematics.py
@@ -210,7 +210,7 @@ def __init__(self, path_database_analysis: str, typean: str):
         # text
         self.text_alice = "ALICE Preliminary, pp, #sqrt{#it{s}} = 13.6 TeV"
         # self.text_alice = "#bf{ALICE}, pp, #sqrt{#it{s}} = 13.6 TeV"
-        self.text_jets = "%s-tagged charged jets, anti-#it{k}_{T}, #it{R} = 0.4" % self.latex_hadron
+        self.text_jets = f"{self.latex_hadron}-tagged charged jets, anti-#it{{k}}_{{T}}, #it{{R}} = 0.4"
         self.text_ptjet = "%g #leq %s < %g GeV/#it{c}, |#it{#eta}_{jet ch}| < 0.5"
         self.text_pth = "%g #leq #it{p}_{T}^{%s} < %g GeV/#it{c}, |#it{y}_{%s}| < 0.8"
         self.text_sd = "Soft drop (#it{z}_{cut} = 0.1, #it{#beta} = 0)"
@@ -275,7 +275,7 @@ def process(self, list_vars: "list[str]"):
         """Do systematics for all variables"""
         for var in list_vars:
             # self.logger.info("Processing observable %s", var)
-            print("Processing observable %s" % var)
+            print(f"Processing observable {var}")
             self.do_jet_systematics(var)
 
     def do_jet_systematics(self, var: str):
@@ -397,8 +397,7 @@ def do_jet_systematics(self, var: str):
                 input_histograms_eff = []
                 for sys_var in range(self.systematic_variations[sys_cat]):
                     print(
-                        "Variation: %s, %s"
-                        % (self.systematic_catnames[sys_cat], self.systematic_varnames[sys_cat][sys_var])
+                        f"Variation: {self.systematic_catnames[sys_cat]}, {self.systematic_varnames[sys_cat][sys_var]}"
                     )
                     name_hist_unfold_2d = f"h_ptjet-{var}_{self.method}_unfolded_data_0"
                     if not (hist_unfold := input_files_sys[sys_cat][sys_var].Get(name_hist_unfold_2d)):
@@ -426,22 +425,10 @@ def do_jet_systematics(self, var: str):
                     print_histogram(sys_var_histo, self.verbose)
                     if self.debug:
                         print(
-                            "Variation: %s, %s: got histogram %s from file %s"
-                            % (
-                                self.systematic_catnames[sys_cat],
-                                self.systematic_varnames[sys_cat][sys_var],
-                                name_his,
-                                path_file,
-                            )
+                            f"Variation: {self.systematic_catnames[sys_cat]}, {self.systematic_varnames[sys_cat][sys_var]}: got histogram {name_his} from file {path_file}"
                         )
                         print(
-                            "Variation: %s, %s: got efficiency histogram %s from file %s"
-                            % (
-                                self.systematic_catnames[sys_cat],
-                                self.systematic_varnames[sys_cat][sys_var],
-                                name_eff,
-                                path_eff_file,
-                            )
+                            f"Variation: {self.systematic_catnames[sys_cat]}, {self.systematic_varnames[sys_cat][sys_var]}: got efficiency histogram {name_eff} from file {path_eff_file}"
                         )
                 input_histograms_syscat.append(input_histograms_syscatvar)
                 input_histograms_syscat_eff.append(input_histograms_eff)
@@ -457,7 +444,7 @@ def do_jet_systematics(self, var: str):
             # plot all the variations together
             suffix = self.get_suffix_ptjet(iptjet)
             nsys = 0
-            csysvar = TCanvas("csysvar_%s" % suffix, "systematic variations" + suffix)
+            csysvar = TCanvas(f"csysvar_{suffix}", "systematic variations" + suffix)
             setup_canvas(csysvar)
             leg_sysvar = TLegend(0.75, 0.15, 0.95, 0.85, "variation")
             setup_legend(leg_sysvar)
@@ -482,38 +469,25 @@ def do_jet_systematics(self, var: str):
             print_histogram(input_histograms_default[iptjet], self.verbose)
 
             self.logger.info("Categories: %d", self.n_sys_cat)
-            print("Categories: %d" % self.n_sys_cat)
+            print(f"Categories: {self.n_sys_cat}")
 
             for sys_cat in range(self.n_sys_cat):
                 self.logger.info("Category: %s", self.systematic_catlabels[sys_cat])
-                print("Category: %s" % self.systematic_catlabels[sys_cat])
+                print(f"Category: {self.systematic_catlabels[sys_cat]}")
                 for sys_var in range(self.systematic_variations[sys_cat]):
                     self.logger.info("Variation: %s", self.systematic_varlabels[sys_cat][sys_var])
-                    print("Variation: %s" % self.systematic_varlabels[sys_cat][sys_var])
+                    print(f"Variation: {self.systematic_varlabels[sys_cat][sys_var]}")
                     leg_sysvar.AddEntry(
                         input_histograms_sys[iptjet][sys_cat][sys_var],
-                        (
-                            "{}, {}".format(
-                                self.systematic_catlabels[sys_cat], self.systematic_varlabels[sys_cat][sys_var]
-                            )
-                        ),
+                        (f"{self.systematic_catlabels[sys_cat]}, {self.systematic_varlabels[sys_cat][sys_var]}"),
                         "P",
                     )
                     self.logger.info(
                         "Adding label %s",
-                        (
-                            "{}, {}".format(
-                                self.systematic_catlabels[sys_cat], self.systematic_varlabels[sys_cat][sys_var]
-                            )
-                        ),
+                        (f"{self.systematic_catlabels[sys_cat]}, {self.systematic_varlabels[sys_cat][sys_var]}"),
                     )
                     print(
-                        "Adding label %s"
-                        % (
-                            "{}, {}".format(
-                                self.systematic_catlabels[sys_cat], self.systematic_varlabels[sys_cat][sys_var]
-                            )
-                        )
+                        f"Adding label {self.systematic_catlabels[sys_cat]}, {self.systematic_varlabels[sys_cat][sys_var]}"
                     )
                     setup_histogram(input_histograms_sys[iptjet][sys_cat][sys_var], get_colour(nsys))
                     input_histograms_sys[iptjet][sys_cat][sys_var].Draw("same")
@@ -522,8 +496,7 @@ def do_jet_systematics(self, var: str):
             latex = TLatex(
                 0.15,
                 0.82,
-                "%g #leq %s < %g GeV/#it{c}"
-                % (self.edges_ptjet_gen_min[iptjet], self.latex_ptjet, self.edges_ptjet_gen_max[iptjet]),
+                f"{self.edges_ptjet_gen_min[iptjet]:g} #leq {self.latex_ptjet} < {self.edges_ptjet_gen_max[iptjet]:g} GeV/#it{{c}}",
             )
             draw_latex(latex)
             # leg_sysvar.Draw("same")
@@ -561,16 +534,10 @@ def do_jet_systematics(self, var: str):
                     leg_sysvar_each.AddEntry(
                         input_histograms_sys[iptjet][sys_cat][sys_var], self.systematic_varlabels[sys_cat][sys_var], "P"
                     )
-                    setup_histogram(
-                        input_histograms_sys[iptjet][sys_cat][sys_var], get_colour(nsys), get_marker(nsys)
-                    )
+                    setup_histogram(input_histograms_sys[iptjet][sys_cat][sys_var], get_colour(nsys), get_marker(nsys))
                     input_histograms_sys[iptjet][sys_cat][sys_var].Draw("same")
                     nsys = nsys + 1
-                latex_text = "{:g} #leq {} < {:g} GeV/#it{{c}}".format(
-                    self.edges_ptjet_gen_min[iptjet],
-                    self.latex_ptjet,
-                    self.edges_ptjet_gen_max[iptjet],
-                )
+                latex_text = f"{self.edges_ptjet_gen_min[iptjet]:g} #leq {self.latex_ptjet} < {self.edges_ptjet_gen_max[iptjet]:g} GeV/#it{{c}}"
                 latex = TLatex(
                     0.15,
                     0.82,
@@ -634,8 +601,7 @@ def do_jet_systematics(self, var: str):
                 latex = TLatex(
                     0.15,
                     0.82,
-                    "%g #leq %s < %g GeV/#it{c}"
-                    % (self.edges_ptjet_gen_min[iptjet], self.latex_ptjet, self.edges_ptjet_gen_max[iptjet]),
+                    f"{self.edges_ptjet_gen_min[iptjet]:g} #leq {self.latex_ptjet} < {self.edges_ptjet_gen_max[iptjet]:g} GeV/#it{{c}}",
                 )
                 draw_latex(latex)
                 # line = TLine(obs_rec_min, 1, obs_rec_max, 1)
@@ -693,8 +659,8 @@ def do_jet_systematics(self, var: str):
                             *get_plot_range(y_min, y_max, y_margin_down, y_margin_up)
                         )
                         eff_default[iptjet].SetTitle("")
-                        eff_default[iptjet].SetXTitle("#it{p}_{T}^{%s} (GeV/#it{c})" % self.latex_hadron)
-                        eff_default[iptjet].SetYTitle("prompt %s-jet efficiency" % self.latex_hadron)
+                        eff_default[iptjet].SetXTitle(f"#it{{p}}_{{T}}^{{{self.latex_hadron}}} (GeV/#it{{c}})")
+                        eff_default[iptjet].SetYTitle(f"prompt {self.latex_hadron}-jet efficiency")
                         eff_default[iptjet].Draw()
                     leg_sysvar_eff.AddEntry(
                         input_histograms_sys_eff[iptjet][sys_cat][sys_var],
@@ -711,8 +677,7 @@ def do_jet_systematics(self, var: str):
                 latex = TLatex(
                     0.15,
                     0.82,
-                    "%g #leq %s < %g GeV/#it{c}"
-                    % (self.edges_ptjet_gen_min[iptjet], self.latex_ptjet, self.edges_ptjet_gen_max[iptjet]),
+                    f"{self.edges_ptjet_gen_min[iptjet]:g} #leq {self.latex_ptjet} < {self.edges_ptjet_gen_max[iptjet]:g} GeV/#it{{c}}",
                 )
                 draw_latex(latex)
                 leg_sysvar_eff.Draw("same")
@@ -763,8 +728,7 @@ def do_jet_systematics(self, var: str):
                 latex = TLatex(
                     0.15,
                     0.82,
-                    "%g #leq %s < %g GeV/#it{c}"
-                    % (self.edges_ptjet_gen_min[iptjet], self.latex_ptjet, self.edges_ptjet_gen_max[iptjet]),
+                    f"{self.edges_ptjet_gen_min[iptjet]:g} #leq {self.latex_ptjet} < {self.edges_ptjet_gen_max[iptjet]:g} GeV/#it{{c}}",
                 )
                 draw_latex(latex)
                 leg_sysvar_eff_ratio.Draw("same")
@@ -1003,14 +967,14 @@ def do_jet_systematics(self, var: str):
             suffix = self.get_suffix_ptjet(iptjet)
             self.file_sys_out.WriteObject(tgsys[iptjet], f"sys_{var}_{suffix}")
             unc_hist_up = TH1F(
-                "unc_hist_up_%s" % suffix,
+                f"unc_hist_up_{suffix}",
                 "",
                 n_bins_obs_gen,
                 obs_gen_min,
                 obs_gen_max,
             )
             unc_hist_down = TH1F(
-                "unc_hist_down_%s" % suffix,
+                f"unc_hist_down_{suffix}",
                 "",
                 n_bins_obs_gen,
                 obs_gen_min,
@@ -1079,25 +1043,18 @@ def do_jet_systematics(self, var: str):
             latex = TLatex(0.15, 0.82, self.text_alice)
             # latex = TLatex(0.15, 0.82, "pp, #sqrt{#it{s}} = 13.6 TeV")
             draw_latex(latex)
-            latex1 = TLatex(0.15, 0.77, "%s in charged jets, anti-#it{k}_{T}, #it{R} = 0.4" % self.latex_hadron)
+            latex1 = TLatex(0.15, 0.77, f"{self.latex_hadron} in charged jets, anti-#it{{k}}_{{T}}, #it{{R}} = 0.4")
             draw_latex(latex1)
             latex2 = TLatex(
                 0.15,
                 0.72,
-                "%g #leq %s < %g GeV/#it{c}, #left|#it{#eta}_{jet}#right| #leq 0.5"
-                % (self.edges_ptjet_rec[iptjet], self.latex_ptjet, self.edges_ptjet_rec[iptjet + 1]),
+                f"{self.edges_ptjet_rec[iptjet]:g} #leq {self.latex_ptjet} < {self.edges_ptjet_rec[iptjet + 1]:g} GeV/#it{{c}}, #left|#it{{#eta}}_{{jet}}#right| #leq 0.5",
             )
             draw_latex(latex2)
             latex3 = TLatex(
                 0.15,
                 0.67,
-                "%g #leq #it{p}_{T}^{%s} < %g GeV/#it{c}, #left|#it{y}_{%s}#right| #leq 0.8"
-                % (
-                    self.edges_pthf_min[0],
-                    self.latex_hadron,
-                    min(self.edges_pthf_max[-1], self.edges_ptjet_rec[iptjet + 1]),
-                    self.latex_hadron,
-                ),
+                f"{self.edges_pthf_min[0]:g} #leq #it{{p}}_{{T}}^{{{self.latex_hadron}}} < {min(self.edges_pthf_max[-1], self.edges_ptjet_rec[iptjet + 1]):g} GeV/#it{{c}}, #left|#it{{y}}_{{{self.latex_hadron}}}#right| #leq 0.8",
             )
             draw_latex(latex3)
             leg_finalwsys.Draw("same")

From 9319df2e0cae7b3c75e7113d4ddba5da5b8ff8c4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?V=C3=ADt=20Ku=C4=8Dera?= <vit.kucera@cern.ch>
Date: Thu, 27 Mar 2025 19:54:04 +0100
Subject: [PATCH 12/13] Ruff: Silence Pylint too-many-... errors

---
 pyproject.toml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pyproject.toml b/pyproject.toml
index 2bd0212ca3..609fed85cf 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -41,6 +41,7 @@ extend-select = [ # in addition to defaults ["E4", "E7", "E9", "F"], see https:/
 ]
 ignore = [
   "PD901", # Avoid using the generic variable name `df` for DataFrames
+  "PLR09", # Too many ...
 ]
 
 [project]

From 61661929e1f96dd9e63ca887be626e23faf30f8d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?V=C3=ADt=20Ku=C4=8Dera?= <vit.kucera@cern.ch>
Date: Thu, 27 Mar 2025 20:15:58 +0100
Subject: [PATCH 13/13] Lint

---
 .../analysis/do_systematics.py                | 42 ++++++++-----------
 .../plotting/plot_jetsubstructure_run3.py     | 14 +++----
 machine_learning_hep/utilities.py             | 38 +++++++----------
 3 files changed, 37 insertions(+), 57 deletions(-)

diff --git a/machine_learning_hep/analysis/do_systematics.py b/machine_learning_hep/analysis/do_systematics.py
index 0bcb9e0f14..273573589f 100644
--- a/machine_learning_hep/analysis/do_systematics.py
+++ b/machine_learning_hep/analysis/do_systematics.py
@@ -15,9 +15,6 @@
 Author: Vit Kucera <vit.kucera@cern.ch>
 """
 
-# pylint: disable=too-many-lines, too-many-instance-attributes, too-many-statements, too-many-locals
-# pylint: disable=too-many-nested-blocks, too-many-branches, consider-using-f-string
-
 import argparse
 import logging
 import os
@@ -94,7 +91,7 @@ def __init__(self, path_database_analysis: str, typean: str):
 
         with open(path_database_analysis, encoding="utf-8") as file_in:
             db_analysis = yaml.safe_load(file_in)
-        case = list(db_analysis.keys())[0]
+        case = next(iter(db_analysis.keys()))
         self.datap = db_analysis[case]
         self.db_typean = self.datap["analysis"][self.typean]
 
@@ -790,28 +787,21 @@ def do_jet_systematics(self, var: str):
                                     count_sys_up = count_sys_up + 1
                             else:
                                 error_var_up = max(error_var_up, error)
-                        else:
-                            if self.systematic_rms[sys_cat] is True:
-                                if self.systematic_rms_both_sides[sys_cat] is True:
-                                    error_var_up += error * error
-                                    if not out_sys:
-                                        count_sys_up = count_sys_up + 1
-                                else:
-                                    error_var_down += error * error
-                                    if not out_sys:
-                                        count_sys_down = count_sys_down + 1
+                        elif self.systematic_rms[sys_cat] is True:
+                            if self.systematic_rms_both_sides[sys_cat] is True:
+                                error_var_up += error * error
+                                if not out_sys:
+                                    count_sys_up = count_sys_up + 1
                             else:
-                                error_var_down = max(error_var_down, abs(error))
-                    if self.systematic_rms[sys_cat] is True:
-                        if count_sys_up != 0:
-                            error_var_up = error_var_up / count_sys_up
+                                error_var_down += error * error
+                                if not out_sys:
+                                    count_sys_down = count_sys_down + 1
                         else:
-                            error_var_up = 0.0
+                            error_var_down = max(error_var_down, abs(error))
+                    if self.systematic_rms[sys_cat] is True:
+                        error_var_up = error_var_up / count_sys_up if count_sys_up != 0 else 0.0
                         error_var_up = sqrt(error_var_up)
-                        if count_sys_down != 0:
-                            error_var_down = error_var_down / count_sys_down
-                        else:
-                            error_var_down = 0.0
+                        error_var_down = error_var_down / count_sys_down if count_sys_down != 0 else 0.0
                         if self.systematic_rms_both_sides[sys_cat] is True:
                             error_var_down = error_var_up
                         else:
@@ -918,7 +908,8 @@ def do_jet_systematics(self, var: str):
                 shapebins_error_down_cat = []
                 for ibinshape in range(n_bins_obs_gen):
                     shapebins_contents_cat.append(0)
-                    if abs(input_histograms_default[iptjet].GetBinContent(ibinshape + 1)) < 1.0e-7:
+                    epsilon_float = 1.0e-7
+                    if abs(input_histograms_default[iptjet].GetBinContent(ibinshape + 1)) < epsilon_float:
                         print("WARNING!!! Input histogram at bin", iptjet, " equal 0", suffix)
                         e_up = 0
                         e_down = 0
@@ -992,7 +983,8 @@ def do_jet_systematics(self, var: str):
             suffix = self.get_suffix_ptjet(iptjet)
             h_default_stat_err.append(input_histograms_default[iptjet].Clone("h_default_stat_err" + suffix))
             for i in range(h_default_stat_err[iptjet].GetNbinsX()):
-                if abs(input_histograms_default[iptjet].GetBinContent(i + 1)) < 1.0e-7:
+                epsilon_float = 1.0e-7
+                if abs(input_histograms_default[iptjet].GetBinContent(i + 1)) < epsilon_float:
                     print("WARNING!!! Input histogram at bin", iptjet, " equal 0", suffix)
                     h_default_stat_err[iptjet].SetBinContent(i + 1, 0)
                     h_default_stat_err[iptjet].SetBinError(i + 1, 0)
diff --git a/machine_learning_hep/plotting/plot_jetsubstructure_run3.py b/machine_learning_hep/plotting/plot_jetsubstructure_run3.py
index d45c634351..abaf202aab 100644
--- a/machine_learning_hep/plotting/plot_jetsubstructure_run3.py
+++ b/machine_learning_hep/plotting/plot_jetsubstructure_run3.py
@@ -15,10 +15,6 @@
 Author: Vit Kucera <vit.kucera@cern.ch>
 """
 
-# pylint: disable=too-many-lines, too-many-instance-attributes, too-many-statements, too-many-locals
-# pylint: disable=too-many-nested-blocks, too-many-branches, consider-using-f-string
-# pylint: disable=unused-variable
-
 import argparse
 import logging
 import os
@@ -106,7 +102,7 @@ def __init__(self, path_input_file: str, path_database_analysis: str, typean: st
 
         with open(path_database_analysis, encoding="utf-8") as file_db:
             db_analysis = yaml.safe_load(file_db)
-        case = list(db_analysis.keys())[0]
+        case = next(iter(db_analysis.keys()))
         self.datap = db_analysis[case]
         self.db_typean = self.datap["analysis"][self.typean]
 
@@ -406,7 +402,7 @@ def get_run3_sim(self) -> dict:
         source = {"monash": "M", "mode2": "SM2"}
         dict_obj = {}
         with TFile.Open(path_file) as file:
-            for s_obs, obs in obs.items():
+            for s_obs, n_obs in obs.items():
                 dict_obj[s_obs] = {}
                 for s_spec, spec in species.items():
                     dict_obj[s_obs][s_spec] = {}
@@ -418,7 +414,7 @@ def get_run3_sim(self) -> dict:
                             name = pattern % (
                                 spec,
                                 src,
-                                obs,
+                                n_obs,
                                 self.edges_ptjet_gen[iptjet],
                                 self.edges_ptjet_gen[iptjet + 1],
                             )
@@ -681,7 +677,7 @@ def plot(self):
                 self.make_plot(f"{self.species}_efficiency_{self.var}")
 
                 bins_ptjet = (0, 1, 2, 3)
-                for cat, label in zip(("pr", "np"), ("prompt", "non-prompt")):
+                for cat, label in zip(("pr", "np"), ("prompt", "non-prompt"), strict=False):
                     self.list_obj = self.get_objects(
                         *(
                             f"h_ptjet-pthf_effnew_{cat}_{string_range_ptjet(get_bin_limits(axis_ptjet, iptjet + 1))}"
@@ -1206,7 +1202,7 @@ def plot(self):
                 # TODO: if plot_run2_lc_ff_data
                 if h_run2 is not None:
                     n_obj = len(self.list_obj)
-                    self.plot_order = list(range(n_obj)) + [-1, -0.5]
+                    self.plot_order = [*list(range(n_obj)), -1, -0.5]
                     self.list_obj += [g_run2, h_run2]
                     self.labels_obj += [f"{self.text_run2}, {self.get_text_range_ptjet(2)}", ""]
                     self.list_colours += [get_colour(-1)] * 2
diff --git a/machine_learning_hep/utilities.py b/machine_learning_hep/utilities.py
index 1ae2d90d3c..9919c0fee0 100644
--- a/machine_learning_hep/utilities.py
+++ b/machine_learning_hep/utilities.py
@@ -128,10 +128,7 @@ def write_df(dfo, path):
 
 def read_df(path, **kwargs):
     try:
-        if path.endswith(".parquet"):
-            df = pd.read_parquet(path, **kwargs)
-        else:
-            df = pickle.load(openfile(path, "rb"))
+        df = pd.read_parquet(path, **kwargs) if path.endswith(".parquet") else pickle.load(openfile(path, "rb"))
     except Exception as e:  # pylint: disable=broad-except
         logger.critical("failed to open file <%s>: %s", path, str(e))
         sys.exit()
@@ -294,12 +291,12 @@ def make_latex_table(column_names, row_names, rows, caption=None, save_path="./t
         columns = "|".join(["c"] * (len(column_names) + 1))
         f.write("\\begin{tabular}{" + columns + "}\n")
         f.write("\\hline\n")
-        columns = "&".join([""] + column_names)
+        columns = "&".join(["", *column_names])
         columns = columns.replace("_", "\\_")
         f.write(columns + "\\\\\n")
         f.write("\\hline\\hline\n")
-        for rn, row in zip(row_names, rows):
-            row_string = "&".join([rn] + row)
+        for rn, row in zip(row_names, rows, strict=False):
+            row_string = "&".join([rn, *row])
             row_string = row_string.replace("_", "\\_")
             f.write(row_string + "\\\\\n")
         f.write("\\end{tabular}\n")
@@ -349,12 +346,12 @@ def make_message_notfound(name, location=None):
 
 
 def z_calc(pt_1, phi_1, eta_1, pt_2, phi_2, eta_2):
-    np_pt_1 = pt_1.values
-    np_pt_2 = pt_2.values
-    np_phi_1 = phi_1.values
-    np_phi_2 = phi_2.values
-    np_eta_1 = eta_1.values
-    np_eta_2 = eta_2.values
+    np_pt_1 = pt_1.to_numpy()
+    np_pt_2 = pt_2.to_numpy()
+    np_phi_1 = phi_1.to_numpy()
+    np_phi_2 = phi_2.to_numpy()
+    np_eta_1 = eta_1.to_numpy()
+    np_eta_2 = eta_2.to_numpy()
 
     cos_phi_1 = np.cos(np_phi_1)
     cos_phi_2 = np.cos(np_phi_2)
@@ -397,10 +394,7 @@ def equal_axis_list(axis1, list2, precision=10):
     bins = get_bins(axis1)
     if len(bins) != len(list2):
         return False
-    for i, j in zip(bins, list2):
-        if round(i, precision) != round(j, precision):
-            return False
-    return True
+    return all(round(i, precision) == round(j, precision) for i, j in zip(bins, list2, strict=False))
 
 
 def equal_binning(his1, his2):
@@ -418,9 +412,7 @@ def equal_binning_lists(his, list_x=None, list_y=None, list_z=None):
         return False
     if list_y is not None and not equal_axis_list(his.GetYaxis(), list_y):
         return False
-    if list_z is not None and not equal_axis_list(his.GetZaxis(), list_z):
-        return False
-    return True
+    return not (list_z is not None and not equal_axis_list(his.GetZaxis(), list_z))
 
 
 def folding(h_input, response_matrix, h_output):
@@ -939,13 +931,13 @@ def plot_latex(latex):
     # set canvas margins
     if isinstance(margins_c, list) and len(margins_c) > 0:
         for setter, value in zip(
-            [can.SetBottomMargin, can.SetLeftMargin, can.SetTopMargin, can.SetRightMargin], margins_c
+            [can.SetBottomMargin, can.SetLeftMargin, can.SetTopMargin, can.SetRightMargin], margins_c, strict=False
         ):
             setter(value)
     # set logarithmic scale for selected axes
     log_y = False
     if isinstance(logscale, str) and len(logscale) > 0:
-        for setter, axis in zip([can.SetLogx, can.SetLogy, can.SetLogz], ["x", "y", "z"]):
+        for setter, axis in zip([can.SetLogx, can.SetLogy, can.SetLogz], ["x", "y", "z"], strict=False):
             if axis in logscale:
                 setter()
                 if axis == "y":
@@ -1349,7 +1341,7 @@ def format_value_with_unc(y, e_stat=None, e_syst_plus=None, e_syst_minus=None, n
         if str_e_syst_plus == str_e_syst_minus:
             str_value += f" ± {str_e_syst_plus} (syst.)"
         else:
-            str_value += f" +{str_e_syst_plus} −{str_e_syst_minus} (syst.)"
+            str_value += f" +{str_e_syst_plus} −{str_e_syst_minus} (syst.)"  # noqa: RUF001
     return str_value