py2ls 0.1.9.2__py3-none-any.whl → 0.1.9.4__py3-none-any.whl

py2ls/.git/COMMIT_EDITMSG

@@ -1 +1 @@
-update ips
+update

py2ls/.git/FETCH_HEAD

@@ -1 +1 @@
-a15389729850729fc7bd78a54f26fce77f30be12		branch 'main' of https://github.com/Jianfengliu0413/py2ls
+6dc2cdf4a84e538e5d4777486aeff87e42f41799		branch 'main' of https://github.com/Jianfengliu0413/py2ls

py2ls/.git/logs/HEAD

@@ -18,3 +18,4 @@ d84688b54c0040a30976b3a6540bc47adf7ce680 32fd627b62fad7cf3b2f9e34ab9777126a0987a
 32fd627b62fad7cf3b2f9e34ab9777126a0987ad 1c3f92adda34344bcbbbf9d409c79855ae2aaea8 Jianfeng <Jianfeng.Liu0413@gmail.com> 1720709655 +0200	commit: Delete dbhandler.py
 1c3f92adda34344bcbbbf9d409c79855ae2aaea8 bf67907e337021ebff434e02b19b30a741c144af Jianfeng <Jianfeng.Liu0413@gmail.com> 1720948339 +0200	commit: update
 bf67907e337021ebff434e02b19b30a741c144af a15389729850729fc7bd78a54f26fce77f30be12 Jianfeng <Jianfeng.Liu0413@gmail.com> 1721137352 +0200	commit: update ips
+a15389729850729fc7bd78a54f26fce77f30be12 6dc2cdf4a84e538e5d4777486aeff87e42f41799 Jianfeng <Jianfeng.Liu0413@gmail.com> 1723527985 +0200	commit: update

py2ls/.git/logs/refs/heads/main

@@ -18,3 +18,4 @@ d84688b54c0040a30976b3a6540bc47adf7ce680 32fd627b62fad7cf3b2f9e34ab9777126a0987a
 32fd627b62fad7cf3b2f9e34ab9777126a0987ad 1c3f92adda34344bcbbbf9d409c79855ae2aaea8 Jianfeng <Jianfeng.Liu0413@gmail.com> 1720709655 +0200	commit: Delete dbhandler.py
 1c3f92adda34344bcbbbf9d409c79855ae2aaea8 bf67907e337021ebff434e02b19b30a741c144af Jianfeng <Jianfeng.Liu0413@gmail.com> 1720948339 +0200	commit: update
 bf67907e337021ebff434e02b19b30a741c144af a15389729850729fc7bd78a54f26fce77f30be12 Jianfeng <Jianfeng.Liu0413@gmail.com> 1721137352 +0200	commit: update ips
+a15389729850729fc7bd78a54f26fce77f30be12 6dc2cdf4a84e538e5d4777486aeff87e42f41799 Jianfeng <Jianfeng.Liu0413@gmail.com> 1723527985 +0200	commit: update

py2ls/.git/logs/refs/remotes/origin/HEAD

@@ -135,3 +135,5 @@ a15389729850729fc7bd78a54f26fce77f30be12 a15389729850729fc7bd78a54f26fce77f30be1
 a15389729850729fc7bd78a54f26fce77f30be12 a15389729850729fc7bd78a54f26fce77f30be12 Jianfeng Liu <macjianfeng@JFLMBP.cin.medizin.uni-tuebingen.de> 1721322143 +0200	remote set-head
 a15389729850729fc7bd78a54f26fce77f30be12 a15389729850729fc7bd78a54f26fce77f30be12 Jianfeng Liu <macjianfeng@JFLMBP.cin.medizin.uni-tuebingen.de> 1721324108 +0200	remote set-head
 a15389729850729fc7bd78a54f26fce77f30be12 a15389729850729fc7bd78a54f26fce77f30be12 Jianfeng Liu <macjianfeng@JFLMBP.cin.medizin.uni-tuebingen.de> 1721326072 +0200	remote set-head
+a15389729850729fc7bd78a54f26fce77f30be12 a15389729850729fc7bd78a54f26fce77f30be12 Jianfeng Liu <macjianfeng@jflmbp.speedport.ip> 1723527981 +0200	remote set-head
+6dc2cdf4a84e538e5d4777486aeff87e42f41799 6dc2cdf4a84e538e5d4777486aeff87e42f41799 Jianfeng Liu <macjianfeng@jflmbp.speedport.ip> 1723527990 +0200	remote set-head

py2ls/.git/logs/refs/remotes/origin/main

@@ -17,3 +17,4 @@ d84688b54c0040a30976b3a6540bc47adf7ce680 32fd627b62fad7cf3b2f9e34ab9777126a0987a
 32fd627b62fad7cf3b2f9e34ab9777126a0987ad 1c3f92adda34344bcbbbf9d409c79855ae2aaea8 Jianfeng <Jianfeng.Liu0413@gmail.com> 1720709657 +0200	update by push
 1c3f92adda34344bcbbbf9d409c79855ae2aaea8 bf67907e337021ebff434e02b19b30a741c144af Jianfeng <Jianfeng.Liu0413@gmail.com> 1720948342 +0200	update by push
 bf67907e337021ebff434e02b19b30a741c144af a15389729850729fc7bd78a54f26fce77f30be12 Jianfeng <Jianfeng.Liu0413@gmail.com> 1721137354 +0200	update by push
+a15389729850729fc7bd78a54f26fce77f30be12 6dc2cdf4a84e538e5d4777486aeff87e42f41799 Jianfeng <Jianfeng.Liu0413@gmail.com> 1723527989 +0200	update by push

py2ls/.git/objects/6d/c2cdf4a84e538e5d4777486aeff87e42f41799

@@ -0,0 +1,2 @@
+x
��M
+� F���AǟQ(���KLtL���`�_7�@7��x|ik�v	/�`���*9(.��#�����K���h�fMb���.I;"BN�-	猁�-�Kb�b������Yi-�.����UOe�y,��gJ[�K�`��ʫ�İ�f���3u_	�FS

py2ls/.git/objects/dc/c2bdbafb3296e09d9ee4955cfa55d275825f94

@@ -0,0 +1,5 @@
+x
�VQo�6�s~ᢐ��Ρ�^�y����ð=��pl:QkK�$7���������Ö�ؔD�#�}��;���dg���ݪ������e�0ڧ��������B�&��ժ������wqcJȣ���[we� Kՠگ�����z/��߭͋?hEw�[G)9�ھ�|S�F�-+m���/����K)4����
+��=*�J`Η���iA#[ZW5TZ=!����~����hPը*�.[�
++(4Jv�}�d�:N�K2�trB�9�J��J�����Y?���|#��d*=v@�B�w�@��'
���Y82��x��̄�d�lE�ݼ����"i��z�ַ��Q
+��
�<"�������@��|±�?��.��R��m�.m�ax���l�M�QEC9��Sܐŧ"~��9E�iTe�!窷��S�':fJ�d^���?n����:f"L݂{4M��o��/^�!�2B
+�?�짲m��0�{k��D��)�D԰��Ю���t�K��#	�v�8g��WA~�
m��r�ڰ��1i�E���<nd����}���Ae��W�#�Iǩ�b

py2ls/.git/objects/e2/f2f8f4c25e62a297fc55f36acc6b01cfbab76f

@@ -0,0 +1,3 @@
+x
e��
+�0D;�+�
+��	����Y����@���x�q7�q{�/)�
��J�2be��uT[����d������<0~��I{���L�#�.�Z�8��<V�y�Ź������:k

py2ls/.git/refs/heads/main

@@ -1 +1 @@
-a15389729850729fc7bd78a54f26fce77f30be12
+6dc2cdf4a84e538e5d4777486aeff87e42f41799

py2ls/.git/refs/remotes/origin/main

@@ -1 +1 @@
-a15389729850729fc7bd78a54f26fce77f30be12
+6dc2cdf4a84e538e5d4777486aeff87e42f41799

py2ls/netfinder.py

@@ -126,10 +126,8 @@ def extract_text_from_content(
                 search_kwargs["class"] = what
             if "attrs" in kwargs:
                 result_set = content.find_all(where, **search_kwargs)
-                print(f"attrs =>{search_kwargs}")
             else:
                 result_set = content.find_all(where, attrs=dict(**search_kwargs))
-                print(f"{search_kwargs}")
 
             if not result_set:
                 print("Failed: check the 'attrs' setting:  attrs={'id':'xample'}")
@@ -594,7 +592,6 @@ def downloader(
             kind[i] = "." + kind[i]
     file_links_all = []
     for kind_ in kind:
-        print(kind_)
         if isinstance(contains, str):
             contains = [contains]
         if isinstance(url, str):
@@ -709,7 +706,6 @@ def find_img(url, driver="request", dir_save="images", rm_folder=False, verbose=
     if rm_folder:
         ips.rm_folder(dir_save)
     content_type, content = fetch_all(url, driver=driver)
-    print(content_type)
     if "html" in content_type.lower():
         # Create the directory if it doesn't exist
         os.makedirs(dir_save, exist_ok=True)
@@ -913,7 +909,6 @@ def fetch(
     output="text",
     **kws,
 ):
-    print(f"output is {output}")
     if "xt" in output.lower():
         for attempt in range(retry):
             if verbose and attempt == 0:
@@ -973,7 +968,6 @@ def fetch(
         try:
             content_type, content = fetch_all(url, parser="html.parser", driver=driver)
             search_kwargs = {**kws}
-            print(search_kwargs)
             if "class_" in search_kwargs:
                 search_kwargs["class"] = search_kwargs["class_"]
                 del search_kwargs["class_"]
@@ -981,10 +975,8 @@ def fetch(
                 search_kwargs["class"] = what
             if "attrs" in kws:
                 result_set = content.find_all(where, **search_kwargs)
-                print(f"attrs =>{search_kwargs}")
             else:
                 result_set = content.find_all(where, attrs=dict(**search_kwargs))
-                print(f"{search_kwargs}")
             return result_set
         except:
             print("got nothing")

py2ls/plot.py

@@ -467,9 +467,12 @@ def catplot(data, *args, **kwargs):
         # custom_order = ['s', 'bx', 'e']
         # full_order = sort_catplot_layers(custom_order)
 
+    ax = kwargs.get("ax", None)
     col = kwargs.get("col", None)
     if not col:
-        # figsets
+        if "ax" not in locals() or ax is None:
+            ax = plt.gca()
+
         kw_figsets = kwargs.get("figsets", None)
         # check the data type
         if isinstance(data, pd.DataFrame):
@@ -478,6 +481,7 @@ def catplot(data, *args, **kwargs):
             y = kwargs.get("y", None)
             hue = kwargs.get("hue", None)
             data = df2array(data=data, x=x, y=y, hue=hue)
+            y_max_loc = np.max(data, axis=0)
             xticklabels = []
             if hue is not None:
                 # for i in df[x].unique().tolist():
@@ -496,8 +500,9 @@ def catplot(data, *args, **kwargs):
                 # ! stats info
                 stats_param = kwargs.get("stats", False)
                 res = pd.DataFrame()  # Initialize an empty DataFrame to store results
+                ihue = 1
                 for i in df[x].unique().tolist():
-                    print(i)
+                    print(i)  # to indicate which 'x'
                     if hue and stats_param:
                         if isinstance(stats_param, dict):
                             if "factor" in stats_param.keys():
@@ -507,15 +512,17 @@ def catplot(data, *args, **kwargs):
                                     data=df[df[x] == i], dv=y, factor=hue, **stats_param
                                 )
                         elif bool(stats_param):
-                            res_tmp = FuncMultiCmpt(data=df, dv=y, factor=hue)
+                            res_tmp = FuncMultiCmpt(
+                                data=df[df[x] == i], dv=y, factor=hue
+                            )
                         else:
                             res_tmp = "did not work properly"
                         display_output(res_tmp)
-                        res_tmp = [{"x": i, **res_tmp}]
                         res = pd.concat(
-                            [res, pd.DataFrame([res_tmp])], ignore_index=True
+                            [res, pd.DataFrame([res_tmp])], ignore_index=True, axis=0
                         )
-                display_output(res)
+                    ihue += 1
+
             else:
                 # ! stats info
                 stats_param = kwargs.get("stats", False)
@@ -529,9 +536,22 @@ def catplot(data, *args, **kwargs):
                 res = None
                 if x and stats_param:
                     if isinstance(stats_param, dict):
-                        res = FuncMultiCmpt(data=df, dv=y, factor=x, **stats_param)
+                        if len(xticklabels) > 2:
+                            res = FuncMultiCmpt(data=df, dv=y, factor=x, **stats_param)
+                        else:
+                            res = FuncCmpt(
+                                x1=df.loc[df[x] == xticklabels[0], y].tolist(),
+                                x2=df.loc[df[x] == xticklabels[1], y].tolist(),
+                                **stats_param,
+                            )
                     elif bool(stats_param):
-                        res = FuncMultiCmpt(data=df, dv=y, factor=x)
+                        if len(xticklabels) > 2:
+                            res = FuncMultiCmpt(data=df, dv=y, factor=x)
+                        else:
+                            res = FuncCmpt(
+                                x1=df.loc[df[x] == xticklabels[0], y].tolist(),
+                                x2=df.loc[df[x] == xticklabels[1], y].tolist(),
+                            )
                     else:
                         res = "did not work properly"
                 display_output(res)
@@ -556,11 +576,28 @@ def catplot(data, *args, **kwargs):
                     "xangle": xangle,
                 }
         else:
-            xticks = np.arange(1, data.shape[1] + 1).tolist()
+            if isinstance(data, np.ndarray):
+                df = array2df(data)
+                x = "group"
+                y = "value"
+            xticklabels = []
+            stats_param = kwargs.get("stats", False)
+            for i in df[x].unique().tolist():
+                xticklabels.append(i)
+            xticks = np.arange(1, len(xticklabels) + 1).tolist()
+            xticks_x_loc = np.arange(1, len(xticklabels) + 1).tolist()
+            legend_hue = xticklabels
+            default_colors = get_color(len(xticklabels))
             default_x_width = 0.5
-            default_colors = get_color(len(xticks))
-            legend_hue = None
-            xangle = 0
+            res = None
+            if x and stats_param:
+                if isinstance(stats_param, dict):
+                    res = FuncMultiCmpt(data=df, dv=y, factor=x, **stats_param)
+                elif bool(stats_param):
+                    res = FuncMultiCmpt(data=df, dv=y, factor=x)
+                else:
+                    res = "did not work properly"
+            display_output(res)
 
         # full_order
         opt = kwargs.get("opt", {})
@@ -580,15 +617,13 @@ def catplot(data, *args, **kwargs):
                 opt.update(style_load)
             except:
                 print(f"cannot find the style'{style_name}'")
-        ax = kwargs.get("ax", None)
-        if "ax" not in locals() or ax is None:
-            ax = plt.gca()
-        opt.setdefault("c", default_colors)
-        # if len(opt["c"]) < data.shape[1]:
-        #     additional_colors = plt.cm.winter(
-        #         np.linspace(0, 1, data.shape[1] - len(opt["c"]))
-        #     )
-        #     opt["c"] = np.vstack([opt["c"], additional_colors[:, :3]])
+
+        color_custom = kwargs.get("c", default_colors)
+        if not isinstance(color_custom, list):
+            color_custom = list(color_custom)
+        # if len(color_custom) < data.shape[1]:
+        #     color_custom.extend(get_color(data.shape[1]-len(color_custom),cmap='tab20'))
+        opt.setdefault("c", color_custom)
 
         opt.setdefault("loc", {})
         opt["loc"].setdefault("go", 0)
@@ -597,15 +632,12 @@ def catplot(data, *args, **kwargs):
         # export setting
         opt.setdefault("style", {})
         opt["style"].setdefault("export", None)
-        print(opt["style"])
-
-        # opt.setdefault('layer', {})
         opt.setdefault("layer", ["b", "bx", "e", "v", "s", "l"])
 
         opt.setdefault("b", {})
         opt["b"].setdefault("go", 1)
         opt["b"].setdefault("loc", "c")
-        opt["b"].setdefault("FaceColor", opt["c"])
+        opt["b"].setdefault("FaceColor", color_custom)
         opt["b"].setdefault("FaceAlpha", 1)
         opt["b"].setdefault("EdgeColor", "k")
         opt["b"].setdefault("EdgeAlpha", 1)
@@ -626,7 +658,7 @@ def catplot(data, *args, **kwargs):
         opt["e"].setdefault("LineColor", "k")
         opt["e"].setdefault("LineJoin", "round")
         opt["e"].setdefault("MarkerSize", "auto")
-        opt["e"].setdefault("FaceColor", opt["c"])
+        opt["e"].setdefault("FaceColor", color_custom)
         opt["e"].setdefault("MarkerEdgeColor", "none")
         opt["e"].setdefault("Visible", True)
         opt["e"].setdefault("Orientation", "vertical")
@@ -656,7 +688,7 @@ def catplot(data, *args, **kwargs):
         opt.setdefault("bx", {})
         opt["bx"].setdefault("go", 0)
         opt["bx"].setdefault("loc", "r")
-        opt["bx"].setdefault("FaceColor", opt["c"])
+        opt["bx"].setdefault("FaceColor", color_custom)
         opt["bx"].setdefault("EdgeColor", "k")
         opt["bx"].setdefault("FaceAlpha", 0.85)
         opt["bx"].setdefault("EdgeAlpha", 1)
@@ -700,7 +732,7 @@ def catplot(data, *args, **kwargs):
         opt["v"].setdefault("x_width", 0.3)
         opt["v"].setdefault("loc", "r")
         opt["v"].setdefault("EdgeColor", "none")
-        opt["v"].setdefault("FaceColor", opt["c"])
+        opt["v"].setdefault("FaceColor", color_custom)
         opt["v"].setdefault("FaceAlpha", 0.3)
         opt["v"].setdefault("BandWidth", "scott")
         opt["v"].setdefault("Function", "pdf")
@@ -723,17 +755,18 @@ def catplot(data, *args, **kwargs):
             xloc = opt["loc"]["xloc"]
         layers = sort_catplot_layers(opt["layer"])
 
-        label_which = kwargs.get("label_which", "barplot")
-        if "b" in label_which:
-            legend_which = "b"
-        elif "s" in label_which:
-            legend_which = "s"
-        elif "bx" in label_which:
-            legend_which = "bx"
-        elif "e" in label_which:
-            legend_which = "e"
-        elif "v" in label_which:
-            legend_which = "v"
+        label = kwargs.get("label", "bar")
+        if label:
+            if "b" in label:
+                legend_which = "b"
+            elif "s" in label:
+                legend_which = "s"
+            elif "bx" in label:
+                legend_which = "bx"
+            elif "e" in label:
+                legend_which = "e"
+            elif "v" in label:
+                legend_which = "v"
         else:
             legend_which = None
         for layer in layers:
@@ -770,6 +803,63 @@ def catplot(data, *args, **kwargs):
         show_legend = kwargs.get("show_legend", True)
         if show_legend:
             ax.legend()
+        # ! add asterisks in the plot
+        if stats_param:
+            if len(xticklabels) >= 1:
+                if hue is None:
+                    add_asterisks(
+                        ax, res, xticks_x_loc, xticklabels, y_loc=np.max(data)
+                    )
+                else:  # hue is not None
+                    ihue = 1
+                    for i in df[x].unique().tolist():
+                        if stats_param:
+                            if isinstance(stats_param, dict):
+                                if "factor" in stats_param.keys():
+                                    res_tmp = FuncMultiCmpt(
+                                        data=df, dv=y, **stats_param
+                                    )
+                                else:
+                                    res_tmp = FuncMultiCmpt(
+                                        data=df[df[x] == i],
+                                        dv=y,
+                                        factor=hue,
+                                        **stats_param,
+                                    )
+                            elif bool(stats_param):
+                                res_tmp = FuncMultiCmpt(
+                                    data=df[df[x] == i], dv=y, factor=hue
+                                )
+                            else:
+                                res_tmp = "did not work properly"
+                            xloc_curr = hue_len * (ihue - 1)
+
+                            add_asterisks(
+                                ax,
+                                res_tmp,
+                                xticks[xloc_curr : xloc_curr + hue_len],
+                                legend_hue,
+                                y_loc=np.max(data),
+                            )
+                        ihue += 1
+            else:  # 240814: still has some bugs
+                if isinstance(res, dict):
+                    tab_res = pd.DataFrame(res[1], index=[0])
+                    x1 = df.loc[df[x] == xticklabels[0], y].tolist()
+                    x2 = df.loc[df[x] == xticklabels[1], y].tolist()
+                    tab_res[f"{xticklabels[0]}(mean±sem)"] = [str_mean_sem(x1)]
+                    tab_res[f"{xticklabels[1]}(mean±sem)"] = [str_mean_sem(x2)]
+                    add_asterisks(
+                        ax, res[1], xticks_x_loc, xticklabels, y_loc=np.max([x1, x2])
+                    )
+                elif isinstance(res, pd.DataFrame):
+                    display(res)
+                    print("still has some bugs")
+                    x1 = df.loc[df[x] == xticklabels[0], y].tolist()
+                    x2 = df.loc[df[x] == xticklabels[1], y].tolist()
+                    add_asterisks(
+                        ax, res, xticks_x_loc, xticklabels, y_loc=np.max([x1, x2])
+                    )
 
         style_export = kwargs.get("style_export", None)
         if style_export and (style_export != style_use):
@@ -806,6 +896,11 @@ def get_cmap():
 
 
 def read_mplstyle(style_file):
+    """
+    example usage:
+    style_file = "/ std-colors.mplstyle"
+    style_dict = read_mplstyle(style_file)
+    """
     # Load the style file
     plt.style.use(style_file)
 
@@ -820,11 +915,6 @@ def read_mplstyle(style_file):
     return style_dict
 
 
-# #example usage:
-# style_file = "/ std-colors.mplstyle"
-# style_dict = read_mplstyle(style_file)
-
-
 def figsets(*args, **kwargs):
     """
     usage:
@@ -900,7 +990,6 @@ def figsets(*args, **kwargs):
     def set_step_1(ax, key, value):
         if ("fo" in key) and (("size" in key) or ("sz" in key)):
             fontsize = value
-            print(fontsize)
             plt.rcParams.update({"font.size": fontsize})
         # style
         if "st" in key.lower() or "th" in key.lower():
@@ -1146,6 +1235,10 @@ def figsets(*args, **kwargs):
             if legend_kws:
                 # https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.legend.html
                 ax.legend(**legend_kws)
+            else:
+                legend = ax.get_legend()
+                if legend is not None:
+                    legend.remove()
 
     for arg in args:
         if isinstance(arg, matplotlib.axes._axes.Axes):
@@ -1620,3 +1713,53 @@ def remove_colors_in_dict(
     if "loc" in data:
         del data["loc"]
     return data
+
+
+def add_asterisks(ax, res, xticks_x_loc, xticklabels, **kwargs_funcstars):
+    if len(xticklabels) > 2:
+        if isinstance(res, dict):
+            pval_groups = res["res_tab"]["p-unc"].tolist()[0]
+        else:
+            pval_groups = res["res_tab"]["PR(>F)"].tolist()[0]
+        if pval_groups <= 0.05:
+            A_list = res["res_posthoc"]["A"].tolist()
+            B_list = res["res_posthoc"]["B"].tolist()
+            xticklabels_array = np.array(xticklabels)
+            yscal_ = 0.99
+            for A, B, P in zip(
+                res["res_posthoc"]["A"].tolist(),
+                res["res_posthoc"]["B"].tolist(),
+                res["res_posthoc"]["p-unc"].tolist(),
+            ):
+                index_A = np.where(xticklabels_array == A)[0][0]
+                index_B = np.where(xticklabels_array == B)[0][0]
+                FuncStars(
+                    ax=ax,
+                    x1=xticks_x_loc[index_A],
+                    x2=xticks_x_loc[index_B],
+                    pval=P,
+                    yscale=yscal_,
+                    **kwargs_funcstars,
+                )
+                if P <= 0.05:
+                    yscal_ -= 0.075
+    else:
+        if isinstance(res, tuple):
+            res = res[1]
+            pval_groups = res["pval"]
+            FuncStars(
+                ax=ax,
+                x1=1,
+                x2=2,
+                pval=pval_groups,
+                **kwargs_funcstars,
+            )
+        else:
+            pval_groups = res["pval"]
+            FuncStars(
+                ax=ax,
+                x1=1,
+                x2=2,
+                pval=pval_groups,
+                **kwargs_funcstars,
+            )

py2ls/stats.py

@@ -12,12 +12,13 @@ warnings.filterwarnings("ignore", category=RuntimeWarning)
 
 # FuncStars --v 0.1.1
 def FuncStars(
-    ax,
+    ax=None,
     pval=None,
     ylim=None,
     xlim=None,
     symbol="*",
     yscale=0.95,
+    y_loc=None,
     x1=0,
     x2=1,
     alpha=0.05,
@@ -32,7 +33,7 @@ def FuncStars(
     linewidth=0.8,
     nsshow="off",
     symbolcolor="k",
-    tailindicator=[0.06, 0.06],
+    tailindicator=[0.05, 0.05],
     report=None,
     report_scale=-0.1,
     report_loc=None,
@@ -48,14 +49,18 @@ def FuncStars(
     if report_scale > 0:
         report_scale = -np.abs(report_scale)
     yscale = np.float64(yscale)
-    y_loc = np.min(ylim) + yscale * (np.max(ylim) - np.min(ylim))
+    if y_loc is None:
+        y_loc = np.min(ylim) + yscale * (np.max(ylim) - np.min(ylim))
+    else:
+        y_loc=y_loc+(1-yscale) * np.abs(np.diff(ylim))+0.1 *y_loc
     xcenter = np.mean([x1, x2])
+
     # ns / *
     if alpha < pval:
         if nsshow == "on":
             ns_str = f"p={round(pval, 3)}" if pval < 0.9 else "ns"
             color = "m" if pval < 0.1 else "k"
-            plt.text(
+            ax.text(
                 xcenter,
                 y_loc,
                 ns_str,
@@ -68,45 +73,43 @@ def FuncStars(
                 # bbox=dict(facecolor=None, edgecolor=None, color=None, linewidth=None)
             )
     elif 0.01 < pval <= alpha:
-        plt.text(
+        ax.text(
             xcenter,
             y_loc,
             symbol,
             ha="center",
-            va="center_baseline",
+            va="top",#"center_baseline",
             fontsize=fontsize,
             fontname=fontname,
             color=symbolcolor,
         )
     elif 0.001 < pval <= 0.01:
-        plt.text(
+        ax.text(
             xcenter,
             y_loc,
             symbol * 2,
             ha="center",
-            va="center_baseline",
+            va="top",#"center_baseline",
             fontsize=fontsize,
             fontname=fontname,
             color=symbolcolor,
         )
     elif 0 < pval <= 0.001:
-        plt.text(
+        ax.text(
             xcenter,
             y_loc,
             symbol * 3,
             ha="center",
-            va="center_baseline",
+            va="top",#"center_baseline",
             fontsize=fontsize,
             fontname=fontname,
             color=symbolcolor,
         )
     # lines indicators
-    if linego:  # and 0 < pval <= 0.05:
-        print(pval)
-        print(linego)
+    if linego and 0 < pval <= 0.05:
         # horizontal line
-        if yscale < 0.99:
-            plt.plot(
+        if yscale <= 0.99:
+            ax.plot(
                 [x1 + np.abs(np.diff(xlim)) * 0.01, x2 - np.abs(np.diff(xlim)) * 0.01],
                 [
                     y_loc - np.abs(np.diff(ylim)) * 0.03,
@@ -117,7 +120,7 @@ def FuncStars(
                 linewidth=linewidth,
             )
             # vertical line
-            plt.plot(
+            ax.plot(
                 [x1 + np.abs(np.diff(xlim)) * 0.01, x1 + np.abs(np.diff(xlim)) * 0.01],
                 [
                     y_loc - np.abs(np.diff(ylim)) * tailindicator[0],
@@ -127,7 +130,7 @@ def FuncStars(
                 color=linecolor,
                 linewidth=linewidth,
             )
-            plt.plot(
+            ax.plot(
                 [x2 - np.abs(np.diff(xlim)) * 0.01, x2 - np.abs(np.diff(xlim)) * 0.01],
                 [
                     y_loc - np.abs(np.diff(ylim)) * tailindicator[1],
@@ -138,7 +141,7 @@ def FuncStars(
                 linewidth=linewidth,
             )
         else:
-            plt.plot(
+            ax.plot(
                 [x1 + np.abs(np.diff(xlim)) * 0.01, x2 - np.abs(np.diff(xlim)) * 0.01],
                 [
                     np.min(ylim)
@@ -153,7 +156,7 @@ def FuncStars(
                 linewidth=linewidth,
             )
             # vertical line
-            plt.plot(
+            ax.plot(
                 [x1 + np.abs(np.diff(xlim)) * 0.01, x1 + np.abs(np.diff(xlim)) * 0.01],
                 [
                     np.min(ylim)
@@ -167,7 +170,7 @@ def FuncStars(
                 color=linecolor,
                 linewidth=linewidth,
             )
-            plt.plot(
+            ax.plot(
                 [x2 - np.abs(np.diff(xlim)) * 0.01, x2 - np.abs(np.diff(xlim)) * 0.01],
                 [
                     np.min(ylim)
@@ -182,7 +185,7 @@ def FuncStars(
                 linewidth=linewidth,
             )
     if values_below is not None:
-        plt.text(
+        ax.text(
             xcenter,
             y_loc * (-0.1),
             values_below,
@@ -194,7 +197,7 @@ def FuncStars(
         )
     # report / comments
     if report is not None:
-        plt.text(
+        ax.text(
             xcenter,
             report_loc,
             report,
@@ -211,45 +214,45 @@ def FuncCmpt(x1, x2, pmc="auto", pair="unpaired", verbose=True):
 
     # pmc correction: 'parametric'/'non-parametric'/'auto'
     # meawhile get the opposite setting (to compare the results)
-    def corr_pmc(pmc):
-        cfg_pmc = None
-        if pmc.lower() in {"pmc", "parametric"} and pmc.lower() not in {
-            "npmc",
-            "nonparametric",
-            "non-parametric",
-        }:
-            cfg_pmc = "parametric"
-        elif pmc.lower() in {
-            "npmc",
-            "nonparametric",
-            "non-parametric",
-        } and pmc.lower() not in {"pmc", "parametric"}:
-            cfg_pmc = "non-parametric"
-        else:
-            cfg_pmc = "auto"
-        return cfg_pmc
-
-    def corr_pair(pair):
-        cfg_pair = None
-        if "pa" in pair.lower() and "np" not in pair.lower():
-            cfg_pair = "paired"
-        elif "np" in pair.lower():
-            cfg_pair = "unpaired"
-        return cfg_pair
-
-    def check_normality(data, verbose=True):
-        stat_shapiro, pval_shapiro = stats.shapiro(data)
-        if pval_shapiro > 0.05:
-            Normality = True
-        else:
-            Normality = False
-        if verbose:
-            (
-                print(f"\n normally distributed\n")
-                if Normality
-                else print(f"\n NOT normally distributed\n")
-            )
-        return Normality
+    # def corr_pmc(pmc):
+    #     cfg_pmc = None
+    #     if pmc.lower() in {"pmc", "parametric"} and pmc.lower() not in {
+    #         "npmc",
+    #         "nonparametric",
+    #         "non-parametric",
+    #     }:
+    #         cfg_pmc = "parametric"
+    #     elif pmc.lower() in {
+    #         "npmc",
+    #         "nonparametric",
+    #         "non-parametric",
+    #     } and pmc.lower() not in {"pmc", "parametric"}:
+    #         cfg_pmc = "non-parametric"
+    #     else:
+    #         cfg_pmc = "auto"
+    #     return cfg_pmc
+
+    # def corr_pair(pair):
+    #     cfg_pair = None
+    #     if "pa" in pair.lower() and "np" not in pair.lower():
+    #         cfg_pair = "paired"
+    #     elif "np" in pair.lower():
+    #         cfg_pair = "unpaired"
+    #     return cfg_pair
+
+    # def check_normality(data, verbose=True):
+    #     stat_shapiro, pval_shapiro = stats.shapiro(data)
+    #     if pval_shapiro > 0.05:
+    #         Normality = True
+    #     else:
+    #         Normality = False
+    #     if verbose:
+    #         (
+    #             print(f"\n normally distributed\n")
+    #             if Normality
+    #             else print(f"\n NOT normally distributed\n")
+    #         )
+    #     return Normality
 
     def sub_cmpt_2group(x1, x2, cfg_pmc="pmc", pair="unpaired", verbose=True):
         output = {}
@@ -261,7 +264,7 @@ def FuncCmpt(x1, x2, pmc="auto", pair="unpaired", verbose=True):
                 x1, x2, center="median", proportiontocut=0.05
             )
             VarType = True if pval_lev > 0.05 and nX1 == nX2 else False
-
+            # print(pair)
             if "np" in pair:  # 'unpaired'
                 if VarType and Normality:
                     # The independent t-test requires that the dependent variable is approximately normally
@@ -278,7 +281,7 @@ def FuncCmpt(x1, x2, pmc="auto", pair="unpaired", verbose=True):
                     )
                     notes_stat = "unpaired t test"
                     notes_APA = (
-                        f"t({nX1+nX2-2})={round(stat_value, 5)},p={round(pval, 5)}"
+                        f"t({nX1+nX2-2})={round(stat_value,3)},p={round(pval,3)}"
                     )
                 else:
                     # If the Levene's Test for Equality of Variances is statistically significant,
@@ -297,7 +300,7 @@ def FuncCmpt(x1, x2, pmc="auto", pair="unpaired", verbose=True):
                     notes_stat = "Welchs t-test"
                     # note: APA FORMAT
                     notes_APA = (
-                        f"t({nX1+nX2-2})={round(stat_value, 5)},p={round(pval, 5)}"
+                        f"t({nX1+nX2-2})={round(stat_value,3)},p={round(pval,3)}"
                     )
             elif "pa" in pair and "np" not in pair:  # 'paired'
                 # the paired-samples t-test is considered “robust” in handling violations of normality
@@ -309,7 +312,7 @@ def FuncCmpt(x1, x2, pmc="auto", pair="unpaired", verbose=True):
                 notes_stat = "paired t test"
                 # note: APA FORMAT
                 notes_APA = (
-                    f"t({sum([nX1-1])})={round(stat_value, 5)},p={round(pval, 5)}"
+                    f"t({sum([nX1-1])})={round(stat_value,3)},p={round(pval,3)}"
                 )
         elif cfg_pmc == "non-parametric":
             if "np" in pair:  # Perform Mann-Whitney
@@ -318,18 +321,18 @@ def FuncCmpt(x1, x2, pmc="auto", pair="unpaired", verbose=True):
                 )
                 notes_stat = "Mann-Whitney U"
                 if nX1 == nX2:
-                    notes_APA = f"U(n={nX1})={round(stat_value, 5)},p={round(pval, 5)}"
+                    notes_APA = f"U(n={nX1})={round(stat_value,3)},p={round(pval,3)}"
                 else:
-                    notes_APA = f"U(n1={nX1},n2={nX2})={round(stat_value, 5)},p={round(pval, 5)}"
+                    notes_APA = f"U(n1={nX1},n2={nX2})={round(stat_value,3)},p={round(pval,3)}"
             elif "pa" in pair and "np" not in pair:  # Wilcoxon signed-rank test
                 stat_value, pval = stats.wilcoxon(
                     x1, x2, method="exact", nan_policy="omit"
                 )
                 notes_stat = "Wilcoxon signed-rank"
                 if nX1 == nX2:
-                    notes_APA = f"Z(n={nX1})={round(stat_value, 5)},p={round(pval, 5)}"
+                    notes_APA = f"Z(n={nX1})={round(stat_value,3)},p={round(pval,3)}"
                 else:
-                    notes_APA = f"Z(n1={nX1},n2={nX2})={round(stat_value, 5)},p={round(pval, 5)}"
+                    notes_APA = f"Z(n1={nX1},n2={nX2})={round(stat_value,3)},p={round(pval,3)}"
 
         # filling output
         output["stat"] = stat_value
@@ -383,7 +386,7 @@ def FuncCmpt(x1, x2, pmc="auto", pair="unpaired", verbose=True):
 # =============================================================================
 
 
-def str_mean_sem(data: list, delimit=5):
+def str_mean_sem(data: list, delimit=3):
     mean_ = np.nanmean(data)
     sem_ = np.nanstd(data, ddof=1) / np.sqrt(sum(~np.isnan(data)))
     return str(round(mean_, delimit)) + "±" + str(round(sem_, delimit))
@@ -404,6 +407,7 @@ def FuncMultiCmpt(
     subject=None,
     group=None,
     verbose=True,
+    post_hoc=False
 ):
     if group is None:
         group = factor
@@ -515,12 +519,12 @@ def FuncMultiCmpt(
         if "np" in cfg_pair:  # 'unpaired'
             res_tab = run_kruskal(data, dv, factor)
             notes_stat = f"Non-parametric Kruskal: {data[factor].nunique()} Way ANOVA"
-            notes_APA = f'H({res_tab.ddof1[0]},n={data.shape[0]})={round(res_tab.H[0], 5)},p={round(res_tab["p-unc"][0], 5)}'
+            notes_APA = f'H({res_tab.ddof1[0]},n={data.shape[0]})={round(res_tab.H[0],3)},p={round(res_tab["p-unc"][0],3)}'
 
         elif "pa" in cfg_pair and "np" not in cfg_pair:  # 'paired'
             res_tab = run_friedman(data, dv, factor, subject, method="chisq")
             notes_stat = f"Non-parametric {data[factor].nunique()} Way Friedman repeated measures ANOVA"
-            notes_APA = f'X^2({res_tab.ddof1[0]})={round(res_tab.Q[0], 5)},p={round(res_tab["p-unc"][0], 5)}'
+            notes_APA = f'X^2({res_tab.ddof1[0]})={round(res_tab.Q[0],3)},p={round(res_tab["p-unc"][0],3)}'
 
     # =============================================================================
     # # Post-hoc
@@ -535,7 +539,10 @@ def FuncMultiCmpt(
     go_mix_between = None if ("pa" in cfg_pair) or ("np" not in cfg_pair) else factor
     go_mix_within = within if ("mix" in cfg_pair) or ("both" in cfg_pair) else None
     go_mix_within = factor if ("pa" in cfg_pair) or ("np" not in cfg_pair) else None
+
     if res_tab["p-unc"][0] <= 0.05:
+        post_hoc=True
+    if post_hoc:
         # Pairwise Comparisons
         method_post_hoc = [
             "bonf",  # 'bonferroni',  # : one-step correction
@@ -602,7 +609,10 @@ def FuncMultiCmpt(
     #     # filling output
     # =============================================================================
 
-    pd.set_option("display.max_columns", None)
+    pd.set_option('display.max_columns', None)  # Show all columns
+    pd.set_option('display.max_colwidth', None)  # No limit on column width
+    pd.set_option('display.expand_frame_repr', False)  # Prevent line-wrapping
+
     output["stat"] = notes_stat
     # print(output['APA'])
     output["APA"] = notes_APA
@@ -616,21 +626,21 @@ def FuncMultiCmpt(
 def display_output(output: dict):
     if isinstance(output, pd.DataFrame):
         output = output.to_dict(orient="list")
-    # ['res_posthoc', 'stat', 'APA', 'pval', 'res_tab']
-    # res_keys = list(output.keys())
-    # display(res_keys)
+    # ['res_posthoc', 'stat', 'APA', 'pval', 'res_tab'] 
+
+    # ? show APA
+    # print(f"\n\ndisplay stat_output")
+    # try:
+    #     print(f"APA: {output["APA"]}")
+    # except:
+    #     pass
     try:
-        print("APA:")
-        display(output["APA"])
-    except:
-        pass
-    try:
-        print("results table:")
+        print("stats table:  ⤵")
         display(output["res_tab"])
     except:
         pass
     try:
-        print("posthoc:")
+        print(f"APA  ⤵\n{output["APA"][0]}  ⤵\npost-hoc analysis ⤵")
         display(output["res_posthoc"])
     except:
         pass
@@ -647,17 +657,18 @@ def corr_pair(pair):
     return cfg_pair
 
 
-def check_normality(data):
+def check_normality(data, verbose=True):
     stat_shapiro, pval_shapiro = stats.shapiro(data)
     if pval_shapiro > 0.05:
         Normality = True
     else:
         Normality = False
-    (
-        print(f"\n normally distributed\n")
-        if Normality
-        else print(f"\n NOT normally distributed\n")
-    )
+    if verbose:
+        (
+            print(f"\n normally distributed\n")
+            if Normality
+            else print(f"\n NOT normally distributed\n")
+        )
     return Normality
 
 
@@ -691,17 +702,17 @@ def extract_apa(res_tab):
     notes_APA = []
     if "ddof1" in res_tab:
         for irow in range(res_tab.shape[0]):
-            note_tmp = f'{res_tab.Source[irow]}:F{round(res_tab.ddof1[irow]),round(res_tab.ddof2[irow])}={round(res_tab.F[irow], 5)},p={round(res_tab["p-unc"][irow], 5)}'
-            notes_APA.append([note_tmp])
+            note_tmp = f'{res_tab.Source[irow]}:F{round(res_tab.ddof1[irow]),round(res_tab.ddof2[irow])}={round(res_tab.F[irow],3)},p={round(res_tab["p-unc"][irow],3)}'
+            notes_APA.append(note_tmp)
     elif "DF" in res_tab:
         for irow in range(res_tab.shape[0] - 1):
-            note_tmp = f'{res_tab.Source[irow]}:F{round(res_tab.DF[irow]),round(res_tab.DF[res_tab.shape[0]-1])}={round(res_tab.F[irow], 5)},p={round(res_tab["p-unc"][irow], 5)}'
-            notes_APA.append([note_tmp])
-        notes_APA.append(["NaN"])
+            note_tmp = f'{res_tab.Source[irow]}:F{round(res_tab.DF[irow]),round(res_tab.DF[res_tab.shape[0]-1])}={round(res_tab.F[irow],3)},p={round(res_tab["p-unc"][irow],3)}'
+            notes_APA.append(note_tmp)
+        notes_APA.append(np.nan)
     elif "DF1" in res_tab:  # in 'mix' case
         for irow in range(res_tab.shape[0]):
-            note_tmp = f'{res_tab.Source[irow]}:F{round(res_tab.DF1[irow]),round(res_tab.DF2[irow])}={round(res_tab.F[irow], 5)},p={round(res_tab["p-unc"][irow], 5)}'
-            notes_APA.append([note_tmp])
+            note_tmp = f'{res_tab.Source[irow]}:F{round(res_tab.DF1[irow]),round(res_tab.DF2[irow])}={round(res_tab.F[irow],3)},p={round(res_tab["p-unc"][irow],3)}'
+            notes_APA.append(note_tmp)
     return notes_APA
 
 
@@ -1130,7 +1141,17 @@ def df2array(data: pd.DataFrame, x, y, hue=None, sort=False):
                 a = padcat(a, new_, axis=0)
         return sort_rows_move_nan(a).T
 
-
+def array2df(data: np.ndarray):
+    df = pd.DataFrame()
+    df["group"] = (
+        np.tile(
+            ["group" + str(i) for i in range(1, data.shape[1] + 1)], [data.shape[0], 1]
+        )
+        .reshape(-1, 1, order="F")[:, 0]
+        .tolist()
+    )
+    df["value"] = data.reshape(-1, 1, order="F")
+    return df
 def padcat(*args, fill_value=np.nan, axis=1, order="row"):
     """
     Concatenate vectors with padding.

{py2ls-0.1.9.2.dist-info → py2ls-0.1.9.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: py2ls
-Version: 0.1.9.2
+Version: 0.1.9.4
 Summary: py(thon)2(too)ls
 Author: Jianfeng
 Author-email: Jianfeng.Liu0413@gmail.com

{py2ls-0.1.9.2.dist-info → py2ls-0.1.9.4.dist-info}/RECORD

@@ -1,6 +1,6 @@
 py2ls/.DS_Store,sha256=l7m93mLt2ckidOORlgzbfdGcDJ5emCexs-GHEiKbEaQ,6148
-py2ls/.git/COMMIT_EDITMSG,sha256=EBFQ6F6FLLKqdBpaLROBL68CNyHmTvOC--uM_TlZ6KI,11
-py2ls/.git/FETCH_HEAD,sha256=ZYJf1HGynl3E4z5mK-iNYPEV63GUwDCoI31sbgjlgL0,100
+py2ls/.git/COMMIT_EDITMSG,sha256=5xj-jWMbrdOc9m7gSn-UcsAQ9FMNvWSbLWSsrOUIO5w,7
+py2ls/.git/FETCH_HEAD,sha256=6cJaQzb6VhkvNNm-KsABX6R28FNKZB8qMmqacDEP_dQ,100
 py2ls/.git/HEAD,sha256=KNJb-Cr0wOK3L1CVmyvrhZ4-YLljCl6MYD2tTdsrboA,21
 py2ls/.git/config,sha256=CL7WR7jU8VRchJwRooCBkXUMvuRoPdf3FWIBAOlap1c,378
 py2ls/.git/description,sha256=ZzMxc0Ca26m45Twn1DDnOHqin5VHEZ9uOTBrScIXSjE,16
@@ -17,25 +17,29 @@ py2ls/.git/hooks/pre-receive.sample,sha256=pMPSuce7P9jRRBwxvU7nGlldZrRPz0ndsxAlI
 py2ls/.git/hooks/prepare-commit-msg.sample,sha256=6d3KpBif3dJe2X_Ix4nsp7bKFjkLI5KuMnbwyOGqRhk,1492
 py2ls/.git/hooks/push-to-checkout.sample,sha256=pT0HQXmLKHxt16-mSu5HPzBeZdP0lGO7nXQI7DsSv18,2783
 py2ls/.git/hooks/update.sample,sha256=jV8vqD4QPPCLV-qmdSHfkZT0XL28s32lKtWGCXoU0QY,3650
-py2ls/.git/index,sha256=XDvwp0KaZw_2pZgn1OPTmqBe78Abnq6O-xcw_aZuOB8,1855
+py2ls/.git/index,sha256=B5IywwCaOb2OVM4Y6a-PbFrE0dw5kWJNBmS_pt5rX64,2663
 py2ls/.git/info/exclude,sha256=ZnH-g7egfIky7okWTR8nk7IxgFjri5jcXAbuClo7DsE,240
-py2ls/.git/logs/HEAD,sha256=0Al8yWeB2OiUKgtEdzKf8Kx9p8_1WI1Mx_X2DXQCbU0,3227
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