py2ls 0.1.9.2__tar.gz → 0.1.9.4__tar.gz

{py2ls-0.1.9.2 → py2ls-0.1.9.4}/PKG-INFO

@@ -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-0.1.9.4/py2ls/.git/COMMIT_EDITMSG

@@ -0,0 +1 @@
+update

py2ls-0.1.9.4/py2ls/.git/FETCH_HEAD

@@ -0,0 +1 @@
+6dc2cdf4a84e538e5d4777486aeff87e42f41799		branch 'main' of https://github.com/Jianfengliu0413/py2ls

{py2ls-0.1.9.2 → py2ls-0.1.9.4}/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-0.1.9.2 → py2ls-0.1.9.4}/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-0.1.9.2 → py2ls-0.1.9.4}/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-0.1.9.2 → py2ls-0.1.9.4}/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-0.1.9.4/py2ls/.git/objects/6d/c2cdf4a84e538e5d4777486aeff87e42f41799

@@ -0,0 +1,2 @@
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py2ls-0.1.9.4/py2ls/.git/objects/dc/c2bdbafb3296e09d9ee4955cfa55d275825f94

@@ -0,0 +1,5 @@
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+��=*�J`Η���iA#[ZW5TZ=!����~����hPը*�.[�
++(4Jv�}�d�:N�K2�trB�9�J��J�����Y?���|#��d*=v@�B�w�@��'
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�<"�������@��|±�?��.��R��m�.m�ax���l�M�QEC9��Sܐŧ"~��9E�iTe�!窷��S�':fJ�d^���?n����:f"L݂{4M��o��/^�!�2B
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py2ls-0.1.9.4/py2ls/.git/objects/e2/f2f8f4c25e62a297fc55f36acc6b01cfbab76f

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+x
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+�0D;�+�
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py2ls-0.1.9.4/py2ls/.git/refs/heads/main

@@ -0,0 +1 @@
+6dc2cdf4a84e538e5d4777486aeff87e42f41799

py2ls-0.1.9.4/py2ls/.git/refs/remotes/origin/main

@@ -0,0 +1 @@
+6dc2cdf4a84e538e5d4777486aeff87e42f41799

{py2ls-0.1.9.2 → py2ls-0.1.9.4}/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-0.1.9.2 → py2ls-0.1.9.4}/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,
+            )