Fix imports (#3)

* :format: format with black

* 🚚 move viz.py changes from phospho project version, lint w/ ruff

* 🐛 fix import. network an wgcna analysis from acore, dendrogram

* 🐛 missing function and start deconvoluting utils, add imports to pkg

* 🎨 port interface adaptions - use plotly figures directly

* 🐛 fix CDCI pipeline (missing imports and 3.13. incompability)

* 🐛 do not allow pyton 3.13 for now

* 🐛 add missing build dependency (for dynamic versioning based on tags)

Author: enryH

.github/workflows/cdci.yml

@@ -14,28 +14,27 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - uses: psf/black@stable
-  # lint:
-  #   name: Lint with ruff
-  #   runs-on: ubuntu-latest
-  #   steps:
-  #     - uses: actions/checkout@v4
+  lint:
+    name: Lint with ruff
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
 
-  #     - uses: actions/setup-python@v5
-  #       with:
-  #         python-version: "3.11"
-  #     - name: Install ruff
-  #       run: | 
-  #         pip install ruff
-  #     - name: Lint with ruff  
-  #       run: |
-  #         # stop the build if there are Python syntax errors or undefined names
-  #         ruff check .
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+      - name: Install ruff
+        run: | 
+          pip install ruff
+      - name: Lint with ruff  
+        run: |
+          ruff check .
   test:
     name: Test
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}

pyproject.toml

@@ -6,7 +6,7 @@ dynamic = ["version"]
 description = "A Python package for plotting related to multimodal molecular data. Works with acore."
 license = { text = "GNU General Public License v3" }
 readme = "README.md"
-requires-python = ">=3.9"
+requires-python = ">=3.9,<3.13"
 classifiers = [
     "Development Status :: 2 - Pre-Alpha",
     "Intended Audience :: Developers",
@@ -27,12 +27,16 @@ dependencies = [
     "beautifulsoup4",
     "requests",
     "dash", # from dash import html
-    # "networkx",
+    "networkx",
     "matplotlib",
-    # "cy-jupyterlab",
-    # "nltk",
-    # "webweb"
-    # "acore",
+    "kaleido",
+    "pyvis",
+    "wordcloud",
+    "cyjupyter",
+    "nltk",
+    "webweb",
+    "acore",
+    "dash-cytoscape",
 ]
 
 [project.optional-dependencies]
@@ -64,5 +68,7 @@ Documentation = "https://analytics-core.readthedocs.io/"
 
 
 [build-system]
-requires = ["setuptools"]
+requires = ["setuptools", "setuptools_scm>=8"]
 build-backend = "setuptools.build_meta"
+
+[tool.setuptools_scm]

src/vuecore/Dendrogram.py

@@ -1,7 +1,7 @@
+from collections import OrderedDict
+
 import numpy as np
 import scipy as scp
-from collections import OrderedDict
-import plotly.graph_objs as go
 
 
 def plot_dendrogram(
@@ -17,7 +17,8 @@ def plot_dendrogram(
     color_threshold=None,
 ):
     """
-    Modified version of Plotly _dendrogram.py that returns a dendrogram Plotly figure object with cutoff line.
+    Modified version of Plotly _dendrogram.py that
+    returns a dendrogram Plotly figure object with cutoff line.
 
     :param Z_dendrogram: Matrix of observations as array of arrays
     :type Z_dendrogram: ndarray
@@ -58,7 +59,7 @@ def plot_dendrogram(
         color_threshold=color_threshold,
     )
 
-    if cutoff_line == True:
+    if cutoff_line:
         dendrogram.layout.update(
             {
                 "shapes": [
@@ -221,7 +222,7 @@ def set_axis_layout(self, axis_key, hide_labels):
 
         self.layout[axis_key].update(axis_defaults)
 
-        if hide_labels == True:
+        if hide_labels:
             self.layout[axis_key].update({"showticklabels": False})
         else:
             pass
@@ -280,8 +281,8 @@ def get_dendrogram_traces(
         icoord = scp.array(Z_dendrogram["icoord"])
         dcoord = scp.array(Z_dendrogram["dcoord"])
         ordered_labels = scp.array(Z_dendrogram["ivl"])
-        color_list = scp.array(Z_dendrogram["color_list"])
-        colors = self.get_color_dict(colorscale)
+        # color_list = scp.array(Z_dendrogram["color_list"])
+        # colors = self.get_color_dict(colorscale)
 
         trace_list = []
 
@@ -295,7 +296,7 @@ def get_dendrogram_traces(
                 ys = dcoord[i]
             else:
                 ys = icoord[i]
-            color_key = color_list[i]
+            # color_key = color_list[i] # not used
             hovertext_label = None
             if hovertext:
                 hovertext_label = hovertext[i]

src/vuecore/linkers.py

@@ -0,0 +1,20 @@
+from io import StringIO
+
+import requests
+
+
+def get_clustergrammer_link(net, filename=None):
+    clustergrammer_url = "http://amp.pharm.mssm.edu/clustergrammer/matrix_upload/"
+    if filename is None:
+        file_string = net.write_matrix_to_tsv()
+        file_obj = StringIO(file_string)
+        if "filename" not in net.dat or net.dat["filename"] is None:
+            fake_filename = "Network.txt"
+        else:
+            fake_filename = net.dat["filename"]
+        r = requests.post(clustergrammer_url, files={"file": (fake_filename, file_obj)})
+    else:
+        file_obj = open(filename, "r")
+        r = requests.post(clustergrammer_url, files={"file": file_obj})
+    link = r.text
+    return link

src/vuecore/translate.py

@@ -0,0 +1,20 @@
+import base64
+import io
+
+from dash import html
+
+
+def hex2rgb(color):
+    _hex = color.lstrip("#")
+    rgb = tuple(int(_hex[i : i + 2], 16) for i in (0, 2, 4))
+    rgba = rgb + (0.6,)
+    return rgba
+
+
+def mpl_to_html_image(plot, width=800):
+    buf = io.BytesIO()
+    plot.savefig(buf, format="png")
+    data = base64.b64encode(buf.getbuffer()).decode("utf8")
+    figure = html.Img(src="data:image/png;base64,{}".format(data), width=f"{width}")
+
+    return figure

src/vuecore/utils.py

@@ -1,15 +1,13 @@
-import base64
-import io
 import random
 from collections import defaultdict
 from urllib import error
 
 import bs4 as bs
-import dash_html_components as html
 import networkx as nx
 import pandas as pd
 import requests
 from Bio import Entrez, Medline
+from dash import html
 from networkx.readwrite import json_graph
 
 # TODO: This should probably be changed to the email of the person installing ckg?
@@ -23,15 +21,6 @@ def check_columns(df, cols):
     return True
 
 
-def mpl_to_html_image(plot, width=800):
-    buf = io.BytesIO()
-    plot.savefig(buf, format="png")
-    data = base64.b64encode(buf.getbuffer()).decode("utf8")
-    figure = html.Img(src="data:image/png;base64,{}".format(data), width="800")
-
-    return figure
-
-
 def generate_html(network):
     """
     This method gets the data structures supporting the nodes, edges,
@@ -151,7 +140,7 @@ def networkx_to_neo4j_document(graph):
                 rel_type = edge["type"]
                 if "type" in graph.nodes()[r]:
                     edge["type"] = graph.nodes()[r]["type"]
-                if not (n, r, edge["type"]) in seen_rels:
+                if (n, r, edge["type"]) not in seen_rels:
                     rels[rel_type].append(edge)
                     seen_rels.update({(n, r, edge["type"]), (r, n, edge["type"])})
                     attr.update(rels)
@@ -268,9 +257,9 @@ def __extract_style(el):
             for k, v in [x.split(": ") for x in el.attrs["style"].split(";") if x != ""]
         }
 
-    if type(el) is str:
+    if isinstance(el, str):
         return convert_html_to_dash(parse_html(el))
-    if type(el) == bs.element.NavigableString:
+    if isinstance(el, bs.element.NavigableString):
         return str(el)
     else:
         name = el.name
@@ -281,13 +270,6 @@ def __extract_style(el):
         return getattr(html, name.title())(contents, style=style)
 
 
-def hex2rgb(color):
-    hex = color.lstrip("#")
-    rgb = tuple(int(hex[i : i + 2], 16) for i in (0, 2, 4))
-    rgba = rgb + (0.6,)
-    return rgba
-
-
 def get_rgb_colors(n):
     colors = []
     r = int(random.random() * 256)