From 33e4164a02ebd9f6f5d0d0b8dc01e71f4e2d07f1 Mon Sep 17 00:00:00 2001
From: Cazabet Remy <remy.cazabet@gmail.com>
Date: Wed, 2 Mar 2022 22:17:49 +0100
Subject: [PATCH 01/23] first try

moved infomap, leidenalg, karate to be optional
---
 cdlib/algorithms/crisp_partition.py | 90 +++++++++++++++++++++++------
 requirements.txt                    |  3 -
 requirements_complete.txt           |  4 ++
 requirements_optional.txt           |  2 -
 4 files changed, 76 insertions(+), 23 deletions(-)
 create mode 100644 requirements_complete.txt

diff --git a/cdlib/algorithms/crisp_partition.py b/cdlib/algorithms/crisp_partition.py
index 075a2b11..7d88d599 100644
--- a/cdlib/algorithms/crisp_partition.py
+++ b/cdlib/algorithms/crisp_partition.py
@@ -1,11 +1,15 @@
+missing_packages={}
+
 try:
     import infomap as imp
 except ModuleNotFoundError:
+    missing_packages.append("infomap")
     imp = None
 
 try:
     from wurlitzer import pipes
 except ModuleNotFoundError:
+    missing_packages.append("wurlitzer")
     pipes = None
 
 try:
@@ -16,20 +20,32 @@
 try:
     import leidenalg
 except ModuleNotFoundError:
+    missing_packages.append("leidenalg")
     leidenalg = None
 
 try:
     import graph_tool.all as gt
 except ModuleNotFoundError:
+    missing_packages.append("graph_tool")
     gt = None
 
+try:
+    import karateclub as kc
+    from karateclub import EdMot, GEMSEC, SCD
+except ModuleNotFoundError:
+    missing_packages.append("karateclub")
+    kc = None
+
+if len(missing_packages)>0:
+    warnings.warn(
+        "Note: to be able to use all methods, you need to install some additional packages: "+missing_packages
+    )
 import warnings
 import numpy as np
 from typing import Callable
 from copy import deepcopy
 from cdlib.algorithms.internal import DER
 import community as louvain_modularity
-import warnings
 from collections import defaultdict
 from cdlib import NodeClustering, FuzzyNodeClustering
 from cdlib.algorithms.internal.belief_prop import detect_belief_communities
@@ -68,7 +84,6 @@
 except ModuleNotFoundError:
     pycombo_part = None
 
-from karateclub import EdMot, GEMSEC, SCD
 import markov_clustering as mc
 from chinese_whispers import chinese_whispers as cw
 from chinese_whispers import aggregate_clusters
@@ -570,10 +585,13 @@ def leiden(
     """
 
     if ig is None or leidenalg is None:
-        raise ModuleNotFoundError(
-            "Optional dependency not satisfied: install igraph and leidenalg to use the "
-            "selected feature."
-        )
+        try:
+            import leidenalg
+        except ModuleNotFoundError:
+            raise ModuleNotFoundError(
+                "Optional dependency not satisfied: install igraph and leidenalg to use the "
+                "selected feature."
+            )
 
     g = convert_graph_formats(g_original, ig.Graph)
 
@@ -1051,13 +1069,19 @@ def infomap(g_original: object, flags: str = "") -> NodeClustering:
     """
 
     if imp is None:
-        raise ModuleNotFoundError(
-            "Optional dependency not satisfied: install infomap to use the selected feature."
-        )
+        try:
+            import infomap as imp
+        except ModuleNotFoundError:
+            raise ModuleNotFoundError(
+                "Optional dependency not satisfied: install infomap to use the selected feature."
+            )
     if pipes is None:
-        raise ModuleNotFoundError(
-            "Optional dependency not satisfied: install package wurlitzer to use infomap."
-        )
+        try:
+            from wurlitzer import pipes
+        except ModuleNotFoundError:
+            raise ModuleNotFoundError(
+                "Optional dependency not satisfied: install package wurlitzer to use infomap."
+            )
 
     g = convert_graph_formats(g_original, nx.Graph, directed=g_original.is_directed())
 
@@ -1499,12 +1523,15 @@ def sbm_dl_nested(
     .. note:: Implementation from graph-tool library, please report to https://graph-tool.skewed.de for details
     """
     if gt is None:
-        raise Exception(
-            "===================================================== \n"
-            "The graph-tool library seems not to be installed (or incorrectly installed). \n"
-            "Please check installation procedure there https://git.skewed.de/count0/graph-tool/wikis/installation-instructions#native-installation \n"
-            "on linux/mac, you can use package managers to do so(apt-get install python3-graph-tool, brew install graph-tool, etc.)"
-        )
+        try:
+            import graph_tool.all as gt
+        except ModuleNotFoundError:
+            raise Exception(
+                "===================================================== \n"
+                "The graph-tool library seems not to be installed (or incorrectly installed). \n"
+                "Please check installation procedure there https://git.skewed.de/count0/graph-tool/wikis/installation-instructions#native-installation \n"
+                "on linux/mac, you can use package managers to do so(apt-get install python3-graph-tool, brew install graph-tool, etc.)"
+            )
     gt_g = convert_graph_formats(g_original, nx.Graph)
     gt_g, label_map = __from_nx_to_graph_tool(gt_g)
     state = gt.minimize_nested_blockmodel_dl(gt_g)
@@ -1717,6 +1744,15 @@ def edmot(
     .. note:: Reference implementation: https://karateclub.readthedocs.io/
     """
 
+    if kc is None:
+        try:
+            from karateclub import EdMot, GEMSEC, SCD
+            kc=True
+        except ModuleNotFoundError:
+            raise ModuleNotFoundError(
+                "Optional dependency not satisfied: install karateclub to use the selected feature."
+            )
+
     g = convert_graph_formats(g_original, nx.Graph)
     model = EdMot(component_count=2, cutoff=10)
 
@@ -2360,6 +2396,15 @@ def gemsec(
 
     .. note:: Reference implementation: https://karateclub.readthedocs.io/
     """
+    if kc is None:
+        try:
+            from karateclub import EdMot, GEMSEC, SCD
+            kc = True
+        except ModuleNotFoundError:
+            raise ModuleNotFoundError(
+                "Optional dependency not satisfied: install karateclub to use the selected feature."
+            )
+
     g = convert_graph_formats(g_original, nx.Graph)
     model = GEMSEC(
         walk_number=walk_number,
@@ -2438,6 +2483,15 @@ def scd(
 
     .. note:: Reference implementation: https://karateclub.readthedocs.io/
     """
+    if kc is None:
+        try:
+            from karateclub import EdMot, GEMSEC, SCD
+            kc=True
+        except ModuleNotFoundError:
+            raise ModuleNotFoundError(
+                "Optional dependency not satisfied: install karateclub to use the selected feature."
+            )
+        
     g = convert_graph_formats(g_original, nx.Graph)
     model = SCD(iterations=iterations, eps=eps, seed=seed)
     model.fit(g)
diff --git a/requirements.txt b/requirements.txt
index ee42ae70..f3caa8c4 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -12,16 +12,13 @@ pulp
 seaborn
 pandas
 eva_lcd
-karateclub
 bimlpa
 markov_clustering
 chinese_whispers
 python-igraph
-leidenalg
 angel-cd
 pooch
 dynetx
-infomap
 wurlitzer
 thresholdclustering
 pyclustering
diff --git a/requirements_complete.txt b/requirements_complete.txt
new file mode 100644
index 00000000..df761dd4
--- /dev/null
+++ b/requirements_complete.txt
@@ -0,0 +1,4 @@
+karateclub
+leidenalg
+infomap
+wurlitzer
\ No newline at end of file
diff --git a/requirements_optional.txt b/requirements_optional.txt
index d90da8d1..570f339a 100644
--- a/requirements_optional.txt
+++ b/requirements_optional.txt
@@ -1,5 +1,3 @@
-infomap>=1.3.0
-wurlitzer>=1.0.2
 GraphRicciCurvature==0.5.2.1
 networkit
 pycombo

From 02b4189256a4da6f9a2ce1185fb41cc2f852b88e Mon Sep 17 00:00:00 2001
From: Cazabet Remy <remy.cazabet@gmail.com>
Date: Wed, 2 Mar 2022 22:31:39 +0100
Subject: [PATCH 02/23] fix

---
 cdlib/algorithms/crisp_partition.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/cdlib/algorithms/crisp_partition.py b/cdlib/algorithms/crisp_partition.py
index 7d88d599..200e810b 100644
--- a/cdlib/algorithms/crisp_partition.py
+++ b/cdlib/algorithms/crisp_partition.py
@@ -1,4 +1,4 @@
-missing_packages={}
+missing_packages=set()
 
 try:
     import infomap as imp
@@ -2491,7 +2491,7 @@ def scd(
             raise ModuleNotFoundError(
                 "Optional dependency not satisfied: install karateclub to use the selected feature."
             )
-        
+
     g = convert_graph_formats(g_original, nx.Graph)
     model = SCD(iterations=iterations, eps=eps, seed=seed)
     model.fit(g)

From b43c614902d94b3031cb32fc11c8a526dbe9ce62 Mon Sep 17 00:00:00 2001
From: Cazabet Remy <remy.cazabet@gmail.com>
Date: Wed, 2 Mar 2022 22:34:24 +0100
Subject: [PATCH 03/23] bug fix

---
 cdlib/algorithms/crisp_partition.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/cdlib/algorithms/crisp_partition.py b/cdlib/algorithms/crisp_partition.py
index 200e810b..1f2421e8 100644
--- a/cdlib/algorithms/crisp_partition.py
+++ b/cdlib/algorithms/crisp_partition.py
@@ -3,13 +3,13 @@
 try:
     import infomap as imp
 except ModuleNotFoundError:
-    missing_packages.append("infomap")
+    missing_packages.add("infomap")
     imp = None
 
 try:
     from wurlitzer import pipes
 except ModuleNotFoundError:
-    missing_packages.append("wurlitzer")
+    missing_packages.add("wurlitzer")
     pipes = None
 
 try:
@@ -20,20 +20,20 @@
 try:
     import leidenalg
 except ModuleNotFoundError:
-    missing_packages.append("leidenalg")
+    missing_packages.add("leidenalg")
     leidenalg = None
 
 try:
     import graph_tool.all as gt
 except ModuleNotFoundError:
-    missing_packages.append("graph_tool")
+    missing_packages.add("graph_tool")
     gt = None
 
 try:
     import karateclub as kc
     from karateclub import EdMot, GEMSEC, SCD
 except ModuleNotFoundError:
-    missing_packages.append("karateclub")
+    missing_packages.add("karateclub")
     kc = None
 
 if len(missing_packages)>0:

From a94bcb2a5eaa855bb5a5416c07fd4396a422d7f7 Mon Sep 17 00:00:00 2001
From: Cazabet Remy <remy.cazabet@gmail.com>
Date: Wed, 2 Mar 2022 22:38:45 +0100
Subject: [PATCH 04/23] bug fix

---
 cdlib/algorithms/crisp_partition.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/cdlib/algorithms/crisp_partition.py b/cdlib/algorithms/crisp_partition.py
index 1f2421e8..2f0dcd7c 100644
--- a/cdlib/algorithms/crisp_partition.py
+++ b/cdlib/algorithms/crisp_partition.py
@@ -36,11 +36,12 @@
     missing_packages.add("karateclub")
     kc = None
 
+import warnings
+
 if len(missing_packages)>0:
     warnings.warn(
         "Note: to be able to use all methods, you need to install some additional packages: "+missing_packages
     )
-import warnings
 import numpy as np
 from typing import Callable
 from copy import deepcopy

From 2ba178ce3061ebae0a080a288cbd003459384fab Mon Sep 17 00:00:00 2001
From: Cazabet Remy <remy.cazabet@gmail.com>
Date: Wed, 2 Mar 2022 22:39:51 +0100
Subject: [PATCH 05/23] bug fix

---
 cdlib/algorithms/crisp_partition.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cdlib/algorithms/crisp_partition.py b/cdlib/algorithms/crisp_partition.py
index 2f0dcd7c..f27a4c15 100644
--- a/cdlib/algorithms/crisp_partition.py
+++ b/cdlib/algorithms/crisp_partition.py
@@ -40,7 +40,7 @@
 
 if len(missing_packages)>0:
     warnings.warn(
-        "Note: to be able to use all methods, you need to install some additional packages: "+missing_packages
+        "Note: to be able to use all methods, you need to install some additional packages: "+ str(missing_packages)
     )
 import numpy as np
 from typing import Callable

From 60e2c5b1789790b757d8c243b2243e919607dd58 Mon Sep 17 00:00:00 2001
From: Cazabet Remy <remy.cazabet@gmail.com>
Date: Wed, 2 Mar 2022 22:52:13 +0100
Subject: [PATCH 06/23] added overlapping karateclub

---
 cdlib/algorithms/overlapping_partition.py | 43 +++++++++++++++++++++--
 1 file changed, 41 insertions(+), 2 deletions(-)

diff --git a/cdlib/algorithms/overlapping_partition.py b/cdlib/algorithms/overlapping_partition.py
index e8734377..ad972498 100644
--- a/cdlib/algorithms/overlapping_partition.py
+++ b/cdlib/algorithms/overlapping_partition.py
@@ -1,3 +1,22 @@
+missing_packages=set()
+
+def try_load_karate(init=False):
+    global kc
+    if kc is None:
+        try:
+            from karateclub import DANMF, EgoNetSplitter, NNSED, MNMF, BigClam, SymmNMF
+            kc=True
+        except ModuleNotFoundError:
+            if init==False:
+                raise ModuleNotFoundError(
+                    "Optional dependency not satisfied: install karateclub to use the selected feature."
+                )
+
+kc=None
+try_load_karate(init=True)
+if kc==None:
+    missing_packages.add("karateclub")
+
 try:
     import igraph as ig
 except ModuleNotFoundError:
@@ -12,6 +31,16 @@
 except ModuleNotFoundError:
     ASLPAw = None
 
+
+import warnings
+
+if len(missing_packages)>0:
+    warnings.warn(
+        "Note: to be able to use all methods, you need to install some additional packages: "+ str(missing_packages)
+    )
+
+
+
 from random import sample
 from demon import Demon
 from cdlib.algorithms.internal.NodePerception import NodePerception
@@ -31,7 +60,6 @@
 from cdlib.algorithms.internal.PercoMCV import percoMVC
 from cdlib.algorithms.internal.LPAM import LPAM
 from cdlib.algorithms.internal.core_exp import findCommunities as core_exp_find
-from karateclub import DANMF, EgoNetSplitter, NNSED, MNMF, BigClam, SymmNMF
 from cdlib.algorithms.internal.weightedCommunity import weightedCommunity
 from cdlib.algorithms.internal.LPANNI import LPANNI, GraphGenerator
 from cdlib.algorithms.internal.DCS import main_dcs
@@ -878,7 +906,7 @@ def big_clam(
 
     .. note:: Reference implementation: https://karateclub.readthedocs.io/
     """
-
+    try_load_karate()
     g = convert_graph_formats(g_original, nx.Graph)
 
     model = BigClam(
@@ -949,6 +977,10 @@ def danmf(
 
     .. note:: Reference implementation: https://karateclub.readthedocs.io/
     """
+
+    try_load_karate()
+
+
     g = convert_graph_formats(g_original, nx.Graph)
     model = DANMF(layers, pre_iterations, iterations, seed, lamb)
 
@@ -1012,6 +1044,8 @@ def egonet_splitter(g_original: object, resolution: float = 1.0) -> NodeClusteri
 
     .. note:: Reference implementation: https://karateclub.readthedocs.io/
     """
+    try_load_karate()
+
     g = convert_graph_formats(g_original, nx.Graph)
     model = EgoNetSplitter(resolution=resolution)
 
@@ -1074,6 +1108,9 @@ def nnsed(
 
     .. note:: Reference implementation: https://karateclub.readthedocs.io/
     """
+
+    try_load_karate()
+
     g = convert_graph_formats(g_original, nx.Graph)
     model = NNSED(dimensions=dimensions, iterations=iterations, seed=seed)
     model.fit(g)
@@ -1148,6 +1185,7 @@ def mnmf(
 
     .. note:: Reference implementation: https://karateclub.readthedocs.io/
     """
+    try_load_karate()
     g = convert_graph_formats(g_original, nx.Graph)
     model = MNMF(
         dimensions=dimensions,
@@ -1601,6 +1639,7 @@ def symmnmf(
 
     .. note:: Reference implementation: https://karateclub.readthedocs.io/
     """
+    try_load_karate()
     g = convert_graph_formats(g_original, nx.Graph)
     model = SymmNMF(dimensions=dimensions, iterations=iterations, rho=rho, seed=seed)
     model.fit(g)

From ead627d7d5022b2fbb61f4a4407a0f01efe9318c Mon Sep 17 00:00:00 2001
From: Cazabet Remy <remy.cazabet@gmail.com>
Date: Wed, 2 Mar 2022 22:56:01 +0100
Subject: [PATCH 07/23] bug fix

---
 cdlib/algorithms/crisp_partition.py | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/cdlib/algorithms/crisp_partition.py b/cdlib/algorithms/crisp_partition.py
index f27a4c15..ac30f212 100644
--- a/cdlib/algorithms/crisp_partition.py
+++ b/cdlib/algorithms/crisp_partition.py
@@ -39,9 +39,8 @@
 import warnings
 
 if len(missing_packages)>0:
-    warnings.warn(
-        "Note: to be able to use all methods, you need to install some additional packages: "+ str(missing_packages)
-    )
+    print("Note: to be able to use all methods, you need to install some additional packages: ", missing_packages)
+    
 import numpy as np
 from typing import Callable
 from copy import deepcopy

From f42bcecf005ac5e4100a46fe1eb89ef673197314 Mon Sep 17 00:00:00 2001
From: Cazabet Remy <remy.cazabet@gmail.com>
Date: Wed, 2 Mar 2022 23:02:08 +0100
Subject: [PATCH 08/23] louvain_fix colab

---
 cdlib/algorithms/crisp_partition.py | 2 +-
 requirements.txt                    | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/cdlib/algorithms/crisp_partition.py b/cdlib/algorithms/crisp_partition.py
index ac30f212..23081378 100644
--- a/cdlib/algorithms/crisp_partition.py
+++ b/cdlib/algorithms/crisp_partition.py
@@ -40,7 +40,7 @@
 
 if len(missing_packages)>0:
     print("Note: to be able to use all methods, you need to install some additional packages: ", missing_packages)
-    
+
 import numpy as np
 from typing import Callable
 from copy import deepcopy
diff --git a/requirements.txt b/requirements.txt
index f3caa8c4..d9706db6 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -5,7 +5,7 @@ scikit-learn
 tqdm
 networkx>=2.4
 demon
-python-louvain
+python-louvain>=0.16
 nf1
 scipy
 pulp

From 9dd928b2b7918aeed29ccf0660fd3bc0b15d518d Mon Sep 17 00:00:00 2001
From: Cazabet Remy <remy.cazabet@gmail.com>
Date: Wed, 2 Mar 2022 23:08:19 +0100
Subject: [PATCH 09/23] louvain update

---
 cdlib/algorithms/crisp_partition.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/cdlib/algorithms/crisp_partition.py b/cdlib/algorithms/crisp_partition.py
index 23081378..d2b581c7 100644
--- a/cdlib/algorithms/crisp_partition.py
+++ b/cdlib/algorithms/crisp_partition.py
@@ -45,7 +45,8 @@
 from typing import Callable
 from copy import deepcopy
 from cdlib.algorithms.internal import DER
-import community as louvain_modularity
+#import community as louvain_modularity
+from community import community_louvain
 from collections import defaultdict
 from cdlib import NodeClustering, FuzzyNodeClustering
 from cdlib.algorithms.internal.belief_prop import detect_belief_communities
@@ -524,7 +525,7 @@ def louvain(
 
     g = convert_graph_formats(g_original, nx.Graph)
 
-    coms = louvain_modularity.best_partition(
+    coms = community_louvain.best_partition(
         g, weight=weight, resolution=resolution, randomize=randomize
     )
 

From ef84d37de96fc905ae7037799ad14c1e64db09ce Mon Sep 17 00:00:00 2001
From: Cazabet Remy <remy.cazabet@gmail.com>
Date: Wed, 2 Mar 2022 23:12:41 +0100
Subject: [PATCH 10/23] bug fix

---
 cdlib/algorithms/crisp_partition.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cdlib/algorithms/crisp_partition.py b/cdlib/algorithms/crisp_partition.py
index d2b581c7..2e6cfcdb 100644
--- a/cdlib/algorithms/crisp_partition.py
+++ b/cdlib/algorithms/crisp_partition.py
@@ -1068,7 +1068,7 @@ def infomap(g_original: object, flags: str = "") -> NodeClustering:
 
     .. note:: Infomap Python API documentation: https://mapequation.github.io/infomap/python/
     """
-
+    global imp,pipes
     if imp is None:
         try:
             import infomap as imp

From b128bf9f7cc88ce65df2e6505f477992b71a06c9 Mon Sep 17 00:00:00 2001
From: Cazabet Remy <remy.cazabet@gmail.com>
Date: Wed, 2 Mar 2022 23:21:45 +0100
Subject: [PATCH 11/23] bug fix

---
 cdlib/algorithms/crisp_partition.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/cdlib/algorithms/crisp_partition.py b/cdlib/algorithms/crisp_partition.py
index 2e6cfcdb..a3619357 100644
--- a/cdlib/algorithms/crisp_partition.py
+++ b/cdlib/algorithms/crisp_partition.py
@@ -584,7 +584,7 @@ def leiden(
 
     .. note:: Reference implementation: https://github.com/vtraag/leidenalg
     """
-
+    global leidenalg
     if ig is None or leidenalg is None:
         try:
             import leidenalg
@@ -1744,7 +1744,7 @@ def edmot(
 
     .. note:: Reference implementation: https://karateclub.readthedocs.io/
     """
-
+    global kc
     if kc is None:
         try:
             from karateclub import EdMot, GEMSEC, SCD
@@ -2397,6 +2397,7 @@ def gemsec(
 
     .. note:: Reference implementation: https://karateclub.readthedocs.io/
     """
+    global kc
     if kc is None:
         try:
             from karateclub import EdMot, GEMSEC, SCD

From 6112ea62f0e8f6a44f7ea608d389813784e26d50 Mon Sep 17 00:00:00 2001
From: Cazabet Remy <remy.cazabet@gmail.com>
Date: Wed, 2 Mar 2022 23:54:58 +0100
Subject: [PATCH 12/23] bug fix

---
 cdlib/algorithms/crisp_partition.py       | 1 +
 cdlib/algorithms/overlapping_partition.py | 5 +----
 2 files changed, 2 insertions(+), 4 deletions(-)

diff --git a/cdlib/algorithms/crisp_partition.py b/cdlib/algorithms/crisp_partition.py
index a3619357..313ce7f5 100644
--- a/cdlib/algorithms/crisp_partition.py
+++ b/cdlib/algorithms/crisp_partition.py
@@ -2485,6 +2485,7 @@ def scd(
 
     .. note:: Reference implementation: https://karateclub.readthedocs.io/
     """
+    global kc
     if kc is None:
         try:
             from karateclub import EdMot, GEMSEC, SCD
diff --git a/cdlib/algorithms/overlapping_partition.py b/cdlib/algorithms/overlapping_partition.py
index ad972498..441875e7 100644
--- a/cdlib/algorithms/overlapping_partition.py
+++ b/cdlib/algorithms/overlapping_partition.py
@@ -34,10 +34,7 @@ def try_load_karate(init=False):
 
 import warnings
 
-if len(missing_packages)>0:
-    warnings.warn(
-        "Note: to be able to use all methods, you need to install some additional packages: "+ str(missing_packages)
-    )
+
 
 
 

From 70a145a842e83afccbd26aef84e4e9755ef87f29 Mon Sep 17 00:00:00 2001
From: Cazabet Remy <remy.cazabet@gmail.com>
Date: Thu, 3 Mar 2022 00:03:44 +0100
Subject: [PATCH 13/23] bug fix

---
 cdlib/algorithms/crisp_partition.py | 29 +++++++++++------------------
 1 file changed, 11 insertions(+), 18 deletions(-)

diff --git a/cdlib/algorithms/crisp_partition.py b/cdlib/algorithms/crisp_partition.py
index 313ce7f5..1bd7d600 100644
--- a/cdlib/algorithms/crisp_partition.py
+++ b/cdlib/algorithms/crisp_partition.py
@@ -30,17 +30,16 @@
     gt = None
 
 try:
-    import karateclub as kc
-    from karateclub import EdMot, GEMSEC, SCD
+    import karateclub
 except ModuleNotFoundError:
     missing_packages.add("karateclub")
-    kc = None
 
 import warnings
 
 if len(missing_packages)>0:
     print("Note: to be able to use all methods, you need to install some additional packages: ", missing_packages)
 
+import sys
 import numpy as np
 from typing import Callable
 from copy import deepcopy
@@ -1744,18 +1743,16 @@ def edmot(
 
     .. note:: Reference implementation: https://karateclub.readthedocs.io/
     """
-    global kc
-    if kc is None:
+    if "karateclub" not in sys.modules:
         try:
-            from karateclub import EdMot, GEMSEC, SCD
-            kc=True
+            import karateclub
         except ModuleNotFoundError:
             raise ModuleNotFoundError(
                 "Optional dependency not satisfied: install karateclub to use the selected feature."
             )
 
     g = convert_graph_formats(g_original, nx.Graph)
-    model = EdMot(component_count=2, cutoff=10)
+    model = karateclub.EdMot(component_count=2, cutoff=10)
 
     model.fit(g)
     members = model.get_memberships()
@@ -2397,18 +2394,16 @@ def gemsec(
 
     .. note:: Reference implementation: https://karateclub.readthedocs.io/
     """
-    global kc
-    if kc is None:
+    if "karateclub" not in sys.modules:
         try:
-            from karateclub import EdMot, GEMSEC, SCD
-            kc = True
+            import karateclub
         except ModuleNotFoundError:
             raise ModuleNotFoundError(
                 "Optional dependency not satisfied: install karateclub to use the selected feature."
             )
 
     g = convert_graph_formats(g_original, nx.Graph)
-    model = GEMSEC(
+    model = karateclub.GEMSEC(
         walk_number=walk_number,
         walk_length=walk_length,
         dimensions=dimensions,
@@ -2485,18 +2480,16 @@ def scd(
 
     .. note:: Reference implementation: https://karateclub.readthedocs.io/
     """
-    global kc
-    if kc is None:
+    if "karateclub" not in sys.modules:
         try:
-            from karateclub import EdMot, GEMSEC, SCD
-            kc=True
+            import karateclub
         except ModuleNotFoundError:
             raise ModuleNotFoundError(
                 "Optional dependency not satisfied: install karateclub to use the selected feature."
             )
 
     g = convert_graph_formats(g_original, nx.Graph)
-    model = SCD(iterations=iterations, eps=eps, seed=seed)
+    model = karateclub.SCD(iterations=iterations, eps=eps, seed=seed)
     model.fit(g)
     members = model.get_memberships()
 

From 2eee970d27bd50c6a03104ad6ff9a3234f553d38 Mon Sep 17 00:00:00 2001
From: Cazabet Remy <remy.cazabet@gmail.com>
Date: Thu, 3 Mar 2022 00:08:54 +0100
Subject: [PATCH 14/23] bug fix

---
 cdlib/algorithms/crisp_partition.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/cdlib/algorithms/crisp_partition.py b/cdlib/algorithms/crisp_partition.py
index 1bd7d600..c7748b03 100644
--- a/cdlib/algorithms/crisp_partition.py
+++ b/cdlib/algorithms/crisp_partition.py
@@ -1743,6 +1743,8 @@ def edmot(
 
     .. note:: Reference implementation: https://karateclub.readthedocs.io/
     """
+    global karateclub
+
     if "karateclub" not in sys.modules:
         try:
             import karateclub
@@ -2394,6 +2396,7 @@ def gemsec(
 
     .. note:: Reference implementation: https://karateclub.readthedocs.io/
     """
+    global karateclub
     if "karateclub" not in sys.modules:
         try:
             import karateclub
@@ -2480,6 +2483,8 @@ def scd(
 
     .. note:: Reference implementation: https://karateclub.readthedocs.io/
     """
+    global karateclub
+
     if "karateclub" not in sys.modules:
         try:
             import karateclub

From 5d371140d819be3149110adbf8f4c89ec7aad743 Mon Sep 17 00:00:00 2001
From: Cazabet Remy <remy.cazabet@gmail.com>
Date: Thu, 3 Mar 2022 00:16:38 +0100
Subject: [PATCH 15/23] change in viz to allow working in colab

---
 cdlib/algorithms/overlapping_partition.py | 8 +++-----
 cdlib/viz/networks.py                     | 4 ++--
 2 files changed, 5 insertions(+), 7 deletions(-)

diff --git a/cdlib/algorithms/overlapping_partition.py b/cdlib/algorithms/overlapping_partition.py
index 441875e7..847bfff3 100644
--- a/cdlib/algorithms/overlapping_partition.py
+++ b/cdlib/algorithms/overlapping_partition.py
@@ -1,18 +1,16 @@
 missing_packages=set()
 
 def try_load_karate(init=False):
-    global kc
-    if kc is None:
+    global karateclub
+    if "karateclub" not in sys.modules:
         try:
-            from karateclub import DANMF, EgoNetSplitter, NNSED, MNMF, BigClam, SymmNMF
-            kc=True
+            import karateclub #import DANMF, EgoNetSplitter, NNSED, MNMF, BigClam, SymmNMF
         except ModuleNotFoundError:
             if init==False:
                 raise ModuleNotFoundError(
                     "Optional dependency not satisfied: install karateclub to use the selected feature."
                 )
 
-kc=None
 try_load_karate(init=True)
 if kc==None:
     missing_packages.add("karateclub")
diff --git a/cdlib/viz/networks.py b/cdlib/viz/networks.py
index 0f9cffc9..ec8eb8bb 100644
--- a/cdlib/viz/networks.py
+++ b/cdlib/viz/networks.py
@@ -5,7 +5,7 @@
 import networkx as nx
 from cdlib import NodeClustering
 from cdlib.utils import convert_graph_formats
-from community import induced_graph
+from community import community_louvain
 
 __all__ = ["plot_network_clusters", "plot_community_graph"]
 
@@ -202,7 +202,7 @@ def plot_community_graph(
     s = nx.subgraph(graph, node_to_com.keys())
 
     # algorithms graph construction
-    c_graph = induced_graph(node_to_com, s)
+    c_graph = community_louvain.induced_graph(node_to_com, s)
     node_cms = [[node] for node in c_graph.nodes()]
 
     return plot_network_clusters(

From 7753cb7c16e95cd6dd4a5e093b8367c441e97ded Mon Sep 17 00:00:00 2001
From: Cazabet Remy <remy.cazabet@gmail.com>
Date: Thu, 3 Mar 2022 00:18:58 +0100
Subject: [PATCH 16/23] bug fix

---
 cdlib/algorithms/overlapping_partition.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/cdlib/algorithms/overlapping_partition.py b/cdlib/algorithms/overlapping_partition.py
index 847bfff3..9d1d7c49 100644
--- a/cdlib/algorithms/overlapping_partition.py
+++ b/cdlib/algorithms/overlapping_partition.py
@@ -1,5 +1,6 @@
 missing_packages=set()
 
+import sys
 def try_load_karate(init=False):
     global karateclub
     if "karateclub" not in sys.modules:
@@ -12,7 +13,7 @@ def try_load_karate(init=False):
                 )
 
 try_load_karate(init=True)
-if kc==None:
+if "karateclub" not in sys.modules:
     missing_packages.add("karateclub")
 
 try:

From 82a9bd8459e71c03a726eec2a643a6cdf10873fd Mon Sep 17 00:00:00 2001
From: Cazabet Remy <remy.cazabet@gmail.com>
Date: Thu, 3 Mar 2022 17:50:25 +0100
Subject: [PATCH 17/23] V1 light

-Removed infomap, leidenalg, karateclub from defaults
-Correct bug with louvain in google colab
-Allow to install a package after loading cdlib (try reloading package when calling the function)
-Display missing package at startup
---
 cdlib/algorithms/overlapping_partition.py | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/cdlib/algorithms/overlapping_partition.py b/cdlib/algorithms/overlapping_partition.py
index 9d1d7c49..702502fb 100644
--- a/cdlib/algorithms/overlapping_partition.py
+++ b/cdlib/algorithms/overlapping_partition.py
@@ -905,7 +905,7 @@ def big_clam(
     try_load_karate()
     g = convert_graph_formats(g_original, nx.Graph)
 
-    model = BigClam(
+    model = karateclub.BigClam(
         dimensions=dimensions, iterations=iterations, learning_rate=learning_rate
     )
     model.fit(g)
@@ -978,7 +978,7 @@ def danmf(
 
 
     g = convert_graph_formats(g_original, nx.Graph)
-    model = DANMF(layers, pre_iterations, iterations, seed, lamb)
+    model = karateclub.DANMF(layers, pre_iterations, iterations, seed, lamb)
 
     mapping = {node: i for i, node in enumerate(g.nodes())}
     rev = {i: node for node, i in mapping.items()}
@@ -1043,7 +1043,7 @@ def egonet_splitter(g_original: object, resolution: float = 1.0) -> NodeClusteri
     try_load_karate()
 
     g = convert_graph_formats(g_original, nx.Graph)
-    model = EgoNetSplitter(resolution=resolution)
+    model = karateclub.EgoNetSplitter(resolution=resolution)
 
     mapping = {node: i for i, node in enumerate(g.nodes())}
     rev = {i: node for node, i in mapping.items()}
@@ -1108,7 +1108,7 @@ def nnsed(
     try_load_karate()
 
     g = convert_graph_formats(g_original, nx.Graph)
-    model = NNSED(dimensions=dimensions, iterations=iterations, seed=seed)
+    model = karateclub.NNSED(dimensions=dimensions, iterations=iterations, seed=seed)
     model.fit(g)
     members = model.get_memberships()
 
@@ -1183,7 +1183,7 @@ def mnmf(
     """
     try_load_karate()
     g = convert_graph_formats(g_original, nx.Graph)
-    model = MNMF(
+    model = karateclub.MNMF(
         dimensions=dimensions,
         clusters=clusters,
         lambd=lambd,
@@ -1637,7 +1637,7 @@ def symmnmf(
     """
     try_load_karate()
     g = convert_graph_formats(g_original, nx.Graph)
-    model = SymmNMF(dimensions=dimensions, iterations=iterations, rho=rho, seed=seed)
+    model = karateclub.SymmNMF(dimensions=dimensions, iterations=iterations, rho=rho, seed=seed)
     model.fit(g)
     members = model.get_memberships()
 

From 0caf0ee432ed0bbf394c22ee1c2e171fc8c83f04 Mon Sep 17 00:00:00 2001
From: Cazabet Remy <remy.cazabet@gmail.com>
Date: Thu, 3 Mar 2022 18:56:56 +0100
Subject: [PATCH 18/23] fixed some bugs

---
 cdlib/algorithms/bipartite_clustering.py  | 39 +++++++++++++++++------
 cdlib/algorithms/crisp_partition.py       |  2 +-
 cdlib/algorithms/overlapping_partition.py | 10 ++++--
 3 files changed, 38 insertions(+), 13 deletions(-)

diff --git a/cdlib/algorithms/bipartite_clustering.py b/cdlib/algorithms/bipartite_clustering.py
index 151744fc..6816af7a 100644
--- a/cdlib/algorithms/bipartite_clustering.py
+++ b/cdlib/algorithms/bipartite_clustering.py
@@ -1,15 +1,18 @@
 from cdlib import BiNodeClustering
+missing_packages=set()
 
 import networkx as nx
 
 try:
     import infomap as imp
 except ModuleNotFoundError:
+    missing_packages.add("infomap")
     imp = None
 
 try:
     from wurlitzer import pipes
 except ModuleNotFoundError:
+    missing_packages.add("wurlitzer")
     pipes = None
 
 try:
@@ -20,8 +23,13 @@
 try:
     import leidenalg
 except ModuleNotFoundError:
+    missing_packages.add("leidenalg")
     leidenalg = None
 
+if len(missing_packages)>0:
+    print("Note: to be able to use all bipartite methods, you need to install some additional packages: ", missing_packages)
+
+
 from cdlib.utils import convert_graph_formats
 from collections import defaultdict
 from cdlib.algorithms.internal.pycondor import condor_object, initial_community, brim
@@ -123,11 +131,15 @@ def CPM_Bipartite(
 
     .. note:: Reference implementation: https://leidenalg.readthedocs.io/en/stable/multiplex.html?highlight=bipartite#bipartite
     """
+    global leidenalg
     if ig is None or leidenalg is None:
-        raise ModuleNotFoundError(
-            "Optional dependency not satisfied: install igraph and leidenalg to use the "
-            "selected feature."
-        )
+        try:
+            import leidenalg
+        except ModuleNotFoundError:
+            raise ModuleNotFoundError(
+                "Optional dependency not satisfied: install igraph and leidenalg to use the "
+                "selected feature."
+            )
 
     g = convert_graph_formats(g_original, ig.Graph)
 
@@ -201,14 +213,21 @@ def infomap_bipartite(g_original: object, flags: str = "") -> BiNodeClustering:
     .. note:: Infomap Python API documentation: https://mapequation.github.io/infomap/python/
     """
 
+    global imp, pipes
     if imp is None:
-        raise ModuleNotFoundError(
-            "Optional dependency not satisfied: install infomap to use the selected feature."
-        )
+        try:
+            import infomap as imp
+        except ModuleNotFoundError:
+            raise ModuleNotFoundError(
+                "Optional dependency not satisfied: install infomap to use the selected feature."
+            )
     if pipes is None:
-        raise ModuleNotFoundError(
-            "Optional dependency not satisfied: install package wurlitzer to use infomap."
-        )
+        try:
+            from wurlitzer import pipes
+        except ModuleNotFoundError:
+            raise ModuleNotFoundError(
+                "Optional dependency not satisfied: install package wurlitzer to use infomap."
+            )
 
     g = convert_graph_formats(g_original, nx.Graph)
 
diff --git a/cdlib/algorithms/crisp_partition.py b/cdlib/algorithms/crisp_partition.py
index c7748b03..3956cf63 100644
--- a/cdlib/algorithms/crisp_partition.py
+++ b/cdlib/algorithms/crisp_partition.py
@@ -37,7 +37,7 @@
 import warnings
 
 if len(missing_packages)>0:
-    print("Note: to be able to use all methods, you need to install some additional packages: ", missing_packages)
+    print("Note: to be able to use all crisp methods, you need to install some additional packages: ", missing_packages)
 
 import sys
 import numpy as np
diff --git a/cdlib/algorithms/overlapping_partition.py b/cdlib/algorithms/overlapping_partition.py
index 702502fb..37a4ffe0 100644
--- a/cdlib/algorithms/overlapping_partition.py
+++ b/cdlib/algorithms/overlapping_partition.py
@@ -1,11 +1,12 @@
 missing_packages=set()
-
 import sys
+
 def try_load_karate(init=False):
     global karateclub
-    if "karateclub" not in sys.modules:
+    if init==True or "karateclub" not in sys.modules:
         try:
             import karateclub #import DANMF, EgoNetSplitter, NNSED, MNMF, BigClam, SymmNMF
+
         except ModuleNotFoundError:
             if init==False:
                 raise ModuleNotFoundError(
@@ -14,8 +15,10 @@ def try_load_karate(init=False):
 
 try_load_karate(init=True)
 if "karateclub" not in sys.modules:
+    karateclub=None
     missing_packages.add("karateclub")
 
+
 try:
     import igraph as ig
 except ModuleNotFoundError:
@@ -29,9 +32,12 @@ def try_load_karate(init=False):
     from ASLPAw_package import ASLPAw
 except ModuleNotFoundError:
     ASLPAw = None
+    missing_packages.add("ASLPAw")
 
 
 import warnings
+if len(missing_packages)>0:
+    print("Note: to be able to use all overlapping methods, you need to install some additional packages: ", missing_packages)
 
 
 

From 13622a5e58389e1632fe7e8f6ac7cac8ecd14d2b Mon Sep 17 00:00:00 2001
From: Cazabet Remy <remy.cazabet@gmail.com>
Date: Fri, 4 Mar 2022 16:18:04 +0100
Subject: [PATCH 19/23] updated requirements and setup.py

---
 requirements.txt          | 1 -
 requirements_complete.txt | 4 ----
 requirements_optional.txt | 4 ++++
 setup.py                  | 2 +-
 4 files changed, 5 insertions(+), 6 deletions(-)
 delete mode 100644 requirements_complete.txt

diff --git a/requirements.txt b/requirements.txt
index d9706db6..229b478c 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -19,7 +19,6 @@ python-igraph
 angel-cd
 pooch
 dynetx
-wurlitzer
 thresholdclustering
 pyclustering
 cython
diff --git a/requirements_complete.txt b/requirements_complete.txt
deleted file mode 100644
index df761dd4..00000000
--- a/requirements_complete.txt
+++ /dev/null
@@ -1,4 +0,0 @@
-karateclub
-leidenalg
-infomap
-wurlitzer
\ No newline at end of file
diff --git a/requirements_optional.txt b/requirements_optional.txt
index 570f339a..c328df25 100644
--- a/requirements_optional.txt
+++ b/requirements_optional.txt
@@ -1,3 +1,7 @@
 GraphRicciCurvature==0.5.2.1
 networkit
 pycombo
+karateclub
+leidenalg
+infomap>=1.3.0
+wurlitzer>=1.0.2
\ No newline at end of file
diff --git a/setup.py b/setup.py
index 786f365c..a60d0484 100644
--- a/setup.py
+++ b/setup.py
@@ -51,7 +51,7 @@
       long_description=long_description,
       long_description_content_type='text/markdown',
       extras_require={
-        'C':  ["infomap>=1.3.0", "wurlitzer>=1.0.2", "GraphRicciCurvature", "networkit", "pycombo"],
+        'C':  ["infomap>=1.3.0", "wurlitzer>=1.0.2", "GraphRicciCurvature", "networkit", "pycombo","leidenalg","karateclub"],
       },
       packages=find_packages(exclude=["*.test", "*.test.*", "test.*", "test", "cdlib.test", "cdlib.test.*"]),
       )

From 72c16e173a1366c210b9300c8d1687c4708df5dc Mon Sep 17 00:00:00 2001
From: Giulio Rossetti <giulio.rossetti@gmail.com>
Date: Tue, 8 Mar 2022 11:25:24 +0100
Subject: [PATCH 20/23] :arrow_up: minor fix

---
 cdlib/algorithms/bipartite_clustering.py  |  19 ++--
 cdlib/algorithms/crisp_partition.py       | 127 ++++++++++++----------
 cdlib/algorithms/overlapping_partition.py | 105 +++++++++---------
 3 files changed, 132 insertions(+), 119 deletions(-)

diff --git a/cdlib/algorithms/bipartite_clustering.py b/cdlib/algorithms/bipartite_clustering.py
index 6816af7a..f608f8ed 100644
--- a/cdlib/algorithms/bipartite_clustering.py
+++ b/cdlib/algorithms/bipartite_clustering.py
@@ -1,7 +1,10 @@
 from cdlib import BiNodeClustering
-missing_packages=set()
-
 import networkx as nx
+from cdlib.utils import convert_graph_formats
+from collections import defaultdict
+from cdlib.algorithms.internal.pycondor import condor_object, initial_community, brim
+
+missing_packages = set()
 
 try:
     import infomap as imp
@@ -26,13 +29,11 @@
     missing_packages.add("leidenalg")
     leidenalg = None
 
-if len(missing_packages)>0:
-    print("Note: to be able to use all bipartite methods, you need to install some additional packages: ", missing_packages)
-
-
-from cdlib.utils import convert_graph_formats
-from collections import defaultdict
-from cdlib.algorithms.internal.pycondor import condor_object, initial_community, brim
+if len(missing_packages) > 0:
+    print(
+        "Note: to be able to use all bipartite methods, you need to install some additional packages: ",
+        missing_packages,
+    )
 
 __all__ = ["bimlpa", "CPM_Bipartite", "infomap_bipartite", "condor"]
 
diff --git a/cdlib/algorithms/crisp_partition.py b/cdlib/algorithms/crisp_partition.py
index 3956cf63..0be2dcba 100644
--- a/cdlib/algorithms/crisp_partition.py
+++ b/cdlib/algorithms/crisp_partition.py
@@ -1,50 +1,10 @@
-missing_packages=set()
-
-try:
-    import infomap as imp
-except ModuleNotFoundError:
-    missing_packages.add("infomap")
-    imp = None
-
-try:
-    from wurlitzer import pipes
-except ModuleNotFoundError:
-    missing_packages.add("wurlitzer")
-    pipes = None
-
-try:
-    import igraph as ig
-except ModuleNotFoundError:
-    ig = None
-
-try:
-    import leidenalg
-except ModuleNotFoundError:
-    missing_packages.add("leidenalg")
-    leidenalg = None
-
-try:
-    import graph_tool.all as gt
-except ModuleNotFoundError:
-    missing_packages.add("graph_tool")
-    gt = None
-
-try:
-    import karateclub
-except ModuleNotFoundError:
-    missing_packages.add("karateclub")
-
-import warnings
-
-if len(missing_packages)>0:
-    print("Note: to be able to use all crisp methods, you need to install some additional packages: ", missing_packages)
-
 import sys
 import numpy as np
 from typing import Callable
 from copy import deepcopy
 from cdlib.algorithms.internal import DER
-#import community as louvain_modularity
+
+# import community as louvain_modularity
 from community import community_louvain
 from collections import defaultdict
 from cdlib import NodeClustering, FuzzyNodeClustering
@@ -73,22 +33,12 @@
 from cdlib.algorithms.internal.principled import principled
 from cdlib.algorithms.internal.MCODE import m_code
 from cdlib.algorithms.internal.RSC import rsc_evaluate_graph
-
-try:
-    from GraphRicciCurvature.OllivierRicci import OllivierRicci
-except ModuleNotFoundError:
-    OllivierRicci = None
-
-try:
-    import pycombo as pycombo_part
-except ModuleNotFoundError:
-    pycombo_part = None
+import warnings
 
 import markov_clustering as mc
 from chinese_whispers import chinese_whispers as cw
 from chinese_whispers import aggregate_clusters
 from thresholdclustering.thresholdclustering import best_partition as th_best_partition
-
 import networkx as nx
 
 from cdlib.utils import (
@@ -98,6 +48,59 @@
     nx_node_integer_mapping,
 )
 
+missing_packages = set()
+
+try:
+    import infomap as imp
+except ModuleNotFoundError:
+    missing_packages.add("infomap")
+    imp = None
+
+try:
+    from wurlitzer import pipes
+except ModuleNotFoundError:
+    missing_packages.add("wurlitzer")
+    pipes = None
+
+try:
+    import igraph as ig
+except ModuleNotFoundError:
+    ig = None
+
+try:
+    import leidenalg
+except ModuleNotFoundError:
+    missing_packages.add("leidenalg")
+    leidenalg = None
+
+try:
+    import graph_tool.all as gt
+except ModuleNotFoundError:
+    missing_packages.add("graph_tool")
+    gt = None
+
+try:
+    import karateclub
+except ModuleNotFoundError:
+    missing_packages.add("karateclub")
+
+
+if len(missing_packages) > 0:
+    print(
+        "Note: to be able to use all crisp methods, you need to install some additional packages: ",
+        missing_packages,
+    )
+
+try:
+    from GraphRicciCurvature.OllivierRicci import OllivierRicci
+except ModuleNotFoundError:
+    OllivierRicci = None
+
+try:
+    import pycombo as pycombo_part
+except ModuleNotFoundError:
+    pycombo_part = None
+
 __all__ = [
     "louvain",
     "leiden",
@@ -1067,7 +1070,7 @@ def infomap(g_original: object, flags: str = "") -> NodeClustering:
 
     .. note:: Infomap Python API documentation: https://mapequation.github.io/infomap/python/
     """
-    global imp,pipes
+    global imp, pipes
     if imp is None:
         try:
             import infomap as imp
@@ -1469,12 +1472,15 @@ def sbm_dl(
 
     .. note:: Implementation from graph-tool library, please report to https://graph-tool.skewed.de for details
     """
+
     if gt is None:
         raise Exception(
             "===================================================== \n"
             "The graph-tool library seems not to be installed (or incorrectly installed). \n"
-            "Please check installation procedure there https://git.skewed.de/count0/graph-tool/wikis/installation-instructions#native-installation \n"
-            "on linux/mac, you can use package managers to do so(apt-get install python3-graph-tool, brew install graph-tool, etc.)"
+            "Please check installation procedure there "
+            "https://git.skewed.de/count0/graph-tool/wikis/installation-instructions#native-installation \n"
+            "on linux/mac, you can use package managers to do so "
+            "(apt-get install python3-graph-tool, brew install graph-tool, etc.)"
         )
     gt_g = convert_graph_formats(g_original, nx.Graph)
     gt_g, label_map = __from_nx_to_graph_tool(gt_g)
@@ -1522,6 +1528,8 @@ def sbm_dl_nested(
 
     .. note:: Implementation from graph-tool library, please report to https://graph-tool.skewed.de for details
     """
+    global gt
+
     if gt is None:
         try:
             import graph_tool.all as gt
@@ -1529,9 +1537,12 @@ def sbm_dl_nested(
             raise Exception(
                 "===================================================== \n"
                 "The graph-tool library seems not to be installed (or incorrectly installed). \n"
-                "Please check installation procedure there https://git.skewed.de/count0/graph-tool/wikis/installation-instructions#native-installation \n"
-                "on linux/mac, you can use package managers to do so(apt-get install python3-graph-tool, brew install graph-tool, etc.)"
+                "Please check installation procedure "
+                "there https://git.skewed.de/count0/graph-tool/wikis/installation-instructions#native-installation \n"
+                "on linux/mac, you can use package managers to do so(apt-get install python3-graph-tool, "
+                "brew install graph-tool, etc.)"
             )
+
     gt_g = convert_graph_formats(g_original, nx.Graph)
     gt_g, label_map = __from_nx_to_graph_tool(gt_g)
     state = gt.minimize_nested_blockmodel_dl(gt_g)
diff --git a/cdlib/algorithms/overlapping_partition.py b/cdlib/algorithms/overlapping_partition.py
index 37a4ffe0..16db1cea 100644
--- a/cdlib/algorithms/overlapping_partition.py
+++ b/cdlib/algorithms/overlapping_partition.py
@@ -1,48 +1,4 @@
-missing_packages=set()
 import sys
-
-def try_load_karate(init=False):
-    global karateclub
-    if init==True or "karateclub" not in sys.modules:
-        try:
-            import karateclub #import DANMF, EgoNetSplitter, NNSED, MNMF, BigClam, SymmNMF
-
-        except ModuleNotFoundError:
-            if init==False:
-                raise ModuleNotFoundError(
-                    "Optional dependency not satisfied: install karateclub to use the selected feature."
-                )
-
-try_load_karate(init=True)
-if "karateclub" not in sys.modules:
-    karateclub=None
-    missing_packages.add("karateclub")
-
-
-try:
-    import igraph as ig
-except ModuleNotFoundError:
-    ig = None
-try:
-    from angel import Angel
-except ModuleNotFoundError:
-    Angel = None
-
-try:
-    from ASLPAw_package import ASLPAw
-except ModuleNotFoundError:
-    ASLPAw = None
-    missing_packages.add("ASLPAw")
-
-
-import warnings
-if len(missing_packages)>0:
-    print("Note: to be able to use all overlapping methods, you need to install some additional packages: ", missing_packages)
-
-
-
-
-
 from random import sample
 from demon import Demon
 from cdlib.algorithms.internal.NodePerception import NodePerception
@@ -76,6 +32,50 @@ def try_load_karate(init=False):
     endntm_find_overlap_cluster,
     endntm_evalFuction,
 )
+import warnings
+
+missing_packages = set()
+
+
+def __try_load_karate(init=False):
+    global karateclub
+    if init == True or "karateclub" not in sys.modules:
+        try:
+            import karateclub
+
+        except ModuleNotFoundError:
+            if not init:
+                raise ModuleNotFoundError(
+                    "Optional dependency not satisfied: install karateclub to use the selected feature."
+                )
+
+
+__try_load_karate(init=True)
+if "karateclub" not in sys.modules:
+    karateclub = None
+    missing_packages.add("karateclub")
+
+
+try:
+    import igraph as ig
+except ModuleNotFoundError:
+    ig = None
+try:
+    from angel import Angel
+except ModuleNotFoundError:
+    Angel = None
+
+try:
+    from ASLPAw_package import ASLPAw
+except ModuleNotFoundError:
+    ASLPAw = None
+    missing_packages.add("ASLPAw")
+
+if len(missing_packages) > 0:
+    print(
+        "Note: to be able to use all overlapping methods, you need to install some additional packages: ",
+        missing_packages,
+    )
 
 __all__ = [
     "ego_networks",
@@ -908,7 +908,7 @@ def big_clam(
 
     .. note:: Reference implementation: https://karateclub.readthedocs.io/
     """
-    try_load_karate()
+    __try_load_karate()
     g = convert_graph_formats(g_original, nx.Graph)
 
     model = karateclub.BigClam(
@@ -980,8 +980,7 @@ def danmf(
     .. note:: Reference implementation: https://karateclub.readthedocs.io/
     """
 
-    try_load_karate()
-
+    __try_load_karate()
 
     g = convert_graph_formats(g_original, nx.Graph)
     model = karateclub.DANMF(layers, pre_iterations, iterations, seed, lamb)
@@ -1046,7 +1045,7 @@ def egonet_splitter(g_original: object, resolution: float = 1.0) -> NodeClusteri
 
     .. note:: Reference implementation: https://karateclub.readthedocs.io/
     """
-    try_load_karate()
+    __try_load_karate()
 
     g = convert_graph_formats(g_original, nx.Graph)
     model = karateclub.EgoNetSplitter(resolution=resolution)
@@ -1111,7 +1110,7 @@ def nnsed(
     .. note:: Reference implementation: https://karateclub.readthedocs.io/
     """
 
-    try_load_karate()
+    __try_load_karate()
 
     g = convert_graph_formats(g_original, nx.Graph)
     model = karateclub.NNSED(dimensions=dimensions, iterations=iterations, seed=seed)
@@ -1187,7 +1186,7 @@ def mnmf(
 
     .. note:: Reference implementation: https://karateclub.readthedocs.io/
     """
-    try_load_karate()
+    __try_load_karate()
     g = convert_graph_formats(g_original, nx.Graph)
     model = karateclub.MNMF(
         dimensions=dimensions,
@@ -1641,9 +1640,11 @@ def symmnmf(
 
     .. note:: Reference implementation: https://karateclub.readthedocs.io/
     """
-    try_load_karate()
+    __try_load_karate()
     g = convert_graph_formats(g_original, nx.Graph)
-    model = karateclub.SymmNMF(dimensions=dimensions, iterations=iterations, rho=rho, seed=seed)
+    model = karateclub.SymmNMF(
+        dimensions=dimensions, iterations=iterations, rho=rho, seed=seed
+    )
     model.fit(g)
     members = model.get_memberships()
 

From b473564a4804ad93e2496e91c60ba722549a9209 Mon Sep 17 00:00:00 2001
From: Giulio Rossetti <giulio.rossetti@gmail.com>
Date: Tue, 8 Mar 2022 14:08:08 +0100
Subject: [PATCH 21/23] :arrow_up: v0.2.6

---
 conda/meta.yaml | 5 +----
 docs/conf.py    | 4 ++--
 environment.yml | 4 ----
 setup.py        | 2 +-
 4 files changed, 4 insertions(+), 11 deletions(-)

diff --git a/conda/meta.yaml b/conda/meta.yaml
index 33400fe4..7d3780ab 100644
--- a/conda/meta.yaml
+++ b/conda/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "cdlib" %}
-{% set version = "0.2.5" %}
+{% set version = "0.2.6" %}
 
 package:
   name: "{{ name|lower }}"
@@ -45,8 +45,6 @@ requirements:
     - demon
     - dynetx
     - eva_lcd
-    - karateclub
-    - leidenalg
     - markov_clustering
     - matplotlib
     - networkx>=2.4
@@ -65,7 +63,6 @@ requirements:
     - seaborn
     - thresholdclustering
     - tqdm
-    - wurlitzer
 
 test:
   imports:
diff --git a/docs/conf.py b/docs/conf.py
index da37cc17..0c48f392 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -134,9 +134,9 @@ def __getattr__(cls, name):
 # built documents.
 #
 # The short X.Y version.
-version = u"0.2.5"
+version = u"0.2.6"
 # The full version, including alpha/beta/rc tags.
-release = u"0.2.5"
+release = u"0.2.6"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
diff --git a/environment.yml b/environment.yml
index 3b737b64..10eae4d6 100644
--- a/environment.yml
+++ b/environment.yml
@@ -14,17 +14,13 @@ dependencies:
 - seaborn
 - pandas
 - eva_lcd
-- karateclub
 - bimlpa
 - markov_clustering
 - chinese_whispers
 - python-igraph
-- leidenalg
 - angel_cd
 - pooch
 - dynetx
-- python-infomap
-- wurlitzer
 - thresholdclustering
 - pyclustering
 - python-Levenshtein
diff --git a/setup.py b/setup.py
index a60d0484..7ac88ec6 100644
--- a/setup.py
+++ b/setup.py
@@ -18,7 +18,7 @@
 
 
 setup(name='cdlib',
-      version='0.2.5',
+      version='0.2.6',
       license='BSD-Clause-2',
       description='Community Discovery Library',
       url='https://github.com/GiulioRossetti/cdlib',

From a27873b9f0329271541a6ddab429a00e26c0f3a5 Mon Sep 17 00:00:00 2001
From: Giulio Rossetti <giulio.rossetti@gmail.com>
Date: Tue, 8 Mar 2022 15:07:46 +0100
Subject: [PATCH 22/23] :arrow_up: minor fix

---
 cdlib/test/test_community_discovery_models.py | 21 ++++++++++++++++++-
 1 file changed, 20 insertions(+), 1 deletion(-)

diff --git a/cdlib/test/test_community_discovery_models.py b/cdlib/test/test_community_discovery_models.py
index 2e52c8e6..2a73d439 100644
--- a/cdlib/test/test_community_discovery_models.py
+++ b/cdlib/test/test_community_discovery_models.py
@@ -348,6 +348,8 @@ def test_markov_clustering(self):
                 self.assertEqual(type(communities.communities[0][0]), int)
 
     def test_bigClam(self):
+        if karateclub is None:
+            return
         g = nx.karate_club_graph()
         coms = algorithms.big_clam(g)
         self.assertEqual(type(coms.communities), list)
@@ -478,6 +480,8 @@ def test_sbm_nested_dl(self):
                 self.assertEqual(type(coms.communities[0][0]), str)
 
     def test_danmf(self):
+        if karateclub is None:
+            return
         g = get_string_graph()
         coms = algorithms.danmf(g)
         self.assertEqual(type(coms.communities), list)
@@ -486,6 +490,8 @@ def test_danmf(self):
             self.assertEqual(type(coms.communities[0][0]), str)
 
     def test_egonet_splitter(self):
+        if karateclub is None:
+            return
         g = get_string_graph()
         coms = algorithms.egonet_splitter(g)
         self.assertEqual(type(coms.communities), list)
@@ -494,6 +500,8 @@ def test_egonet_splitter(self):
             self.assertEqual(type(coms.communities[0][0]), str)
 
     def test_nnsed(self):
+        if karateclub is None:
+            return
         g = nx.karate_club_graph()
         coms = algorithms.nnsed(g)
         self.assertEqual(type(coms.communities), list)
@@ -502,6 +510,8 @@ def test_nnsed(self):
             self.assertEqual(type(coms.communities[0][0]), int)
 
     def test_mnmf(self):
+        if karateclub is None:
+            return
         g = nx.karate_club_graph()
         coms = algorithms.mnmf(g)
         self.assertEqual(type(coms.communities), list)
@@ -510,6 +520,8 @@ def test_mnmf(self):
             self.assertEqual(type(coms.communities[0][0]), int)
 
     def test_edmot(self):
+        if karateclub is None:
+            return
         g = nx.karate_club_graph()
         coms = algorithms.edmot(g)
         self.assertEqual(type(coms.communities), list)
@@ -625,7 +637,8 @@ def test_CPM_Bipartite(self):
         g = ig.Graph.Erdos_Renyi(n=80, m=600)
         g.vs["type"] = 0
         g.vs[15:]["type"] = 1
-
+        if leidenalg is None:
+            return
         coms = algorithms.CPM_Bipartite(g, 0.3)
         self.assertEqual(type(coms.communities), list)
         if len(coms.communities) > 0:
@@ -640,6 +653,8 @@ def test_CPM_Bipartite(self):
             self.assertEqual(type(coms.communities[0][0]), int)
 
     def test_infomap_Bipartite(self):
+        if infomap is None:
+            return
         g = nx.algorithms.bipartite.random_graph(300, 100, 0.2)
         coms = algorithms.infomap_bipartite(g)
         self.assertEqual(type(coms.communities), list)
@@ -788,6 +803,8 @@ def test_kcut(self):
             print("Kcut error to be checked (conda packaging)")
 
     def test_symmnmf(self):
+        if karateclub is None:
+            return
         G = nx.karate_club_graph()
 
         coms = algorithms.symmnmf(G)
@@ -806,6 +823,8 @@ def test_scd(self):
             self.assertEqual(type(coms.communities[0][0]), int)
 
     def test_gemsec(self):
+        if karateclub is None:
+            return
         G = nx.karate_club_graph()
 
         coms = algorithms.gemsec(G)

From f5d8376de34dd1f4f98fc266f27fcc24aa27f9c4 Mon Sep 17 00:00:00 2001
From: Giulio Rossetti <giulio.rossetti@gmail.com>
Date: Tue, 8 Mar 2022 15:17:15 +0100
Subject: [PATCH 23/23] :arrow_up: minor fix

---
 cdlib/test/test_community_discovery_models.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/cdlib/test/test_community_discovery_models.py b/cdlib/test/test_community_discovery_models.py
index 2a73d439..232b87e4 100644
--- a/cdlib/test/test_community_discovery_models.py
+++ b/cdlib/test/test_community_discovery_models.py
@@ -5,6 +5,11 @@
 import random
 import os
 
+try:
+    import karateclub
+except ModuleNotFoundError:
+    karateclub = None
+
 try:
     import pycombo as pycombo_part
 except ModuleNotFoundError: