Merge pull request #141 from faridrashidi/develop

release v0.2.2

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.2.1
+current_version = 0.2.2
 commit = True
 message = [skip ci] {current_version} → {new_version}
 tag = False

.scripts/ci/install.sh

@@ -32,7 +32,7 @@ elif [[ "$OS" == "ubuntu-latest" ]]; then
   sudo apt-get update -y
   sudo apt-get install libopenblas-base r-base r-base-dev -y
   sudo apt-get install libcurl4-openssl-dev libssl-dev -y
-  pip install rpy2>=3.3.0
+  pip install "rpy2<=3.5.10"
   sudo Rscript -e 'install.packages("devtools")'
   sudo Rscript -e 'install.packages("BiocManager")'
   sudo Rscript -e 'install.packages("tidyverse")'

setup.py

@@ -12,7 +12,7 @@
     __author__ = ", ".join(["Farid Rashidi"])
     __maintainer__ = ", ".join(["Farid Rashidi"])
     __email__ = ", ".join(["[email protected]"])
-    __version__ = "0.2.1"
+    __version__ = "0.2.2"
 
 if platform == "linux" or platform == "linux2":
     os.environ["CC"] = "g++"

trisicell/__init__.py

@@ -7,5 +7,5 @@
 __author__ = ", ".join(["Farid Rashidi"])
 __maintainer__ = ", ".join(["Farid Rashidi"])
 __email__ = ", ".join(["[email protected]"])
-__version__ = "0.2.1"
+__version__ = "0.2.2"
 __all__ = (datasets, io, logg, pl, pp, settings, tl, ul)

trisicell/tl/consensus/_consensus_day.py

@@ -85,7 +85,7 @@ def consensus_day(sc1, sc2):
     soin1 = _find_set_of_internal_nodes(cnt_tree1)
     soin2 = _find_set_of_internal_nodes(cnt_tree2)
 
-    intersection = list(np.intersect1d(soin1, soin2))
+    intersection = [x for x in soin1 if x in soin2]
     intersection_len = list(map(len, intersection))
     valmax = max(intersection_len)
     argmax = intersection_len.index(valmax)

trisicell/tl/solver/_bnb.py

@@ -109,7 +109,7 @@ def all_None(*args):
 
 
 def calculate_column_intersections(matrix, for_loop=False, row_by_row=False):
-    ret = np.empty((matrix.shape[1], matrix.shape[1]), dtype=np.bool)
+    ret = np.empty((matrix.shape[1], matrix.shape[1]), dtype=bool)
     mask_1 = matrix == 1
 
     if for_loop:
@@ -463,7 +463,7 @@ def make_constraints_np_matrix(
                     if not compact_formulation:
                         # len(r01) * len(r10) * (len(r01) * len(r10)) many constraints
                         # will be added
-                        x = np.empty((r01.shape[0] + r10.shape[0], 2), dtype=np.int)
+                        x = np.empty((r01.shape[0] + r10.shape[0], 2), dtype=int)
                         x[: len(r01), 0] = r01
                         x[: len(r01), 1] = p
                         x[-len(r10) :, 0] = r10
@@ -519,7 +519,7 @@ def make_constraints_np_matrix(
         "F map_f2ij zero_vars na_vars hard_constraints col_pair complete_version",
     )
     for ind in range(n_levels):
-        hard_constraints[ind] = np.array(hard_constraints[ind], dtype=np.int)
+        hard_constraints[ind] = np.array(hard_constraints[ind], dtype=int)
     return return_type(
         F, map_f2ij, zero_vars, na_vars, hard_constraints, col_pair, complete_version
     )

trisicell/tl/solver/booster/_booster.py

@@ -13,7 +13,7 @@ def booster(
     solver="SCITE",
     sample_on="muts",
     sample_size=10,
-    n_samples=None,
+    n_samples=10,
     begin_index=0,
     n_jobs=10,
     dep_weight=50,

trisicell/tl/solver/booster/_reconstruct_big_tree.py

@@ -188,7 +188,7 @@ def get_CF_matrix_from_parent_vector(parent, D, alpha, beta):
         best_score = score[ROOT]
         best_mut = ROOT
 
-        muts_to_visit = children[ROOT]
+        muts_to_visit = list(child_id for child_id in children[ROOT])
         while len(muts_to_visit) > 0:
             mut_id = muts_to_visit.pop(0)
             parent_id = parent[mut_id]