From c6395d1295eeda12d3036c4bf15bb23e714af266 Mon Sep 17 00:00:00 2001
From: "Daniel N. Baker" <dnb@cs.jhu.edu>
Date: Mon, 9 Sep 2024 15:14:59 -0700
Subject: [PATCH] Update for more recent pybind11.

---
 bioseq/__init__.py | 4 ----
 bioseq/poa_util.py | 6 +++++-
 requirements.txt   | 6 +++---
 setup.py           | 8 ++++----
 src/poa.cpp        | 2 +-
 5 files changed, 13 insertions(+), 13 deletions(-)

diff --git a/bioseq/__init__.py b/bioseq/__init__.py
index 158cfe0..2c863c8 100644
--- a/bioseq/__init__.py
+++ b/bioseq/__init__.py
@@ -1,9 +1,5 @@
 import cbioseq
 from cbioseq import *
-#from .tax import get_taxid
-#import bioseq.tax as tax
-#import bioseq.decoders as decoders
-#import bioseq.hattn as hattn
 import bioseq.poa_util as poa_util
 import bioseq.softmax as softmax
 import bioseq.loaders as loaders
diff --git a/bioseq/poa_util.py b/bioseq/poa_util.py
index a24f1ab..31ebb6e 100644
--- a/bioseq/poa_util.py
+++ b/bioseq/poa_util.py
@@ -1,6 +1,5 @@
 import networkx as nx
 import torch
-import pytorch_geometric as pyg
 
 class FastxSeq:
     trans = str.maketrans("U", "T")
@@ -61,6 +60,11 @@ def __init__(self, tok, emb_dim=128):
 
     # Takes the output of bioseq.SequenceGraph().matrix() and creates the data for GAT
     def embed_graph(self, mat):
+        try:
+            import pytorch_geometric as pyg
+        except ImportError:
+            print("Cannot import pytorch_geometric")
+            raise
         x, data = self.to_x_data(mat)
         return pyg.Data(x, data)
 
diff --git a/requirements.txt b/requirements.txt
index 4c19dfe..a75594c 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,12 +1,12 @@
-linear_attention_transformer
-fast_transformer_pytorch
 einops
+numpy
+torch
 x-transformers>=0.19
 entmax
-product-key-memory
 local-attention
 numpy
 pybind11==2.7.1
 feedback-transformer-pytorch
 memcnn
 e2cnn
+pysam
diff --git a/setup.py b/setup.py
index db97fa3..2b031e5 100644
--- a/setup.py
+++ b/setup.py
@@ -45,7 +45,7 @@ def cpp_flag(compiler):
     raise RuntimeError('Unsupported compiler -- at least C++11 support '
                        'is needed!')
 
-#full_gomp_path = subprocess.check_output("realpath `$CXX --print-file-name=libgomp.a`", shell=True).decode('utf-8')
+full_gomp_path = subprocess.check_output("realpath `$CXX --print-file-name=libgomp.a`", shell=True).decode('utf-8').strip()
 
 extra_compile_args = ['-march=native',
                       '-Wno-char-subscripts', '-Wno-unused-function', '-Wno-ignored-qualifiers',
@@ -54,7 +54,7 @@ def cpp_flag(compiler):
                       '-lz', '-fopenmp',
                       "-pipe", '-O0', '-DNDEBUG']
 
-extra_link_opts = ["-fopenmp", "-lz", "-lgomp"]
+extra_link_opts = ["-fopenmp", "-lz"]
 
 
 class BuildExt(build_ext):
@@ -90,7 +90,7 @@ def build_extensions(self):
             ext.extra_compile_args = opts
             ext.extra_compile_args += extra_compile_args
             ext.extra_link_args = link_opts + extra_link_opts
-            # ext.extra_objects = [full_gomp_path]
+            ext.extra_objects = [full_gomp_path, "spoa/lib/libspoa.a"]
         build_ext.build_extensions(self)
 
 
@@ -104,7 +104,7 @@ def build_spoa():
     __version__ = "0.1.8"
     build_spoa()
     include_dirs = [get_pybind_include(), get_pybind_include(True), "./", "spoa/include"]
-    ext_modules = [Extension("cbioseq", ["src/bioseq.cpp", "src/poa.cpp", "src/tokenize.cpp", "src/omp.cpp", 'src/fxstats.cpp'], include_dirs=include_dirs, language='c++', extra_objects=["spoa/lib/libspoa.a"])]
+    ext_modules = [Extension("cbioseq", ["src/bioseq.cpp", "src/poa.cpp", "src/tokenize.cpp", "src/omp.cpp", 'src/fxstats.cpp'], include_dirs=include_dirs, language='c++')]
     setup(
         name='bioseq',
         version=__version__,
diff --git a/src/poa.cpp b/src/poa.cpp
index 4e4b6bb..589a90a 100644
--- a/src/poa.cpp
+++ b/src/poa.cpp
@@ -162,7 +162,7 @@ struct SequenceGroup {
             *destPtr++ = (edge.first << 32) >> 32;
             *destPtr++ = edge.second;
         }
-        matrixCOOPy = matrixCOOPy.reshape(std::vector<int64_t>{{static_cast<int64_t>(edges.size()), 3}});
+        matrixCOOPy.resize(std::vector<int64_t>{{static_cast<int64_t>(edges.size()), 3}});
 
         std::transform(std::cbegin(bases), std::cend(bases), std::begin(bases), [&](const char base) -> char {return graph->decoder(base);});