Bump embedded FAMSA to v2.2.3

patches/sequence.cpp.patch

@@ -1,6 +1,10 @@
-@@ -19,6 +19,18 @@
-
-
+diff --git a/src/core/sequence.cpp b/src/core/sequence.cpp
+index 54401be..83d0f2f 100644
+--- a/src/core/sequence.cpp
++++ b/src/core/sequence.cpp
+@@ -19,6 +19,18 @@ char CGappedSequence::mapping_table[25] = "ARNDCQEGHILKMFPSTWYVBZX*";
+
+
  // *******************************************************************
 +CSequence::CSequence()
 +	:
@@ -15,12 +19,12 @@
 +{}
 +
  CSequence::CSequence(const string& _id, const string& seq, int sequence_no, memory_monotonic_safe* mma)
- 	:
- 	length(0),
-@@ -79,6 +91,39 @@
+ 	: 
+ 	length(0), 
+@@ -79,6 +91,39 @@ CSequence::CSequence(const string& _id, const string& seq, int sequence_no, memo
  	}
  }
-
+ 
 +// *******************************************************************
 +CSequence::CSequence(const CSequence& x)
 +{
@@ -55,57 +59,25 @@
 +}
 +
  // *******************************************************************
- CSequence::CSequence(CSequence&& x) noexcept
+ CSequence::CSequence(CSequence&& x) noexcept 
  	:
-@@ -105,10 +150,11 @@
-
-
+@@ -105,10 +150,10 @@ CSequence::CSequence(CSequence&& x) noexcept
+ 
+ 
  // *******************************************************************
 -/*
-+
  CSequence& CSequence::operator=(CSequence&& x) noexcept
  {
  	this->sequence_no = move(x.sequence_no);
 +	this->original_no = move(x.original_no);
  	this->length = move(x.length);
  	this->id = move(x.id);
-
-@@ -127,7 +173,7 @@
-
+ 
+@@ -127,7 +172,6 @@ CSequence& CSequence::operator=(CSequence&& x) noexcept
+ 
  	return *this;
  }
 -*/
-+
-
+
  // *******************************************************************
  CSequence::~CSequence()
-@@ -231,6 +277,7 @@
- 			symbols=(symbol_t*)mma->allocate(symbols_size + 1);}
- 		else {
- 			symbols=new symbol_t[symbols_size +1];}
-+		*symbols = GUARD;
- 	}
- 	else {
- 		symbols=nullptr;
-@@ -255,10 +302,10 @@
- 			char* q = find(mapping_table, mapping_table + 25, c);
- 			if (q == mapping_table + 25) {
- 				extra_symbols.emplace_back(is, c); // save non-standard symbol
--				symbols[is] = (symbol_t)UNKNOWN_SYMBOL;
-+				symbols[is+1] = (symbol_t)UNKNOWN_SYMBOL;
- 			}
- 			else {
--				symbols[is] = (symbol_t)(q - mapping_table);
-+				symbols[is+1] = (symbol_t)(q - mapping_table);
- 			}
-
- 			++is;
-@@ -313,7 +360,7 @@
- 		symbols = new symbol_t[symbols_size + 1];
-
-
--	copy_n(_gapped_sequence.symbols, symbols_size, symbols);
-+	copy_n(_gapped_sequence.symbols, symbols_size + 1, symbols);
-
- 	n_gaps = _gapped_sequence.n_gaps;
- 	dps = _gapped_sequence.dps;

patches/sequence.h.patch

@@ -1,7 +1,17 @@
-@@ -35,1 +35,1 @@
+diff --git a/src/core/sequence.h b/src/core/sequence.h
+index ac37942..e17620e 100644
+--- a/src/core/sequence.h
++++ b/src/core/sequence.h
+@@ -32,7 +32,7 @@ public:
+ 	bit_vec_t *p_bit_masks;
+ 	uint32_t p_bv_len;
+
 -	const int original_no;
 +	int original_no;
-@@ -42,15 +42,15 @@
+ 	int sequence_no;
+ 	string id;
+
+@@ -42,15 +42,15 @@ public:
  	vector<std::pair<int, char>> extra_symbols;
 
  public:
@@ -12,8 +22,7 @@
  	// sequences are not copyable
 -	CSequence(const CSequence& x) noexcept = delete;
 +	CSequence(const CSequence& x);
--	CSequence& operator=(const CSequence& x) noexcept = delete;
-+	// CSequence& operator=(const CSequence& x) noexcept;
+ 	CSequence& operator=(const CSequence& x) noexcept = delete;
 
  	CSequence(CSequence&& x) noexcept;
 -	CSequence& operator=(CSequence&& x) noexcept = delete; 

pyfamsa/_famsa.pyx

@@ -102,9 +102,9 @@ def famsa_info():
     Example:
         >>> info = famsa_info()
         >>> info.version
-        '2.2.2'
+        '2.2.3'
         >>> info.date
-        datetime.date(2022, 10, 9)
+        datetime.date(2024, 9, 17)
 
     """
     _VersionInfo = collections.namedtuple("_VersionInfo", ["major", "minor", "micro"])

setup.py

@@ -69,7 +69,7 @@ def _detect_target_system(platform):
 
 # --- Utils ------------------------------------------------------------------
 
-_HEADER_PATTERN = re.compile(r"^@@ -(\d+),?(\d+)? \+(\d+),?(\d+)? @@$")
+_HEADER_PATTERN = re.compile(r"^@@ -(\d+),?(\d+)? \+(\d+),?(\d+)? @@")
 
 
 def _eprint(*args, **kwargs):
@@ -102,7 +102,7 @@ def _apply_patch(s,patch,revert=False):
     i = 0
     sl = 0
     midx, sign = (1,'+') if not revert else (3,'-')
-    while i < len(p) and p[i].startswith(("---","+++")):
+    while i < len(p) and not p[i].startswith("@@"):
         i += 1 # skip header lines
 
     while i < len(p):
@@ -781,7 +781,7 @@ def run(self):
                 os.path.join(SETUP_FOLDER, "vendor", "FAMSA", "src", "core", "profile_seq.cpp"),
                 os.path.join(SETUP_FOLDER, "vendor", "FAMSA", "src", "core", "sequence.cpp"),
                 os.path.join(SETUP_FOLDER, "vendor", "FAMSA", "src", "core", "queues.cpp"),
-                os.path.join(SETUP_FOLDER, "vendor", "FAMSA", "libs", "mimalloc", "static.cpp"),
+                os.path.join(SETUP_FOLDER, "vendor", "FAMSA", "libs", "mimalloc", "src", "static.c"),
                 # LCS_OBJS
                 os.path.join(SETUP_FOLDER, "vendor", "FAMSA", "src", "lcs", "lcsbp.cpp"),
                 os.path.join(SETUP_FOLDER, "vendor", "FAMSA", "src", "lcs", "lcsbp_classic.cpp"),
@@ -792,7 +792,7 @@ def run(self):
                 os.path.join(SETUP_FOLDER, "vendor", "FAMSA", "src", "tree"),
                 os.path.join(SETUP_FOLDER, "vendor", "FAMSA", "src", "utils"),
                 os.path.join(SETUP_FOLDER, "vendor", "FAMSA", "src"),
-                os.path.join(SETUP_FOLDER, "vendor", "FAMSA", "libs", "mimalloc"),
+                os.path.join(SETUP_FOLDER, "vendor", "FAMSA", "libs", "mimalloc", "include"),
                 os.path.join(SETUP_FOLDER, "vendor", "FAMSA", "libs"),
                 os.path.join(SETUP_FOLDER, "include"),
             ],