2.0.0 release (libnano#113)

* migrated primer3 header file Cython extern imports to `thermoanalysis.pxi` (libnano#100)

Optional C structure string argument `c_ascii_structure` added to `_ThermoAnalysis`
methods to enable 3rd party use for structures

version bump to 2.0.0a1 due to breaking change

* fix for issue 108 whereby no_structure is not correctly 1 set to 1 when no secondary structure in found (libnano#109)

* Issue 50 update to add list version of (libnano#110)

PRIMER_{PAIR, LEFT, RIGHT, INTERNAL} output dictionary keys.
Retaining original keys as well for compatibility

version bump to 2.0.0

updated CHANGES and cython_help.md for a note about the
`c_ascii_structure` argument

Consistent free of `c_ascii_structure` in thermoanalysis.pyx methods

* fixes missing `thal_result.sec_struct` and `dpal_results.sec_struct` (libnano#112)

initialization to `NULL` in `recalc_primer_sec_struct` in `libprimer3.c`
and `libprimer3flex.c`.  `CHANGES` updated

* doc string update for _ThermoAnalysis.run_design for new list based keys

CHANGES

@@ -1,9 +1,20 @@
 # Changelog
 
+## Version 2.0.0 (May 30, 2023)
+
+- Migrated primer3 header file Cython extern imports to `thermoanalysis.pxi`
+- Optional C structure string argument `c_ascii_structure` added to `_ThermoAnalysis` methods to enable 3rd party use for structures
+- Version bump to 2.0.0 due to breaking change
+- Fix issue whereby no_structure is not correctly 1 set to 1 when no secondary structure in found
+- Add list version of `PRIMER_{PAIR, LEFT, RIGHT, INTERNAL}` to design output dictionary keys.Retaining original keys as well for compatibility.
+- Fix for  missing `thal_result.sec_struct` and `dpal_results.sec_struct` initialization to `NULL` in `recalc_primer_sec_struct`
+
 ## Version 1.2.2 (May 16, 2023)
+
 - Bug fixes for output formatting related to penalty, "problem", and mispriming fields
 
 ## Version 1.2.1 (April 28, 2023)
+
 - Bug fixes for `pdh_create_seq_lib` to correct missing `seq_lib` datastructure allocation and variable name typos.
 - Increase test coverage to include `misprime_lib` and `mishyb_lib` arguments
 
@@ -18,6 +29,7 @@
 - `setup.py` `package_data` and `MANIFEST.in` to assist with future builds from `tar.gz` (`conda`)
 
 ## Version 1.1.0 (March 1, 2023)
+
  - Added specificity to error non-N IUPAC error for issue #59
  - Wheel build support for python 3.8 to move towards following the CPython EOL model for issue #88. See https://devguide.python.org/versions/
 

MANIFEST.in

@@ -1,6 +1,6 @@
 include README.md LICENSE CHANGES AUTHORS setup.py
 include .pre-commit-config.yaml dev-requirements.txt setup.cfg
-include primer3/*.pxd primer3/*.pyx primer3/*.h
+include primer3/*.pxd primer3/*.pxi primer3/*.pyx primer3/*.h
 include primer3/src/libprimer3/*.h primer3/src/libprimer3/*.c
 include primer3/src/libprimer3/klib/khash.h
 include primer3/src/libprimer3/klib/README.md

docs/cython_help.md

@@ -40,4 +40,8 @@ and to build/install using a standard `setup.py` add the lines (fill in the ...s
         ...)
 ```
 
-and it should work
+and it should work.
+
+## Notes
+- Many `_ThermoAnalysis` methods (e.g. `calc_heterodimer_c`) have C string argument
+`c_ascii_structure` to enable 3rd party use for structures reuse

primer3/__init__.py

@@ -26,7 +26,7 @@
 from typing import List
 
 # Per PEP-440 https://peps.python.org/pep-0440/#public-version-identifiers
-__version__ = '1.2.2'
+__version__ = '2.0.0'
 __author__ = 'Ben Pruitt, Nick Conway'
 __copyright__ = (
     'Copyright 2014-2023, Ben Pruitt & Nick Conway; 2014-2018 Wyss Institute'

primer3/bindings.py

@@ -532,6 +532,7 @@ def design_primers(
         mishyb_lib: Optional[Dict[str, Any]] = None,
 ) -> Dict[str, Any]:
     '''Run the Primer3 design process.
+    This is a wrapper around :meth:`_ThermoAnalysis.run_design`.
 
     Args:
         seq_args: Primer3 sequence/design args as per Primer3 docs

primer3/src/libprimer3/libprimer3.c

@@ -5283,8 +5283,7 @@ recalc_secundary_structures(
     num_print = retval->best_pairs.num_pairs;
     for (int i = 0 ; i < num_print ; i++) {
       recalc_primer_sec_struct(
-        retval->best_pairs.pairs[i].
-        left,
+        retval->best_pairs.pairs[i].left,
         0,
         pa,
         sa,
@@ -5381,6 +5380,10 @@ recalc_primer_sec_struct(
 
   if (pa->thermodynamic_oligo_alignment==0) {
     dpal_results any, end;
+    /* NOTE: important to set these values to NULL to prevent segfaults */
+    any.sec_struct = NULL;
+    end.sec_struct = NULL;
+
     if (p_rec->self_any > 0.0) {
       dpal((const unsigned char *) s1, (const unsigned char *) s1_rev,
            dpal_arg_to_use->local, DPM_STRUCT, &any);
@@ -5397,6 +5400,11 @@ recalc_primer_sec_struct(
   /* Thermodynamic approach, fwd-primer */
   if (pa->thermodynamic_oligo_alignment==1) {
     thal_results any, end, hair;
+    /* NOTE: important to set these values to NULL to prevent segfaults */
+    any.sec_struct = NULL;
+    end.sec_struct = NULL;
+    hair.sec_struct = NULL;
+
     if (p_rec->self_any > 0.0 ) {
       thal(
         (const unsigned char *) s1,

primer3/src/libprimer3/libprimer3flex.c

@@ -6182,8 +6182,7 @@ recalc_secundary_structures(
     num_print = retval->best_pairs.num_pairs;
     for (int i = 0 ; i < num_print ; i++) {
       recalc_primer_sec_struct(
-        retval->best_pairs.pairs[i].
-        left,
+        retval->best_pairs.pairs[i].left,
         0,
         pa,
         sa,
@@ -6232,7 +6231,7 @@ recalc_primer_sec_struct(
   char s1[THAL_MAX_ALIGN+1], s1_rev[THAL_MAX_ALIGN+1];
   int overhang_len;
   /* s1 is the forward oligo. */
-  if (primer_type == 0) {  /*left */
+  if (primer_type == 0) {  /* left */
     if (NULL != sa->overhang_left) {
       overhang_len = strlen(sa->overhang_left);
       strcpy(s1, sa->overhang_left);
@@ -6287,9 +6286,11 @@ recalc_primer_sec_struct(
     }
     p3_reverse_complement(s1_rev, s1);
   }
-
   if (pa->thermodynamic_oligo_alignment==0) {
     dpal_results any, end;
+    /* NOTE: important to set these values to NULL to prevent segfaults */
+    any.sec_struct = NULL;
+    end.sec_struct = NULL;
     if (p_rec->self_any > 0.0) {
       dpal(
         (const unsigned char*) s1,
@@ -6322,6 +6323,11 @@ recalc_primer_sec_struct(
   /* Thermodynamic approach, fwd-primer */
   if (pa->thermodynamic_oligo_alignment==1) {
     thal_results any, end, hair;
+    /* NOTE: important to set these values to NULL to prevent segfaults */
+    any.sec_struct = NULL;
+    end.sec_struct = NULL;
+    hair.sec_struct = NULL;
+
     if (p_rec->self_any > 0.0 ) {
       thal(
         (const unsigned char*) s1,

primer3/src/libprimer3/thal.c

@@ -496,7 +496,7 @@ thal(const unsigned char *oligo_f,
      const thal_args *a,
      const thal_mode mode,
      thal_results *o,
-     const int print_output)  /* primer3-py modification argumen */
+     const int print_output)  /* primer3-py modification argument */
 {
   double* SH;
   int i, j;
@@ -680,6 +680,7 @@ thal(const unsigned char *oligo_f,
         if (print_output == 1) { /* primer3-py update to supress undesired printing */
           fputs("No secondary structure could be calculated\n", stderr);
         }
+        o->no_structure = 1;
     }
 
     if(o->temp == -_INFINITY && (!strcmp(o->msg, ""))) { o->temp=0.0; }

primer3/src/libprimer3/thalflex.c

@@ -652,6 +652,7 @@ thal(
         if (print_output == 1) { /* primer3-py update to supress undesired printing */
           fputs("No secondary structure could be calculated\n", stderr);
         }
+        o->no_structure = 1;
     }
 
     if(o->temp == -_INFINITY && (!strcmp(o->msg, ""))) { o->temp=0.0; }