From 0d222793500ef5d5bb01bdb6029fba6cb537cb72 Mon Sep 17 00:00:00 2001
From: BiocondaBot <47040946+BiocondaBot@users.noreply.github.com>
Date: Tue, 2 Jul 2024 21:11:46 +0000
Subject: [PATCH 01/19] Update primerforge to 1.2.5

---
 recipes/primerforge/meta.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/recipes/primerforge/meta.yaml b/recipes/primerforge/meta.yaml
index ee7e23d85787f..20a5a81158d34 100644
--- a/recipes/primerforge/meta.yaml
+++ b/recipes/primerforge/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "primerForge" %}
-{% set version = "1.1.1" %}
+{% set version = "1.2.5" %}
 
 package:
   name: "{{ name|lower }}"
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://github.com/dr-joe-wirth/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: b13a26e006f7790f80937178a311cfbb95a9f69ee8ab97a0d21139bd197fec13
+  sha256: 428a2712466a7c64296c893cb525ab092dd943ace5728b8c09e3c0c7bfe15300
 
 build:
   number: 0

From b5d778c4e894b326fa34120e189659bcf32ea91b Mon Sep 17 00:00:00 2001
From: "Joe Wirth (Joseph S. Wirth)"
 <71667025+dr-joe-wirth@users.noreply.github.com>
Date: Tue, 2 Jul 2024 17:36:23 -0400
Subject: [PATCH 02/19] added `khmer` as a dependency

---
 recipes/primerforge/meta.yaml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/recipes/primerforge/meta.yaml b/recipes/primerforge/meta.yaml
index 20a5a81158d34..c5f5724a6d9a4 100644
--- a/recipes/primerforge/meta.yaml
+++ b/recipes/primerforge/meta.yaml
@@ -28,6 +28,8 @@ requirements:
     - numpy
     - primer3-py >=2.0
     - scipy >=1.10
+    - pip:
+      - khmer >=2.1
 
 test:
   commands:

From f1f32a35b392cee7a8ab07c747f5a40eb19958bb Mon Sep 17 00:00:00 2001
From: Martin Grigorov <martin-g@users.noreply.github.com>
Date: Wed, 3 Jul 2024 10:11:29 +0300
Subject: [PATCH 03/19] Fix yaml syntax

---
 recipes/primerforge/meta.yaml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/recipes/primerforge/meta.yaml b/recipes/primerforge/meta.yaml
index c5f5724a6d9a4..aa447de84cf36 100644
--- a/recipes/primerforge/meta.yaml
+++ b/recipes/primerforge/meta.yaml
@@ -28,8 +28,7 @@ requirements:
     - numpy
     - primer3-py >=2.0
     - scipy >=1.10
-    - pip:
-      - khmer >=2.1
+    - khmer >=2.1
 
 test:
   commands:

From 4226fd16e6b0e7154267187c10375100696624f9 Mon Sep 17 00:00:00 2001
From: Martin Grigorov <martin-g@users.noreply.github.com>
Date: Wed, 3 Jul 2024 10:29:45 +0300
Subject: [PATCH 04/19] Ping kmer between 2.1 and 3

---
 recipes/primerforge/meta.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/recipes/primerforge/meta.yaml b/recipes/primerforge/meta.yaml
index aa447de84cf36..3bf9014defa59 100644
--- a/recipes/primerforge/meta.yaml
+++ b/recipes/primerforge/meta.yaml
@@ -28,7 +28,7 @@ requirements:
     - numpy
     - primer3-py >=2.0
     - scipy >=1.10
-    - khmer >=2.1
+    - khmer >=2.1,<3
 
 test:
   commands:

From 3b58a113c066cc6e091a11eee27fd92667c2050e Mon Sep 17 00:00:00 2001
From: "Joe Wirth (Joseph S. Wirth)"
 <71667025+dr-joe-wirth@users.noreply.github.com>
Date: Wed, 3 Jul 2024 13:49:39 -0400
Subject: [PATCH 05/19] updated compatible python versions

---
 recipes/primerforge/meta.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/recipes/primerforge/meta.yaml b/recipes/primerforge/meta.yaml
index 3bf9014defa59..2b9f8bc9170c0 100644
--- a/recipes/primerforge/meta.yaml
+++ b/recipes/primerforge/meta.yaml
@@ -20,10 +20,10 @@ build:
 
 requirements:
   host:
-    - python >=3.11
+    - python >=3.9,<3.12
     - pip
   run:
-    - python >=3.11
+    - python >=3.9,<3.12
     - biopython ==1.81
     - numpy
     - primer3-py >=2.0

From f67865935112b48996c91ef7741d891bcd9815aa Mon Sep 17 00:00:00 2001
From: dr-joe-wirth <dr.joe.wirth@gmail.com>
Date: Wed, 3 Jul 2024 18:06:44 -0400
Subject: [PATCH 06/19] started working on a `build.sh` file...not yet working

---
 recipes/primerforge/build.sh  | 11 +++++++++++
 recipes/primerforge/meta.yaml |  3 +--
 2 files changed, 12 insertions(+), 2 deletions(-)
 create mode 100644 recipes/primerforge/build.sh

diff --git a/recipes/primerforge/build.sh b/recipes/primerforge/build.sh
new file mode 100644
index 0000000000000..9917414dea90b
--- /dev/null
+++ b/recipes/primerforge/build.sh
@@ -0,0 +1,11 @@
+#!/bin/bash
+set -e
+
+# Install primerforge using pip
+python3 -m pip install $SRC_DIR --no-deps --no-build-isolation -vvv
+
+# Install khmer
+wget https://github.com/dib-lab/khmer/archive/refs/tags/v2.1.1.tar.gz
+tar xzf v2.1.1.tar.gz
+cd khmer-2.1.1
+python3 setup.py install
diff --git a/recipes/primerforge/meta.yaml b/recipes/primerforge/meta.yaml
index 2b9f8bc9170c0..aea3d164656b6 100644
--- a/recipes/primerforge/meta.yaml
+++ b/recipes/primerforge/meta.yaml
@@ -12,7 +12,7 @@ source:
 build:
   number: 0
   noarch: python
-  script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv"
+  #script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv && {{ PYTHON }} -m pip install khmer"
   entry_points:
     - primerForge=bin.main:main
   run_exports:
@@ -28,7 +28,6 @@ requirements:
     - numpy
     - primer3-py >=2.0
     - scipy >=1.10
-    - khmer >=2.1,<3
 
 test:
   commands:

From 0497ae5ddc62e37397afe66fc064bde00586e9fd Mon Sep 17 00:00:00 2001
From: dr-joe-wirth <dr.joe.wirth@gmail.com>
Date: Mon, 8 Jul 2024 11:00:22 -0400
Subject: [PATCH 07/19] removing attempts to install khmer with pip; recipe
 does not work

---
 recipes/primerforge/build.sh  | 11 -----------
 recipes/primerforge/meta.yaml |  3 ++-
 2 files changed, 2 insertions(+), 12 deletions(-)
 delete mode 100644 recipes/primerforge/build.sh

diff --git a/recipes/primerforge/build.sh b/recipes/primerforge/build.sh
deleted file mode 100644
index 9917414dea90b..0000000000000
--- a/recipes/primerforge/build.sh
+++ /dev/null
@@ -1,11 +0,0 @@
-#!/bin/bash
-set -e
-
-# Install primerforge using pip
-python3 -m pip install $SRC_DIR --no-deps --no-build-isolation -vvv
-
-# Install khmer
-wget https://github.com/dib-lab/khmer/archive/refs/tags/v2.1.1.tar.gz
-tar xzf v2.1.1.tar.gz
-cd khmer-2.1.1
-python3 setup.py install
diff --git a/recipes/primerforge/meta.yaml b/recipes/primerforge/meta.yaml
index aea3d164656b6..6712a5aa986e1 100644
--- a/recipes/primerforge/meta.yaml
+++ b/recipes/primerforge/meta.yaml
@@ -12,7 +12,7 @@ source:
 build:
   number: 0
   noarch: python
-  #script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv && {{ PYTHON }} -m pip install khmer"
+  script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv"
   entry_points:
     - primerForge=bin.main:main
   run_exports:
@@ -25,6 +25,7 @@ requirements:
   run:
     - python >=3.9,<3.12
     - biopython ==1.81
+    - khmer >=2.1.1
     - numpy
     - primer3-py >=2.0
     - scipy >=1.10

From fdb959469b736eeb544934477a167d4e4ddfd5a8 Mon Sep 17 00:00:00 2001
From: BiocondaBot <47040946+BiocondaBot@users.noreply.github.com>
Date: Tue, 16 Jul 2024 21:06:32 +0000
Subject: [PATCH 08/19] Update primerforge to 1.2.7

---
 recipes/primerforge/meta.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/recipes/primerforge/meta.yaml b/recipes/primerforge/meta.yaml
index 6712a5aa986e1..0442baf54ae41 100644
--- a/recipes/primerforge/meta.yaml
+++ b/recipes/primerforge/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "primerForge" %}
-{% set version = "1.2.5" %}
+{% set version = "1.2.7" %}
 
 package:
   name: "{{ name|lower }}"
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://github.com/dr-joe-wirth/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: 428a2712466a7c64296c893cb525ab092dd943ace5728b8c09e3c0c7bfe15300
+  sha256: 27295871c8a3e0d51ec0dfc0776227d1e254e12ab94b4e9181d59295d2b0f81f
 
 build:
   number: 0

From e917499c339bbb69ab65fb41f9c7ae56cfa6d677 Mon Sep 17 00:00:00 2001
From: "Joe Wirth (Joseph S. Wirth)"
 <71667025+dr-joe-wirth@users.noreply.github.com>
Date: Tue, 16 Jul 2024 21:33:48 -0400
Subject: [PATCH 09/19] Added `pyahocorasick` requirement

---
 recipes/primerforge/meta.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/recipes/primerforge/meta.yaml b/recipes/primerforge/meta.yaml
index 0442baf54ae41..1ad12b4b3d0b0 100644
--- a/recipes/primerforge/meta.yaml
+++ b/recipes/primerforge/meta.yaml
@@ -28,6 +28,7 @@ requirements:
     - khmer >=2.1.1
     - numpy
     - primer3-py >=2.0
+    - pyahocorasick
     - scipy >=1.10
 
 test:

From 318594c17ba2f3cff5f41787df48699b0f52e539 Mon Sep 17 00:00:00 2001
From: BiocondaBot <47040946+BiocondaBot@users.noreply.github.com>
Date: Mon, 29 Jul 2024 18:17:25 +0000
Subject: [PATCH 10/19] Update primerforge to 1.3.1

---
 recipes/primerforge/meta.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/recipes/primerforge/meta.yaml b/recipes/primerforge/meta.yaml
index 1ad12b4b3d0b0..feeca7caee1f8 100644
--- a/recipes/primerforge/meta.yaml
+++ b/recipes/primerforge/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "primerForge" %}
-{% set version = "1.2.7" %}
+{% set version = "1.3.1" %}
 
 package:
   name: "{{ name|lower }}"
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://github.com/dr-joe-wirth/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: 27295871c8a3e0d51ec0dfc0776227d1e254e12ab94b4e9181d59295d2b0f81f
+  sha256: 497244b225c9f3c6604a824b61a25a25a885f5bf913e364c0eb2b38e7c1cf627
 
 build:
   number: 0

From 236bd98736375511f82655822bf4e92e48d3a3eb Mon Sep 17 00:00:00 2001
From: "Joe Wirth (Joseph S. Wirth)"
 <71667025+dr-joe-wirth@users.noreply.github.com>
Date: Mon, 29 Jul 2024 14:31:20 -0400
Subject: [PATCH 11/19] added `isPcr` dependency

---
 recipes/primerforge/meta.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/recipes/primerforge/meta.yaml b/recipes/primerforge/meta.yaml
index feeca7caee1f8..ce000732e26d6 100644
--- a/recipes/primerforge/meta.yaml
+++ b/recipes/primerforge/meta.yaml
@@ -25,6 +25,7 @@ requirements:
   run:
     - python >=3.9,<3.12
     - biopython ==1.81
+    - ispcr
     - khmer >=2.1.1
     - numpy
     - primer3-py >=2.0

From 59575cbc4b89d8a4f0a9b0034eb953b20ff932ac Mon Sep 17 00:00:00 2001
From: BiocondaBot <47040946+BiocondaBot@users.noreply.github.com>
Date: Tue, 30 Jul 2024 19:10:36 +0000
Subject: [PATCH 12/19] Update primerforge to 1.3.2

---
 recipes/primerforge/meta.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/recipes/primerforge/meta.yaml b/recipes/primerforge/meta.yaml
index ce000732e26d6..97ca1efc1b288 100644
--- a/recipes/primerforge/meta.yaml
+++ b/recipes/primerforge/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "primerForge" %}
-{% set version = "1.3.1" %}
+{% set version = "1.3.2" %}
 
 package:
   name: "{{ name|lower }}"
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://github.com/dr-joe-wirth/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: 497244b225c9f3c6604a824b61a25a25a885f5bf913e364c0eb2b38e7c1cf627
+  sha256: 6aa32a2b59b90390429a04689c7712420b38fc17443b809b95f167d2533dcefa
 
 build:
   number: 0

From 2fdc207ce5eb6a213cff4b177b701d49408663c4 Mon Sep 17 00:00:00 2001
From: BiocondaBot <47040946+BiocondaBot@users.noreply.github.com>
Date: Fri, 2 Aug 2024 18:15:36 +0000
Subject: [PATCH 13/19] Update primerforge to 1.3.3

---
 recipes/primerforge/meta.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/recipes/primerforge/meta.yaml b/recipes/primerforge/meta.yaml
index 97ca1efc1b288..d13852591380b 100644
--- a/recipes/primerforge/meta.yaml
+++ b/recipes/primerforge/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "primerForge" %}
-{% set version = "1.3.2" %}
+{% set version = "1.3.3" %}
 
 package:
   name: "{{ name|lower }}"
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://github.com/dr-joe-wirth/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: 6aa32a2b59b90390429a04689c7712420b38fc17443b809b95f167d2533dcefa
+  sha256: a54faa2bdf583a988c0c08a88bbb93d870c9bb245f217f0bea11b0015199a9bc
 
 build:
   number: 0

From b1c925d55849a53c0104588e0726bc0ce24c3d1a Mon Sep 17 00:00:00 2001
From: BiocondaBot <47040946+BiocondaBot@users.noreply.github.com>
Date: Mon, 12 Aug 2024 18:07:17 +0000
Subject: [PATCH 14/19] Update primerforge to 1.3.4

---
 recipes/primerforge/meta.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/recipes/primerforge/meta.yaml b/recipes/primerforge/meta.yaml
index d13852591380b..b9fd5b2d4e61a 100644
--- a/recipes/primerforge/meta.yaml
+++ b/recipes/primerforge/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "primerForge" %}
-{% set version = "1.3.3" %}
+{% set version = "1.3.4" %}
 
 package:
   name: "{{ name|lower }}"
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://github.com/dr-joe-wirth/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: a54faa2bdf583a988c0c08a88bbb93d870c9bb245f217f0bea11b0015199a9bc
+  sha256: fc11721a5ece13621c4eadec55d412ba18f89abd40bfb1a4c64a42fb45512089
 
 build:
   number: 0

From fd8f362bf2c4ca11aa8224b848338d5a71e89255 Mon Sep 17 00:00:00 2001
From: BiocondaBot <47040946+BiocondaBot@users.noreply.github.com>
Date: Tue, 13 Aug 2024 22:16:06 +0000
Subject: [PATCH 15/19] Update primerforge to 1.3.5

---
 recipes/primerforge/meta.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/recipes/primerforge/meta.yaml b/recipes/primerforge/meta.yaml
index b9fd5b2d4e61a..b44086ea8c8c5 100644
--- a/recipes/primerforge/meta.yaml
+++ b/recipes/primerforge/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "primerForge" %}
-{% set version = "1.3.4" %}
+{% set version = "1.3.5" %}
 
 package:
   name: "{{ name|lower }}"
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://github.com/dr-joe-wirth/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: fc11721a5ece13621c4eadec55d412ba18f89abd40bfb1a4c64a42fb45512089
+  sha256: 8d8c49186568541a6426da6042e1576c9250baeaabfbd078163325cb01feb483
 
 build:
   number: 0

From 11a46198663c70aca26cb634d513a1c71ad4718d Mon Sep 17 00:00:00 2001
From: BiocondaBot <47040946+BiocondaBot@users.noreply.github.com>
Date: Thu, 22 Aug 2024 19:05:24 +0000
Subject: [PATCH 16/19] Update primerforge to 1.3.6

---
 recipes/primerforge/meta.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/recipes/primerforge/meta.yaml b/recipes/primerforge/meta.yaml
index b44086ea8c8c5..0bcdf112d447a 100644
--- a/recipes/primerforge/meta.yaml
+++ b/recipes/primerforge/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "primerForge" %}
-{% set version = "1.3.5" %}
+{% set version = "1.3.6" %}
 
 package:
   name: "{{ name|lower }}"
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://github.com/dr-joe-wirth/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: 8d8c49186568541a6426da6042e1576c9250baeaabfbd078163325cb01feb483
+  sha256: a37a225a278bd0a96c035b1c0a7d74a8c73d95aecf60e9dfbe246addd1f74b82
 
 build:
   number: 0

From 4f3a8c97065d8a8a8f9ac95b1431dd92d18dcb74 Mon Sep 17 00:00:00 2001
From: BiocondaBot <47040946+BiocondaBot@users.noreply.github.com>
Date: Mon, 16 Sep 2024 18:16:47 +0000
Subject: [PATCH 17/19] Update primerforge to 1.3.7

---
 recipes/primerforge/meta.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/recipes/primerforge/meta.yaml b/recipes/primerforge/meta.yaml
index 0bcdf112d447a..0dbd546a77284 100644
--- a/recipes/primerforge/meta.yaml
+++ b/recipes/primerforge/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "primerForge" %}
-{% set version = "1.3.6" %}
+{% set version = "1.3.7" %}
 
 package:
   name: "{{ name|lower }}"
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://github.com/dr-joe-wirth/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: a37a225a278bd0a96c035b1c0a7d74a8c73d95aecf60e9dfbe246addd1f74b82
+  sha256: 9c80041491433ed5896104c402c9c2f739c4c4342aae090df40794fd42be1e8e
 
 build:
   number: 0

From 459b4a42e3c099ce16fa822535aa1dfb5ff4e50d Mon Sep 17 00:00:00 2001
From: BiocondaBot <47040946+BiocondaBot@users.noreply.github.com>
Date: Mon, 7 Oct 2024 19:14:10 +0000
Subject: [PATCH 18/19] Update primerforge to 1.4.3

---
 recipes/primerforge/meta.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/recipes/primerforge/meta.yaml b/recipes/primerforge/meta.yaml
index 0dbd546a77284..a1a4178447f9d 100644
--- a/recipes/primerforge/meta.yaml
+++ b/recipes/primerforge/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "primerForge" %}
-{% set version = "1.3.7" %}
+{% set version = "1.4.3" %}
 
 package:
   name: "{{ name|lower }}"
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://github.com/dr-joe-wirth/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: 9c80041491433ed5896104c402c9c2f739c4c4342aae090df40794fd42be1e8e
+  sha256: 80e858976d94c8fb8578a43c51da3700d2ba3718cdbb109cfe176f942e222ae6
 
 build:
   number: 0

From 02a31d198ef77e20f62281191c696f383d7fd5da Mon Sep 17 00:00:00 2001
From: BiocondaBot <47040946+BiocondaBot@users.noreply.github.com>
Date: Wed, 9 Oct 2024 20:13:21 +0000
Subject: [PATCH 19/19] Update primerforge to 1.5.1

---
 recipes/primerforge/meta.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/recipes/primerforge/meta.yaml b/recipes/primerforge/meta.yaml
index a1a4178447f9d..f9b7b2dbe4706 100644
--- a/recipes/primerforge/meta.yaml
+++ b/recipes/primerforge/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "primerForge" %}
-{% set version = "1.4.3" %}
+{% set version = "1.5.1" %}
 
 package:
   name: "{{ name|lower }}"
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://github.com/dr-joe-wirth/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: 80e858976d94c8fb8578a43c51da3700d2ba3718cdbb109cfe176f942e222ae6
+  sha256: ec71ade593e9f3d342ac884ad469f4468540dbe61b9f9b0a932769195fcdf486
 
 build:
   number: 0