From fe29d63985a4b3c5987ed858b0b91510510c67d2 Mon Sep 17 00:00:00 2001
From: BiocondaBot <47040946+BiocondaBot@users.noreply.github.com>
Date: Tue, 16 Jul 2024 14:11:32 +0000
Subject: [PATCH 01/10] Update ms2rescore-rs to 0.2.1

---
 recipes/ms2rescore-rs/meta.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/recipes/ms2rescore-rs/meta.yaml b/recipes/ms2rescore-rs/meta.yaml
index 1a0a2afa568f4..469fc1b8457f3 100644
--- a/recipes/ms2rescore-rs/meta.yaml
+++ b/recipes/ms2rescore-rs/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "ms2rescore-rs" %}
-{% set version = "0.2.0" %}
-{% set sha256 = "561ed92f58fd7ecccc78b3e4b1bc91ffa36d0f2e58d54f7ea317898f3ea55560" %}
+{% set version = "0.2.1" %}
+{% set sha256 = "574b65ac20000ef1a5acc2332174e9fc7fbacc36bc314eedfea8ed8d9220c51d" %}
 
 package:
   name: {{ name|lower }}
@@ -11,7 +11,7 @@ source:
   sha256: {{ sha256 }}
 
 build:
-  number: 1
+  number: 0
   skip: True  # [py < 37]
   run_exports:
     - {{ pin_subpackage(name|lower, max_pin="x.x") }}

From df9fd3175d4f484d438edfa1136b7b81d2b2a018 Mon Sep 17 00:00:00 2001
From: mencian <joshua.zhuang@yahoo.com>
Date: Tue, 16 Jul 2024 10:29:28 -0500
Subject: [PATCH 02/10] clean up recipe

---
 recipes/ms2rescore-rs/build.sh  | 10 ++++------
 recipes/ms2rescore-rs/meta.yaml |  7 ++-----
 2 files changed, 6 insertions(+), 11 deletions(-)

diff --git a/recipes/ms2rescore-rs/build.sh b/recipes/ms2rescore-rs/build.sh
index 89752b0073526..2e0f071d05457 100644
--- a/recipes/ms2rescore-rs/build.sh
+++ b/recipes/ms2rescore-rs/build.sh
@@ -4,18 +4,16 @@
 # -x = print every executed command
 set -ex
 
-# Add workaround for SSH-based Git connections from Rust/cargo.  See https://github.com/rust-lang/cargo/issues/2078 for details.
-# We set CARGO_HOME because we don't pass on HOME to conda-build, thus rendering the default "${HOME}/.cargo" defunct.
-export CARGO_NET_GIT_FETCH_WITH_CLI=true CARGO_HOME="${BUILD_PREFIX}/.cargo"
-
 # Use a custom temporary directory as home on macOS.
 # (not sure why this is useful, but people use it in bioconda recipes)
 if [ `uname` == Darwin ]; then
   export HOME=`mktemp -d`
 fi
 
+# build statically linked binary with Rust
+RUST_BACKTRACE=1
 # Build the package using maturin - should produce *.whl files.
-maturin build --interpreter $PYTHON --release
+maturin build --interpreter $PYTHON -b pyo3 --release --strip
 
 # Install *.whl files using pip
-$PYTHON -m pip install target/wheels/*.whl --no-deps --ignore-installed -vv
+$PYTHON -m pip install target/wheels/*.whl --no-deps --no-build-isolation --no-cache-dir -vvv
diff --git a/recipes/ms2rescore-rs/meta.yaml b/recipes/ms2rescore-rs/meta.yaml
index 469fc1b8457f3..b39727bf9338c 100644
--- a/recipes/ms2rescore-rs/meta.yaml
+++ b/recipes/ms2rescore-rs/meta.yaml
@@ -12,7 +12,7 @@ source:
 
 build:
   number: 0
-  skip: True  # [py < 37]
+  skip: True  # [py < 38]
   run_exports:
     - {{ pin_subpackage(name|lower, max_pin="x.x") }}
 
@@ -33,15 +33,12 @@ requirements:
 test:
   imports:
     - ms2rescore_rs
-  commands:
-    - pip check
-  requires:
-    - pip
 
 about:
   home: https://github.com/compomics/ms2rescore-rs
   summary: "Rust functionality for the MS²Rescore package"
   license: Apache-2.0
+  license_family: APACHE
   license_file: LICENSE
 
 extra:

From cf86464398e03a16a04e4c4078baa14b13357f07 Mon Sep 17 00:00:00 2001
From: BiocondaBot <47040946+BiocondaBot@users.noreply.github.com>
Date: Wed, 17 Jul 2024 21:14:09 +0000
Subject: [PATCH 03/10] Update ms2rescore-rs to 0.3.0

---
 recipes/ms2rescore-rs/meta.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/recipes/ms2rescore-rs/meta.yaml b/recipes/ms2rescore-rs/meta.yaml
index b39727bf9338c..c27d55e162c5e 100644
--- a/recipes/ms2rescore-rs/meta.yaml
+++ b/recipes/ms2rescore-rs/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "ms2rescore-rs" %}
-{% set version = "0.2.1" %}
-{% set sha256 = "574b65ac20000ef1a5acc2332174e9fc7fbacc36bc314eedfea8ed8d9220c51d" %}
+{% set version = "0.3.0" %}
+{% set sha256 = "be77217a777ce7a05ec68e228fdc07e3f17e340b5608704b0adcdba8eea86963" %}
 
 package:
   name: {{ name|lower }}

From 8c2a36bdee36f7c8e7478aebedc90e084659310d Mon Sep 17 00:00:00 2001
From: BiocondaBot <47040946+BiocondaBot@users.noreply.github.com>
Date: Thu, 24 Oct 2024 16:06:01 +0000
Subject: [PATCH 04/10] Update ms2rescore-rs to 0.4.0

---
 recipes/ms2rescore-rs/meta.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/recipes/ms2rescore-rs/meta.yaml b/recipes/ms2rescore-rs/meta.yaml
index c27d55e162c5e..c91f881651330 100644
--- a/recipes/ms2rescore-rs/meta.yaml
+++ b/recipes/ms2rescore-rs/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "ms2rescore-rs" %}
-{% set version = "0.3.0" %}
-{% set sha256 = "be77217a777ce7a05ec68e228fdc07e3f17e340b5608704b0adcdba8eea86963" %}
+{% set version = "0.4.0" %}
+{% set sha256 = "9bdf673a625b520a18dda633487cb48e1b3970ea3df5390d0c79fda9eaf2bc9b" %}
 
 package:
   name: {{ name|lower }}

From 75465c8d96cfcd51cd42d09bacb8b3a5d9fbdfca Mon Sep 17 00:00:00 2001
From: mencian <joshua.zhuang@yahoo.com>
Date: Wed, 20 Nov 2024 02:47:00 -0600
Subject: [PATCH 05/10] clean up recipe

---
 recipes/ms2rescore-rs/build.sh    |  8 +-------
 recipes/ms2rescore-rs/meta.yaml   |  3 +++
 recipes/ms2rescore-rs/setup.patch | 27 +++++++++++++++++++++++++++
 3 files changed, 31 insertions(+), 7 deletions(-)
 create mode 100644 recipes/ms2rescore-rs/setup.patch

diff --git a/recipes/ms2rescore-rs/build.sh b/recipes/ms2rescore-rs/build.sh
index 2e0f071d05457..95c3de4df1c0e 100644
--- a/recipes/ms2rescore-rs/build.sh
+++ b/recipes/ms2rescore-rs/build.sh
@@ -4,16 +4,10 @@
 # -x = print every executed command
 set -ex
 
-# Use a custom temporary directory as home on macOS.
-# (not sure why this is useful, but people use it in bioconda recipes)
-if [ `uname` == Darwin ]; then
-  export HOME=`mktemp -d`
-fi
-
 # build statically linked binary with Rust
 RUST_BACKTRACE=1
 # Build the package using maturin - should produce *.whl files.
-maturin build --interpreter $PYTHON -b pyo3 --release --strip
+maturin build --interpreter "${PYTHON}" -b pyo3 --release --strip
 
 # Install *.whl files using pip
 $PYTHON -m pip install target/wheels/*.whl --no-deps --no-build-isolation --no-cache-dir -vvv
diff --git a/recipes/ms2rescore-rs/meta.yaml b/recipes/ms2rescore-rs/meta.yaml
index c91f881651330..87c94b5ca28d2 100644
--- a/recipes/ms2rescore-rs/meta.yaml
+++ b/recipes/ms2rescore-rs/meta.yaml
@@ -9,6 +9,8 @@ package:
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/ms2rescore_rs-{{ version }}.tar.gz
   sha256: {{ sha256 }}
+  patches:
+    - setup.patch
 
 build:
   number: 0
@@ -40,6 +42,7 @@ about:
   license: Apache-2.0
   license_family: APACHE
   license_file: LICENSE
+  dev_url: https://github.com/compomics/ms2rescore-rs
 
 extra:
   recipe-maintainers:
diff --git a/recipes/ms2rescore-rs/setup.patch b/recipes/ms2rescore-rs/setup.patch
new file mode 100644
index 0000000000000..a88fbd3deaf20
--- /dev/null
+++ b/recipes/ms2rescore-rs/setup.patch
@@ -0,0 +1,27 @@
+diff --git a/pyproject.toml b/pyproject.toml
+index 460b2bc..7940aa3 100644
+--- a/pyproject.toml
++++ b/pyproject.toml
+@@ -16,4 +16,7 @@ dynamic = ["version"]
+ test = ["pytest"]
+ 
+ [tool.maturin]
++python-source = "python"
+ features = ["pyo3/extension-module"]
++strip = true
++profile = "release"
+diff --git a/Cargo.toml b/Cargo.toml
+index 7900ad4..be46176 100644
+--- a/Cargo.toml
++++ b/Cargo.toml
+@@ -14,6 +14,9 @@ default = ["thermo"]
+ thermo = ["mzdata/thermo"]
+ 
+ [dependencies]
+-pyo3 = "0.20.0"
+ mzdata = "0.33.0"
+ timsrust = "0.3.0"
++
++[dependencies.pyo3]
++version = "0.21.2"
++features = ["anyhow"]

From aa46d2cf71db305bf6cb654e1001c69633982d4e Mon Sep 17 00:00:00 2001
From: BiocondaBot <47040946+BiocondaBot@users.noreply.github.com>
Date: Wed, 20 Nov 2024 09:16:41 +0000
Subject: [PATCH 06/10] Update ms2rescore-rs to 0.4.0.post1

---
 recipes/ms2rescore-rs/meta.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/recipes/ms2rescore-rs/meta.yaml b/recipes/ms2rescore-rs/meta.yaml
index 87c94b5ca28d2..850b985299421 100644
--- a/recipes/ms2rescore-rs/meta.yaml
+++ b/recipes/ms2rescore-rs/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "ms2rescore-rs" %}
-{% set version = "0.4.0" %}
-{% set sha256 = "9bdf673a625b520a18dda633487cb48e1b3970ea3df5390d0c79fda9eaf2bc9b" %}
+{% set version = "0.4.0.post1" %}
+{% set sha256 = "5453415180e3f58b9498897a34da174a2641500986b953dbc0f6034dc775e099" %}
 
 package:
   name: {{ name|lower }}

From 55bd49891342f39603b5bec470c7ed2a2decb24b Mon Sep 17 00:00:00 2001
From: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
Date: Mon, 9 Dec 2024 11:36:43 -0600
Subject: [PATCH 07/10] Update build.sh

---
 recipes/ms2rescore-rs/build.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/recipes/ms2rescore-rs/build.sh b/recipes/ms2rescore-rs/build.sh
index 95c3de4df1c0e..fc003fa3432ac 100644
--- a/recipes/ms2rescore-rs/build.sh
+++ b/recipes/ms2rescore-rs/build.sh
@@ -7,7 +7,7 @@ set -ex
 # build statically linked binary with Rust
 RUST_BACKTRACE=1
 # Build the package using maturin - should produce *.whl files.
-maturin build --interpreter "${PYTHON}" -b pyo3 --release --strip
+maturin build --interpreter "${PYTHON}" -b pyo3 --release --strip --compatibility "manylinux2014"
 
 # Install *.whl files using pip
 $PYTHON -m pip install target/wheels/*.whl --no-deps --no-build-isolation --no-cache-dir -vvv

From 5ce6ab89c6c1556042288f2861780eb951ad934f Mon Sep 17 00:00:00 2001
From: mencian <joshua.zhuang@yahoo.com>
Date: Mon, 9 Dec 2024 18:07:01 -0600
Subject: [PATCH 08/10] fix patch

---
 recipes/ms2rescore-rs/setup.patch | 15 ++++++---------
 1 file changed, 6 insertions(+), 9 deletions(-)

diff --git a/recipes/ms2rescore-rs/setup.patch b/recipes/ms2rescore-rs/setup.patch
index a88fbd3deaf20..f2fb44cfcca13 100644
--- a/recipes/ms2rescore-rs/setup.patch
+++ b/recipes/ms2rescore-rs/setup.patch
@@ -1,17 +1,14 @@
 diff --git a/pyproject.toml b/pyproject.toml
-index 460b2bc..7940aa3 100644
+index 460b2bc..61b4d10 100644
 --- a/pyproject.toml
 +++ b/pyproject.toml
-@@ -16,4 +16,7 @@ dynamic = ["version"]
- test = ["pytest"]
+@@ -17,3 +17,4 @@ test = ["pytest"]
  
  [tool.maturin]
-+python-source = "python"
  features = ["pyo3/extension-module"]
-+strip = true
-+profile = "release"
++bindings = "pyo3"
 diff --git a/Cargo.toml b/Cargo.toml
-index 7900ad4..be46176 100644
+index 994665b..aa8e064 100644
 --- a/Cargo.toml
 +++ b/Cargo.toml
 @@ -14,6 +14,9 @@ default = ["thermo"]
@@ -23,5 +20,5 @@ index 7900ad4..be46176 100644
  timsrust = "0.3.0"
 +
 +[dependencies.pyo3]
-+version = "0.21.2"
-+features = ["anyhow"]
++version = "0.23.3"
++features = ["auto-initialize", "anyhow"]

From 0dc6cdb1c30732a883c5d4014f05fbc2bdd6b190 Mon Sep 17 00:00:00 2001
From: mencian <joshua.zhuang@yahoo.com>
Date: Mon, 9 Dec 2024 18:40:45 -0600
Subject: [PATCH 09/10] fix patches

---
 recipes/ms2rescore-rs/build.sh        | 2 +-
 recipes/ms2rescore-rs/manylinux.patch | 9 +++++++++
 recipes/ms2rescore-rs/meta.yaml       | 1 +
 recipes/ms2rescore-rs/setup.patch     | 2 +-
 4 files changed, 12 insertions(+), 2 deletions(-)
 create mode 100644 recipes/ms2rescore-rs/manylinux.patch

diff --git a/recipes/ms2rescore-rs/build.sh b/recipes/ms2rescore-rs/build.sh
index fc003fa3432ac..95c3de4df1c0e 100644
--- a/recipes/ms2rescore-rs/build.sh
+++ b/recipes/ms2rescore-rs/build.sh
@@ -7,7 +7,7 @@ set -ex
 # build statically linked binary with Rust
 RUST_BACKTRACE=1
 # Build the package using maturin - should produce *.whl files.
-maturin build --interpreter "${PYTHON}" -b pyo3 --release --strip --compatibility "manylinux2014"
+maturin build --interpreter "${PYTHON}" -b pyo3 --release --strip
 
 # Install *.whl files using pip
 $PYTHON -m pip install target/wheels/*.whl --no-deps --no-build-isolation --no-cache-dir -vvv
diff --git a/recipes/ms2rescore-rs/manylinux.patch b/recipes/ms2rescore-rs/manylinux.patch
new file mode 100644
index 0000000000000..fb9009846ba3f
--- /dev/null
+++ b/recipes/ms2rescore-rs/manylinux.patch
@@ -0,0 +1,9 @@
+diff --git a/pyproject.toml b/pyproject.toml
+index 61b4d10..c007322 100644
+--- a/pyproject.toml
++++ b/pyproject.toml
+@@ -18,3 +18,4 @@ test = ["pytest"]
+ [tool.maturin]
+ features = ["pyo3/extension-module"]
+ bindings = "pyo3"
++compatibility = "manylinux2014"
diff --git a/recipes/ms2rescore-rs/meta.yaml b/recipes/ms2rescore-rs/meta.yaml
index 850b985299421..9b25ed3c6e0d8 100644
--- a/recipes/ms2rescore-rs/meta.yaml
+++ b/recipes/ms2rescore-rs/meta.yaml
@@ -11,6 +11,7 @@ source:
   sha256: {{ sha256 }}
   patches:
     - setup.patch
+    - manylinux.patch  # [linux]
 
 build:
   number: 0
diff --git a/recipes/ms2rescore-rs/setup.patch b/recipes/ms2rescore-rs/setup.patch
index f2fb44cfcca13..cdc1172bf3645 100644
--- a/recipes/ms2rescore-rs/setup.patch
+++ b/recipes/ms2rescore-rs/setup.patch
@@ -20,5 +20,5 @@ index 994665b..aa8e064 100644
  timsrust = "0.3.0"
 +
 +[dependencies.pyo3]
-+version = "0.23.3"
++version = "0.21.2"
 +features = ["auto-initialize", "anyhow"]

From e88dbe7771c1916f2bf8d94958fe7220008c66bc Mon Sep 17 00:00:00 2001
From: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
Date: Mon, 9 Dec 2024 19:09:24 -0600
Subject: [PATCH 10/10] Update meta.yaml

---
 recipes/ms2rescore-rs/meta.yaml | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/recipes/ms2rescore-rs/meta.yaml b/recipes/ms2rescore-rs/meta.yaml
index 9b25ed3c6e0d8..eeb0dc6143cbd 100644
--- a/recipes/ms2rescore-rs/meta.yaml
+++ b/recipes/ms2rescore-rs/meta.yaml
@@ -25,13 +25,16 @@ requirements:
     - {{ compiler('rust') }}
     - make
     - cmake
+    - sysroot_linux-64 =2.17 # [linux]
   host:
     - zlib
     - python
     - maturin >=1.5,<2.0
     - pip
+    - sysroot_linux-64 =2.17 # [linux]
   run:
     - python
+    - sysroot_linux-64 =2.17 # [linux]
 
 test:
   imports:
@@ -39,8 +42,8 @@ test:
 
 about:
   home: https://github.com/compomics/ms2rescore-rs
-  summary: "Rust functionality for the MS²Rescore package"
-  license: Apache-2.0
+  summary: "Rust functionality for the MS²Rescore package."
+  license: "Apache-2.0"
   license_family: APACHE
   license_file: LICENSE
   dev_url: https://github.com/compomics/ms2rescore-rs