From 20519ea7da9818b9c64a098a9ead772467b964f6 Mon Sep 17 00:00:00 2001
From: Thomas-Otavio Peulen <thomas.otavio.peulen@gmail.com>
Date: Tue, 5 Nov 2024 08:49:44 +0100
Subject: [PATCH 01/18] Add tttrlib recipe

---
 recipes/tttrlib/LICENSE.txt   |  27 ++++++
 recipes/tttrlib/app_wrapper.c | 175 ++++++++++++++++++++++++++++++++++
 recipes/tttrlib/bld.bat       |  32 +++++++
 recipes/tttrlib/build.sh      |  26 +++++
 recipes/tttrlib/meta.yaml     |  68 +++++++++++++
 5 files changed, 328 insertions(+)
 create mode 100644 recipes/tttrlib/LICENSE.txt
 create mode 100644 recipes/tttrlib/app_wrapper.c
 create mode 100755 recipes/tttrlib/bld.bat
 create mode 100755 recipes/tttrlib/build.sh
 create mode 100644 recipes/tttrlib/meta.yaml

diff --git a/recipes/tttrlib/LICENSE.txt b/recipes/tttrlib/LICENSE.txt
new file mode 100644
index 0000000000000..66fe31cc38cc1
--- /dev/null
+++ b/recipes/tttrlib/LICENSE.txt
@@ -0,0 +1,27 @@
+BSD-3-Clause license
+Copyright (c) 2015-2022, conda-forge contributors
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+  1. Redistributions of source code must retain the above copyright notice,
+     this list of conditions and the following disclaimer.
+  2. Redistributions in binary form must reproduce the above copyright
+     notice, this list of conditions and the following disclaimer in the
+     documentation and/or other materials provided with the distribution.
+  3. Neither the name of the copyright holder nor the names of its
+     contributors may be used to endorse or promote products derived from
+     this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS OR CONTRIBUTORS BE LIABLE FOR
+ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+DAMAGE.
\ No newline at end of file
diff --git a/recipes/tttrlib/app_wrapper.c b/recipes/tttrlib/app_wrapper.c
new file mode 100644
index 0000000000000..326dceb63e296
--- /dev/null
+++ b/recipes/tttrlib/app_wrapper.c
@@ -0,0 +1,175 @@
+#include <stdio.h>
+#include <windows.h>
+#include <string.h>
+#include <stdlib.h>
+
+/*
+   See: https://github.com/conda-forge/imp-feedstock/tree/main/recipe
+   IMP Python command line tools on Unix/Linux/Mac are typically named
+   without a .py extension (e.g. 'myapp' not 'myapp.py') and rely on a
+   #!/usr/bin/python line at the start of the file to tell the OS that
+   they are Python files. This doesn't work on Windows though, since
+   Windows relies on the file extension.
+
+   To remedy this problem, we provide this wrapper. Compile with
+      cl app_wrapper.c shell32.lib
+   then copy the resulting app_wrapper.exe to myapp.exe and install in
+   the top-level Anaconda directory. Then a user should be able to simply
+   type 'myapp', and the right Python tool will be run.
+*/
+
+/* Get full path to fname in topdir */
+static char *get_new_full_path(const char *topdir, const char *fname)
+{
+    char *newpath = malloc(strlen(topdir) + strlen(fname) + 2);
+    strcpy(newpath, topdir);
+    strcat(newpath, "\\");
+    strcat(newpath, fname);
+    return newpath;
+}
+
+/* Get full path to this binary */
+static void get_full_path(char **dir, char **fname)
+{
+    char path[MAX_PATH * 2];
+    size_t l;
+    char *ch;
+    DWORD ret = GetModuleFileName(NULL, path, MAX_PATH * 2);
+    if (ret == 0) {
+        fprintf(stderr, "Failed to get executable name, code %d\n", GetLastError());
+        exit(1);
+    }
+    l = strlen(path);
+    if (l > 4 && path[l - 4] == '.') {
+        /* Remove extension */
+        path[l-4] = '\0';
+    }
+    ch = strrchr(path, '\\');
+    if (ch) {
+        *ch = '\0';
+        *fname = strdup(ch + 1);
+    } else {
+        *fname = strdup("");
+    }
+    *dir = strdup(path);
+}
+
+/* Find where the parameters start in the command line (skip past the
+   executable name) */
+static char *find_param_start(char *cmdline)
+{
+    BOOL in_quote = FALSE, in_space = FALSE;
+    for (; *cmdline; cmdline++) {
+        /* Ignore spaces that are quoted */
+        if (*cmdline == ' ' && !in_quote) {
+            in_space = TRUE;
+        } else if (*cmdline == '"') {
+            in_quote = !in_quote;
+        }
+        /* Return the first nonspace that follows a space */
+        if (in_space && *cmdline != ' ') {
+            break;
+        }
+    }
+    return cmdline;
+}
+
+/* Convert original parameters into those that python.exe wants (i.e. prepend
+   the name of the Python script) */
+static char *make_python_parameters(const char *orig_param, const char *binary)
+{
+    char *param = malloc(strlen(orig_param) + strlen(binary) + 4);
+    strcpy(param, "\"");
+    strcat(param, binary);
+    strcat(param, "\" ");
+    strcat(param, orig_param);
+    /*printf("python param %s\n", param);*/
+    return param;
+}
+
+/* Remove the last component of the path in place */
+static void remove_last_component(char *dir)
+{
+    char *pt;
+    if (!dir || !*dir) return;
+    /* Remove trailing slash if present */
+    if (dir[strlen(dir)-1] == '\\') {
+        dir[strlen(dir)-1] = '\0';
+    }
+    /* Remove everything after the last slash */
+    pt = strrchr(dir, '\\');
+    if (pt) {
+        *pt = '\0';
+    }
+}
+
+/* Get the full path to the Anaconda Python. */
+static char* get_python_binary(const char *topdir)
+{
+    char *python = malloc(strlen(topdir) + 12);
+    strcpy(python, topdir);
+    /* Remove last two components of the path (we are in Library/bin; python
+       is in the top-level directory) */
+    remove_last_component(python);
+    remove_last_component(python);
+    strcat(python, "\\python.exe");
+    return python;
+}
+
+/* Run the given Python script, passing it the parameters we ourselves
+   were given. */
+static DWORD run_binary(const char *binary, const char *topdir)
+{
+    SHELLEXECUTEINFO si;
+    BOOL bResult;
+    char *param, *python = NULL;
+    param = strdup(GetCommandLine());
+
+    ZeroMemory(&si, sizeof(SHELLEXECUTEINFO));
+    si.cbSize = sizeof(SHELLEXECUTEINFO);
+    /* Wait for the spawned process to finish, so that any output goes to the
+       console *before* the next command prompt */
+    si.fMask = SEE_MASK_NO_CONSOLE | SEE_MASK_NOASYNC | SEE_MASK_NOCLOSEPROCESS;
+    {
+        char *orig_param = param;
+        python = get_python_binary(topdir);
+        si.lpFile = python;
+        param = make_python_parameters(find_param_start(param), binary);
+        free(orig_param);
+        si.lpParameters = param;
+    }
+    si.nShow = SW_SHOWNA;
+    bResult = ShellExecuteEx(&si);
+    free(param);
+    free(python);
+
+    if (bResult) {
+        if (si.hProcess) {
+            DWORD exit_code;
+            WaitForSingleObject(si.hProcess, INFINITE);
+            GetExitCodeProcess(si.hProcess, &exit_code);
+            CloseHandle(si.hProcess);
+            return exit_code;
+        }
+    } else {
+        fprintf(stderr, "Failed to start process, code %d\n", GetLastError());
+        exit(1);
+    }
+    return 0;
+}
+
+int main(int argc, char *argv[]) {
+    int is_python;
+    char *dir, *fname, *new_full_path;
+    DWORD return_code;
+
+    get_full_path(&dir, &fname);
+    /*printf("%s, %s\n", dir, fname);*/
+    new_full_path = get_new_full_path(dir, fname);
+    /*printf("new full path %s, %d\n", new_full_path, is_python);*/
+    return_code = run_binary(new_full_path, dir);
+    free(dir);
+    free(fname);
+    free(new_full_path);
+    return return_code;
+}
diff --git a/recipes/tttrlib/bld.bat b/recipes/tttrlib/bld.bat
new file mode 100755
index 0000000000000..2abc2a7c890fd
--- /dev/null
+++ b/recipes/tttrlib/bld.bat
@@ -0,0 +1,32 @@
+cd %SRC_DIR%
+git submodule update --recursive --init --remote
+
+echo "Build app wrapper"
+:: build app wrapper
+copy "%RECIPE_DIR%\app_wrapper.c" .
+cl app_wrapper.c shell32.lib
+if errorlevel 1 exit 1
+
+rmdir b2 /s /q
+mkdir b2
+cd b2
+for /f %%A in ('python -c "import platform; print(platform.python_version())"') do set python_version=%%A
+echo Python version: %python_version%
+cmake .. -G "NMake Makefiles" ^
+ -DCMAKE_INSTALL_PREFIX="%LIBRARY_PREFIX%" ^
+ -DCMAKE_PREFIX_PATH="%PREFIX%" ^
+ -DBUILD_PYTHON_INTERFACE=ON ^
+ -DCMAKE_BUILD_TYPE=Release ^
+ -DCMAKE_LIBRARY_OUTPUT_DIRECTORY="%SP_DIR%" ^
+ -DCMAKE_SWIG_OUTDIR="%SP_DIR%" ^
+ -DPYTHON_VERSION="%python_version%" ^
+ -DBUILD_LIBRARY=ON
+nmake install
+
+
+:: Add wrappers to path for each Python command line tool
+:: (all files without an extension)
+cd %SRC_DIR%\bin
+for /f %%f in ('dir /b *.py') do copy "%SRC_DIR%\bin\%%f" "%PREFIX%\Library\bin\%%f"
+for /f %%f in ('dir /b *.') do copy "%SRC_DIR%\app_wrapper.exe" "%PREFIX%\Library\bin\%%f.exe"
+if errorlevel 1 exit 1
diff --git a/recipes/tttrlib/build.sh b/recipes/tttrlib/build.sh
new file mode 100755
index 0000000000000..d0d2e2583e50b
--- /dev/null
+++ b/recipes/tttrlib/build.sh
@@ -0,0 +1,26 @@
+mkdir b2 && cd b2
+
+if [[ "${target_platform}" == osx-* ]]; then
+  # See https://conda-forge.org/docs/maintainer/knowledge_base.html#newer-c-features-with-old-sdk
+  CXXFLAGS="${CXXFLAGS} -D_LIBCPP_DISABLE_AVAILABILITY"
+fi
+
+cmake \
+ -DCMAKE_INSTALL_PREFIX="$PREFIX" \
+ -DCMAKE_PREFIX_PATH="$PREFIX" \
+ -DBUILD_PYTHON_INTERFACE=ON \
+ -DCMAKE_BUILD_TYPE=Release \
+ -DCMAKE_LIBRARY_OUTPUT_DIRECTORY="$SP_DIR" \
+ -DCMAKE_SWIG_OUTDIR="$SP_DIR" \
+ -DBUILD_LIBRARY=ON \
+ -DPYTHON_VERSION=$(python -c 'import platform; print(platform.python_version())')\
+ -G Ninja ..
+
+# On some platforms (notably aarch64 with Drone) builds can fail due to
+# running out of memory. If this happens, try the build again; if it
+# still fails, restrict to one core.
+ninja install -k 0 || ninja install -k 0 || ninja install -j 1
+
+# Copy programs to bin
+cd $PREFIX/bin
+cp $SRC_DIR/bin/* .
\ No newline at end of file
diff --git a/recipes/tttrlib/meta.yaml b/recipes/tttrlib/meta.yaml
new file mode 100644
index 0000000000000..bb0183895212a
--- /dev/null
+++ b/recipes/tttrlib/meta.yaml
@@ -0,0 +1,68 @@
+{% set name = "tttrlib" %}
+{% set version = "0.25.0" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://github.com/Fluorescence-Tools/tttrlib/archive/refs/tags/v{{ version }}.tar.gz
+  sha256: e15604ef063257cd87d3bdf266c1d5a448189508f51cdc4156a93cb2b46fe807
+
+build:
+  number: 0
+
+requirements:
+  build:
+    - {{ compiler('c') }}
+    - {{ compiler('cxx') }}
+    - {{ stdlib("c") }}
+    - llvm-openmp        # [osx]
+    - libgomp            # [linux]
+    - pkg-config         # [not win]
+    - cmake
+    - ninja
+    - make               # [linux]
+    - doxygen
+    - swig 4.2.*
+    - python
+    - numpy
+  host:
+    - libboost-devel
+    - hdf5
+    - python
+    - setuptools
+    - numpy
+  run:
+    - python
+    - tqdm
+    - click
+    - click-didyoumean
+    - {{ pin_compatible('numpy') }}
+    - scikit-image
+    - matplotlib-base
+    - hdf5
+
+test:
+  imports:
+    - tttrlib
+  commands:
+    - tttrlib --help      # [not win]
+
+about:
+  home: https://github.com/fluorescence-tools/tttrlib
+  summary: 'A file format agnostic library for time-resolved imaging and spectroscopic data'
+  description: |
+    tttrlib is a simple, fast, libray to read, write and process
+    time-resolved imaging and spectroscopic data. For speed, it 
+    is written in C++ and wrapped for Python via SWIG.
+  license: BSD-3-Clause
+  license_family: BSD
+  license_file: LICENSE.txt
+  doc_url: https://tttrlib.readthedocs.io/
+  dev_url: https://github.com/fluorescence-tools/tttrlib
+
+extra:
+  recipe-maintainers:
+    - tpeulen
+    - khemmen

From aaaf15afb18d8b113f29715e5c26fd27cdd70c6e Mon Sep 17 00:00:00 2001
From: Thomas-Otavio Peulen <thomas.otavio.peulen@gmail.com>
Date: Tue, 5 Nov 2024 09:23:45 +0100
Subject: [PATCH 02/18] Remove bld.bat

---
 recipes/tttrlib/bld.bat | 32 --------------------------------
 1 file changed, 32 deletions(-)
 delete mode 100755 recipes/tttrlib/bld.bat

diff --git a/recipes/tttrlib/bld.bat b/recipes/tttrlib/bld.bat
deleted file mode 100755
index 2abc2a7c890fd..0000000000000
--- a/recipes/tttrlib/bld.bat
+++ /dev/null
@@ -1,32 +0,0 @@
-cd %SRC_DIR%
-git submodule update --recursive --init --remote
-
-echo "Build app wrapper"
-:: build app wrapper
-copy "%RECIPE_DIR%\app_wrapper.c" .
-cl app_wrapper.c shell32.lib
-if errorlevel 1 exit 1
-
-rmdir b2 /s /q
-mkdir b2
-cd b2
-for /f %%A in ('python -c "import platform; print(platform.python_version())"') do set python_version=%%A
-echo Python version: %python_version%
-cmake .. -G "NMake Makefiles" ^
- -DCMAKE_INSTALL_PREFIX="%LIBRARY_PREFIX%" ^
- -DCMAKE_PREFIX_PATH="%PREFIX%" ^
- -DBUILD_PYTHON_INTERFACE=ON ^
- -DCMAKE_BUILD_TYPE=Release ^
- -DCMAKE_LIBRARY_OUTPUT_DIRECTORY="%SP_DIR%" ^
- -DCMAKE_SWIG_OUTDIR="%SP_DIR%" ^
- -DPYTHON_VERSION="%python_version%" ^
- -DBUILD_LIBRARY=ON
-nmake install
-
-
-:: Add wrappers to path for each Python command line tool
-:: (all files without an extension)
-cd %SRC_DIR%\bin
-for /f %%f in ('dir /b *.py') do copy "%SRC_DIR%\bin\%%f" "%PREFIX%\Library\bin\%%f"
-for /f %%f in ('dir /b *.') do copy "%SRC_DIR%\app_wrapper.exe" "%PREFIX%\Library\bin\%%f.exe"
-if errorlevel 1 exit 1

From 828daf7920e399ebcf91b5ead40ad07cfee9b4c3 Mon Sep 17 00:00:00 2001
From: Thomas-Otavio Peulen <thomas.otavio.peulen@gmail.com>
Date: Tue, 5 Nov 2024 09:24:01 +0100
Subject: [PATCH 03/18] Fix version issues

---
 recipes/tttrlib/meta.yaml | 22 ++++++++++------------
 1 file changed, 10 insertions(+), 12 deletions(-)

diff --git a/recipes/tttrlib/meta.yaml b/recipes/tttrlib/meta.yaml
index bb0183895212a..96222679fc565 100644
--- a/recipes/tttrlib/meta.yaml
+++ b/recipes/tttrlib/meta.yaml
@@ -1,30 +1,28 @@
-{% set name = "tttrlib" %}
-{% set version = "0.25.0" %}
-
 package:
-  name: {{ name|lower }}
-  version: {{ version }}
+  name: tttrlib
+  version: "0.25.0"
 
 source:
-  url: https://github.com/Fluorescence-Tools/tttrlib/archive/refs/tags/v{{ version }}.tar.gz
+  url: https://github.com/Fluorescence-Tools/tttrlib/archive/refs/tags/v0.25.0.tar.gz
   sha256: e15604ef063257cd87d3bdf266c1d5a448189508f51cdc4156a93cb2b46fe807
 
 build:
   number: 0
+  run_exports: '{{ pin_subpackage("tttrlib", max_pin="x.x") }}'
 
 requirements:
   build:
     - {{ compiler('c') }}
     - {{ compiler('cxx') }}
     - {{ stdlib("c") }}
-    - llvm-openmp        # [osx]
-    - libgomp            # [linux]
-    - pkg-config         # [not win]
+    - llvm-openmp  # [osx]
+    - libgomp  # [linux]
+    - pkg-config
     - cmake
     - ninja
-    - make               # [linux]
+    - make  # [linux]
     - doxygen
-    - swig 4.2.*
+    - swig <4.3.0
     - python
     - numpy
   host:
@@ -47,7 +45,7 @@ test:
   imports:
     - tttrlib
   commands:
-    - tttrlib --help      # [not win]
+    - tttrlib --help
 
 about:
   home: https://github.com/fluorescence-tools/tttrlib

From def59b27e94279c1548e7718afa88baf6b1baead Mon Sep 17 00:00:00 2001
From: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
Date: Tue, 5 Nov 2024 03:16:35 -0600
Subject: [PATCH 04/18] Update meta.yaml

---
 recipes/tttrlib/meta.yaml | 24 ++++++++++++------------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/recipes/tttrlib/meta.yaml b/recipes/tttrlib/meta.yaml
index 96222679fc565..5c29d252d3b54 100644
--- a/recipes/tttrlib/meta.yaml
+++ b/recipes/tttrlib/meta.yaml
@@ -1,9 +1,12 @@
+{% set name = "tttrlib" %}
+{% set version = "0.25.0" %}
+
 package:
-  name: tttrlib
-  version: "0.25.0"
+  name: {{ name }}
+  version: {{ version }}
 
 source:
-  url: https://github.com/Fluorescence-Tools/tttrlib/archive/refs/tags/v0.25.0.tar.gz
+  url: https://github.com/Fluorescence-Tools/tttrlib/archive/refs/tags/v{{ version }}.tar.gz
   sha256: e15604ef063257cd87d3bdf266c1d5a448189508f51cdc4156a93cb2b46fe807
 
 build:
@@ -14,22 +17,19 @@ requirements:
   build:
     - {{ compiler('c') }}
     - {{ compiler('cxx') }}
-    - {{ stdlib("c") }}
-    - llvm-openmp  # [osx]
-    - libgomp  # [linux]
     - pkg-config
     - cmake
     - ninja
     - make  # [linux]
     - doxygen
     - swig <4.3.0
-    - python
-    - numpy
   host:
-    - libboost-devel
+    - llvm-openmp   # [osx]
+    - libgomp   # [linux]
+    - libboost-cpp
     - hdf5
     - python
-    - setuptools
+    - pip
     - numpy
   run:
     - python
@@ -49,7 +49,7 @@ test:
 
 about:
   home: https://github.com/fluorescence-tools/tttrlib
-  summary: 'A file format agnostic library for time-resolved imaging and spectroscopic data'
+  summary: 'A file format agnostic library for time-resolved imaging and spectroscopic data.'
   description: |
     tttrlib is a simple, fast, libray to read, write and process
     time-resolved imaging and spectroscopic data. For speed, it 
@@ -57,7 +57,7 @@ about:
   license: BSD-3-Clause
   license_family: BSD
   license_file: LICENSE.txt
-  doc_url: https://tttrlib.readthedocs.io/
+  doc_url: https://tttrlib.readthedocs.io
   dev_url: https://github.com/fluorescence-tools/tttrlib
 
 extra:

From a3e7d406fc5fa17a58ccd6de3c1aebb3cee5eb95 Mon Sep 17 00:00:00 2001
From: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
Date: Tue, 5 Nov 2024 03:22:54 -0600
Subject: [PATCH 05/18] Update build.sh

---
 recipes/tttrlib/build.sh | 32 +++++++++++++++++++-------------
 1 file changed, 19 insertions(+), 13 deletions(-)

diff --git a/recipes/tttrlib/build.sh b/recipes/tttrlib/build.sh
index d0d2e2583e50b..20ecefe97b93a 100755
--- a/recipes/tttrlib/build.sh
+++ b/recipes/tttrlib/build.sh
@@ -1,26 +1,32 @@
+#!/bin/bash
+
 mkdir b2 && cd b2
 
 if [[ "${target_platform}" == osx-* ]]; then
   # See https://conda-forge.org/docs/maintainer/knowledge_base.html#newer-c-features-with-old-sdk
   CXXFLAGS="${CXXFLAGS} -D_LIBCPP_DISABLE_AVAILABILITY"
+  export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER"
+else
+  export CONFIG_ARGS=""
 fi
 
-cmake \
- -DCMAKE_INSTALL_PREFIX="$PREFIX" \
- -DCMAKE_PREFIX_PATH="$PREFIX" \
- -DBUILD_PYTHON_INTERFACE=ON \
- -DCMAKE_BUILD_TYPE=Release \
- -DCMAKE_LIBRARY_OUTPUT_DIRECTORY="$SP_DIR" \
- -DCMAKE_SWIG_OUTDIR="$SP_DIR" \
- -DBUILD_LIBRARY=ON \
- -DPYTHON_VERSION=$(python -c 'import platform; print(platform.python_version())')\
- -G Ninja ..
+cmake -S .. -B . \
+  -DCMAKE_CXX_COMPILER="${CXX}" \
+  -DCMAKE_INSTALL_PREFIX="$PREFIX" \
+  -DBUILD_PYTHON_INTERFACE=ON \
+  -DCMAKE_BUILD_TYPE=Release \
+  -DCMAKE_LIBRARY_OUTPUT_DIRECTORY="$SP_DIR" \
+  -DCMAKE_SWIG_OUTDIR="$SP_DIR" \
+  -DBUILD_LIBRARY=ON \
+  -DPYTHON_VERSION=$(python -c 'import platform; print(platform.python_version())') \
+  -G Ninja \
+  "${CONFIG_ARGS}"
 
 # On some platforms (notably aarch64 with Drone) builds can fail due to
 # running out of memory. If this happens, try the build again; if it
 # still fails, restrict to one core.
-ninja install -k 0 || ninja install -k 0 || ninja install -j 1
+ninja install -k 0 || ninja install -k 0 || ninja install -j ${CPU_COUNT}
 
 # Copy programs to bin
-cd $PREFIX/bin
-cp $SRC_DIR/bin/* .
\ No newline at end of file
+chmod 0755 $SRC_DIR/bin/*
+cp -f $SRC_DIR/bin/* $PREFIX/bin

From f5611f3fa2351e27d89e1a0a08fc188713ca9479 Mon Sep 17 00:00:00 2001
From: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
Date: Tue, 5 Nov 2024 03:23:29 -0600
Subject: [PATCH 06/18] Delete recipes/tttrlib/LICENSE.txt

---
 recipes/tttrlib/LICENSE.txt | 27 ---------------------------
 1 file changed, 27 deletions(-)
 delete mode 100644 recipes/tttrlib/LICENSE.txt

diff --git a/recipes/tttrlib/LICENSE.txt b/recipes/tttrlib/LICENSE.txt
deleted file mode 100644
index 66fe31cc38cc1..0000000000000
--- a/recipes/tttrlib/LICENSE.txt
+++ /dev/null
@@ -1,27 +0,0 @@
-BSD-3-Clause license
-Copyright (c) 2015-2022, conda-forge contributors
-All rights reserved.
-
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are met:
-
-  1. Redistributions of source code must retain the above copyright notice,
-     this list of conditions and the following disclaimer.
-  2. Redistributions in binary form must reproduce the above copyright
-     notice, this list of conditions and the following disclaimer in the
-     documentation and/or other materials provided with the distribution.
-  3. Neither the name of the copyright holder nor the names of its
-     contributors may be used to endorse or promote products derived from
-     this software without specific prior written permission.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS OR CONTRIBUTORS BE LIABLE FOR
-ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-DAMAGE.
\ No newline at end of file

From db042c3bd7db0f898b6607c9db3b0f9c1574988f Mon Sep 17 00:00:00 2001
From: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
Date: Tue, 5 Nov 2024 03:30:31 -0600
Subject: [PATCH 07/18] Update meta.yaml

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

diff --git a/recipes/tttrlib/meta.yaml b/recipes/tttrlib/meta.yaml
index 5c29d252d3b54..e172baf18d8b4 100644
--- a/recipes/tttrlib/meta.yaml
+++ b/recipes/tttrlib/meta.yaml
@@ -26,7 +26,7 @@ requirements:
   host:
     - llvm-openmp   # [osx]
     - libgomp   # [linux]
-    - libboost-cpp
+    - boost-cpp
     - hdf5
     - python
     - pip

From 78a75c8e7ebc4f6f697f7319fe234fd819d8e45d Mon Sep 17 00:00:00 2001
From: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
Date: Tue, 5 Nov 2024 03:49:56 -0600
Subject: [PATCH 08/18] Update build.sh

---
 recipes/tttrlib/build.sh | 2 --
 1 file changed, 2 deletions(-)

diff --git a/recipes/tttrlib/build.sh b/recipes/tttrlib/build.sh
index 20ecefe97b93a..4d381437b4311 100755
--- a/recipes/tttrlib/build.sh
+++ b/recipes/tttrlib/build.sh
@@ -15,8 +15,6 @@ cmake -S .. -B . \
   -DCMAKE_INSTALL_PREFIX="$PREFIX" \
   -DBUILD_PYTHON_INTERFACE=ON \
   -DCMAKE_BUILD_TYPE=Release \
-  -DCMAKE_LIBRARY_OUTPUT_DIRECTORY="$SP_DIR" \
-  -DCMAKE_SWIG_OUTDIR="$SP_DIR" \
   -DBUILD_LIBRARY=ON \
   -DPYTHON_VERSION=$(python -c 'import platform; print(platform.python_version())') \
   -G Ninja \

From 2f0d38ca2dc1e0f234a0cf4876118d9537254300 Mon Sep 17 00:00:00 2001
From: Thomas-Otavio Peulen <thomas.otavio.peulen@gmail.com>
Date: Tue, 5 Nov 2024 13:20:45 +0100
Subject: [PATCH 09/18] Build environment uses python/numpy

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

diff --git a/recipes/tttrlib/meta.yaml b/recipes/tttrlib/meta.yaml
index e172baf18d8b4..b44412d22ee67 100644
--- a/recipes/tttrlib/meta.yaml
+++ b/recipes/tttrlib/meta.yaml
@@ -23,6 +23,8 @@ requirements:
     - make  # [linux]
     - doxygen
     - swig <4.3.0
+    - python
+    - numpy
   host:
     - llvm-openmp   # [osx]
     - libgomp   # [linux]

From e23517a2b7c8fe0ecb644387b30c598c04c0e508 Mon Sep 17 00:00:00 2001
From: Thomas-Otavio Peulen <thomas.otavio.peulen@gmail.com>
Date: Tue, 5 Nov 2024 13:21:45 +0100
Subject: [PATCH 10/18] Remove Windows app wrapper

bioconda does not build for windows
-> remove windows app wrapper.
---
 recipes/tttrlib/app_wrapper.c | 175 ----------------------------------
 1 file changed, 175 deletions(-)
 delete mode 100644 recipes/tttrlib/app_wrapper.c

diff --git a/recipes/tttrlib/app_wrapper.c b/recipes/tttrlib/app_wrapper.c
deleted file mode 100644
index 326dceb63e296..0000000000000
--- a/recipes/tttrlib/app_wrapper.c
+++ /dev/null
@@ -1,175 +0,0 @@
-#include <stdio.h>
-#include <windows.h>
-#include <string.h>
-#include <stdlib.h>
-
-/*
-   See: https://github.com/conda-forge/imp-feedstock/tree/main/recipe
-   IMP Python command line tools on Unix/Linux/Mac are typically named
-   without a .py extension (e.g. 'myapp' not 'myapp.py') and rely on a
-   #!/usr/bin/python line at the start of the file to tell the OS that
-   they are Python files. This doesn't work on Windows though, since
-   Windows relies on the file extension.
-
-   To remedy this problem, we provide this wrapper. Compile with
-      cl app_wrapper.c shell32.lib
-   then copy the resulting app_wrapper.exe to myapp.exe and install in
-   the top-level Anaconda directory. Then a user should be able to simply
-   type 'myapp', and the right Python tool will be run.
-*/
-
-/* Get full path to fname in topdir */
-static char *get_new_full_path(const char *topdir, const char *fname)
-{
-    char *newpath = malloc(strlen(topdir) + strlen(fname) + 2);
-    strcpy(newpath, topdir);
-    strcat(newpath, "\\");
-    strcat(newpath, fname);
-    return newpath;
-}
-
-/* Get full path to this binary */
-static void get_full_path(char **dir, char **fname)
-{
-    char path[MAX_PATH * 2];
-    size_t l;
-    char *ch;
-    DWORD ret = GetModuleFileName(NULL, path, MAX_PATH * 2);
-    if (ret == 0) {
-        fprintf(stderr, "Failed to get executable name, code %d\n", GetLastError());
-        exit(1);
-    }
-    l = strlen(path);
-    if (l > 4 && path[l - 4] == '.') {
-        /* Remove extension */
-        path[l-4] = '\0';
-    }
-    ch = strrchr(path, '\\');
-    if (ch) {
-        *ch = '\0';
-        *fname = strdup(ch + 1);
-    } else {
-        *fname = strdup("");
-    }
-    *dir = strdup(path);
-}
-
-/* Find where the parameters start in the command line (skip past the
-   executable name) */
-static char *find_param_start(char *cmdline)
-{
-    BOOL in_quote = FALSE, in_space = FALSE;
-    for (; *cmdline; cmdline++) {
-        /* Ignore spaces that are quoted */
-        if (*cmdline == ' ' && !in_quote) {
-            in_space = TRUE;
-        } else if (*cmdline == '"') {
-            in_quote = !in_quote;
-        }
-        /* Return the first nonspace that follows a space */
-        if (in_space && *cmdline != ' ') {
-            break;
-        }
-    }
-    return cmdline;
-}
-
-/* Convert original parameters into those that python.exe wants (i.e. prepend
-   the name of the Python script) */
-static char *make_python_parameters(const char *orig_param, const char *binary)
-{
-    char *param = malloc(strlen(orig_param) + strlen(binary) + 4);
-    strcpy(param, "\"");
-    strcat(param, binary);
-    strcat(param, "\" ");
-    strcat(param, orig_param);
-    /*printf("python param %s\n", param);*/
-    return param;
-}
-
-/* Remove the last component of the path in place */
-static void remove_last_component(char *dir)
-{
-    char *pt;
-    if (!dir || !*dir) return;
-    /* Remove trailing slash if present */
-    if (dir[strlen(dir)-1] == '\\') {
-        dir[strlen(dir)-1] = '\0';
-    }
-    /* Remove everything after the last slash */
-    pt = strrchr(dir, '\\');
-    if (pt) {
-        *pt = '\0';
-    }
-}
-
-/* Get the full path to the Anaconda Python. */
-static char* get_python_binary(const char *topdir)
-{
-    char *python = malloc(strlen(topdir) + 12);
-    strcpy(python, topdir);
-    /* Remove last two components of the path (we are in Library/bin; python
-       is in the top-level directory) */
-    remove_last_component(python);
-    remove_last_component(python);
-    strcat(python, "\\python.exe");
-    return python;
-}
-
-/* Run the given Python script, passing it the parameters we ourselves
-   were given. */
-static DWORD run_binary(const char *binary, const char *topdir)
-{
-    SHELLEXECUTEINFO si;
-    BOOL bResult;
-    char *param, *python = NULL;
-    param = strdup(GetCommandLine());
-
-    ZeroMemory(&si, sizeof(SHELLEXECUTEINFO));
-    si.cbSize = sizeof(SHELLEXECUTEINFO);
-    /* Wait for the spawned process to finish, so that any output goes to the
-       console *before* the next command prompt */
-    si.fMask = SEE_MASK_NO_CONSOLE | SEE_MASK_NOASYNC | SEE_MASK_NOCLOSEPROCESS;
-    {
-        char *orig_param = param;
-        python = get_python_binary(topdir);
-        si.lpFile = python;
-        param = make_python_parameters(find_param_start(param), binary);
-        free(orig_param);
-        si.lpParameters = param;
-    }
-    si.nShow = SW_SHOWNA;
-    bResult = ShellExecuteEx(&si);
-    free(param);
-    free(python);
-
-    if (bResult) {
-        if (si.hProcess) {
-            DWORD exit_code;
-            WaitForSingleObject(si.hProcess, INFINITE);
-            GetExitCodeProcess(si.hProcess, &exit_code);
-            CloseHandle(si.hProcess);
-            return exit_code;
-        }
-    } else {
-        fprintf(stderr, "Failed to start process, code %d\n", GetLastError());
-        exit(1);
-    }
-    return 0;
-}
-
-int main(int argc, char *argv[]) {
-    int is_python;
-    char *dir, *fname, *new_full_path;
-    DWORD return_code;
-
-    get_full_path(&dir, &fname);
-    /*printf("%s, %s\n", dir, fname);*/
-    new_full_path = get_new_full_path(dir, fname);
-    /*printf("new full path %s, %d\n", new_full_path, is_python);*/
-    return_code = run_binary(new_full_path, dir);
-    free(dir);
-    free(fname);
-    free(new_full_path);
-    return return_code;
-}

From 9bf368a3b6f834b7cc7c106be92668d3a193e90b Mon Sep 17 00:00:00 2001
From: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
Date: Tue, 5 Nov 2024 14:59:13 -0600
Subject: [PATCH 11/18] Update meta.yaml

---
 recipes/tttrlib/meta.yaml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/recipes/tttrlib/meta.yaml b/recipes/tttrlib/meta.yaml
index b44412d22ee67..7dc514b52a873 100644
--- a/recipes/tttrlib/meta.yaml
+++ b/recipes/tttrlib/meta.yaml
@@ -20,12 +20,10 @@ requirements:
     - pkg-config
     - cmake
     - ninja
-    - make  # [linux]
-    - doxygen
-    - swig <4.3.0
-    - python
-    - numpy
+    - make
   host:
+    - swig <4.3.0
+    - doxygen
     - llvm-openmp   # [osx]
     - libgomp   # [linux]
     - boost-cpp
@@ -35,6 +33,8 @@ requirements:
     - numpy
   run:
     - python
+    - llvm-openmp   # [osx]
+    - libgomp   # [linux]
     - tqdm
     - click
     - click-didyoumean

From c239340823f3e311bd13859b37392e4a80f0c801 Mon Sep 17 00:00:00 2001
From: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
Date: Tue, 12 Nov 2024 05:36:19 -0600
Subject: [PATCH 12/18] try swig in build section

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

diff --git a/recipes/tttrlib/meta.yaml b/recipes/tttrlib/meta.yaml
index 7dc514b52a873..4ee787a5aae00 100644
--- a/recipes/tttrlib/meta.yaml
+++ b/recipes/tttrlib/meta.yaml
@@ -21,8 +21,8 @@ requirements:
     - cmake
     - ninja
     - make
+    - swig
   host:
-    - swig <4.3.0
     - doxygen
     - llvm-openmp   # [osx]
     - libgomp   # [linux]

From 2158694d598e8d12616100fd0b648d0266affc42 Mon Sep 17 00:00:00 2001
From: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
Date: Tue, 12 Nov 2024 05:50:26 -0600
Subject: [PATCH 13/18] pin swig <4.3.0

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

diff --git a/recipes/tttrlib/meta.yaml b/recipes/tttrlib/meta.yaml
index 4ee787a5aae00..1a0c71a0c94c3 100644
--- a/recipes/tttrlib/meta.yaml
+++ b/recipes/tttrlib/meta.yaml
@@ -21,7 +21,7 @@ requirements:
     - cmake
     - ninja
     - make
-    - swig
+    - swig <4.3.0
   host:
     - doxygen
     - llvm-openmp   # [osx]

From e35d14b1eb46b687fe38f0e4f12247c33e6f9947 Mon Sep 17 00:00:00 2001
From: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
Date: Tue, 12 Nov 2024 09:36:14 -0600
Subject: [PATCH 14/18] Update meta.yaml

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

diff --git a/recipes/tttrlib/meta.yaml b/recipes/tttrlib/meta.yaml
index 1a0c71a0c94c3..7dc514b52a873 100644
--- a/recipes/tttrlib/meta.yaml
+++ b/recipes/tttrlib/meta.yaml
@@ -21,8 +21,8 @@ requirements:
     - cmake
     - ninja
     - make
-    - swig <4.3.0
   host:
+    - swig <4.3.0
     - doxygen
     - llvm-openmp   # [osx]
     - libgomp   # [linux]

From 6f8c5936c7cfd4b9a592a549c5f0716f0d0be636 Mon Sep 17 00:00:00 2001
From: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
Date: Tue, 12 Nov 2024 09:37:40 -0600
Subject: [PATCH 15/18] Update build.sh

---
 recipes/tttrlib/build.sh | 1 +
 1 file changed, 1 insertion(+)

diff --git a/recipes/tttrlib/build.sh b/recipes/tttrlib/build.sh
index 4d381437b4311..1d728a4c8de2c 100755
--- a/recipes/tttrlib/build.sh
+++ b/recipes/tttrlib/build.sh
@@ -17,6 +17,7 @@ cmake -S .. -B . \
   -DCMAKE_BUILD_TYPE=Release \
   -DBUILD_LIBRARY=ON \
   -DPYTHON_VERSION=$(python -c 'import platform; print(platform.python_version())') \
+  -DPython3_ROOT_DIR="${PYTHON}" \
   -G Ninja \
   "${CONFIG_ARGS}"
 

From 4a0ae5fd5145fccd485e77035a977448da7c73ff Mon Sep 17 00:00:00 2001
From: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
Date: Tue, 12 Nov 2024 09:44:45 -0600
Subject: [PATCH 16/18] Update build.sh

---
 recipes/tttrlib/build.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/recipes/tttrlib/build.sh b/recipes/tttrlib/build.sh
index 1d728a4c8de2c..d27bf1de117b3 100755
--- a/recipes/tttrlib/build.sh
+++ b/recipes/tttrlib/build.sh
@@ -12,12 +12,12 @@ fi
 
 cmake -S .. -B . \
   -DCMAKE_CXX_COMPILER="${CXX}" \
-  -DCMAKE_INSTALL_PREFIX="$PREFIX" \
+  -DCMAKE_INSTALL_PREFIX="${PREFIX}" \
   -DBUILD_PYTHON_INTERFACE=ON \
   -DCMAKE_BUILD_TYPE=Release \
   -DBUILD_LIBRARY=ON \
   -DPYTHON_VERSION=$(python -c 'import platform; print(platform.python_version())') \
-  -DPython3_ROOT_DIR="${PYTHON}" \
+  -DPython3_ROOT_DIR="${PREFIX}/bin" \
   -G Ninja \
   "${CONFIG_ARGS}"
 

From ec34809c403bd32ec9f6b040173028da0f40d9a3 Mon Sep 17 00:00:00 2001
From: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
Date: Tue, 12 Nov 2024 19:26:21 -0600
Subject: [PATCH 17/18] Update build.sh

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

diff --git a/recipes/tttrlib/build.sh b/recipes/tttrlib/build.sh
index d27bf1de117b3..b4013e98b4ad8 100755
--- a/recipes/tttrlib/build.sh
+++ b/recipes/tttrlib/build.sh
@@ -17,7 +17,7 @@ cmake -S .. -B . \
   -DCMAKE_BUILD_TYPE=Release \
   -DBUILD_LIBRARY=ON \
   -DPYTHON_VERSION=$(python -c 'import platform; print(platform.python_version())') \
-  -DPython3_ROOT_DIR="${PREFIX}/bin" \
+  -DPython_ROOT_DIR="${PREFIX}/bin" \
   -G Ninja \
   "${CONFIG_ARGS}"
 

From f000548c0d51a018ac89c2c292e5ff70608d8224 Mon Sep 17 00:00:00 2001
From: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
Date: Tue, 12 Nov 2024 20:30:24 -0600
Subject: [PATCH 18/18] Update meta.yaml

---
 recipes/tttrlib/meta.yaml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/recipes/tttrlib/meta.yaml b/recipes/tttrlib/meta.yaml
index 7dc514b52a873..d9b4c5bcb9146 100644
--- a/recipes/tttrlib/meta.yaml
+++ b/recipes/tttrlib/meta.yaml
@@ -11,6 +11,7 @@ source:
 
 build:
   number: 0
+  skip: True  # [osx and py > 310]
   run_exports: '{{ pin_subpackage("tttrlib", max_pin="x.x") }}'
 
 requirements:
@@ -35,10 +36,11 @@ requirements:
     - python
     - llvm-openmp   # [osx]
     - libgomp   # [linux]
+    - boost-cpp
     - tqdm
     - click
     - click-didyoumean
-    - {{ pin_compatible('numpy') }}
+    - numpy
     - scikit-image
     - matplotlib-base
     - hdf5