Add tttrlib

recipes/tttrlib/LICENSE.txt

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+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.

recipes/tttrlib/app_wrapper.c

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+#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;
+}

recipes/tttrlib/build.sh

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+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/* .

recipes/tttrlib/meta.yaml

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+{% set name = "tttrlib" %}
+{% set version = "0.25.0" %}
+
+package:
+  name: {{ name }}
+  version: {{ version }}
+
+source:
+  url: https://github.com/Fluorescence-Tools/tttrlib/archive/refs/tags/v{{ version }}.tar.gz
+  sha256: e15604ef063257cd87d3bdf266c1d5a448189508f51cdc4156a93cb2b46fe807
+
+build:
+  number: 0
+  run_exports: '{{ pin_subpackage("tttrlib", max_pin="x.x") }}'
+
+requirements:
+  build:
+    - {{ compiler('c') }}
+    - {{ compiler('cxx') }}
+    - pkg-config
+    - cmake
+    - ninja
+    - make  # [linux]
+    - doxygen
+    - swig <4.3.0
+  host:
+    - llvm-openmp   # [osx]
+    - libgomp   # [linux]
+    - libboost-cpp
+    - hdf5
+    - python
+    - pip
+    - numpy
+  run:
+    - python
+    - tqdm
+    - click
+    - click-didyoumean
+    - {{ pin_compatible('numpy') }}
+    - scikit-image
+    - matplotlib-base
+    - hdf5
+
+test:
+  imports:
+    - tttrlib
+  commands:
+    - tttrlib --help
+
+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