fix ci and add formatting (#48)

* add dependency

* dont run blocking zmq example and add formatting

* format files

.github/workflows/common-workflow.yml

@@ -45,7 +45,7 @@ jobs:
           pwd
           export PROJECT_ROOT_DIR="."
           ls build/examples/*_example
-          find build/examples -name "*_example"  | xargs -I {} -n 1 -t  bash -c {}
+          find build/examples -name "*_example" -not -name "zmq_example" | xargs -I {} -n 1 -t  bash -c {}
 
 
 

.github/workflows/format.yml

@@ -0,0 +1,19 @@
+name: test-formatting
+on: 
+  push:
+
+jobs:
+  test-formatting:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: check if files are formatted
+        # find all examples in build/examples and run them
+        run: |
+          pwd
+          find -name "*.cpp" -not -path "./build/*" | xargs -I {} -n 1 -P 10 clang-format  {}  -Werror --dry-run -style='file:.clang-format'
+
+          
+
+
+

aare-environment.yml

@@ -7,3 +7,4 @@ dependencies:
   - pybind11
   - nlohmann_json
   - catch2
+  - zeromq

core/src/DType.cpp

@@ -4,7 +4,6 @@
 
 namespace aare {
 
-
 DType::DType(const std::type_info &t) {
     if (t == typeid(int8_t))
         m_type = TypeIndex::INT8;
@@ -29,8 +28,7 @@ DType::DType(const std::type_info &t) {
     else if (t == typeid(double))
         m_type = TypeIndex::DOUBLE;
     else
-        throw std::runtime_error(
+        throw std::runtime_error("Could not construct data type. Type not supported.");
-            "Could not construct data type. Type not supported.");
 }
 
 uint8_t DType::bitdepth() const {
@@ -56,7 +54,6 @@ uint8_t DType::bitdepth()const {
     default:
         throw std::runtime_error(LOCATION + "Could not get bitdepth. Type not supported.");
     }
-
 }
 
 DType::DType(DType::TypeIndex ti) : m_type(ti) {}
@@ -99,8 +96,7 @@ DType::DType(std::string_view sv) {
     else if (sv == "f8")
         m_type = TypeIndex::DOUBLE;
     else
-        throw std::runtime_error(
+        throw std::runtime_error("Could not construct data type. Type no supported.");
-            "Could not construct data type. Type no supported.");
 }
 
 std::string DType::str() const {
@@ -138,18 +134,10 @@ std::string DType::str() const {
     return {};
 }
 
-bool DType::operator==(const DType &other) const noexcept {
+bool DType::operator==(const DType &other) const noexcept { return m_type == other.m_type; }
-    return m_type == other.m_type;
+bool DType::operator!=(const DType &other) const noexcept { return !(*this == other); }
-}
-bool DType::operator!=(const DType &other) const noexcept {
-    return !(*this == other);
-}
 
-bool DType::operator==(const std::type_info &t) const {
+bool DType::operator==(const std::type_info &t) const { return DType(t) == *this; }
-    return DType(t) == *this;
+bool DType::operator!=(const std::type_info &t) const { return DType(t) != *this; }
-}
-bool DType::operator!=(const std::type_info &t) const {
-    return DType(t) != *this;
-}
 
-} // namespace pl
+} // namespace aare

core/src/Frame.cpp

@@ -1,24 +1,21 @@
 #include "aare/Frame.hpp"
 #include "aare/utils/logger.hpp"
-#include <iostream>
 #include <cassert>
+#include <iostream>
 
 namespace aare {
 
-Frame::Frame(std::byte* bytes, ssize_t rows, ssize_t cols, ssize_t bitdepth):
+Frame::Frame(std::byte *bytes, ssize_t rows, ssize_t cols, ssize_t bitdepth)
-  m_rows(rows), m_cols(cols), m_bitdepth(bitdepth) {
+    : m_rows(rows), m_cols(cols), m_bitdepth(bitdepth) {
     m_data = new std::byte[rows * cols * bitdepth / 8];
     std::memcpy(m_data, bytes, rows * cols * bitdepth / 8);
 }
 
-Frame::Frame(ssize_t rows, ssize_t cols, ssize_t bitdepth):
+Frame::Frame(ssize_t rows, ssize_t cols, ssize_t bitdepth) : m_rows(rows), m_cols(cols), m_bitdepth(bitdepth) {
-  m_rows(rows), m_cols(cols), m_bitdepth(bitdepth) {
     m_data = new std::byte[rows * cols * bitdepth / 8];
     std::memset(m_data, 0, rows * cols * bitdepth / 8);
 }
 
-
-
 std::byte *Frame::get(int row, int col) {
     if (row < 0 || row >= m_rows || col < 0 || col >= m_cols) {
         std::cerr << "Invalid row or column index" << std::endl;
@@ -27,5 +24,4 @@ std::byte* Frame::get(int row, int col) {
     return m_data + (row * m_cols + col) * (m_bitdepth / 8);
 }
 
-
 } // namespace aare

core/src/ZmqSocket.cpp

@@ -1,10 +1,9 @@
 #include "aare/ZmqSocket.hpp"
-#include <zmq.h>
 #include <fmt/core.h>
+#include <zmq.h>
 
 namespace aare {
 
-
 ZmqSocket::ZmqSocket(const std::string &endpoint) : m_endpoint(endpoint) {
     memset(m_header_buffer, 0, m_max_header_size);
 }
@@ -40,13 +39,9 @@ ZmqSocket::~ZmqSocket(){
     delete[] m_header_buffer;
 }
 
-void ZmqSocket::set_zmq_hwm(int hwm){
+void ZmqSocket::set_zmq_hwm(int hwm) { m_zmq_hwm = hwm; }
-    m_zmq_hwm = hwm;
-}
 
-void ZmqSocket::set_timeout_ms(int n){
+void ZmqSocket::set_timeout_ms(int n) { m_timeout_ms = n; }
-    m_timeout_ms = n;
-}   
 
 int ZmqSocket::receive(zmqHeader &header, std::byte *data) {
 

core/test/DType.test.cpp

@@ -6,8 +6,6 @@
 using aare::DType;
 using aare::endian;
 
-
-
 TEST_CASE("Construct from typeid") {
     REQUIRE(DType(typeid(int)) == typeid(int));
     REQUIRE(DType(typeid(int)) != typeid(double));
@@ -45,7 +43,6 @@ TEST_CASE("Construct from string") {
         REQUIRE(DType("f4") == typeid(float));
         REQUIRE(DType("f8") == typeid(double));
     }
-
 }
 
 TEST_CASE("Construct from string with endianess") {
@@ -54,5 +51,4 @@ TEST_CASE("Construct from string with endianess"){
     REQUIRE_THROWS(DType(">i4") == typeid(int32_t));
 }
 
-
 TEST_CASE("Convert to string") { REQUIRE(DType(typeid(int)).str() == "<i4"); }

core/test/Frame.test.cpp

@@ -15,7 +15,6 @@ TEST_CASE("Construct a frame"){
     REQUIRE(frame.bitdepth() == bitdepth);
     REQUIRE(frame.size() == rows * cols * bitdepth / 8);
 
-
     // data should be initialized to 0
     for (int i = 0; i < rows; i++) {
         for (int j = 0; j < cols; j++) {
@@ -37,7 +36,6 @@ TEST_CASE("Set a value in a 8 bit frame"){
     uint8_t value = 255;
     frame.set(5, 7, value);
 
-
     // only the value we did set should be non-zero
     for (int i = 0; i < rows; i++) {
         for (int j = 0; j < cols; j++) {
@@ -63,7 +61,6 @@ TEST_CASE("Set a value in a 64 bit frame"){
     uint64_t value = 255;
     frame.set(5, 7, value);
 
-
     // only the value we did set should be non-zero
     for (int i = 0; i < rows; i++) {
         for (int j = 0; j < cols; j++) {
@@ -78,7 +75,6 @@ TEST_CASE("Set a value in a 64 bit frame"){
     }
 }
 
-
 TEST_CASE("Move construct a frame") {
     ssize_t rows = 10;
     ssize_t cols = 10;

core/test/NDArray.test.cpp

@@ -1,21 +1,17 @@
-#include <catch2/catch_test_macros.hpp>
 #include "aare/NDArray.hpp"
 #include <array>
-
+#include <catch2/catch_test_macros.hpp>
 
 using aare::NDArray;
 using aare::NDView;
 using aare::Shape;
 
-
+TEST_CASE("Initial size is zero if no size is specified") {
-TEST_CASE("Initial size is zero if no size is specified")
-{
     NDArray<double> a;
     REQUIRE(a.size() == 0);
     REQUIRE(a.shape() == Shape<2>{0, 0});
 }
 
-
 TEST_CASE("Construct from a DataSpan") {
     std::vector<int> some_data(9, 42);
     NDView<int, 2> view(some_data.data(), Shape<2>{3, 3});
@@ -35,8 +31,6 @@ TEST_CASE("Construct from a DataSpan"){
     for (int i = 0; i < image.size(); ++i) {
         REQUIRE(image(i) != view(i));
     }
-
-
 }
 
 TEST_CASE("1D image") {
@@ -44,7 +38,6 @@ TEST_CASE("1D image"){
     NDArray<short, 1> img(shape, 3);
     REQUIRE(img.size() == 20);
     REQUIRE(img(5) == 3);
-
 }
 
 TEST_CASE("Accessing a const object") {
@@ -55,11 +48,9 @@ TEST_CASE("Accessing a const object"){
     REQUIRE(img.shape(0) == 3);
     REQUIRE(img.shape(1) == 4);
     REQUIRE(img.shape(2) == 5);
-
 }
 
-TEST_CASE("Indexing of a 2D image")
+TEST_CASE("Indexing of a 2D image") {
-{
     std::array<ssize_t, 2> shape{{3, 7}};
     NDArray<long> img(shape, 5);
     for (int i = 0; i != img.size(); ++i) {
@@ -74,8 +65,7 @@ TEST_CASE("Indexing of a 2D image")
     REQUIRE(img(1, 0) == 7);
 }
 
-TEST_CASE("Indexing of a 3D image")
+TEST_CASE("Indexing of a 3D image") {
-{
     NDArray<float, 3> img{{{3, 4, 2}}, 5.0f};
     for (int i = 0; i != img.size(); ++i) {
         REQUIRE(img(i) == 5.0f);
@@ -101,11 +91,9 @@ TEST_CASE("Divide double by int"){
     for (auto it : a) {
         REQUIRE(it == 1.0);
     }
-
 }
 
-TEST_CASE("Elementwise multiplication of 3D image")
+TEST_CASE("Elementwise multiplication of 3D image") {
-{
     std::array<ssize_t, 3> shape{3, 4, 2};
     NDArray<double, 3> a{shape};
     NDArray<double, 3> b{shape};
@@ -121,8 +109,7 @@ TEST_CASE("Elementwise multiplication of 3D image")
     REQUIRE(c(2, 3, 1) == 23 * 23);
 }
 
-TEST_CASE("Compare two images")
+TEST_CASE("Compare two images") {
-{
     NDArray<int> a;
     NDArray<int> b;
     CHECK(a == b);
@@ -137,8 +124,7 @@ TEST_CASE("Compare two images")
     CHECK(a != b);
 }
 
-TEST_CASE("Size and shape matches")
+TEST_CASE("Size and shape matches") {
-{
     ssize_t w = 15;
     ssize_t h = 75;
     std::array<ssize_t, 2> shape{w, h};
@@ -147,8 +133,7 @@ TEST_CASE("Size and shape matches")
     REQUIRE(a.shape() == shape);
 }
 
-TEST_CASE("Initial value matches for all elements")
+TEST_CASE("Initial value matches for all elements") {
-{
     double v = 4.35;
     NDArray<double> a{{5, 5}, v};
     for (int i = 0; i < a.size(); ++i) {
@@ -165,7 +150,6 @@ TEST_CASE("Data layout of 3D image, fast index last"){
         *ptr++ = 10 + i;
         REQUIRE(a(0, 0, i) == 10 + i);
         REQUIRE(a(i) == 10 + i);
-
     }
 }
 
@@ -182,7 +166,6 @@ TEST_CASE("Bitwise and on data"){
     REQUIRE(a(0) == 300);
     REQUIRE(a(1) == 300);
     REQUIRE(a(2) == 384);
-
 }
 
 // TEST_CASE("Benchmarks")
@@ -220,14 +203,12 @@ TEST_CASE("Bitwise and on data"){
 //     }
 // }
 
-TEST_CASE("Elementwise operatios on images")
+TEST_CASE("Elementwise operatios on images") {
-{
     std::array<ssize_t, 2> shape{5, 5};
     double a_val = 3.0;
     double b_val = 8.0;
 
-    SECTION("Add two images")
+    SECTION("Add two images") {
-    {
         NDArray<double> A(shape, a_val);
         NDArray<double> B(shape, b_val);
 
@@ -252,8 +233,7 @@ TEST_CASE("Elementwise operatios on images")
         REQUIRE(A.data() != B.data());
         REQUIRE(B.data() != C.data());
     }
-    SECTION("Subtract two images")
+    SECTION("Subtract two images") {
-    {
         NDArray<double> A(shape, a_val);
         NDArray<double> B(shape, b_val);
         auto C = A - B;
@@ -277,8 +257,7 @@ TEST_CASE("Elementwise operatios on images")
         REQUIRE(A.data() != B.data());
         REQUIRE(B.data() != C.data());
     }
-    SECTION("Multiply two images")
+    SECTION("Multiply two images") {
-    {
         NDArray<double> A(shape, a_val);
         NDArray<double> B(shape, b_val);
         auto C = A * B;
@@ -302,8 +281,7 @@ TEST_CASE("Elementwise operatios on images")
         REQUIRE(A.data() != B.data());
         REQUIRE(B.data() != C.data());
     }
-    SECTION("Divide two images")
+    SECTION("Divide two images") {
-    {
         NDArray<double> A(shape, a_val);
         NDArray<double> B(shape, b_val);
         auto C = A / B;
@@ -328,8 +306,7 @@ TEST_CASE("Elementwise operatios on images")
         REQUIRE(B.data() != C.data());
     }
 
-    SECTION("subtract scalar")
+    SECTION("subtract scalar") {
-    {
         NDArray<double> A(shape, a_val);
         NDArray<double> B(shape, b_val);
         double v = 1.0;
@@ -346,8 +323,7 @@ TEST_CASE("Elementwise operatios on images")
             REQUIRE(A(i) == a_val);
         }
     }
-    SECTION("add scalar")
+    SECTION("add scalar") {
-    {
         NDArray<double> A(shape, a_val);
         NDArray<double> B(shape, b_val);
         double v = 1.0;
@@ -364,8 +340,7 @@ TEST_CASE("Elementwise operatios on images")
             REQUIRE(A(i) == a_val);
         }
     }
-    SECTION("divide with scalar")
+    SECTION("divide with scalar") {
-    {
         NDArray<double> A(shape, a_val);
         NDArray<double> B(shape, b_val);
         double v = 3.7;
@@ -382,8 +357,7 @@ TEST_CASE("Elementwise operatios on images")
             REQUIRE(A(i) == a_val);
         }
     }
-    SECTION("multiply with scalar")
+    SECTION("multiply with scalar") {
-    {
         NDArray<double> A(shape, a_val);
         NDArray<double> B(shape, b_val);
         double v = 3.7;

core/test/NDView.test.cpp

@@ -142,7 +142,6 @@ TEST_CASE("iterators") {
     }
 }
 
-
 TEST_CASE("shape from vector") {
     std::vector<int> vec;
     for (int i = 0; i != 12; ++i) {
@@ -175,7 +174,6 @@ TEST_CASE("Retrieve shape"){
     NDView<int, 2> data(vec.data(), Shape<2>{3, 4});
     REQUIRE(data.shape()[0] == 3);
     REQUIRE(data.shape()[1] == 4);
-
 }
 
 TEST_CASE("compare two views") {

core/test/ProducerConsumerQueue.test.cpp

@@ -1,5 +1,5 @@
- #include <catch2/catch_all.hpp>
 #include "aare/ProducerConsumerQueue.hpp"
+#include <catch2/catch_all.hpp>
 
 // using arve::SimpleQueue;
 TEST_CASE("push pop") {

core/test/defs.test.cpp

@@ -1,6 +1,6 @@
+#include "aare/defs.hpp"
 #include <catch2/catch_test_macros.hpp>
 #include <string>
-#include "aare/defs.hpp"
 TEST_CASE("Enum to string conversion") {
     // By the way I don't think the enum string conversions should be in the defs.hpp file
     // but let's use this to show a test

core/test/wrappers.test.cpp

@@ -1,12 +1,11 @@
-#include <aare/NDView.hpp>
 #include <aare/Frame.hpp>
 #include <aare/NDView.hpp>
 #include <catch2/catch_test_macros.hpp>
 #include <cstdint>
 
 using aare::Frame;
-using aare::NDView;
 using aare::NDArray;
+using aare::NDView;
 
 TEST_CASE("Frame") {
     auto data = new uint16_t[100];

examples/logger_example.cpp

@@ -1,6 +1,6 @@
 #include "aare/utils/logger.hpp"
-#include <iostream>
 #include <fstream>
+#include <iostream>
 
 int main() {
     aare::logger::debug(LOCATION, "hello", 1, "world", std::vector<long>{1, 2, 3, 4, 5});
@@ -9,15 +9,12 @@ int main() {
     aare::logger::debug(LOCATION, "NOTHING SHOULD BE PRINTED");
     aare::logger::info(LOCATION, "info printed");
 
-
     // writing to file
     std::ofstream textfile;
     textfile.open("Test.txt");
     aare::logger::set_streams(textfile.rdbuf());
     aare::logger::info(LOCATION, "info printed to file");
 
-
-
     // writing with a local logger instance
     aare::logger::Logger logger;
     logger.set_verbosity(aare::logger::WARNING);
@@ -27,7 +24,6 @@ int main() {
     aare::logger::info(LOCATION, "info printed in file ##");
     textfile.close();
 
-
     // setting file output by path
     // user doesn't have to close file
     aare::logger::set_output_file("Test2.txt");

examples/multiport_example.cpp

@@ -2,7 +2,6 @@
 #include "aare/File.hpp"
 #include "aare/utils/logger.hpp"
 #include <iostream>
-#include <iostream>
 
 #define AARE_ROOT_DIR_VAR "PROJECT_ROOT_DIR"
 

examples/numpy_write_example.cpp

@@ -9,7 +9,6 @@ using aare::File;
 using aare::FileConfig;
 using aare::Frame;
 
-
 int main() {
     auto path = std::filesystem::path("/tmp/test.npy");
     auto dtype = aare::DType(typeid(uint32_t));
@@ -25,7 +24,4 @@ int main() {
     npy.write(f);
     npy.write(f);
     return 0;
-    
-
-
 }

examples/raw_example.cpp

@@ -1,7 +1,7 @@
 // Your First C++ Program
 #include "aare/File.hpp"
-#include <iostream>
 #include "aare/utils/logger.hpp"
+#include <iostream>
 
 #define AARE_ROOT_DIR_VAR "PROJECT_ROOT_DIR"
 
@@ -21,7 +21,8 @@ int main() {
     if (PROJECT_ROOT_DIR.empty()) {
         throw std::runtime_error("environment variable PROJECT_ROOT_DIR is not set");
     }
-    std::filesystem::path fpath(PROJECT_ROOT_DIR / "data" /"moench"/ "moench04_noise_200V_sto_both_100us_no_light_thresh_900_master_0.raw");
+    std::filesystem::path fpath(PROJECT_ROOT_DIR / "data" / "moench" /
+                                "moench04_noise_200V_sto_both_100us_no_light_thresh_900_master_0.raw");
     File file(fpath, "r");
     test(file, 0);
     test(file, 2);

examples/zmq_example.cpp

@@ -1,8 +1,6 @@
-#include <string>
-#include <fmt/core.h>
 #include "aare/ZmqSocket.hpp"
-
+#include <fmt/core.h>
-
+#include <string>
 
 int main() {
     std::string endpoint = "tcp://localhost:5555";
@@ -12,7 +10,6 @@ int main(){
     aare::zmqHeader header;
     while (true) {
         int rc = socket.receive(header, reinterpret_cast<std::byte *>(data));
-
     }
     delete[] data;
     return 0;

file_io/src/File.cpp

@@ -33,4 +33,4 @@ File::File(File &&other) {
 
 // write move assignment operator
 
-}
+} // namespace aare

file_io/src/FileFactory.cpp

@@ -1,8 +1,7 @@
 #include "aare/FileFactory.hpp"
 #include "aare/FileInterface.hpp"
-#include "aare/RawFileFactory.hpp"
 #include "aare/NumpyFileFactory.hpp"
-#include "aare/utils/logger.hpp"
+#include "aare/RawFileFactory.hpp"
 #include "aare/utils/logger.hpp"
 #include <iostream>
 
@@ -27,5 +26,3 @@ FileFactory *FileFactory::get_factory(std::filesystem::path fpath) {
 }
 
 } // namespace aare
-
-

file_io/src/NumpyFile.cpp

@@ -26,8 +26,7 @@ NumpyFile::NumpyFile(FileConfig config, header_t header) {
         throw std::runtime_error(fmt::format("Could not open: {} for reading", m_fname.c_str()));
     }
 
-    initial_header_len =
+    initial_header_len = aare::NumpyHelpers::write_header(std::filesystem::path(m_fname.c_str()), header);
-        aare::NumpyHelpers::write_header(std::filesystem::path(m_fname.c_str()), header);
 }
 
 void NumpyFile::write(Frame &frame) {
@@ -41,8 +40,6 @@ void NumpyFile::write(Frame &frame) {
     fwrite(frame.data(), frame.size(), 1, fp);
 }
 
-
-
 Frame NumpyFile::get_frame(size_t frame_number) {
     Frame frame(m_header.shape[1], m_header.shape[2], m_header.dtype.bitdepth());
     get_frame_into(frame_number, frame.data());
@@ -97,13 +94,10 @@ NumpyFile::~NumpyFile() {
         std::string header_str = ss.str();
         // write header
         fwrite(header_str.c_str(), header_str.size(), 1, fp);
-
-        
     }
 
     if (fp != nullptr) {
         fclose(fp);
-        
     }
 }
 
@@ -142,7 +136,6 @@ void NumpyFile::load_metadata(){
     std::string header(header_len, '\0');
     fread(header.data(), header_len, 1, fp);
 
-
     // parse header
     std::vector<std::string> keys{"descr", "fortran_order", "shape"};
     aare::logger::debug("original header: \"header\"");
@@ -171,5 +164,4 @@ void NumpyFile::load_metadata(){
     m_header = {dtype, fortran_order, shape};
 }
 
-
 } // namespace aare

file_io/src/NumpyFileFactory.cpp

@@ -5,7 +5,6 @@ namespace aare {
 
 NumpyFileFactory::NumpyFileFactory(std::filesystem::path fpath) { this->m_fpath = fpath; }
 
-
 NumpyFile *NumpyFileFactory::load_file_read() {
     NumpyFile *file = new NumpyFile(this->m_fpath);
     return file;
@@ -14,8 +13,6 @@ NumpyFile *NumpyFileFactory::load_file_read() {
 NumpyFile *NumpyFileFactory::load_file_write(FileConfig config) {
     NumpyFile *file = new NumpyFile(config, {config.dtype, false, {config.rows, config.cols}});
 
-
-
     return file;
 };
 

file_io/src/NumpyHelpers.cpp

@@ -214,7 +214,6 @@ size_t write_header(std::filesystem::path fname, const header_t &header) {
     return write_header(out, header);
 }
 
-
 size_t write_header(std::ostream &out, const header_t &header) {
     std::string header_dict = write_header_dict(header.dtype.str(), header.fortran_order, header.shape);
 

file_io/src/RawFile.cpp

@@ -62,8 +62,6 @@ void RawFile::read_into(std::byte *image_buf, size_t n_frames) {
     }
 }
 
-
-
 size_t RawFile::frame_number(size_t frame_index) {
     if (frame_index > this->m_total_frames) {
         throw std::runtime_error(LOCATION + "Frame number out of range");

file_io/src/RawFileFactory.cpp

@@ -114,8 +114,8 @@ void RawFileFactory::open_subfiles(FileInterface *_file) {
     for (size_t i = 0; i != file->n_subfiles; ++i) {
         auto v = std::vector<SubFile *>(file->n_subfile_parts);
         for (size_t j = 0; j != file->n_subfile_parts; ++j) {
-            v[j] =
+            v[j] = new SubFile(file->data_fname(i, j), file->m_type, file->subfile_rows, file->subfile_cols,
-                new SubFile(file->data_fname(i, j), file->m_type, file->subfile_rows, file->subfile_cols, file->bitdepth());
+                               file->bitdepth());
         }
         file->subfiles.push_back(v);
     }
@@ -147,7 +147,6 @@ sls_detector_header RawFileFactory::read_header(const std::filesystem::path &fna
     return h;
 }
 
-
 void RawFileFactory::find_geometry(FileInterface *_file) {
     auto file = dynamic_cast<RawFile *>(_file);
     uint16_t r{};

file_io/src/SubFile.cpp

@@ -12,7 +12,8 @@ SubFile::SubFile(std::filesystem::path fname, DetectorType detector, ssize_t row
     this->m_bitdepth = bitdepth;
     this->n_frames = std::filesystem::file_size(fname) / (sizeof(sls_detector_header) + rows * cols * bitdepth / 8);
     if (read_impl_map.find({detector, bitdepth}) == read_impl_map.end()) {
-        auto error_msg = LOCATION + "No read_impl function found for detector: " + toString(detector) + " and bitdepth: " + std::to_string(bitdepth);
+        auto error_msg = LOCATION + "No read_impl function found for detector: " + toString(detector) +
+                         " and bitdepth: " + std::to_string(bitdepth);
         throw std::runtime_error(error_msg);
     }
     this->read_impl = read_impl_map.at({detector, bitdepth});

file_io/test/NumpyFile.test.cpp

@@ -1,11 +1,11 @@
-#include <catch2/catch_test_macros.hpp>
 #include "aare/NumpyFile.hpp"
 #include "aare/NDArray.hpp"
+#include <catch2/catch_test_macros.hpp>
 
 #include "test_config.hpp"
 
-using aare::NumpyFile;
 using aare::DType;
+using aare::NumpyFile;
 TEST_CASE("Read a 1D numpy file with int32 data type") {
 
     auto fpath = test_data_path() / "numpy" / "test_1d_int32.npy";
@@ -22,7 +22,6 @@ TEST_CASE("Read a 1D numpy file with int32 data type"){
     for (size_t i = 0; i < 10; i++) {
         REQUIRE(data(i) == i);
     }
-
 }
 
 TEST_CASE("Read a 3D numpy file with np.double data type") {
@@ -48,6 +47,4 @@ TEST_CASE("Read a 3D numpy file with np.double data type"){
     REQUIRE(data(0, 0, 1) == 2.0);
     REQUIRE(data(0, 1, 0) == 72.0);
     REQUIRE(data(2, 0, 4) == 63.0);
-    
-
 }

file_io/test/NumpyHelpers.test.cpp

@@ -1,5 +1,5 @@
-#include <catch2/catch_test_macros.hpp>
 #include "aare/NumpyHelpers.hpp" //Is this really a public header?
+#include <catch2/catch_test_macros.hpp>
 
 using namespace aare::NumpyHelpers;
 
@@ -19,9 +19,7 @@ TEST_CASE("Check for quotes and return stripped string"){
     REQUIRE(parse_str("''") == "");
 }
 
-TEST_CASE("parsing a string without quotes throws"){
+TEST_CASE("parsing a string without quotes throws") { REQUIRE_THROWS(parse_str("hej")); }
-    REQUIRE_THROWS(parse_str("hej"));
-}
 
 TEST_CASE("trim whitespace") {
     REQUIRE(trim(" hej ") == "hej");

python/src/bindings.cpp

@@ -4,17 +4,15 @@
 #include <pybind11/stl.h>
 #include <string>
 
-#include "aare/defs.hpp"
-#include "aare/Frame.hpp"
 #include "aare/FileHandler.hpp"
+#include "aare/Frame.hpp"
+#include "aare/defs.hpp"
 
 namespace py = pybind11;
 
-
 PYBIND11_MODULE(_aare, m) {
     // helps to convert from std::string to std::filesystem::path
-    py::class_<std::filesystem::path>(m, "Path")
+    py::class_<std::filesystem::path>(m, "Path").def(py::init<std::string>());
-        .def(py::init<std::string>());
     py::implicitly_convertible<std::string, std::filesystem::path>();
 
     // TODO: find a solution to avoid code duplication and include other detectors
@@ -22,7 +20,6 @@ PYBIND11_MODULE(_aare, m) {
         .def(py::init<std::filesystem::path>())
         .def("get_frame", &FileHandler::get_frame);
 
-    
     py::enum_<DetectorType>(m, "DetectorType");
 
     py::class_<Frame>(m, "_Frame")
@@ -31,14 +28,4 @@ PYBIND11_MODULE(_aare, m) {
         .def_property_readonly("rows", &Frame::rows)
         .def_property_readonly("cols", &Frame::cols)
         .def_property_readonly("bitdepth", &Frame::bitdepth);
-
-    
-
-
-
-    
-
-    
 }
-
-