Better progress reporting

Co-authored-by: Sebastian Deorowicz <sebastian.deorowicz@polsl.pl>
refresh-bio · Nov 25, 2024 · c898e1e · c898e1e
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commit c898e1e
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diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml
@@ -17,6 +17,8 @@ jobs:
     runs-on: [self-hosted, lz-ani, '${{ matrix.machine }}']
 
     steps:
+    - name: clean
+      run: rm -rf ${{ github.workspace }}/*
     - uses: actions/checkout@v4
       with:
         submodules: recursive
@@ -47,10 +49,9 @@ jobs:
     steps:
     - name: make 
       run: |
-        make clean
-        make -j32 CXX=${{matrix.compiler}} STATIC_LINK=true PLATFORM=${{ matrix.platform }}
+        gmake -j32 CXX=${{matrix.compiler}} STATIC_LINK=true PLATFORM=${{ matrix.platform }}
     - name: tar artifacts
-      run: tar -cvzf lz-ani.tar.gz lz-ani LICENSE
+      run: tar -cvzf lz-ani.tar.gz LICENSE -C ./bin lz-ani
 
 
 ########################################################################################
@@ -65,7 +66,7 @@ jobs:
 
     steps:
     - name: help
-      run: ./lz-ani
+      run: ./bin/lz-ani
 
 ########################################################################################
   upload:

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -1,4 +1,4 @@
-name: GitHub Actions CI
+name: Build and tests
 
 on:
   push:
@@ -15,20 +15,25 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        machine: [ubuntu-latest, macOS-12]
+        machine: [ubuntu-latest]
+        gmake_install_command: ['gmake --version']
+        include:
+        - {machine: macOS-13, gmake_install_command: 'brew install make && gmake --version'}
     runs-on: ['${{ matrix.machine }}']   
 
     steps:
     - uses: actions/checkout@v4
       with:
         submodules: recursive
+
+    - name: install gmake
+      run: ${{ matrix.gmake_install_command }}        
     - name: make
       run: | 
-        g++ --version
-        make -j CXX=g++-12
+        gmake -j CXX=g++-12 CC=gcc-12 STATIC_LINK=true
 
     - name: tar artifacts
-      run: tar -cvf lz-ani.tar ./lz-ani ./test
+      run: tar -cvf lz-ani.tar ./test -C ./bin lz-ani
 
     - uses: actions/upload-artifact@v4
       with:
@@ -42,7 +47,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        machine: [ubuntu-latest, macOS-12]
+        machine: [ubuntu-latest, macOS-13]
     runs-on: ['${{ matrix.machine }}']
 
     steps:

diff --git a/.github/workflows/self-hosted.yml b/.github/workflows/self-hosted.yml
@@ -18,6 +18,8 @@ jobs:
     runs-on: [self-hosted, lz-ani, '${{ matrix.machine }}']
 
     steps:
+    - name: clean
+      run: rm -rf ${{ github.workspace }}/*
     - uses: actions/checkout@v4
       with:
         submodules: recursive
@@ -31,28 +33,24 @@ jobs:
       fail-fast: false
       matrix:
         machine: [x64_linux, x64_mac, arm64_linux, arm64_mac]
-        compiler: [g++-11, g++-12, g++-13]
+        compiler: [11, 12, 13]
         include:
-        - machine: x64_linux
-          platform: avx2
-        - machine: arm64_linux
-          platform: arm8
-        - machine: x64_mac
-          platform: avx2
-        - machine: arm64_mac
-          platform: m1
+        - {machine: x64_linux, platform: avx2, compiler: 14}
+        - {machine: x64_linux, platform: avx2}
+        - {machine: arm64_linux, platform: arm8}
+        - {machine: x64_mac, platform: avx2}
+        - {machine: arm64_mac, platform: m1}
         exclude:
-        - machine: arm64_linux
-          compiler: g++-13
+        - {machine: arm64_linux, compiler: 13}
 
     runs-on: [self-hosted, lz-ani, '${{ matrix.machine }}']  
 
     steps:
     - name: make
       run: | 
-        make -j32 CXX=${{matrix.compiler}} PLATFORM=${{ matrix.platform }}
-        cp ./lz-ani ./lz-ani-${{matrix.compiler}}
-        make clean
+        gmake -j32 CXX=g++-${{matrix.compiler}} CC=gcc-${{matrix.compiler}} PLATFORM=${{ matrix.platform }} STATIC_LINK=true
+        cp ./bin/lz-ani ./lz-ani-${{matrix.compiler}}
+        gmake clean
         
 ########################################################################################
   help:
@@ -62,10 +60,11 @@ jobs:
       fail-fast: false
       matrix:
         machine: [x64_linux, x64_mac, arm64_linux, arm64_mac]
-        compiler: [g++-11, g++-12, g++-13]
+        compiler: [11, 12, 13]
+        include:
+        - {machine: x64_linux, platform: avx2, compiler: 14}
         exclude:
-        - machine: arm64_linux
-          compiler: g++-13
+        - {machine: arm64_linux, compiler: 13}
 
     runs-on: [self-hosted, lz-ani, '${{ matrix.machine }}']
 
@@ -74,9 +73,9 @@ jobs:
 
     steps:
     - name: help
-      run: | 
-       ${EXEC} 
-
+      run: ${EXEC} 
+    - name: version
+      run: ${EXEC} -version  
 
  ########################################################################################
   vir61:
@@ -86,10 +85,11 @@ jobs:
       fail-fast: false
       matrix:
         machine: [x64_linux, x64_mac, arm64_linux, arm64_mac]
-        compiler: [g++-11, g++-12, g++-13]
+        compiler: [11, 12, 13]
+        include:
+        - {machine: x64_linux, platform: avx2, compiler: 14}
         exclude:
-        - machine: arm64_linux
-          compiler: g++-13
+        - {machine: arm64_linux, compiler: 13}
 
     runs-on: [self-hosted, lz-ani, '${{ matrix.machine }}']
 

diff --git a/README.md b/README.md
@@ -2,7 +2,7 @@
 
 [![GitHub downloads](https://img.shields.io/github/downloads/refresh-bio/lz-ani/total.svg?style=flag&label=GitHub%20downloads)](https://github.com/refresh-bio/LZ-ANI/releases)
 [![Bioconda downloads](https://img.shields.io/conda/dn/bioconda/lz-ani.svg?style=flag&label=Bioconda%20downloads)](https://anaconda.org/bioconda/lz-ani)
-[![GitHub Actions CI](../../workflows/GitHub%20Actions%20CI/badge.svg)](../../actions/workflows/main.yml)
+[![Build and tests](../../workflows/Build%20and%20tests/badge.svg)](../../actions/workflows/main.yml)
 
 [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
 

diff --git a/libs/refresh/compression/lib/file_wrapper.h b/libs/refresh/compression/lib/file_wrapper.h
@@ -1,16 +1,11 @@
-// *******************************************************************************************
-// This file is a part of LZ-ANI software distributed under GNU GPL 3 license.
-// The homepage of the LZ-ANI project is https://github.com/refresh-bio/LZ-ANI
-//
-// Copyright(C) 2024-2024, S.Deorowicz, A.Gudys
-//
-// Version: 1.0.0
-// Date   : 2024-05-15
-// *******************************************************************************************
-
 #ifndef _FILE_WRAPPER_H
 #define _FILE_WRAPPER_H
 
+// *** History of updates
+// *** v. 1.0.1 (2024-03-11) - bug fix (wrong zlib initialization)
+// *** v. 1.0.2 (2024-05-01) - bug fix (wrong reading from file)
+// ***
+
 #include <cstdint>
 #include <cstring>
 #include <cstdio>
@@ -46,9 +41,9 @@
 
 #ifdef REFRESH_STREAM_DECOMPRESSION_ENABLE_ZLIB
 #ifdef _WIN32
-#include "../libs/zlib-ng/build-vs/zlib.h"
+#include <zlib-ng/build-vs/zlib.h>
 #else
-#include "../zlib-ng/zlib.h"
+#include <zlib-ng/zlib.h>
 #endif
 #endif
 
@@ -150,17 +145,30 @@ namespace refresh
 	{
 		std::string file_name;
 		size_t io_buffer_size;
-		FILE* file = nullptr;
-		bool test_extension = true;
+		FILE* file;
+		bool test_extension;
+
+		void _open()
+		{
+			file = fopen(file_name.c_str(), "rb");
+
+			if (!file)
+				return;
+
+			setvbuf(file, nullptr, _IOFBF, io_buffer_size);
+			buffer_released = true;
+		}
 
 	public:
 		stream_in_file(const std::string& file_name, size_t io_buffer_size = 16 << 20, size_t buffer_size = 8 << 20, bool test_extension = true) :
 			stream_in_buffered(buffer_size),
-			file_name(file_name),
-			io_buffer_size(io_buffer_size),
-			test_extension(test_extension)
+			file_name{ file_name },
+			io_buffer_size{ io_buffer_size },
+			file{ nullptr },
+			test_extension{test_extension}
 		{
-			open(file_name);
+//			open(file_name);
+			_open();
 		}
 
 		virtual ~stream_in_file()
@@ -175,16 +183,9 @@ namespace refresh
 			if (file)
 				close();
 
-			file = fopen(file_name.c_str(), "rb");
-
-			if (!file)
-				return false;
-
-			setvbuf(file, nullptr, _IOFBF, io_buffer_size);
-
-			buffer_released = true;
+			_open();
 
-			return true;
+			return file != nullptr;
 		}
 
 		virtual bool close()