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agudyssebastiandeorowicz
agudys
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sebastiandeorowicz
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Better progress reporting
Co-authored-by: Sebastian Deorowicz <[email protected]>
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‎.github/workflows/deploy.yml‎

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@@ -17,6 +17,8 @@ jobs:
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runs-on: [self-hosted, lz-ani, '${{ matrix.machine }}']
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steps:
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- name: clean
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run: rm -rf ${{ github.workspace }}/*
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- uses: actions/checkout@v4
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with:
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submodules: recursive
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steps:
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- name: make
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run: |
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make clean
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make -j32 CXX=${{matrix.compiler}} STATIC_LINK=true PLATFORM=${{ matrix.platform }}
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gmake -j32 CXX=${{matrix.compiler}} STATIC_LINK=true PLATFORM=${{ matrix.platform }}
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- name: tar artifacts
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run: tar -cvzf lz-ani.tar.gz lz-ani LICENSE
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run: tar -cvzf lz-ani.tar.gz LICENSE -C ./bin lz-ani
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########################################################################################
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steps:
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- name: help
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run: ./lz-ani
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run: ./bin/lz-ani
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########################################################################################
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upload:

‎.github/workflows/main.yml‎

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

‎.github/workflows/self-hosted.yml‎

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Original file line numberDiff line numberDiff line change
@@ -18,6 +18,8 @@ jobs:
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runs-on: [self-hosted, lz-ani, '${{ matrix.machine }}']
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steps:
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- name: clean
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run: rm -rf ${{ github.workspace }}/*
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- uses: actions/checkout@v4
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with:
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submodules: recursive
@@ -31,28 +33,24 @@ jobs:
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fail-fast: false
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matrix:
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machine: [x64_linux, x64_mac, arm64_linux, arm64_mac]
34-
compiler: [g++-11, g++-12, g++-13]
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compiler: [11, 12, 13]
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include:
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- machine: x64_linux
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platform: avx2
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- machine: arm64_linux
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platform: arm8
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- machine: x64_mac
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platform: avx2
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- machine: arm64_mac
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platform: m1
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- {machine: x64_linux, platform: avx2, compiler: 14}
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- {machine: x64_linux, platform: avx2}
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- {machine: arm64_linux, platform: arm8}
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- {machine: x64_mac, platform: avx2}
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- {machine: arm64_mac, platform: m1}
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exclude:
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- machine: arm64_linux
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compiler: g++-13
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- {machine: arm64_linux, compiler: 13}
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runs-on: [self-hosted, lz-ani, '${{ matrix.machine }}']
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steps:
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- name: make
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run: |
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make -j32 CXX=${{matrix.compiler}} PLATFORM=${{ matrix.platform }}
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cp ./lz-ani ./lz-ani-${{matrix.compiler}}
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make clean
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gmake -j32 CXX=g++-${{matrix.compiler}} CC=gcc-${{matrix.compiler}} PLATFORM=${{ matrix.platform }} STATIC_LINK=true
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cp ./bin/lz-ani ./lz-ani-${{matrix.compiler}}
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gmake clean
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########################################################################################
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help:
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fail-fast: false
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matrix:
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machine: [x64_linux, x64_mac, arm64_linux, arm64_mac]
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compiler: [g++-11, g++-12, g++-13]
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compiler: [11, 12, 13]
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include:
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- {machine: x64_linux, platform: avx2, compiler: 14}
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exclude:
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- machine: arm64_linux
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compiler: g++-13
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- {machine: arm64_linux, compiler: 13}
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runs-on: [self-hosted, lz-ani, '${{ matrix.machine }}']
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steps:
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- name: help
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run: |
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${EXEC}
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run: ${EXEC}
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- name: version
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run: ${EXEC} -version
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########################################################################################
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vir61:
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fail-fast: false
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matrix:
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machine: [x64_linux, x64_mac, arm64_linux, arm64_mac]
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compiler: [g++-11, g++-12, g++-13]
88+
compiler: [11, 12, 13]
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include:
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- {machine: x64_linux, platform: avx2, compiler: 14}
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exclude:
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- machine: arm64_linux
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compiler: g++-13
92+
- {machine: arm64_linux, compiler: 13}
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runs-on: [self-hosted, lz-ani, '${{ matrix.machine }}']
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‎README.md‎

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@@ -2,7 +2,7 @@
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[![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)
44
[![Bioconda downloads](https://img.shields.io/conda/dn/bioconda/lz-ani.svg?style=flag&label=Bioconda%20downloads)](https://anaconda.org/bioconda/lz-ani)
5-
[![GitHub Actions CI](../../workflows/GitHub%20Actions%20CI/badge.svg)](../../actions/workflows/main.yml)
5+
[![Build and tests](../../workflows/Build%20and%20tests/badge.svg)](../../actions/workflows/main.yml)
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[![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
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‎libs/refresh/compression/lib/file_wrapper.h‎

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Original file line numberDiff line numberDiff line change
@@ -1,16 +1,11 @@
1-
// *******************************************************************************************
2-
// This file is a part of LZ-ANI software distributed under GNU GPL 3 license.
3-
// The homepage of the LZ-ANI project is https://github.com/refresh-bio/LZ-ANI
4-
//
5-
// Copyright(C) 2024-2024, S.Deorowicz, A.Gudys
6-
//
7-
// Version: 1.0.0
8-
// Date : 2024-05-15
9-
// *******************************************************************************************
10-
111
#ifndef _FILE_WRAPPER_H
122
#define _FILE_WRAPPER_H
133

4+
// *** History of updates
5+
// *** v. 1.0.1 (2024-03-11) - bug fix (wrong zlib initialization)
6+
// *** v. 1.0.2 (2024-05-01) - bug fix (wrong reading from file)
7+
// ***
8+
149
#include <cstdint>
1510
#include <cstring>
1611
#include <cstdio>
@@ -46,9 +41,9 @@
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#ifdef REFRESH_STREAM_DECOMPRESSION_ENABLE_ZLIB
4843
#ifdef _WIN32
49-
#include "../libs/zlib-ng/build-vs/zlib.h"
44+
#include <zlib-ng/build-vs/zlib.h>
5045
#else
51-
#include "../zlib-ng/zlib.h"
46+
#include <zlib-ng/zlib.h>
5247
#endif
5348
#endif
5449

@@ -150,17 +145,30 @@ namespace refresh
150145
{
151146
std::string file_name;
152147
size_t io_buffer_size;
153-
FILE* file = nullptr;
154-
bool test_extension = true;
148+
FILE* file;
149+
bool test_extension;
150+
151+
void _open()
152+
{
153+
file = fopen(file_name.c_str(), "rb");
154+
155+
if (!file)
156+
return;
157+
158+
setvbuf(file, nullptr, _IOFBF, io_buffer_size);
159+
buffer_released = true;
160+
}
155161

156162
public:
157163
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) :
158164
stream_in_buffered(buffer_size),
159-
file_name(file_name),
160-
io_buffer_size(io_buffer_size),
161-
test_extension(test_extension)
165+
file_name{ file_name },
166+
io_buffer_size{ io_buffer_size },
167+
file{ nullptr },
168+
test_extension{test_extension}
162169
{
163-
open(file_name);
170+
// open(file_name);
171+
_open();
164172
}
165173

166174
virtual ~stream_in_file()
@@ -175,16 +183,9 @@ namespace refresh
175183
if (file)
176184
close();
177185

178-
file = fopen(file_name.c_str(), "rb");
179-
180-
if (!file)
181-
return false;
182-
183-
setvbuf(file, nullptr, _IOFBF, io_buffer_size);
184-
185-
buffer_released = true;
186+
_open();
186187

187-
return true;
188+
return file != nullptr;
188189
}
189190

190191
virtual bool close()

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