From de19571d8130b76c7718edb8be72370d3af78518 Mon Sep 17 00:00:00 2001 From: "Leonardo de Oliveira Martins (QIB)" Date: Mon, 14 Sep 2020 11:11:45 +0100 Subject: [PATCH] updating makefiles --- .travis.yml | 14 +- Dockerfile | 10 +- autom4te.cache/output.1 | 20 +- autom4te.cache/output.3 | 20 +- autom4te.cache/requests | 1094 +++++++++++++++++++-------------------- autom4te.cache/traces.1 | 2 +- configure | 20 +- environment.yml | 3 +- recipe/build.sh | 9 +- requirements.txt | 2 + setup.py | 12 +- src/Makefile.am | 4 +- src/Makefile.in | 4 +- submodules/biomcmc-lib | 2 +- tauari/__init__.py | 1 - tauari/tauari.py | 15 + 16 files changed, 628 insertions(+), 604 deletions(-) create mode 100644 requirements.txt diff --git a/.travis.yml b/.travis.yml index 03481dc..e80e6ea 100644 --- a/.travis.yml +++ b/.travis.yml @@ -1,4 +1,12 @@ -language: c +language: python +python: + - "2.7" + - "3.4" + - "3.5" + - "3.6" # current default Python on Travis CI + - "3.7" + - "3.8" + git: submodules: true #install: make get-deps # @@ -9,10 +17,12 @@ before_install: - sudo apt-get update - sudo apt-get install -y check - sudo apt-get install -y autotools-dev + - sudo apt-get install -y python-dev install: - autoreconf script: - - "mkdir build; cd build; ../configure && make && make check" + - pip install -r requirements.txt + - pip install . branches: only: diff --git a/Dockerfile b/Dockerfile index 3e3cb04..b0571e4 100644 --- a/Dockerfile +++ b/Dockerfile @@ -7,11 +7,11 @@ RUN apt-get update && apt-get install -y \ giflib-dbg \ check \ build-essential \ + python-dev \ automake && \ apt-get clean && \ rm -rf /var/lib/apt/lists/* -RUN git clone --recursive https://github.com/leomrtns/super_distance.git && \ - mkdir build && \ - cd build && \ - ../super_distance/configure --prefix=/ && \ - make && make install +RUN git clone --recursive https://github.com/leomrtns/tauari.git && \ + cd tauari && \ + pip install -r requirements.txt && \ + pip install . diff --git a/autom4te.cache/output.1 b/autom4te.cache/output.1 index eb892a8..b43883b 100644 --- a/autom4te.cache/output.1 +++ b/autom4te.cache/output.1 @@ -1,6 +1,6 @@ @%:@! /bin/sh @%:@ Guess values for system-dependent variables and create Makefiles. -@%:@ Generated by GNU Autoconf 2.69 for tauari_c 1.0.0. +@%:@ Generated by GNU Autoconf 2.69 for tauari_c 0.0.1. @%:@ @%:@ Report bugs to . @%:@ @@ -590,8 +590,8 @@ MAKEFLAGS= # Identity of this package. PACKAGE_NAME='tauari_c' PACKAGE_TARNAME='tauari_c' -PACKAGE_VERSION='1.0.0' -PACKAGE_STRING='tauari_c 1.0.0' +PACKAGE_VERSION='0.0.1' +PACKAGE_STRING='tauari_c 0.0.1' PACKAGE_BUGREPORT='leomrtns@gmail.com' PACKAGE_URL='https://github.com/quadram-institute-bioscience/tauari' @@ -1365,7 +1365,7 @@ if test "$ac_init_help" = "long"; then # Omit some internal or obsolete options to make the list less imposing. # This message is too long to be a string in the A/UX 3.1 sh. cat <<_ACEOF -\`configure' configures tauari_c 1.0.0 to adapt to many kinds of systems. +\`configure' configures tauari_c 0.0.1 to adapt to many kinds of systems. Usage: $0 [OPTION]... [VAR=VALUE]... @@ -1436,7 +1436,7 @@ fi if test -n "$ac_init_help"; then case $ac_init_help in - short | recursive ) echo "Configuration of tauari_c 1.0.0:";; + short | recursive ) echo "Configuration of tauari_c 0.0.1:";; esac cat <<\_ACEOF @@ -1564,7 +1564,7 @@ fi test -n "$ac_init_help" && exit $ac_status if $ac_init_version; then cat <<\_ACEOF -tauari_c configure 1.0.0 +tauari_c configure 0.0.1 generated by GNU Autoconf 2.69 Copyright (C) 2012 Free Software Foundation, Inc. @@ -1933,7 +1933,7 @@ cat >config.log <<_ACEOF This file contains any messages produced by compilers while running configure, to aid debugging if configure makes a mistake. -It was created by tauari_c $as_me 1.0.0, which was +It was created by tauari_c $as_me 0.0.1, which was generated by GNU Autoconf 2.69. Invocation command line was $ $0 $@ @@ -2805,7 +2805,7 @@ fi # Define the identity of the package. PACKAGE='tauari_c' - VERSION='1.0.0' + VERSION='0.0.1' cat >>confdefs.h <<_ACEOF @@ -14272,7 +14272,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 # report actual input values of CONFIG_FILES etc. instead of their # values after options handling. ac_log=" -This file was extended by tauari_c $as_me 1.0.0, which was +This file was extended by tauari_c $as_me 0.0.1, which was generated by GNU Autoconf 2.69. Invocation command line was CONFIG_FILES = $CONFIG_FILES @@ -14339,7 +14339,7 @@ _ACEOF cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`" ac_cs_version="\\ -tauari_c config.status 1.0.0 +tauari_c config.status 0.0.1 configured by $0, generated by GNU Autoconf 2.69, with options \\"\$ac_cs_config\\" diff --git a/autom4te.cache/output.3 b/autom4te.cache/output.3 index eb892a8..b43883b 100644 --- a/autom4te.cache/output.3 +++ b/autom4te.cache/output.3 @@ -1,6 +1,6 @@ @%:@! /bin/sh @%:@ Guess values for system-dependent variables and create Makefiles. -@%:@ Generated by GNU Autoconf 2.69 for tauari_c 1.0.0. +@%:@ Generated by GNU Autoconf 2.69 for tauari_c 0.0.1. @%:@ @%:@ Report bugs to . @%:@ @@ -590,8 +590,8 @@ MAKEFLAGS= # Identity of this package. PACKAGE_NAME='tauari_c' PACKAGE_TARNAME='tauari_c' -PACKAGE_VERSION='1.0.0' -PACKAGE_STRING='tauari_c 1.0.0' +PACKAGE_VERSION='0.0.1' +PACKAGE_STRING='tauari_c 0.0.1' PACKAGE_BUGREPORT='leomrtns@gmail.com' PACKAGE_URL='https://github.com/quadram-institute-bioscience/tauari' @@ -1365,7 +1365,7 @@ if test "$ac_init_help" = "long"; then # Omit some internal or obsolete options to make the list less imposing. # This message is too long to be a string in the A/UX 3.1 sh. cat <<_ACEOF -\`configure' configures tauari_c 1.0.0 to adapt to many kinds of systems. +\`configure' configures tauari_c 0.0.1 to adapt to many kinds of systems. Usage: $0 [OPTION]... [VAR=VALUE]... @@ -1436,7 +1436,7 @@ fi if test -n "$ac_init_help"; then case $ac_init_help in - short | recursive ) echo "Configuration of tauari_c 1.0.0:";; + short | recursive ) echo "Configuration of tauari_c 0.0.1:";; esac cat <<\_ACEOF @@ -1564,7 +1564,7 @@ fi test -n "$ac_init_help" && exit $ac_status if $ac_init_version; then cat <<\_ACEOF -tauari_c configure 1.0.0 +tauari_c configure 0.0.1 generated by GNU Autoconf 2.69 Copyright (C) 2012 Free Software Foundation, Inc. @@ -1933,7 +1933,7 @@ cat >config.log <<_ACEOF This file contains any messages produced by compilers while running configure, to aid debugging if configure makes a mistake. -It was created by tauari_c $as_me 1.0.0, which was +It was created by tauari_c $as_me 0.0.1, which was generated by GNU Autoconf 2.69. Invocation command line was $ $0 $@ @@ -2805,7 +2805,7 @@ fi # Define the identity of the package. PACKAGE='tauari_c' - VERSION='1.0.0' + VERSION='0.0.1' cat >>confdefs.h <<_ACEOF @@ -14272,7 +14272,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 # report actual input values of CONFIG_FILES etc. instead of their # values after options handling. ac_log=" -This file was extended by tauari_c $as_me 1.0.0, which was +This file was extended by tauari_c $as_me 0.0.1, which was generated by GNU Autoconf 2.69. Invocation command line was CONFIG_FILES = $CONFIG_FILES @@ -14339,7 +14339,7 @@ _ACEOF cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`" ac_cs_version="\\ -tauari_c config.status 1.0.0 +tauari_c config.status 0.0.1 configured by $0, generated by GNU Autoconf 2.69, with options \\"\$ac_cs_config\\" diff --git a/autom4te.cache/requests b/autom4te.cache/requests index 5a05037..d21e2df 100644 --- a/autom4te.cache/requests +++ b/autom4te.cache/requests @@ -44,195 +44,195 @@ 'configure.ac' ], { - '_AM_CONFIG_MACRO_DIRS' => 1, - 'AC_LIBTOOL_SYS_DYNAMIC_LINKER' => 1, - 'AC_DISABLE_STATIC' => 1, - '_AM_SET_OPTION' => 1, - 'AU_DEFUN' => 1, - '_LT_AC_PROG_CXXCPP' => 1, - 'm4_pattern_forbid' => 1, - 'AM_PROG_INSTALL_SH' => 1, - 'LTDL_CONVENIENCE' => 1, - 'LT_PATH_LD' => 1, - 'PKG_INSTALLDIR' => 1, - 'AC_LIBTOOL_SETUP' => 1, - 'AM_PROG_LD' => 1, - 'AC_LIBTOOL_SYS_HARD_LINK_LOCKS' => 1, - 'AC_PROG_LD' => 1, + '_LT_PREPARE_SED_QUOTE_VARS' => 1, + 'AC_LIBTOOL_F77' => 1, + '_LT_LINKER_BOILERPLATE' => 1, + 'AC_LIBTOOL_PROG_CC_C_O' => 1, + 'LT_AC_PROG_EGREP' => 1, + 'AM_DISABLE_SHARED' => 1, + 'AM_SILENT_RULES' => 1, + 'PKG_CHECK_VAR' => 1, + '_LT_AC_FILE_LTDLL_C' => 1, 'AC_LIBTOOL_PICMODE' => 1, + 'AC_PROG_NM' => 1, + '_AM_IF_OPTION' => 1, + 'LT_SUPPORTED_TAG' => 1, + 'AC_LIBTOOL_WIN32_DLL' => 1, + 'AC_LIBLTDL_CONVENIENCE' => 1, + '_LT_AC_LANG_GCJ_CONFIG' => 1, + 'LT_FUNC_DLSYM_USCORE' => 1, + 'LT_SYS_MODULE_EXT' => 1, + '_LT_DLL_DEF_P' => 1, + 'AM_SET_DEPDIR' => 1, + '_LT_COMPILER_BOILERPLATE' => 1, + 'PKG_NOARCH_INSTALLDIR' => 1, 'AM_SUBST_NOTMAKE' => 1, - 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'LT_AC_PROG_GCJ' => 1 + 'AC_DEFUN' => 1, + '_LT_COMPILER_OPTION' => 1, + 'AC_LIBTOOL_LINKER_OPTION' => 1, + 'AC_PROG_LD_GNU' => 1, + '_AC_AM_CONFIG_HEADER_HOOK' => 1, + 'AM_ENABLE_STATIC' => 1, + 'AC_DEPLIBS_CHECK_METHOD' => 1, + '_LT_AC_LANG_F77_CONFIG' => 1 } ], 'Autom4te::Request' ) ); diff --git a/autom4te.cache/traces.1 b/autom4te.cache/traces.1 index 7f33d43..e6cefa6 100644 --- a/autom4te.cache/traces.1 +++ b/autom4te.cache/traces.1 @@ -3,7 +3,7 @@ m4trace:aclocal.m4:1762: -1- m4_include([m4/ltoptions.m4]) m4trace:aclocal.m4:1763: -1- m4_include([m4/ltsugar.m4]) m4trace:aclocal.m4:1764: -1- m4_include([m4/ltversion.m4]) m4trace:aclocal.m4:1765: -1- m4_include([m4/lt~obsolete.m4]) -m4trace:configure.ac:1: -1- AC_INIT([tauari_c], [1.0.0], [leomrtns@gmail.com], [], [https://github.com/quadram-institute-bioscience/tauari]) +m4trace:configure.ac:1: -1- AC_INIT([tauari_c], [0.0.1], [leomrtns@gmail.com], [], [https://github.com/quadram-institute-bioscience/tauari]) m4trace:configure.ac:1: -1- m4_pattern_forbid([^_?A[CHUM]_]) m4trace:configure.ac:1: -1- m4_pattern_forbid([_AC_]) m4trace:configure.ac:1: -1- m4_pattern_forbid([^LIBOBJS$], [do not use LIBOBJS directly, use AC_LIBOBJ (see section `AC_LIBOBJ vs LIBOBJS']) diff --git a/configure b/configure index 0057214..8ea5166 100755 --- a/configure +++ b/configure @@ -1,6 +1,6 @@ #! /bin/sh # Guess values for system-dependent variables and create Makefiles. -# Generated by GNU Autoconf 2.69 for tauari_c 1.0.0. +# Generated by GNU Autoconf 2.69 for tauari_c 0.0.1. # # Report bugs to . # @@ -590,8 +590,8 @@ MAKEFLAGS= # Identity of this package. PACKAGE_NAME='tauari_c' PACKAGE_TARNAME='tauari_c' -PACKAGE_VERSION='1.0.0' -PACKAGE_STRING='tauari_c 1.0.0' +PACKAGE_VERSION='0.0.1' +PACKAGE_STRING='tauari_c 0.0.1' PACKAGE_BUGREPORT='leomrtns@gmail.com' PACKAGE_URL='https://github.com/quadram-institute-bioscience/tauari' @@ -1365,7 +1365,7 @@ if test "$ac_init_help" = "long"; then # Omit some internal or obsolete options to make the list less imposing. # This message is too long to be a string in the A/UX 3.1 sh. cat <<_ACEOF -\`configure' configures tauari_c 1.0.0 to adapt to many kinds of systems. +\`configure' configures tauari_c 0.0.1 to adapt to many kinds of systems. Usage: $0 [OPTION]... [VAR=VALUE]... @@ -1436,7 +1436,7 @@ fi if test -n "$ac_init_help"; then case $ac_init_help in - short | recursive ) echo "Configuration of tauari_c 1.0.0:";; + short | recursive ) echo "Configuration of tauari_c 0.0.1:";; esac cat <<\_ACEOF @@ -1564,7 +1564,7 @@ fi test -n "$ac_init_help" && exit $ac_status if $ac_init_version; then cat <<\_ACEOF -tauari_c configure 1.0.0 +tauari_c configure 0.0.1 generated by GNU Autoconf 2.69 Copyright (C) 2012 Free Software Foundation, Inc. @@ -1933,7 +1933,7 @@ cat >config.log <<_ACEOF This file contains any messages produced by compilers while running configure, to aid debugging if configure makes a mistake. -It was created by tauari_c $as_me 1.0.0, which was +It was created by tauari_c $as_me 0.0.1, which was generated by GNU Autoconf 2.69. Invocation command line was $ $0 $@ @@ -2805,7 +2805,7 @@ fi # Define the identity of the package. PACKAGE='tauari_c' - VERSION='1.0.0' + VERSION='0.0.1' cat >>confdefs.h <<_ACEOF @@ -14272,7 +14272,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 # report actual input values of CONFIG_FILES etc. instead of their # values after options handling. ac_log=" -This file was extended by tauari_c $as_me 1.0.0, which was +This file was extended by tauari_c $as_me 0.0.1, which was generated by GNU Autoconf 2.69. Invocation command line was CONFIG_FILES = $CONFIG_FILES @@ -14339,7 +14339,7 @@ _ACEOF cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`" ac_cs_version="\\ -tauari_c config.status 1.0.0 +tauari_c config.status 0.0.1 configured by $0, generated by GNU Autoconf 2.69, with options \\"\$ac_cs_config\\" diff --git a/environment.yml b/environment.yml index 3abb550..0dfa98f 100644 --- a/environment.yml +++ b/environment.yml @@ -5,8 +5,9 @@ channels: - defaults dependencies: - pip + - setuptools - python>=3.6 # includes python-dev - - biopython>1.68 + - treeswift>=1.0 - automake - make - zlib diff --git a/recipe/build.sh b/recipe/build.sh index 90eb8a5..39d6027 100644 --- a/recipe/build.sh +++ b/recipe/build.sh @@ -5,11 +5,4 @@ export CFLAGS="-I$PREFIX/include" export LDFLAGS="-L$PREFIX/lib" export CPATH=${PREFIX}/include -# cd to location of Makefile and source -mkdir build -cd build -# assumes autoreconf was run and thus configure.sh is present -$SRC_DIR/configure --prefix=$PREFIX -make -make install - +pip install . diff --git a/requirements.txt b/requirements.txt new file mode 100644 index 0000000..0ae5bbb --- /dev/null +++ b/requirements.txt @@ -0,0 +1,2 @@ +treeswift >= 1.0 +biopython >= 1.70 diff --git a/setup.py b/setup.py index 864ef9d..72c3fea 100644 --- a/setup.py +++ b/setup.py @@ -1,9 +1,8 @@ -import pathlib, setuptools, sys, os +import pathlib, setuptools, sys, os, re import setuptools.command.develop import setuptools.command.install import setuptools.command.egg_info import subprocess -from tauari import __version__ ## right now it uses "local" copy of biomcmc but also needs system global-wide one (cant copy to sys.path) ## I'll end up installing biomcmc with autotools and setup.py only when needed @@ -22,6 +21,10 @@ build_path = f"{base_dir}/build_setup" biomcmc_path = f"{build_path}/biomcmc-lib" +# first line of configure.ac is "AC_INIT([tauari_c], [0.0.1], [leomrtns@gmail.com]" +version_txt = open(f"{base_dir}/configure.ac").readline() +version_txt = re.findall(r'\[(.*?)\]',version_txt)[1] + # Eval the version file to get __version__; avoids importing our own package with readme_file.open(encoding = "utf-8") as f: long_description = f.read() @@ -56,7 +59,7 @@ def run(self): setuptools.setup( name = "tauari", - version = __version__, + version = version_txt, author = "Leonardo de Oliveira Martins", author_email = "Leonardo.de-Oliveira-Martins@quadram.ac.uk", description = "Python bindings for biomcmc-lib, a C library for phylogenetics", @@ -74,7 +77,8 @@ def run(self): python_requires = '>={}'.format('.'.join(str(n) for n in min_version)), license='GPLv3+', install_requires=[ - 'biopython >= 1.68' + 'treeswift >= 1.0', + 'biopython >= 1.70' ], classifiers = [ "Development Status :: 2 - Pre-Alpha", diff --git a/src/Makefile.am b/src/Makefile.am index 31669de..64df00f 100644 --- a/src/Makefile.am +++ b/src/Makefile.am @@ -1,6 +1,6 @@ -AM_CPPFLAGS = $(GTKDEPS_CFLAGS) @OPENMP_CPPFLAGS@ -I$(srcdir)/../@BIOMCMCLIB@/lib +AM_CPPFLAGS = $(GTKDEPS_CFLAGS) @OPENMP_CPPFLAGS@ -I$(top_srcdir)/@BIOMCMCLIB@/lib AM_CFLAGS = @AM_CFLAGS@ @OPENMP_CFLAGS@ @PYTHON_CFLAGS@ -LIBBIOMC_LA = ../@BIOMCMCLIB@/lib/libbiomcmc_static.la +LIBBIOMC_LA = $(top_builddir)/@BIOMCMCLIB@/lib/libbiomcmc_static.la LDADD = $(LIBBIOMC_LA) $(GTKDEPS_LIBS) $(AM_LDFLAGS) @PYTHON_LIBS@ common_headers =#tauari_module.h diff --git a/src/Makefile.in b/src/Makefile.in index 1e8ebe2..bcc6cc4 100644 --- a/src/Makefile.in +++ b/src/Makefile.in @@ -349,8 +349,8 @@ target_alias = @target_alias@ top_build_prefix = @top_build_prefix@ top_builddir = @top_builddir@ top_srcdir = @top_srcdir@ -AM_CPPFLAGS = $(GTKDEPS_CFLAGS) @OPENMP_CPPFLAGS@ -I$(srcdir)/../@BIOMCMCLIB@/lib -LIBBIOMC_LA = ../@BIOMCMCLIB@/lib/libbiomcmc_static.la +AM_CPPFLAGS = $(GTKDEPS_CFLAGS) @OPENMP_CPPFLAGS@ -I$(top_srcdir)/@BIOMCMCLIB@/lib +LIBBIOMC_LA = $(top_builddir)/@BIOMCMCLIB@/lib/libbiomcmc_static.la LDADD = $(LIBBIOMC_LA) $(GTKDEPS_LIBS) $(AM_LDFLAGS) @PYTHON_LIBS@ common_headers = #tauari_module.h common_src = tauari_module.c diff --git a/submodules/biomcmc-lib b/submodules/biomcmc-lib index d766ace..b88eab5 160000 --- a/submodules/biomcmc-lib +++ b/submodules/biomcmc-lib @@ -1 +1 @@ -Subproject commit d766ace82091b7a2ea8010b60cc3131a013daa02 +Subproject commit b88eab5e3c7629f4827983962fc62dd3502e24c7 diff --git a/tauari/__init__.py b/tauari/__init__.py index 0775c7b..a364486 100644 --- a/tauari/__init__.py +++ b/tauari/__init__.py @@ -1,2 +1 @@ from .tauari import * -__version__ = '0.0.1' diff --git a/tauari/tauari.py b/tauari/tauari.py index c3cd1bd..5e368ac 100644 --- a/tauari/tauari.py +++ b/tauari/tauari.py @@ -2,9 +2,24 @@ import tauari_c except: print ("Tauari:: could not load C library 'tauari_c', maybe it's not compiled yet") +import logging +logger = logging.getLogger(__name__) +logger.propagate = False +stream_log = logging.StreamHandler() +log_format = logging.Formatter(fmt='Tauari %(asctime)s [%(levelname)s] %(message)s', datefmt="%Y-%m-%d %H:%M") +stream_log.setFormatter(log_format) +stream_log.setLevel(logging.WARNING) +logger.addHandler(stream_log) def tauaritest(s1 = None, s2 = None): print(tauari_c.testfunction(s1, s2)) def tauaritest2(): print(tauari_c.test2()) + +def get_version (): + import pkg_resources # part of setuptools + return pkg_resources.require("tauari")[0].version + +if __name__ == '__main__': + print (f"Tauari version ", get_version())