pip now installs successfully

.gitignore

@@ -1,5 +1,4 @@
-/biomcmc-lib
-/build
+/build/*
 
 ## suggested by github
 # Byte-compiled / optimized / DLL files

README.md

@@ -10,54 +10,54 @@ It will contain python bindings for the low-level [biomcmc-lib](https://github.c
 phylogenetic library in C.
 Very beta at the moment. Empty, to be precise. 
 
-
 **tauari** is the name of an endangered Brazilian timber tree. Tree → towa-ree → tauari. 
 
+### Dependencies
+
+* python development package (with the API python/C library).  Installed with your python conda installation or as `python-dev` from linux. 
+* `automake`, the `check` unit test framework, and `zlib` are required for installing the lowlevel `biomcmc-lib`.
+* python > 3.6 and a C compiler, e.g. `gcc`
+* The lowlevel phylogenetic library [biomcmc-lib](https://github.com/quadram-institute-bioscience/biomcmc-lib), which should be included here
+(it will be compiled as well). 
+For a more up-to-date list you may need to check the conda/docker files once they are complete.
+
 # Installation
 
 Make sure you clone this repository recursively:
 ```
 git clone --recursive  https://github.com/leomrtns/tauari.git
 ```
-Right now I am testing two ways of installing it, I'll probably use the second one (autotools).
-Needless to say the instructions are incomplete at this point. 
-
-### Dependencies
 
-* development package with the API python/C library, which is installed with your python conda installation or as `python-dev` from linux. 
-* `automake`, the `check` unit test framework, and `zlib` are required for installing the lowlevel `biomcmc-lib`.
-* python > 3.6 and a C compiler, e.g. `gcc`
-* The lowlevel phylogenetic library [biomcmc-lib](https://github.com/quadram-institute-bioscience/biomcmc-lib), which is installed together
-
-## installation using `pip` 
-
-You can create a conda environment 
+**tl;dr:** You can create a conda environment (or not) and then run `pip install .`  
 ```bash
 conda update -n base -c defaults conda # probably not needed, but some machines complained about it
 conda env create -f environment.yml
 conda activate tauari
 pip install .
 
-## since this software is under development, these two commands are also quite useful:
+## since this software is under development, I find these two commands quite useful:
 
 conda env update -f environment.yml # updat conda evironment after changing dependencies
 pip install -e . # installs in development mode (modifications to python files are live)
 python setup.py develop # same as above, but more verbose and overwriting ./build_setup directory
 ```
 
-However this method assumes that `biomcmc-lib` is installed globally, which is not its original or main purpose (to be
-an auxiliary, lowlevel library).
-I won't write the details here because I'll probably abandon this approach.
-
 ## autotools-based installation 
-This will probably be the default approach once this software becomes useful, since it compiles the lowlevel
-`biomcmc-lib` together with the C components of *tauari* and generates a dynamic library. 
-It still needs `setuptools` to install the python components. 
-
-`autotools` can find the shared library installation path relative to the environment root (e.g. `conda info --base` when installing
-locally or `/` if installing it system-wide).
-Or it can install a regular libotool library (the difference is `pyexec_LTLIBRARIES` or `lib_`)
-I plan to also generate a pre-install step in `setup.py` that runs autotools if library is absent. 
+
+Originally `biomcmc-lib` is an auxiliary, lowlevel library, and as such should not be directly exposed to the user or
+shared system-wide (you can do it, btw, but it's intended as a "subdir" for autotools).
+Therefore **tauari** compiles `biomcmc-lib` together with its C components, generating a dynamic library.
+Just like [setuptools.Extension](https://docs.python.org/3/extending/building.html), but using autotools.
+It still needs `setuptools` to install the python components and move the library to the correct location.  
+
+Calling `pip install .` (or `python setup.py install`) will run autotools in the background, but if you want you can run it by hand:
+```bash
+cd build_setup
+../configure --prefix="." 
+make && make install
+ls lib/
+```
+The file "tauari_c.so" can be imported in python.
 
 # License 
 SPDX-License-Identifier: GPL-3.0-or-later

clean_dist.sh

@@ -1,6 +1,6 @@
 #!/bin/sh 
 rm -f build_setup/config.log build_setup/config.status build_setup/libtool build_setup/Makefile 
-rm -rf build_setup/lib build_setup/include 
+rm -rf build_setup/lib build_setup/include build_setup/src build_setup/build_setup 
 rm -rf build_setup/lib.* build_setup/temp.*
 rm -rf build_setup/tests
 rm -rf tauari.egg-info 

setup.py

@@ -21,33 +21,23 @@
 readme_file  = base_dir/"README.md"
 build_path   = f"{base_dir}/build_setup"
 biomcmc_path = f"{build_path}/biomcmc-lib"
-source_files = ["tauari_module.c"]
-source_files = [f"src/{x}" for x in source_files]
 
 # 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()
 
-module_c = setuptools.Extension('_tauari_c',
-    include_dirs = ["build_setup/include/biomcmc"], 
-    library_dirs =  ["build_setup/lib"],
-    runtime_library_dirs = ["build_setup/lib"], 
-    libraries = ['biomcmc'], # dynamic libraries only
-    undef_macros = [ "NDEBUG" ],
-    extra_objects = ["build_setup/lib/libbiomcmc.so", "build_setup/lib/libbiomcmc.a"], # redundant with 'libraries' tbh
-    #extra_compile_args = ["-Bstatic -lbiomcmc -Wl"],
-    sources = source_files)
-
 if not os.path.exists(biomcmc_path): # developers can have their own links (without submodule)
     source = f"{base_dir}/submodules/biomcmc-lib/"
     if not os.path.exists(source):
         sys.exit(f"Tauari:: No '{source}' found;\n You must download this repository with 'git clone --recursive' or add biomcmc-lib by hand to {biomcmc_path}")
     print (f"Tauari:: Creating a link '{biomcmc_path}' pointing to '{source}'")
     os.symlink(source, biomcmc_path)
 
-def biomc2_compilation (options = ""):
-    autoconf_path = f"{biomcmc_path}/configure"
-    subprocess.call(f"{autoconf_path} --prefix={build_path} {options}".split(), cwd=build_path) # --program-prefix=PREFIX 
-    subprocess.call(f"make install".split(), cwd=build_path) # libbiomcmc.a will be installed in {build_path}
+def biomc2_compilation (options = ""):     
+    if not os.path.isfile(f"{build_path}/lib/tauari_c.so"):
+        subprocess.call(f"../configure --prefix={build_path} {options}".split(), cwd=build_path) # --program-prefix=PREFIX 
+        subprocess.call(f"make".split(), cwd=build_path)
+        subprocess.call(f"make install".split(), cwd=build_path) # tauari_c.so* will be installed in {build_path}
+
 class PrePostDevelopCompile(setuptools.command.develop.develop):
     """pre- and post-compilation for development mode (only pre- currently)"""
     def run(self):
@@ -78,9 +68,8 @@ def run(self):
         "Source": "https://github.com/quadram-institute-bioscience",
     },
     packages = setuptools.find_packages(),
-    #include_package_data=True,
-    package_dir = {'tauari':"build_setup/lib"}, ## copy to root (site-packages)
-    package_data = {'': ["libbiomcmc.so*"]}, # , "build_setup/include/*", "build_setup/include/biomcmc/*"]}, # relative paths to setup.py only 
+#    package_dir = {'tauari':"build_setup/lib"}, # copy to site-packages/tauari 
+    package_data = {'tauari': ["build_setup/lib/tauari_c.so*"]},      # relative paths to setup.py only 
     data_files = [("", ["LICENSE"])],
     python_requires = '>={}'.format('.'.join(str(n) for n in min_version)),
     license='GPLv3+',
@@ -97,11 +86,11 @@ def run(self):
         "Programming Language :: Python :: 3.8",
     ],
     # Install a "tauari" program which calls tauari.__main__.main()
-    #entry_points = { "console_scripts": ["tauari = tauari.tauari:main"]},
+    # entry_points = { "console_scripts": ["tauari = tauari.tauari:main"]},
+    # ext_modules = [module_c], 
     cmdclass={
         'develop':  PrePostDevelopCompile,
         'install':  PrePostInstallCompile,
         'egg_info':  PrePostEggInfoCompile,
-    },
-    ext_modules = [module_c]
+    } 
 )

src/tauari_module.c

@@ -52,7 +52,7 @@ PyInit_tauari_c (void) /* it has to be named PyInit_<module name in python> */
   m = PyModule_Create(&tauarimodule);
   if (m == NULL) return NULL;
 
-  TauariError = PyErr_NewException("_tauari_c.error", NULL, NULL);
+  TauariError = PyErr_NewException("tauari_c.error", NULL, NULL);
   Py_INCREF(TauariError);
   PyModule_AddObject(m, "error", TauariError);
   return m;

tauari/__init__.py

@@ -1 +1,2 @@
+from .tauari import *
 __version__ = '0.0.1'

tauari/tauari.py

@@ -1,7 +1,10 @@
-import _tauari_c
+try:
+    import tauari_c
+except:
+    print ("Tauari:: could not load C library 'tauari_c', maybe it's not compiled yet")
 
 def tauaritest(s1 = None, s2 = None):
-    print(_tauari_c.testfunction(s1, s2))
+    print(tauari_c.testfunction(s1, s2))
 
 def tauaritest2():
-    print(_tauari_c.test2())
+    print(tauari_c.test2())