diff options
Diffstat (limited to 'reproduce/src/make/dependencies-python.mk')
| -rw-r--r-- | reproduce/src/make/dependencies-python.mk | 213 |
1 files changed, 109 insertions, 104 deletions
diff --git a/reproduce/src/make/dependencies-python.mk b/reproduce/src/make/dependencies-python.mk index 946c047..6711d17 100644 --- a/reproduce/src/make/dependencies-python.mk +++ b/reproduce/src/make/dependencies-python.mk @@ -29,51 +29,6 @@ -# Top level environment -include reproduce/config/pipeline/LOCAL.mk -include reproduce/src/make/dependencies-build-rules.mk -include reproduce/config/pipeline/dependency-versions.mk - -ddir = $(BDIR)/dependencies -tdir = $(BDIR)/dependencies/tarballs -idir = $(BDIR)/dependencies/installed -ibdir = $(BDIR)/dependencies/installed/bin -ildir = $(BDIR)/dependencies/installed/lib -ilidir = $(BDIR)/dependencies/installed/lib/built -ipydir = $(BDIR)/dependencies/installed/lib/built/python - -# Define the top-level programs to build (installed in `.local/bin'). -top-level-python = astroquery matplotlib #scipy -all: $(foreach p, $(top-level-python), $(ipydir)/$(p)) - -# Other basic environment settings: We are only including the host -# operating system's PATH environment variable (after our own!) for the -# compiler and linker. For the library binaries and headers, we are only -# using our internally built libraries. -# -# To investigate: -# -# 1) Set SHELL to `$(ibdir)/env - NAME=VALUE $(ibdir)/bash' and set all -# the parameters defined bellow as `NAME=VALUE' statements before -# calling Bash. This will enable us to completely ignore the user's -# native environment. -# -# 2) Add `--noprofile --norc' to `.SHELLFLAGS' so doesn't load the -# user's environment. -.ONESHELL: -.SHELLFLAGS := --noprofile --norc -ec -export CCACHE_DISABLE := 1 -export PATH := $(ibdir) -export LD_RUN_PATH := $(ildir) -export LD_LIBRARY_PATH := $(ildir) -export SHELL := $(ibdir)/bash -export CPPFLAGS := -I$(idir)/include -export PKG_CONFIG_PATH := $(ildir)/pkgconfig -export PKG_CONFIG_LIBDIR := $(ildir)/pkgconfig -export LDFLAGS := $(rpath_command) -L$(ildir) - - - # Python enviroment @@ -84,9 +39,9 @@ export LDFLAGS := $(rpath_command) -L$(ildir) # systems which might interfere. To be safe, we are removing all their # values. export PYTHONPATH := $(installdir)/lib/python/site-packages +export PYTHONPATH2 := $(PYTHONPATH) export PYTHONPATH3 := $(PYTHONPATH) export _LMFILES_ := -export PYTHONPATH2 := export LOADEDMODULES := export MPI_PYTHON_SITEARCH := export MPI_PYTHON2_SITEARCH := @@ -106,7 +61,7 @@ export MPI_PYTHON3_SITEARCH := # convention, but include the name/version in their tarball names with # another format, we'll do the modification before the download so the # downloaded file has our desired format. -tarballs = $(foreach t, asn1crypto-$(asn1crypto-version).tar.gz \ +pytarballs = $(foreach t, asn1crypto-$(asn1crypto-version).tar.gz \ astroquery-$(astroquery-version).tar.gz \ astropy-$(astropy-version).tar.gz \ beautifulsoup4-$(beautifulsoup4-version).tar.gz \ @@ -116,6 +71,7 @@ tarballs = $(foreach t, asn1crypto-$(asn1crypto-version).tar.gz \ cryptography-$(cryptography-version).tar.gz \ cycler-$(cycler-version).tar.gz \ entrypoints-$(entrypoints-version).tar.gz \ + h5py-$(h5py-version).tar.gz \ html5lib-$(html5lib-version).tar.gz \ idna-$(idna-version).tar.gz \ jeepney-$(jeepney-version).tar.gz \ @@ -123,6 +79,7 @@ tarballs = $(foreach t, asn1crypto-$(asn1crypto-version).tar.gz \ keyring-$(keyring-version).tar.gz \ libffi-$(libffi-version).tar.gz \ matplotlib-$(matplotlib-version).tar.gz \ + mpi4py-$(mpi4py-version).tar.gz \ numpy-$(numpy-version).zip \ pip-$(pip-version).tar.gz \ pycparser-$(pycparser-version).tar.gz \ @@ -140,8 +97,8 @@ tarballs = $(foreach t, asn1crypto-$(asn1crypto-version).tar.gz \ webencodings-$(webencodings-version).tar.gz \ virtualenv-$(virtualenv-version).tar.gz \ , $(tdir)/$(t) ) -topurl=https://files.pythonhosted.org/packages -$(tarballs): $(tdir)/%: +pytopurl=https://files.pythonhosted.org/packages +$(pytarballs): $(tdir)/%: if [ -f $(DEPENDENCIES-DIR)/$* ]; then cp $(DEPENDENCIES-DIR)/$* $@ else @@ -157,7 +114,10 @@ $(tarballs): $(tdir)/%: # because the tokenization above will produce `python' as the # first string. if [ $* = python-dateutil-$(python-dateutil-version).tar.gz ]; then - n=dateutil + n=dateutil + elif [ $* = h5py-$(h5py-version).tar.gz ]; then + n=h5py + # elif [ $* = strange-tarball5name-version.tar.gz ]; then # n=strange5-name else @@ -180,7 +140,7 @@ $(tarballs): $(tdir)/%: elif [ $$n = secretstorage ]; then mergenames=0 hash=a6/89/df343dbc2957a317127e7ff2983230dc5336273be34f2e1911519d85aeb5 - h=$(topurl)/$$hash/SecretStorage-$(secretstorage-version).tar.gz + h=$(pytopurl)/$$hash/SecretStorage-$(secretstorage-version).tar.gz elif [ $$n = asn ]; then h=fc/f1/8db7daa71f414ddabfa056c4ef792e1461ff655c2ae2928a2b675bfed6b4 elif [ $$n = astroquery ]; then h=61/50/a7a08f9e54d7d9d97e69433cd88231e1ad2901811c9d1ae9ac7ccaef9396 elif [ $$n = astropy ]; then h=eb/f7/1251bf6881861f24239efe0c24cbcfc4191ccdbb69ac3e9bb740d0c23352 @@ -191,13 +151,15 @@ $(tarballs): $(tdir)/%: elif [ $$n = cryptography ]; then h=07/ca/bc827c5e55918ad223d59d299fff92f3563476c3b00d0a9157d9c0217449 elif [ $$n = cycler ]; then h=c2/4b/137dea450d6e1e3d474e1d873cd1d4f7d3beed7e0dc973b06e8e10d32488 elif [ $$n = entrypoints ]; then h=b4/ef/063484f1f9ba3081e920ec9972c96664e2edb9fdc3d8669b0e3b8fc0ad7c + elif [ $$n = h5py ]; then h=43/27/a6e7dcb8ae20a4dbf3725321058923fec262b6f7835179d78ccc8d98deec elif [ $$n = html ]; then h=85/3e/cf449cf1b5004e87510b9368e7a5f1acd8831c2d6691edd3c62a0823f98f elif [ $$n = idna ]; then h=ad/13/eb56951b6f7950cadb579ca166e448ba77f9d24efc03edd7e55fa57d04b7 elif [ $$n = jeepney ]; then h=16/1d/74adf3b164a8d19a60d0fcf706a751ffa2a1eaa8e5bbb1b6705c92a05263 elif [ $$n = keyring ]; then h=15/88/c6ce9509438bc02d54cf214923cfba814412f90c31c95028af852b19f9b2 elif [ $$n = kiwisolver ]; then h=31/60/494fcce70d60a598c32ee00e71542e52e27c978e5f8219fae0d4ac6e2864 elif [ $$n = matplotlib ]; then h=89/0c/653aec68e9cfb775c4fbae8f71011206e5e7fe4d60fcf01ea1a9d3bc957f - elif [ $$n = numpy ]; then h=2b/26/07472b0de91851b6656cbc86e2f0d5d3a3128e7580f23295ef58b6862d6c + elif [ $$n = mpi ]; then h=55/a2/c827b196070e161357b49287fa46d69f25641930fd5f854722319d431843 + elif [ $$n = numpy ]; then h=cf/8d/6345b4f32b37945fedc1e027e83970005fc9c699068d2f566b82826515f2 elif [ $$n = pip ]; then h=4c/4d/88bc9413da11702cbbace3ccc51350ae099bb351febae8acc85fec34f9af elif [ $$n = pycparser ]; then h=68/9e/49196946aee219aead1290e00d1e7fdeab8567783e83e1b9ab5585e6206a elif [ $$n = pyparsing ]; then h=b9/b8/6b32b3e84014148dcd60dd05795e35c2e7f4b72f918616c61fdce83d27fc @@ -212,7 +174,7 @@ $(tarballs): $(tdir)/%: elif [ $$n = urllib ]; then h=b1/53/37d82ab391393565f2f831b8eedbffd57db5a718216f82f1a8b4d381a1c1 elif [ $$n = virtualenv ]; then h=51/aa/c395a6e6eaaedfa5a04723b6446a1df783b16cca6fec66e671cede514688 elif [ $$n = webencodings ]; then h=0b/02/ae6ceac1baeda530866a85075641cec12989bd8d31af6d5ab4a3e8c92f47 -# elif [ $$n = strange5-name ]; then h=XXXXX +# elif [ $$n = strange5-name ]; then h=XXXXX else echo; echo; echo; echo "'$$n' not recognized as a dependency name to download." @@ -227,7 +189,7 @@ $(tarballs): $(tdir)/%: # storing all the tarballs in one directory, we want it to have # the same naming convention, so we'll download it to a temporary # name, then rename that. - if [ $$mergenames = 1 ]; then tarballurl=$(topurl)/$$h/"$*" + if [ $$mergenames = 1 ]; then tarballurl=$(pytopurl)/$$h/"$*" else tarballurl=$$h fi @@ -249,18 +211,24 @@ $(tarballs): $(tdir)/%: # -------------------- # # To build Python packages with direct access to a `setup.py' (if no direct -# access to `setup.py' is needed, pip can be used) +# access to `setup.py' is needed, pip can be used). # Arguments of this function are the numbers # 1) Unpack command # 2) Package name # 3) Unpacked directory name after unpacking the tarball -pybuild = cd $(ddir); rm -rf $(3); \ - if ! $(1) $(2); then echo; echo "Tar error"; exit 1; fi; \ - cd $(3); \ - python3 setup.py build && \ - python3 setup.py install && \ - cd .. && rm -rf $(3) && \ - echo "done!" > $@ +# 4) site.cfg file (optional) +pybuild = cd $(ddir); rm -rf $(3); \ + if ! $(1) $(2); then echo; echo "Tar error"; exit 1; fi; \ + cd $(3); \ + if [ "x$(4)" != x ]; then \ + sed -e 's|@LIBDIR[@]|'"$(ildir)"'|' \ + -e 's|@INCDIR[@]|'"$(idir)/include"'|' \ + $(4) > site.cfg; \ + fi; \ + python3 setup.py build \ + && python3 setup.py install \ + && cd .. && rm -rf $(3) \ + && echo "done!" > $@ @@ -271,24 +239,27 @@ pybuild = cd $(ddir); rm -rf $(3); \ # # While this Makefile is for Python programs, in some cases, we need # certain programs (like Python itself), or libraries for the modules. -$(ibdir)/python3: $(tdir)/python-$(python-version).tar.gz +$(ilidir)/libffi: $(tdir)/libffi-$(libffi-version).tar.gz + $(call gbuild, $<, libffi-$(libffi-version)) \ + echo "libffi is built" > $@ + +$(ibdir)/python3: $(tdir)/python-$(python-version).tar.gz \ + $(ilidir)/libffi # On Mac systems, the build complains about `clang' specific # features, so we can't use our own GCC build here. -# if [ x$(on_mac_os) = xyes ]; then \ -# export CC=clang; \ -# export CXX=clang++; \ -# fi; \ - - $(call gbuild, $<, Python-$(python-version)) \ + if [ x$(on_mac_os) = xyes ]; then \ + export CC=clang; \ + export CXX=clang++; \ + fi; \ + $(call gbuild, $<, Python-$(python-version),, \ + --without-ensurepip \ + --with-system-ffi \ + --enable-shared) \ && v=$$(echo $(python-version) | awk 'BEGIN{FS="."} \ {printf "%d.%d\n", $$1, $$2}') \ && ln -s $(ildir)/python$$v $(ildir)/python \ && rm -rf $(ipydir) && mkdir $(ipydir) -$(ilidir)/libffi: $(tdir)/libffi-$(libffi-version).tar.gz - $(call gbuild, $<, libffi-$(libffi-version)) \ - echo "libffi is built" > $@ - @@ -297,7 +268,7 @@ $(ilidir)/libffi: $(tdir)/libffi-$(libffi-version).tar.gz # # All the necessary Python modules go here. $(ipydir)/asn1crypto: $(tdir)/asn1crypto-$(asn1crypto-version).tar.gz \ - $(ibdir)/python3 + $(ipydir)/setuptools $(call pybuild, tar xf, $<, asn1crypto-$(asn1crypto-version)) $(ipydir)/astroquery: $(tdir)/astroquery-$(astroquery-version).tar.gz \ @@ -310,7 +281,9 @@ $(ipydir)/astroquery: $(tdir)/astroquery-$(astroquery-version).tar.gz \ $(call pybuild, tar xf, $<, astroquery-$(astroquery-version)) $(ipydir)/astropy: $(tdir)/astropy-$(astropy-version).tar.gz \ - $(ipydir)/numpy + $(ipydir)/h5py \ + $(ipydir)/numpy \ + $(ipydir)/scipy $(call pybuild, tar xf, $<, astropy-$(astropy-version)) $(ipydir)/beautifulsoup4: $(tdir)/beautifulsoup4-$(beautifulsoup4-version).tar.gz \ @@ -318,81 +291,107 @@ $(ipydir)/beautifulsoup4: $(tdir)/beautifulsoup4-$(beautifulsoup4-version).tar.g $(call pybuild, tar xf, $<, beautifulsoup4-$(beautifulsoup4-version)) $(ipydir)/certifi: $(tdir)/certifi-$(certifi-version).tar.gz \ - $(ibdir)/python3 + $(ipydir)/setuptools $(call pybuild, tar xf, $<, certifi-$(certifi-version)) $(ipydir)/cffi: $(tdir)/cffi-$(cffi-version).tar.gz \ - $(ipydir)/pycparser \ - $(ilidir)/libffi + $(ilidir)/libffi \ + $(ipydir)/pycparser $(call pybuild, tar xf, $<, cffi-$(cffi-version)) $(ipydir)/chardet: $(tdir)/chardet-$(chardet-version).tar.gz \ - $(ibdir)/python3 + $(ipydir)/setuptools $(call pybuild, tar xf, $<, chardet-$(chardet-version)) $(ipydir)/cryptography: $(tdir)/cryptography-$(cryptography-version).tar.gz \ - $(ipydir)/cffi \ - $(ipydir)/asn1crypto + $(ipydir)/asn1crypto \ + $(ipydir)/cffi $(call pybuild, tar xf, $<, cryptography-$(cryptography-version)) $(ipydir)/cycler: $(tdir)/cycler-$(cycler-version).tar.gz \ - $(ipydir)/six + $(ipydir)/six $(call pybuild, tar xf, $<, cycler-$(cycler-version)) $(ipydir)/entrypoints: $(tdir)/entrypoints-$(entrypoints-version).tar.gz \ - $(ibdir)/python3 + $(ipydir)/setuptools $(call pybuild, tar xf, $<, entrypoints-$(entrypoints-version)) +$(ipydir)/h5py: $(tdir)/h5py-$(h5py-version).tar.gz \ + $(ipydir)/setuptools \ + $(ilidir)/hdf5 + # $(ipydir)/mpi4py # AFTER its problem is fixed. + #export HDF5_MPI=ON; # AFTER its problem is fixed. + export HDF5_DIR=$(ildir); \ + $(call pybuild, tar xf, $<, h5py-$(h5py-version)) + $(ipydir)/html5lib: $(tdir)/html5lib-$(html5lib-version).tar.gz \ $(ipydir)/six \ $(ipydir)/webencodings $(call pybuild, tar xf, $<, html5lib-$(html5lib-version)) $(ipydir)/idna: $(tdir)/idna-$(idna-version).tar.gz \ - $(ibdir)/python3 + $(ipydir)/setuptools $(call pybuild, tar xf, $<, idna-$(idna-version)) $(ipydir)/jeepney: $(tdir)/jeepney-$(jeepney-version).tar.gz \ - $(ibdir)/python3 + $(ipydir)/setuptools $(call pybuild, tar xf, $<, jeepney-$(jeepney-version)) $(ipydir)/keyring: $(tdir)/keyring-$(keyring-version).tar.gz \ - $(ipydir)/setuptools_scm \ + $(ipydir)/entrypoints \ $(ipydir)/secretstorage \ - $(ipydir)/entrypoints + $(ipydir)/setuptools_scm $(call pybuild, tar xf, $<, keyring-$(keyring-version)) $(ipydir)/kiwisolver: $(tdir)/kiwisolver-$(kiwisolver-version).tar.gz \ - $(ipydir)/setuptools + $(ipydir)/setuptools $(call pybuild, tar xf, $<, kiwisolver-$(kiwisolver-version)) - $(ipydir)/matplotlib: $(tdir)/matplotlib-$(matplotlib-version).tar.gz \ $(ipydir)/cycler \ $(ilidir)/freetype \ + $(ipydir)/kiwisolver \ $(ipydir)/numpy \ $(ipydir)/pyparsing \ - $(ipydir)/python-dateutil \ - $(ipydir)/kiwisolver + $(ipydir)/python-dateutil $(call pybuild, tar xf, $<, matplotlib-$(matplotlib-version)) +# Currently mpi4py doesn't build because of some conflict with OpenMPI: +# +# In file included from src/mpi4py.MPI.c:591, +# from src/MPI.c:4: +# src/mpi4py.MPI.c: In function '__pyx_f_6mpi4py_3MPI_del_Datatype': +# src/mpi4py.MPI.c:15094:36: error: expected expression before '_Static_assert' +# __pyx_t_1 = (((__pyx_v_ob[0]) == MPI_UB) != 0); +# +# But atleast on my system it fails. +$(ipydir)/mpi4py: $(tdir)/mpi4py-$(mpi4py-version).tar.gz \ + $(ipydir)/setuptools \ + $(ilidir)/openmpi + $(call pybuild, tar xf, $<, mpi4py-$(mpi4py-version)) + $(ipydir)/numpy: $(tdir)/numpy-$(numpy-version).zip \ - $(ibdir)/python3 - export BLAS=None; \ - export ATLAS=None; \ - export LAPACK=None; \ - $(call pybuild, unzip, $<, numpy-$(numpy-version)) + $(ipydir)/setuptools \ + $(ilidir)/openblas \ + $(ilidir)/fftw + if [ x$(on_mac_os) = xyes ]; then \ + export LDFLAGS="$(LDFLAGS) -undefined dynamic_lookup -bundle"; \ + else \ + export LDFLAGS="$(LDFLAGS) -shared"; \ + fi; \ + conf="$$(pwd)/reproduce/config/pipeline/dependency-numpy-scipy.cfg"; \ + $(call pybuild, unzip, $<, numpy-$(numpy-version),$$conf) $(ibdir)/pip3: $(tdir)/pip-$(pip-version).tar.gz \ - $(ibdir)/python3 + $(ipydir)/setuptools $(call pybuild, tar xf, $<, pip-$(pip-version)) $(ipydir)/pycparser: $(tdir)/pycparser-$(pycparser-version).tar.gz \ - $(ibdir)/python3 + $(ipydir)/setuptools $(call pybuild, tar xf, $<, pycparser-$(pycparser-version)) $(ipydir)/pyparsing: $(tdir)/pyparsing-$(pyparsing-version).tar.gz \ - $(ibdir)/python3 + $(ipydir)/setuptools $(call pybuild, tar xf, $<, pyparsing-$(pyparsing-version)) $(ipydir)/python-dateutil: $(tdir)/python-dateutil-$(python-dateutil-version).tar.gz \ @@ -410,7 +409,13 @@ $(ipydir)/requests: $(tdir)/requests-$(requests-version).tar.gz \ $(ipydir)/scipy: $(tdir)/scipy-$(scipy-version).tar.gz \ $(ipydir)/numpy - $(call pybuild, tar xf, $<, scipy-$(scipy-version)) + if [ x$(on_mac_os) = xyes ]; then \ + export LDFLAGS="$(LDFLAGS) -undefined dynamic_lookup -bundle"; \ + else \ + export LDFLAGS="$(LDFLAGS) -shared"; \ + fi; \ + conf="$$(pwd)/reproduce/config/pipeline/dependency-numpy-scipy.cfg"; \ + $(call pybuild, tar xf, $<, scipy-$(scipy-version),$$conf) $(ipydir)/secretstorage: $(tdir)/secretstorage-$(secretstorage-version).tar.gz \ $(ipydir)/cryptography \ @@ -426,17 +431,17 @@ $(ipydir)/setuptools_scm: $(tdir)/setuptools_scm-$(setuptools_scm-version).tar.g $(call pybuild, tar xf, $<, setuptools_scm-$(setuptools_scm-version)) $(ipydir)/six: $(tdir)/six-$(six-version).tar.gz \ - $(ibdir)/python3 + $(ipydir)/setuptools $(call pybuild, tar xf, $<, six-$(six-version)) $(ipydir)/soupsieve: $(tdir)/soupsieve-$(soupsieve-version).tar.gz \ - $(ibdir)/python3 + $(ipydir)/setuptools $(call pybuild, tar xf, $<, soupsieve-$(soupsieve-version)) $(ipydir)/urllib3: $(tdir)/urllib3-$(urllib3-version).tar.gz \ - $(ibdir)/python3 + $(ipydir)/setuptools $(call pybuild, tar xf, $<, urllib3-$(urllib3-version)) $(ipydir)/webencodings: $(tdir)/webencodings-$(webencodings-version).tar.gz \ - $(ibdir)/python3 + $(ipydir)/setuptools $(call pybuild, tar xf, $<, webencodings-$(webencodings-version)) |