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authorRaul Infante-Sainz <infantesainz@gmail.com>2019-03-06 17:12:19 +0000
committerRaul Infante-Sainz <infantesainz@gmail.com>2019-03-06 17:12:19 +0000
commit41865272cd80856eb466daef029a669225dbf139 (patch)
treebc77d553e92432c91530c9bbc4a466e16fa0d67d /reproduce/src
parenta57c91cfdb05cf5cd790823f40d443648f3fc21a (diff)
Astroquery, astropy, matplotlib and numpy are now in the pipeline
Until this commit, we had some of the python packages intalled but they did not work properly because of the `PYTHONPATH' variables. That is, the pipeline's `python' was the `python' of the system instead of the pipeline's `python'. With this commit this issue has been fixed by setting the correct `PYTHONPATH'. In this commit we also modify the installation of `bzip2' because `CMake' was complaining about some libraries built statically.
Diffstat (limited to 'reproduce/src')
-rw-r--r--reproduce/src/make/dependencies-basic.mk37
-rw-r--r--reproduce/src/make/dependencies-python.mk1
-rw-r--r--reproduce/src/make/dependencies.mk3
-rw-r--r--reproduce/src/make/initialize.mk13
4 files changed, 44 insertions, 10 deletions
diff --git a/reproduce/src/make/dependencies-basic.mk b/reproduce/src/make/dependencies-basic.mk
index f02f68f..fefda6f 100644
--- a/reproduce/src/make/dependencies-basic.mk
+++ b/reproduce/src/make/dependencies-basic.mk
@@ -288,15 +288,34 @@ $(ibdir)/xz: $(tdir)/xz-$(xz-version).tar.gz
$(call gbuild, $<, xz-$(xz-version), static)
$(ibdir)/bzip2: $(tdir)/bzip2-$(bzip2-version).tar.gz
- tdir=bzip2-$(bzip2-version); \
- if [ $(static_build) = yes ]; then \
- makecommand="make LDFLAGS=-static"; \
- else \
- makecommand="make"; \
- fi; \
- cd $(ddir) && rm -rf $$tdir && tar xf $< && cd $$tdir && \
- $$makecommand && make install PREFIX=$(idir) && \
- cd .. && rm -rf $$tdir
+ # Bzip2 doesn't have a `./configure' script, and its Makefile
+ # doesn't build a shared library. So we can't use the `gbuild'
+ # function here and we need to take some extra steps (inspired
+ # from the "Linux from Scratch" guide for Bzip2):
+ # 1) The `sed' call is for relative installed symbolic links.
+ # 2) The special Makefile-libbz2_so builds the shared library.
+ #
+ # NOTE: the major version number appears in the final symbolic
+ # link.
+ tdir=bzip2-$(bzip2-version); \
+ if [ $(static_build) = yes ]; then \
+ makecommand="make LDFLAGS=-static"; \
+ makeshared="echo no-shared"; \
+ else \
+ makecommand="make"; \
+ makeshared="make -f Makefile-libbz2_so"; \
+ fi; \
+ cd $(ddir) && rm -rf $$tdir && tar xf $< && cd $$tdir \
+ && sed -i 's@\(ln -s -f \)$$(PREFIX)/bin/@\1@' Makefile \
+ && $$makeshared \
+ && cp -a libbz2* $(ildir)/ \
+ && make clean \
+ && $$makecommand \
+ && make install PREFIX=$(idir) \
+ && cd .. \
+ && rm -rf $$tdir \
+ && cd $(ildir) \
+ && ln -fs libbz2.so.1.0 libbz2.so
# GNU Tar: When built statically, tar gives a segmentation fault on
# unpacking Bash. So we'll build it dynamically.
diff --git a/reproduce/src/make/dependencies-python.mk b/reproduce/src/make/dependencies-python.mk
index c45cc13..1e4f611 100644
--- a/reproduce/src/make/dependencies-python.mk
+++ b/reproduce/src/make/dependencies-python.mk
@@ -302,6 +302,7 @@ $(ipydir)/kiwisolver: $(tdir)/kiwisolver-$(kiwisolver-version).tar.gz \
$(ipydir)/matplotlib: $(tdir)/matplotlib-$(matplotlib-version).tar.gz \
$(ipydir)/cycler \
$(ilidir)/freetype \
+ $(ipydir)/numpy \
$(ipydir)/pyparsing \
$(ipydir)/python-dateutil \
$(ipydir)/kiwisolver
diff --git a/reproduce/src/make/dependencies.mk b/reproduce/src/make/dependencies.mk
index e1b409e..deb9f39 100644
--- a/reproduce/src/make/dependencies.mk
+++ b/reproduce/src/make/dependencies.mk
@@ -242,7 +242,8 @@ $(ilidir)/libjpeg: $(tdir)/jpegsrc.$(libjpeg-version).tar.gz
$(call gbuild, $<, jpeg-9b, static) && echo "Libjpeg is built" > $@
$(ilidir)/libpng: $(tdir)/libpng-$(libpng-version).tar.xz
- $(call gbuild, $<, libpng, static) && echo "Libpng is built" > $@
+ $(call gbuild, $<, libpng-$(libpng-version), static) \
+ && echo "Libpng is built" > $@
$(ilidir)/libtiff: $(tdir)/tiff-$(libtiff-version).tar.gz \
$(ilidir)/libjpeg
diff --git a/reproduce/src/make/initialize.mk b/reproduce/src/make/initialize.mk
index 71cdbb8..638338b 100644
--- a/reproduce/src/make/initialize.mk
+++ b/reproduce/src/make/initialize.mk
@@ -116,6 +116,19 @@ export LDFLAGS := -L$(installdir)/lib
export SHELL := $(installdir)/bin/bash
export CPPFLAGS := -I$(installdir)/include
+# Python enviroment
+# So far we have found several other Python-related environment
+# variables which might interfere. So we are just removing all
+# of their values within the pipeline.
+export PYTHONPATH := $(installdir)/lib/python/site-packages
+export PYTHONPATH3 := $(PYTHONPATH)
+export _LMFILES_ :=
+export PYTHONPATH2 :=
+export LOADEDMODULES :=
+export MPI_PYTHON_SITEARCH :=
+export MPI_PYTHON2_SITEARCH :=
+export MPI_PYTHON3_SITEARCH :=
+