From 41865272cd80856eb466daef029a669225dbf139 Mon Sep 17 00:00:00 2001
From: Raul Infante-Sainz <infantesainz@gmail.com>
Date: Wed, 6 Mar 2019 17:12:19 +0000
Subject: 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.
---
.file-metadata | Bin 16853304 -> 3721 bytes
reproduce/config/pipeline/dependency-versions.mk | 9 +++---
reproduce/src/make/dependencies-basic.mk | 37 +++++++++++++++++------
reproduce/src/make/dependencies-python.mk | 1 +
reproduce/src/make/dependencies.mk | 3 +-
reproduce/src/make/initialize.mk | 13 ++++++++
6 files changed, 48 insertions(+), 15 deletions(-)
diff --git a/.file-metadata b/.file-metadata
index 525a090..1176014 100644
Binary files a/.file-metadata and b/.file-metadata differ
diff --git a/reproduce/config/pipeline/dependency-versions.mk b/reproduce/config/pipeline/dependency-versions.mk
index 655d44e..9104852 100644
--- a/reproduce/config/pipeline/dependency-versions.mk
+++ b/reproduce/config/pipeline/dependency-versions.mk
@@ -3,7 +3,6 @@
# Programs
bash-version = 5.0
binutils-version = 2.31.1
-bzip2-version = 1.0.6
cmake-version = 3.12.4
coreutils-version = 8.30
diffutils-version = 3.7
@@ -83,9 +82,9 @@ webencodings-version = 0.5.1
# Special libraries
# -----------------
#
-# The shared library name of the following libraries is explicity mentioned
-# the software build Makefiles (`reproduce/src/make/dependencies*.mk'). If
-# you change their version, also please change the explicit shared library
-# names also.
+# When updating the version of these libraries, please look into the build
+# rule first: In one way or another, the version string becomes necessary
+# during their build and must be accounted for.
+bzip2-version = 1.0.6
libgit2-version = 0.26.0
wcslib-version = 6.2
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 :=
+
--
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