Installed astroquery in the pipeline

All dependencies for building astroquery package have been done.

Until nowthe Python dependencies were built in the same Makefile
as the high level libraries and programs. But, because astroquery
has many dependencies we split the Python and Python packages
installation in a new Makefile.

The installation of differents packages are done using Python and
not pip, because we found some problems when doing it with pip.
Apparently there are some interferences between the packages
installed by the pip of the system and the pip installed as part
of Python in the pipeline.

6 files changed, 332 insertions, 50 deletions

diff --git a/.file-metadata b/.file-metadata
index 517973d..8d70351 100644
--- a/.file-metadata
+++ b/.file-metadata
diff --git a/configure b/configure
index 268ee4c..c8e2b63 100755
--- a/configure
+++ b/configure
@@ -718,6 +718,24 @@ numthreads=$($instdir/bin/nproc)
 
 
 
+# Python dependencies
+# -------------------
+#
+# Python has its own installation program. To help in managing the
+# dependencies we make the installation of packages as a separate
+# Makefile.
+./.local/bin/make -f reproduce/src/make/dependencies-python.mk    \
+                  rpath_command=$rpath_command                    \
+                  static_build=$static_build                      \
+                  on_mac_os=$on_mac_os                            \
+                  numthreads=$numthreads                          \
+                  -j$numthreads
+
+
+
+
+
+
 # Make sure TeX Live installed successfully
 # -----------------------------------------
 #
diff --git a/reproduce/config/pipeline/dependency-versions.mk b/reproduce/config/pipeline/dependency-versions.mk
index f0774bc..0aaceaf 100644
--- a/reproduce/config/pipeline/dependency-versions.mk
+++ b/reproduce/config/pipeline/dependency-versions.mk
@@ -52,8 +52,25 @@ zlib-version               = 1.2.11
 #
 # IMPORTANT: Fix url in `reproduce/src/make/dependencies.mk'
 # if changing the version
+astroquery-version         = 0.3.9
 astropy-version            = 3.1.1
+beautifulsoup4-version     = 4.7.1
+certifi-version            = 2018.11.29
+chardet-version            = 3.0.4
+entrypoints-version        = 0.3
+html5lib-version           = 1.0.1
+idna-version               = 2.8
+keyring-version            = 18.0.0
 numpy-version              = 1.16.1
+pip-version                = 19.0.2
+requests-version           = 2.21.0
+setuptools-version         = 40.8.0
+setuptools_scm-version     = 3.2.0
+six-version                = 1.12.0
+soupsieve-version          = 1.8
+urllib3-version            = 1.24.1
+virtualenv-version         = 16.4.0
+webencodings-version       = 0.5.1
 
 # Special libraries
 # -----------------
diff --git a/reproduce/src/make/dependencies-build-rules.mk b/reproduce/src/make/dependencies-build-rules.mk
index 2247518..5216488 100644
--- a/reproduce/src/make/dependencies-build-rules.mk
+++ b/reproduce/src/make/dependencies-build-rules.mk
@@ -102,23 +102,6 @@ gbuild = if [ x$(static_build) = xyes ] && [ "x$(3)" = xstatic ]; then        \
 
 
 
-
-# Python
-# ------
-#
-# To build Python packages with direct access to a `setup.py' (if no direct
-# access to `setup.py' is needed, pip can be used)
-pybuild = cd $(ddir); rm -rf $(2);                                        \
-	 if ! tar xf $(1); then echo; echo "Tar error"; exit 1; fi;           \
-	 cd $(2);                                                             \
-	 python3 setup.py build &&                                            \
-	 python3 setup.py install &&                                          \
-	 cd .. && rm -rf $(2)
-
-
-
-
-
 # CMake
 # -----
 #
diff --git a/reproduce/src/make/dependencies-python.mk b/reproduce/src/make/dependencies-python.mk
new file mode 100644
index 0000000..3e69ac6
--- /dev/null
+++ b/reproduce/src/make/dependencies-python.mk
@@ -0,0 +1,294 @@
+# Build the reproduction pipeline Python dependencies.
+#
+# ------------------------------------------------------------------------
+#                      !!!!! IMPORTANT NOTES !!!!!
+#
+# This Makefile will be run by the initial `./configure' script. It is not
+# included into the reproduction pipe after that.
+#
+# ------------------------------------------------------------------------
+#
+# Original author:
+#     Raul Infante-Sainz <infantesainz@gmail.com>
+# Contributing author(s):
+#     Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2019, Your Name.
+#
+# This Makefile is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by the
+# Free Software Foundation, either version 3 of the License, or (at your
+# option) any later version.
+#
+# This Makefile is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General
+# Public License for more details.
+#
+# A copy of the GNU General Public License is available at
+# <http://www.gnu.org/licenses/>.
+
+
+
+# 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
+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)
+
+
+
+
+
+# Tarballs
+# --------
+#
+# All the necessary tarballs are defined and prepared with this rule.
+#
+# Note that we want the tarballs to follow the convention of NAME-VERSION
+# before the `tar.XX' prefix. For those programs that don't follow this
+# 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 = $(foreach t, astroquery-$(astroquery-version).tar.gz           \
+                        astropy-$(astropy-version).tar.gz                 \
+                        beautifulsoup4-$(beautifulsoup4-version).tar.gz   \
+                        certifi-$(certifi-version).tar.gz                 \
+                        chardet-$(chardet-version).tar.gz                 \
+                        entrypoints-$(entrypoints-version).tar.gz         \
+                        html5lib-$(html5lib-version).tar.gz               \
+                        idna-$(idna-version).tar.gz                       \
+                        keyring-$(keyring-version).tar.gz                 \
+                        numpy-$(numpy-version).zip                        \
+                        pip-$(pip-version).tar.gz                         \
+                        python-$(python-version).tar.gz                   \
+                        requests-$(requests-version).tar.gz               \
+                        setuptools-$(setuptools-version).zip              \
+                        setuptools_scm-$(setuptools_scm-version).tar.gz   \
+                        six-$(six-version).tar.gz                         \
+                        soupsieve-$(soupsieve-version).tar.gz             \
+                        urllib3-$(urllib3-version).tar.gz                 \
+                        webencodings-$(webencodings-version).tar.gz       \
+                        virtualenv-$(virtualenv-version).tar.gz           \
+                      , $(tdir)/$(t) )
+topurl=https://files.pythonhosted.org/packages
+$(tarballs): $(tdir)/%:
+	if [ -f $(DEPENDENCIES-DIR)/$* ]; then
+	  cp $(DEPENDENCIES-DIR)/$* $@
+	else
+          # Remove all numbers, `-' and `.' from the tarball name so we can
+          # search more easily only with the program name.
+	  n=$$(echo $* | sed -e's/[0-9\-]/ /g' -e's/\./ /g'           \
+	               | awk '{print $$1}' )
+
+          # Set the top download link of the requested tarball.
+	  mergenames=1
+	  if [ $$n = python           ]; then
+	    mergenames=0
+	    w=https://www.python.org/ftp/python/$(python-version)/Python-$(python-version).tgz
+	  elif [ $$n = astroquery     ]; then h=61/50/a7a08f9e54d7d9d97e69433cd88231e1ad2901811c9d1ae9ac7ccaef9396
+	  elif [ $$n = astropy        ]; then h=eb/f7/1251bf6881861f24239efe0c24cbcfc4191ccdbb69ac3e9bb740d0c23352
+	  elif [ $$n = beautifulsoup  ]; then h=80/f2/f6aca7f1b209bb9a7ef069d68813b091c8c3620642b568dac4eb0e507748
+	  elif [ $$n = certifi        ]; then h=55/54/3ce77783acba5979ce16674fc98b1920d00b01d337cfaaf5db22543505ed
+	  elif [ $$n = chardet        ]; then h=fc/bb/a5768c230f9ddb03acc9ef3f0d4a3cf93462473795d18e9535498c8f929d
+	  elif [ $$n = entrypoints    ]; then h=b4/ef/063484f1f9ba3081e920ec9972c96664e2edb9fdc3d8669b0e3b8fc0ad7c
+	  elif [ $$n = html           ]; then h=85/3e/cf449cf1b5004e87510b9368e7a5f1acd8831c2d6691edd3c62a0823f98f
+	  elif [ $$n = idna           ]; then h=ad/13/eb56951b6f7950cadb579ca166e448ba77f9d24efc03edd7e55fa57d04b7
+	  elif [ $$n = keyring        ]; then h=15/88/c6ce9509438bc02d54cf214923cfba814412f90c31c95028af852b19f9b2
+	  elif [ $$n = numpy          ]; then h=2b/26/07472b0de91851b6656cbc86e2f0d5d3a3128e7580f23295ef58b6862d6c
+	  elif [ $$n = pip            ]; then h=4c/4d/88bc9413da11702cbbace3ccc51350ae099bb351febae8acc85fec34f9af
+	  elif [ $$n = requests       ]; then h=52/2c/514e4ac25da2b08ca5a464c50463682126385c4272c18193876e91f4bc38
+	  elif [ $$n = setuptools     ]; then h=c2/f7/c7b501b783e5a74cf1768bc174ee4fb0a8a6ee5af6afa92274ff964703e0
+	  elif [ $$n = setuptools_scm ]; then h=54/85/514ba3ca2a022bddd68819f187ae826986051d130ec5b972076e4f58a9f3
+	  elif [ $$n = six            ]; then h=dd/bf/4138e7bfb757de47d1f4b6994648ec67a51efe58fa907c1e11e350cddfca
+	  elif [ $$n = soupsieve      ]; then h=0c/52/e9088bb9b96e2d39fc3b33fcda5b4fde9d71473536ac660a1ca9a0958a2f
+	  elif [ $$n = virtualenv     ]; then h=51/aa/c395a6e6eaaedfa5a04723b6446a1df783b16cca6fec66e671cede514688
+	  elif [ $$n = webencodings   ]; then h=0b/02/ae6ceac1baeda530866a85075641cec12989bd8d31af6d5ab4a3e8c92f47
+	  else
+	    echo; echo; echo;
+	    echo "'$$n' not recognized as a dependency name to download."
+	    echo; echo; echo;
+	    exit 1
+	  fi
+
+          # Download the requested tarball. Note that some packages may not
+          # follow our naming convention (where the package name is merged
+          # with its version number). In such cases, `w' will be the full
+          # address, not just the top directory address. But since we are
+          # 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/"$*"
+	  else                           tarballurl=$$h
+	  fi
+
+          # If the download fails, Wget will write the error message in the
+          # target file, so Make will think that its done! To avoid this
+          # problem, we'll rename the output.
+	  echo "Downloading $$tarballurl"
+	  if ! wget --no-use-server-timestamps -O$@ $$tarballurl; then
+	     rm -f $@
+	     echo; echo "DOWNLOAD FAILED: $$tarballurl"; echo; exit 1
+	  fi
+	fi
+
+
+
+
+
+# Install without pip
+# --------------------
+#
+# To build Python packages with direct access to a `setup.py' (if no direct
+# 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!" > $@
+
+
+
+
+
+# Python installation
+# -------------------
+#
+$(ibdir)/python3: $(tdir)/python-$(python-version).tar.gz
+	$(call gbuild, $<, Python-$(python-version))        \
+	&& v=$$(echo $(python-version) | awk 'BEGIN{FS="."} \
+	    {printf "%d.%d\n", $$1, $$2}')                  \
+	&& ln -s $(ildir)/python$$v $(ildir)/python         \
+	&& rm -rf $(ipydir) && mkdir $(ipydir)
+
+
+
+
+# Python packages
+# ---------------
+#
+$(ipydir)/astroquery: $(tdir)/astroquery-$(astroquery-version).tar.gz  \
+                      $(ipydir)/astropy                                \
+                      $(ipydir)/beautifulsoup4                         \
+                      $(ipydir)/html5lib                               \
+                      $(ipydir)/keyring                                \
+                      $(ipydir)/numpy                                  \
+                      $(ipydir)/requests
+	$(call pybuild, tar xf, $<, astroquery-$(astroquery-version))
+
+$(ipydir)/astropy: $(tdir)/astropy-$(astropy-version).tar.gz \
+                   $(ipydir)/numpy
+	$(call pybuild, tar xf, $<, astropy-$(astropy-version))
+
+$(ipydir)/beautifulsoup4: $(tdir)/beautifulsoup4-$(beautifulsoup4-version).tar.gz \
+                          $(ipydir)/soupsieve
+	$(call pybuild, tar xf, $<, beautifulsoup4-$(beautifulsoup4-version))
+
+$(ipydir)/certifi: $(tdir)/certifi-$(certifi-version).tar.gz \
+                   $(ibdir)/python3
+	$(call pybuild, tar xf, $<, certifi-$(certifi-version))
+
+$(ipydir)/chardet: $(tdir)/chardet-$(chardet-version).tar.gz \
+                   $(ibdir)/python3
+	$(call pybuild, tar xf, $<, chardet-$(chardet-version))
+
+$(ipydir)/entrypoints: $(tdir)/entrypoints-$(entrypoints-version).tar.gz \
+                       $(ibdir)/python3
+	$(call pybuild, tar xf, $<, entrypoints-$(entrypoints-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
+	$(call pybuild, tar xf, $<, idna-$(idna-version))
+
+$(ipydir)/keyring: $(tdir)/keyring-$(keyring-version).tar.gz    \
+                   $(ipydir)/entrypoints                        \
+                   $(ipydir)/setuptools_scm
+	$(call pybuild, tar xf, $<, keyring-$(keyring-version))
+
+$(ipydir)/numpy: $(tdir)/numpy-$(numpy-version).zip \
+                 $(ibdir)/python3
+	$(call pybuild, unzip, $<, numpy-$(numpy-version))
+
+$(ibdir)/pip3: $(tdir)/pip-$(pip-version).tar.gz \
+               $(ibdir)/python3
+	$(call pybuild, tar xf, $<, pip-$(pip-version))
+
+$(ipydir)/requests: $(tdir)/requests-$(requests-version).tar.gz   \
+                    $(ipydir)/certifi                             \
+                    $(ipydir)/chardet                             \
+                    $(ipydir)/idna                                \
+                    $(ipydir)/numpy                               \
+                    $(ipydir)/urllib3
+	$(call pybuild, tar xf, $<, requests-$(requests-version))
+
+$(ipydir)/setuptools: $(tdir)/setuptools-$(setuptools-version).zip \
+                      $(ibdir)/python3
+	$(call pybuild, unzip, $<, setuptools-$(setuptools-version))
+
+$(ipydir)/setuptools_scm: $(tdir)/setuptools_scm-$(setuptools_scm-version).tar.gz \
+                          $(ipydir)/setuptools
+	$(call pybuild, tar xf, $<, setuptools_scm-$(setuptools_scm-version))
+
+$(ipydir)/six: $(tdir)/six-$(six-version).tar.gz \
+               $(ibdir)/python3
+	$(call pybuild, tar xf, $<, six-$(six-version))
+
+$(ipydir)/soupsieve: $(tdir)/soupsieve-$(soupsieve-version).tar.gz \
+                     $(ibdir)/python3
+	$(call pybuild, tar xf, $<, soupsieve-$(soupsieve-version))
+
+$(ipydir)/urllib3: $(tdir)/urllib3-$(urllib3-version).tar.gz \
+                   $(ibdir)/python3
+	$(call pybuild, tar xf, $<, urllib3-$(urllib3-version))
+
+$(ipydir)/webencodings: $(tdir)/webencodings-$(webencodings-version).tar.gz \
+                        $(ibdir)/python3
+	$(call pybuild, tar xf, $<, webencodings-$(webencodings-version))
+
diff --git a/reproduce/src/make/dependencies.mk b/reproduce/src/make/dependencies.mk
index 92febb1..d227dcc 100644
--- a/reproduce/src/make/dependencies.mk
+++ b/reproduce/src/make/dependencies.mk
@@ -43,10 +43,8 @@ ildir  = $(BDIR)/dependencies/installed/lib
 ilidir = $(BDIR)/dependencies/installed/lib/built
 
 # Define the top-level programs to build (installed in `.local/bin').
-top-level-python   = astropy
-top-level-programs = astnoisechisel metastore flock unzip zip
+top-level-programs = astnoisechisel flock metastore unzip zip
 all: $(ddir)/texlive-versions.tex                       \
-     $(foreach p, $(top-level-python),   $(ilidir)/$(p)) \
      $(foreach p, $(top-level-programs), $(ibdir)/$(p))
 
 # Other basic environment settings: We are only including the host
@@ -89,8 +87,7 @@ export LDFLAGS           := $(rpath_command) -L$(ildir)
 # 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 = $(foreach t, astropy-$(astropy-version).tar.gz                  \
-                        cfitsio-$(cfitsio-version).tar.gz                  \
+tarballs = $(foreach t, cfitsio-$(cfitsio-version).tar.gz                  \
                         cmake-$(cmake-version).tar.gz                      \
                         curl-$(curl-version).tar.gz                        \
                         flock-$(flock-version).tar.xz                      \
@@ -104,8 +101,6 @@ tarballs = $(foreach t, astropy-$(astropy-version).tar.gz                  \
                         libtool-$(libtool-version).tar.xz                  \
                         libgit2-$(libgit2-version).tar.gz                  \
                         metastore-$(metastore-version).tar.gz              \
-                        numpy-$(numpy-version).zip                         \
-                        python-$(python-version).tar.gz                    \
                         unzip-$(unzip-version).tar.gz                      \
                         tiff-$(libtiff-version).tar.gz                     \
                         wcslib-$(wcslib-version).tar.bz2                   \
@@ -122,8 +117,7 @@ $(tarballs): $(tdir)/%:
 
           # Set the top download link of the requested tarball.
 	  mergenames=1
-	  if   [ $$n = astropy     ]; then w=https://files.pythonhosted.org/packages/eb/f7/1251bf6881861f24239efe0c24cbcfc4191ccdbb69ac3e9bb740d0c23352
-	  elif [ $$n = cfitsio     ]; then
+	  if [ $$n = cfitsio     ]; then
 	    mergenames=0
 	    v=$$(echo $(cfitsio-version) | sed -e's/\.//'             \
 	              | awk '{l=length($$1);                          \
@@ -147,10 +141,6 @@ $(tarballs): $(tdir)/%:
 	    mergenames=0
 	    w=https://github.com/libgit2/libgit2/archive/v$(libgit2-version).tar.gz
 	  elif [ $$n = metastore   ]; then w=http://akhlaghi.org/src
-	  elif [ $$n = numpy       ]; then w=https://files.pythonhosted.org/packages/2b/26/07472b0de91851b6656cbc86e2f0d5d3a3128e7580f23295ef58b6862d6c
-	  elif [ $$n = python      ]; then
-	    mergenames=0
-	    w=https://www.python.org/ftp/python/$(python-version)/Python-$(python-version).tgz
 	  elif [ $$n = tiff        ]; then w=https://download.osgeo.org/libtiff
 	  elif [ $$n = unzip       ]; then w=ftp://ftp.info-zip.org/pub/infozip/src
 	    mergenames=0; v=$$(echo $(unzip-version) | sed -e's/\.//')
@@ -456,12 +446,6 @@ endif
 	               $$staticopts, -j$(numthreads),                \
 	               make check -j$(numthreads))
 
-$(ibdir)/python3: $(tdir)/python-$(python-version).tar.gz
-	$(call gbuild, $<, Python-$(python-version))        \
-	&& v=$$(echo $(python-version) | awk 'BEGIN{FS="."} \
-            {printf "%d.%d\n", $$1, $$2}')              \
-    && ln -s $(ildir)/python$$v $(ildir)/python
-
 $(ibdir)/unzip: $(tdir)/unzip-$(unzip-version).tar.gz
 	v=$$(echo $(unzip-version) | sed -e's/\.//')
 	$(call gbuild, $<, unzip$$v, static,,          \
@@ -482,20 +466,6 @@ $(ibdir)/zip: $(tdir)/zip-$(zip-version).tar.gz
 
 
 
-# Python packages
-# ---------------
-$(ilidir)/numpy: $(tdir)/numpy-$(numpy-version).zip \
-                 $(ibdir)/python3
-	pip3 install $< --verbose && echo "numpy is built" > $@
-
-$(ilidir)/astropy: $(tdir)/astropy-$(astropy-version).tar.gz \
-                   $(ilidir)/numpy
-	pip3 install $< --verbose && echo "astropy is built" > $@
-
-
-
-
-
 # Since we want to avoid complicating the PATH, we are putting a symbolic
 # link of all the TeX Live executables in $(ibdir). But symbolic links are
 # hard to track for Make (as a target). Also, TeX in general is optional