Imported recent work in master, minor conflict fixed in paper.mk

Only two conflicts came up in the newly added comments of 'paper.mk' in the
Maneage branch. It happened because in this project we don't use
'pdflatex', but 'latex' alone.

1 files changed, 49 insertions, 44 deletions

diff --git a/reproduce/software/config/versions.conf b/reproduce/software/config/versions.conf
index 1a4172a..b395e0f 100644
--- a/reproduce/software/config/versions.conf
+++ b/reproduce/software/config/versions.conf
@@ -14,6 +14,8 @@
 
 # Basic/low-level programs and libraires (installed in any case)
 # --------------------------------------------------------------
+#
+# CLASS:BASIC (important identifier, don't modify this line)
 bash-version = 5.0.11
 binutils-version = 2.32
 coreutils-version = 8.31
@@ -22,6 +24,7 @@ dash-version = 0.5.10.2
 diffutils-version = 3.7
 file-version = 5.36
 findutils-version = 4.7.0
+flock-version = 0.2.3
 gawk-version = 5.0.1
 gcc-version = 9.2.0
 gettext-version = 0.20.2
@@ -35,8 +38,8 @@ libiconv-version = 1.16
 libtool-version = 2.4.6
 libunistring-version = 0.9.10
 libxml2-version = 2.9.9
-lzip-version = 1.20
-m4-version = 1.4.18
+lzip-version = 1.22-rc2
+m4-version = 1.4.18-patched
 make-version = 4.3
 metastore-version = 1.1.2-23-fa9170b
 mpc-version = 1.1.0
@@ -56,6 +59,14 @@ xz-version = 5.2.4
 zip-version = 3.0
 zlib-version = 1.2.11
 
+# Version-dependent build
+# -----------------------
+#
+# When updating the version of these programs/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
+
 
 
 
@@ -67,6 +78,8 @@ zlib-version = 1.2.11
 # `reproduce/software/config/TARGETS.conf' will be built as
 # part of a project. To specify a software there, just remove the
 # `-version' suffix from the list below.
+#
+# CLASS:HIGHLEVEL (important identifier, don't modify this line.)
 apachelog4cxx-version = 0.10.0-603-014954db
 apr-version = 1.7.0
 apr-util-version = 1.6.1
@@ -75,7 +88,7 @@ atlas-version = 3.10.3
 autoconf-version = 2.69.200-babc
 automake-version = 1.16.1
 bison-version = 3.4.2
-boost-version = 1.71.0
+boost-version = 1.73.0
 cairo-version = 1.16.0
 cdsclient-version = 3.84
 cfitsio-version = 3.47
@@ -83,8 +96,7 @@ cmake-version = 3.17.0
 eigen-version = 3.3.7
 expat-version = 2.2.9
 fftw-version = 3.3.8
-flex-version = 2.6.4
-flock-version = 0.2.3
+flex-version = 2.6.4-91-ga631f5d
 freetype-version = 2.9
 gdb-version = 8.3
 ghostscript-version = 9.50
@@ -98,14 +110,16 @@ imfit-version = 1.6.1
 libffi-version = 3.2.1
 libjpeg-version = v9b
 libnsl-version = 1.2.0-4a062cf
+libpaper-version = 1.1.28
 libpng-version = 1.6.37
 libtiff-version = 4.0.10
-libtirpc-version = 1.1.4
+libtirpc-version = 1.2.6
 missfits-version = 2.8.0
-openblas-version = 0.3.5
+openblas-version = 0.3.10
 openmpi-version = 4.0.1
 openssh-version = 8.0p1
 patch-version = 2.7.6
+pcre-version = 8.44
 pixman-version = 0.38.0
 python-version = 3.7.4
 R-version = 3.6.2
@@ -119,6 +133,29 @@ tides-version = 2.0
 xlsxio-version = 0.2.21
 yaml-version = 0.2.2
 
+# Version-dependent build
+# -----------------------
+lapack-version = 3.8.0
+libgit2-version = 0.28.2
+wcslib-version = 6.4
+
+# Netpbm's questions in the configure steps maybe change with different or
+# new versions.
+netpbm-version = 10.86.99
+
+# Minizip is installed with the same `zlib' tarball, and they have the same
+# version.
+minizip-version = $(zlib-version)
+
+# From version 1.2 OpenSSL may not need a manual addition, as described in
+# its comments and `https://savannah.nongnu.org/bugs/?58263'. If it doesn't
+# cause problems, put it back in the list of "Basic/low-level" tools.
+openssl-version = 1.1.1a
+
+# Version 3.15.0 needs two patches, please check if they are necessary on
+# any future release.
+valgrind-version = 3.15.0
+
 
 
 
@@ -131,6 +168,8 @@ yaml-version = 0.2.2
 # IMPORTANT: If you intend to change the version of any of the Python
 # modules/libraries below, please fix the hash strings of the respective
 # URL in `reproduce/software/make/python.mk'.
+#
+# CLASS:PYTHON (important identifier, don't modify this line.)
 asn1crypto-version = 0.24.0
 asteval-version = 0.9.16
 astropy-version = 4.0
@@ -151,7 +190,6 @@ flake8-version = 3.7.8
 future-version = 0.18.1
 galsim-version = 2.2.1
 h5py-version = 2.9.0
-healpy-version = installed-with-healpix
 html5lib-version = 1.0.1
 idna-version = 2.8
 jeepney-version = 0.4
@@ -184,42 +222,9 @@ soupsieve-version = 1.8
 sympy-version = 1.4
 uncertainties-version = 3.1.2
 urllib3-version = 1.24.1
-virtualenv-version = 16.4.0
 webencodings-version = 0.5.1
 
-
-
-
-
-# Special programs and libraries
-# ------------------------------
-#
-# 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.
+# Special Python modules:
 #
-# Special notes:
-#   - `netpbm' questions in the configure steps maybe change with different
-#   or new versions.
-
-# Basic/low-level
-bzip2-version = 1.0.6
-
-# Optional/high-level
-lapack-version = 3.8.0
-libgit2-version = 0.28.2
-netpbm-version = 10.86.99
-wcslib-version = 6.4
-
-# Minizip is installed with the same `zlib' tarball, and they have the same
-# version.
-minizip-version = $(zlib-version)
-
-# From version 1.2 OpenSSL may not need a manual addition, as described in
-# its comments and `https://savannah.nongnu.org/bugs/?58263'. If it doesn't
-# cause problems, put it back in the list of "Basic/low-level" tools.
-openssl-version = 1.1.1a
-
-# Version 3.15.0 needs two patches, please check if they are necessary on
-# any future release.
-valgrind-version = 3.15.0
+# Healpy: When any Python module is requested, healpix will also build its
+#         Python module Healpy.