diff options
Diffstat (limited to 'reproduce')
20 files changed, 51 insertions, 50 deletions
diff --git a/reproduce/analysis/config/INPUTS.mk b/reproduce/analysis/config/INPUTS.conf index 6ddaec7..6ddaec7 100644 --- a/reproduce/analysis/config/INPUTS.mk +++ b/reproduce/analysis/config/INPUTS.conf diff --git a/reproduce/analysis/config/delete-me-num.mk b/reproduce/analysis/config/delete-me-num.conf index 17f608c..17f608c 100644 --- a/reproduce/analysis/config/delete-me-num.mk +++ b/reproduce/analysis/config/delete-me-num.conf diff --git a/reproduce/analysis/config/pdf-build.mk b/reproduce/analysis/config/pdf-build.conf index e2d59cc..e2d59cc 100644 --- a/reproduce/analysis/config/pdf-build.mk +++ b/reproduce/analysis/config/pdf-build.conf diff --git a/reproduce/analysis/config/verify-outputs.mk b/reproduce/analysis/config/verify-outputs.conf index 5d8eff1..4f99661 100644 --- a/reproduce/analysis/config/verify-outputs.mk +++ b/reproduce/analysis/config/verify-outputs.conf @@ -1,3 +1,2 @@ # To disable verification of output datasets set this variable to yes - verify-outputs = yes diff --git a/reproduce/analysis/make/delete-me.mk b/reproduce/analysis/make/delete-me.mk index 3ba4909..8b97673 100644 --- a/reproduce/analysis/make/delete-me.mk +++ b/reproduce/analysis/make/delete-me.mk @@ -26,7 +26,7 @@ delete-numdir = $(texdir)/delete-me-num delete-num = $(delete-numdir)/data.txt $(delete-numdir): | $(texdir); mkdir $@ -$(delete-num): $(pconfdir)/delete-me-num.mk | $(delete-numdir) +$(delete-num): $(pconfdir)/delete-me-num.conf | $(delete-numdir) # When the plotted values are re-made, it is necessary to also # delete the TiKZ externalized files so the plot is also re-made. diff --git a/reproduce/analysis/make/download.mk b/reproduce/analysis/make/download.mk index 7c290f4..07e9f27 100644 --- a/reproduce/analysis/make/download.mk +++ b/reproduce/analysis/make/download.mk @@ -24,9 +24,10 @@ # Download input data # -------------------- # -# The input dataset properties are defined in `$(pconfdir)/INPUTS.mk'. For -# this template we only have one dataset to enable easy processing, so all -# the extra checks in this rule may seem redundant. +# The input dataset properties are defined in +# `$(pconfdir)/INPUTS.conf'. For this template we only have one dataset to +# enable easy processing, so all the extra checks in this rule may seem +# redundant. # # In a real project, you will need more than one dataset. In that case, # just add them to the target list and add an `elif' statement to define it @@ -93,5 +94,5 @@ $(inputdatasets): $(indir)/%.fits: | $(indir) $(lockdir) # # It is very important to mention the address where the data were # downloaded in the final report. -$(mtexdir)/download.tex: $(pconfdir)/INPUTS.mk | $(mtexdir) +$(mtexdir)/download.tex: $(pconfdir)/INPUTS.conf | $(mtexdir) echo "\\newcommand{\\wfpctwourl}{$(WFPC2URL)}" > $@ diff --git a/reproduce/analysis/make/initialize.mk b/reproduce/analysis/make/initialize.mk index cdf2129..fa39699 100644 --- a/reproduce/analysis/make/initialize.mk +++ b/reproduce/analysis/make/initialize.mk @@ -241,7 +241,7 @@ distclean: clean # `rm', not our own. $$sys_rm -rf $(BDIR) $$sys_rm -f Makefile .gnuastro .local .build - $$sys_rm -f $(pconfdir)/LOCAL.mk $(gconfdir)/gnuastro-local.conf + $$sys_rm -f $(pconfdir)/LOCAL.conf $(gconfdir)/gnuastro-local.conf @@ -298,10 +298,11 @@ $(packagecontents): paper.pdf | $(texdir) # directories (when building in a group structure, there will be # `build-user1', `build-user2' and etc), are just temporary LaTeX # build files and don't have any relevant/hand-written files in - # them. 2) The `LOCAL.mk' and `gnuastro-local.conf' files just have - # this machine's local settings and are irrelevant for anyone else. + # them. 2) The `LOCAL.conf' and `gnuastro-local.conf' files just + # have this machine's local settings and are irrelevant for anyone + # else. rm -rf $$dir/tex/build/build* - rm $$dir/reproduce/software/config/installation/LOCAL.mk + rm $$dir/reproduce/software/config/installation/LOCAL.conf rm $$dir/reproduce/software/config/gnuastro/gnuastro-local.conf # When submitting to places like arXiv, they will just run LaTeX diff --git a/reproduce/analysis/make/paper.mk b/reproduce/analysis/make/paper.mk index a4eeb2e..8a14573 100644 --- a/reproduce/analysis/make/paper.mk +++ b/reproduce/analysis/make/paper.mk @@ -38,7 +38,7 @@ # # Note that if you don't want the final PDF and just want the processing # and file outputs, you can remove the value of `pdf-build-final' in -# `reproduce/analysis/config/pdf-build.mk'. +# `reproduce/analysis/config/pdf-build.conf'. $(mtexdir)/project.tex: $(mtexdir)/verify.tex # If no PDF is requested, or if LaTeX isn't available, don't @@ -62,7 +62,7 @@ $(mtexdir)/project.tex: $(mtexdir)/verify.tex echo "can check by running './.local/bin/latex --version'), _AND_" echo "make sure that the 'pdf-build-final' variable has a value." echo "'pdf-build-final' is defined in: " - echo "'reproduce/analysis/config/pdf-build.mk'." + echo "'reproduce/analysis/config/pdf-build.conf'." echo echo "If you don't have LaTeX within the project, please re-run" echo "'./project configure -e' when you have internet access." diff --git a/reproduce/analysis/make/top-make.mk b/reproduce/analysis/make/top-make.mk index 0292d3c..6c940b8 100644 --- a/reproduce/analysis/make/top-make.mk +++ b/reproduce/analysis/make/top-make.mk @@ -21,7 +21,7 @@ # Load the local configuration (created after running # `./project configure'). -include reproduce/software/config/installation/LOCAL.mk +include reproduce/software/config/installation/LOCAL.conf @@ -50,7 +50,7 @@ include reproduce/software/config/installation/LOCAL.mk # # Controlling this requires two variables that are available at this stage: # -# - `GROUP-NAME': from `LOCAL.mk' (which was built by `./project configure'). +# - `GROUP-NAME': from `LOCAL.conf' (which was built by `./project configure'). # - `reproducible_paper_group_name': value to the `--group' option. # # The analysis is only done when both have the same group name. Note that @@ -63,7 +63,7 @@ include reproduce/software/config/installation/LOCAL.mk # # If you are just interested in the processing and don't want to build the # PDF, you can skip the creatation of the final PDF by removing the value -# of `pdf-build-final' in `reproduce/analysis/config/pdf-build.mk'. +# of `pdf-build-final' in `reproduce/analysis/config/pdf-build.conf'. ifeq (x$(reproducible_paper_group_name),x$(GROUP-NAME)) all: paper.pdf else @@ -132,5 +132,5 @@ makesrc = initialize \ # But before that, we need to identify the phase for the Makefiles that are # run both in `./project prepare' and `./project make'. project-phase = make -include reproduce/analysis/config/*.mk +include reproduce/analysis/config/*.conf include $(foreach s,$(makesrc), reproduce/analysis/make/$(s).mk) diff --git a/reproduce/analysis/make/top-prepare.mk b/reproduce/analysis/make/top-prepare.mk index 5ce120d..cefbc6b 100644 --- a/reproduce/analysis/make/top-prepare.mk +++ b/reproduce/analysis/make/top-prepare.mk @@ -25,7 +25,7 @@ # Load the local configuration (created after running # `./project configure'). -include reproduce/software/config/installation/LOCAL.mk +include reproduce/software/config/installation/LOCAL.conf @@ -87,5 +87,5 @@ makesrc = initialize \ # # See `top-make.mk' for complete explanation. project-phase = prepare -include reproduce/analysis/config/*.mk +include reproduce/analysis/config/*.conf include $(foreach s,$(makesrc), reproduce/analysis/make/$(s).mk) diff --git a/reproduce/analysis/make/verify.mk b/reproduce/analysis/make/verify.mk index a4afd45..d11dcbf 100644 --- a/reproduce/analysis/make/verify.mk +++ b/reproduce/analysis/make/verify.mk @@ -33,7 +33,7 @@ verify-print-tips = \ echo "If you are still developing your project, you can disable"; \ echo "verification by removing the value of the variable in the"; \ echo "following file (from the top project source directory):"; \ - echo " reproduce/analysis/config/verify-outputs.mk"; \ + echo " reproduce/analysis/config/verify-outputs.conf"; \ echo; \ echo "If this is the final version of the file, you can just copy"; \ echo "and paste the calculated checksum (above) for the file in"; \ diff --git a/reproduce/software/bash/configure.sh b/reproduce/software/bash/configure.sh index 8cdd744..c681298 100755 --- a/reproduce/software/bash/configure.sh +++ b/reproduce/software/bash/configure.sh @@ -38,11 +38,11 @@ cdir=reproduce/software/config sbdir=$cdir/installation -pconf=$sbdir/LOCAL.mk -ptconf=$sbdir/LOCAL_tmp.mk -poconf=$sbdir/LOCAL_old.mk -depverfile=$cdir/installation/versions.mk -depshafile=$cdir/installation/checksums.mk +pconf=$sbdir/LOCAL.conf +ptconf=$sbdir/LOCAL_tmp.conf +poconf=$sbdir/LOCAL_old.conf +depverfile=$cdir/installation/versions.conf +depshafile=$cdir/installation/checksums.conf # --------- Delete for no Gnuastro --------- glconf=$cdir/gnuastro/gnuastro-local.conf # ------------------------------------------ @@ -117,7 +117,7 @@ EOF # What to do with possibly existing configuration file # ---------------------------------------------------- # -# `LOCAL.mk' is the top-most local configuration for the project. If it +# `LOCAL.conf' is the top-most local configuration for the project. If it # already exists when this script is run, we'll make a copy of it as backup # (for example the user might have ran `./project configure' by mistake). printnotice=yes @@ -299,10 +299,10 @@ if [ x"$input_dir" = x ]; then else indir=$input_dir fi -wfpc2name=$(awk '!/^#/ && $1=="WFPC2IMAGE" {print $3}' $adir/INPUTS.mk) -wfpc2md5=$(awk '!/^#/ && $1=="WFPC2MD5" {print $3}' $adir/INPUTS.mk) -wfpc2size=$(awk '!/^#/ && $1=="WFPC2SIZE" {print $3}' $adir/INPUTS.mk) -wfpc2url=$(awk '!/^#/ && $1=="WFPC2URL" {print $3}' $adir/INPUTS.mk) +wfpc2name=$(awk '!/^#/ && $1=="WFPC2IMAGE" {print $3}' $adir/INPUTS.conf) +wfpc2md5=$(awk '!/^#/ && $1=="WFPC2MD5" {print $3}' $adir/INPUTS.conf) +wfpc2size=$(awk '!/^#/ && $1=="WFPC2SIZE" {print $3}' $adir/INPUTS.conf) +wfpc2url=$(awk '!/^#/ && $1=="WFPC2URL" {print $3}' $adir/INPUTS.conf) if [ $rewritepconfig = yes ] && [ x"$input_dir" = x ]; then cat <<EOF diff --git a/reproduce/software/config/installation/LOCAL.mk.in b/reproduce/software/config/installation/LOCAL.conf.in index 1045f72..1045f72 100644 --- a/reproduce/software/config/installation/LOCAL.mk.in +++ b/reproduce/software/config/installation/LOCAL.conf.in diff --git a/reproduce/software/config/installation/TARGETS.mk b/reproduce/software/config/installation/TARGETS.conf index 164d606..d2d5e2c 100644 --- a/reproduce/software/config/installation/TARGETS.mk +++ b/reproduce/software/config/installation/TARGETS.conf @@ -18,17 +18,17 @@ # All software that are currently available for installation can be seen in # the following file. # -# reproduce/software/config/installation/versions.mk +# reproduce/software/config/installation/versions.conf # # Please add any software that you need for your project in the respective -# part below (using its name in `versions.mk', but without the `-version' +# part below (using its name in `versions.conf', but without the `-version' # part). Just note that if a program/library is a dependency of another, # you don't need to include it here (it will be installed before the # higher-level software anyway). # # Note that many low-level software will be installed before those that are # installed in this step. They are clearly distinguished from the -# higher-level (optional) software in `versions.mk'. These low-level +# higher-level (optional) software in `versions.conf'. These low-level # software MUST NOT be added here. diff --git a/reproduce/software/config/installation/checksums.mk b/reproduce/software/config/installation/checksums.conf index 28980e1..406ec1b 100644 --- a/reproduce/software/config/installation/checksums.mk +++ b/reproduce/software/config/installation/checksums.conf @@ -71,9 +71,9 @@ zlib-checksum = 73fd3fff4adeccd4894084c15ddac89890cd10ef105dd5e1835e1e9bbb6a49ff # ------------------------------------------ # # These are programs and libraries that are optional, The ones in -# `reproduce/software/config/installation/TARGETS.mk' will be built as part -# of a project. To specify a software there, just remove the `-checksum' -# suffix from the list below. +# `reproduce/software/config/installation/TARGETS.conf' will be built as +# part of a project. To specify a software there, just remove the +# `-checksum' suffix from the list below. apachelog4cxx-checksum = aa59ce549c2c5cbeec031361dfce09cdfc3e62ee3bc9ecbc809507b7ec878c14409b98536b7d13c27690809c8e9d5ebafc3589c9fb5e4aecd5cc064943ae7d6b apr-checksum = daa140c83c7e2c45c3980d9dc81d34fa662bebd050653562c39572d0ddf2eaedb71767c518a59d77f59db9b32e00221ef48b9f72ec3666c4521dd511969f3706 apr-util-checksum = 84da76e9b64da2de0996d4d6f3ab3f23db3724eb6352d218e0e8196bcc0b0a5d4fe791f41b4cc350ce3d04cce3bb3cf8bfb513d777d0cd030928368e6b55a536 diff --git a/reproduce/software/config/installation/texlive.mk b/reproduce/software/config/installation/texlive-packages.conf index c53e170..c53e170 100644 --- a/reproduce/software/config/installation/texlive.mk +++ b/reproduce/software/config/installation/texlive-packages.conf diff --git a/reproduce/software/config/installation/versions.mk b/reproduce/software/config/installation/versions.conf index 348a61c..565f1a4 100644 --- a/reproduce/software/config/installation/versions.mk +++ b/reproduce/software/config/installation/versions.conf @@ -69,9 +69,9 @@ zlib-version = 1.2.11 # ------------------------------------------ # # These are programs and libraries that are optional, The ones in -# `reproduce/software/config/installation/TARGETS.mk' will be built as part -# of a project. To specify a software there, just remove the `-version' -# suffix from the list below. +# `reproduce/software/config/installation/TARGETS.conf' will be built as +# part of a project. To specify a software there, just remove the +# `-version' suffix from the list below. apachelog4cxx-version = 0.10.0-603-014954db apr-version = 1.7.0 apr-util-version = 1.6.1 diff --git a/reproduce/software/make/basic.mk b/reproduce/software/make/basic.mk index 343b3b0..93dcdc2 100644 --- a/reproduce/software/make/basic.mk +++ b/reproduce/software/make/basic.mk @@ -34,9 +34,9 @@ # Top level environment include reproduce/software/make/build-rules.mk -include reproduce/software/config/installation/LOCAL.mk -include reproduce/software/config/installation/versions.mk -include reproduce/software/config/installation/checksums.mk +include reproduce/software/config/installation/LOCAL.conf +include reproduce/software/config/installation/versions.conf +include reproduce/software/config/installation/checksums.conf lockdir = $(BDIR)/locks tdir = $(BDIR)/software/tarballs diff --git a/reproduce/software/make/build-rules.mk b/reproduce/software/make/build-rules.mk index cbde70b..f3ca7d2 100644 --- a/reproduce/software/make/build-rules.mk +++ b/reproduce/software/make/build-rules.mk @@ -1,7 +1,7 @@ # Generic configurable recipes to build packages with GNU Build system or # CMake. This is Makefile is not intended to be run directly, it will be -# imported into `dependencies-basic.mk' and `dependencies.mk'. They should -# be activated with Make's `Call' function. +# imported into `basic.mk' and `high-level.mk'. They should be activated +# with Make's `Call' function. # # Copyright (C) 2018-2020 Mohammad Akhlaghi <mohammad@akhlaghi.org> # diff --git a/reproduce/software/make/high-level.mk b/reproduce/software/make/high-level.mk index 0afeaba..bc77dab 100644 --- a/reproduce/software/make/high-level.mk +++ b/reproduce/software/make/high-level.mk @@ -28,11 +28,11 @@ # Top level environment include reproduce/software/make/build-rules.mk -include reproduce/software/config/installation/LOCAL.mk -include reproduce/software/config/installation/TARGETS.mk -include reproduce/software/config/installation/texlive.mk -include reproduce/software/config/installation/versions.mk -include reproduce/software/config/installation/checksums.mk +include reproduce/software/config/installation/LOCAL.conf +include reproduce/software/config/installation/TARGETS.conf +include reproduce/software/config/installation/versions.conf +include reproduce/software/config/installation/checksums.conf +include reproduce/software/config/installation/texlive-packages.conf lockdir = $(BDIR)/locks tdir = $(BDIR)/software/tarballs @@ -588,7 +588,7 @@ $(ibidir)/hdf5: $(ibidir)/openmpi \ # HEALPix includes the source of its C, C++, Python (and several other # languages) libraries within one tarball. We will include the Python # installation only when any other Python module is requested (in -# `TARGETS.mk'). +# `TARGETS.conf'). # # Note that the default `./configure' script is an interactive script which # is hard to automate. So we need to go into the `autotools' directory of @@ -1191,7 +1191,7 @@ $(itidir)/texlive-ready-tlmgr: reproduce/software/config/installation/texlive.co #else #forbiber = $(ibidir)/libnsl #endif -$(itidir)/texlive: reproduce/software/config/installation/texlive.mk \ +$(itidir)/texlive: reproduce/software/config/installation/texlive-packages.conf \ $(itidir)/texlive-ready-tlmgr \ $(forbiber) |