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76 files changed, 1335 insertions, 525 deletions
diff --git a/README-hacking.md b/README-hacking.md index bd1d988..8897333 100644 --- a/README-hacking.md +++ b/README-hacking.md @@ -1,8 +1,8 @@ Maneage: managing data lineage ============================== -Copyright (C) 2018-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>\ -Copyright (C) 2020-2022 Raul Infante-Sainz <infantesainz@gmail.com>\ +Copyright (C) 2018-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org>\ +Copyright (C) 2020-2023 Raul Infante-Sainz <infantesainz@gmail.com>\ See the end of the file for license conditions. Maneage is a **fully working template** for doing reproducible research (or @@ -762,8 +762,8 @@ First custom commit and generally, all the files you modified in the previous step. ``` - Copyright (C) 2018-2022 Existing Name <existing@email.address> - Copyright (C) 2022 YOUR NAME <YOUR@EMAIL.ADDRESS> + Copyright (C) 2018-2023 Existing Name <existing@email.address> + Copyright (C) 2023 YOUR NAME <YOUR@EMAIL.ADDRESS> ``` 9. **Configure Git for fist time**: If this is the first time you are @@ -1,7 +1,7 @@ Reproducible source for XXXXXXXXXXXXXXXXX ------------------------------------------------------------------------- -Copyright (C) 2018-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>\ +Copyright (C) 2018-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org>\ See the end of the file for license conditions. This is the reproducible project source for the paper titled "**XXX XXXXX @@ -188,6 +188,56 @@ analysis and finally create the final paper). + + + + + +### Building on older systems (+10 year old compilers) + +Maneage builds almost all its software itself. But to do that, it needs a C +and C++ compiler on the host. The C++ standard in particular is updated +regularly. Therefore, gradually the basic software packages (that are used +to build the internal Maneage C compiler and other necessary tools) will +start using the newer language features in their newer versions. As a +result, if a host doesn't update its compiler for more than a decade, some +of the basic software may not get built. + +Note that this is only a problem for the "basic" software of Maneage (that +are used to build Maneage's own C compiler), not the high-level (or +science) software. On GNU/Linux systems, the high-level software get built +with Maneage's own C compiler. Therefore once Maneage's C compiler is +built, you don't need to worry about the versions of the high-level +software. + +One solution to such cases is to downgrade the versions of the basic +software that can't be built. For example, when building Maneage in August +2022 on a old Debian GNU/Linux system from 2010 (with GCC 4.4.5 and GNU C +Library 2.11.3 and Linux kernel 2.6.32-5 on an amd64 architecture), the +following low-level packages needed to be downgraded to slightly earlier +versions. + +| Program name | 2022-08 version | Version for old system | +|:------------------------------|:---------------:|:----------------------:| +| PatchELF | 0.13 | 0.9 | +| GNU Binutils | 2.39 | 2.37 | +| GNU Compiler Collection (GCC) | 12.1.0 | 10.2.0 | + +As you can see above, fortunately most basic software in Maneage respect ++10 year old compilers and are build-able there. So your higher-level +science software should be buildable with out changing their versions. It +is _highly improbable_ that these downgrades will affect your final science +result. + + + + + + + + + + ### Building on ARM As of 2021-10-13, very little testing of Maneage has been done on arm64 @@ -237,6 +287,11 @@ light and should be very fast. + + + + + ### Building in Docker containers Docker containers are a common way to build projects in an independent @@ -534,7 +589,12 @@ steps. following contents. Just replace `UID` with your user ID (found in step 1 above). Note that we are manually setting the `maneager` (user) password to `123` and the root password to '456' (both should be - repeated because they must be confirmed by `passwd`). + repeated because they must be confirmed by `passwd`). To install other + operating systems, just change the contents on the `FROM` line. For + example, for CentOS 7 you can use `FROM centos:centos7`, for the + latest CentOS, you can use `FROM centos:latest` (you may need to add + this line `RUN yum install -y passwd` before the `RUN useradd ...` + line.). ``` FROM debian:stable-slim @@ -658,7 +718,11 @@ steps. versions of both and will use them. But for the very first packages, they are necessary. In the process, by setting the `PS1` environment variable, we'll define a color-coding for the interactive shell prompt - (red for root and purple for the user). + (red for root and purple for the user). If you build another operating + system, replace the `apt` commands accordingly (for example on CentOS, + you don't need the `apt update` line and you should use `yum install + -y gcc gcc-c++ wget glibc-static` to install the three basic + dependencies). ```shell su @@ -1,4 +1,4 @@ -%% Copyright (C) 2018-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org> +%% Copyright (C) 2018-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org> %% See the end of the file for license conditions. \documentclass[10pt, twocolumn]{article} @@ -3,8 +3,8 @@ # High-level script to manage the project. # Run './project --help' for a description of how to use it. # -# Copyright (C) 2019-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org> -# Copyright (C) 2021-2022 Raul Infante-Sainz <infantesainz@gmail.com> +# Copyright (C) 2019-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2021-2023 Raul Infante-Sainz <infantesainz@gmail.com> # # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by @@ -516,20 +516,25 @@ case $operation in # tools like some text editors. bdir=`.local/bin/realpath .build` instdir="$bdir"/software/installed + bindir="$bdir"/software/installed/bin + rcfile=$(pwd)/reproduce/software/shell/bashrc.sh .local/bin/env -i \ HOME="$bdir" \ TERM="$TERM" \ + PATH="$bindir" \ CCACHE_DISABLE=1 \ - PATH="$instdir"/bin \ + PROJECT_STATUS=shell \ + SHELL="$bindir"/bash \ + COLORTERM="$COLORTERM" \ + PROJECT_RCFILE="$rcfile" \ LDFLAGS=-L"$instdir"/lib \ - SHELL="$instdir"/bin/bash \ CPPFLAGS=-I"$instdir"/include \ LD_LIBRARY_PATH="$instdir"/lib \ OMPI_MCA_plm_rsh_agent=/bin/false \ PYTHONPATH="$instdir"/lib/python/site-packages \ PYTHONPATH3="$instdir"/lib/python/site-packages \ PS1="[\[\033[01;35m\]maneage@\h \W\[\033[32m\]\[\033[00m\]]$ " \ - "$instdir"/bin/bash --noprofile --norc + "$bindir"/bash --noprofile --rcfile "$rcfile" ;; diff --git a/reproduce/analysis/bash/download-multi-try b/reproduce/analysis/bash/download-multi-try index 994a8fa..d7e9be2 100755 --- a/reproduce/analysis/bash/download-multi-try +++ b/reproduce/analysis/bash/download-multi-try @@ -26,7 +26,7 @@ # reason, you don't want to use a lock file, set the 'lockfile' name to # 'nolock'. # -# Copyright (C) 2019-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2019-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by @@ -123,7 +123,7 @@ while [ ! -f "$outname" ]; do else # Try downloading from the requested URL. flock "$lockfile" sh -c \ - "if ! $downloader $outname $inurl; then rm -f $outname; fi" + "if ! $downloader $outname \"$inurl\"; then rm -f $outname; fi" fi # If the download failed, try the backup server(s). diff --git a/reproduce/analysis/config/INPUTS.conf b/reproduce/analysis/config/INPUTS.conf index 75e24de..1090e44 100644 --- a/reproduce/analysis/config/INPUTS.conf +++ b/reproduce/analysis/config/INPUTS.conf @@ -1,9 +1,10 @@ # This project's input file information (metadata). # # For each input (external) data file that is used within the project, -# three variables are suggested here (two of them are mandatory). These -# variables will be used by 'reproduce/analysis/make/download.mk' to import -# the dataset into the project (within the build directory): +# three variables are suggested here (only the verification variable is +# strictly mandatory). These variables will be used by the download rule of +# 'reproduce/analysis/make/initialize.mk' to import the dataset into the +# project (within the build directory): # # - If the file already exists locally in '$(INDIR)' (the optional input # directory that may have been specified at configuration time with @@ -12,27 +13,53 @@ # files are large. # # - If the file doesn't exist in '$(INDIR)', or no input directory was -# specified at configuration time, then the file is downloaded from a -# specific URL. +# specified at configuration time, then the file is downloaded from the +# specified URL for that dataset. # # In both cases, before placing the file (or its link) in the build -# directory, 'reproduce/analysis/make/download.mk' will check the SHA256 -# checksum of the dataset and if it differs from the pre-defined value (set -# for that file, here), it will abort (since this is not the intended -# dataset). -# -# Therefore, the two variables specifying the URL and SHA256 checksum of -# the file are MANDATORY. The third variable (INPUT-%-size) showing the -# human-readable size of the file (from 'ls -lh') is optional (but -# recommended: because it gives future scientists to get a feeling of the -# volume of data they need to input: will become important if the -# size/number of files is large). +# directory, the download rule of 'reproduce/analysis/make/initialize.mk' +# will check the verification of the dataset and if it differs from the +# pre-defined value (set for that file, here), it will abort (since this is +# not the intended dataset). # +# Verification (two modes) +# ------------------------ +# - SHA256 checksum. This will check the full contents of the file, and +# is generic to any data format. However, if the server inserts custom +# headers like the query date or query code and etc, this form of +# validation is not useful: because every download will have different +# headers. In such cases, you should use the other verification methods +# below. In other words, this method is only good for files that are +# "static" on the server (and left there unchanged). If the file is +# generated at request time, the server usually inserts custom run-time +# dependent headers; making it impossible to verify with an SHA +# checksum of the whole file. +# - The FITS Standard's 'DATASUM' (which will only check the data, not +# the headers). According to the FITS standard, this sum ignores all +# headers, and is only calculated on a HDU's data. By default, this +# will require Gnuastro (which can easily calculate and return the +# value on the command-line), and it assumes HDU number 1 (counting +# from 0). You can modify the defaults by modifying the rule in +# 'reproduce/analysis/make/initialize.mk'. +# +# Automatic writing of verification +# --------------------------------- +# In case you would like Maneage to find the checksum upon downloading, put +# the string '--auto-replace--' instead of a checksum. This can be helpful +# for large datasets; where downloading only for adding the checksum is not +# easy/possible and can be buggy. In this scenario, upon downloading the +# file its checksum will be calculated and will be replaced with the +# '--auto-replace--' in this file. But since this file is under version +# control, be sure to commit all the updated checksums after your downloads +# are finished! +# +# Variable description +# -------------------- # The naming convension is critical for the input files to be properly -# imported into the project. In the patterns below, the '%' is the full -# file name (including its suffix): for example in the demo input of this -# file in the 'maneage' branch, we have 'INPUT-wfpc2.fits-sha256': -# therefore, the input file (within the project's '$(indir)') is called +# imported into Maneage. In the patterns below, the '%' is the full file +# name (including its suffix): for example in the demo input of this file +# in the 'maneage' branch, we have 'INPUT-wfpc2.fits-sha256': therefore, +# the input file (within the project's '$(indir)') is called # 'wfpc2.fits'. This allows you to simply set '$(indir)/wfpc2.fits' as the # pre-requisite of any recipe that needs the input file: you will rarely # (if at all!) need to use these variables directly. @@ -40,23 +67,17 @@ # INPUT-%-sha256: The sha256 checksum of the file. You can generate the # SHA256 checksum of a file with the 'sha256sum FILENAME' # command (where 'FILENAME' is the name of your -# file). this is very important for an automatic -# verification of the file: that it hasn't changed -# between different runs of the project (locally or in -# the URL). There are more robust checksum algorithms -# like the 'SHA' standards. -# -# AUTOMATIC CHEKSUM CALCULATION: In case you would like -# Maneage to find the checksum upon downloading, put the -# string '--auto-replace--' instead of a checksum. This -# can be helpful for large datasets; where downloading -# only for adding the checksum is not easy/possible and -# can be buggy. In this scenario, upon downloading the -# file its checksum will be calculated and will be -# replaced with the '--auto-replace--' in this file. But -# since this file is under version control, be sure to -# commit all the updated checksums after your downloads -# are finished! +# file). Don't use this if you give the 'fitsdatasum' +# keyvalue. +# +# INPUT-%-fitsdatasum: The FITS standard DATASUM value for HDU number 1 +# of the FITS file (counting from 0). Don't use this +# if you give the 'sha256' keyword. +# +# INPUT-%-fitshdu: The HDU identifier (counter from 0, or name) to use +# for the verification. This is only relevant in the +# 'fitsdatasum' verification method and optional (if not +# given, HDU number 1 is used; counting from 0). # # INPUT-%-url: The URL to download the file if it is not available # locally. It can happen that during the first phases of @@ -70,13 +91,20 @@ # good feeling of the necessary network and storage # capacity that is necessary to start the project. # +# Therefore, the the verification variable is MANDATORY in any case. The +# variable with a URL is only necessary if you do not have the file +# locally. However, The size variable is optional (but recommended: because +# it gives future scientists a feeling of the volume of data they need to +# input to run your project: will become important if the size/number of +# files is large). +# # The input dataset's name (that goes into the '%') can be different from # the URL's file name (last component of the URL, after the last '/'). Just # note that it is assumed that the local copy (outside of your project) is # also called '%' (if your local copy of the input dataset and the only # repository names are the same, be sure to set '%' accordingly). # -# Copyright (C) 2018-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2018-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # Copying and distribution of this file, with or without modification, are # permitted in any medium without royalty provided the copyright notice and @@ -87,7 +115,18 @@ -# Demo dataset used in the histogram plot (remove when customizing). +# Demo dataset used in the histogram plot +# --------------------------------------- +# +# Remove this part while you are entering your project's datasets. +# +# Since the demonstration dataset is a FITS file, we have also added the +# two '$(INPUT-%-fits*)' variables as a demonstration. But they are +# commented because the SHA256 method is also possible for this file (its +# not generated on the server at query time; it is a static file on the +# server). INPUT-wfpc2.fits-size = 62K INPUT-wfpc2.fits-url = https://fits.gsfc.nasa.gov/samples/WFPC2ASSNu5780205bx.fits INPUT-wfpc2.fits-sha256 = 9851bc2bf9a42008ea606ec532d04900b60865daaff2f233e5c8565dac56ad5f +#INPUT-wfpc2.fits-fitshdu = 0 +#INPUT-wfpc2.fits-fitsdatasum = 2218330266 diff --git a/reproduce/analysis/config/delete-me-squared-num.conf b/reproduce/analysis/config/delete-me-squared-num.conf index 4df2101..c2fa79c 100644 --- a/reproduce/analysis/config/delete-me-squared-num.conf +++ b/reproduce/analysis/config/delete-me-squared-num.conf @@ -1,6 +1,6 @@ # Number of samples in the demonstration analysis (to be deleted). # -# Copyright (C) 2019-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2019-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # Copying and distribution of this file, with or without modification, are # permitted in any medium without royalty provided the copyright notice and diff --git a/reproduce/analysis/config/metadata.conf b/reproduce/analysis/config/metadata.conf index 0241136..7bafc4b 100644 --- a/reproduce/analysis/config/metadata.conf +++ b/reproduce/analysis/config/metadata.conf @@ -15,7 +15,7 @@ # and the copyright license name and standard link to the fully copyright # license. # -# Copyright (C) 2020-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2020-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # Copying and distribution of this file, with or without modification, are # permitted in any medium without royalty provided the copyright notice and diff --git a/reproduce/analysis/config/pdf-build.conf b/reproduce/analysis/config/pdf-build.conf index a57b529..2aa2e9a 100644 --- a/reproduce/analysis/config/pdf-build.conf +++ b/reproduce/analysis/config/pdf-build.conf @@ -12,7 +12,7 @@ # LaTeX. Otherwise, a notice will just printed that, no PDF will be # created. # -# Copyright (C) 2018-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2018-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # Copying and distribution of this file, with or without modification, are # permitted in any medium without royalty provided the copyright notice and diff --git a/reproduce/analysis/config/verify-outputs.conf b/reproduce/analysis/config/verify-outputs.conf index 37fc43c..db7751d 100644 --- a/reproduce/analysis/config/verify-outputs.conf +++ b/reproduce/analysis/config/verify-outputs.conf @@ -1,6 +1,6 @@ # To enable verification of output datasets set this variable to 'yes'. # -# Copyright (C) 2019-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2019-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # Copying and distribution of this file, with or without modification, are # permitted in any medium without royalty provided the copyright notice and diff --git a/reproduce/analysis/make/delete-me.mk b/reproduce/analysis/make/delete-me.mk index f4c8600..325280d 100644 --- a/reproduce/analysis/make/delete-me.mk +++ b/reproduce/analysis/make/delete-me.mk @@ -1,6 +1,6 @@ # Dummy Makefile to create a random dataset for plotting. # -# Copyright (C) 2018-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2018-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # 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 diff --git a/reproduce/analysis/make/initialize.mk b/reproduce/analysis/make/initialize.mk index eb5f2ff..9e8db4a 100644 --- a/reproduce/analysis/make/initialize.mk +++ b/reproduce/analysis/make/initialize.mk @@ -1,6 +1,6 @@ # Project initialization. # -# Copyright (C) 2018-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2018-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # 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 @@ -63,15 +63,18 @@ pconfdir = reproduce/analysis/config # loaded. # # If your project doesn't need any preparation, you can ignore this. +# +# The '-' behind the include commands is used for adding the files only if +# it is possible (they exist). This is necessary because sometimes the user +# will have only '*.conf' or '*.mk' files, or with 'make clean' (where the +# preparation Makefile may call initialize.mk before the main +# 'top-make.mk'). If the '-' is not used, Make will complain about not +# finding these files. ifeq (x$(project-phase),xprepare) $(prepdir):; mkdir $@ else -include $(bsdir)/preparation-done.mk +-include $(bsdir)/preparation-done.mk ifeq (x$(include-prepare-results),xyes) -# The '-' behind the include is The '-' is used for adding the files only -# if it is possible (they exist). This is necessary because sometimes the -# user will have only '*.conf' or '*.mk' files. So, if the '-' is not used, -# Make will complain about not finding these files. -include $(prepdir)/*.mk $(prepdir)/*.conf endif endif @@ -227,7 +230,7 @@ project-commit-hash := $(shell \ export LD_LIBRARY_PATH="$(installdir)/lib"; \ echo $$($(installdir)/bin/git describe --dirty --always --long); \ else echo NOGIT; fi) -project-package-name := maneaged-$(project-commit-hash) +project-package-name = maneaged-$(project-commit-hash) project-package-contents = $(texdir)/$(project-package-name) @@ -438,13 +441,15 @@ dist-software: -# Download input data -# -------------------- +# Import input data +# ----------------- # -# 'reproduce/analysis/config/INPUTS.conf' contains the input dataset -# properties. In most cases, you will not need to edit this rule. Simply -# follow the instructions of 'INPUTS.conf' and set the variables names -# according to the described standards and everything should be fine. +# The list files to be imported (downloaded from a server, or linked from a +# local location), are listed in 'reproduce/analysis/config/INPUTS.conf' +# along with their URLs and verification checksums. In most cases, you will +# not need to edit this rule. Simply follow the instructions at the top of +# 'INPUTS.conf' and set the variables names according to the described +# standards and everything should be fine. # # TECHNICAL NOTE on the '$(foreach, n ...)' loop of 'inputdatasets': we are # using several (relatively complex!) features particular to Make: In GNU @@ -465,16 +470,60 @@ dist-software: # progress at every moment. $(indir):; mkdir $@ downloadwrapper = $(bashdir)/download-multi-try -inputdatasets = $(foreach i, \ - $(patsubst INPUT-%-sha256,%, \ - $(filter INPUT-%-sha256,$(.VARIABLES))), \ - $(indir)/$(i)) +inputdatasets := $(foreach i, \ + $(patsubst INPUT-%-sha256,%, \ + $(filter INPUT-%-sha256,$(.VARIABLES))) \ + $(patsubst INPUT-%-fitsdatasum,%, \ + $(filter INPUT-%-fitsdatasum,$(.VARIABLES))), \ + $(indir)/$(i)) $(inputdatasets): $(indir)/%: | $(indir) $(lockdir) -# Set the necessary parameters for this input file as shell variables -# (to help in readability). - url=$(INPUT-$*-url) - sha=$(INPUT-$*-sha256) +# Starting rule with '@': In case there is a username or password +# given for the database, we don't want the values to be printed in +# the terminal as the pipeline is running. We are therefore starting +# this recipe with an '@' (so Make doesn't print the used +# commands). To help the user know what is happening (in case they +# can't tell from the Wget outputs), we'll just start the recipe with +# a notice on what is being imported. + @echo "Importing $@" + +# If a username or password has been provided, add them to the WGET +# command. The two variables are defined in the local configuation +# file 'reproduce/software/config/LOCAL.conf' that is not under +# version control. Different servers may use different authentication +# formats. If the default one doesn't work for your server, comment +# it and uncomment the one that works. If your serve needs a +# different kind of authentication format, please add it yourself. In +# case you need a new format, we encourage you to send the format to +# us using the link below: +# https://savannah.nongnu.org/support/?group=reproduce&func=additem + authopt="" + if [ x"$(DATABASEAUTHTYPE)" != x ]; then + case "$(DATABASEAUTHTYPE)" in + +# Format: '--user=XXXX --password=YYYY' + userpass) + if [ x'$(DATABASEUSER)' != x ]; then + authopt="--user='$(DATABASEUSER)'"; fi + if [ x'$(DATABASEPASS)' != x ]; then + authopt="$$authopt --password='$(DATABASEPASS)'"; fi + ;; + +# Format: --post-data 'username=XXXX&password=YYYY' + postdata) + if [ x'$(DATABASEUSER)' != x ]; then + authopt="--post-data 'username=$(DATABASEUSER)"; fi + if [ x'$(DATABASEPASS)' != x ]; then + authopt="$$authopt""&password=$(DATABASEPASS)'"; + else authopt="$$authopt'" # To close the single quote + fi + ;; + +# Unrecognized format. + *) + echo "Maneage: 'DATABASEAUTHTYPE' format not recognized! Please see the description of this variable in 'reproduce/software/config/LOCAL.conf' for the acceptable values."; exit 1;; + esac + fi # Download (or make the link to) the input dataset. If the file # exists in 'INDIR', it may be a symbolic link to some other place in @@ -488,13 +537,29 @@ $(inputdatasets): $(indir)/%: | $(indir) $(lockdir) ln -fs $$(readlink -f $(INDIR)/$*) $$unchecked else touch $(lockdir)/download - $(downloadwrapper) "wget --no-use-server-timestamps -O" \ - $(lockdir)/download $$url $$unchecked + $(downloadwrapper) "wget $$authopt --no-use-server-timestamps -O" \ + $(lockdir)/download "$(INPUT-$*-url)" $$unchecked + fi + +# Set the checksum related variables. + if [ x"$(INPUT-$*-sha256)" != x ]; then + suffix=sha256 + sumin=$(INPUT-$*-sha256) + verifname="SHA256 checksum" + sum=$$(sha256sum $$unchecked | awk '{print $$1}') + elif [ x"$(INPUT-$*-fitsdatasum)" != x ]; then + suffix=fitsdatasum + sumin=$(INPUT-$*-fitsdatasum) + verifname="FITS standard DATASUM" + if [ x"$(INPUT-$*-fitshdu)" = x ]; then hdu=1; + else hdu="$(INPUT-$*-fitshdu)"; fi + sum=$$(astfits $$unchecked -h$$hdu --datasum | awk '{print $$1}') + else + echo "$@: checksum for verifyication not recognized!"; exit 1 fi -# Check the checksum to see if this is the proper dataset. - sum=$$(sha256sum $$unchecked | awk '{print $$1}') - if [ $$sum = $$sha ]; then +# Verify the input. + if [ $$sum = $$sumin ]; then mv $$unchecked $@ echo "Integrity confirmed, using $@ in this project." @@ -502,11 +567,11 @@ $(inputdatasets): $(indir)/%: | $(indir) $(lockdir) else # The user has asked to update the checksum in 'INPUTS.conf'. - if [ $$sha = "--auto-replace--" ]; then + if [ $$sumin = "--auto-replace--" ]; then # Put the updated 'INPUTS.conf' in a temporary file. inputstmp=$@.inputs - awk '{if($$1 == "INPUT-$*-sha256") \ + awk '{if($$1 == "INPUT-$*-'$$suffix'") \ $$3="'$$sum'"; print}' \ $(pconfdir)/INPUTS.conf > $$inputstmp @@ -520,10 +585,10 @@ $(inputdatasets): $(indir)/%: | $(indir) $(lockdir) # Error on non-matching checksums. else echo; echo; - echo "Wrong SHA256 checksum for input file '$*':" + echo "Wrong $$verifname for input file '$*':" echo " File location: $$unchecked"; \ - echo " Expected SHA256 checksum: $$sha"; \ - echo " Calculated SHA256 checksum: $$sum"; \ + echo " Expected $$verifname: $$sumin"; \ + echo " Calculated $$verifname: $$sum"; \ echo; exit 1 fi fi diff --git a/reproduce/analysis/make/paper.mk b/reproduce/analysis/make/paper.mk index 740dc7d..791108b 100644 --- a/reproduce/analysis/make/paper.mk +++ b/reproduce/analysis/make/paper.mk @@ -1,6 +1,6 @@ # Build the final PDF paper/report. # -# Copyright (C) 2018-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2018-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # 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 diff --git a/reproduce/analysis/make/prepare.mk b/reproduce/analysis/make/prepare.mk index ebc2b4d..36f5294 100644 --- a/reproduce/analysis/make/prepare.mk +++ b/reproduce/analysis/make/prepare.mk @@ -1,6 +1,6 @@ # Basic preparations, called by './project make'. # -# Copyright (C) 2019-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2019-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # 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 diff --git a/reproduce/analysis/make/top-make.mk b/reproduce/analysis/make/top-make.mk index d6e3822..460433b 100644 --- a/reproduce/analysis/make/top-make.mk +++ b/reproduce/analysis/make/top-make.mk @@ -1,6 +1,6 @@ # Top-level Makefile (first to be loaded). # -# Copyright (C) 2018-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2018-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # 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 diff --git a/reproduce/analysis/make/top-prepare.mk b/reproduce/analysis/make/top-prepare.mk index 28dfc4a..930c2a9 100644 --- a/reproduce/analysis/make/top-prepare.mk +++ b/reproduce/analysis/make/top-prepare.mk @@ -4,7 +4,7 @@ # are not included here. Please see that file for thorough comments on each # step. # -# Copyright (C) 2019-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2019-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # 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 diff --git a/reproduce/analysis/make/verify.mk b/reproduce/analysis/make/verify.mk index 25b3bec..aa026b5 100644 --- a/reproduce/analysis/make/verify.mk +++ b/reproduce/analysis/make/verify.mk @@ -1,6 +1,6 @@ # Verify the project outputs before building the paper. # -# Copyright (C) 2020-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2020-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # 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 diff --git a/reproduce/software/bibtex/astrometrynet.tex b/reproduce/software/bibtex/astrometrynet.tex index 26d211b..10b487e 100644 --- a/reproduce/software/bibtex/astrometrynet.tex +++ b/reproduce/software/bibtex/astrometrynet.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2019-2022 Raul Infante-Sainz <infantesainz@gmail.com> +%% Copyright (C) 2019-2023 Raul Infante-Sainz <infantesainz@gmail.com> %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright @@ -6,15 +6,19 @@ %% without any warranty. @ARTICLE{astrometrynet, - doi = {10.1088/0004-6256/139/5/1782}, - url = {https://doi.org/10.1088%2F0004-6256%2F139%2F5%2F1782}, - year = 2010, - month = {mar}, - publisher = {{IOP} Publishing}, - volume = {139}, - number = {5}, - pages = {1782}, - author = {Dustin Lang and David W. Hogg and Keir Mierle and Michael Blanton and Sam Roweis}, - title = {{ASTROMETRY}.{NET}: {BLIND} {ASTROMETRIC} {CALIBRATION} {OF} {ARBITRARY} {ASTRONOMICAL} {IMAGES}}, - journal = {AJ} + author = {{Lang}, Dustin and {Hogg}, David W. and {Mierle}, Keir and {Blanton}, Michael and {Roweis}, Sam}, + title = "{Astrometry.net: Blind Astrometric Calibration of Arbitrary Astronomical Images}", + journal = {AJ}, + keywords = {astrometry, catalogs, instrumentation: miscellaneous, methods: data analysis, methods: statistical, techniques: image processing, Astrophysics - Instrumentation and Methods for Astrophysics}, + year = 2010, + month = may, + volume = {139}, + number = {5}, + pages = {1782-1800}, + doi = {10.1088/0004-6256/139/5/1782}, +archivePrefix = {arXiv}, + eprint = {0910.2233}, + primaryClass = {astro-ph.IM}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2010AJ....139.1782L}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} } diff --git a/reproduce/software/bibtex/astropy.tex b/reproduce/software/bibtex/astropy.tex index 2041fc3..f0b8349 100644 --- a/reproduce/software/bibtex/astropy.tex +++ b/reproduce/software/bibtex/astropy.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2019-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org> +%% Copyright (C) 2019-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org> %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/corner.tex b/reproduce/software/bibtex/corner.tex index f6b4f22..5eda23d 100644 --- a/reproduce/software/bibtex/corner.tex +++ b/reproduce/software/bibtex/corner.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2019-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org> +%% Copyright (C) 2019-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org> %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/cython.tex b/reproduce/software/bibtex/cython.tex index 30a0713..6103028 100644 --- a/reproduce/software/bibtex/cython.tex +++ b/reproduce/software/bibtex/cython.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2019-2022 Raul Infante-Sainz <infantesainz@gmail.com> +%% Copyright (C) 2019-2023 Raul Infante-Sainz <infantesainz@gmail.com> %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright @@ -6,16 +6,15 @@ %% without any warranty. @ARTICLE{cython2011, - author = {{Behnel}, S. and {Bradshaw}, R. and {Citro}, C. and {Dalcin}, L. and - {Seljebotn}, D.~S. and {Smith}, K.}, - title = "{Cython: The Best of Both Worlds}", - journal = {CiSE}, - year = 2011, - month = mar, - volume = 13, - number = 2, - pages = {31}, - doi = {10.1109/MCSE.2010.118}, - adsurl = {http://ui.adsabs.harvard.edu/abs/2011CSE....13b..31B}, - adsnote = {Provided by the SAO/NASA Astrophysics Data System} + author = {{Behnel}, Stefan and {Bradshaw}, Robert and {Citro}, Craig and {Dalcin}, Lisandro and {Seljebotn}, Dag Sverre and {Smith}, Kurt}, + title = "{Cython: The Best of Both Worlds}", + journal = {Computing in Science and Engineering}, + year = 2011, + month = mar, + volume = {13}, + number = {2}, + pages = {31-39}, + doi = {10.1109/MCSE.2010.118}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2011CSE....13b..31B}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} } diff --git a/reproduce/software/bibtex/fftw.tex b/reproduce/software/bibtex/fftw.tex index 1186efa..e1e9bf8 100644 --- a/reproduce/software/bibtex/fftw.tex +++ b/reproduce/software/bibtex/fftw.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2019-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org> +%% Copyright (C) 2019-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org> %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright @@ -12,7 +12,7 @@ year = {2005}, volume = {93}, number = {2}, - pages = {216}, + pages = {216-231}, doi = {10.1109/JPROC.2004.840301}, ISSN = {0018-9219}, month = {Feb}, diff --git a/reproduce/software/bibtex/galsim.tex b/reproduce/software/bibtex/galsim.tex index 8fceda8..6ca9b45 100644 --- a/reproduce/software/bibtex/galsim.tex +++ b/reproduce/software/bibtex/galsim.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2019-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org> +%% Copyright (C) 2019-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org> %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/gnuastro.tex b/reproduce/software/bibtex/gnuastro.tex index 018a35b..5fd87e4 100644 --- a/reproduce/software/bibtex/gnuastro.tex +++ b/reproduce/software/bibtex/gnuastro.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2019-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org> +%% Copyright (C) 2019-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org> %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright @@ -6,19 +6,20 @@ %% without any warranty. @ARTICLE{gnuastro, - author = {{Akhlaghi}, M. and {Ichikawa}, T.}, - title = "{Noise-based Detection and Segmentation of Nebulous Objects}", - journal = {ApJS}, -archivePrefix = "arXiv", - eprint = {1505.01664}, - primaryClass = "astro-ph.IM", - keywords = {galaxies: irregular, galaxies: photometry, galaxies: structure, methods: data analysis, techniques: image processing, techniques: photometric}, - year = 2015, - month = sep, - volume = 220, - eid = {1}, - pages = {1}, - doi = {10.1088/0067-0049/220/1/1}, - adsurl = {http://ui.adsabs.harvard.edu/abs/2015ApJS..220....1A}, - adsnote = {Provided by the SAO/NASA Astrophysics Data System} + author = {{Akhlaghi}, Mohammad and {Ichikawa}, Takashi}, + title = "{Noise-based Detection and Segmentation of Nebulous Objects}", + journal = {ApJS}, + keywords = {galaxies: irregular, galaxies: photometry, galaxies: structure, methods: data analysis, techniques: image processing, techniques: photometric, Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - Cosmology and Nongalactic Astrophysics, Astrophysics - Astrophysics of Galaxies}, + year = 2015, + month = sep, + volume = {220}, + number = {1}, + eid = {1}, + pages = {1}, + doi = {10.1088/0067-0049/220/1/1}, +archivePrefix = {arXiv}, + eprint = {1505.01664}, + primaryClass = {astro-ph.IM}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2015ApJS..220....1A}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} } diff --git a/reproduce/software/bibtex/healpix.tex b/reproduce/software/bibtex/healpix.tex index 77471c5..cfb96c0 100644 --- a/reproduce/software/bibtex/healpix.tex +++ b/reproduce/software/bibtex/healpix.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2019-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org> +%% Copyright (C) 2019-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org> %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright @@ -6,16 +6,15 @@ %% without any warranty. @ARTICLE{healpix, - author = {{G{\'o}rski}, K.~M. and {Hivon}, E. and {Banday}, A.~J. and {Wand - elt}, B.~D. and {Hansen}, F.~K. and {Reinecke}, M. and {Bartelmann}, M.}, + author = {{G{\'o}rski}, K.~M. and {Hivon}, E. and {Banday}, A.~J. and {Wandelt}, B.~D. and {Hansen}, F.~K. and {Reinecke}, M. and {Bartelmann}, M.}, title = "{HEALPix: A Framework for High-Resolution Discretization and Fast Analysis of Data Distributed on the Sphere}", journal = {ApJ}, keywords = {Cosmology: Cosmic Microwave Background, Cosmology: Observations, Methods: Statistical, Astrophysics}, - year = "2005", - month = "Apr", + year = 2005, + month = apr, volume = {622}, number = {2}, - pages = {759}, + pages = {759-771}, doi = {10.1086/427976}, archivePrefix = {arXiv}, eprint = {astro-ph/0409513}, diff --git a/reproduce/software/bibtex/imfit.tex b/reproduce/software/bibtex/imfit.tex index 167586d..f35ee69 100644 --- a/reproduce/software/bibtex/imfit.tex +++ b/reproduce/software/bibtex/imfit.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2019-2022 Raul Infante-Sainz <infantesainz@gmail.com> +%% Copyright (C) 2019-2023 Raul Infante-Sainz <infantesainz@gmail.com> %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright @@ -6,19 +6,20 @@ %% without any warranty. @ARTICLE{imfit2015, - author = {{Erwin}, P.}, - title = "{IMFIT: A Fast, Flexible New Program for Astronomical Image Fitting}", - journal = {ApJ}, -archivePrefix = "arXiv", - eprint = {1408.1097}, - primaryClass = "astro-ph.IM", - keywords = {galaxies: bulges, galaxies: photometry, galaxies: structure, methods: data analysis, techniques: image processing, techniques: photometric }, - year = 2015, - month = feb, - volume = 799, - eid = {226}, - pages = {226}, - doi = {10.1088/0004-637X/799/2/226}, - adsurl = {https://ui.adsabs.harvard.edu/abs/2015ApJ...799..226E}, - adsnote = {Provided by the SAO/NASA Astrophysics Data System} + author = {{Erwin}, Peter}, + title = "{IMFIT: A Fast, Flexible New Program for Astronomical Image Fitting}", + journal = {ApJ}, + keywords = {galaxies: bulges, galaxies: photometry, galaxies: structure, methods: data analysis, techniques: image processing, techniques: photometric, Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - Astrophysics of Galaxies}, + year = 2015, + month = feb, + volume = {799}, + number = {2}, + eid = {226}, + pages = {226}, + doi = {10.1088/0004-637X/799/2/226}, +archivePrefix = {arXiv}, + eprint = {1408.1097}, + primaryClass = {astro-ph.IM}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2015ApJ...799..226E}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} } diff --git a/reproduce/software/bibtex/matplotlib.tex b/reproduce/software/bibtex/matplotlib.tex index aab2c04..9873c57 100644 --- a/reproduce/software/bibtex/matplotlib.tex +++ b/reproduce/software/bibtex/matplotlib.tex @@ -1,18 +1,21 @@ -%% Copyright (C) 2019-2022 Raul Infante-Sainz <infantesainz@gmail.com> +%% Copyright (C) 2019-2023 Raul Infante-Sainz <infantesainz@gmail.com> %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright %% notice and this notice are preserved. This file is offered as-is, %% without any warranty. -@Article{matplotlib2007, - Author = {Hunter, J. D.}, - Title = {Matplotlib: A 2D graphics environment}, - Journal = {CiSE}, - Volume = {9}, - Number = {3}, - Pages = {90}, - publisher = {IEEE COMPUTER SOC}, - doi = {10.1109/MCSE.2007.55}, - year = 2007 +@ARTICLE{matplotlib2007, + author = {{Hunter}, John D.}, + title = "{Matplotlib: A 2D Graphics Environment}", + journal = {CiSE}, + keywords = {Python, Scripting languages, Application development, Scientific programming}, + year = 2007, + month = may, + volume = {9}, + number = {3}, + pages = {90-95}, + doi = {10.1109/MCSE.2007.55}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2007CSE.....9...90H}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} } diff --git a/reproduce/software/bibtex/missfits.tex b/reproduce/software/bibtex/missfits.tex index 470cf8a..64704e6 100644 --- a/reproduce/software/bibtex/missfits.tex +++ b/reproduce/software/bibtex/missfits.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2020-2022 Surena Fatemi <surena.fatemi@ipm.ir> +%% Copyright (C) 2020-2023 Surena Fatemi <surena.fatemi@ipm.ir> %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/mpi4py.tex b/reproduce/software/bibtex/mpi4py.tex index 598bbda..cc6bcb9 100644 --- a/reproduce/software/bibtex/mpi4py.tex +++ b/reproduce/software/bibtex/mpi4py.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2019-2022 Raul Infante-Sainz <infantesainz@gmail.com> +%% Copyright (C) 2019-2023 Raul Infante-Sainz <infantesainz@gmail.com> %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright @@ -6,15 +6,15 @@ %% without any warranty. @ARTICLE{mpi4py2011, - author = {{Dalcin}, L.~D. and {Paz}, R.~R. and {Kler}, P.~A. and {Cosimo}, A. - }, - title = "{Parallel distributed computing using Python}", - journal = {AdvWatRes}, - year = 2011, - month = sep, - volume = 34, - pages = {1124}, - doi = {10.1016/j.advwatres.2011.04.013}, - adsurl = {http://ui.adsabs.harvard.edu/abs/2011AdWR...34.1124D}, - adsnote = {Provided by the SAO/NASA Astrophysics Data System} + author = {{Dalcin}, Lisandro D. and {Paz}, Rodrigo R. and {Kler}, Pablo A. and {Cosimo}, Alejandro}, + title = "{Parallel distributed computing using Python}", + journal = {Advances in Water Resources}, + year = 2011, + month = sep, + volume = {34}, + number = {9}, + pages = {1124-1139}, + doi = {10.1016/j.advwatres.2011.04.013}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2011AdWR...34.1124D}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} } diff --git a/reproduce/software/bibtex/numpy.tex b/reproduce/software/bibtex/numpy.tex index 0dee489..da54330 100644 --- a/reproduce/software/bibtex/numpy.tex +++ b/reproduce/software/bibtex/numpy.tex @@ -1,23 +1,24 @@ -%% Copyright (C) 2019-2022 Raul Infante-Sainz <infantesainz@gmail.com> +%% Copyright (C) 2019-2023 Raul Infante-Sainz <infantesainz@gmail.com> %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright %% notice and this notice are preserved. This file is offered as-is, %% without any warranty. -@ARTICLE{numpy2011, - author = {{van der Walt}, S. and {Colbert}, S.~C. and {Varoquaux}, G.}, - title = "{The NumPy Array: A Structure for Efficient Numerical Computation}", - journal = {CiSE}, -archivePrefix = "arXiv", - eprint = {1102.1523}, - primaryClass = "cs.MS", - year = 2011, - month = mar, - volume = 13, - number = 2, - pages = {22}, - doi = {10.1109/MCSE.2011.37}, - adsurl = {http://ui.adsabs.harvard.edu/abs/2011CSE....13b..22V}, - adsnote = {Provided by the SAO/NASA Astrophysics Data System} +@ARTICLE{numpy2020, + author = {{Harris}, Charles R. and {Millman}, K. Jarrod and {van der Walt}, St{\'e}fan J. and {Gommers}, Ralf and {Virtanen}, Pauli and {Cournapeau}, David and {Wieser}, Eric and {Taylor}, Julian and {Berg}, Sebastian and {Smith}, Nathaniel J. and {Kern}, Robert and {Picus}, Matti and {Hoyer}, Stephan and {van Kerkwijk}, Marten H. and {Brett}, Matthew and {Haldane}, Allan and {del R{\'\i}o}, Jaime Fern{\'a}ndez and {Wiebe}, Mark and {Peterson}, Pearu and {G{\'e}rard-Marchant}, Pierre and {Sheppard}, Kevin and {Reddy}, Tyler and {Weckesser}, Warren and {Abbasi}, Hameer and {Gohlke}, Christoph and {Oliphant}, Travis E.}, + title = "{Array programming with NumPy}", + journal = {Nature}, + keywords = {Computer Science - Mathematical Software, Statistics - Computation}, + year = 2020, + month = sep, + volume = {585}, + number = {7825}, + pages = {357-362}, + doi = {10.1038/s41586-020-2649-2}, +archivePrefix = {arXiv}, + eprint = {2006.10256}, + primaryClass = {cs.MS}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2020Natur.585..357H}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} } diff --git a/reproduce/software/bibtex/r-cran.tex b/reproduce/software/bibtex/r-cran.tex index cf74a8e..8d691c1 100644 --- a/reproduce/software/bibtex/r-cran.tex +++ b/reproduce/software/bibtex/r-cran.tex @@ -1,5 +1,5 @@ -%% Copyright (C) 2022 Boud Roukema <boud@cosmo.torun.pl> -%% Copyright (C) 2022 Mohammad Akhlaghi <mohammad@akhlaghi.org> +%% Copyright (C) 2022-2023 Boud Roukema <boud@cosmo.torun.pl> +%% Copyright (C) 2022-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org> %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/scamp.tex b/reproduce/software/bibtex/scamp.tex index 62e910c..5e5be91 100644 --- a/reproduce/software/bibtex/scamp.tex +++ b/reproduce/software/bibtex/scamp.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2019-2022 Raul Infante-Sainz <infantesainz@gmail.com> +%% Copyright (C) 2019-2023 Raul Infante-Sainz <infantesainz@gmail.com> %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/scipy.tex b/reproduce/software/bibtex/scipy.tex index 4b1292d..c92bbec 100644 --- a/reproduce/software/bibtex/scipy.tex +++ b/reproduce/software/bibtex/scipy.tex @@ -1,34 +1,23 @@ -%% Copyright (C) 2019-2022 Raul Infante-Sainz <infantesainz@gmail.com> +%% Copyright (C) 2019-2023 Raul Infante-Sainz <infantesainz@gmail.com> %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright %% notice and this notice are preserved. This file is offered as-is, %% without any warranty. -@ARTICLE{scipy2011, - author = {K. J. {Millman} and M. {Aivazis}}, - journal = {CiSE}, - title = {Python for Scientists and Engineers}, - year = {2011}, - volume = {13}, - number = {2}, - pages = {9}, - keywords = {Special issues and sections;Computer languages;Programming;Scientific computing;Numerical models;Programming languages;Python;Scientific computing;interactive research;Python libraries;Python tools}, - doi = {10.1109/MCSE.2011.36}, - ISSN = {1521-9615}, - month ={March}, -} - -@ARTICLE{scipy2007, - author = {T. E. {Oliphant}}, - journal = {CiSE}, - title = {Python for Scientific Computing}, - year = {2007}, - volume = {9}, - number = {3}, - pages = {10}, - keywords = {high level languages;Python;scientific computing;steering language;scientific codes;high-level language;Scientific computing;High level languages;Libraries;Writing;Application software;Embedded software;Software standards;Standards development;Internet;Prototypes;Python;computer languages;scientific programming;scientific computing}, - doi = {10.1109/MCSE.2007.58}, - ISSN = {1521-9615}, - month = {May}, +@ARTICLE{scipy2020, + author = {{Virtanen}, Pauli and {Gommers}, Ralf and {Oliphant}, Travis E. and {Haberland}, Matt and {Reddy}, Tyler and {Cournapeau}, David and {Burovski}, Evgeni and {Peterson}, Pearu and {Weckesser}, Warren and {Bright}, Jonathan and {van der Walt}, St{\'e}fan J. and {Brett}, Matthew and {Wilson}, Joshua and {Millman}, K. Jarrod and {Mayorov}, Nikolay and {Nelson}, Andrew R.~J. and {Jones}, Eric and {Kern}, Robert and {Larson}, Eric and {Carey}, C.~J. and {Polat}, {\.I}lhan and {Feng}, Yu and {Moore}, Eric W. and {VanderPlas}, Jake and {Laxalde}, Denis and {Perktold}, Josef and {Cimrman}, Robert and {Henriksen}, Ian and {Quintero}, E.~A. and {Harris}, Charles R. and {Archibald}, Anne M. and {Ribeiro}, Ant{\^o}nio H. and {Pedregosa}, Fabian and {van Mulbregt}, Paul and {SciPy 1. 0 Contributors}}, + title = "{SciPy 1.0: fundamental algorithms for scientific computing in Python}", + journal = {Nature Methods}, + keywords = {Computer Science - Mathematical Software, Computer Science - Data Structures and Algorithms, Computer Science - Software Engineering, Physics - Computational Physics}, + year = 2020, + month = feb, + volume = {17}, + pages = {261-272}, + doi = {10.1038/s41592-019-0686-2}, +archivePrefix = {arXiv}, + eprint = {1907.10121}, + primaryClass = {cs.MS}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2020NatMe..17..261V}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} } diff --git a/reproduce/software/bibtex/sextractor.tex b/reproduce/software/bibtex/sextractor.tex index 8905be8..cdffe74 100644 --- a/reproduce/software/bibtex/sextractor.tex +++ b/reproduce/software/bibtex/sextractor.tex @@ -1,5 +1,5 @@ -%% Copyright (C) 2019-2022 Raul Infante-Sainz <infantesainz@gmail.com> -%% Copyright (C) 2019-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org> +%% Copyright (C) 2019-2023 Raul Infante-Sainz <infantesainz@gmail.com> +%% Copyright (C) 2019-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org> %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright @@ -11,10 +11,10 @@ title = "{SExtractor: Software for source extraction.}", journal = {A\&AS}, keywords = {METHODS: DATA ANALYSIS, TECHNIQUES: IMAGE PROCESSING, GALAXIES: PHOTOMETRY}, - year = "1996", - month = "Jun", + year = 1996, + month = jun, volume = {117}, - pages = {393}, + pages = {393-404}, doi = {10.1051/aas:1996164}, adsurl = {https://ui.adsabs.harvard.edu/abs/1996A&AS..117..393B}, adsnote = {Provided by the SAO/NASA Astrophysics Data System} diff --git a/reproduce/software/bibtex/sip_tpv.tex b/reproduce/software/bibtex/sip_tpv.tex index 2a5b68b..d13d7a5 100644 --- a/reproduce/software/bibtex/sip_tpv.tex +++ b/reproduce/software/bibtex/sip_tpv.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2019-2022 Raul Infante-Sainz <infantesainz@gmail.com> +%% Copyright (C) 2019-2023 Raul Infante-Sainz <infantesainz@gmail.com> %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/swarp.tex b/reproduce/software/bibtex/swarp.tex index f645bb3..ecac1a7 100644 --- a/reproduce/software/bibtex/swarp.tex +++ b/reproduce/software/bibtex/swarp.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2019-2022 Raul Infante-Sainz <infantesainz@gmail.com> +%% Copyright (C) 2019-2023 Raul Infante-Sainz <infantesainz@gmail.com> %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/sympy.tex b/reproduce/software/bibtex/sympy.tex index 3ce064a..27ea9ac 100644 --- a/reproduce/software/bibtex/sympy.tex +++ b/reproduce/software/bibtex/sympy.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2019-2022 Raul Infante-Sainz <infantesainz@gmail.com> +%% Copyright (C) 2019-2023 Raul Infante-Sainz <infantesainz@gmail.com> %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/tides.tex b/reproduce/software/bibtex/tides.tex index b97762a..dfa8eb8 100644 --- a/reproduce/software/bibtex/tides.tex +++ b/reproduce/software/bibtex/tides.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2019-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org> +%% Copyright (C) 2019-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org> %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright @@ -13,7 +13,7 @@ month = nov, volume = 39, eid = {5}, - pages = {5:1}, + pages = {1-28}, doi = {10.1145/2382585.2382590}, keywords = {Taylor series method, automatic differentiation, high precision, numerical integration of ODEs, variational equations}, } diff --git a/reproduce/software/config/LOCAL.conf.in b/reproduce/software/config/LOCAL.conf.in index a7434ea..5ee1ff7 100644 --- a/reproduce/software/config/LOCAL.conf.in +++ b/reproduce/software/config/LOCAL.conf.in @@ -3,7 +3,7 @@ # This is just a template for the './project configure' script to fill # in. Please don't make any change to this file. # -# Copyright (C) 2018-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2018-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # Copying and distribution of this file, with or without modification, are # permitted in any medium without royalty provided the copyright notice and @@ -15,3 +15,46 @@ DEPENDENCIES-DIR = @ddir@ SYS_CPATH = @sys_cpath@ DOWNLOADER = @downloader@ GROUP-NAME = @groupname@ + + + + + +# Server authentication/identification +# ------------------------------------ +# +# If you need to identify yourself to the database server (when downloading +# input files), you can write your user name and password in the two +# variables below. When these two variables are defined, the download rule +# (in 'reproduce/analysis/make/initialize.mk') will pass their values to +# the '--user' and '--password' options of WGET.\ +# +# The 'DATABASEAUTHTYPE' specifies which type of authentication is +# recognized by the database with the 'wget' command. It can take the +# following values: +# 'userpass': Assumes --user='XXXX' --password='YYYY' +# 'postdata': Assumes --post-data 'username=XXXX&password=YYYY' +# +# SPECIAL CHARACTERS IN PASSWORD: if your password has special characters +# like '#' or '$' (that can have special meaning for Make), then comment +# them with a back-slash. For example if your password is 'ab#cd', write it +# below as 'ab\#cd'. Within 'initialize.mk', the user name and password are +# placed inside single quotes before being used, so special characters +# won't be problematic. However, if your password includes characters like +# the single quote itself, this can be problematic. In this case, you can +# temporarily (without committing!) directly enter the password in the +# respective rule of 'initialize.mk' and after downloading, undo the change +# (which is easy with 'git restore'). If you have any ideas on how to +# account for such characters in a generic way, please let us know and +# we'll suggest them here for future users. +# +# SECURITY WARNING: only set the values of these two variables in +# 'LOCAL.conf' (which is _not_ under version control), _not_ +# 'LOCAL.conf.in' (which is under version control). It is also recommended +# to remove the ID and password values from 'LOCAL.conf' immediately after +# your downloads finish: even though 'LOCAL.conf' is not under version +# control, it will still be on your computer, which may be accessed by +# others or (mistakenly) shared with others. +DATABASEUSER = +DATABASEPASS = +DATABASEAUTHTYPE = diff --git a/reproduce/software/config/TARGETS.conf b/reproduce/software/config/TARGETS.conf index ef95f57..3d35eed 100644 --- a/reproduce/software/config/TARGETS.conf +++ b/reproduce/software/config/TARGETS.conf @@ -1,7 +1,7 @@ # Necessary high-level software to build in this project. # -# Copyright (C) 2018-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org> -# Copyright (C) 2019-2022 Raul Infante-Sainz <infantesainz@gmail.com> +# Copyright (C) 2018-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2019-2023 Raul Infante-Sainz <infantesainz@gmail.com> # # Copying and distribution of this file, with or without modification, are # permitted in any medium without royalty provided the copyright notice and @@ -36,10 +36,10 @@ # Programs and libraries (for Python or R modules, use respective variable). -top-level-programs = gnuastro +top-level-programs = gnuastro # Python libraries/modules. -top-level-python = +top-level-python = # R libraries/modules # [For developers 2022-01-02: 'r-cran-cowplot r-cran-gridExtra' for all] diff --git a/reproduce/software/config/checksums.conf b/reproduce/software/config/checksums.conf index 736a5e5..e34d9b8 100644 --- a/reproduce/software/config/checksums.conf +++ b/reproduce/software/config/checksums.conf @@ -1,8 +1,8 @@ # sha512 checksums of all the necessary software tarballs. # -# Copyright (C) 2018-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org> -# Copyright (C) 2019-2022 Raul Infante-Sainz <infantesainz@gmail.com> -# Copyright (C) 2022 Pedram Ashofteh Ardakani <pedramardakani@pm.me> +# Copyright (C) 2018-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2019-2023 Raul Infante-Sainz <infantesainz@gmail.com> +# Copyright (C) 2022-2023 Pedram Ashofteh Ardakani <pedramardakani@pm.me> # # Copying and distribution of this file, with or without modification, are # permitted in any medium without royalty provided the copyright notice and @@ -15,28 +15,28 @@ # Basic/low-level programs and libraires (installed in any case) # -------------------------------------------------------------- -bash-checksum = 409843172032fbe7ef50004ddc30934e12d864e30935fa501dd8a2792c0c12c9c00e1108c05a95ba84b5ab4dd146d92e793b684df1f49ba51eba40f39d47f14d -binutils-checksum = f3c10d8aeb50872278ece6ad31f7369bf12b2d09618812322b35e6750024b45f77fc32d498a9c579df3c152ce3da382f480281743eb5b53639aa287b7166aba3 +bash-checksum = 2ce67af3ff6b6c9d87b2e98986da937ee100a4cecefd50f01ccdbaeb53e45ff80b1e84d5861619dd3058259223a1f0748e5850aa2dab13b3350fb8a955c3024e +binutils-checksum = 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flake8-checksum = a25076bb7f978ca23af0f2016b30bf5fe4680371b4c0939361a6f8c496f3c846cf98ecadee35fc2dedd588116c8cd982529972dd2411ab139621912b69132a1e future-checksum = c70565a660cf87c5e7e994bae0d4eb0b2b8b607ecb5ce65521c027bf0a39ce5699f0578413bd3c7edd5d01aeb1617de48dcea098a9e9021d8487a73007573030 -galsim-checksum = d7e354778de87cf5c8964a7f252025eeeabc04ef2fb673c35adc536b449442aca261e2bd96befaaa872065376ac79cbe23d1ee7d034bcab5916f74b98112b8b8 +galsim-checksum = 65393c4bcf52a3e723604a956aac5f58f490e41c7d5ddbd5d61660658738e2496aa30f632d4d83b765aaf1e46ac691fcd02fc827380e07c8f921c160a9f6a6fd gast-checksum = 8311f48788daf060bee54ad8986eae054c2a426adcf97f1503cde37c4da2827cd0f664188e51f5c2f932a0a4ded78166a8466465595a640106060c8b6c7072a5 h5py-checksum = c49b04f7dcddf03f36d4f063d79ecbe544e0b1daee432d4a76cfa83dac3a1f2cb144f40a74fb85ea17cb5b778f57f709969ea5d1a2afc5bdd5aecbc9d732898d healpy-checksum = installed-with-healpix @@ -224,8 +225,8 @@ requests-checksum = 385e1d80993a21c09e7c4682500ca8c24155962ba41ecd8e73612722b2ff scipy-checksum = ed7956f5686b13689d9a8246a8c3afa64a33f993b38fe0e9ed9e880d49298fea6014f10bc3e1a280f1474155cd691ee0409d133254c5f8cd133805d41b2f1ed4 secretstorage-checksum = 295e0f75c772edf153480730dc20051f06e60e040a18f169620cb4aaa37b8c1a254a496464d3794a38cf49fa884a7b561fe364816f0d12a5b2622c77259f03cf setuptools-checksum = 92040b907eb5d15ae6a95f73c2f2229e7d4c1941c82890ce3920fcb5549240223433db6e1388b1131ba574540a55a0487ae9b802c9e43d0c1cfde699167ef3e6 -setuptools_scm-checksum = 196d4785a1802875d89b9e54ae788e791a9c5cb685109784059955b691242984e42b96d77075116790935f56be82259bc2588d95d65ecbb101261d76daddb83c setuptools-rust-checksum = cdebf61a2d55846104a3f2ff5eb0c1e268285d2e1f074dc0080b99faf74e3bfa55af9dd5ecd12aba97b37888b8bf5d7388d7b42f2b0b9e906c9860309ea5aceb +setuptools_scm-checksum = 196d4785a1802875d89b9e54ae788e791a9c5cb685109784059955b691242984e42b96d77075116790935f56be82259bc2588d95d65ecbb101261d76daddb83c sip_tpv-checksum = 5e03279cb3650dd506332dfcb31aa4a20f23f55b8a29fd18da5c6d422d1b7dc49e12362ceae2ff7417c874401b5e87a73ca1ac0f3c8747c8984e4269cad56c3f six-checksum = 903334a9dcde08d654e5bf8f2bc06aa4d72449bd2b667505b9c191c38eb5b8259233fc791215584393cc70aea92ea29035460880a6a151f5defce5db084da1af soupsieve-checksum = abdcbb6a13563e7afadd3056141587fdc3d7d644e346f789bca0a16242d860219e462491b0c624b287300af960fb8e3f85c79f5137580939a9fc8c3d6961478c @@ -246,6 +247,9 @@ wheel-checksum = 0a900806b97c368a6fdb763353c14a54e1fb629443af11432cbbaba5f2d7fa7 # 'reproduce/software/conf/versions.conf'. If you update the version and are # confident that the new version is safe to use, then you can update the # hash here. +r-cran-MASS-checksum = 0d22ff69cff1414bf52d11aefd75b442c9c8fecb343fe3733c7b28a6b881f3c87ac8b6e4b0d76709c36e612523ef386d207d403c2292881c083e03d21b3709ec +r-cran-R6-checksum = 5986510ff19c1e0129bb0b88d72020d30255e26d6da9a40c123b7b0c42c3e121188c8de34b79ad5eb0e0390eb4d59f2b7f0224b58679459bec0c4d677dec6ea9 +r-cran-RColorBrewer-checksum = 62aae85a0cf349a58ff51922886f71e2a9dc7b9548b061390f3b370f240bcec72340b3ebc03077a0374ce18ccf16121247e0500eca875ef2ab2f755c809e8f28 r-cran-cli-checksum = 29782b4cb00a94536c871276835a5f762f3deca8355c35b9366434cd2873604ea20f2746ef624eb4e6ec1514cb9079e8c101e50ace85fb1336f3befcf77be244 r-cran-colorspace-checksum = b6c24e1dd104d444e09049df61fcaac680aafc1f530bcff07fc8ce5f2bcfc9a3521aac032a506b61dd10de885a914ed82c4095ee95113e407ffd0cd43662f098 r-cran-cowplot-checksum = 39e3b29078ffa67e03911c21b4cc09a8dcfe0bf38fb180691e82f2ff87c993e78f89173a750dcf08424fa1e0ab39ae5d07fc59af792ac0333ef02cd9ea8afc03 @@ -262,13 +266,10 @@ r-cran-isoband-checksum = 253d0b768492b64d5c32ab20f3b896cfe206305b8a53b31055813b r-cran-labeling-checksum = 0ba0cb33863f79868ec6f2289f29ddc742cc620b7ed85364099448d39d71a51cce45028097100aeeaf8a8a7e4ad0982b459ef20a15faed9c5c7db79e9f9b01fe r-cran-lifecycle-checksum = 1ac7aafb41925d19abfd78f454d1acd5102a72ee7017840f14cf54d035cf3999d5b6dc2979b00214358e3c26dfac3407c8b525b434e8882c123a92a132bb07df r-cran-magrittr-checksum = b0bca6000602b90c996efc3681799a8a965a5bb90eb5e3436b7a26be15e5a219ef6300f4086f0b6efda734272775688a8ca77a4094eda429926a9179125b87c7 -r-cran-MASS-checksum = 0d22ff69cff1414bf52d11aefd75b442c9c8fecb343fe3733c7b28a6b881f3c87ac8b6e4b0d76709c36e612523ef386d207d403c2292881c083e03d21b3709ec r-cran-mgcv-checksum = 83df262152d9ee5081b3d16711b5cae3860f7dd879f97db014b987edd6b110b11219bac0e07f8ca04169181291aea76399d465b9bf0e96a1b6aaf83692fdf5bc r-cran-munsell-checksum = 59536096c637d84b80f097bf400bcbb9fcb7ddf6267ce6b026e3c7b3cbcf548caef118439a1928dd8833359a18b14e49f38fe90ea7919c28c215b3b297c036a3 r-cran-pillar-checksum = dd2bc53539ec6838cb8d5bb5ddf30cff9c43c5de0f8d148374d5a394385429a06243db48e7cf6bdb463bad7a130fb47b172ceaac8d04ca3205b4c4210ab672ff r-cran-pkgconfig-checksum = 0b636d9b1233a00974ac93eb2a1e0ad6b552fa043bfe9743ec74ef884c1d01a73c372586516abca8772a836c50dcd9eed4d10c50f6883fc68ba2494e79872aaf -r-cran-R6-checksum = 5986510ff19c1e0129bb0b88d72020d30255e26d6da9a40c123b7b0c42c3e121188c8de34b79ad5eb0e0390eb4d59f2b7f0224b58679459bec0c4d677dec6ea9 -r-cran-RColorBrewer-checksum = 62aae85a0cf349a58ff51922886f71e2a9dc7b9548b061390f3b370f240bcec72340b3ebc03077a0374ce18ccf16121247e0500eca875ef2ab2f755c809e8f28 r-cran-rlang-checksum = 8dc647e59dc767471345f9cfda7b77316215b0bf5a96e28f63e216d80f239ba9ed260b90926d175080e256d645f9a1b621d7602bfe27c32d0151758753b6cac8 r-cran-scales-checksum = a1c693f993010613a33b9a165d5f853ad5f4fbbd790deae2bd5b19adc6ea0adbf27962e0f56807297ec56a71a6a5f57e3aa0ef78c266e74dc600da34c24d16e8 r-cran-tibble-checksum = 4a4953b9083064ba10e240e304617f0b2c65039eb188f56761cfac228e99186054b543aef045607b63e5ebf9da2d20255f0ae724fd974c497507706d21a92864 diff --git a/reproduce/software/config/numpy-scipy.cfg b/reproduce/software/config/numpy-scipy.cfg index 09c1627..5ad5112 100644 --- a/reproduce/software/config/numpy-scipy.cfg +++ b/reproduce/software/config/numpy-scipy.cfg @@ -7,8 +7,8 @@ # appropriate sections. Not all packages will use all sections so you # should leave out sections that your package does not use. # -# Copyright (C) 2018-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org> -# Copyright (C) 2019-2022 Raul Infante-Sainz <infantesainz@gmail.com> +# Copyright (C) 2018-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2019-2023 Raul Infante-Sainz <infantesainz@gmail.com> # # Copying and distribution of this file, with or without modification, are # permitted in any medium without royalty provided the copyright notice and diff --git a/reproduce/software/config/servers-backup.conf b/reproduce/software/config/servers-backup.conf index 64de818..67eff44 100644 --- a/reproduce/software/config/servers-backup.conf +++ b/reproduce/software/config/servers-backup.conf @@ -3,7 +3,7 @@ # is irrelevant). Note that this is not a to be read as a variable but will # be parsed as a list. # -# Copyright (C) 2020-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2020-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # Copying and distribution of this file, with or without modification, are # permitted in any medium without royalty provided the copyright notice and diff --git a/reproduce/software/config/software_acknowledge_context.sh b/reproduce/software/config/software_acknowledge_context.sh index 4dfb407..043d9aa 100755 --- a/reproduce/software/config/software_acknowledge_context.sh +++ b/reproduce/software/config/software_acknowledge_context.sh @@ -10,8 +10,8 @@ # your project to make a smoothly readable English text. Afterwards, please # feel free to modify them as you wish. # -# Copyright (C) 2021-2022 Boud Roukema <boud@cosmo.torun.pl> -# Copyright (C) 2021-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2021-2023 Boud Roukema <boud@cosmo.torun.pl> +# Copyright (C) 2021-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # This script is free software: you can redistribute it and/or modify it # under the terms of the GNU General Public License as published by the diff --git a/reproduce/software/config/texlive-packages.conf b/reproduce/software/config/texlive-packages.conf index ff3dad0..250a4e6 100644 --- a/reproduce/software/config/texlive-packages.conf +++ b/reproduce/software/config/texlive-packages.conf @@ -4,7 +4,7 @@ # name to this variable (you can check in 'ctan.org' to find the official # name). # -# Copyright (C) 2018-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2018-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # Copying and distribution of this file, with or without modification, are # permitted in any medium without royalty provided the copyright notice and diff --git a/reproduce/software/config/texlive.conf b/reproduce/software/config/texlive.conf index 950dd4f..71878e5 100644 --- a/reproduce/software/config/texlive.conf +++ b/reproduce/software/config/texlive.conf @@ -2,7 +2,7 @@ # # installdir: Install directory # -# Copyright (C) 2018-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2018-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # Copying and distribution of this file, with or without modification, are # permitted in any medium without royalty provided the copyright notice and diff --git a/reproduce/software/config/urls.conf b/reproduce/software/config/urls.conf index 7177411..3a86d2d 100644 --- a/reproduce/software/config/urls.conf +++ b/reproduce/software/config/urls.conf @@ -3,8 +3,8 @@ # If un-commented the URLs of this file will be used. Otherwise default # servers (primarily on 'zenodo.org') will be checked for the tarball. # -# Copyright (C) 2020-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org> -# Copyright (C) 2020-2022 Raul Infante-Sainz <infantesainz@gmail.com> +# Copyright (C) 2020-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2020-2023 Raul Infante-Sainz <infantesainz@gmail.com> # # Copying and distribution of this file, with or without modification, are # permitted in any medium without royalty provided the copyright notice and @@ -41,7 +41,7 @@ #libtool-url = http://ftp.gnu.org/gnu/libtool #libunistring-url = http://ftp.gnu.org/gnu/libunistring #libxml2-url = ftp://xmlsoft.org/libxml2 -#lzip-url = http://akhlaghi.org/src +#lzip-url = https://download.savannah.gnu.org/releases/lzip/ #m4-url = http://akhlaghi.org/maneage-software #make-url = http://akhlaghi.org/src #mpc-url = http://ftp.gnu.org/gnu/mpc @@ -149,15 +149,17 @@ # Xorg packages # ------------- #fontconfig-url = https://www.freedesktop.org/software/fontconfig/release +#libice-url = https://www.x.org/archive/individual/lib/ #libpthread-stubs-url = https://xcb.freedesktop.org/dist +#libsm-url = https://www.x.org/archive/individual/lib/ #libx11-url = https://www.x.org/pub/individual/lib #libxau-url = https://www.x.org/pub/individual/lib +#libxcb-url = https://xcb.freedesktop.org/dist/ #libxdmcp-url = https://www.x.org/pub/individual/lib #libxext-url = https://www.x.org/pub/individual/lib -#libice-url = https://www.x.org/archive/individual/lib/ +#libxext-url = https://www.x.org/archive/individual/lib/ #util-macros-url = https://www.x.org/pub/individual/util #xcb-proto-url = https://xorg.freedesktop.org/archive/individual/proto -#libxcb-url = https://xcb.freedesktop.org/dist/ #xorgproto-url = https://xorg.freedesktop.org/archive/individual/proto #xtrans-url = https://www.x.org/pub/individual/lib diff --git a/reproduce/software/config/versions.conf b/reproduce/software/config/versions.conf index 04de56f..afb0535 100644 --- a/reproduce/software/config/versions.conf +++ b/reproduce/software/config/versions.conf @@ -1,8 +1,8 @@ # Versions of the various dependencies # -# Copyright (C) 2018-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org> -# Copyright (C) 2019-2022 Raul Infante-Sainz <infantesainz@gmail.com> -# Copyright (C) 2022 Pedram Ashofteh Ardakani <pedramardakani@pm.me> +# Copyright (C) 2018-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2019-2023 Raul Infante-Sainz <infantesainz@gmail.com> +# Copyright (C) 2022-2023 Pedram Ashofteh Ardakani <pedramardakani@pm.me> # # Copying and distribution of this file, with or without modification, are # permitted in any medium without royalty provided the copyright notice and @@ -17,26 +17,28 @@ # -------------------------------------------------------------- # # CLASS:BASIC (important identifier for 'awk'; don't modify this line) -bash-version = 5.1.8 -binutils-version = 2.37 +bash-version = 5.2-rc2 +binutils-version = 2.39 +bison-version = 3.8.2 coreutils-version = 9.1 -curl-version = 7.79.1 -dash-version = 0.5.11.5 +curl-version = 7.84.0 +dash-version = 0.5.11-057cd65 diffutils-version = 3.8 -file-version = 5.41 -findutils-version = 4.8.0 +file-version = 5.42 +findutils-version = 4.9.0 flock-version = 0.4.0 -gawk-version = 5.1.0 -gcc-version = 11.2.0 +gawk-version = 5.1.1 +gcc-version = 12.1.0 gettext-version = 0.21 -git-version = 2.36.0 +git-version = 2.37.1 gmp-version = 6.2.1 grep-version = 3.7 -gzip-version = 1.11 -isl-version = 0.18 +gzip-version = 1.12 +help2man-version = 1.49.2 +isl-version = 0.24 less-version = 590 -libiconv-version = 1.16 -libtool-version = 2.4.6 +libiconv-version = 1.17 +libtool-version = 2.4.7 libunistring-version = 1.0 libxml2-version = 2.9.12 lzip-version = 1.23 @@ -44,14 +46,13 @@ m4-version = 1.4.19 make-version = 4.3 mpc-version = 1.2.1 mpfr-version = 4.1.0 -nano-version = 6.0 +nano-version = 6.4 ncurses-version = 6.3 -openssl-version = 3.0.0 -patchelf-version = 0.13 -perl-version = 5.34.0 +openssl-version = 3.0.5 +perl-version = 5.36.0 pkgconfig-version = 0.29.2 podlators-version = 4.14 -readline-version = 8.1.1 +readline-version = 8.2-rc2 sed-version = 4.8 tar-version = 1.34 texinfo-version = 6.8 @@ -79,6 +80,15 @@ bzip2-version = 1.0.8 # the date that is also equal to the version. certpem-version = 2021-10-15 +# PatchELF +# -------- +# +# PatchELF 0.15 requires a C++ compiler with the 2017 standard. There are +# still systems that don't have such compilers and there hasn't been any +# Maneage-related bug in PatchELF that would need newer versions. So we'll +# stick to this version until the stdc++17 compilers are more commonly +# supported. +patchelf-version = 0.13 @@ -93,18 +103,17 @@ certpem-version = 2021-10-15 # # CLASS:HIGHLEVEL (important identifier for 'awk'; don't modify this line) apachelog4cxx-version = 0.12.1 -apr-version = 1.7.0 apr-util-version = 1.6.1 -astrometrynet-version = 0.89 +apr-version = 1.7.0 +astrometrynet-version = 0.91 atlas-version = 3.10.3 autoconf-version = 2.71 automake-version = 1.16.5 -bison-version = 3.8.2 boost-version = 1.77.0 cairo-version = 1.16.0 cdsclient-version = 3.84 -cfitsio-version = 4.0.0 -cmake-version = 3.21.4 +cfitsio-version = 4.1.0 +cmake-version = 3.24.0 eigen-version = 3.4.0 emacs-version = 28.1 expat-version = 2.4.1 @@ -112,70 +121,70 @@ fftw-version = 3.3.10 flex-version = 2.6.4-410-74a89fd freetype-version = 2.11.0 gdb-version = 11.1 -ghostscript-version = 9.55.0 ghostscript-fonts-gnu-version = 6.0 ghostscript-fonts-std-version = 8.11 -gnuastro-version = 0.16.1-e0f1 +ghostscript-version = 9.56.1 +gnuastro-version = 0.18 gperf-version = 3.1 gsl-version = 2.7 -help2man-version = 1.48.5 icu-version = 70.1 imagemagick-version = 7.1.0-13 imfit-version = 1.6.1 libbsd-version = 0.11.3 libffi-version = 3.4.2 libidn-version = 1.38 -libjpeg-version = 9d +libjpeg-version = 9e libmd-version = 1.0.4 libnsl-version = 1.2.0-4a062cf libpaper-version = 1.1.28 libpng-version = 1.6.37 -libtiff-version = 4.3.0 +libtiff-version = 4.4.0 libtirpc-version = 1.2.6 metastore-version = 1.1.2-23-fa9170b missfits-version = 2.8.0 -openblas-version = 0.3.18 +openblas-version = 0.3.21 openmpi-version = 4.1.1 openssh-version = 8.0p1 patch-version = 2.7.6 pcre-version = 8.44 pixman-version = 0.40.0 -python-version = 3.10.0 +plplot-version = 5.15.0 +python-version = 3.10.6 r-cran-version = 4.1.2 rpcsvc-proto-version = 1.4 -scamp-version = 2.6.7 +scamp-version = 2.10.0 scons-version = 3.0.5 sextractor-version = 2.25.0 -swarp-version = 2.38.0 +swarp-version = 2.41.5 swig-version = 4.0.2 tides-version = 2.0 -util-linux-version = 2.37.2 +util-linux-version = 2.38.1 valgrind-version = 3.18.1 -vim-version = 8.2 +vim-version = 9.0 +wcslib-version = 7.11 xlsxio-version = 0.2.21 yaml-version = 0.2.5 # Xorg packages -util-macros-version = 1.19.3 -xorgproto-version = 2021.5 +fontconfig-version = 2.14.0 +libice-version = 1.0.10 +libpthread-stubs-version = 0.4 +libsm-version = 1.2.3 +libx11-version = 1.8 libxau-version = 1.0.9 +libxcb-version = 1.15 libxdmcp-version = 1.1.3 -xcb-proto-version = 1.14.1 -libxcb-version = 1.14 -fontconfig-version = 2.13.94 -xtrans-version = 1.4.0 -libx11-version = 1.7.2 libxext-version = 1.3.4 -libice-version = 1.0.10 -libsm-version = 1.2.3 libxt-version = 1.2.1 -libpthread-stubs-version = 0.4 +util-macros-version = 1.19.3 +xcb-proto-version = 1.15 +xorgproto-version = 2022.1 +xtrans-version = 1.4.0 # Version-dependent build # ----------------------- lapack-version = 3.8.0 libgit2-version = 1.3.0 -wcslib-version = 7.7 # Netpbm's questions in the configure steps maybe change with different or # new versions. @@ -188,7 +197,7 @@ minizip-version = $(zlib-version) # Be careful with updateing hdf5 because h5py 2.10.0 doesn't work with # version 1.12.0. -hdf5-version = 1.10.5 +hdf5-version = 1.13.1 @@ -206,7 +215,7 @@ hdf5-version = 1.10.5 # CLASS:PYTHON-START (important identifier for 'awk'; don't modify this line) asn1crypto-version = 0.24.0 asteval-version = 0.9.16 -astropy-version = 5.0 +astropy-version = 5.1 beautifulsoup4-version = 4.10.0 beniget-version = 0.4.1 certifi-version = 2018.11.29 @@ -222,7 +231,7 @@ esutil-version = 0.6.9 extension-helpers-version = 0.1 flake8-version = 3.7.8 future-version = 0.18.1 -galsim-version = 2.3.3 +galsim-version = 2.3.5 gast-version = 0.5.3 h5py-version = 2.10.0 html5lib-version = 1.0.1 @@ -233,7 +242,6 @@ kiwisolver-version = 1.0.1 lmfit-version = 0.9.14 lsstdesccoord-version = 1.2.0 markupsafe-version = 2.0.1 -matplotlib-version = 3.3.0 mpi4py-version = 3.1.3 mpmath-version = 1.1.0 numpy-version = 1.21.3 @@ -242,18 +250,17 @@ pexpect-version = 4.7.0 pillow-version = 8.4.0 pip-version = 19.0.2 ply-version = 3.11 +pybind11-version = 2.5.0 pycodestyle-version = 2.5.0 pycparser-version = 2.19 pyerfa-version = 2.0.0.1 pyflakes-version = 2.1.1 -pybind11-version = 2.5.0 pyparsing-version = 3.0.4 pypkgconfig-version = 1.5.1 python-dateutil-version = 2.8.0 pythran-version = 0.11.0 pyyaml-version = 5.1 requests-version = 2.21.0 -scipy-version = 1.7.3 setuptools-version = 58.3.0 setuptools_scm-version = 3.3.3 sip_tpv-version = 1.1 @@ -264,6 +271,12 @@ uncertainties-version = 3.1.6 urllib3-version = 1.24.1 webencodings-version = 0.5.1 wheel-version = 0.37.0 + +# More recent versions of Matplotlib and Scipy have issues with finding +# dependencies in our Python build system. +scipy-version = 1.7.3 +matplotlib-version = 3.3.0 + # CLASS:PYTHON-END (important identifier for 'awk'; don't modify this line) # Special Python modules: @@ -309,11 +322,14 @@ wheel-version = 0.37.0 # called 'R-CRAN' (or 'r-cran') in Maneage, because searching on a single # letter string 'R' is extremely inefficient. # -# IMPORTANT: If you intend to change the version of any of the R-CRAN -# modules/libraries below, please fix the hash strings of the respective -# packages in 'reproduce/software/conf/checksums.conf'. +# IMPORTANT: Similar to all software, if you intend to change the version +# of any of the R-CRAN modules/libraries below, please fix the hash strings +# of the respective packages in 'reproduce/software/conf/checksums.conf'. # # CLASS:R-CRAN-START (important identifier for 'awk'; don't modify this line) +r-cran-MASS-version = 7.3-54 +r-cran-R6-version = 2.5.0 +r-cran-RColorBrewer-version = 1.1-2 r-cran-cli-version = 2.5.0 r-cran-colorspace-version = 2.0-1 r-cran-cowplot-version = 1.1.1 @@ -330,13 +346,10 @@ r-cran-isoband-version = 0.2.4 r-cran-labeling-version = 0.4.2 r-cran-lifecycle-version = 1.0.0 r-cran-magrittr-version = 2.0.1 -r-cran-MASS-version = 7.3-54 r-cran-mgcv-version = 1.8-36 r-cran-munsell-version = 0.5.0 r-cran-pillar-version = 1.6.1 r-cran-pkgconfig-version = 2.0.3 -r-cran-R6-version = 2.5.0 -r-cran-RColorBrewer-version = 1.1-2 r-cran-rlang-version = 0.4.11 r-cran-scales-version = 1.1.1 r-cran-tibble-version = 3.1.2 diff --git a/reproduce/software/make/README.md b/reproduce/software/make/README.md index 76ab5c1..d2b6952 100644 --- a/reproduce/software/make/README.md +++ b/reproduce/software/make/README.md @@ -1,7 +1,7 @@ Software building instructions ------------------------------ -Copyright (C) 2019-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>\ +Copyright (C) 2019-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org>\ See the end of the file for license conditions. This directory contains Makefiles that are called by the high-level diff --git a/reproduce/software/make/atlas-multiple.mk b/reproduce/software/make/atlas-multiple.mk index b92fbfc..5c8f14c 100644 --- a/reproduce/software/make/atlas-multiple.mk +++ b/reproduce/software/make/atlas-multiple.mk @@ -8,7 +8,7 @@ # # ------------------------------------------------------------------------ # -# Copyright (C) 2019-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2019-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # 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 diff --git a/reproduce/software/make/atlas-single.mk b/reproduce/software/make/atlas-single.mk index 720bad6..4e2b04a 100644 --- a/reproduce/software/make/atlas-single.mk +++ b/reproduce/software/make/atlas-single.mk @@ -8,7 +8,7 @@ # # ------------------------------------------------------------------------ # -# Copyright (C) 2019-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2019-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # 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 diff --git a/reproduce/software/make/basic.mk b/reproduce/software/make/basic.mk index d90d945..99e81d2 100644 --- a/reproduce/software/make/basic.mk +++ b/reproduce/software/make/basic.mk @@ -21,9 +21,9 @@ # # ------------------------------------------------------------------------ # -# Copyright (C) 2018-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org> -# Copyright (C) 2019-2022 Raul Infante-Sainz <infantesainz@gmail.com> -# Copyright (C) 2022 Pedram Ashofteh Ardakani <pedramardakani@pm.me> +# Copyright (C) 2018-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2019-2023 Raul Infante-Sainz <infantesainz@gmail.com> +# Copyright (C) 2022-2023 Pedram Ashofteh Ardakani <pedramardakani@pm.me> # # 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 @@ -55,6 +55,7 @@ ddir = $(BDIR)/software/build-tmp idir = $(BDIR)/software/installed ibdir = $(BDIR)/software/installed/bin ildir = $(BDIR)/software/installed/lib +iidir = $(BDIR)/software/installed/include ibidir = $(BDIR)/software/installed/version-info/proglib # Ultimate Makefile target. GNU Nano (a simple and very light-weight text @@ -87,13 +88,18 @@ export SHELL := $(ibdir)/dash export PATH := $(ibdir):$(PATH) export PKG_CONFIG_PATH := $(ildir)/pkgconfig export PKG_CONFIG_LIBDIR := $(ildir)/pkgconfig -export CPPFLAGS := -I$(idir)/include $(CPPFLAGS) \ - -Wno-nullability-completeness export LDFLAGS := $(rpath_command) -L$(ildir) $(LDFLAGS) # Disable built-in rules (which are not needed here!) .SUFFIXES: +# See description of '-Wno-nullability-completeness' in +# 'reproduce/software/shell/configure.sh'. +ifeq ($(on_mac_os),yes) + noccwarnings=-Wno-nullability-completeness +endif +export CPPFLAGS := -I$(idir)/include $(CPPFLAGS) $(noccwarnings) + # This is the "basic" tools where we are relying on the host operating # system, but are slowly populating our basic software envirnoment. To run # (system or template) programs, 'LD_LIBRARY_PATH' is necessary, so here, @@ -202,6 +208,7 @@ $(ibidir)/low-level-links: $(ibidir)/grep-$(grep-version) \ $(call makelink,xcrun) $(call makelink,sysctl) $(call makelink,sw_vers) + $(call makelink,codesign) $(call makelink,dsymutil) $(call makelink,install_name_tool) @@ -222,6 +229,10 @@ $(ibidir)/low-level-links: $(ibidir)/grep-$(grep-version) \ fi done +# Useful tools: 'ldd' (list libraries linked by binary on GNU +# systems) + $(call makelink,ldd) + # We want this to be empty (so it doesn't interefere with the other # files in 'ibidir'. touch $@ @@ -252,10 +263,46 @@ $(ibidir)/gzip-$(gzip-version): | $(ibdir) $(ildir) $(lockdir) $(call gbuild, gzip-$(gzip-version), static, , V=1) echo "GNU Gzip $(gzip-version)" > $@ +# 2022-07-14 B Roukema +# +# xz-5.2.5 fails on (at least) CentOS 7 (Redhat) systems while trying +# to compile 'cmake' in Maneage - this is Maneage bug 62700 [1]. +# +# The fix appears to be just a few lines, although it's not clear +# how robust or long-term it is. Since we don't yet have 'patch' in +# 'basic.mk', this file has to be copied into place rather than patched. + +# xz-5.2.5_src_liblzma_liblzma.map is a patched +# version of xz-5.2.5/src/liblzma/liblzma.map based on discussion at +# [1] + [2] + the patch file [3]. +# +# [1] https://savannah.nongnu.org/bugs/index.php?62700 +# [2] https://github.com/easybuilders/easybuild-easyconfigs/issues/14991 +# [3] https://raw.githubusercontent.com/easybuilders/easybuild-easyconfigs/bcebb3320ffb63f9804ca8d4d64d1822ec7c9792/easybuild/easyconfigs/x/XZ/XZ-5.2.5_compat-libs.patch $(ibidir)/xz-$(xz-version): $(ibidir)/gzip-$(gzip-version) + +# Prepare the tarball. tarball=xz-$(xz-version).tar.lz $(call import-source, $(xz-url), $(xz-checksum)) - $(call gbuild, xz-$(xz-version), static) + +# Until the bug mentioned above is fixed, we'll can't use the generic +# rule. +# $(call gbuild, xz-$(xz-version), static) + +# Configure and build with patched file. + srcdir=$$(pwd) + unpackdir=xz-$(xz-version) + patchedfile=xz-5.2.5_src_liblzma_liblzma.map + cd $(ddir) + rm -rf $$unpackdir + tar -x -f $(tdir)/$$tarball + cd $$unpackdir + cp -pv $$srcdir/reproduce/software/patches/$$patchedfile \ + src/liblzma/liblzma.map # copy the fixed file into place + ./configure --prefix=$(idir) + make install + cd .. + rm -rf $$unpackdir echo "XZ Utils $(xz-version)" > $@ $(ibidir)/bzip2-$(bzip2-version): $(ibidir)/gzip-$(gzip-version) @@ -303,26 +350,6 @@ $(ibidir)/bzip2-$(bzip2-version): $(ibidir)/gzip-$(gzip-version) ln -fs libbz2.so.$(bzip2-version) libbz2.so echo "Bzip2 $(bzip2-version)" > $@ -$(ibidir)/unzip-$(unzip-version): $(ibidir)/gzip-$(gzip-version) - tarball=unzip-$(unzip-version).tar.lz - $(call import-source, $(unzip-url), $(unzip-checksum)) - $(call gbuild, unzip-$(unzip-version), static,, \ - -f unix/Makefile generic \ - CFLAGS="-DBIG_MEM -DMMAP",,pwd, \ - -f unix/Makefile generic \ - BINDIR=$(ibdir) MANDIR=$(idir)/man/man1 ) - echo "Unzip $(unzip-version)" > $@ - -$(ibidir)/zip-$(zip-version): $(ibidir)/gzip-$(gzip-version) - tarball=zip-$(zip-version).tar.lz - $(call import-source, $(zip-url), $(zip-checksum)) - $(call gbuild, zip-$(zip-version), static,, \ - -f unix/Makefile generic \ - CFLAGS="-DBIG_MEM -DMMAP",,pwd, \ - -f unix/Makefile generic \ - BINDIR=$(ibdir) MANDIR=$(idir)/man/man1 ) - echo "Zip $(zip-version)" > $@ - # Some programs (like Wget and CMake) that use zlib need it to be dynamic # so they use our custom build. So we won't force a static-only build. # @@ -341,11 +368,9 @@ $(ibidir)/zlib-$(zlib-version): $(ibidir)/gzip-$(gzip-version) # software to be built). $(ibidir)/tar-$(tar-version): \ $(ibidir)/xz-$(xz-version) \ - $(ibidir)/zip-$(zip-version) \ $(ibidir)/gzip-$(gzip-version) \ $(ibidir)/zlib-$(zlib-version) \ - $(ibidir)/bzip2-$(bzip2-version) \ - $(ibidir)/unzip-$(unzip-version) + $(ibidir)/bzip2-$(bzip2-version) # Since all later programs depend on Tar, the configuration will hit # a bottleneck here: only making Tar. So its more efficient to built @@ -629,7 +654,7 @@ $(ibidir)/perl-$(perl-version): $(ibidir)/patchelf-$(patchelf-version) -Dcccdlflags='-fPIC' \ $(perl-conflddlflags) \ -Dldflags="$$LDFLAGS" - make -j$(numthreads) + make -j$(numthreads) V=1 make install cd .. rm -rf perl-$(perl-version) @@ -807,6 +832,8 @@ $(ibidir)/curl-$(curl-version): $(ibidir)/coreutils-$(coreutils-version) --without-librtmp \ --without-libidn2 \ --without-wolfssl \ + --without-nghttp2 \ + --without-nghttp3 \ --without-brotli \ --without-gnutls \ --without-cyassl \ @@ -814,6 +841,7 @@ $(ibidir)/curl-$(curl-version): $(ibidir)/coreutils-$(coreutils-version) --without-axtls \ --disable-ldaps \ --disable-ldap \ + --without-zstd \ --without-nss, V=1) if [ -f $(ibdir)/patchelf ]; then @@ -875,6 +903,12 @@ $(ibidir)/wget-$(wget-version): \ # process of the higher-level programs and libraries. Note that during the # building of those higher-level programs (after this Makefile finishes), # there is no access to the system's PATH. +$(ibidir)/bison-$(bison-version): $(ibidir)/help2man-$(help2man-version) + tarball=bison-$(bison-version).tar.lz + $(call import-source, $(bison-url), $(bison-checksum)) + $(call gbuild, bison-$(bison-version), static, ,V=1 -j$(numthreads)) + echo "GNU Bison $(bison-version)" > $@ + $(ibidir)/diffutils-$(diffutils-version): \ $(ibidir)/coreutils-$(coreutils-version) tarball=diffutils-$(diffutils-version).tar.lz @@ -928,6 +962,13 @@ $(ibidir)/gawk-$(gawk-version): \ # Build final target. echo "GNU AWK $(gawk-version)" > $@ +$(ibidir)/help2man-$(help2man-version): \ + $(ibidir)/coreutils-$(coreutils-version) + tarball=help2man-$(help2man-version).tar.lz + $(call import-source, $(help2man-url), $(help2man-checksum)) + $(call gbuild, help2man-$(help2man-version), static, ,V=1) + echo "Help2man $(Help2man-version)" > $@ + $(ibidir)/libiconv-$(libiconv-version): \ $(ibidir)/pkg-config-$(pkgconfig-version) tarball=libiconv-$(libiconv-version).tar.lz @@ -998,7 +1039,19 @@ $(ibidir)/gmp-$(gmp-version): \ $(ibidir)/less-$(less-version): $(ibidir)/ncurses-$(ncurses-version) tarball=less-$(less-version).tar.lz $(call import-source, $(less-url), $(less-checksum)) - $(call gbuild, less-$(less-version), static,,-j$(numthreads)) + +# Without the '--with-regex=posix' option, the build will depend on +# PCRE (perl compatible regular expressions) which are not available +# on some systems/compilers and can cause a crash. Maneage was +# successfully built with the POSIX regular expression (regex), and +# 'less' is generally, an interactive software, not a batch-mode +# software (it is just added in 'basic.mk' because Git uses it to +# display things. Again, this is an interactive meta-operation in +# maneage (operations you only do when you are developing Maneage +# within Maneage interactively, and will not affect into the actual +# reproducible analysis!) + $(call gbuild, less-$(less-version), static, \ + --with-regex=posix,-j$(numthreads)) if [ -f $(ibdir)/patchelf ]; then $(ibdir)/patchelf --set-rpath $(ildir) $(ibdir)/less; fi @@ -1032,7 +1085,7 @@ $(ibidir)/m4-$(m4-version): $(ibidir)/patchelf-$(patchelf-version) $(ibidir)/mpfr-$(mpfr-version): $(ibidir)/gmp-$(gmp-version) tarball=mpfr-$(mpfr-version).tar.lz $(call import-source, $(mpfr-url), $(mpfr-checksum)) - $(call gbuild, mpfr-$(mpfr-version), static, , , make check) + $(call gbuild, mpfr-$(mpfr-version), static) echo "GNU Multiple Precision Floating-Point Reliably $(mpfr-version)" > $@ $(ibidir)/pkg-config-$(pkgconfig-version): $(ibidir)/patchelf-$(patchelf-version) @@ -1070,6 +1123,17 @@ $(ibidir)/sed-$(sed-version): $(ibidir)/coreutils-$(coreutils-version) $(ibidir)/texinfo-$(texinfo-version): \ $(ibidir)/perl-$(perl-version) \ $(ibidir)/gettext-$(gettext-version) + +# Setting for the XS sub-package. "This is because in theory, the XS +# module could be built with a different compiler to the rest of the +# project, needing completely different flags" (part of [1]) +# +# [1] https://lists.gnu.org/archive/html/bug-texinfo/2022-08/msg00068.html + export PERL="$(ibdir)/perl" + export PERL_EXT_LDFLAGS="-L$(ildir)" + export PERL_EXT_CPPFLAGS="-I$(iidir)" + +# Basic build commands. tarball=texinfo-$(texinfo-version).tar.lz $(call import-source, $(texinfo-url), $(texinfo-checksum)) $(call gbuild, texinfo-$(texinfo-version), static) @@ -1136,6 +1200,7 @@ $(ibidir)/binutils-$(binutils-version): \ $(ibidir)/gawk-$(gawk-version) \ $(ibidir)/grep-$(grep-version) \ $(ibidir)/wget-$(wget-version) \ + $(ibidir)/bison-$(bison-version) \ $(ibidir)/which-$(which-version) \ $(ibidir)/libtool-$(libtool-version) \ $(ibidir)/texinfo-$(texinfo-version) \ @@ -1164,7 +1229,7 @@ $(ibidir)/binutils-$(binutils-version): \ # Build binutils with the standard 'gbuild' function. $(call gbuild, binutils-$(binutils-version), static, \ --with-lib-path=$(sys_library_path), \ - -j$(numthreads) ) + -j$(numthreads) V=1) # The 'ld' linker of Binutils needs several '*crt*.o' files from # the host's GNU C Library to run. On some systems these object @@ -1287,20 +1352,35 @@ $(ibidir)/gcc-$(gcc-version): $(ibidir)/binutils-$(binutils-version) current_dir=$$(pwd) # By default 'ddir' (where GCC is decompressed and built) is in the -# RAM (on systems that support '/dev/shm'). This is done to avoid -# building so many small/temporary files and possibly harming the -# hard-drive or SSD. But if the RAM doesn't have enough space, we -# should use the hard-drive or SSD. During its build GCC's build -# directory will become about 7GB (multiple of 1024 bytes, for GCC -# 11.2.0). So at this step, we are making sure we have more than -# 7.5GiB (multiple of 1000 bytes, which corresponds to 7.32GB) -# before GCC starts to build. Note that the 4th column of 'df' is -# the "available" space at the time of running, not the full -# space. So the background RAM that the OS will be using during -# Maneage is accounted for. Also consider that GCC is built alone -# (no other Maneage software is built at the same time as GCC). - in_ram=$$(df $(ddir) \ - | awk 'NR==2{print ($$4>7500000) ? "yes" : "no"}'); \ +# RAM (on systems that support a '/dev/shm' RAM disk). This is done +# to avoid building so many small/temporary files and possibly +# harming the hard-drive or SSD. But if the RAM doesn't have enough +# space, we should use the hard-drive or SSD. During its build, +# GCC's build directory will become about 7GiB (in units of 1024^3 +# bytes, for GCC 12.1.0, which corresponds to 7.5GB, in units of +# 1000^3 bytes). So at this step, we make sure that we have more +# than 12GiB before GCC starts to build. See the figure in the link +# below for GCC's RAM consumption as a function of time: +# +# https://savannah.nongnu.org/task/?16244#comment12 +# +# For POSIX portability and longevity (default sizes might change), +# we use the '-P' option, and we use the environment variable +# POSIXLY_CORRECT=1, so the 'block size' is 512 bytes. We'll also +# allow for about ~0.5 GB at the start. +# +# So we need 8 GiB * 1024^3 (B/GiB) / 512 blocks/B = 16777216 +# blocks, in blocks of 512 bytes. +# +# The 4th column of 'df' is the "available" space at the time of +# running, not the full space. So the 'RAM disk' that the OS +# will be using as "pretend" disk space (e.g. using 'tmpfs'; this +# is physically RAM, but appears as if it is disk space) +# during this stage of Maneage is accounted for. GCC is built +# alone - no other Maneage software is built at the same time as +# GCC - so this amount of RAM should be enough. + in_ram=$$(POSIXLY_CORRECT=1 df -P $(ddir) \ + | awk 'NR==2{print ($$4>16777216) ? "yes" : "no"}'); \ if [ $$in_ram = "yes" ]; then odir=$(ddir) else odir=$(BDIR)/software/build-tmp-gcc-due-to-lack-of-space @@ -1308,9 +1388,11 @@ $(ibidir)/gcc-$(gcc-version): $(ibidir)/binutils-$(binutils-version) mkdir $$odir fi -# Go into the proper directory, unpack GCC and prepare the 'build' -# directory inside it for all the built files. +# Go into the directory to uncompress GCC. cd $$odir + +# Unpack GCC and prepare the 'build' directory inside it for all +# the built files. rm -rf gcc-$(gcc-version) tar -xf $(tdir)/$$tarball if [ $$odir != $(ddir) ]; then @@ -1318,6 +1400,34 @@ $(ibidir)/gcc-$(gcc-version): $(ibidir)/binutils-$(binutils-version) fi cd gcc-$(gcc-version) +# Unfortunately binutils installs headers like 'ansidecl.h' that +# have been seen to conflict with GCC's internal versions of those +# headers. For example in the 'ansidecl.h' of Binutils 2.39, the +# 'PTR' macro isn't defined, while the same file in GCC 12.1.0 has +# defined it. Therefore, without this change, GCC will include the +# file installed from Binutils, not find what it needs and crash! +# Therefore, with the 'CPPFLAGS' modification below, we tell GCC to +# first look into its own 'include' directory before anything else. + export CPPFLAGS="-I$$(pwd)/include $(CPPFLAGS)" + +# In the GNU C Library 2.36 (which is more recent than GCC 12.1.0), +# the 'linux/mount.h' (loaded by 'linux/fs.h', which is loaded by +# 'libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cpp' +# in GCC) conflicts with 'sys/mount.h' which is directly loaded by +# the same file! This is a known conflict in glibc 2.36 (see +# [1]). As described in [1], one solution is the final job done in +# [2]. We therefore do this process here: 1) Not loading +# 'linux/fs.h', and adding the necessary macros directly. +# +# [1] https://sourceware.org/glibc/wiki/Release/2.36#Usage_of_.3Clinux.2Fmount.h.3E_and_.3Csys.2Fmount.h.3E +# [2] https://reviews.llvm.org/D129471 + sed -e's|\#include <linux/fs.h>||' \ + -e"s|FS_IOC_GETFLAGS;|_IOR('f', 1, long);|" \ + -e"s|FS_IOC_GETVERSION;|_IOR('v', 1, long);|" \ + -e"s|FS_IOC_SETFLAGS;|_IOW('f', 2, long);|" \ + -e"s|FS_IOC_SETVERSION;|_IOW('v', 2, long);|" \ + -i libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cpp + # Set the build directory for the processing. mkdir build cd build @@ -1396,6 +1506,25 @@ $(ibidir)/gcc-$(gcc-version): $(ibidir)/binutils-$(binutils-version) +# Software that need re-compilation (to use our own libraries) +$(ibidir)/lzip-$(lzip-version): $(ibidir)/gcc-$(gcc-version) + tarball=lzip-$(lzip-version).tar + unpackdir=lzip-$(lzip-version) + cd $(ddir) + rm -rf $$unpackdir + tar -xf $(tdir)/$$tarball + cd $$unpackdir + ./configure --build --check --installdir="$(ibdir)" + if [ -f $(ibdir)/patchelf ]; then + $(ibdir)/patchelf --set-rpath $(ildir) $(ibdir)/lzip; + fi + cd .. + rm -rf $$unpackdir + echo "Lzip $(lzip-version)" > $@ + + + + @@ -1418,7 +1547,7 @@ $(ibidir)/gcc-$(gcc-version): $(ibidir)/binutils-$(binutils-version) # nano (and use their own optional high-level text editor). To do this, you # can just have to manually remove 'nano' from 'targets-proglib' above and # add their optional text editor in 'TARGETS.conf'. -$(ibidir)/nano-$(nano-version): $(ibidir)/gcc-$(gcc-version) +$(ibidir)/nano-$(nano-version): $(ibidir)/lzip-$(lzip-version) tarball=nano-$(nano-version).tar.lz $(call import-source, $(nano-url), $(nano-checksum)) $(call gbuild, nano-$(nano-version), static) diff --git a/reproduce/software/make/build-rules.mk b/reproduce/software/make/build-rules.mk index c25dfb1..c160d33 100644 --- a/reproduce/software/make/build-rules.mk +++ b/reproduce/software/make/build-rules.mk @@ -3,7 +3,7 @@ # imported into 'basic.mk' and 'high-level.mk'. They should be activated # with Make's 'Call' function. # -# Copyright (C) 2018-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2018-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # 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 diff --git a/reproduce/software/make/high-level.mk b/reproduce/software/make/high-level.mk index 966ea9b..3f9c40c 100644 --- a/reproduce/software/make/high-level.mk +++ b/reproduce/software/make/high-level.mk @@ -12,8 +12,8 @@ # # ------------------------------------------------------------------------ # -# Copyright (C) 2018-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org> -# Copyright (C) 2019-2022 Raul Infante-Sainz <infantesainz@gmail.com> +# Copyright (C) 2018-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2019-2023 Raul Infante-Sainz <infantesainz@gmail.com> # # 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 @@ -49,6 +49,7 @@ ddir = $(BDIR)/software/build-tmp idir = $(BDIR)/software/installed ibdir = $(BDIR)/software/installed/bin ildir = $(BDIR)/software/installed/lib +iidir = $(BDIR)/software/installed/include ibidir = $(BDIR)/software/installed/version-info/proglib # Basic directories (specific to this Makefile). @@ -147,7 +148,6 @@ export SHELL := $(ibdir)/bash .SHELLFLAGS := --noprofile --norc -ec export LDFLAGS := $(rpath_command) -L$(ildir) export PKG_CONFIG_LIBDIR := $(ildir)/pkgconfig -export CPPFLAGS := -I$(idir)/include -Wno-nullability-completeness export PKG_CONFIG_PATH := $(ildir)/pkgconfig:$(idir)/share/pkgconfig # Disable built-in rules (which are not needed here!) @@ -160,6 +160,13 @@ export F77 := $(ibdir)/gfortran export LD_RUN_PATH := $(ildir):$(il64dir) export LD_LIBRARY_PATH := $(ildir):$(il64dir) +# See description of '-Wno-nullability-completeness' in +# 'reproduce/software/shell/configure.sh'. +ifeq ($(on_mac_os),yes) + noccwarnings=-Wno-nullability-completeness +endif +export CPPFLAGS := -I$(idir)/include $(noccwarnings) + # In macOS, if a directory exists in both 'C_INCLUDE_PATH' and 'CPPFLAGS' # it will be ignored in 'CPPFLAGS' (which has higher precedence). So, we # should not define 'C_INCLUDE_PATH' on macOS. This happened with clang @@ -429,6 +436,7 @@ $(ibidir)/cfitsio-$(cfitsio-version): echo "CFITSIO $(cfitsio-version)" > $@ $(ibidir)/cairo-$(cairo-version): \ + $(ibidir)/libxt-$(libxt-version) \ $(ibidir)/pixman-$(pixman-version) \ $(ibidir)/libpng-$(libpng-version) \ $(ibidir)/freetype-$(freetype-version) @@ -448,7 +456,8 @@ $(ibidir)/eigen-$(eigen-version): topdir=$(pwd); cd $(ddir); tar -xf $(tdir)/$$tarball cd eigen-$(eigen-version) if ! [ -d $(iidir)/eigen3 ]; then mkdir $(iidir)/eigen3; fi - cp -r Eigen/* $(iidir)/eigen3/ + cp -r Eigen/* $(iidir)/eigen3/ # Some expect 'eigen3'. + ln -s $(iidir)/eigen3 $(iidir)/Eigen # Others expect 'Eigen'. cd $$topdir rm -rf $(ddir)/eigen-$(eigen-version) echo "Eigen $(eigen-version)" > $@ @@ -529,7 +538,7 @@ $(ibidir)/gsl-$(gsl-version): $(ibidir)/hdf5-$(hdf5-version): $(ibidir)/openmpi-$(openmpi-version) export CC=mpicc export FC=mpif90 - tarball=hdf5-$(hdf5-version).tar.gz + tarball=hdf5-$(hdf5-version).tar.lz $(call import-source, $(hdf5-url), $(hdf5-checksum)) $(call gbuild, hdf5-$(hdf5-version), static, \ --enable-parallel \ @@ -907,20 +916,27 @@ $(ibidir)/wcslib-$(wcslib-version): $(ibidir)/cfitsio-$(cfitsio-version) tarball=wcslib-$(wcslib-version).tar.lz $(call import-source, $(wcslib-url), $(wcslib-checksum)) -# If Fortran isn't present, don't build WCSLIB with it. - if type gfortran &> /dev/null; then fortranopt=""; - else fortranopt="--disable-fortran" - fi - -# Build WCSLIB. +# Build WCSLIB while disabling some features: +# - Fortran is disabled because as of May 2023, on macOS systems +# where we do not install GCC (and thus a standard 'gfortran'), the +# LLVM Fortran compiler is not complete and will cause a crash. If +# you use the Fortran features of WCSLIB, feel free to remove +# '--disable-fortran', but be careful with portability on other +# systems. Hopefully some time in the future, GCC will also be +# install-able on macOS within Maneage or LLVM's 'gfortran' will +# also be complete and will not cause a crash. +# - PGPLOT is disabled because it has many manual steps in its +# installation. Therefore, we currently do not build PGPlots in +# Maneage. Once (if) it is added, we can remove '--without-pgplot'. $(call gbuild, wcslib-$(wcslib-version), , \ LIBS="-pthread -lcurl -lm" \ + --without-pgplot \ + --disable-fortran \ --with-cfitsiolib=$(ildir) \ - --with-cfitsioinc=$(idir)/include \ - --without-pgplot $$fortranopt) + --with-cfitsioinc=$(idir)/include) if [ x$(on_mac_os) = xyes ]; then - install_name_tool -id $(ildir)/libwcs.7.7.dylib \ - $(ildir)/libwcs.7.7.dylib + install_name_tool -id $(ildir)/libwcs.$(wcslib-version).dylib \ + $(ildir)/libwcs.$(wcslib-version).dylib fi echo "WCSLIB $(wcslib-version)" > $@ @@ -938,15 +954,44 @@ $(ibidir)/wcslib-$(wcslib-version): $(ibidir)/cfitsio-$(cfitsio-version) # # Astrometry-net contains a lot of programs. We need to specify the # installation directory and the Python executable (by default it will look -# for /usr/bin/python) +# for /usr/bin/python). +# +# An optional dependency is 'netpbm' but it has many dependencies and a +# crazy build system. So, it is not in the default preprequisites. If you +# need it you can add it as a prerequisite and pray that it will work. +# +# A consequence of not having 'netpbm' is that for obtaining the +# astrometric solution of one image using 'solve-field', it is necessary to +# build a catalog of sources with image coordinates and flux (x,y,flux) in +# advance. The catalog has to be sorted by flux. Finally, when invoking +# 'solve-field', the width and heigh of the original image have to be +# provided. +# +# More explicitly, raw basic steps using Gnuastro: +# +# - Obtain a catalog with image coordinates and flux (x,y,brightness): +# $ astnoisechisel img.fits -o det.fits +# $ astsegment det.fits -o seg.fits +# $ astmkcatalog seg.fits --clumpscat --x --y --brightness -o cat-raw.fits +# +# - Sort by flux: +# $ asttable cat-raw.fits --hdu 2 --sort brightness --descending \ +# --output cat.fits +# +# - Get the x-size and y-size from the header: +# $ xsize=$(astfits img.fits --keyvalue NAXIS1 --quiet) +# $ ysize=$(astfits img.fits --keyvalue NAXIS2 --quiet) +# +# - Run 'solve-field' to obtain the astrometric solution: +# $ solve-field cat.fits --width $xsize --height $ysize [--other-parameters] $(ibidir)/astrometrynet-$(astrometrynet-version): \ $(ibidir)/gsl-$(gsl-version) \ $(ibidir)/swig-$(swig-version) \ $(ipydir)/numpy-$(numpy-version) \ $(ibidir)/cairo-$(cairo-version) \ $(ibidir)/libpng-$(libpng-version) \ - $(ibidir)/netpbm-$(netpbm-version) \ $(ibidir)/wcslib-$(wcslib-version) \ + $(ipydir)/astropy-$(astropy-version) \ $(ibidir)/cfitsio-$(cfitsio-version) \ $(ibidir)/libjpeg-$(libjpeg-version) @@ -986,12 +1031,6 @@ $(ibidir)/automake-$(automake-version): $(ibidir)/autoconf-$(autoconf-version) $(call gbuild, automake-$(automake-version), static, ,V=1) echo "GNU Automake $(automake-version)" > $@ -$(ibidir)/bison-$(bison-version): $(ibidir)/help2man-$(help2man-version) - tarball=bison-$(bison-version).tar.lz - $(call import-source, $(bison-url), $(bison-checksum)) - $(call gbuild, bison-$(bison-version), static, ,V=1 -j$(numthreads)) - echo "GNU Bison $(bison-version)" > $@ - # cdsclient is a set of software written in c to interact with astronomical # database servers. It is a dependency of 'scamp' to be able to download # reference catalogues. @@ -1048,7 +1087,11 @@ $(ibidir)/cmake-$(cmake-version): $(ibidir)/flex-$(flex-version): $(ibidir)/bison-$(bison-version) tarball=flex-$(flex-version).tar.lz $(call import-source, $(flex-url), $(flex-checksum)) - $(call gbuild, flex-$(flex-version), static, ,V=1 -j$(numthreads)) + $(call gbuild, flex-$(flex-version), static, \ + --with-libiconv-prefix=$(idir) \ + --with-libintl-prefix=$(idir) \ + --disable-dependency-tracking, \ + V=1 -j$(numthreads)) echo "Flex $(flex-version)" > $@ $(ibidir)/gdb-$(gdb-version): $(ibidir)/python-$(python-version) @@ -1127,13 +1170,7 @@ $(ibidir)/gnuastro-$(gnuastro-version): \ $(call gbuild, gnuastro-$(gnuastro-version), static, , \ -j$(numthreads)) cp $(dtexdir)/gnuastro.tex $(ictdir)/ - echo "GNU Astronomy Utilities $(gnuastro-version) \citep{gnuastro}" > $@ - -$(ibidir)/help2man-$(help2man-version): - tarball=help2man-$(help2man-version).tar.lz - $(call import-source, $(help2man-url), $(help2man-checksum)) - $(call gbuild, help2man-$(help2man-version), static, ,V=1) - echo "Help2man $(Help2man-version)" > $@ + echo "GNU Astronomy Utilities $(gnuastro-version) \citep{gnuastro,akhlaghi19}" > $@ $(ibidir)/icu-$(icu-version): $(ibidir)/python-$(python-version) @@ -1167,8 +1204,25 @@ $(ibidir)/imagemagick-$(imagemagick-version): \ tarball=ImageMagick-$(imagemagick-version).tar.lz $(call import-source, $(imagemagick-url), $(imagemagick-checksum)) $(call gbuild, ImageMagick-$(imagemagick-version), static, \ - --with-gslib --without-x --disable-openmp, \ + --without-x \ + --with-gslib \ + --disable-openmp \ + --with-libstdc=$(ildir), \ V=1 -j$(numthreads)) + +# On macOS, an executable and several libraries are not properly +# linked with the Ghostscript library (libgs), so we need to fix it +# manually. + if [ x$(on_mac_os) = xyes ]; then + gsversion=$$(echo $(ghostscript-version) \ + | awk -F'.' '{print $$1"."$$2}') + libMagicks=$$(ls -l $(ildir)/libMagick*.dylib \ + | awk '/^-/{print $$NF}') + libMagicks_all="$(ibdir)/magick $$libMagicks" + for f in $$libMagicks_all; do \ + install_name_tool -change libgs.dylib.$$gsversion \ + $(ildir)/libgs.dylib.$$gsversion $$f; done + fi echo "ImageMagick $(imagemagick-version)" > $@ # 'imfit' doesn't use the traditional 'configure' and 'make' to install @@ -1280,12 +1334,12 @@ $(ibidir)/missfits-$(missfits-version): cp $(dtexdir)/missfits.tex $(ictdir)/ echo "MissFITS $(missfits-version) \citep{missfits}" > $@ -# Netpbm is a prerequisite of Astrometry-net, it contains a lot of programs. -# This program has a crazy dialogue installation which is override using the -# printf statment. Each '\n' is a new question that the installation process -# ask to the user. We give all answers with a pipe to the scripts (configure -# and install). The questions are different depending on the system (tested -# on GNU/Linux and Mac OS). +# Netpbm is an optional prerequisite of Astrometry-net, it contains a lot +# of programs. This program has a crazy dialogue installation which is +# override using the printf statment. Each '\n' is a new question that the +# installation process ask to the user. We give all answers with a pipe to +# the scripts (configure and install). The questions are different +# depending on the system (tested on GNU/Linux and Mac OS). $(ibidir)/netpbm-$(netpbm-version): \ $(ibidir)/flex-$(flex-version) \ $(ibidir)/libpng-$(libpng-version) \ @@ -1351,15 +1405,43 @@ $(ibidir)/pcre-$(pcre-version): , V=1 -j$(numthreads)) echo "Perl Compatible Regular Expressions $(pcre-version)" > $@ -# 2022-01-01 The rules for building R - identified as r-cran to avoid the -# difficulties in searching text for a one-letter string - were shifted to -# 'r-cran.mk'. +# On macOS 12.3 Monterey with AppleClang 13.1.6.13160021, Plplot 5.15.0 +# needs the 'finite' function of 'math.h' which has been deprecated in +# macOS. By manually adding "#define finite isfinite" in 'math.h' like +# below, we fixed this problem but still it can't find 'exit' during the +# configuration phase so we stopped trying to port it to macOS. It means +# that on macOS Plplot is not available. For other OSs it should be fine. +# On macOS, the file 'tmath.h' can be found with 'xcrun --show-sdk-path'. +# +# cp /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/math.h \ +# $(iidir)/math.h +# awk '{if($$0 ~ /#define isinf\(x\)/) {print "#define finite isfinite"; print $$0} else print $$0 }' \ +# $(iidir)/math.h > $(iidir)/math-tmp.h +# mv $(iidir)/math-tmp.h $(iidir)/math.h +$(ibidir)/plplot-$(plplot-version): \ + $(ibidir)/cairo-$(cairo-version) \ + $(ibidir)/freetype-$(freetype-version) + tarball=plplot-$(plplot-version).tar.lz + $(call import-source, $(plplot-url), $(plplot-checksum)) + $(call cbuild, plplot-$(plplot-version), static, \ + -DDEFAULT_NO_BINDINGS:BOOL=ON \ + -DENABLE_cxx:BOOL=ON \ + -DENABLE_fortran:BOOL=ON \ + -DDEFAULT_NO_QT_DEVICES:BOOL=ON) + echo "PLplot $(pcre-version)" > $@ # SCAMP documentation says ATLAS is a mandatory prerequisite for using # SCAMP. We have ATLAS into the project but there are some problems with the # libraries that are not yet solved. However, we tried to install it with # the option --enable-openblas and it worked (same issue happened with # 'sextractor'. +# +# Plplot in SCAMP cannot be built for macOS. See comments on top of Plplot. +# But if you are not using macOS and want to enable plots, follow the +# steps below: +# +# 1. Add '$(ibidir)/plplot-$(plplot-version)' to the prerequisites +# 2. Remove the option '--enable-plplot=no' from the call of 'gbuild' $(ibidir)/scamp-$(scamp-version): \ $(ibidir)/fftw-$(fftw-version) \ $(ibidir)/openblas-$(openblas-version) \ @@ -1429,32 +1511,56 @@ $(ibidir)/scons-$(scons-version): $(ibidir)/python-$(python-version) echo "SCons $(scons-version)" > $@ # Sextractor crashes complaining about not linking with some ATLAS -# libraries. But we can override this issue since we have Openblas +# libraries. But we can override this issue since we have OpenBLAS # installed, it is just necessary to explicity tell sextractor to use it in # the configuration step. -# -# The '-fcommon' is a necessary C compilation flag for GCC 10 and above. It -# is necessary for astromatic libraries, otherwise their build will crash. $(ibidir)/sextractor-$(sextractor-version): \ $(ibidir)/fftw-$(fftw-version) \ $(ibidir)/openblas-$(openblas-version) +# Import the source. tarball=sextractor-$(sextractor-version).tar.lz $(call import-source, $(sextractor-url), $(sextractor-checksum)) +# Unpack the tarball and enter the directory. + unpackdir=sextractor-$(sextractor-version) + cd $(ddir) + rm -rf $$unpackdir + tar -xf $(tdir)/$$tarball + cd $$unpackdir + # See comment above 'missfits' for '-fcommon'. - $(call gbuild, sextractor-$(sextractor-version), static, \ - CFLAGS="-fcommon" \ - --enable-threads \ - --enable-openblas \ - --with-openblas-libdir=$(ildir) \ - --with-openblas-incdir=$(idir)/include) + ./configure --prefix="$(idir)" \ + CFLAGS="-fcommon" \ + --enable-threads \ + --enable-openblas \ + --libdir=$(ildir) \ + --includedir=$(iidir) \ + --with-openblas-libdir=$(ildir) \ + --with-openblas-incdir=$(iidir) + +# On macOS we need to manually change 'finite' to 'isfinite' in the +# header file 'src/levmar/compiler.h'. Until this problem is +# hopefully fixed in next releases, we are doing it manually using +# 'sed'. Consequently we are not installing it using 'gbuild'. Once +# this is fixed upstream, we can use the standard 'gbuild'. + sed -i -e's|define LM_FINITE finite |define LM_FINITE isfinite |' \ + src/levmar/compiler.h + +# Build, install and delete the temporary files. + make V=1 + make install + cd .. + rm -rf $$unpackdir + +# Make links for other possibly used names, copy citation and build +# the final target. ln -fs $(ibdir)/sex $(ibdir)/sextractor ln -fs $(ibdir)/sex $(ibdir)/source-extractor cp $(dtexdir)/sextractor.tex $(ictdir)/ echo "SExtractor $(sextractor-version) \citep{sextractor}" > $@ $(ibidir)/swarp-$(swarp-version): $(ibidir)/fftw-$(fftw-version) - tarball=swarp-$(swarp-version).tar.gz + tarball=swarp-$(swarp-version).tar.lz $(call import-source, $(swarp-url), $(swarp-checksum)) # See comment above 'missfits' for '-fcommon'. @@ -1519,6 +1625,29 @@ $(ibidir)/util-linux-$(util-linux-version): | $(idircustom) cd $(ddir) tar -xf $(tdir)/$$tarball cd util-linux-$(util-linux-version) + +# If a patch exists for the current version, apply it. + if [ -f $(patchdir)/util-linux-$(util-linux-version)-macos.patch ]; then + cp $(patchdir)/util-linux-$(util-linux-version)-macos.patch \ + util-linux-$(util-linux-version)-macos.patch + git apply util-linux-$(util-linux-version)-macos.patch + fi + +# The 'mkswap' feature needs low-level file system and kernel headers +# that are not always available (in particular on older Linux +# kernels). Also, creating SWAP space will need root permissions, so +# its not something a Maneager may need! Unfortunately there is no +# configuration option to disable this so we'll have to disable it +# manually by commenting the relevant files in the +# 'configure.ac'. Having a more recent 'configure.ac' will trigger +# the './configure' script to be re-created after the first run, but +# it is pretty fast and not a problem. + sed -e's|UL_BUILD_INIT(\[mkswap\], \[yes\])|UL_BUILD_INIT(\[mkswap\], \[no\])|' \ + -i configure.ac + + +# Configure Util-linux + export CONFIG_SHELL=$(ibdir)/bash ./configure --prefix=$(idircustom)/util-linux \ --disable-dependency-tracking \ --enable-libmount-support-mtab \ @@ -1592,12 +1721,12 @@ $(ibidir)/xlsxio-$(xlsxio-version): \ # useful in projects during its development, for more see the comment above # GNU Emacs. $(ibidir)/vim-$(vim-version): - tarball=vim-$(vim-version).tar.bz2 + tarball=vim-$(vim-version).tar.lz $(call import-source, $(vim-url), $(vim-checksum)) cd $(ddir) tar -xf $(tdir)/$$tarball - n=$$(echo $(vim-version) | sed -e's|\.||') - cd $(ddir)/vim$$n + unpackdir=vim-$(vim-version) + cd $(ddir)/$$unpackdir ./configure --prefix=$(idir) \ --disable-canberra \ --enable-multibyte \ @@ -1610,9 +1739,29 @@ $(ibidir)/vim-$(vim-version): make -j$(numthreads) make install cd .. - rm -rf vim$$n + rm -rf $$unpackdir echo "VIM $(vim-version)" > $@ +$(ibidir)/unzip-$(unzip-version): $(ibidir)/gzip-$(gzip-version) + tarball=unzip-$(unzip-version).tar.lz + $(call import-source, $(unzip-url), $(unzip-checksum)) + $(call gbuild, unzip-$(unzip-version), static,, \ + -f unix/Makefile generic \ + CFLAGS="-DBIG_MEM -DMMAP",,pwd, \ + -f unix/Makefile generic \ + BINDIR=$(ibdir) MANDIR=$(idir)/man/man1 ) + echo "Unzip $(unzip-version)" > $@ + +$(ibidir)/zip-$(zip-version): $(ibidir)/gzip-$(gzip-version) + tarball=zip-$(zip-version).tar.lz + $(call import-source, $(zip-url), $(zip-checksum)) + $(call gbuild, zip-$(zip-version), static,, \ + -f unix/Makefile generic \ + CFLAGS="-DBIG_MEM -DMMAP",,pwd, \ + -f unix/Makefile generic \ + BINDIR=$(ibdir) MANDIR=$(idir)/man/man1 ) + echo "Zip $(zip-version)" > $@ + diff --git a/reproduce/software/make/python.mk b/reproduce/software/make/python.mk index 6766744..936fab1 100644 --- a/reproduce/software/make/python.mk +++ b/reproduce/software/make/python.mk @@ -12,8 +12,8 @@ # # ------------------------------------------------------------------------ # -# Copyright (C) 2019-2022 Raul Infante-Sainz <infantesainz@gmail.com> -# Copyright (C) 2019-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2019-2023 Raul Infante-Sainz <infantesainz@gmail.com> +# Copyright (C) 2019-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # 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 @@ -172,8 +172,10 @@ $(ipydir)/astroquery-$(astroquery-version): \ $(call pybuild, tar -xf, astroquery-$(astroquery-version), , \ Astroquery $(astroquery-version)) +# The optional dependency 'h5py' that is necessary for writting tables in +# HDF5 format has been removed from Astropy because on macOS it cannot be +# installed. $(ipydir)/astropy-$(astropy-version): \ - $(ipydir)/h5py-$(h5py-version) \ $(ibidir)/expat-$(expat-version) \ $(ipydir)/scipy-$(scipy-version) \ $(ipydir)/numpy-$(numpy-version) \ @@ -283,7 +285,8 @@ $(ipydir)/entrypoints-$(entrypoints-version): \ EntryPoints $(entrypoints-version)) $(ipydir)/extension-helpers-$(extension-helpers-version): \ - $(ipydir)/setuptools-$(setuptools-version) + $(ipydir)/setuptools-$(setuptools-version) \ + $(ipydir)/setuptools_scm-$(setuptools_scm-version) tarball=extension-helpers-$(extension-helpers-version).tar.lz $(call import-source, $(extension-helpers-url), $(extension-helpers-checksum)) $(call pybuild, tar -xf, extension-helpers-$(extension-helpers-version), , \ @@ -400,7 +403,9 @@ $(ipydir)/lmfit-$(lmfit-version): \ LMFIT $(lmfit-version)) $(ipydir)/lsstdesccoord-$(lsstdesccoord-version): \ - $(ipydir)/cython-$(cython-version) + $(ipydir)/cffi-$(cffi-version) \ + $(ipydir)/numpy-$(numpy-version) \ + $(ipydir)/future-$(future-version) tarball=lsstdesccoord-$(lsstdesccoord-version).tar.gz $(call import-source, $(lsstdesccoord-url), $(lsstdesccoord-checksum)) $(call pybuild, tar -xf, LSSTDESC.Coord-$(lsstdesccoord-version), , \ @@ -455,7 +460,6 @@ $(ipydir)/mpmath-$(mpmath-version): $(ipydir)/setuptools-$(setuptools-version) mpmath $(mpmath-version)) $(ipydir)/numpy-$(numpy-version): \ - $(ibidir)/unzip-$(unzip-version) \ $(ipydir)/cython-$(cython-version) \ $(ibidir)/openblas-$(openblas-version) \ $(ipydir)/setuptools-$(setuptools-version) @@ -471,7 +475,7 @@ $(ipydir)/numpy-$(numpy-version): \ $(call pybuild, tar -xf, numpy-$(numpy-version),$$conf, \ Numpy $(numpy-version)) cp $(dtexdir)/numpy.tex $(ictdir)/ - echo "Numpy $(numpy-version) \citep{numpy2011}" > $@ + echo "Numpy $(numpy-version) \citep{numpy2020}" > $@ $(ipydir)/packaging-$(packaging-version): \ $(ipydir)/pyparsing-$(pyparsing-version) @@ -532,7 +536,8 @@ $(ipydir)/pycparser-$(pycparser-version): $(ipydir)/setuptools-$(setuptools-vers $(ipydir)/pyerfa-$(pyerfa-version): \ $(ipydir)/numpy-$(numpy-version) \ - $(ipydir)/packaging-$(packaging-version) + $(ipydir)/packaging-$(packaging-version) \ + $(ipydir)/setuptools_scm-$(setuptools_scm-version) tarball=pyerfa-$(pyerfa-version).tar.lz $(call import-source, $(pyerfa-url), $(pyerfa-checksum)) $(call pybuild, tar -xf, pyerfa-$(pyerfa-version), , \ @@ -594,9 +599,12 @@ $(ipydir)/requests-$(requests-version): $(ipydir)/idna-$(idna-version) \ $(call pybuild, tar -xf, requests-$(requests-version), , \ Requests $(requests-version)) +# 'pythran' is disabled in the build of Scipy because of complications it +# caused on some systems. It is explicitly disabled using the environmental +# variable. If for some reason it is needed, set the environment variable +# to 1, and add it as a prerequisite of 'scipy'. $(ipydir)/scipy-$(scipy-version): \ $(ipydir)/numpy-$(numpy-version) \ - $(ipydir)/pythran-$(pythran-version) \ $(ipydir)/pybind11-$(pybind11-version) tarball=scipy-$(scipy-version).tar.lz $(call import-source, $(scipy-url), $(scipy-checksum)) @@ -605,10 +613,11 @@ $(ipydir)/scipy-$(scipy-version): \ else export LDFLAGS="$(LDFLAGS) -shared" fi + export SCIPY_USE_PYTHRAN=0 conf="$$(pwd)/reproduce/software/config/numpy-scipy.cfg" $(call pybuild, tar -xf, scipy-$(scipy-version),$$conf) cp $(dtexdir)/scipy.tex $(ictdir)/ - echo "Scipy $(scipy-version) \citep{scipy2007,scipy2011}" > $@ + echo "Scipy $(scipy-version) \citep{scipy2020}" > $@ $(ipydir)/secretstorage-$(secretstorage-version): \ $(ipydir)/jeepney-$(jeepney-version) \ @@ -619,7 +628,6 @@ $(ipydir)/secretstorage-$(secretstorage-version): \ SecretStorage $(secretstorage-version)) $(ipydir)/setuptools-$(setuptools-version): \ - $(ibidir)/unzip-$(unzip-version) \ $(ibidir)/python-$(python-version) tarball=setuptools-$(setuptools-version).tar.lz $(call import-source, $(setuptools-url), $(setuptools-checksum)) diff --git a/reproduce/software/make/r-cran.mk b/reproduce/software/make/r-cran.mk index 617b8de..484fe74 100644 --- a/reproduce/software/make/r-cran.mk +++ b/reproduce/software/make/r-cran.mk @@ -12,8 +12,8 @@ # # ------------------------------------------------------------------------ # -# Copyright (C) 2022 Boud Roukema <boud@cosmo.torun.pl> -# Copyright (C) 2022 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2022-2023 Boud Roukema <boud@cosmo.torun.pl> +# Copyright (C) 2022-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # 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 diff --git a/reproduce/software/make/xorg.mk b/reproduce/software/make/xorg.mk index dd707e5..1cc87a5 100644 --- a/reproduce/software/make/xorg.mk +++ b/reproduce/software/make/xorg.mk @@ -14,8 +14,8 @@ # # ------------------------------------------------------------------------ # -# Copyright (C) 2021-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org> -# Copyright (C) 2021-2022 Raul Infante-Sainz <infantesainz@gmail.com> +# Copyright (C) 2021-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2021-2023 Raul Infante-Sainz <infantesainz@gmail.com> # # 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 diff --git a/reproduce/software/patches/README.xz-5.2.5_src_liblzma_liblzma.map b/reproduce/software/patches/README.xz-5.2.5_src_liblzma_liblzma.map new file mode 100644 index 0000000..15e2787 --- /dev/null +++ b/reproduce/software/patches/README.xz-5.2.5_src_liblzma_liblzma.map @@ -0,0 +1,8 @@ +2022-07-14 B Roukema +xz-5.2.5_src_liblzma_liblzma.map is a patched version of xz-5.2.5/src/liblzma/liblzma.map +based on discussion at https://savannah.nongnu.org/bugs/index.php?62700 +and https://github.com/easybuilders/easybuild-easyconfigs/issues/14991 and +https://raw.githubusercontent.com/easybuilders/easybuild-easyconfigs/bcebb3320ffb63f9804ca8d4d64d1822ec7c9792/easybuild/easyconfigs/x/XZ/XZ-5.2.5_compat-libs.patch + +Since we don't yet have 'patch' in 'basic.mk', this file has to be copied +into place rather than patched. diff --git a/reproduce/software/patches/util-linux-2.38.1-macos.patch b/reproduce/software/patches/util-linux-2.38.1-macos.patch new file mode 100644 index 0000000..d89422d --- /dev/null +++ b/reproduce/software/patches/util-linux-2.38.1-macos.patch @@ -0,0 +1,114 @@ +From 3671d4a878fb58aa953810ecf9af41809317294f Mon Sep 17 00:00:00 2001 +From: Karel Zak <kzak@redhat.com> +Date: Mon, 4 Apr 2022 13:17:44 +0200 +Subject: [PATCH] build-sys: improve dependences for lib/procfs.c + +* add #ifdefs when use statfs() and include statfs.h or vfs.h + +Addresses: https://github.com/util-linux/util-linux/issues/1634 +Signed-off-by: Karel Zak <kzak@redhat.com> +--- + configure.ac | 2 ++ + include/statfs_magic.h | 4 +++- + lib/procfs.c | 15 +++++++++++++-- + misc-utils/hardlink.c | 2 +- + 4 files changed, 19 insertions(+), 4 deletions(-) + +diff --git a/configure.ac b/configure.ac +index 3fba95336a5b60b277d90615089093901fec723e..11c86b9a70809cbade98539b17fb2e1186984ebb 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -346,6 +346,7 @@ AC_CHECK_HEADERS([ \ + sys/socket.h \ + sys/sockio.h \ + sys/stat.h \ ++ sys/statfs.h \ + sys/swap.h \ + sys/syscall.h \ + sys/sysmacros.h \ +@@ -355,6 +356,7 @@ AC_CHECK_HEADERS([ \ + sys/types.h \ + sys/ucred.h \ + sys/un.h \ ++ sys/vfs.h \ + sys/xattr.h \ + unistd.h \ + utmp.h \ +diff --git a/include/statfs_magic.h b/include/statfs_magic.h +index b6b0225e865aeb3c04610ecab177f3e95f1cc61a..67ad0af2595862795299f0bcdb7baa5778742185 100644 +--- a/include/statfs_magic.h ++++ b/include/statfs_magic.h +@@ -1,7 +1,9 @@ + #ifndef UTIL_LINUX_STATFS_MAGIC_H + #define UTIL_LINUX_STATFS_MAGIC_H + +-#include <sys/statfs.h> ++#ifdef HAVE_SYS_STATFS_H ++# include <sys/statfs.h> ++#endif + + /* + * If possible then don't depend on internal libc __SWORD_TYPE type. +diff --git a/lib/procfs.c b/lib/procfs.c +index 4d6d25b6d78eba56aada4cd9acacee4d2e69f656..0d58857c83b378cb1cb3baf00f88f992ff8dce1e 100644 +--- a/lib/procfs.c ++++ b/lib/procfs.c +@@ -6,9 +6,13 @@ + */ + #include <ctype.h> + #include <unistd.h> +-#include <sys/vfs.h> + #include <errno.h> + ++#ifdef HAVE_SYS_VFS_H ++# include <sys/vfs.h> ++# include "statfs_magic.h" ++#endif ++ + #include "c.h" + #include "pathnames.h" + #include "procfs.h" +@@ -16,7 +20,6 @@ + #include "all-io.h" + #include "debug.h" + #include "strutils.h" +-#include "statfs_magic.h" + + static void procfs_process_deinit_path(struct path_cxt *pc); + +@@ -356,6 +359,7 @@ int procfs_dirent_match_name(DIR *procfs, struct dirent *d, const char *name) + return 0; + } + ++#ifdef HAVE_SYS_VFS_H + /* checks if fd is file in a procfs; + * returns 1 if true, 0 if false or couldn't determine */ + int fd_is_procfs(int fd) +@@ -375,7 +379,14 @@ int fd_is_procfs(int fd) + } while (ret != 0); + + return st.f_type == STATFS_PROC_MAGIC; ++ return 0; + } ++#else ++int fd_is_procfs(int fd __attribute__((__unused__))) ++{ ++ return 0; ++} ++#endif + + static char *strdup_procfs_file(pid_t pid, const char *name) + { +diff --git a/misc-utils/hardlink.c b/misc-utils/hardlink.c +index dd55af12aab7903e6025d0a39ea020c2400300e8..08af2882c1359e41fba37377a08c9a18647b0f9f 100644 +--- a/misc-utils/hardlink.c ++++ b/misc-utils/hardlink.c +@@ -38,7 +38,7 @@ + #include <ctype.h> /* tolower() */ + #include <sys/ioctl.h> + +-#if defined(HAVE_LINUX_FIEMAP_H) ++#if defined(HAVE_LINUX_FIEMAP_H) && defined(HAVE_SYS_VFS_H) + # include <linux/fs.h> + # include <linux/fiemap.h> + # ifdef FICLONE diff --git a/reproduce/software/patches/xz-5.2.5_src_liblzma_liblzma.map b/reproduce/software/patches/xz-5.2.5_src_liblzma_liblzma.map new file mode 100644 index 0000000..8df17a9 --- /dev/null +++ b/reproduce/software/patches/xz-5.2.5_src_liblzma_liblzma.map @@ -0,0 +1,115 @@ +XZ_5.0 { +global: + lzma_alone_decoder; + lzma_alone_encoder; + lzma_auto_decoder; + lzma_block_buffer_bound; + lzma_block_buffer_decode; + lzma_block_buffer_encode; + lzma_block_compressed_size; + lzma_block_decoder; + lzma_block_encoder; + lzma_block_header_decode; + lzma_block_header_encode; + lzma_block_header_size; + lzma_block_total_size; + lzma_block_unpadded_size; + lzma_check_is_supported; + lzma_check_size; + lzma_code; + lzma_crc32; + lzma_crc64; + lzma_easy_buffer_encode; + lzma_easy_decoder_memusage; + lzma_easy_encoder; + lzma_easy_encoder_memusage; + lzma_end; + lzma_filter_decoder_is_supported; + lzma_filter_encoder_is_supported; + lzma_filter_flags_decode; + lzma_filter_flags_encode; + lzma_filter_flags_size; + lzma_filters_copy; + lzma_filters_update; + lzma_get_check; + lzma_index_append; + lzma_index_block_count; + lzma_index_buffer_decode; + lzma_index_buffer_encode; + lzma_index_cat; + lzma_index_checks; + lzma_index_decoder; + lzma_index_dup; + lzma_index_encoder; + lzma_index_end; + lzma_index_file_size; + lzma_index_hash_append; + lzma_index_hash_decode; + lzma_index_hash_end; + lzma_index_hash_init; + lzma_index_hash_size; + lzma_index_init; + lzma_index_iter_init; + lzma_index_iter_locate; + lzma_index_iter_next; + lzma_index_iter_rewind; + lzma_index_memusage; + lzma_index_memused; + lzma_index_size; + lzma_index_stream_count; + lzma_index_stream_flags; + lzma_index_stream_padding; + lzma_index_stream_size; + lzma_index_total_size; + lzma_index_uncompressed_size; + lzma_lzma_preset; + lzma_memlimit_get; + lzma_memlimit_set; + lzma_memusage; + lzma_mf_is_supported; + lzma_mode_is_supported; + lzma_physmem; + lzma_properties_decode; + lzma_properties_encode; + lzma_properties_size; + lzma_raw_buffer_decode; + lzma_raw_buffer_encode; + lzma_raw_decoder; + lzma_raw_decoder_memusage; + lzma_raw_encoder; + lzma_raw_encoder_memusage; + lzma_stream_buffer_bound; + lzma_stream_buffer_decode; + lzma_stream_buffer_encode; + lzma_stream_decoder; + lzma_stream_encoder; + lzma_stream_flags_compare; + lzma_stream_footer_decode; + lzma_stream_footer_encode; + lzma_stream_header_decode; + lzma_stream_header_encode; + lzma_version_number; + lzma_version_string; + lzma_vli_decode; + lzma_vli_encode; + lzma_vli_size; +}; + +XZ_5.1.2alpha { +global: + lzma_stream_encoder_mt; + lzma_stream_encoder_mt_memusage; +} XZ_5.0; + +XZ_5.2.2 { +global: + lzma_block_uncomp_encode; + lzma_cputhreads; + lzma_get_progress; + +local: + *; +} XZ_5.1.2alpha; + +XZ_5.2 { +} XZ_5.2.2; diff --git a/reproduce/software/shell/bashrc.sh b/reproduce/software/shell/bashrc.sh index 6bb871b..814de2c 100755 --- a/reproduce/software/shell/bashrc.sh +++ b/reproduce/software/shell/bashrc.sh @@ -28,8 +28,13 @@ # When doing the project's analysis: all software have known # versions. # +# shell +# ----- +# When the user has activated the interactive shell (with './project +# shell'). # -# Copyright (C) 2019-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# +# Copyright (C) 2019-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # This script is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by @@ -43,3 +48,48 @@ # # You should have received a copy of the GNU General Public License # along with this script. If not, see <http://www.gnu.org/licenses/>. + + + + + +# Interactive mode settings. We don't want these within the pipeline +# because they are useless there (for example the introduction message or +# prompt) and can un-necessarily slow down the running jobs (recall that +# the shell is executed at the start of each recipe). +if [ x$PROJECT_STATUS = xshell ]; then + + # A small introductory message. + echo "----------------------------------------------------------------------" + echo "Welcome to the Maneage interactive shell for this project, running" + echo " $(sh --version | awk 'NR==1')" + echo + echo "This shell's home directory is the project's build directory:" + echo " HOME: $HOME" + echo + echo "This shell's startup file is in the project's source directory:" + echo " $PROJECT_RCFILE" + echo + echo "To return to your host shell, run the 'exit' command." + echo "----------------------------------------------------------------------" + + # To activate colors in generic commands. + alias ls='ls --color=auto' + alias grep='grep --color=auto' + + # Add the Git branch information to the command prompt only when Git is + # present. Also set the command-prompt color to purple for normal users + # and red when the root is running it. + if git --version &> /dev/null; then + parse_git_branch() { + git branch 2> /dev/null | sed -e '/^[^*]/d' -e 's/* \(.*\)/ (\1)/' + } + else + parse_git_branch() { echo &> /dev/null; } + fi + if [ x$(whoami) = xroot ]; then + export PS1="[\[\033[01;31m\]\u@\h \W\[\033[32m\]\$(parse_git_branch)\[\033[00m\]]# " + else + export PS1="[\[\033[01;35m\]maneage@\h \W\[\033[32m\]\$(parse_git_branch)\[\033[00m\]]$ " + fi +fi diff --git a/reproduce/software/shell/configure.sh b/reproduce/software/shell/configure.sh index b946c3b..4f71bee 100755 --- a/reproduce/software/shell/configure.sh +++ b/reproduce/software/shell/configure.sh @@ -2,9 +2,9 @@ # # Necessary preparations/configurations for the reproducible project. # -# Copyright (C) 2018-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org> -# Copyright (C) 2021-2022 Raul Infante-Sainz <infantesainz@gmail.com> -# Copyright (C) 2022 Pedram Ashofteh Ardakani <pedramardakani@pm.me> +# Copyright (C) 2018-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2021-2023 Raul Infante-Sainz <infantesainz@gmail.com> +# Copyright (C) 2022-2023 Pedram Ashofteh Ardakani <pedramardakani@pm.me> # # This script is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by @@ -446,7 +446,9 @@ if ! [ -d $compilertestdir ]; then mkdir $compilertestdir; fi # also harmless for our test here, so it is generally added. testprog=$compilertestdir/test testsource=$compilertestdir/test.c -noccwarnings="-Wno-nullability-completeness" +if [ x$on_mac_os = xyes ]; then + noccwarnings="-Wno-nullability-completeness" +fi echo; echo; echo "Checking host C compiler ('$CC')..."; cat > $testsource <<EOF #include <stdio.h> diff --git a/reproduce/software/shell/git-post-checkout b/reproduce/software/shell/git-post-checkout index d49504d..a1340d7 100755 --- a/reproduce/software/shell/git-post-checkout +++ b/reproduce/software/shell/git-post-checkout @@ -4,7 +4,7 @@ # controlled files (with each commit) using the 'metastore' program. # # Copyright (C) 2016 Przemyslaw Pawelczyk <przemoc@gmail.com> -# Copyright (C) 2018-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2018-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # This script is taken from the 'examples/hooks/pre-commit' file of the # 'metastore' package (installed within the project, with an MIT license diff --git a/reproduce/software/shell/git-pre-commit b/reproduce/software/shell/git-pre-commit index 10ad710..02ba488 100755 --- a/reproduce/software/shell/git-pre-commit +++ b/reproduce/software/shell/git-pre-commit @@ -4,7 +4,7 @@ # controlled files (with each commit) using the 'metastore' program. # # Copyright (C) 2016 Przemyslaw Pawelczyk <przemoc@gmail.com> -# Copyright (C) 2018-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2018-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # WARNING: # diff --git a/reproduce/software/shell/pre-make-build.sh b/reproduce/software/shell/pre-make-build.sh index e7de93d..808429b 100755 --- a/reproduce/software/shell/pre-make-build.sh +++ b/reproduce/software/shell/pre-make-build.sh @@ -2,7 +2,7 @@ # # Very basic tools necessary to start Maneage's default building. # -# Copyright (C) 2020-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2020-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # This script is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by @@ -230,7 +230,7 @@ build_program() { # (without compression it is just ~400Kb). So we use its '.tar' file and # won't rely on the host's compression tools at all. progname="lzip" -progname_tex="Lzip" +progname_tex="" # Lzip re-built after GCC (empty string to avoid repetition) url=$(awk '/^'$progname'-url/{print $3}' $urlfile) version=$(awk '/^'$progname'-version/{print $3}' "$versionsfile") tarball=$progname-$version.tar diff --git a/reproduce/software/shell/run-parts.in b/reproduce/software/shell/run-parts.in index a6db9e0..a7b7705 100755 --- a/reproduce/software/shell/run-parts.in +++ b/reproduce/software/shell/run-parts.in @@ -10,8 +10,8 @@ # However, it didn't have a copyright statement. So one is being added # here. # -# Copyright (C) 2022 Authors mentioned above. -# Copyright (C) 2020-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2023 Authors mentioned above. +# Copyright (C) 2020-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # This script is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by diff --git a/reproduce/software/shell/tarball-prepare.sh b/reproduce/software/shell/tarball-prepare.sh index 69e6afa..472b4c0 100755 --- a/reproduce/software/shell/tarball-prepare.sh +++ b/reproduce/software/shell/tarball-prepare.sh @@ -15,8 +15,8 @@ # # Discussion: https://savannah.nongnu.org/task/?15699 # -# Copyright (C) 2022 Mohammad Akhlaghi <mohammad@akhlaghi.org> -# Copyright (C) 2022 Pedram Ashofteh Ardakani <pedramardakani@pm.me> +# Copyright (C) 2022-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2022-2023 Pedram Ashofteh Ardakani <pedramardakani@pm.me> # Released under GNU GPLv3+ # Abort the script in case of an error. @@ -154,9 +154,10 @@ fi # Process all files for f in $allfiles; do - # Seperate name and version number - name=$(echo $f | sed -e 's/.tar.*//' \ - | awk 'BEGIN { FS = "[-_ ]" } {print $1 "-" $2}') + # Extract the name and version (while replacing any possible '_' with + # '-' because some software separate name and version with '_'). + name=$(echo $(basename $f) \ + | sed -e 's/.tar.*//' -e's/_/-/') # Skip previously packed files if [ -f $odir/$name.tar.lz ]; then @@ -202,6 +203,11 @@ for f in $allfiles; do mv * $name/ fi + # Put the current date on all the files because some packagers will not + # add dates to their release tarballs, resulting in dates of the + # Unix-time zero'th second (1970-01-01 at 00:00:00)! + touch $(find "$name"/ -type f) + # Pack with recommended options tar -c -Hustar --owner=root --group=root \ -f $name.tar $name/ @@ -215,5 +221,5 @@ for f in $allfiles; do echo $(sha512sum $odir/$name.tar.lz) # Clean up the temporary directory - rm -r $tmpdir + rm -rf $tmpdir done diff --git a/tex/README.md b/tex/README.md index 6f30839..4963bf5 100644 --- a/tex/README.md +++ b/tex/README.md @@ -1,7 +1,7 @@ Directory containing LaTeX-related files ---------------------------------------- -Copyright (C) 2018-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>\ +Copyright (C) 2018-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org>\ See the end of the file for license conditions. This directory contains directories to various components the LaTeX part of diff --git a/tex/src/delete-me-image-histogram.tex b/tex/src/delete-me-image-histogram.tex index 4648fe6..37618ec 100644 --- a/tex/src/delete-me-image-histogram.tex +++ b/tex/src/delete-me-image-histogram.tex @@ -1,6 +1,6 @@ %% Plot the demonstration image and its histogram. % -%% Copyright (C) 2019-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org> +%% Copyright (C) 2019-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org> % %% This file is free software: you can redistribute it and/or modify it %% under the terms of the GNU General Public License as published by the diff --git a/tex/src/delete-me-squared.tex b/tex/src/delete-me-squared.tex index f8e29cc..968b4d7 100644 --- a/tex/src/delete-me-squared.tex +++ b/tex/src/delete-me-squared.tex @@ -1,6 +1,6 @@ %% PGFPlots code to plot a random set of numbers as demo %% -%% Copyright (C) 2019-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org> +%% Copyright (C) 2019-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org> % %% This file is free software: you can redistribute it and/or modify it %% under the terms of the GNU General Public License as published by the diff --git a/tex/src/preamble-biblatex.tex b/tex/src/preamble-biblatex.tex index 2ac18d9..fd4bf9d 100644 --- a/tex/src/preamble-biblatex.tex +++ b/tex/src/preamble-biblatex.tex @@ -12,7 +12,7 @@ %% helps in clearly identifying the files and avoiding places that %% complain about '.bib' files. % -%% Copyright (C) 2018-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org> +%% Copyright (C) 2018-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org> % %% This file is free software: you can redistribute it and/or modify it %% under the terms of the GNU General Public License as published by the diff --git a/tex/src/preamble-maneage-default-style.tex b/tex/src/preamble-maneage-default-style.tex index 10a61ad..f811743 100644 --- a/tex/src/preamble-maneage-default-style.tex +++ b/tex/src/preamble-maneage-default-style.tex @@ -6,7 +6,7 @@ %% style defined here as a preamble. To ignore it, uncomment or delete the %% respective line in 'paper.tex'. % -%% Copyright (C) 2019-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org> +%% Copyright (C) 2019-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org> % %% This file is free software: you can redistribute it and/or modify it %% under the terms of the GNU General Public License as published by the diff --git a/tex/src/preamble-maneage.tex b/tex/src/preamble-maneage.tex index 6875e37..5dc89fe 100644 --- a/tex/src/preamble-maneage.tex +++ b/tex/src/preamble-maneage.tex @@ -1,6 +1,6 @@ %% Preamble for Maneage-related features. % -%% Copyright (C) 2020-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org> +%% Copyright (C) 2020-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org> % %% This LaTeX file is part of Maneage. Maneage is free software: you can %% redistribute it and/or modify it under the terms of the GNU General diff --git a/tex/src/preamble-pgfplots.tex b/tex/src/preamble-pgfplots.tex index c200845..86f649c 100644 --- a/tex/src/preamble-pgfplots.tex +++ b/tex/src/preamble-pgfplots.tex @@ -40,7 +40,7 @@ %% hasn't changed since the last build. TiKZ/PGFPlots won't rebuild the %% plot. % -%% Copyright (C) 2018-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org> +%% Copyright (C) 2018-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org> % %% This file is part of Maneage (https://maneage.org). % diff --git a/tex/src/preamble-project.tex b/tex/src/preamble-project.tex index a596aec..76603f2 100644 --- a/tex/src/preamble-project.tex +++ b/tex/src/preamble-project.tex @@ -4,7 +4,7 @@ %% LaTeX usages. However, if any are not needed in your work, please feel %% free to remove them. % -%% Copyright (C) 2018-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org> +%% Copyright (C) 2018-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org> %% Copyright (C) YYYY Your Name <your@email.address> % %% This file is free software: you can redistribute it and/or modify it diff --git a/tex/src/references.tex b/tex/src/references.tex index b38706b..e4117ae 100644 --- a/tex/src/references.tex +++ b/tex/src/references.tex @@ -1,7 +1,7 @@ %% Non-software BibTeX entries. The software-specific BibTeX entries are %% stored in a '*.tex' file under the 'tex/dependencies' directory. % -%% Copyright (C) 2018-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org> +%% Copyright (C) 2018-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org> % %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright @@ -13,7 +13,7 @@ {Roukema}, Boudewijn F. and {Khellat}, Mohammadreza and {Valls-Gabaud}, David and {Baena-Galle}, Roberto}, title = "{Toward Long-Term and Archivable Reproducibility}", - journal = {Computing in Science and Engineering}, + journal = {CiSE}, keywords = {Computer Science - Digital Libraries}, year = 2021, month = may, |