From 8463df97c6f26ec4d22cd5828bb0574fd5e450d2 Mon Sep 17 00:00:00 2001 From: Mohammad Akhlaghi Date: Mon, 4 Oct 2021 02:51:45 +0200 Subject: IMPORTANT: Updates to almost all software This commit primarily affects the configuration step of Maneage'd projects, and in particular, updated versions of the many of the software (see P.S.). So it shouldn't affect your high-level analysis other than the version bumps of the software you use (and the software's possibly improve/changed behavior). The following software (and thus their dependencies) couldn't be updated as described below: - Cryptography: isn't building because it depends on a new setuptools-rust package that has problems (https://savannah.nongnu.org/bugs/index.php?61731), so it has been commented in 'versions.conf'. - SecretStorage: because it depends on Cryptography. - Keyring: because it depends on SecretStorage. - Astroquery: because it depends on Keyring. This is a "squashed" commit after rebasing a development branch of 60 commits corresponding to a roughly two-month time interval. The following people contributed to this branch. - Boudewijn Roukema added all the R software infrastructure and the R packages, as well as greatly helping in fixing many bugs during the update. - Raul Infante-Sainz helped in testing and debugging the build. - Pedram Ashofteh Ardakani found and fixed a bug. - Zahra Sharbaf helped in testing and found several bugs. Below a description of the most noteworthy points is given. - Software tarballs: all updated software now have a unified format tarball (ustar; if not possible, pax) and unified compression (Lzip) in Maneage's software repository in Zenodo (https://doi.org/10.5281/zenodo.3883409). For more on this See https://savannah.nongnu.org/task/?15699 . This won't affect any extra software you would like to add; you can use any format recognized by GNU Tar, and all common compression algorithms. This new requirement is only for software that get merged to the core Maneage branch. - Metastore (and thus libbsd and libmd) moved to highlevel: Metastore (and the packages it depends on) is a high-level product that is only relevant during the project development (like Emacs!): when the user wants the file meta data (like dates) to be unchanged after checking out branches. So it should be considered a high-level software, not basic. Metastore also usually causes many more headaches and error messages, so personally, I have stopped using it! Instead I simply merge my branches in a separate clone, then pull the merge commit: in this way, the files of my project aren't re-written during the checkout phase and therefore their dates are untouched (which can conflict with Make's dates on configuration files). - The un-official cloned version of Flex (2.6.4-91 until this commit) was causing problems in the building of Netpbm, so with this commit, it has been moved back to version 2.6.4. - Netpbm's official page had version 10.73.38 as the latest stable tarball that was just released in late 2021. But I couldn't find our previously-used version 10.86.99 anywhere (to see when it was released and why we used it! Its at last more than one year old!). So the official stable version is being used now. - Improved instructions in 'README.md' for building software environment in a Docker container (while having project source and output data products on the local system; including the usage of the host's '/dev/shm' to speed up temporary operations). - Until now, the convention in Maneage was to put eight SPACE characters before the comment lines within recipes. This was done because by default GNU Emacs (also many other editors) show a TAB as eight characters. However, in other text editors, online browsers, or even the Git diff, a TAB can correspond to a different number of characters. In such cases, the Maneage recipes wouldn't look too interesting (the comments and the recipe commands would show a different indentation!). With this commit, all the comment lines in the Makefiles within the core Maneage branch have a hash ('#') as their first character and a TAB as the second. This allows the comment lines in recipes to have the same indentation as code; making the code much more easier to read in a general scenario including a 'git diff' (editor agnostic!). P.S. List of updated software with their old and new versions - Software with no version update are not mentioned. - The old version of newly added software are shown with '--'. Name (Basic) Old version New version ------------ ----------- ----------- Bzip2 1.0.6 1.0.8 CURL 7.71.1 7.79.1 Dash 0.5.10.2 0.5.11.5 File 5.39 5.41 Flock 0.2.3 0.4.0 GNU Bash 5.0.18 5.1.8 GNU Binutils 2.35 2.37 GNU Coreutils 8.32 9.0 GNU GCC 10.2.0 11.2.0 GNU M4 1.4.18 1.4.19 GNU Readline 8.0 8.1.1 GNU Tar 1.32 1.34 GNU Texinfo 6.7 6.8 GNU diffutils 3.7 3.8 GNU findutils 4.7.0 4.8.0 GNU gmp 6.2.0 6.2.1 GNU grep 3.4 3.7 GNU gzip 1.10 1.11 GNU libunistring 0.9.10 1.0 GNU mpc 1.1.0 1.2.1 GNU mpfr 4.0.2 4.1.0 GNU nano 5.2 6.0 GNU ncurses 6.2 6.3 GNU wget 1.20.3 1.21.2 Git 2.28.0 2.34.0 Less 563 590 Libxml2 2.9.9 2.9.12 Lzip 1.22-rc2 1.22 OpenSLL 1.1.1a 3.0.0 Patchelf 0.10 0.13 Perl 5.32.0 5.34.0 Podlators -- 4.14 Name (Highlevel) Old version New version ---------------- ----------- ----------- Apachelog4cxx 0.10.0-603 0.12.1 Astrometry.net 0.80 0.85 Boost 1.73.0 1.77.0 CFITSIO 3.48 4.0.0 Cmake 3.18.1 3.21.4 Eigen 3.3.7 3.4.0 Expat 2.2.9 2.4.1 FFTW 3.3.8 3.3.10 Flex 2.6.4-91 2.6.4 Fontconfig 2.13.1 2.13.94 Freetype 2.10.2 2.11.0 GNU Astronomy Utilities 0.12 0.16.1-e0f1 GNU Autoconf 2.69.200-babc 2.71 GNU Automake 1.16.2 1.16.5 GNU Bison 3.7 3.8.2 GNU Emacs 27.1 27.2 GNU GDB 9.2 11.1 GNU GSL 2.6 2.7 GNU Help2man 1.47.11 1.48.5 Ghostscript 9.52 9.55.0 ICU -- 70.1 ImageMagick 7.0.8-67 7.1.0-13 Libbsd 0.10.0 0.11.3 Libffi 3.2.1 3.4.2 Libgit2 1.0.1 1.3.0 Libidn 1.36 1.38 Libjpeg 9b 9d Libmd -- 1.0.4 Libtiff 4.0.10 4.3.0 Libx11 1.6.9 1.7.2 Libxt 1.2.0 1.2.1 Netpbm 10.86.99 10.73.38 OpenBLAS 0.3.10 0.3.18 OpenMPI 4.0.4 4.1.1 Pixman 0.38.0 0.40.0 Python 3.8.5 3.10.0 R 4.0.2 4.1.2 SWIG 3.0.12 4.0.2 Util-linux 2.35 2.37.2 Util-macros 1.19.2 1.19.3 Valgrind 3.15.0 3.18.1 WCSLIB 7.3 7.7 Xcb-proto 1.14 1.14.1 Xorgproto 2020.1 2021.5 Name (Python) Old version New version ------------- ----------- ----------- Astropy 4.0 5.0 Beautifulsoup4 4.7.1 4.10.0 Beniget -- 0.4.1 Cffi 1.12.2 1.15.0 Cryptography 2.6.1 36.0.1 Cycler 0.10.0 0.11.0+} Cython 0.29.21 0.29.24 Esutil 0.6.4 0.6.9 Extension-helpers -- 0.1 Galsim 2.2.1 2.3.3 Gast -- 0.5.3 Jinja2 -- 3.0.3 MPI4py 3.0.3 3.1.3 Markupsafe -- 2.0.1 Numpy 1.19.1 1.21.3 Packaging -- 21.3 Pillow -- 8.4.0 Ply -- 3.11 Pyerfa -- 2.0.0.1 Pyparsing 2.3.1 3.0.4 Pythran -- 0.11.0 Scipy 1.5.2 1.7.3 Setuptools 41.6.0 58.3.0 Six 1.12.0 1.16.0 Uncertainties 3.1.2 3.1.6 Wheel -- 0.37.0 Name (R) Old version New version -------- ----------- ----------- Cli -- 2.5.0 Colorspace -- 2.0-1 Cowplot -- 1.1.1 Crayon -- 1.4.1 Digest -- 0.6.27 Ellipsis -- 0.3.2 Fansi -- 0.5.0 Farver -- 2.1.0 Ggplot2 -- 3.3.4 Glue -- 1.4.2 GridExtra -- 2.3 Gtable -- 0.3.0 Isoband -- 0.2.4 Labeling -- 0.4.2 Lifecycle -- 1.0.0 Magrittr -- 2.0.1 MASS -- 7.3-54 Mgcv -- 1.8-36 Munsell -- 0.5.0 Pillar -- 1.6.1 R-Pkgconfig -- 2.0.3 R6 -- 2.5.0 RColorBrewer -- 1.1-2 Rlang -- 0.4.11 Scales -- 1.1.1 Tibble -- 3.1.2 Utf8 -- 1.2.1 Vctrs -- 0.3.8 ViridisLite -- 0.4.0 Withr -- 2.4.2 --- reproduce/analysis/bash/download-multi-try | 14 +- reproduce/analysis/config/INPUTS.conf | 2 +- .../analysis/config/delete-me-squared-num.conf | 2 +- reproduce/analysis/config/metadata.conf | 2 +- reproduce/analysis/config/pdf-build.conf | 2 +- reproduce/analysis/config/verify-outputs.conf | 2 +- reproduce/analysis/make/delete-me.mk | 64 +++---- reproduce/analysis/make/download.mk | 26 +-- reproduce/analysis/make/initialize.mk | 204 ++++++++++----------- reproduce/analysis/make/paper.mk | 83 ++++----- reproduce/analysis/make/prepare.mk | 47 +++-- reproduce/analysis/make/top-make.mk | 20 +- reproduce/analysis/make/top-prepare.mk | 20 +- reproduce/analysis/make/verify.mk | 40 ++-- 14 files changed, 262 insertions(+), 266 deletions(-) (limited to 'reproduce/analysis') diff --git a/reproduce/analysis/bash/download-multi-try b/reproduce/analysis/bash/download-multi-try index 76eb859..994a8fa 100755 --- a/reproduce/analysis/bash/download-multi-try +++ b/reproduce/analysis/bash/download-multi-try @@ -6,7 +6,7 @@ # # $ /path/to/download-multi-try downloader lockfile input-url downloaded-name # -# NOTE: The `downloader' must contain the option to specify the output name +# NOTE: The 'downloader' must contain the option to specify the output name # in its end. For example "wget -O". Any other option can also be placed in # the middle. # @@ -20,13 +20,13 @@ # world, downloading is done much faster in serial, not in parallel. But # the project's processing may be done in parallel (with multiple threads # needing to download different files at the same time). Therefore, this -# script uses the `flock' program to only do one download at a time. To +# script uses the 'flock' program to only do one download at a time. To # benefit from it, any call to this script must be given the same lock # file. If your system has multiple ports to the internet, or for any -# reason, you don't want to use a lock file, set the `lockfile' name to -# `nolock'. +# reason, you don't want to use a lock file, set the 'lockfile' name to +# 'nolock'. # -# Copyright (C) 2019-2021 Mohammad Akhlaghi +# Copyright (C) 2019-2022 Mohammad Akhlaghi # # 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 @@ -114,9 +114,9 @@ while [ ! -f "$outname" ]; do sleep $tstep fi - # Attempt downloading the file. Note that the `downloader' ends with + # Attempt downloading the file. Note that the 'downloader' ends with # the respective option to specify the output name. For example "wget - # -O" (so `outname', that comes after it) will be the name of the + # -O" (so 'outname', that comes after it) will be the name of the # downloaded file. if [ x"$lockfile" = xnolock ]; then if ! $downloader $outname $inurl; then rm -f $outname; fi diff --git a/reproduce/analysis/config/INPUTS.conf b/reproduce/analysis/config/INPUTS.conf index b969945..936f5f9 100644 --- a/reproduce/analysis/config/INPUTS.conf +++ b/reproduce/analysis/config/INPUTS.conf @@ -36,7 +36,7 @@ # (including the file-name) that can be used to download the dataset # when necessary. Also, see the description above on local filename. # -# Copyright (C) 2018-2021 Mohammad Akhlaghi +# Copyright (C) 2018-2022 Mohammad Akhlaghi # # 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/delete-me-squared-num.conf b/reproduce/analysis/config/delete-me-squared-num.conf index 13068e4..4df2101 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) 2019-2021 Mohammad Akhlaghi +# Copyright (C) 2019-2022 Mohammad Akhlaghi # # 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 aaf2ca0..0241136 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) 2020-2021 Mohammad Akhlaghi +# Copyright (C) 2020-2022 Mohammad Akhlaghi # # 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 015bf2e..a57b529 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) 2018-2021 Mohammad Akhlaghi +# Copyright (C) 2018-2022 Mohammad Akhlaghi # # 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 d96f293..37fc43c 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) 2019-2021 Mohammad Akhlaghi +# Copyright (C) 2019-2022 Mohammad Akhlaghi # # 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 c160e51..f4c8600 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) 2018-2021 Mohammad Akhlaghi +# Copyright (C) 2018-2022 Mohammad Akhlaghi # # 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 @@ -30,16 +30,16 @@ dm-squared = $(tex-publish-dir)/squared.txt $(dm-squared): $(pconfdir)/delete-me-squared-num.conf | $(tex-publish-dir) - # When the plotted values are re-made, it is necessary to also - # delete the TiKZ externalized files so the plot is also re-made by - # PGFPlots. +# When the plotted values are re-made, it is necessary to also delete +# the TiKZ externalized files so the plot is also re-made by +# PGFPlots. rm -f $(tikzdir)/delete-me-squared.pdf - # Write the column metadata in a temporary file name (appending - # '.tmp' to the actual target name). Once all steps are done, it is - # renamed to the final target. We do this because if there is an - # error in the middle, Make will not consider the job to be - # complete and will stop here. +# Write the column metadata in a temporary file name (appending +# '.tmp' to the actual target name). Once all steps are done, it is +# renamed to the final target. We do this because if there is an +# error in the middle, Make will not consider the job to be complete +# and will stop here. echo "# Data for demonstration plot of default Maneage (MANaging data linEAGE)." > $@.tmp echo "# It is a simple plot, showing the power of two: y=x^2! " >> $@.tmp echo "# " >> $@.tmp @@ -50,11 +50,11 @@ $(dm-squared): $(pconfdir)/delete-me-squared-num.conf | $(tex-publish-dir) echo "# " >> $@.tmp $(call print-general-metadata, $@.tmp) - # Generate the table of random values. +# Generate the table of random values. awk 'BEGIN {for(i=1;i<=$(delete-me-squared-num);i+=0.5) \ printf("%-8.1f%.2f\n", i, i*i); }' >> $@.tmp - # Write it into the final target +# Write it into the final target mv $@.tmp $@ @@ -71,11 +71,11 @@ $(dm-histdir): | $(texdir); mkdir $@ dm-img-pdf = $(dm-histdir)/wfpc2.pdf $(dm-img-pdf): $(dm-histdir)/%.pdf: $(indir)/%.fits | $(dm-histdir) - # When the plotted values are re-made, it is necessary to also - # delete the TiKZ externalized files so the plot is also re-made. +# When the plotted values are re-made, it is necessary to also +# delete the TiKZ externalized files so the plot is also re-made. rm -f $(tikzdir)/delete-me-image-histogram.pdf - # Convert the dataset to a PDF. +# Convert the dataset to a PDF. astconvertt --colormap=gray --fluxhigh=4 $< -h0 -o$@ @@ -92,15 +92,15 @@ dm-img-histogram = $(tex-publish-dir)/wfpc2-histogram.txt $(dm-img-histogram): $(tex-publish-dir)/%-histogram.txt: $(indir)/%.fits \ | $(tex-publish-dir) - # When the plotted values are re-made, it is necessary to also - # delete the TiKZ externalized files so the plot is also re-made. +# When the plotted values are re-made, it is necessary to also delete +# the TiKZ externalized files so the plot is also re-made. rm -f $(tikzdir)/delete-me-image-histogram.pdf - # Generate the pixel value histogram. +# Generate the pixel value histogram. aststatistics --lessthan=5 $< -h0 --histogram -o$@.data - # Put a two-line description of the dataset, copy the column - # metadata from '$@.data', and add copyright. +# Put a two-line description of the dataset, copy the column metadata +# from '$@.data', and add copyright. echo "# Histogram of example image to demonstrate Maneage (MANaging data linEAGE)." \ > $@.tmp echo "# Example image URL: $(DEMO-URL)" >> $@.tmp @@ -109,8 +109,8 @@ $(dm-img-histogram): $(tex-publish-dir)/%-histogram.txt: $(indir)/%.fits \ echo "# " >> $@.tmp $(call print-general-metadata, $@.tmp) - # Add the column numbers in a formatted manner, rename it to the - # output and clean up. +# Add the column numbers in a formatted manner, rename it to the +# output and clean up. awk '!/^#/{printf("%-15.4f%d\n", $$1, $$2)}' $@.data >> $@.tmp mv $@.tmp $@ rm $@.data @@ -123,7 +123,7 @@ $(dm-img-histogram): $(tex-publish-dir)/%-histogram.txt: $(indir)/%.fits \ # ---------------- # # This is just as a demonstration on how to get analysic configuration -# parameters from variables defined in `reproduce/analysis/config/'. +# parameters from variables defined in 'reproduce/analysis/config/'. dm-img-stats = $(dm-histdir)/wfpc2-stats.txt $(dm-img-stats): $(dm-histdir)/%-stats.txt: $(indir)/%.fits \ | $(dm-histdir) @@ -143,17 +143,17 @@ $(dm-img-stats): $(dm-histdir)/%-stats.txt: $(indir)/%.fits \ $(mtexdir)/delete-me.tex: $(dm-squared) $(dm-img-pdf) $(dm-img-histogram) \ $(dm-img-stats) - # Write the number of random values used. +# Write the number of random values used. echo "\newcommand{\deletemenum}{$(delete-me-squared-num)}" > $@ - # Note that since Make variables start with a `$(', if you want to - # use `$' within the shell (not Make), you have to quote any - # occurance of `$' with another `$'. That is why there are `$$' in - # the AWK command below. - # - # Here, we are first using AWK to find the minimum and maximum - # values, then using it again to read each separately to use in the - # macro definition. +# Note that since Make variables start with a '$(', if you want to +# use '$' within the shell (not Make), you have to quote any +# occurance of '$' with another '$'. That is why there are '$$' in +# the AWK command below. +# +# Here, we are first using AWK to find the minimum and maximum +# values, then using it again to read each separately to use in the +# macro definition. mm=$$(awk 'BEGIN{min=99999; max=-min} !/^#/{if($$2>max) max=$$2; if($$2> $@ - # Write the statistics of the demo image as a macro. +# Write the statistics of the demo image as a macro. mean=$$(awk '{printf("%.2f", $$1)}' $(dm-img-stats)) echo "\newcommand{\deletemewfpctwomean}{$$mean}" >> $@ median=$$(awk '{printf("%.2f", $$2)}' $(dm-img-stats)) diff --git a/reproduce/analysis/make/download.mk b/reproduce/analysis/make/download.mk index 0ea3432..e652c17 100644 --- a/reproduce/analysis/make/download.mk +++ b/reproduce/analysis/make/download.mk @@ -5,7 +5,7 @@ # recipes in this Makefile all use a single file lock to have one download # script running at every instant. # -# Copyright (C) 2018-2021 Mohammad Akhlaghi +# Copyright (C) 2018-2022 Mohammad Akhlaghi # # 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 @@ -28,12 +28,12 @@ # -------------------- # # The input dataset properties are defined in -# `$(pconfdir)/INPUTS.conf'. For this template we only have one dataset to +# '$(pconfdir)/INPUTS.conf'. For this template we only have one dataset to # enable easy processing, so all the extra checks in this rule may seem # redundant. # # In a real project, you will need more than one dataset. In that case, -# just add them to the target list and add an `elif' statement to define it +# just add them to the target list and add an 'elif' statement to define it # in the recipe. # # Files in a server usually have very long names, which are mainly designed @@ -48,7 +48,7 @@ # internet, therefore downloading is inherently done in series. As a # result, when more than one dataset is necessary for download, if they are # done in parallel, the speed will be slower than downloading them in -# series. We thus use the `flock' program to tie/lock the downloading +# series. We thus use the 'flock' program to tie/lock the downloading # process with a file and make sure that only one downloading event is in # progress at every moment. $(indir):; mkdir $@ @@ -56,7 +56,7 @@ downloadwrapper = $(bashdir)/download-multi-try inputdatasets = $(foreach i, wfpc2, $(indir)/$(i).fits) $(inputdatasets): $(indir)/%.fits: | $(indir) $(lockdir) - # Set the necessary parameters for this input file. +# Set the necessary parameters for this input file. if [ $* = wfpc2 ]; then localname=$(DEMO-DATA); url=$(DEMO-URL); mdf=$(DEMO-MD5); else @@ -64,13 +64,13 @@ $(inputdatasets): $(indir)/%.fits: | $(indir) $(lockdir) echo; echo; exit 1 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 the filesystem. To avoid too many links when using these files - # during processing, we'll use `readlink -f' so the link we make - # here points to the final file directly (note that `readlink' is - # part of GNU Coreutils). If its not a link, the `readlink' part - # has no effect. +# 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 +# the filesystem. To avoid too many links when using these files +# during processing, we'll use 'readlink -f' so the link we make here +# points to the final file directly (note that 'readlink' is part of +# GNU Coreutils). If its not a link, the 'readlink' part has no +# effect. unchecked=$@.unchecked if [ -f $(INDIR)/$$localname ]; then ln -fs $$(readlink -f $(INDIR)/$$localname) $$unchecked @@ -80,7 +80,7 @@ $(inputdatasets): $(indir)/%.fits: | $(indir) $(lockdir) $(lockdir)/download $$url $$unchecked fi - # Check the md5 sum to see if this is the proper dataset. +# Check the md5 sum to see if this is the proper dataset. sum=$$(md5sum $$unchecked | awk '{print $$1}') if [ $$sum = $$mdf ]; then mv $$unchecked $@ diff --git a/reproduce/analysis/make/initialize.mk b/reproduce/analysis/make/initialize.mk index 744ecbf..4823e3a 100644 --- a/reproduce/analysis/make/initialize.mk +++ b/reproduce/analysis/make/initialize.mk @@ -1,6 +1,6 @@ # Project initialization. # -# Copyright (C) 2018-2021 Mohammad Akhlaghi +# Copyright (C) 2018-2022 Mohammad Akhlaghi # # 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 @@ -25,10 +25,10 @@ # Basic directories that are used throughout the project. # # Locks are used to make sure that an operation is done in series not in -# parallel (even if Make is run in parallel with the `-j' option). The most +# parallel (even if Make is run in parallel with the '-j' option). The most # common case is downloads which are better done in series and not in # parallel. Also, some programs may not be thread-safe, therefore it will -# be necessary to put a lock on them. This project uses the `flock' program +# be necessary to put a lock on them. This project uses the 'flock' program # to achieve this. # # To help with modularity and clarity of the build directory (not mixing @@ -56,10 +56,10 @@ pconfdir = reproduce/analysis/config # Preparation phase # ----------------- # -# This Makefile is loaded both for the `prepare' phase and the `make' +# This Makefile is loaded both for the 'prepare' phase and the 'make' # phase. But the preparation files should be dealt with differently -# (depending on the phase). In the `prepare' phase, the main directory -# should be created, and in the `make' phase, its contents should be +# (depending on the phase). In the 'prepare' phase, the main directory +# should be created, and in the 'make' phase, its contents should be # loaded. # # If you don't need any preparation, please simply comment these lines. @@ -89,9 +89,9 @@ endif # create a separate LaTeX build directory for each user. # # The same logic applies to the final paper PDF: each user will create a -# separte final PDF (for example `paper-user1.pdf' and `paper-user2.pdf') -# and no `paper.pdf' will be built. This isn't a problem because -# `initialize.tex' is a .PHONY prerequisite, so the rule to build the final +# separte final PDF (for example 'paper-user1.pdf' and 'paper-user2.pdf') +# and no 'paper.pdf' will be built. This isn't a problem because +# 'initialize.tex' is a .PHONY prerequisite, so the rule to build the final # paper is always executed (even if it is present and nothing has # changed). So in terms of over-all efficiency and processing steps, this # doesn't change anything. @@ -114,7 +114,7 @@ tikzdir = $(texbdir)/tikz # --------------------------- # # Before defining the local sub-environment here, we'll need to save the -# system's environment for some scenarios (for example after `clean'ing the +# system's environment for some scenarios (for example after 'clean'ing the # built programs). curdir := $(shell echo $$(pwd)) @@ -127,16 +127,16 @@ curdir := $(shell echo $$(pwd)) # # We want the full recipe to be executed in one call to the shell. Also we # want Make to run the specific version of Bash that we have installed -# during `./project configure' time. +# during './project configure' time. # # Regarding the directories, this project builds its major dependencies # itself and doesn't use the local system's default tools. With these # environment variables, we are setting it to prefer the software we have # build here. # -# `TEXINPUTS': we have to remove all possible user-specified directories to -# avoid conflicts with existing TeX Live solutions. Later (in `paper.mk'), -# we are also going to overwrite `TEXINPUTS' just before `pdflatex'. +# 'TEXINPUTS': we have to remove all possible user-specified directories to +# avoid conflicts with existing TeX Live solutions. Later (in 'paper.mk'), +# we are also going to overwrite 'TEXINPUTS' just before 'pdflatex'. .ONESHELL: .SHELLFLAGS = -ec export TEXINPUTS := @@ -153,12 +153,12 @@ export LD_LIBRARY_PATH := $(installdir)/lib # will be empty. export CPATH := $(SYS_CPATH) -# RPATH is automatically written in macOS, so `DYLD_LIBRARY_PATH' is +# RPATH is automatically written in macOS, so 'DYLD_LIBRARY_PATH' is # ultimately redundant. But on some systems, even having a single value # causes crashs (see bug #56682). So we'll just give it no value at all. export DYLD_LIBRARY_PATH := -# OpenMPI can depend on an existing `ssh' or `rsh' binary. However, because +# OpenMPI can depend on an existing 'ssh' or 'rsh' binary. However, because # of security reasons, its best to not install them, disable any # remote-shell accesss through this environment variable. export OMPI_MCA_plm_rsh_agent=/bin/false @@ -172,7 +172,7 @@ export BASH_ENV := $(shell pwd)/reproduce/software/shell/bashrc.sh # Python enviroment # ----------------- # -# The main Python environment variable is `PYTHONPATH'. However, so far we +# The main Python environment variable is 'PYTHONPATH'. However, so far we # have found several other Python-related environment variables on some # systems which might interfere. To be safe, we are removing all their # values. @@ -196,10 +196,10 @@ export MPI_PYTHON3_SITEARCH := # directories (or possible sub-directories) for individual steps will be # defined and added within their own Makefiles. # -# The `.SUFFIXES' rule with no prerequisite is defined to eliminate all the +# The '.SUFFIXES' rule with no prerequisite is defined to eliminate all the # default implicit rules. The default implicit rules are to do with -# programming (for example converting `.c' files to `.o' files). The -# problem they cause is when you want to debug the make command with `-d' +# programming (for example converting '.c' files to '.o' files). The +# problem they cause is when you want to debug the make command with '-d' # option: they add too many extra checks that make it hard to find what you # are looking for in the outputs. .SUFFIXES: @@ -222,10 +222,10 @@ project-package-contents = $(texdir)/$(project-package-name) # High-level Makefile management # ------------------------------ # -# About `.PHONY': these are targets that must be built even if a file with +# About '.PHONY': these are targets that must be built even if a file with # their name exists. # -# Only `$(mtexdir)/initialize.tex' corresponds to a file. This is because +# Only '$(mtexdir)/initialize.tex' corresponds to a file. This is because # we want to ensure that the file is always built in every run: it contains # the project version which may change between two separate runs, even when # no file actually differs. @@ -238,14 +238,14 @@ texclean: mkdir $(texdir)/build/tikz # 'tikz' is assumed to already exist. clean: - # Delete the top-level PDF file. +# Delete the top-level PDF file. rm -f *.pdf - # Delete all the built outputs except the dependency - # programs. We'll use Bash's extended options builtin (`shopt') to - # enable "extended glob" (for listing of files). It allows extended - # features like ignoring the listing of a file with `!()' that we - # are using afterwards. +# Delete all the built outputs except the dependency programs. We'll +# use Bash's extended options builtin ('shopt') to enable "extended +# glob" (for listing of files). It allows extended features like +# ignoring the listing of a file with '!()' that we are using +# afterwards. shopt -s extglob rm -rf $(texdir)/macros/!(dependencies.tex|dependencies-bib.tex|hardware-parameters.tex) rm -rf $(badir)/!(tex) $(texdir)/!(macros|$(texbtopdir)) @@ -253,14 +253,13 @@ clean: rm -rf $(bsdir)/preparation-done.mk distclean: clean - # Without cleaning the Git hooks, we won't be able to easily - # commit or checkout after this task is done. So we'll remove them - # first. +# Without cleaning the Git hooks, we won't be able to easily commit +# or checkout after this task is done. So we'll remove them first. rm -f .git/hooks/post-checkout .git/hooks/pre-commit - # We'll be deleting the built environent programs and just need the - # `rm' program. So for this recipe, we'll use the host system's - # `rm', not our own. +# We'll be deleting the built environent programs and just need the +# 'rm' program. So for this recipe, we'll use the host system's 'rm', +# not our own. $$sys_rm -rf $(BDIR) $$sys_rm -f .local .build $(pconfdir)/LOCAL.conf @@ -277,14 +276,14 @@ distclean: clean # without having to worry about the technicalities of the analysis. $(project-package-contents): paper.pdf | $(texdir) - # Set up the output directory, delete it if it exists and remake it - # to fill with new contents. +# Set up the output directory, delete it if it exists and remake it +# to fill with new contents. dir=$@ rm -rf $$dir mkdir $$dir - # Build a small Makefile to help in automatizing the paper building - # (including the bibliography). +# Build a small Makefile to help in automatizing the paper building +# (including the bibliography). m=$$dir/Makefile echo "paper.pdf: paper.tex paper.bbl" > $$m printf "\tpdflatex -shell-escape -halt-on-error paper\n" >> $$m @@ -296,91 +295,89 @@ $(project-package-contents): paper.pdf | $(texdir) printf "\trm -f *.aux *.auxlock *.bbl *.bcf\n" >> $$m printf "\trm -f *.blg *.log *.out *.run.xml\n" >> $$m - # Copy the top-level contents (see next step for `paper.tex'). +# Copy the top-level contents (see next step for 'paper.tex'). cp COPYING project README.md README-hacking.md $$dir/ - # Since the packaging is mainly intended for high-level building of - # the PDF with LaTeX, we'll comment the `makepdf' LaTeX macro in - # the paper. This will disable usage of TiKZ. +# Since the packaging is mainly intended for high-level building of +# the PDF with LaTeX, we'll comment the 'makepdf' LaTeX macro in the +# paper. This will disable usage of TiKZ. sed -e's|\\newcommand{\\makepdf}{}|%\\newcommand{\\makepdf}{}|' \ paper.tex > $$dir/paper.tex - # Copy ONLY the version-controlled files in 'reproduce' and - # 'tex/src'. This is important because files like 'LOCAL.conf' (in - # 'reproduce/software/config') should not be archived, they contain - # information about the host computer and are irrelevant for - # others. Also some project authors may have temporary files here - # that are not under version control and thus shouldn't be archived - # (although this is bad practice, but that is up to the user). - # - # To keep the sub-directory structure, we are packaging the files - # with Tar, piping it, and unpacking it in the archive - # directory. So afterwards we need to come back to the current - # directory. +# Copy ONLY the version-controlled files in 'reproduce' and +# 'tex/src'. This is important because files like 'LOCAL.conf' (in +# 'reproduce/software/config') should not be archived, they contain +# information about the host computer and are irrelevant for +# others. Also some project authors may have temporary files here +# that are not under version control and thus shouldn't be archived +# (although this is bad practice, but that is up to the user). +# +# To keep the sub-directory structure, we are packaging the files +# with Tar, piping it, and unpacking it in the archive directory. So +# afterwards we need to come back to the current directory. tar -c -f - $$(git ls-files reproduce tex/src) \ | (cd $$dir ; tar -x -f -) cd $(curdir) - # Build the other two subdirectories of 'tex/' that we need in the - # archive (in the actual project, these are symbolic links to the - # build directory). +# Build the other two subdirectories of 'tex/' that we need in the +# archive (in the actual project, these are symbolic links to the +# build directory). mkdir $$dir/tex/tikz $$dir/tex/build - # Copy the 'tex/build' directory into the archive (excluding the - # temporary archive directory that we are now copying to). We will - # be using Bash's extended globbing ('extglob') for excluding this - # directory. +# Copy the 'tex/build' directory into the archive (excluding the +# temporary archive directory that we are now copying to). We will be +# using Bash's extended globbing ('extglob') for excluding this +# directory. shopt -s extglob cp -r tex/build/!($(project-package-name)) $$dir/tex/build - # Clean up the $(texdir)/build* directories in the archive (when - # building in a group structure, there will be `build-user1', - # `build-user2' and etc). These are just temporary LaTeX build - # files and don't have any relevant/hand-written files in them. +# Clean up the $(texdir)/build* directories in the archive (when +# building in a group structure, there will be 'build-user1', +# 'build-user2' and etc). These are just temporary LaTeX build files +# and don't have any relevant/hand-written files in them. rm -rf $$dir/tex/build/build* - # If the project has any PDFs in its 'tex/tikz' directory (TiKZ or - # PGFPlots was used to generate them), copy them too. +# If the project has any PDFs in its 'tex/tikz' directory (TiKZ or +# PGFPlots was used to generate them), copy them too. if ls tex/tikz/*.pdf &> /dev/null; then cp tex/tikz/*.pdf $$dir/tex/tikz fi - # When submitting to places like arXiv, they will just run LaTeX - # once and won't run `biber'. So we need to also keep the `.bbl' - # file into the distributing tarball. However, BibLaTeX is - # particularly sensitive to versioning (a `.bbl' file has to be - # read by the same BibLaTeX version that created it). This is hard - # to do with non-up-to-date places like arXiv. Therefore, we thus - # just copy the whole of BibLaTeX's source (the version we are - # using) into the top tarball directory. In this way, arXiv's LaTeX - # engine will use the same BibLaTeX version to interpret the `.bbl' - # file. TIP: you can use the same strategy for other LaTeX packages - # that may cause problems on the arXiv server. +# When submitting to places like arXiv, they will just run LaTeX once +# and won't run 'biber'. So we need to also keep the '.bbl' file into +# the distributing tarball. However, BibLaTeX is particularly +# sensitive to versioning (a '.bbl' file has to be read by the same +# BibLaTeX version that created it). This is hard to do with +# non-up-to-date places like arXiv. Therefore, we thus just copy the +# whole of BibLaTeX's source (the version we are using) into the top +# tarball directory. In this way, arXiv's LaTeX engine will use the +# same BibLaTeX version to interpret the '.bbl' file. TIP: you can +# use the same strategy for other LaTeX packages that may cause +# problems on the arXiv server. cp tex/build/build/paper.bbl $$dir/ tltopdir=.local/texlive/maneage/texmf-dist/tex/latex find $$tltopdir/biblatex/ -maxdepth 1 -type f -print0 \ | xargs -0 cp -t $$dir - # Just in case the package users want to rebuild some of the - # figures (manually un-comment the `makepdf' command we commented - # above), correct the TikZ external directory, so the figures can - # be rebuilt. +# Just in case the package users want to rebuild some of the figures +# (manually un-comment the 'makepdf' command we commented above), +# correct the TikZ external directory, so the figures can be rebuilt. pgfsettings="$$dir/tex/src/preamble-pgfplots.tex" sed -e's|{tikz/}|{tex/tikz/}|' $$pgfsettings > $$pgfsettings.new mv $$pgfsettings.new $$pgfsettings - # PROJECT SPECIFIC - # ---------------- - # Put any project-specific distribution steps here. +# PROJECT SPECIFIC +# ---------------- +# Put any project-specific distribution steps here. - # ---------------- +# ---------------- - # Clean temporary files that may have been created by text editors. +# Clean temporary files that may have been created by text editors. cd $(texdir) find $(project-package-name) -name \*~ -delete find $(project-package-name) -name \*.swp -delete -# Package into `.tar.gz' or '.tar.lz'. +# Package into '.tar.gz' or '.tar.lz'. dist dist-lzip: $(project-package-contents) curdir=$$(pwd) cd $(texdir) @@ -396,7 +393,7 @@ dist dist-lzip: $(project-package-contents) cd $$curdir mv $(texdir)/$(project-package-name).tar.$$suffix ./ -# Package into `.zip'. +# Package into '.zip'. dist-zip: $(project-package-contents) curdir=$$(pwd) cd $(texdir) @@ -497,13 +494,13 @@ print-general-metadata = \ # This file will store some basic info about the project that is necessary # for the final PDF. Since these are not version controlled, it must be # calculated everytime the project is run. So even though this file -# actually exists, it is also aded as a `.PHONY' target above. +# actually exists, it is also aded as a '.PHONY' target above. $(mtexdir)/initialize.tex: | $(mtexdir) - # Version and title of project. About the starting '@': since these - # commands are run every time with './project make', it is annoying - # to print them on the standard output every time. With the '@', - # make will not print the commands that it runs in this recipe. +# Version and title of project. About the starting '@': since these +# commands are run every time with './project make', it is annoying +# to print them on the standard output every time. With the '@', make +# will not print the commands that it runs in this recipe. @d=$$(git show -s --format=%aD HEAD | awk '{print $$2, $$3, $$4}') echo "\newcommand{\projectdate}{$$d}" > $@ echo "\newcommand{\projecttitle}{$(metadata-title)}" >> $@ @@ -511,16 +508,15 @@ $(mtexdir)/initialize.tex: | $(mtexdir) echo "\newcommand{\projectgitrepo}{$(metadata-git-repository)}" >> $@ echo "\newcommand{\projectcopyrightowner}{$(metadata-copyright-owner)}" >> $@ - # Calculate the latest Maneage commit used to build this - # project: - # - The project may not have the 'maneage' branch (for example - # after cloning from a fork that didn't include it!). In this - # case, we'll print a descriptive warning, telling the user what - # should be done (reporting the last merged commit and its date - # is very useful for the future). - # - The '--dirty' option (used in 'project-commit-hash') isn't - # applicable to "commit-ishes" (direct quote from Git's error - # message!). +# Calculate the latest Maneage commit used to build this project: +# - The project may not have the 'maneage' branch (for example +# after cloning from a fork that didn't include it!). In this +# case, we'll print a descriptive warning, telling the user what +# should be done (reporting the last merged commit and its date +# is very useful for the future). +# - The '--dirty' option (used in 'project-commit-hash') isn't +# applicable to "commit-ishes" (direct quote from Git's error +# message!). if git log maneage -1 &> /dev/null; then c=$$(git merge-base HEAD maneage) v=$$(git describe --always --long $$c) diff --git a/reproduce/analysis/make/paper.mk b/reproduce/analysis/make/paper.mk index b5b5b29..740dc7d 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) 2018-2021 Mohammad Akhlaghi +# Copyright (C) 2018-2022 Mohammad Akhlaghi # # 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 @@ -23,14 +23,14 @@ # # To report the input settings and results, the final report's PDF (final # target of this project) uses macros generated from various steps of the -# project. All these macros are defined through `$(mtexdir)/project.tex'. +# project. All these macros are defined through '$(mtexdir)/project.tex'. # -# `$(mtexdir)/project.tex' is actually just a combination of separate files +# '$(mtexdir)/project.tex' is actually just a combination of separate files # that keep the LaTeX macros related to each workhorse Makefile (in -# `reproduce/src/make/*.mk'). Those individual macros are pre-requisites to -# `$(mtexdir)/verify.tex' which will check them before starting to build +# 'reproduce/src/make/*.mk'). Those individual macros are pre-requisites to +# '$(mtexdir)/verify.tex' which will check them before starting to build # the paper. The only workhorse Makefile that doesn't need to produce LaTeX -# macros is this Makefile (`reproduce/src/make/paper.mk'). +# macros is this Makefile ('reproduce/src/make/paper.mk'). # # This file is thus the interface between the analysis/processing steps and # the final PDF: when we get to this point, all the processing has been @@ -38,33 +38,33 @@ # # Note that if you don't want the final PDF and just want the processing # and file outputs, you can give any value other than 'yes' to -# 'pdf-build-final' in `reproduce/analysis/config/pdf-build.conf'. +# 'pdf-build-final' in 'reproduce/analysis/config/pdf-build.conf'. $(mtexdir)/project.tex: $(mtexdir)/verify.tex - # If no PDF is requested, or if LaTeX isn't available, don't - # continue to building the final PDF. Otherwise, merge all the TeX - # macros into one for building the PDF. +# If no PDF is requested, or if LaTeX isn't available, don't continue +# to building the final PDF. Otherwise, merge all the TeX macros into +# one for building the PDF. @if [ -f .local/bin/pdflatex ] && [ x"$(pdf-build-final)" = xyes ]; then - # Put a LaTeX input command for all the necessary macro files. - # 'hardware-parameters.tex' is created in 'configure.sh'. +# Put a LaTeX input command for all the necessary macro files. +# 'hardware-parameters.tex' is created in 'configure.sh'. projecttex=$(mtexdir)/project.tex rm -f $$projecttex for t in $(subst paper,,$(makesrc)) hardware-parameters; do echo "\input{tex/build/macros/$$t.tex}" >> $$projecttex done - # Possibly highlight the '\new' parts of the text. +# Possibly highlight the '\new' parts of the text. if [ x"$(highlightnew)" = x1 ]; then echo "\newcommand{\highlightnew}{}" >> $$projecttex fi - # Possibly show the text within '\tonote'. +# Possibly show the text within '\tonote'. if [ x"$(highlightnotes)" = x1 ]; then echo "\newcommand{\highlightnotes}{}" >> $$projecttex fi - # The paper shouldn't be built. +# The paper shouldn't be built. else echo echo "-----" @@ -95,39 +95,39 @@ $(mtexdir)/project.tex: $(mtexdir)/verify.tex # The bibliography # ---------------- # -# We need to run the `biber' program on the output of LaTeX to generate the +# We need to run the 'biber' program on the output of LaTeX to generate the # necessary bibliography before making the final paper. So we'll first have -# one run of LaTeX (similar to the `paper.pdf' recipe), then `biber'. +# one run of LaTeX (similar to the 'paper.pdf' recipe), then 'biber'. # -# NOTE: `$(mtexdir)/project.tex' is an order-only-prerequisite for -# `paper.bbl'. This is because we need to run LaTeX in both the `paper.bbl' -# recipe and the `paper.pdf' recipe. But if `tex/src/references.tex' hasn't +# NOTE: '$(mtexdir)/project.tex' is an order-only-prerequisite for +# 'paper.bbl'. This is because we need to run LaTeX in both the 'paper.bbl' +# recipe and the 'paper.pdf' recipe. But if 'tex/src/references.tex' hasn't # been modified, we don't want to re-build the bibliography, only the final # PDF. $(texbdir)/paper.bbl: tex/src/references.tex $(mtexdir)/dependencies-bib.tex \ | $(mtexdir)/project.tex - # If `$(mtexdir)/project.tex' is empty, don't build PDF. +# If '$(mtexdir)/project.tex' is empty, don't build PDF. @macros=$$(cat $(mtexdir)/project.tex) if [ x"$$macros" != x ]; then - # We'll run LaTeX first to generate the `.bcf' file (necessary - # for `biber') and then run `biber' to generate the `.bbl' file. +# We'll run LaTeX first to generate the '.bcf' file (necessary for +# 'biber') and then run 'biber' to generate the '.bbl' file. p=$$(pwd) export TEXINPUTS=$$p: cd $(texbdir); - # Delete any possibly existing target (a '.bbl' file) to avoid - # complications with LaTeX being run before the command that - # generates it. Otherwise users will have to manually delete - # it. It will be built anyway once this rule is done. +# Delete any possibly existing target (a '.bbl' file) to avoid +# complications with LaTeX being run before the command that +# generates it. Otherwise users will have to manually delete it. It +# will be built anyway once this rule is done. rm -f $@ - # The pdflatex option '-shell-escape' is "normally disallowed for - # security reasons" according to the `info pdflatex' manual, but - # is enabled here in order to allow the use of PGFPlots. If you - # do not use PGFPlots, then you should remove the `-shell-escape' - # option for better security. See - # https://savannah.nongnu.org/task/?15694 for details. +# The pdflatex option '-shell-escape' is "normally disallowed for +# security reasons" according to the 'info pdflatex' manual, but is +# enabled here in order to allow the use of PGFPlots. If you do not +# use PGFPlots, then you should remove the '-shell-escape' option +# for better security. See https://savannah.nongnu.org/task/?15694 +# for details. pdflatex -shell-escape -halt-on-error "$$p"/paper.tex biber paper @@ -140,27 +140,28 @@ $(texbdir)/paper.bbl: tex/src/references.tex $(mtexdir)/dependencies-bib.tex \ # The final paper # --------------- # -# Run LaTeX in the `$(texbdir)' directory so all the intermediate and +# Run LaTeX in the '$(texbdir)' directory so all the intermediate and # auxiliary files stay there and keep the top directory clean. To be able # to run everything cleanly from there, it is necessary to add the current -# directory (top project directory) to the `TEXINPUTS' environment +# directory (top project directory) to the 'TEXINPUTS' environment # variable. paper.pdf: $(mtexdir)/project.tex paper.tex $(texbdir)/paper.bbl - # If `$(mtexdir)/project.tex' is empty, don't build the PDF. +# If '$(mtexdir)/project.tex' is empty, don't build the PDF. @macros=$$(cat $(mtexdir)/project.tex) if [ x"$$macros" != x ]; then - # Go into the top TeX build directory and make the paper. +# Go into the top TeX build directory and make the paper. p=$$(pwd) export TEXINPUTS=$$p: cd $(texbdir) - # See above for a warning and brief discussion on the the - # pdflatex option `-shell-escape'. + +# See above for a warning and brief discussion on the the pdflatex +# option '-shell-escape'. pdflatex -shell-escape -halt-on-error "$$p"/paper.tex - # Come back to the top project directory and copy the built PDF - # file here. +# Come back to the top project directory and copy the built PDF +# file here. cd "$$p" cp $(texbdir)/$@ $(final-paper) diff --git a/reproduce/analysis/make/prepare.mk b/reproduce/analysis/make/prepare.mk index d0b61d9..ecb6842 100644 --- a/reproduce/analysis/make/prepare.mk +++ b/reproduce/analysis/make/prepare.mk @@ -1,6 +1,6 @@ -# Basic preparations, called by `./project prepare'. +# Basic preparations, called by './project prepare'. # -# Copyright (C) 2019-2021 Mohammad Akhlaghi +# Copyright (C) 2019-2022 Mohammad Akhlaghi # # 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 @@ -21,30 +21,29 @@ # Final-target # -# Without this file, `./project make' won't work. +# Without this file, './project make' won't work. prepare-dep = $(subst prepare, ,$(makesrc)) $(bsdir)/preparation-done.mk: \ $(foreach s, $(prepare-dep), $(mtexdir)/$(s).tex) - # If you need to add preparations define targets above to do the - # preparations, then set the value below to `yes'. Recall that just - # like `./project make', before loading this file, `./project - # prepare' loads loads `initialize.mk' and `download.mk', so you - # can safely assume everything that is defined there in the - # preparation phase also. - # - # TIP: the targets can actually be automatically generated - # Makefiles that are used by `./project make'. They can include - # variables, or automatically generated rules. Just make sure that - # those Makefiles aren't written in the source directory. Even - # though they are Makefiles, they are automatically built, so they - # don't belong in the source. `$(prepdir)' has been defined for - # this purpose (see `initialize.mk'), we recommend that you put all - # automatically generated Makefiles under this directory. In the - # `make' phase, `initialize.mk' will automatically load all the - # `*.mk' files. If you need to load your generated - # configuration-makefiles before automatically generated Makefiles - # containing rules, you can use some naming convension like - # `conf-*.mk' and `rule-*.mk', or you can put them in - # subdirectories. +# If you need to add preparations define targets above to do the +# preparations, then set the value below to 'yes'. Recall that just +# like './project make', before loading this file, './project +# prepare' loads loads 'initialize.mk' and 'download.mk', so you can +# safely assume everything that is defined there in the preparation +# phase also. +# +# TIP: the targets can actually be automatically generated Makefiles +# that are used by './project make'. They can include variables, or +# automatically generated rules. Just make sure that those Makefiles +# aren't written in the source directory. Even though they are +# Makefiles, they are automatically built, so they don't belong in +# the source. '$(prepdir)' has been defined for this purpose (see +# 'initialize.mk'), we recommend that you put all automatically +# generated Makefiles under this directory. In the 'make' phase, +# 'initialize.mk' will automatically load all the '*.mk' files. If +# you need to load your generated configuration-makefiles before +# automatically generated Makefiles containing rules, you can use +# some naming convension like 'conf-*.mk' and 'rule-*.mk', or you can +# put them in subdirectories. @echo "include-prepare-results = no" > $@ diff --git a/reproduce/analysis/make/top-make.mk b/reproduce/analysis/make/top-make.mk index 596cc0d..4e95c54 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) 2018-2021 Mohammad Akhlaghi +# Copyright (C) 2018-2022 Mohammad Akhlaghi # # 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 @@ -20,7 +20,7 @@ # Load the local configuration (created after running -# `./project configure'). +# './project configure'). include reproduce/software/config/LOCAL.conf @@ -30,7 +30,7 @@ include reproduce/software/config/LOCAL.conf # Ultimate target of this project # ------------------------------- # -# The final paper/report (`paper.pdf') is the main target of this +# The final paper/report ('paper.pdf') is the main target of this # project. As defined in the Make paradigm, it must be the first target # that Make encounters (immediately after loading the local configuration # settings, necessary for a group building scenario mentioned next). @@ -50,8 +50,8 @@ include reproduce/software/config/LOCAL.conf # # Controlling this requires two variables that are available at this stage: # -# - `GROUP-NAME': from `LOCAL.conf' (which was built by `./project configure'). -# - `maneage_group_name': value to the `--group' option. +# - 'GROUP-NAME': from 'LOCAL.conf' (which was built by './project configure'). +# - 'maneage_group_name': value to the '--group' option. # # The analysis is only done when both have the same group name. Note that # when the project isn't being built for a group, both variables will be an @@ -63,7 +63,7 @@ include reproduce/software/config/LOCAL.conf # # If you are just interested in the processing and don't want to build the # PDF, you can skip the creation of the final PDF by giving a value of -# `yes' to `pdf-build-final' in `reproduce/analysis/config/pdf-build.conf'. +# 'yes' to 'pdf-build-final' in 'reproduce/analysis/config/pdf-build.conf'. ifeq (x$(maneage_group_name),x$(GROUP-NAME)) all: paper.pdf else @@ -87,13 +87,13 @@ endif # To keep things clean, managable and readable, each set of operations # is (and must be) classified (modularized) by context into separate # Makefiles: the more the better. These modular steps are then -# included in this top-level Makefile through the `include' command of +# included in this top-level Makefile through the 'include' command of # the next step. Each Makefile should also produce a LaTeX macro file # with the same fixed name (used to keep all the parameters and # relevant outputs of the steps in it for the final paper). # # In the rare case that no special LaTeX macros are necessary in a -# workhorse Makefile, you can simply make an empty file with `touch +# workhorse Makefile, you can simply make an empty file with 'touch # $@'. This will not add any lines to the final combined LaTeX macros # file, but will create the file that is a prerequisite to the final # paper generation. @@ -107,7 +107,7 @@ endif # IMPORTANT NOTE: order matters in the inclusion of the processing # Makefiles. As the project grows, some Makefiles will define # variables/dependencies that later Makefiles need. Therefore we are using -# a `foreach' loop in the next step to explicitly request loading them in +# a 'foreach' loop in the next step to explicitly request loading them in # the same order that they are defined here (we aren't just using a # wild-card like the configuration Makefiles). makesrc = initialize \ @@ -130,7 +130,7 @@ makesrc = initialize \ # contain rules to actually do this project's processing. # # But before that, we need to identify the phase for the Makefiles that are -# run both in `./project prepare' and `./project make'. +# run both in './project prepare' and './project make'. project-phase = make include reproduce/analysis/config/*.conf include $(foreach s,$(makesrc), reproduce/analysis/make/$(s).mk) diff --git a/reproduce/analysis/make/top-prepare.mk b/reproduce/analysis/make/top-prepare.mk index fb5700e..3950bf1 100644 --- a/reproduce/analysis/make/top-prepare.mk +++ b/reproduce/analysis/make/top-prepare.mk @@ -1,10 +1,10 @@ # Do basic preparations to optimize the project's running. # -# NOTE: This file is very similar to `top-make.mk', so the large comments +# NOTE: This file is very similar to 'top-make.mk', so the large comments # are not included here. Please see that file for thorough comments on each # step. # -# Copyright (C) 2019-2021 Mohammad Akhlaghi +# Copyright (C) 2019-2022 Mohammad Akhlaghi # # 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 @@ -24,7 +24,7 @@ # Load the local configuration (created after running -# `./project configure'). +# './project configure'). include reproduce/software/config/LOCAL.conf @@ -34,7 +34,7 @@ include reproduce/software/config/LOCAL.conf # Ultimate target of this project # ------------------------------- # -# See `top-make.mk' for complete explanation. +# See 'top-make.mk' for complete explanation. ifeq (x$(maneage_group_name),x$(GROUP-NAME)) all: $(BDIR)/software/preparation-done.mk @echo "Project preparation is complete."; @@ -57,12 +57,12 @@ endif # Define source Makefiles # ----------------------- # -# See `top-make.mk' for complete explanation. +# See 'top-make.mk' for complete explanation. # -# To ensure that `prepare' and `make' have the same basic definitions and -# environment and that all `downloads' are managed in one place, both -# `./project prepare' and `./project make' will first read `initialize.mk' -# and `downloads.mk'. +# To ensure that 'prepare' and 'make' have the same basic definitions and +# environment and that all 'downloads' are managed in one place, both +# './project prepare' and './project make' will first read 'initialize.mk' +# and 'downloads.mk'. makesrc = initialize \ download \ prepare @@ -74,7 +74,7 @@ makesrc = initialize \ # Include all analysis Makefiles # ------------------------------ # -# See `top-make.mk' for complete explanation. +# See 'top-make.mk' for complete explanation. project-phase = prepare include reproduce/analysis/config/*.conf include $(foreach s,$(makesrc), reproduce/analysis/make/$(s).mk) diff --git a/reproduce/analysis/make/verify.mk b/reproduce/analysis/make/verify.mk index 7e16add..d3f3282 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) 2020-2021 Mohammad Akhlaghi +# Copyright (C) 2020-2022 Mohammad Akhlaghi # # 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 @@ -94,7 +94,7 @@ verify-txt-no-comments-no-space = \ # (generated in various stages of the analysis. # # Since each analysis step's data files are already prerequisites of their -# respective TeX macro file, its enough for `verify.tex' to depend on the +# respective TeX macro file, its enough for 'verify.tex' to depend on the # final TeX macro. # # USEFUL TIP: during the early phases of your research (when you are @@ -103,40 +103,40 @@ verify-txt-no-comments-no-space = \ # # Here is a description of the variables defined here. # -# verify-dep: The major step dependencies of `verify.tex', this includes +# verify-dep: The major step dependencies of 'verify.tex', this includes # all the steps that must be finished before it. # # verify-changes: The files whose contents are important. This is -# essentially the same as `verify-dep', but it has removed -# the `initialize' step (which is information about the +# essentially the same as 'verify-dep', but it has removed +# the 'initialize' step (which is information about the # pipeline, not the results). verify-dep = $(subst verify,,$(subst paper,,$(makesrc))) verify-check = $(subst initialize,,$(verify-dep)) $(mtexdir)/verify.tex: $(foreach s, $(verify-dep), $(mtexdir)/$(s).tex) - # Make sure that verification is actually requested, the '@' at the - # start of the recipe is added so Make doesn't print the commands - # on the standard output because this recipe is run on every call - # to the project and can be annoying (get mixed in the middle of - # the analysis outputs or the LaTeX outputs). +# Make sure that verification is actually requested, the '@' at the +# start of the recipe is added so Make doesn't print the commands on +# the standard output because this recipe is run on every call to the +# project and can be annoying (get mixed in the middle of the +# analysis outputs or the LaTeX outputs). @if [ x"$(verify-outputs)" = xyes ]; then - # Make sure the temporary output doesn't exist (because we want - # to append to it). We are making a temporary output target so if - # there is a crash in the middle, Make will not continue. If we - # write in the final target progressively, the file will exist, - # and its date will be more recent than all prerequisites, so - # next time the project is run, Make will continue and ignore the - # rest of the checks. +# Make sure the temporary output doesn't exist (because we want to +# append to it). We are making a temporary output target so if +# there is a crash in the middle, Make will not continue. If we +# write in the final target progressively, the file will exist, and +# its date will be more recent than all prerequisites, so next time +# the project is run, Make will continue and ignore the rest of the +# checks. rm -f $@.tmp - # Verify the figure datasets. +# Verify the figure datasets. $(call verify-txt-no-comments-no-space, \ $(dm-squared), 6b6d3b0f9c351de53606507b59bca5d1, $@.tmp) $(call verify-txt-no-comments-no-space, \ $(dm-img-histogram), b1f9c413f915a1ad96078fee8767b16c, $@.tmp) - # Verify TeX macros (the values that go into the PDF text). +# Verify TeX macros (the values that go into the PDF text). for m in $(verify-check); do file=$(mtexdir)/$$m.tex if [ $$m == download ]; then s=49e4e9f049aa9da0453a67203d798587 @@ -146,7 +146,7 @@ $(mtexdir)/verify.tex: $(foreach s, $(verify-dep), $(mtexdir)/$(s).tex) $(call verify-txt-no-comments-no-space, $$file, $$s, $@.tmp) done - # Move temporary file to final target. +# Move temporary file to final target. mv $@.tmp $@ else echo "% Verification was DISABLED!" > $@ -- cgit v1.2.1