| 11b5f36 | Boud Roukema | 18 April 2021, 20:25:46 UTC | Merge branch 'maneage-d-merge' into postreferee_corrections | 18 April 2021, 20:25:46 UTC |
| 926e498 | Marius Peper | 18 April 2021, 17:31:27 UTC | Add a sentence to highlight the significant velocity of test particles away from the elaphrocentre | 18 April 2021, 17:31:27 UTC |
| a34748f | Boud Roukema | 11 April 2021, 19:22:18 UTC | Update Maneage paper reference The main Maneage paper is formally accepted. This commit inserts the journal name, inserts the year 2021, and adds the DOI (not yet live, but it's assigned and IEEE is very unlikely to make a mistake with something like a DOI). | 11 April 2021, 19:22:18 UTC |
| 7c9a7e3 | Boud Roukema | 10 April 2021, 21:26:08 UTC | Merge branch 'maneage' into maneage-d-merge This merge has not yet been tested. You have been warned! | 10 April 2021, 21:26:08 UTC |
| 0280929 | Boud Roukema | 08 April 2021, 21:31:55 UTC | Acknowledgments; label fonts This commit adds the anonymous referee to our acknowledgments; converts the subscript 'eff' to roman font for several figures; and switches from Mph/h (miles per hour per hubble constant?) to the more conventional Mpc/h. | 08 April 2021, 21:31:55 UTC |
| fd947c4 | Boud Roukema | 08 April 2021, 19:45:01 UTC | Fix --remove-some-fits and replace dist-mnras This commit fixes a minor bug in '--remove-some-fits, and appears to work correctly for me. The 'dist-mnras' rule is removed, and instead, the 'paper-full.pdf' command should cause '$(project-package-name)-journal.tar.gz' to be created for simple enough journal submission formats. | 08 April 2021, 19:45:16 UTC |
| f497df0 | Boud Roukema | 08 April 2021, 13:48:25 UTC | Add rule for dist-mnras This commit adds a rule for './project make dist-mnras' to `reproduce/analysis/make/initialize.mk`, for creating the .tar.gz package for MNRAS resubmission. Two plot files that haven't been used for a long time are removed by this commit from the list of postscript files in `reproduce/analysis/make/analyse-plot.mk`. | 08 April 2021, 13:48:25 UTC |
| e989af9 | Boud Roukema | 08 April 2021, 13:26:02 UTC | Merge branch 'postreferee_corrections' of codeberg:boud/elaphrocentre into postreferee_corrections | 08 April 2021, 13:26:02 UTC |
| 6193ac2 | Boud Roukema | 08 April 2021, 13:19:58 UTC | First try at --remove-some-fits option This commit has not yet been tested; it attempts to implement the '--remove-some-fits' option, so that default plotting and inclusion in the paper avoids selection bias, but the referee's preference can optionally be enabled, as an opt-in option. modified: paper.tex modified: project modified: reproduce/analysis/make/analyse-plot.mk modified: reproduce/analysis/make/paper.mk modified: reproduce/analysis/python/plot_voidgals_properties.py | 08 April 2021, 13:19:58 UTC |
| 2710e70 | Boud Roukema | 07 April 2021, 20:23:45 UTC | Typo: curves Minor: fixes a typo. | 07 April 2021, 20:23:45 UTC |
| 96733da | Marius Peper | 07 April 2021, 15:46:56 UTC | Minor updates to the differential halo mass figure This commit rearanges the label so that the order of the labels is the same as in the text and further makes a dashed line for non-void haloes and a dash-dotted line for void haloes. | 07 April 2021, 15:46:56 UTC |
| d92c3ee | Boud Roukema | 06 April 2021, 23:09:30 UTC | Minor fixes to most recent edit These are further minor wording changes to the last edit. | 06 April 2021, 23:09:30 UTC |
| c65b8ff | Marius Peper | 06 April 2021, 19:56:53 UTC | Minor clearifications about the meaning of the fits | 06 April 2021, 19:56:53 UTC |
| 99ccd5f | Boud Roukema | 06 April 2021, 17:15:30 UTC | Fix option --highlight-new The option '--highlight-new' to './project make' will now highlight the changes for revision 2 = B; this is an *opt-in* option. (It will not apply the changes for revision 1.) | 06 April 2021, 17:15:30 UTC |
| 013891c | Boud Roukema | 06 April 2021, 16:44:34 UTC | Fig 3 caption, refer to Fig 2 This commit further works on the caption of Figure 3, the halo mulitiplicity function. It also adds a text reference to Fig 2, since without that, we would be required to remove the figure. Some of the minor changes in figure captions in which we removed the fits are de-highlighted in this commit, because the referee appears to have shown no interest in reading the captions and looking at the values and uncertainties stated there; highlighting these minor changes might provoke the referee unnecessarily. | 06 April 2021, 16:44:34 UTC |
| d936cb0 | Boud Roukema | 05 April 2021, 22:13:55 UTC | Halo mass function - minor smoothing This commit does some minor smoothing in the caption and text for the halo mass function plot. The plot is shifted earlier, since the order of referring to figures in the text has to match the order of seeing them displayed. This commit has not yet been tested for correct LaTeXing. | 05 April 2021, 22:13:55 UTC |
| 146ce1c | Marius Peper | 05 April 2021, 20:15:30 UTC | Update the figure for the differential halo counts This commit avoids to show the lines dropping to -\infty. | 05 April 2021, 20:15:30 UTC |
| 583782f | Marius Peper | 05 April 2021, 16:40:18 UTC | Remove DiffHaloCounts.py from analyse-plot.mk The previous commit removed DiffHaloCounts.py from the software package because the routine was obsolete. This commit also removes it from the python-package-list specified in analyse-plot.mk to avoid a crash when the script tries to copy the file into the build-directory. | 05 April 2021, 16:40:18 UTC |
| 0111305 | Marius Peper | 05 April 2021, 15:49:21 UTC | Merge branch 'postreferee_corrections' of codeberg:boud/elaphrocentre into postreferee_corrections | 05 April 2021, 15:49:21 UTC |
| f3edd77 | Marius Peper | 05 April 2021, 15:46:24 UTC | Update the figure we want to add for points 13 & 14 of the referee report The updated figure shows the differential halo mass function for all haloes, and for the haloes in voids/outside voids seperately. It visualises the distribution of halo masses. | 05 April 2021, 15:46:24 UTC |
| 990797e | Boud Roukema | 04 April 2021, 22:49:59 UTC | Handle several more referee comments This commit updates the text to handle most of the later specific comments by the referee, such as how J and E are calculated and putting more caveats in the conclusion. | 04 April 2021, 22:49:59 UTC |
| f755b14 | Marius Peper | 04 April 2021, 20:59:52 UTC | Avoid multiplying the factor for the halo mass twice when creating the figure for the distribution of halo masses This commit removes a wrong prefactor that was multiplied to the halo masses when creating the histograms of the distribution of halo masses of void galaxies and non-void galaxies. | 04 April 2021, 20:59:52 UTC |
| 31db0b5 | Marius Peper | 04 April 2021, 19:58:06 UTC | Add an equation how the effective radius is defined to paper.tex | 04 April 2021, 19:58:06 UTC |
| 55d2267 | Boud Roukema | 04 April 2021, 19:50:27 UTC | Explanatory text in caption of Fig 3 This commit does some minor LaTeX fixes and puts an explanation in the caption of Fig 3 to explain why some plots arbitrarily have their fit hidden. | 04 April 2021, 19:50:27 UTC |
| f27fa20 | Boud Roukema | 04 April 2021, 16:28:11 UTC | Arbitrarily hide some fits to make referee happy The referee is not convinced by the need to avoid selection bias, so this commit mostly follows the referee's requests to hide the robust best fits in some plots. This commit also fixes some minor typos in the previous commit and in the Mpc/h axis label. This commit has not yet been tested. | 04 April 2021, 16:28:11 UTC |
| 97afad0 | Boud Roukema | 04 April 2021, 02:12:40 UTC | Points 1 to 9 of the referee This commit makes changes in the text of paper.tex that update/propose/complete responses to points 1 to 9 of the referee's second report. A histogram of \dot{v}_parallel might be useful. This commit has *not* been tested for correct LaTeX compilation, since I'm still waiting for a new plotting run to finish. | 04 April 2021, 02:12:40 UTC |
| 20b6273 | Mohammad Akhlaghi | 28 March 2021, 11:55:03 UTC | Configuration: corrected check of group name When built in 'group' mode, the write permissions of all created files will be activated for a certain group of users in the host operating system. The user specifies the name of the group with the '--group' option at configure time. At the very start, the './project' script checks to see if the given group name actually exists or not (to avoid hard-to-debug errors popping up later). Until now, the checking 'sg' command (that was used to build the project with group-writable permissions) would always fail due to the excessive number of redirections. Therefore, it would always print the error message and abort. With this commit, the output of 'sg' is no longer re-directed (which also helps users in debuggin). If the group does actually exist, it will just print a small statement saying so, and if it fails, the error message is printed. This fixed the problem, allowing maneage to be built in group-mode. I also noticed that the variable name keeping the group name ('reproducible_paper_group_name') used the old name for the project (which was "Reproducible paper template"! So it has been changed/corrected to 'maneage_group_name'. | 28 March 2021, 11:55:03 UTC |
| 611c2f1 | Mohammad Akhlaghi | 26 March 2021, 20:37:35 UTC | Initialization: removed other Gnuastro-specific features In the previous commit, some Gnuastro-specific initializations were removed but a few more cases remained that are removed with this commit. | 26 March 2021, 20:39:48 UTC |
| ac8890d | Mohammad Akhlaghi | 26 March 2021, 18:19:22 UTC | ./project: unused --minmapsize option is removed Until now, the './project' script included an '--minmapsize' option which is an option to one of the original programs that was used in Maneage (Gnuastro). Such an option doesn't exist in many other programs, so it is not a suitable option for the generic Maneage project (and can just cause confusion). It was also not used in any part of Maneage any more! With this commit, this option is removed from the core Maneage './project' script and if any project uses it, they can implement it in their own branch. | 26 March 2021, 18:19:22 UTC |
| 66453b4 | Mohammad Akhlaghi | 24 March 2021, 21:01:35 UTC | Maneage installation: removed TCL as a dependency of SWIG Until now the SWIG software would use the host operating system's packages to find the TCL configuraiton (which we don't install yet in Maneage). In particular, you can see the error during its configuration here: .... checking for pkg-config... pkg-config checking for Tcl configuration... found /usr/lib/tclConfig.sh /usr/lib/tclConfig.sh: line 2: dpkg-architecture: command not found /usr/lib//tcl8.6/tclConfig.sh: line 2: dpkg-architecture: com. not found With this commit, TCL has been disabled when building SWIG with the '--without-tcl' option. Later, when we add TCL in Maneage, we can remove this option. | 24 March 2021, 21:01:35 UTC |
| a981196 | Raul Infante-Sainz | 19 March 2021, 18:11:12 UTC | Configuration: nullability-completeness warnings suppressed With a recent update of macOS systems (macOS Big Sur 11.2.3 and Xcode 12.4), there are many warnings when building C programs (for example the simple program we compile to check the compiler, or some of the software like `gzip'). It prints hundreds of warning lines for every source file that are irrelevant for our builds, but really clutters the output. With this commit, these warnings are disabled by adding `-Wno-nullability-completeness' to the 'CPPFLAGS' environment variable. This has also been added to the very first check of the C compiler in the configure step. | 20 March 2021, 01:08:21 UTC |
| c3e82b1 | Raul Infante-Sainz | 19 March 2021, 17:52:08 UTC | Configuration: --debug option available in this phase also Until now, each time there was a problem in the configuration of Maneage'd projects and debugging was necessary, we had to take the following changes: - Run the configuration on a single thread ('-j1') to see the building of only the problematic software. - Disable the Zenodo check manually by commenting those parts of 'reproduce/software/shell/configure.sh'. Because the internet connection wastes a few seconds and is thus very annoying during repeated runs! - Manually remove the '-k' option that was passed to Make (when building the software). With the '-k', Make keeps going with the execution of other targets if something crashes and this usually causes confusions during the debugging. Doing the manual changes within the code was both very annoying and prone to errors (forgetting to correct it!). With this commit, the existing '--debug' option has been generalized to the software configuration phase of Maneage also. Until now, it was only available in the analysis phase (and would directly be passed to the 'make' command that would run the analysis). When this option is used, and the project is in the software configuration phase, the Zenodo check won't be done, it will use one single thread ('-j1'), and it will stop the execution as soon as an error occurs (Make is not run with '-k'). | 20 March 2021, 00:53:37 UTC |
| 1524213 | Mohammad Akhlaghi | 12 February 2021, 23:49:16 UTC | Installation: minor correction in links to system libraries Until now when making a link to the system's 'dl' and 'pthread' libraries we were simply linking the installed location on the system (in '/usr/lib'). However, in some systems, these may themselves be links to other locations and this could cause linking problems. With this commit, we now use 'realpath' to extract the absolute address of the final file that the libraries may link to, and directly link to them. A minor cosmetic correction was also made in the build rule for CFITSIO: the long line was broken into two! | 12 February 2021, 23:49:16 UTC |
| 76ed8bc | Marius Peper | 06 February 2021, 00:44:42 UTC | Minor edits to clearify the how we estimate an expression for the comsic variance This commit adds the information that we use 10 runs to estimate a naive expression for the cosmic variance in order to check if the results of a future run are agree with our published results statistically. | 06 February 2021, 00:44:42 UTC |
| 9ae04ed | Marius Peper | 04 February 2021, 23:16:25 UTC | Add a figure of the halo mass distribution of galaxies and of the differential halo mass function This commit adresses the remarks of the referee to add a figure of the differential halo mass function and to visualise the distribution of host halo masses for galaxies that are identified in voids and those that not lie in voids. | 04 February 2021, 23:16:25 UTC |
| 5d776ae | Marius Peper | 03 February 2021, 22:06:24 UTC | Modify the abstract as suggested by the referee This commit adds a new command for the 2nd correction and modifies the abstract as suggested by the referee. | 03 February 2021, 22:06:24 UTC |
| 442b039 | Marius Peper | 03 February 2021, 20:17:18 UTC | Add a rule to only show the fits which have a significant slope This routine adds a routine that decides for every scatter plot if the slope of the theil-sen fit is significant enough to be shown in the created pdf. | 03 February 2021, 20:17:18 UTC |
| ecbaadc | Mohammad Akhlaghi | 12 January 2021, 16:15:47 UTC | Default LaTeX preamble: some packages moved to preamble-project.tex Until now, important LaTeX packages like 'caption' (for managing figure captions), 'hyperref' (for managing links) and 'xcolor' (for managing colors) were being loaded inside the optional 'tex/src/preamble-maneagge-defualt-style.tex' file. We recommend to remove this file from loading when you use custom journal sytels. However, these packages will often be necessary after loading special journal styles also. With this commit, these packages are now loaded into LaTeX as part of the 'tex/src/preamble-project.tex' file. This file is in charge of LaTeX settings that are custom to the project and independent of its style. Several other small corrections are made with this commit: - I noticed that './project make texclean' crashes if no PDF exists in the working directory! So a '-f' was added to the 'rm' command of the 'texclean' rule. - As part of the LaTeX Hyperref, we can set general metadata or properties for the PDF (that aren't written into the printable PDF, but into the file metadata). They can be viewed in many PDF viewers as PDF properties. Until now, we were only using the '\projecttitle' macro here to write the paper's title. However, thanks to the recently added 'reproduce/analysis/config/metadata.conf', we now have a lot of useful information that can also go here. So the 'metadata-copyright-owner' is now used to define the PDF author, and the project's 'metadata-git-repository' and commit hash are written into the PDF subject. But to import these, it was necessary to define them as LaTeX macros, hence the addition of these macros in 'initialize.mk'. - Some extra packages that aren't necessary to build the default PDF were removed in 'preamble-project.tex'. | 12 January 2021, 16:17:18 UTC |
| cbe3030 | Mohammad Akhlaghi | 10 January 2021, 03:32:54 UTC | make dist: removing temp files moved after project-specific files Until now, when you ran './project make dist', first it would delete the temporary files (like files ending in '~' or '.swp' created by some editors), then it had a place to add project-specific operations for the distribution. However, in the process of cleaning the temporary files, it would 'cd' into the directory that would later be packaged. So project-specific operations would first have to 'cd' back into the top source directory. This was prone to hard-to-find bugs. With this commit, to avoid the problem the project-specific operations are now placed before the cleaning phase. This is also technically good because in the project-specific operations there may also be temporary files that shouldn't go into the distribution tarball. | 10 January 2021, 03:32:54 UTC |
| 334c16b | Boud Roukema | 09 January 2021, 22:03:03 UTC | Final pre-submission checklist This commit fixes some of the rules in `reproduce/analysis/make/initialize.mk` for creating the archive type files to upload to Zenodo. The '-committed-only' name in variables is for archiving commands that use git and ignore any uncommitted changes. The '-dirty' suffix is irrelevant in this case. Some utf-8 (unicode) characters that accidentally crept into `tex/src/references.tex` are fixed; and '\&' is replaced by 'and' in paper.tex. The sequence of creating/listing files for uploading to Zenodo should be: ./project make clean-paper ./project make dist-arXiv ./project make git-bundle ./project make dist-software # Wait! typically 0.5 Gb! ls -lt .build/data-to-publish/ In the elaphrocentre project, remember to 'touch' the initial conditions file to prevent a new simulation from being run, e.g. touch --date=2010-02-03 reproduce/analysis/config/init-conditions-params.conf unless you really do want to run a new simulation. | 09 January 2021, 22:03:03 UTC |
| a40cf08 | Marius Peper | 09 January 2021, 21:00:17 UTC | Add the new zenodo ID for the updated (corrected) version of the project | 09 January 2021, 21:00:17 UTC |
| d9a6855 | Mohammad Akhlaghi | 09 January 2021, 01:34:15 UTC | IMPORTANT: analysis outputs written in BDIR/analysis Until now, the build directory contained a 'software/' directory (that hosted all the built software), a 'tex/' subdirectory for the final building of the paper, and many other directories containing intermediate/final data of the specific project. But this mixing of built software and data is against our modularity and minimal complexity principles: built software and built data are separate things and keeping them separate will enable many optimizations. With this commit, the build directory of the core Maneage branch will only contain two sub-directories: 'software/' and 'analysis/'. The 'software/' directory has the same contents as before and is not touched in this commit. However, the 'analysis/' directory is new and everything created in the './project make' phase of the project will be created inside of this directory. To facilitate easy access to these top-level built directories, two new variables are defined at the top of 'initialize.mk': 'badir', which is short for "built-analysis directory" and 'bsdir', which is short for "built-software directory". HOW TO IMPLEMENT THIS CHANGE IN YOUR PROJECT. It is easy: simply replace all occurances of '$(BDIR)' in your project's subMakefiles (except the ones below) to '$(badir)'. To confirm if everything is fine before building your project from scratch after merging, you can run the following command to see where 'BDIR' is used and confirm the only remaning cases. $ grep -r BDIR reproduce/analysis/* --> make/verify.mk: innobdir=$$(echo $$infile | sed -e's|$(BDIR)/||g'); \ --> make/initialize.mk:badir=$(BDIR)/analysis --> make/initialize.mk:bsdir=$(BDIR)/software --> make/initialize.mk: $$sys_rm -rf $(BDIR) --> make/top-prepare.mk:all: $(BDIR)/software/preparation-done.mk 'BDIR' should only be present in lines of the files above. If you see '$(BDIR)' used anywhere else, simply change it to '$(badir)'. Ofcourse, if your project assumes BDIR in other contexts, feel free to keep it, it will not conflict. If anything un-expected happens, please post a comment on the link below (you need to be registered on Savannah to post a comment): https://savannah.nongnu.org/task/?15855 One consequence of this change is that the 'analysis/' subdirectory can be optionally mounted on a separate partition. The need for this actually came up for some new users of Maneage in a Docker image. Docker can fix portability problems on systems that we haven't yet supported (even Windows!), or had a chance to fix low-level issues on. However, Docker doesn't have a GUI interface. So to see the built PDF or intermediate data, it was necessary to copy the built data to the host system after every change, which is annoying during working on a project. It would also need two copies of the source: one in the host, one in the container. All these frustrations can be fixed with this new feature. To describe this scenario, README.md now has a new section titled "Only software environment in the Docker image". It explains step-by-step how you can make a Docker image to only host the built software environment. While your project's source, software tarballs and 'BDIR/analysis' directories are on your host operating system. It has been tested before this commit and works very nicely. | 09 January 2021, 03:00:15 UTC |
| b2f6bf2 | Boud Roukema | 06 January 2021, 19:03:37 UTC | Selection not apophenic bias; Pustilnik comment in 4.4 This commit fixes the description of the bias that would potentially be introduced by showing the fits in the diagrams in only the cases that look convincing: I think this is 'selection bias'. 'Apophenia' is about seeing patterns where there are none, and here in fact, this is what a naive astronomer may worry about. This commit also adds a brief comment on Pustilnik in Section 4.4 for possible extensions, in the Discussion section. | 06 January 2021, 19:03:37 UTC |
| 0b5f57a | Boud Roukema | 06 January 2021, 17:46:19 UTC | Merge branch 'maneage' into maneage-c-merge This commit is a merge that should bring elaphrocentre up-to-date with the latest maneage commit, b91af98. | 06 January 2021, 17:46:19 UTC |
| c89421f | Boud Roukema | 05 January 2021, 23:00:54 UTC | Title; abstract context; cosmic variance; explain fits This commit switches to a title more likely to satisfy the referee and less vague than our previous revised title; it increases the focus on void galaxies in the first sentence of the abstract; it updates to using cosmic variance for infall rate dependance on the elaphrocentric distance; and it better explains why we show fits consistently for all plots rather than selecting only a few of them. | 05 January 2021, 23:00:54 UTC |
| b91af98 | Mohammad Akhlaghi | 05 January 2021, 18:01:19 UTC | Configuration: GNU Binutils linking bug on some systems fixed Until now, when building GNU Binutils on GNU Linux operating systems, we would simply put a link to the host's core C library components (the '*crt*' files). However, the symbolic link wasn't "forced"! So if it already existed in the build directory, it would crash. With this commit a '-f' option has been added to the 'ln' command and this fixed the problem. This bug was reported by Zahra Sharbaf. | 05 January 2021, 18:01:19 UTC |
| 43509c0 | Boud Roukema | 05 January 2021, 13:39:33 UTC | Single commit verification set This commit introduces a new set of verification files, calculated with commit e93569c. One parameter \PlotsSizeiRAvgVoidsTotalvalue is shifted from canonical value checking to cosmic variance checking, because it failed the canonical check. The value of n_verify_sigmas is increased to 5.0, to (heuristically) take into account possible non-Gaussianity of the distributions. A comment on the computer endianness and architecture is added in the final paragraph of the introduction. (Some software assumes a given endianness, and fails if the computer uses the opposite.) | 05 January 2021, 13:39:33 UTC |
| a1a966a | Mohammad Akhlaghi | 04 January 2021, 03:32:38 UTC | Building of Less program now uses patchelf to ensure good linking After correctly setting Less to depend on 'ncurses', I noticed its still not linking to Maneage's 'ncurses', but pointing to my host system's 'ncurses' (that happens to have the same version! So it would crash on a system with a different version). This shows that like some other software, we need to manually correct the RPATH inside Less. With this command, the necessary call to 'patchelf' has been added and with it, the installed 'less' command properly linked to Maneage's internal build of 'ncurses'. | 04 January 2021, 03:32:38 UTC |
| dc4aa8c | Mohammad Akhlaghi | 04 January 2021, 03:21:03 UTC | README-hacking.md: edits and improvements to publication checklist After going through the publication checklist, some edits were made to make things more clear. Also, an item was added to remind the project author that the commit hashes on the uploaded data files should be the same. | 04 January 2021, 03:21:03 UTC |
| 02e53b9 | Mohammad Akhlaghi | 04 January 2021, 02:58:05 UTC | README.md: summary Dockerfile with all necessary lines in one step Until now, the description in 'README.md' to build the Dockerfile in 'README.md' had one item per line, thoroughly describing the reason behind that line. But in many cases, the user is already familiar with Docker (or has already read through the items) and just wants to have the Dockerfile ready fast. In these cases, all those extra explanations are annoying. With this commit, an item '0' has been added at the start of the item list for summary. It only contains the necessary Dockerfile contents with no extra explanation. | 04 January 2021, 02:58:05 UTC |
| 31f4ea3 | Mohammad Akhlaghi | 04 January 2021, 01:52:25 UTC | Building of less software depends on ncurses Until now, the 'less' software package (used to view large files easily on the command-line and used by Git for things like 'git diff' or 'git log') only depended on 'patchelf' (which is a very low-level software). However, as Boud reported in bug #59811 [1], building less would crash with an error saying "Cannot find terminal libraries" in some systems (including the proposed Docker image of 'README.md' which I confirmed afterwards). Looking into the 'configure' script of 'less', I noticed that 'less' is actually just checking for some functions provided by the ncurses library! With this commit, 'less' depends on 'ncurses'. I was able to confirm that with this change, 'less' successfully builds within the Docker image. [1] https://savannah.nongnu.org/bugs/?59811 | 04 January 2021, 01:52:25 UTC |
| e93569c | Boud Roukema | 03 January 2021, 21:13:29 UTC | Restore reasonable value of n_verify_sigmas This commit restores n_verify_sigmas to the reasonable value of 4.0 . The value of 1000.0 is *only* for testing without verification, e.g. for 32^3 runs. | 03 January 2021, 21:13:29 UTC |
| 287a672 | Boud Roukema | 03 January 2021, 20:56:34 UTC | Restore preamble-style.tex; enable verification The file `tex/src/preamble-style.tex` was accidentally deleted in the merge; this is restored in this commit. The verification system is re-enabled in this commit, and an explanation given to the user, in `reproduce/analysis/config/verify-outputs.conf`, because paper.tex requires the verification input parameters and the cosmic variances to be calculated and inserted into what becomes the final pdf file. | 03 January 2021, 20:56:34 UTC |
| 49ca75b | Boud Roukema | 03 January 2021, 19:49:53 UTC | Merge branch 'maneage' into maneage-c-merge This merge aims to update elaphrocentre (branch: postreferee_corrections) to the most recent commit of maneage, b1bd282 of 2 Jan 2021, first going through a test branch. | 03 January 2021, 19:49:53 UTC |
| f4a6b51 | Boud Roukema | 03 January 2021, 16:50:30 UTC | Abstract s/LSBG/galaxy/; verification clarification This commit does some final tidying prior to resubmission. Once instance of "LSBG" in the abstract is changed to "galaxy". Section 2.4 on the verification procedure is clarified (strictly speaking, the older version was incorrect), and a cross-reference to it is provided in Table 2, where we now have one parameter that needs cosmic variance for its verification. Two other minor changes done: "higher than"; and spacing in the 'project' help info. | 03 January 2021, 16:50:30 UTC |
| 182679f | Marius Peper | 02 January 2021, 17:35:00 UTC | Minor changes to paper.tex This commit adds more information in the caption of Table 4 and makes a few more changes to smoothen the text. | 02 January 2021, 17:35:00 UTC |
| b1bd282 | Mohammad Akhlaghi | 02 January 2021, 15:59:49 UTC | ./project make: new texclean target Until now there was only a 'clean' (to delete all files created during the 'make' phase) and the 'distclean' (to delete all files during configuration and make). But sometimes we don't want to delete all the files created during the full 'make' phase, we only want to delete the files that were created by LaTeX for building the paper. Witht this commit, a new target has been added for this job. You can now run the following command for this job: ./project make texclean Only the files in '$(BDIR)/tex/build' will be deleted (and the 'tikz' directory under that location is recreated, ready for a future build). | 02 January 2021, 15:59:49 UTC |
| ff43476 | Mohammad Akhlaghi | 02 January 2021, 15:52:31 UTC | Copyright year updated in all source files Having entered 2021, it was necessary to update the copyright years at the top of the source files. We recommend that you do this for all your project-specific source files also. | 02 January 2021, 15:52:31 UTC |
| 169768c | Boud Roukema | 30 December 2020, 21:45:43 UTC | Allow switching highlighting on/off without changing commit ID With this commit, `./project make --highlight-new` uses a new rule in `reproduce/analysis/make/paper.mk` to switch on highlighting for the revised version of the paper. By default, there is no highlighting. This avoids having to have different commit IDs for the highlighted and unhighlighted versions, which would be confusing in terms of the submission procedure. An accepted article is allowed only minimal changes, and modifying the commit ID would look strange given the whole point of reproducibility. | 30 December 2020, 21:45:43 UTC |
| c9c7b23 | Boud Roukema | 27 December 2020, 11:04:45 UTC | Conclu: somewhat smaller; fix Rong+2017 age quotes This commit writes the conclusion sentence more carefully about making 'diffuse, somewhat smaller' galaxies; and fixes our reversed quote of Rong+2017 ages vs epochs of ordinary dwarfs; plus some minor copyediting. | 27 December 2020, 11:04:45 UTC |
| 9b9f13a | Boud Roukema | 25 December 2020, 10:59:08 UTC | Rework conclusion; RviriErrorRvirAvgVoidsTotal cosmic variance This commit is mostly a reworking of the conclusion: * some compression; * give more attention to the referee's point about void galaxies being smaller (it is actually useful); * add the numbers for the difference in epochs, since we don't have a subsection or table or formula to point to. One run failed to verify RviriErrorRvirAvgVoidsTotal, so this is now checked for cosmic variance. | 25 December 2020, 10:59:08 UTC |
| 724d9d0 | Boud Roukema | 25 December 2020, 09:10:06 UTC | Add a tenth verification simulation | 25 December 2020, 09:10:06 UTC |
| b910b2e | Mohammad Akhlaghi | 14 December 2020, 02:14:34 UTC | Better warnings when maneage branch not present and PDF not built Until now, there was no warning when the 'maneage' branch didn't exist in the Git history. This can happen when you forget to push the 'maneage' branch to a remote for your project, and you later clone your project from that remote (for example on another computer). We use the 'maneage' branch to report the latest commit hash and date in the final paper (which can greatly help future readers). Since we check the 'maneage' branch on every run of './project make' (in 'initialize.mk') this would result in a printed statement like this: fatal: Not a valid object name maneage Also until now, the description of what to do when TeXLive wasn't installed properly wasn't complete: it didn't mention that it is necessary to delete the TeXLive target files. This could confuse users (they would re-run './project configure -e', but with no effect). With this commit, for the 'maneage' branch issue a complete warning will be printed. Telling the user what to do to get the 'maneage' branch (and thus fix this warning). Also, the LaTeX macros that go in the paper are now red when the 'maneage' branch doesn't exist, telling the user to see the printed warning (thus encouraging the user to get the branch). For the TeXLive issue, the necessary commands to run are now also printed in the warning. | 14 December 2020, 02:28:14 UTC |
| cce4016 | Raul Infante-Sainz | 09 December 2020, 20:09:43 UTC | Configuration: not settting C_INCLUDE_PATH on macOS Until now, when building the high-level (optional) software, we would give both 'CPPFLAGS' and 'C_INCLUDE_PATH' the same value/directory in 'high-level.mk'. But we recently found that on macOS's C compiler ('clang'), if a directory is included in both 'CPPFLAGS' and 'C_INCLUDE_PATH', then that directory is ignored in 'CPPFLAGS' (which has higher priority). This caused linking problems when the version of a software on the host was different from the Maneage version. With this commit, 'C_INCLUDE_PATH' is not set on macOS any more and this fixed the problem on the reported systems. This bug was fixed with the help of Mohammad Akhlaghi and Mahdieh Navabi. | 09 December 2020, 22:44:13 UTC |
| 2f56ad2 | Marius Peper | 07 December 2020, 14:53:59 UTC | Use Malin 1 like test halo instead of a Milky-Way like halo and edit the elaphro-acc paragraph This commit tries to clearify how we estimate the elaphro-acceleration. I assume that the idea how we use the test halo was not clear before. This commit also exchanges all references to the Milky-Way by references to Malin 1. | 07 December 2020, 14:53:59 UTC |
| 39a21a9 | Boud Roukema | 06 December 2020, 03:45:10 UTC | Add 9th realisation for verification - 7c2aea8 This commit adds another realisation of commit 7c2aea8, making the 9th. We should add one more realisation to get a reasonable round number. | 06 December 2020, 03:45:10 UTC |
| f338a76 | Marius Peper | 04 December 2020, 19:29:20 UTC | Edit the conclusion and discussion This commit shortens the conclusion. Large parts of the former conclusion are moved to the discussion. Several small changes were done to add the paragraphs from the conclusion to the discussion. The conclusion now is roughly half a page. | 04 December 2020, 19:29:20 UTC |
| 238d8d7 | Boud Roukema | 03 December 2020, 20:09:11 UTC | Add verification file v1-34-g7c2aea8_16341512 | 03 December 2020, 20:09:11 UTC |
| aeb0458 | Boud Roukema | 03 December 2020, 19:57:24 UTC | Fix statistical difference of two estimates In `reproduce/analysis/bash/verify-parameter-statistically.sh`, we by default compare two individual realisations (a new one versus an old one), but if requested, we compare a new one to the mean of an ensemble of old realisations. In the former case, the error distribution of the difference, for Gaussian distributions, should be \sqrt{2} times the standard deviation of the parameter being measured; in the latter case, the standard error in the mean should be a lot smaller than the standard deviation. This commit corrects the handling of the former case by increasing the "number of sigmas" by a factor of sqrt{2}. No change is made for the latter case. | 03 December 2020, 19:57:24 UTC |
| a34a1d5 | Boud Roukema | 03 December 2020, 02:20:39 UTC | Allow compare_centres to be disabled This commit makes the production of the pdf file contingent upon whether or not 'compare_centres' is enabled in 'reproduce/analysis/config/analyse-plot-params.conf'. The default remains 'YES', but 'NO' (or anything different to 'YES') should disable the option. A comment is added to 'README.md' to clarify that the default that we will retain in the official version 2 commit will aim to reproduce the submitted version 2, but that we recommend that users who do not feel the need for Table 4 and the final paragraph in Section 4.2 should disable 'compare_centres'. We leave the calculation times to those for the disabled state of compare_centres. This commit also adds the timing estimate for a 256^3 simulation in README.md, warning the user that this is very unwise with the current state of the full pipeline. Full testing of switching between the YES and NO states is best done with a `./project make clean-analyse-conf` step in between. This works for me. | 03 December 2020, 02:20:39 UTC |
| 0721453 | Boud Roukema | 03 December 2020, 00:44:47 UTC | Table 4 and comments: minor changes This commit bypasses the "protection" in terms of font size and colour on parts of the table environment, to make sure that all of Table 4 is nicely highlighted to bring it to the attention of the referee and possibly editor. The sentences are changed a bit too. | 03 December 2020, 00:44:47 UTC |
| 7c2aea8 | Boud Roukema | 02 December 2020, 23:41:42 UTC | Three more verification files This commit adds three more realisations, and renames one, for consistency of style. | 02 December 2020, 23:41:42 UTC |
| 59d1276 | Boud Roukema | 02 December 2020, 03:36:24 UTC | Add two more realisations for verification This commit adds to more verification files. The commit IDs are slightly different, but there are no changes in the project calculation routines between these two files, or between them and the other two 'v1-[23]*' files. A wildcard asterisk can be used for the commit ID for cases such as this, as long as 'make' and 'bash' treat the asterisk appropriately. | 02 December 2020, 03:36:24 UTC |
| 59c9e30 | Boud Roukema | 02 December 2020, 01:25:17 UTC | Copyedit of recent fixes to paper; restore 4-sigma verification This commit does a bit of copyediting on Marius' recent changes to the text that respond to some more of the concerns of the referee. It also restores the "4-sigma" value in the verification configure file. This has not yet been tested on a more solid set of updated verification files, but it will be within a few days. | 02 December 2020, 01:25:17 UTC |
| 021ff34 | Mohammad Akhlaghi | 02 December 2020, 01:01:45 UTC | Less is now built as a basic software Less is rarely used in non-interactive mode and is primarily intended for interactively viewing large files. So its need within Maneage (for batch processing) wasn't often felt until now. However, when running './project shell' (which completely closes-off the outside environment), or building a Maneage'd project within a minimal container that doesn't have less, it becomes hard to use Git (and in particular its 'diff' output which depends on 'less'). With this commit, Less has been added as a dependency of Git in 'basic.mk'. In total its built product is roughly 800KB and builds within a second or two. So it isn't a burden on any project. But it can be very useful when the projects are being developed within the Maneage environment itself. | 02 December 2020, 01:01:45 UTC |
| 1f4083e | Boud Roukema | 01 December 2020, 23:54:59 UTC | High n_verify_sigmas for guaranteed valid realisations This commit is for generating realisations that will later be used for checking cosmic variance. The value of n_verify_sigmas is set to a ridiculously high value. For real verification, the value has to be reset to a reasonable value. A minor improvement in the documentation of the statistical verification script is added here too. | 01 December 2020, 23:54:59 UTC |
| d720c7b | Boud Roukema | 01 December 2020, 23:29:58 UTC | Merge branch 'postreferee_corrections' of codeberg:boud/elaphrocentre into postreferee_corrections | 01 December 2020, 23:29:58 UTC |
| 04451b2 | Boud Roukema | 01 December 2020, 23:26:40 UTC | Modularise statistical verification script This commit shifts the statistical verification script into the file `reproduce/analysis/bash/verify-parameter-statistically.sh`; improves the documentation of the parameters of the script; and adds a rough guide on how to set up a set of realisations to start off with, in order to benefit from the statistics over repeated realisations. In the cosmology context, this is called "cosmic variance", but the general idea should apply to any quantitative scientific project in which statistical reproducibility is felt to be more relevant than byte-for-byte reproducibility. This commit is fresh and might still have bugs. | 01 December 2020, 23:26:40 UTC |
| 2e33629 | Marius Peper | 01 December 2020, 21:42:31 UTC | Add a table that compares the best fit parameters for the three different centres This commit adds a table with the best fit parameters for r_disk, R_vir and lambda against the relative position r/R_eff for each centre. Once we have results based on several 128^3 runs we should add a few sentences based on how the best fit parameter compare to each other. | 01 December 2020, 21:42:31 UTC |
| 1ee1d66 | Mohammad Akhlaghi | 01 December 2020, 17:32:44 UTC | Installation: m4 no longer depends on Texinfo In a recent build on a macOS, we recognized that Texinfo needs the 'libintl.h' headers of Gettext. However, Gettext depends on M4, and until now we had set M4 to depend on Texinfo. Therefore adding Gettext as a dependency of Texinfo would cause a circular dependency. On the macOS, we temporarily disabled M4's Texinfo dependency, and the build went through. I also checked on my GNU/Linux system: temporarily renamed all Texinfo built files from my system and done a clean build of M4 and it succeeded. To be further safe, I built Maneage from this commit (where M4 doesn't depend on Texinfo) in a Docker container, and it went through with no problems. So the current M4 version indeed doesn't need Texinfo. I think adding Texinfo as a dependency of M4 was a historic issue from the early days. In the process, I also cleaned 'basic.mk' a little: - A "# Level N" comment was added on top of each group of software that can be built in parallel (generally). - GNU Nano was moved to the end of the file (to be "Level 6"). - Some comments were edited in some places. | 01 December 2020, 18:53:22 UTC |
| 2a1a717 | Boud Roukema | 01 December 2020, 16:47:36 UTC | Merge branch 'postreferee_corrections' of codeberg:boud/elaphrocentre into postreferee_corrections | 01 December 2020, 16:47:36 UTC |
| e796e6f | Mohammad Akhlaghi | 01 December 2020, 16:42:50 UTC | README-hacking.md: recommended to push maneage after merging Until now at the end of the updating process, we hadn't explicity talked about pushing the branches. So people would usually only push their 'master' branch to their remote. While the merged 'master' branch does contain the commits from the core Maneage branch, having a no-updated 'maneage' branch reference on their remote can be confusing. With this commit, at the end of the process to merge with the 'maneage' branch we explicitly recommend to push both the 'master' and 'maneage' branches. | 01 December 2020, 16:47:31 UTC |
| 631c375 | Boud Roukema | 01 December 2020, 16:46:03 UTC | Initialise statistical verification For initialising the verification system, a set of realisations that necessarily "pass" is required. This commit illustrates (hopefully) that setting n_verify_sigmas = 1000.0 is temporarily necessary for this step. | 01 December 2020, 16:46:03 UTC |
| 3b78a73 | Marius Peper | 01 December 2020, 12:01:06 UTC | Mention the conversion of M_vir to R_vir encoded in sage This commit adds that sage uses the virial mass to estimate the virial radius, see line 166 of model_misc.c . | 01 December 2020, 12:01:06 UTC |
| ac8eee9 | Mohammad Akhlaghi | 01 December 2020, 11:43:04 UTC | Default paper: macros available for date of commits cited Until now, Maneage only provided the commit hashes (of the project and Maneage) as LaTeX macros to use in your paper. However, they are too cryptic and not really human friendly (unless you have access to the Git history on a computer). With this commit, to make things easier for the readers, the date of both commits are also available as LaTeX macros for use in the paper. The date of the Maneage commit is also included in the acknowledgements. Also, the paragraph above the acknowledgements has been updated with better explanation on why adding this acknowledgement in the science papers is good/necessary. | 01 December 2020, 11:43:04 UTC |
| 6ca2fbf | Mohammad Akhlaghi | 30 November 2020, 23:50:38 UTC | IMPORTANT: organizational improvements in Maneage TeX sources This only concerns the TeX sources in the default branch. In case you don't use them, there should only be a clean conflict in 'paper.tex' (that is obvious and easy to fix). Conflicts may only happen in some of the 'tex/src/preamble-*.tex' files if you have actually changed them for your project. But generally any conflict that does arise by this commit with your project branch should be very clear and easy to fix and test. In short, from now on things will even be easier: any LaTeX configuration that you want to do for your project can be done in 'tex/src/preamble-project.tex', so you don't have to worry about any other LaTeX preamble file. They are either templates (like the ones for PGFPlots and BibLaTeX) or low-level things directly related to Maneage. Until now, this distinction wasn't too clear. Here is a summary of the improvements: - Two new options to './project make': with '--highlight-new' and '--highlight-notes' it is now possible to activate highlighting on the command-line. Until now, there was a LaTeX macro for this at the start of 'paper.tex' (\highlightchanges). But changing that line would change the Git commit hash, making it hard for the readers to trust that this is the same PDF. With these two new run-time options, the printed commit hash will not changed. - paper.tex: the sentences are formatted as one sentence per line (and one line per sentence). This helps in version controlling narrative and following the changes per sentence. A description of this format (and its advantages) is also included in the default text. - The internal Maneage preambles have been modified: - 'tex/src/preamble-header.tex' and 'tex/src/preamble-style.tex' have been merged into one preamble file called 'tex/src/preamble-maneage-default-style.tex'. This helps a lot in simply removing it when you use a journal style file for example. - Things like the options to highlight parts of the text are now put in a special 'tex/src/preamble-maneage.tex'. This helps highlight that these are Maneage-specific features that are independent of the style used in the paper. - There is a new 'tex/src/preamble-project.tex' that is the place you can add your project-specific customizations. | 01 December 2020, 00:12:11 UTC |
| f01e9f9 | Marius Peper | 30 November 2020, 21:09:39 UTC | Merge branch 'postreferee_corrections' of codeberg:boud/elaphrocentre into postreferee_corrections | 30 November 2020, 21:09:39 UTC |
| cf71a15 | Marius Peper | 30 November 2020, 21:06:58 UTC | Edit the section 2.3.2 making clear why we chose an exponential This commit adds the explanation that we fit the matter infall rate to an exponential and gives a rough reasoning og how the SFR and the matter infall are related. | 30 November 2020, 21:06:58 UTC |
| 3d35a71 | Boud Roukema | 30 November 2020, 16:06:44 UTC | Commit to set new standard values This commit should be usable to generate a new set of realisations with values to be used as the new standards. | 30 November 2020, 16:06:44 UTC |
| c4ea538 | Boud Roukema | 30 November 2020, 15:42:17 UTC | Clarify updating stat-verifiability Step 8 in the previous edit description should point out that the grep of VERIFIED should apply to .build/tex/macros/verify.tex . This commit processes the new parameters in `reproduce/analysis/make/verify.mk`. | 30 November 2020, 15:42:17 UTC |
| e5b32ed | Boud Roukema | 30 November 2020, 15:00:53 UTC | Merge branch 'postreferee_corrections' of codeberg:boud/elaphrocentre into postreferee_corrections | 30 November 2020, 15:00:53 UTC |
| de807a7 | Boud Roukema | 30 November 2020, 14:47:29 UTC | Step 1 in updating statistically verifiable values To extend the set of 'statistically verifiable' values, we need to do something like: 1. extra the new values in the LaTeX extraction list in `reproduce/analysis/make/analyse-plot.mk` keeping in mind the need for unique greppable names [this is crucial!] 2. disable verify-outputs and set the commit ID to empty in `reproduce/analysis/config/verify-outputs.conf` 3. rm .build/tex/macros/analyse-plot.tex 4. ./project make # this is unlikely to complete without error 5. check the new `.build/tex/macros/analyse-plot.tex` file; if it's OK, then copy it to `reproduce/analysis/verify/analyse-plot.tex.verify` 6. enable verify-outputs in `reproduce/analysis/config/verify-outputs.conf` 7. ./project make # this is unlikely to complete without error 8. Repeat the above for an independent run, and grep the VERIFIED lines, rename files, and when you're ready, set the new commit ID in `reproduce/analysis/config/verify-outputs.conf`. | 30 November 2020, 14:47:29 UTC |
| 667ffc4 | Boud Roukema | 30 November 2020, 02:40:23 UTC | Comment 10 done - Section 3.1, 3.3 This commit proposes a fix for referee specific comment 10 and major comment 3. The term LSBG is removed from Section 3.1. Comparisons with the Bootes and SDSS void surveys are added to Section 3.3. | 30 November 2020, 02:40:23 UTC |
| 9fcccc6 | Boud Roukema | 30 November 2020, 00:59:44 UTC | Introduction condensed: finishes on page 2 With this commit, and highlighting disabled (\togglefalse{postreferee}), the introduction finishes on page 2. | 30 November 2020, 00:59:44 UTC |
| f77da44 | Marius Peper | 29 November 2020, 20:51:22 UTC | Merge branch 'postreferee_corrections' of codeberg:boud/elaphrocentre into postreferee_corrections | 29 November 2020, 20:51:22 UTC |
| 6c1a173 | Boud Roukema | 29 November 2020, 17:52:31 UTC | Proposed fix for calculating tree_number There was a bug in using a wrong python string cleaning function. The function 'strip' was used instead of something more appropriate like 'replace'. This commit aims to fix that. | 29 November 2020, 17:52:31 UTC |
| e8b1094 | Marius Peper | 29 November 2020, 12:40:52 UTC | Merge branch 'postreferee_corrections' of codeberg:boud/elaphrocentre into postreferee_corrections | 29 November 2020, 12:40:52 UTC |
| 171376a | Marius Peper | 29 November 2020, 12:31:29 UTC | Rearrange the introduction This commit tries to rearrange the introduction in order to put void galaxies into the focus of the paper. It rearranges the paragraphs about voids and the theoretical assumptions to the beginning of the introduction. The introduction now explains the general effect that voids should have on all void galaxies and then explains why we think this is benefitial to form giant low surface brightness galaxies. I think now there are less "jumps" in the introduction making it clearer. I haven't been able to shorten the introduction a lot, I removed a few sentences but also added a few new sentences. | 29 November 2020, 12:31:29 UTC |
| 5f3d1d9 | Boud Roukema | 29 November 2020, 00:49:53 UTC | Try again to fix bary/geom issue | 29 November 2020, 00:49:53 UTC |
| c312f4e | Mohammad Akhlaghi | 28 November 2020, 22:18:36 UTC | README-hacking.md: updated paper to cite for using Maneage Until now, we were asking the users of Maneage to cite the first paper that used its primoridal version (arXiv:1505:01664). But there is now a paper that fully describes the concept (arXiv:2006.03018). With this commit, in the 'citation' section of 'README-hacking.md' we now ask to cite the new paper. | 28 November 2020, 22:18:36 UTC |
