| 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 |
| 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 |
| 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 |
| 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 |
| b4a273b | Boud Roukema | 28 November 2020, 17:58:33 UTC | Another try to fix modern_revolver_hacks.patch | 28 November 2020, 17:58:33 UTC |
| 87d6d0f | Boud Roukema | 28 November 2020, 17:44:37 UTC | Try to fix modern_revolver_hacks.patch This commit tries to fix modern_revolver_hacks.patch. | 28 November 2020, 17:44:37 UTC |
| fbab1ed | Boud Roukema | 28 November 2020, 17:15:11 UTC | Try to fix bary/geom confusion Unless we want to completely revise revolver for the confusing terminology "barycenter" that refers to geometrical centres, we can at least write "geom" for the files used in this particular project. This commit aims to do that. This commit also uses a loop for run-plots instead of repeated code. This commit has not yet been tested. | 28 November 2020, 17:15:11 UTC |
| 789d849 | Boud Roukema | 28 November 2020, 03:20:06 UTC | Merge branch 'prereferee_changes' into postreferee_corrections This commit merges the elaphrocentre definition improvement and the extra Nadathur reference. | 28 November 2020, 03:20:06 UTC |
| 80c5aa9 | Boud Roukema | 28 November 2020, 03:01:11 UTC | Highlighting changes done so far This commit does some further modification of the small number of changes made to the text so far and adds highlighting with \postrefereechanges{ ... } to highlight the changes for the referee + editor, who are not expected to do git diffs. | 28 November 2020, 03:01:11 UTC |
| 43c51f2 | Marius Peper | 16 November 2020, 09:48:19 UTC | Start on trivial corrections and add comments where we have to modify the text This commit starts to solve a few of the trivial corrections. It also starts to mark which parts of the text need to be overworked from my point of view. | 16 November 2020, 09:48:19 UTC |
| fcc77a7 | Mohammad Akhlaghi | 15 November 2020, 13:28:57 UTC | Building final PDF: pdf-build-final has to be given an explicit yes Until now, when the 'pdf-build-final' configuration variable (defined in 'reproduce/analysis/config/pdf-build.conf') was given any string a PDF would be built. This was very confusing, because people could put a 'no' and the PDF would still be built! With this commit, only when this variable has a value of 'yes' will the PDF be built. If given any other string (or no string at all), it will not produce a PDF. This issue was reported by Zahra Sharbaf. | 15 November 2020, 13:32:57 UTC |
| 9cfb8d3 | Mohammad Akhlaghi | 13 November 2020, 19:11:18 UTC | README.md: added commands to delete all Docker images Until now we had described the basic commands on how to create and use Docker images, but we hadn't mentioned how you can delete them. With this commit the commands necessary for deleting Docker images have also been added at the bottom of the section on Docker. | 13 November 2020, 19:11:18 UTC |
| 07ca2b7 | Marius Peper | 12 November 2020, 02:18:51 UTC | Enable the pipeline to perform allresults_LSBGs.py for all three centres in one run This commit lets allresults_LSBGs.py run on all three output-files of revolver. It will do the analysis for all three centres. A new version of the revolver hack is needed hence before we have not created a file containing the IDs of the DM particles laying in a fixed sphere around the barycentre. This commit directly deals with point 7 of the referees report. | 12 November 2020, 02:18:51 UTC |
| 2b39a67 | Mohammad Akhlaghi | 18 October 2020, 13:37:16 UTC | Recipes for final initialize and verify targets not on stdout The LaTeX macro files for these two subMakefiles are created on every run of './project make'. So their commands are also printed every time and hardly ever will a normal user want to modify or change these. So to avoid populating the standard output of a Maneaged project with all these extra lines every time (possibly getting mixed with the important analysis or LaTeX outputs), an '@' has been placed at the start of the recipes. With an '@' at the start of the recipe, Make is instructed to not print the commands it wants to run in the standard output. | 18 October 2020, 13:37:16 UTC |
| 3be9c0b | Boud Roukema | 11 October 2020, 11:01:22 UTC | Add missing ref Nadathur19BOSSRevolver for Revolver | 11 October 2020, 11:01:22 UTC |
| c473a5e | Boud Roukema | 11 October 2020, 10:45:06 UTC | Clarify definition of elaphrocentre This commit clarifies in the text that the definition of the elaphrocentre uses potentials calculated per particle by RAMSES. | 11 October 2020, 10:45:06 UTC |
| 04bda5a | Boud Roukema | 09 October 2020, 10:33:58 UTC | Update README-hacking.md with elaphrocentre ArXiv:2010.03742 This commit updates README-hacking.md with the URIs for the 'elaphrocentre' galaxy formation pipeline paper arXiv:2010.03742. This makes three papers currently in the peer review pipeline: arXiv:2006.03018, arXiv:2007.11779, and arXiv:2010.03742, each chronologically corresponding to various stages of the review process. | 09 October 2020, 13:28:21 UTC |
| 540f29b | Boud Roukema | 09 October 2020, 08:38:31 UTC | Restore parameters for N = 32^3 | 09 October 2020, 08:38:31 UTC |
| 19839a6 | Boud Roukema | 09 October 2020, 07:07:18 UTC | Update README.md with ArXiv and SWH IDs This commit updates README.md with the ArXiv and SWH IDs of the paper. The source URLs of the references are placed close to the citations, since some people will read README.md as a plain text file (and may not scroll all the way down), without making the paragraph itself too messy to read in plain text. The markdown rendered version should, in principle, not show the list of references; it should only show the URLs as live links. | 09 October 2020, 07:07:18 UTC |
| 6d86ff9 | Boud Roukema | 08 October 2020, 04:14:30 UTC | cleaner arXiv version | 08 October 2020, 04:14:30 UTC |
| cd3bd7d | Boud Roukema | 08 October 2020, 04:11:15 UTC | Data Availability Statement MNRAS new requirement | 08 October 2020, 04:11:15 UTC |
| 724a7c8 | Boud Roukema | 08 October 2020, 00:40:55 UTC | Add softwareheritage (swh) ID and URL | 08 October 2020, 00:40:55 UTC |
| 5621d99 | Boud Roukema | 07 October 2020, 22:22:48 UTC | Fix my error in terms of packages; minor fix in title | 07 October 2020, 22:22:48 UTC |
| 5665f48 | Boud Roukema | 07 October 2020, 22:12:09 UTC | Minor smoothing of log file instructions in README.md | 07 October 2020, 22:12:09 UTC |
| 2b097c5 | Boud Roukema | 07 October 2020, 22:05:17 UTC | Merge branch 'N128cubed' of codeberg:boud/elaphrocentre into N128cubed | 07 October 2020, 22:05:17 UTC |
| 6bbc299 | Marius Peper | 07 October 2020, 22:02:55 UTC | Minor edit of README.md This commit recommends the user to create logs when running/configuring the pipeline. | 07 October 2020, 22:02:55 UTC |
| b3f433d | Boud Roukema | 07 October 2020, 22:01:27 UTC | Fix make dist-arXiv for this paper With this commit, the command `./project make dist-arXiv` or `./project make dist-arxiv` should correctly create a tar.gz file for ArXiv. However, if you have old files in `.build/tex/build/` or `.build/tex/build/fig`, they may be included too. So double-check and clean those out first, or tidy up the tar.gz file, or improve the `make` rule. | 07 October 2020, 22:01:27 UTC |
| 7e5a841 | Boud Roukema | 07 October 2020, 21:27:25 UTC | Update README.md - paper name; elaphrocentre specific info This commit adds some updates to README.md - paper name, Zenodo ID; info specific to the elaphrocentre galaxy pipeline project; overall directory structure (which is not at all obvious to people new to Maneage). | 07 October 2020, 21:27:25 UTC |
| a8bccd5 | Boud Roukema | 07 October 2020, 20:44:19 UTC | Explain strong tail of insignificant values of GalsizeFracSlope | 07 October 2020, 20:44:19 UTC |
| 81e4878 | Boud Roukema | 07 October 2020, 20:05:53 UTC | Add cos variance to infall tau slope The cosmic variance for the infall tau slope is high enough that we need to state it. This commit calculates and states this value. | 07 October 2020, 20:05:53 UTC |
| f95ad34 | Boud Roukema | 06 October 2020, 19:06:36 UTC | Merge branch 'elaphro' into N128cubed | 06 October 2020, 19:06:36 UTC |
| c6b5713 | Boud Roukema | 06 October 2020, 14:00:32 UTC | Minor text smoothing This commit removes the "A closer examination ..." sentence and does some other minor text smoothing. | 06 October 2020, 19:05:41 UTC |
| 374c6b8 | Marius Peper | 06 October 2020, 11:28:21 UTC | Fix a small typo in the text | 06 October 2020, 19:05:34 UTC |
| 42ed3ef | Boud Roukema | 05 October 2020, 18:09:47 UTC | Text smoothing: 3. results, 4. discussion, 5. conclusion Minor text smoothing; some corrections of wrong summaries/inferences or somewhat misleading or confusing text. Trivia: two cases of LSGB corrected to LSBG; MNRAS wants 3-author papers to be cited with '*' the first time, to list all three authors (if I remember correctly). | 06 October 2020, 19:05:26 UTC |
