Reproducible paper template =========================== Copyright (C) 2018-2019 Mohammad Akhlaghi See the end of the file for license conditions. This project contains a **fully working template** for doing reproducible research (or writing a reproducible paper) as defined in the link below. If the link below is not accessible at the time of reading, please see the appendix at the end of this file for a portion of its introduction. Some [slides](http://akhlaghi.org/pdf/reproducible-paper.pdf) are also available to help demonstrate the concept implemented here. http://akhlaghi.org/reproducible-science.html This template is created with the aim of supporting reproducible research by making it easy to start a project in this framework. As shown below, it is very easy to customize this reproducible paper template for any particular (research) project and expand it as it starts and evolves. It can be run with no modification (as described in `README.md`) as a demonstration and customized for use in any project as fully described below. A project designed using this template will download and build all the necessary libraries and programs for working in a closed environment (highly independent of the host operating system) with fixed versions of the necessary dependencies. The tarballs for building the local environment are also collected in a [separate repository](https://gitlab.com/makhlaghi/reproducible-paper-dependencies). The final output of the project is [a paper](https://gitlab.com/makhlaghi/reproducible-paper-output/raw/master/paper.pdf). Notice the last paragraph of the Acknowledgments where all the necessary software are mentioned with their versions. Below, we start with a discussion of why Make was chosen as the high-level language/framework for project management and how to learn and master Make easily (and freely). The general architecture and design of the project is then discussed to help you navigate the files and their contents. This is followed by a checklist for the easy/fast customization of this template to your exciting research. We continue with some tips and guidelines on how to manage or extend your project as it grows based on our experiences with it so far. The main body concludes with a description of possible future improvements that are planned for the template (but not yet implemented). As discussed above, we end with a short introduction on the necessity of reproducible science in the appendix. Please don't forget to share your thoughts, suggestions and criticisms on this template. Maintaining and designing this template is itself a separate project, so please join us if you are interested. Once it is mature enough, we will describe it in a paper (written by all contributors) for a formal introduction to the community. Why Make? --------- When batch processing is necessary (no manual intervention, as in a reproducible project), shell scripts are usually the first solution that come to mind. However, the inherent complexity and non-linearity of progress in a scientific project (where experimentation is key) make it hard to manage the script(s) as the project evolves. For example, a script will start from the top/start every time it is run. So if you have already completed 90% of a research project and want to run the remaining 10% that you have newly added, you have to run the whole script from the start again. Only then will you see the effects of the last new steps (to find possible errors, or better solutions and etc). It is possible to manually ignore/comment parts of a script to only do a special part. However, such checks/comments will only add to the complexity of the script and will discourage you to play-with/change an already completed part of the project when an idea suddenly comes up. It is also prone to very serious bugs in the end (when trying to reproduce from scratch). Such bugs are very hard to notice during the work and frustrating to find in the end. The Make paradigm, on the other hand, starts from the end: the final *target*. It builds a dependency tree internally, and finds where it should start each time the project is run. Therefore, in the scenario above, a researcher that has just added the final 10% of steps of her research to her Makefile, will only have to run those extra steps. With Make, it is also trivial to change the processing of any intermediate (already written) *rule* (or step) in the middle of an already written analysis: the next time Make is run, only rules that are affected by the changes/additions will be re-run, not the whole analysis/project. This greatly speeds up the processing (enabling creative changes), while keeping all the dependencies clearly documented (as part of the Make language), and most importantly, enabling full reproducibility from scratch with no changes in the project code that was working during the research. This will allow robust results and let the scientists get to what they do best: experiment and be critical to the methods/analysis without having to waste energy and time on technical problems that come up as a result of that experimentation in scripts. Since the dependencies are clearly demarcated in Make, it can identify independent steps and run them in parallel. This further speeds up the processing. Make was designed for this purpose. It is how huge projects like all Unix-like operating systems (including GNU/Linux or Mac OS operating systems) and their core components are built. Therefore, Make is a highly mature paradigm/system with robust and highly efficient implementations in various operating systems perfectly suited for a complex non-linear research project. Make is a small language with the aim of defining *rules* containing *targets*, *prerequisites* and *recipes*. It comes with some nice features like functions or automatic-variables to greatly facilitate the management of text (filenames for example) or any of those constructs. For a more detailed (yet still general) introduction see the article on Wikipedia: https://en.wikipedia.org/wiki/Make_(software) Make is a +40 year old software that is still evolving, therefore many implementations of Make exist. The only difference in them is some extra features over the [standard definition](https://pubs.opengroup.org/onlinepubs/009695399/utilities/make.html) (which is shared in all of them). This template has been created for GNU Make which is the most common, most actively developed, and most advanced implementation. Just note that this template downloads, builds, internally installs, and uses its own dependencies (including GNU Make), so you don't have to have it installed before you try it out. How can I learn Make? --------------------- The GNU Make book/manual (links below) is arguably the best place to learn Make. It is an excellent and non-technical book to help get started (it is only non-technical in its first few chapters to get you started easily). It is freely available and always up to date with the current GNU Make release. It also clearly explains which features are specific to GNU Make and which are general in all implementations. So the first few chapters regarding the generalities are useful for all implementations. The first link below points to the GNU Make manual in various formats and in the second, you can download it in PDF (which may be easier for a first time reading). https://www.gnu.org/software/make/manual/ https://www.gnu.org/software/make/manual/make.pdf If you use GNU Make, you also have the whole GNU Make manual on the command-line with the following command (you can come out of the "Info" environment by pressing `q`). ```shell $ info make ``` If you aren't familiar with the Info documentation format, we strongly recommend running `$ info info` and reading along. In less than an hour, you will become highly proficient in it (it is very simple and has a great manual for itself). Info greatly simplifies your access (without taking your hands off the keyboard!) to many manuals that are installed on your system, allowing you to be much more efficient as you work. If you use the GNU Emacs text editor (or any of its variants), you also have access to all Info manuals while you are writing your projects (again, without taking your hands off the keyboard!). Published works using this template ----------------------------------- The list below shows some of the works that have already been published with (earlier versions of) this template. Note that this template is evolving, so some details may be different in them. The more recent ones can be used as a good working example besides the default template. - Infante-Sainz et al. ([2019](https://arxiv.org/abs/1911.01430)), accepted for publication in MNRAS. The version controlled project source is available [on GitLab](https://gitlab.com/infantesainz/sdss-extended-psfs-paper) and is also archived on Zenodo with all the necessary software tarballs: [zenodo.3524937](https://zenodo.org/record/3524937). - Akhlaghi ([2019](https://arxiv.org/abs/1909.11230), IAU Symposium 355). The version controlled project source is available [on GitLab](https://gitlab.com/makhlaghi/iau-symposium-355) and is also archived on Zenodo with all the necessary software tarballs: [zenodo.3408481](https://doi.org/10.5281/zenodo.3408481). - Section 7.3 of Bacon et al. ([2017](http://adsabs.harvard.edu/abs/2017A%26A...608A...1B), A&A 608, A1): The version controlled project source is available [on GitLab](https://gitlab.com/makhlaghi/muse-udf-origin-only-hst-magnitudes) and a snapshot of the project along with all the necessary input datasets and outputs is available in [zenodo.1164774](https://doi.org/10.5281/zenodo.1164774). - Section 4 of Bacon et al. ([2017](http://adsabs.harvard.edu/abs/2017A%26A...608A...1B), A&A, 608, A1): The version controlled project is available [on GitLab](https://gitlab.com/makhlaghi/muse-udf-photometry-astrometry) and a snapshot of the project along with all the necessary input datasets is available in [zenodo.1163746](https://doi.org/10.5281/zenodo.1163746). - Akhlaghi & Ichikawa ([2015](http://adsabs.harvard.edu/abs/2015ApJS..220....1A), ApJS, 220, 1): The version controlled project is available [on GitLab](https://gitlab.com/makhlaghi/NoiseChisel-paper). This is the very first (and much less mature!) implementation of this template: the history of this template started more than two years after this paper was published. It is a very rudimentary/initial implementation, thus it is only included here for historical reasons. However, the project source is complete, accurate and uploaded to arXiv along with the paper. Citation -------- A paper will be published to fully describe this reproducible paper template. Until then, if you used this template in your work, please cite the paper that implemented its first version: Akhlaghi & Ichikawa ([2015](http://adsabs.harvard.edu/abs/2015ApJS..220....1A), ApJS, 220, 1). The experience gained with this template after several more implementations will be used to make it robust enough for a complete and useful paper to introduce to the community afterwards. Also, when your paper is published, don't forget to add a notice in your own paper (in coordination with the publishing editor) that the paper is fully reproducible and possibly add a sentence or paragraph in the end of the paper shortly describing the concept. This will help spread the word and encourage other scientists to also manage and publish their projects in a reproducible manner. Project architecture ==================== In order to customize this template to your research, it is important to first understand its architecture so you can navigate your way in the directories and understand how to implement your research project within its framework: where to add new files and which existing files to modify for what purpose. But if this the first time you are using this template, before reading this theoretical discussion, please run the template once from scratch without any chages (described in `README.md`). You will see how it works (note that the configure step builds all necessary software, so it can take long, but you can continue reading while its working). The project has two top-level directories: `reproduce` and `tex`. `reproduce` hosts all the software building and analysis steps. `tex` contains all the final paper's components to be compiled into a PDF using LaTeX. The `reproduce` directory has two sub-directories: `software` and `analysis`. As the name says, the former contains all the instructions to download, build and install (independent of the host operating system) the necessary software (these are called by the `./project configure` command). The latter contains instructions on how to use those software to do your project's analysis. After it finishes, `./project configure` will create the following symbolic links in the project's top source directory: `.build` which points to the top build directory and `.local` for easy access to the custom built software installation directory. With these you can easily access the build directory and project-specific software from your top source directory. For example if you run `.local/bin/ls` you will be using the `ls` of the template, which is problably different from your system's `ls` (run them both with `--version` to check). Once the project is configured for your system, `./project prepare` and `./project make` will do the basic preparations and run the project's analysis with the custom version of software. The `project` script is just a wrapper, and with the commands above, it will call `top-prepare.mk` and `top-make.mk` (both are in the `reproduce/analysis/make` directory). In the template, no particular preparation is necessary, so it will immediately finish and instruct you to run `./project make`. But in some projects, it can be very useful to do some very basic preparatory steps on the input data that can greatly optimize running of `./project make`. For example, you may need to query a server, to find how many input files there are. Once that number is known in the preparation phase, `./project make` can parallelize the analysis much more effectively. In terms of organization, `top-prepare.mk` and `top-make.mk` have an identical design, only a minor difference. So, let's continue the template's architecture with `top-make.mk`. Once you understand that, you'll clearly understand `top-prepare.mk` also. These very high-level files are relatively short and heavily commented so hopefully the descriptions in each comment will be enough to understand the general details. As you read this section, please also look at the contents of the mentioned files and directories to fully understand what is going on. Before starting to look into the top `top-make.mk`, it is important to recall that Make defines dependencies by files. Therefore, the input/prerequisite and output of every step/rule must be a file. Also recall that Make will use the modification date of the prerequisite(s) and target files to see if the target must be re-built or not. Therefore during the processing, _many_ intermediate files will be created (see the tips section below on a good strategy to deal with large/huge files). To keep the source and (intermediate) built files separate, the user _must_ define a top-level build directory variable (or `$(BDIR)`) to host all the intermediate files (you defined it during `./project configure`). This directory doesn't need to be version controlled or even synchronized, or backed-up in other servers: its contents are all products, and can be easily re-created any time. As you define targets for your new rules, it is thus important to place them all under sub-directories of `$(BDIR)`. As mentioned above, you always have fast access to this "build"-directory with the `.build` symbolic link. Also, beware to *never* make any manual change in the files of the build-directory, just delete them (so they are re-built). In this architecture, we have two types of Makefiles that are loaded into the top `Makefile`: _configuration-Makefiles_ (only independent variables/configurations) and _workhorse-Makefiles_ (Makefiles that actually contain analysis/processing rules). The configuration-Makefiles are those that satisfy these two wildcards: `reproduce/software/config/installation/*.mk` (for building the necessary software when you run `./project configure`) and `reproduce/analysis/config/*.mk` (for the high-level analysis, when you run `./project make`). These Makefiles don't actually have any rules, they just have values for various free parameters throughout the configuration or analysis. Open a few of them to see for yourself. These Makefiles must only contain raw Make variables (project configurations). By "raw" we mean that the Make variables in these files must not depend on variables in any other configuration-Makefile. This is because we don't want to assume any order in reading them. It is also very important to *not* define any rule, or other Make construct, in these configuration-Makefiles. Following this rule-of-thumb enables you to set these configure-Makefiles as a prerequisite to any target that depends on their variable values. Therefore, if you change any of their values, all targets that depend on those values will be re-built. This is very convenient as your project scales up and gets more complex. The workhorse-Makefiles are those satisfying this wildcard `reproduce/software/make/*.mk` and `reproduce/analysis/make/*.mk`. They contain the details of the processing steps (Makefiles containing rules). Therefore, in this phase *order is important*, because the prerequisites of most rules will be the targets of other rules that will be defined prior to them (not a fixed name like `paper.pdf`). The lower-level rules must be imported into Make before the higher-level ones. All processing steps are assumed to ultimately (usually after many rules) end up in some number, image, figure, or table that will be included in the paper. The writing of these results into the final report/paper is managed through separate LaTeX files that only contain macros (a name given to a number/string to be used in the LaTeX source, which will be replaced when compiling it to the final PDF). So the last target in a workhorse-Makefile is a `.tex` file (with the same base-name as the Makefile, but in `$(BDIR)/tex/macros`). As a result, if the targets in a workhorse-Makefile aren't directly a prerequisite of other workhorse-Makefile targets, they can be a pre-requisite of that intermediate LaTeX macro file and thus be called when necessary. Otherwise, they will be ignored by Make. This template also has a mode to share the build directory between several users of a Unix group (when working on large computer clusters). In this scenario, each user can have their own cloned project source, but share the large built files between each other. To do this, it is necessary for all built files to give full permission to group members while not allowing any other users access to the contents. Therefore the `./project configure` and `./project make` steps must be called with special conditions which are managed in the `--group` option. Let's see how this design is implemented. Please open and inspect `top-make.mk` it as we go along here. The first step (un-commented line) is to import the local configuration (your answers to the questions of `./project configure`). They are defined in the configuration-Makefile `reproduce/software/config/installation/LOCAL.mk` which was also built by `./project configure` (based on the `LOCAL.mk.in` template of the same directory). The next non-commented set of the top `Makefile` defines the ultimate target of the whole project (`paper.pdf`). But to avoid mistakes, a sanity check is necessary to see if Make is being run with the same group settings as the configure script (for example when the project is configured for group access using the `./for-group` script, but Make isn't). Therefore we use a Make conditional to define the `all` target based on the group permissions. Having defined the top/ultimate target, our next step is to include all the other necessary Makefiles. However, order matters in the importing of workhorse-Makefiles and each must also have a TeX macro file with the same base name (without a suffix). Therefore, the next step in the top-level Makefile is to define the `makesrc` variable to keep the base names (without a `.mk` suffix) of the workhorse-Makefiles that must be imported, in the proper order. Finally, we import all the necessary remaining Makefiles: 1) All the analysis configuration-Makefiles with a wildcard. 2) The software configuration-Makefile that contains their version (just in case its necessary). 3) All workhorse-Makefiles in the proper order using a Make `foreach` loop. In short, to keep things modular, readable and manageable, follow these recommendations: 1) Set clear-to-understand names for the configuration-Makefiles, and workhorse-Makefiles, 2) Only import other Makefiles from top Makefile. These will let you know/remember generally which step you are taking before or after another. Projects will scale up very fast. Thus if you don't start and continue with a clean and robust convention like this, in the end it will become very dirty and hard to manage/understand (even for yourself). As a general rule of thumb, break your rules into as many logically-similar but independent steps as possible. The `reproduce/analysis/make/paper.mk` Makefile must be the final Makefile that is included. This workhorse Makefile ends with the rule to build `paper.pdf` (final target of the whole project). If you look in it, you will notice that it starts with a rule to create `$(mtexdir)/project.tex` (`mtexdir` is just a shorthand name for `$(BDIR)/tex/macros` mentioned before). `$(mtexdir)/project.tex` is the connection between the processing/analysis steps of the project, and the steps to build the final PDF. As you see, `$(mtexdir)/project.tex` only instructs LaTeX to import the LaTeX macros of each high-level processing step during the analysis (the separate work-horse Makefiles that you defined and included). During the research, it often happens that you want to test a step that is not a prerequisite of any higher-level operation. In such cases, you can (temporarily) define that processing as a rule in the most relevant workhorse-Makefile and set its target as a prerequisite of its TeX macro. If your test gives a promising result and you want to include it in your research, set it as prerequisites to other rules and remove it from the list of prerequisites for TeX macro file. In fact, this is how a project is designed to grow in this framework. File modification dates (meta data) ----------------------------------- While git does an excellent job at keeping a history of the contents of files, it makes no effort in keeping the file meta data, and in particular the dates of files. Therefore when you checkout to a different branch, files that are re-written by Git will have a newer date than the other project files. However, file dates are important in the current design of the template: Make uses file dates of the pre-requisits and targets to see if the target should be re-built. To fix this problem, for this template we use a forked version of [Metastore](https://github.com/mohammad-akhlaghi/metastore). Metastore use a binary database file (which is called `.file-metadata`) to keep the modification dates of all the files under version control. This file is also under version control, but is hidden (because it shouldn't be modified by hand). During the project's configuration, the template installs to Git hooks to run Metastore 1) before making a commit to update its database with the file dates in a branch, and 2) after doing a checkout, to reset the file-dates after the checkout is complete and re-set the file dates back to what they were. In practice, Metastore should work almost fully invisiablly within your project. The only place you might notice its presence is that you'll see `.file-metadata` in the list of modified/staged files (commonly after merging your branches). Since its a binary file, Git also won't show you the changed contents. In a merge, you can simply accept any changes with `git add -u`. But if Git is telling you that it has changed without a merge (for example if you started a commit, but cancelled it in the middle), you can just do `git checkout .file-metadata` and set it back to its original state. Summary ------- Based on the explanation above, some major design points you should have in mind are listed below. - Define new `reproduce/analysis/make/XXXXXX.mk` workhorse-Makefile(s) with good and human-friendly name(s) replacing `XXXXXX`. - Add `XXXXXX`, as a new line, to the values in `makesrc` of the top-level `Makefile`. - Do not use any constant numbers (or important names like filter names) in the workhorse-Makefiles or paper's LaTeX source. Define such constants as logically-grouped, separate configuration-Makefiles in `reproduce/analysis/config/XXXXX.mk`. Then set this configuration-Makefiles file as a pre-requisite to any rule that uses the variable defined in it. - Through any number of intermediate prerequisites, all processing steps should end in (be a prerequisite of) `$(mtexdir)/project.tex` (defined in `reproduce/analysis/make/paper.mk`). `$(mtexdir)/project.tex` is the bridge between the processing steps and PDF-building steps. Customization checklist ======================= Take the following steps to fully customize this template for your research project. After finishing the list, be sure to run `./project configure` and `project make` to see if everything works correctly. If you notice anything missing or any in-correct part (probably a change that has not been explained here), please let us know to correct it. As described above, the concept of reproducibility (during a project) heavily relies on [version control](https://en.wikipedia.org/wiki/Version_control). Currently this template uses Git as its main version control system. If you are not already familiar with Git, please read the first three chapters of the [ProGit book](https://git-scm.com/book/en/v2) which provides a wonderful practical understanding of the basics. You can read later chapters as you get more advanced in later stages of your work. First custom commit ------------------- - **Get this repository and its history** (if you don't already have it): Arguably the easiest way to start is to clone this repository as shown below. As you see, after the cloning some further corrections to your clone's Git settings are necessary: first, you need to remove all possibly existing Git tags from the template's history. Then you need to rename the conventional `origin` remote server, and the `master` branch. This renaming allows you to use these standard names for your own customized project (which greatly helps because this convention is widely used). ```shell $ git clone git://git.sv.gnu.org/reproduce # Clone/copy the project and its history. $ mv reproduce my-project # Change the name to your project's name. $ cd my-project # Go into the cloned directory. $ git tag | xargs git tag -d # Delete all template tags. $ git config remote.origin.tagopt --no-tags # No tags in future fetch/pull from this template. $ git remote rename origin template-origin # Rename current/only remote to "template-origin". $ git branch -m template # Rename current/only branch to "template". $ git checkout -b master # Create and enter new "master" branch. ``` - **Test the template**: Before making any changes, it is important to test it and see if everything works properly with the commands below. If there is any problem in the `./project configure` or `./project make` steps, please contact us to fix the problem before continuing. Since the building of dependencies in configuration can take long, you can take the next few steps (editing the files) while its working (they don't affect the configuration). After `./project make` is finished, open `paper.pdf`. If it looks fine, you are ready to start customizing the template for your project. But before that, clean all the extra template outputs with `make clean` as shown below. ```shell $ ./project configure # Build the project's software environment (can take an hour or so). $ ./project prepare # Pre-processing preparations (doing nothing in the raw template). $ ./project make # Do the processing and build paper (just a simple demo in the template). # Open 'paper.pdf' and see if everything is ok. ``` - **Software building status**: While the `./project configure` command of the step above is busy building all the different software, you can check the status by running the following command in another terminal (but same project source directory). See the "Inspecting status" section below for more. ```shell $ while true; do echo; date; ls .build/software/build-tmp; sleep 1; done ``` - **Setup the remote**: You can use any [hosting facility](https://en.wikipedia.org/wiki/Comparison_of_source_code_hosting_facilities) that supports Git to keep an online copy of your project's version controlled history. We recommend [GitLab](https://gitlab.com) because it is [more ethical (although not perfect)](https://www.gnu.org/software/repo-criteria-evaluation.html), and later you can also host GitLab on your own server. Anyway, create an account in your favorite hosting facility (if you don't already have one), and define a new project there. It will give you a URL (usually starting with `git@` and ending in `.git`), put this URL in place of `XXXXXXXXXX` in the first command below. With the second command, "push" your `master` branch to your `origin` remote, and (with the `--set-upstream` option) set them to track/follow each other. However, the `template` branch is currently tracking/following your `template-origin` remote (automatically set when you cloned the template). So when pushing the `template` branch to your `origin` remote, you _shouldn't_ use `--set-upstream`. With the last command, you can actually check this (which local and remote branches are tracking each other). ```shell git remote add origin XXXXXXXXXX # Newly created repo is now called 'origin'. git push --set-upstream origin master # Push 'master' branch to 'origin' (enable tracking). git push origin template # Push 'template' branch to 'origin' (no tracking). ``` - **Title**, **short description** and **author**: The title and basic information of your project's output PDF paper should be added in `paper.tex`. You should see the relevant place in the preamble (prior to `\begin{document}`. After you are done, run the `./project make` command again to see your changes in the final PDF, and make sure that your changes don't cause a crash in LaTeX. Of course, if you use a different LaTeX package/style for managing the title and authors (in particular a specific journal's style), please feel free to use it your own methods after finishing this checklist and doing your first commit. - **Delete dummy parts (can be done later)**: The template contains some parts that are only for the initial/test run, mainly as a demonstration of important steps. They not for any real analysis. You can remove these parts in the file below - `paper.tex`: 1) Delete the text of the abstract (from `\includeabstract{` to `\vspace{0.25cm}`) and start writing your own (a single sentence can be enough now). 2) Add some keywords under it in the keywords part. 3) Delete everything between `%% Start of main body.` and `%% End of main body.`. 4) Remove the notice in the "Acknowledgments" section (in `\new{}`) and add Acknowledge your funding sources. Just don't delete the existing acknowledgment statement: this template was designed by funding from many grants. Since you are using it in your work, it is necessary to acknowledge them in your work also. - `reproduce/analysis/make/top-make.mk`: Delete the `delete-me` line in the `makesrc` definition. Just make sure there is no empty line between the `download \` and `paper` lines. - Delete all `delete-me*` files in the following directories: ```shell $ rm tex/src/delete-me* $ rm reproduce/analysis/make/delete-me* $ rm reproduce/analysis/config/delete-me* ``` - Re-make the project (after a cleaning) to see if you haven't introduced any errors. ```shell $ ./project make clean $ ./project make ``` - **Copyright and License notice**: To be usable/modifiable by others after publication, _all_ the "copyright-able" files in your project (those larger than 10 lines) must have a copyright notice and license notice. Please take a moment to look at several existing files to see a few examples. The copyright notice is usually close to the start of the file, it is the line starting with `Copyright (C)` and containing a year and the author's name. The License notice is a short (or full, when its not too long, like the MIT license) description of the copyright license, usually less than three paragraphs. Don't forget to add these _two_ notices to any new file you add to this template for your project. When you modify an existing template file (which already has the notices), just add a copyright notice in your name under the existing one(s), like the line with capital letters below. Please add this line with your name and email address to `paper.tex` and `tex/src/preamble-header.tex`. ``` Copyright (C) 2018-2019 Mohammad Akhlaghi Copyright (C) 2019 YOUR NAME ``` - **Your first commit**: You have already made some small and basic changes in the steps above and you are in the `master` branch. So, you can officially make your first commit in your project's history. But before that you need to make sure that there are no problems in the project (this is a good habit to always re-build the system before a commit to be sure it works as expected). ```shell $ git status # See which files you have changed. $ git diff # See the lines you have added/changed. $ ./project make # Make sure everything builds successfully. $ git add -u # Put all tracked changes in staging area. $ git status # Make sure everything is fine. $ git commit # Your first commit, add a nice description. $ git tag -a v0 # Tag this as the zero-th version of your project. ``` - **Push to the remote**: Push your first commit and its tag to your remote repository with these commands. Since we have setup your `master` branch to follow `origin/master`, you can just use `git push` from now on. ```shell $ git push $ git push --tags ``` - **Start your exciting research**: You are now ready to add flesh and blood to this raw skeleton by further modifying and adding your exciting research steps. You can use the "published works" section in the introduction (above) as some fully working models to learn from. Also, don't hesitate to contact us if you have any questions. Other basic customizations -------------------------- - **High-level software**: The template installs all the software that your project needs. You can specify which software your project needs in `reproduce/software/config/installation/TARGETS.mk`. The necessary software are classified into two classes: 1) programs or libraries (usually written in C/C++) which are run directly by the operating system. 2) Python modules/libraries that are run within Python. By default `TARGETS.mk` only has GNU Astronomy Utilities (Gnuastro) as one scientific program and Astropy as one scientific Python module. Both have many dependencies which will be installed into your project during the configuration step. To see a list of software that are currently ready to be built in the template, see `reproduce/software/config/installation/versions.mk` (which has their versions also), the comments in `TARGETS.mk` describe how to use the software name from `versions.mk`. Currently the raw pipeline just uses Gnuastro to make the demonstration plots. Therefore if you don't need Gnuastro, go through the analysis steps in `reproduce/analysis` and remove all its use cases (clearly marked). - **Input dataset**: The input datasets are managed through the `reproduce/analysis/config/INPUTS.mk` file. It is best to gather all the information regarding all the input datasets into this one central file. To ensure that the proper dataset is being downloaded and used by the project, it is also recommended get an [MD5 checksum](https://en.wikipedia.org/wiki/MD5) of the file and include that in `INPUTS.mk` so the project can check it automatically. The preparation/downloading of the input datasets is done in `reproduce/analysis/make/download.mk`. Have a look there to see how these values are to be used. This information about the input datasets is also used in the initial `configure` script (to inform the users), so also modify that file. You can find all occurrences of the template dataset with the command below and replace it with your input's dataset. ```shell $ grep -ir wfpc2 ./* ``` - **`README.md`**: Correct all the `XXXXX` place holders (name of your project, your own name, address of the template's online/remote repository, link to download dependencies and etc). Generally, read over the text and update it where necessary to fit your project. Don't forget that this is the first file that is displayed on your online repository and also your colleagues will first be drawn to read this file. Therefore, make it as easy as possible for them to start with. Also check and update this file one last time when you are ready to publish your project's paper/source. - **Feedback**: As you use the template you will notice many things that if implemented from the start would have been very useful for your work. This can be in the actual scripting and architecture of the template, or useful implementation and usage tips, like those below. In any case, please share your thoughts and suggestions with us, so we can add them here for everyone's benefit. - **Updating TeXLive**: Currently the only software package that the template doesn't build is TeXLive (since its not part of the analysis, only for demonstration: building the PDf). So when a new version of TeXLive comes (once every year), if you would like to build the paper, its necessary to update it in your project (otherwise the configure script will crash). To do that, just modify the years in `reproduce/software/config/installation/texlive.conf`, then delete `.build/software/tarballs/install-tl-unx.tar.gz`. The next time you run `./project configure`, the new TeXLive will be installed and used. - **Pre-publication: add notice on reproducibility**: Add a notice somewhere prominent in the first page within your paper, informing the reader that your research is fully reproducible. For example in the end of the abstract, or under the keywords with a title like "reproducible paper". This will encourage them to publish their own works in this manner also and also will help spread the word. Tips for designing your project =============================== The following is a list of design points, tips, or recommendations that have been learned after some experience with this type of project management. Please don't hesitate to share any experience you gain after using it with us. In this way, we can add it here (with full giving credit) for the benefit of others. - **Modularity**: Modularity is the key to easy and clean growth of a project. So it is always best to break up a job into as many sub-components as reasonable. Here are some tips to stay modular. - *Short recipes*: if you see the recipe of a rule becoming more than a handful of lines which involve significant processing, it is probably a good sign that you should break up the rule into its main components. Try to only have one major processing step per rule. - *Context-based (many) Makefiles*: For maximum modularity, this design allows easy inclusion of many Makefiles: in `reproduce/analysis/make/*.mk` for analysis steps, and `reproduce/software/make/*.mk` for building software. So keep the rules for closely related parts of the processing in separate Makefiles. - *Descriptive names*: Be very clear and descriptive with the naming of the files and the variables because a few months after the processing, it will be very hard to remember what each one was for. Also this helps others (your collaborators or other people reading the project source after it is published) to more easily understand your work and find their way around. - *Naming convention*: As the project grows, following a single standard or convention in naming the files is very useful. Try best to use multiple word filenames for anything that is non-trivial (separating the words with a `-`). For example if you have a Makefile for creating a catalog and another two for processing it under models A and B, you can name them like this: `catalog-create.mk`, `catalog-model-a.mk` and `catalog-model-b.mk`. In this way, when listing the contents of `reproduce/analysis/make` to see all the Makefiles, those related to the catalog will all be close to each other and thus easily found. This also helps in auto-completions by the shell or text editors like Emacs. - *Source directories*: If you need to add files in other languages for example in shell, Python, AWK or C, keep the files in the same language in a separate directory under `reproduce/analysis`, with the appropriate name. - *Configuration files*: If your research uses special programs as part of the processing, put all their configuration files in a devoted directory (with the program's name) within `reproduce/software/config`. Similar to the `reproduce/software/config/gnuastro` directory (which is put in the template as a demo in case you use GNU Astronomy Utilities). It is much cleaner and readable (thus less buggy) to avoid mixing the configuration files, even if there is no technical necessity. - **Contents**: It is good practice to follow the following recommendations on the contents of your files, whether they are source code for a program, Makefiles, scripts or configuration files (copyrights aren't necessary for the latter). - *Copyright*: Always start a file containing programming constructs with a copyright statement like the ones that this template starts with (for example in the top level `Makefile`). - *Comments*: Comments are vital for readability (by yourself in two months, or others). Describe everything you can about why you are doing something, how you are doing it, and what you expect the result to be. Write the comments as if it was what you would say to describe the variable, recipe or rule to a friend sitting beside you. When writing the project it is very tempting to just steam ahead with commands and codes, but be patient and write comments before the rules or recipes. This will also allow you to think more about what you should be doing. Also, in several months when you come back to the code, you will appreciate the effort of writing them. Just don't forget to also read and update the comment first if you later want to make changes to the code (variable, recipe or rule). As a general rule of thumb: first the comments, then the code. - *File title*: In general, it is good practice to start all files with a single line description of what that particular file does. If further information about the totality of the file is necessary, add it after a blank line. This will help a fast inspection where you don't care about the details, but just want to remember/see what that file is (generally) for. This information must of course be commented (its for a human), but this is kept separate from the general recommendation on comments, because this is a comment for the whole file, not each step within it. - **Make programming**: Here are some experiences that we have come to learn over the years in using Make and are useful/handy in research contexts. - *Environment of each recipe*: If you need to define a special environment (or alises, or scripts to run) for all the recipes in your Makefiles, you can use the Bash startup file `reproduce/software/bash/bashrc.sh`. This file is loaded before every Make recipe is run, just like the `.bashrc` in your home directory is loaded everytime you start a new interactive, non-login terminal. See the comments in that file for more. - *Automatic variables*: These are wonderful and very useful Make constructs that greatly shrink the text, while helping in read-ability, robustness (less bugs in typos for example) and generalization. For example even when a rule only has one target or one prerequisite, always use `$@` instead of the target's name, `$<` instead of the first prerequisite, `$^` instead of the full list of prerequisites and etc. You can see the full list of automatic variables [here](https://www.gnu.org/software/make/manual/html_node/Automatic-Variables.html). If you use GNU Make, you can also see this page on your command-line: ```shell $ info make "automatic variables" ``` - *Debug*: Since Make doesn't follow the common top-down paradigm, it can be a little hard to get accustomed to why you get an error or un-expected behavior. In such cases, run Make with the `-d` option. With this option, Make prints a full list of exactly which prerequisites are being checked for which targets. Looking (patiently) through this output and searching for the faulty file/step will clearly show you any mistake you might have made in defining the targets or prerequisites. - *Large files*: If you are dealing with very large files (thus having multiple copies of them for intermediate steps is not possible), one solution is the following strategy (Also see the next item on "Fast access to temporary files"). Set a small plain text file as the actual target and delete the large file when it is no longer needed by the project (in the last rule that needs it). Below is a simple demonstration of doing this. In it, we use Gnuastro's Arithmetic program to add all pixels of the input image with 2 and create `large1.fits`. We then subtract 2 from `large1.fits` to create `large2.fits` and delete `large1.fits` in the same rule (when its no longer needed). We can later do the same with `large2.fits` when it is no longer needed and so on. ``` large1.fits.txt: input.fits astarithmetic $< 2 + --output=$(subst .txt,,$@) echo "done" > $@ large2.fits.txt: large1.fits.txt astarithmetic $(subst .txt,,$<) 2 - --output=$(subst .txt,,$@) rm $(subst .txt,,$<) echo "done" > $@ ``` A more advanced Make programmer will use Make's [call function](https://www.gnu.org/software/make/manual/html_node/Call-Function.html) to define a wrapper in `reproduce/analysis/make/initialize.mk`. This wrapper will replace `$(subst .txt,,XXXXX)`. Therefore, it will be possible to greatly simplify this repetitive statement and make the code even more readable throughout the whole project. - *Fast access to temporary files*: Most Unix-like operating systems will give you a special shared-memory device (directory): on systems using the GNU C Library (all GNU/Linux system), it is `/dev/shm`. The contents of this directory are actually in your RAM, not in your persistance storage like the HDD or SSD. Reading and writing from/to the RAM is much faster than persistant storage, so if you have enough RAM available, it can be very beneficial for large temporary files to be put there. You can use the `mktemp` program to give the temporary files a randomly-set name, and use text files as targets to keep that name (as described in the item above under "Large files") for later deletion. For example, see the minimal working example Makefile below (which you can actually put in a `Makefile` and run if you have an `input.fits` in the same directory, and Gnuastro is installed). ``` .ONESHELL: .SHELLFLAGS = -ec all: mean-std.txt shm-template = /dev/shm/$(shell whoami)-XXXXXXXXXX large1.txt: input.fits out=$$(mktemp $(shm-template)) astarithmetic $< 2 + --output=$$out.fits echo "$$out" > $@ large2.txt: large1.txt input=$$(cat $<) out=$$(mktemp $(shm-template)) astarithmetic $$input.fits 2 - --output=$$out.fits rm $$input.fits $$input echo "$$out" > $@ mean-std.txt: large2.txt input=$$(cat $<) aststatistics $$input.fits --mean --std > $@ rm $$input.fits $$input ``` The important point here is that the temporary name template (`shm-template`) has no suffix. So you can add the suffix corresponding to your desired format afterwards (for example `$$out.fits`, or `$$out.txt`). But more importantly, when `mktemp` sets the random name, it also checks if no file exists with that name and creates a file with that exact name at that moment. So at the end of each recipe above, you'll have two files in your `/dev/shm`, one empty file with no suffix one with a suffix. The role of the file without a suffix is just to ensure that the randomly set name will not be used by other calls to `mktemp` (when running in parallel) and it should be deleted with the file containing a suffix. This is the reason behind the `rm $$input.fits $$input` command above: to make sure that first the file with a suffix is deleted, then the core random file (note that when working in parallel on powerful systems, in the time between deleting two files of a single `rm` command, many things can happen!). When using this template, you can put the definition of `shm-template` in `reproduce/analysis/make/initialize.mk` to be usable in all the different Makefiles of your analysis, and you won't need the three lines above it. **Finally, BE RESPONSIBLE:** after you are finished, be sure to clean up any possibly remaining files (due to crashes in the processing while you are working), otherwise your RAM may fill up very fast. You can do it easily with a command like this on your command-line: `rm -f /dev/shm/$(whoami)-*`. - **Software tarballs and raw inputs**: It is critically important to document the raw inputs to your project (software tarballs and raw input data): - *Keep the source tarball of dependencies*: After configuration finishes, the `.build/software/tarballs` directory will contain all the software tarballs that were necessary for your project. You can mirror the contents of this directory to keep a backup of all the software tarballs used in your project (possibly as another version controlled repository) that is also published with your project. Note that software web-pages are not written in stone and can suddenly go offline or not be accessible in some conditions. This backup is thus very important. If you intend to release your project in a place like Zenodo, you can upload/keep all the necessary tarballs (and data) there with your project. [zenodo.1163746](https://doi.org/10.5281/zenodo.1163746) is one example of how the data, Gnuastro (main software used) and all major Gnuastro's dependencies have been uploaded with the project's source. Just note that this is only possible for free and open-source software. - *Keep your input data*: The input data is also critical to the project's reproducibility, so like the above for software, make sure you have a backup of them, or their persistent identifiers (PIDs). - **Version control**: Version control is a critical component of this template. Here are some tips to help in effectively using it. - *Regular commits*: It is important (and extremely useful) to have the history of your project under version control. So try to make commits regularly (after any meaningful change/step/result). - *Keep template up-to-date*: In time, this template is going to become more and more mature and robust (thanks to your feedback and the feedback of other users). Bugs will be fixed and new/improved features will be added. So every once and a while, you can run the commands below to pull new work that is done in this template. If the changes are useful for your work, you can merge them with your project to benefit from them. Just pay **very close attention** to resolving possible **conflicts** which might happen in the merge (updated settings that you have customized in the template). ```shell $ git checkout template $ git pull # Get recent work in the template $ git log XXXXXX..XXXXXX --reverse # Inspect new work (replace XXXXXXs with hashs mentioned in output of previous command). $ git log --oneline --graph --decorate --all # General view of branches. $ git checkout master # Go to your top working branch. $ git merge template # Import all the work into master. ``` - *Adding this template to a fork of your project*: As you and your colleagues continue your project, it will be necessary to have separate forks/clones of it. But when you clone your own project on a different system, or a colleague clones it to collaborate with you, the clone won't have the `template-origin` remote that you started the project with. As shown in the previous item above, you need this remote to be able to pull recent updates from the template. The steps below will setup the `template-origin` remote, and a local `template` branch to track it, on the new clone. ```shell $ git remote add template-origin git://git.sv.gnu.org/reproduce $ git fetch template-origin $ git checkout -b template --track template-origin/master ``` - *Commit message*: The commit message is a very important and useful aspect of version control. To make the commit message useful for others (or yourself, one year later), it is good to follow a consistent style. The template already has a consistent formatting (described below), which you can also follow in your project if you like. You can see many examples by running `git log` in the `template` branch. If you intend to push commits to the main template, for the consistency of the template, it is necessary to follow these guidelines. 1) No line should be more than 75 characters (to enable easy reading of the message when you run `git log` on the standard 80-character terminal). 2) The first line is the title of the commit and should summarize it (so `git log --oneline` can be useful). The title should also not end with a point (`.`, because its a short single sentence, so a point is not necessary and only wastes space). 3) After the title, leave an empty line and start the body of your message (possibly containing many paragraphs). 4) Describe the context of your commit (the problem it is trying to solve) as much as possible, then go onto how you solved it. One suggestion is to start the main body of your commit with "Until now ...", and continue describing the problem in the first paragraph(s). Afterwards, start the next paragraph with "With this commit ...". - *Tags*: To help manage the history, tag all major commits. This helps make a more human-friendly output of `git describe`: for example `v1-4-gaafdb04` states that we are on commit `aafdb04` which is 4 commits after tag `v1`. The output of `git describe` is included in your final PDF as part of this project. Also, if you use reproducibility-friendly software like Gnuastro, this value will also be included in all output files, see the description of `COMMIT` in [Output headers](https://www.gnu.org/software/gnuastro/manual/html_node/Output-headers.html). In the checklist above, you tagged the first commit of your project with `v0`. Here is one suggestion on when to tag: when you have fully adopted the template and have got the first (initial) results, you can make a `v1` tag. Subsequently when you first start reporting the results to your colleagues, you can tag the commit as `v2` and increment the version on every later circulation, or referee submission. - *Project outputs*: During your research, it is possible to checkout a specific commit and reproduce its results. However, the processing can be time consuming. Therefore, it is useful to also keep track of the final outputs of your project (at minimum, the paper's PDF) in important points of history. However, keeping a snapshot of these (most probably large volume) outputs in the main history of the project can unreasonably bloat it. It is thus recommended to make a separate Git repo to keep those files and keep your project's source as small as possible. For example if your project is called `my-exciting-project`, the name of the outputs repository can be `my-exciting-project-output`. This enables easy sharing of the output files with your co-authors (with necessary permissions) and not having to bloat your email archive with extra attachments also (you can just share the link to the online repo in your communications). After the research is published, you can also release the outputs repository, or you can just delete it if it is too large or un-necessary (it was just for convenience, and fully reproducible after all). For example this template's output is available for demonstration in the separate [reproducible-paper-output](https://gitlab.com/makhlaghi/reproducible-paper-output) repository. - *Full Git history in one file*: When you are publishing your project (for example to Zenodo for long term preservation), it is more convenient to have the whole project's Git history into one file to save with your datasets. Afterall, you can't be sure that your current Git server (for example Gitlab, Github, or Bitbucket) will be active forever. While they are good for the immediate future, you can't rely on them for archival purposes. Fortunately keeping your whole history in one file is easy with Git using the following commands. To learn more about it, run `git help bundle`. - "bundle" your project's history into one file (just don't forget to change `my-project-git.bundle` to a descriptive name of your project): ```shell $ git bundle create my-project-git.bundle --all ``` - You can easily upload `my-project-git.bundle` anywhere. Later, if you need to unbundle it, you can use the following command. ```shell $ git clone my-project-git.bundle ``` - **Inspecting software building status**: When you run `./project configure`, several programs and libraries start to get configured and build (in many cases, simultaneously). To understand the building process, or for debugging a strange situation, it is sometimes useful to know which programs are being built at every moment. To do this, you can look into the `.build/software/build-tmp` directory (from the top project directory). This temporary directory is only present while building the software. At every moment, it contains the unpacked source tarball directories of the all the packages that are being built. After a software is successfully installed in your project, it is removed from this directory. To automatically get a listing of this directory every second, you can run the command below (on another terminal while the software are being built). Press `CTRL-C` to stop it and return back to the command-line). ```shell $ while true; do echo; date; ls .build/software/build-tmp; sleep 1; done ``` Future improvements =================== This is an evolving project and as time goes on, it will evolve and become more robust. Some of the most prominent issues we plan to implement in the future are listed below, please join us if you are interested. Package management ------------------ It is important to have control of the environment of the project. The current template builds the higher-level programs (for example GNU Bash, GNU Make, GNU AWK and domain-specific software) it needs, then sets `PATH` so the analysis is done only with the project's built software. But currently the configuration of each program is in the Makefile rules that build it. This is not good because a change in the build configuration does not automatically cause a re-build. Also, each separate project on a system needs to have its own built tools (that can waste a lot of space). A good solution is based on the [Nix package manager](https://nixos.org/nix/about.html): a separate file is present for each software, containing all the necessary info to build it (including its URL, its tarball MD5 hash, dependencies, configuration parameters, build steps and etc). Using this file, a script can automatically generate the Make rules to download, build and install program and its dependencies (along with the dependencies of those dependencies and etc). All the software are installed in a "store". Each installed file (library or executable) is prefixed by a hash of this configuration (and the OS architecture) and the standard program name. For example (from the Nix webpage): ``` /nix/store/b6gvzjyb2pg0kjfwrjmg1vfhh54ad73z-firefox-33.1/ ``` The important thing is that the "store" is *not* in the project's search path. After the complete installation of the software, symbolic links are made to populate each project's program and library search paths without a hash. This hash will be unique to that particular software and its particular configuration. So simply by searching for this hash in the installed directory, we can find the installed files of that software to generate the links. This scenario has several advantages: 1) a change in a software's build configuration triggers a rebuild. 2) a single "store" can be used in many projects, thus saving space and configuration time for new projects (that commonly have large overlaps in lower-level programs). Appendix: Necessity of exact reproduction in scientific research ================================================================ In case [the link above](http://akhlaghi.org/reproducible-science.html) is not accessible at the time of reading, here is a copy of the introduction of that link, describing the necessity for a reproducible project like this (copied on February 7th, 2018): The most important element of a "scientific" statement/result is the fact that others should be able to falsify it. The Tsunami of data that has engulfed astronomers in the last two decades, combined with faster processors and faster internet connections has made it much more easier to obtain a result. However, these factors have also increased the complexity of a scientific analysis, such that it is no longer possible to describe all the steps of an analysis in the published paper. Citing this difficulty, many authors suffice to describing the generalities of their analysis in their papers. However, It is impossible to falsify (or even study) a result if you can't exactly reproduce it. The complexity of modern science makes it vitally important to exactly reproduce the final result. Because even a small deviation can be due to many different parts of an analysis. Nature is already a black box which we are trying so hard to comprehend. Not letting other scientists see the exact steps taken to reach a result, or not allowing them to modify it (do experiments on it) is a self-imposed black box, which only exacerbates our ignorance. Other scientists should be able to reproduce, check and experiment on the results of anything that is to carry the "scientific" label. Any result that is not reproducible (due to incomplete information by the author) is not scientific: the readers have to have faith in the subjective experience of the authors in the very important choice of configuration values and order of operations: this is contrary to the scientific spirit. Copyright information --------------------- This file is part of the reproducible paper template http://savannah.nongnu.org/projects/reproduce This template is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This template is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with Template. If not, see .