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diff --git a/README-hacking.md b/README-hacking.md new file mode 100644 index 0000000..7fb42a2 --- /dev/null +++ b/README-hacking.md @@ -0,0 +1,999 @@ +Reproducible paper template +=========================== + +This project contains a **fully working template** for a high-level +research reproduction pipeline, or 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 template reproducible paper pipeline for any +particular research/job 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. + +The pipeline 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 reproducible paper +output](https://gitlab.com/makhlaghi/reproducible-paper-output/raw/master/paper.pdf) +of this pipeline is also present in [a separate +repository](https://gitlab.com/makhlaghi/reproducible-paper-output). Notice +the last paragraph of the Acknowledgments where all the dependencies are +mentioned with their versions. + +Below, we start with a discussion of why Make was chosen as the high-level +language/framework for this research reproduction pipeline and how to learn +and master Make easily (and freely). The general architecture and design of +the pipeline 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 pipeline to your exciting research. We continue with some tips and +guidelines on how to manage or extend the pipeline as your research 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 +pipeline (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 pipeline. Maintaining and designing this pipeline 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 +reproduction pipeline), 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 pipeline 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/pipeline. + +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 pipeline 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 pipeline has been created for GNU +Make which is the most common, most actively developed, and most advanced +implementation. Just note that this pipeline 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 pipeline +----------------------------------- + +The links below will guide you to some of the works that have already been +published using the method of this pipeline. Note that this pipeline is +evolving, so some small details may be different in them, but they can be +used as a good working model to build your own. + + - Section 7.3 of Bacon et + al. ([2017](http://adsabs.harvard.edu/abs/2017A%26A...608A...1B), A&A + 608, A1): The version controlled reproduction pipeline is available [on + Gitlab](https://gitlab.com/makhlaghi/muse-udf-origin-only-hst-magnitudes) + and a snapshot of the pipeline 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 reproduction pipeline is available [on + Gitlab](https://gitlab.com/makhlaghi/muse-udf-photometry-astrometry) and + a snapshot of the pipeline 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 reproduction pipeline is available [on + Gitlab](https://gitlab.com/makhlaghi/NoiseChisel-paper). This is the + very first (and much less mature) implementation of this pipeline: the + history of this template pipeline started more than two years after that + paper was published. It is a very rudimentary/initial implementation, + thus it is only included here for historical reasons. However, the + pipeline is complete and accurate and uploaded to arXiv along with the + paper. See the more recent implementations if you want to get ideas for + your version of this pipeline. + + + + + +Citation +-------- + +A paper will be published to fully describe this reproduction +pipeline. Until then, if this pipeline is useful in your work, please cite +the paper that implemented the first version of this pipeline: 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 this pipeline 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 publish their reproduction +pipelines. + + + + + + + + + + +Reproduction pipeline architecture +================================== + +In order to adopt this pipeline 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. But before reading this theoretical discussion, please run the +pipeline (described in `README.md`: first run `./configure`, then +`.local/bin/make -j8`) without any change, just to see how it works. + +In order to obtain a reproducible result it is important to have an +identical environment (for example same versions of the programs that it +will use). Therefore, the pipeline builds its own dependencies during the +`./configure` step. Building of the dependencies is managed by +`reproduce/src/make/dependencies-basic.mk` and +`reproduce/src/make/dependencies.mk`. These Makefiles are called by the +`./configure` script and not used afterwards. The first is intended for +downloading and building the most basic tools like GNU Bash, GNU Make, and +GNU Tar. Therefore it must only contain very basic and portable Make and +shell features. The second is called after the first, thus enabling usage +of the modern and advanced features of GNU Bash and GNU Make, similar to +the rest of the pipeline. Later, if you add a new program/library for your +research, you will need to include a rule on how to download and build it +(in `reproduce/src/make/dependencies.mk`). + +After it finishes, `./configure` will create a `Makefile` in the top +directory (a symbolic link to `reproduce/src/make/top.mk`) and a `.local` +directory (a link for easy access to the custom built software +packages). The `.local/bin/make` command will then use our custom version +of GNU Make to do the analysis. The first file that is read by Make is the +top-level `Makefile`. Therefore, we'll start our navigation/discussion with +this file. This file is 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 `Makefile`, 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 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, you _must_ +define a top-level build directory variable (or `$(BDIR)`) to host all the +intermediate files (it was defined in `./configure`). This directory +doesn't need to be version controlled or even synchronized, or backed-up in +other servers: its contents are all products of the pipeline, and can be +easily re-created any time. As you define targets for your new rules, it is +thus important to place them all under sub-directories of `$(BDIR)`. + +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 rules). + +The configuration-Makefiles are those that satisfy this wildcard: +`reproduce/config/pipeline/*.mk`. These Makefiles don't actually have any +rules, they just have values for various free parameters throughout the +analysis/processing. Open a few of them to see for your self. These +Makefiles must only contain raw Make variables (pipeline +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 any of these +configuration-Makefiles. + +These conditions will enable 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/src/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 are to 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 pipeline 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 pipeline 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 `./configure` and +Make steps must be called with special conditions which are managed in the +`for-group` file. + +Let's see how this design is implemented. When the `./configure` finishes, +it makes a `Makefile` in the top directory. This Makefile is just a +symbolic link to `reproduce/src/make/top.mk`. Please open and inspect it as +we go along here. The first step (un-commented line) is to import the local +configuration (answers to the questions `./configure` asked you). They are +defined in the configuration-Makefile `reproduce/config/pipeline/LOCAL.mk` +which was also built by `./configure` (based on the `LOCAL.mk.in` +template). + +The next non-commented set of lines define the ultimate target of the whole +pipeline (`paper.pdf`). But a sanity check is necessary for situations when +the user is not careful (for example has configured the pipeline for group +access but forgets to run the pipeline with `./for-group`, or the +opposite). Therefore we use a Make conditional to define the `all` target +based on the group permissions being consistent between the initial +configuration and the current run. + +If there is a problem `all` will not depend on anything and will just print +a warning to inform you of the problem. When the group conditions are fine, +`all` will depend on `paper.pdf` (which is defined in +`reproduce/src/make/paper.mk` and will be imported into this top Makefile +later). + +Having defined the top target, our next step is to include all the other +necessary Makefiles. But 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 a `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'll just import all the configuration-Makefiles with a wildcard +(while ignoring `LOCAL.mk` that was imported before). Also, all +workhorse-Makefiles are imported in the proper order using a Make `foreach` +loop. This finishes the general view of the pipeline's implementation. + +In short, to keep things modular, readable and managable, 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/src/make/paper.mk` Makefile must be the final Makefile that +is included. It ends with the rule to build `paper.pdf` (final target of +the whole reproduction pipeline). If look in it, you will notice that it +starts with a rule to create `tex/pipeline.tex`. `tex/pipeline.tex` is the +connection between the processing/analysis steps of the pipeline, and the +steps to build the final PDF. As you see, `tex/pipeline.tex` is only a +merging/concatenation of LaTeX macros defined as the output of each +high-level processing step (the separate work-horse Makefiles that you +included). + +One of the LaTeX macros created by `reproduce/src/make/initialize.mk` is +`\bdir`. It is the location of the build directory. In some cases you want +tables and images to also be included in the final PDF. To keep these +necessary LaTeX inputs, you can define other directories under +`$(BDIR)/tex` in the relevant workhorse-Makefile. You can then easily guide +LaTeX to look into the proper directory to import an image for example +through the `\bdir` macro. + +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. + +When working within a group, more than one person may want to work with the +pipeline outputs (in the build directory). For example each person is +developing part of the higher-level steps of the pipeline in their own Git +branch of the pipeline, but using the same build directory. Therefore, the +lower-level parts of the built outputs, can be shared between them. In such +scenarios, this pipeline comes with a `for-group` script (in the top +directory) which is just a simple wrapper to run the configure and building +steps. You can specify a group name within this file. Therefore, when you +use it (fully described in the comments at the start of the file), it will +ensure that all group members have write access to the created files. + + + + +Summary +------- + +Based on the explanation above, some major design points you should have in +mind are listed below. + + - Define new `reproduce/src/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/config/pipeline`. Then set the respective + 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) `tex/pipeline.tex` (defined in + `reproduce/src/make/paper.mk`). `tex/pipeline.tex` is the bridge between + the processing steps and PDF-building steps. + + + + + + + + + + +Checklist to customize the pipeline +=================================== + +Take the following steps to fully customize this pipeline for your research +project. After finishing the list, be sure to run `./configure` and `make` +to see if everything works correctly before expanding it. 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 a reproduction pipeline heavily relies +on [version +control](https://en.wikipedia.org/wiki/Version_control). Currently this +pipeline 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. + + - **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. The main branch of this pipeline is called `pipeline`. This + allows you to use the common branch name `master` for your own + research, while keeping up to date with improvements in the pipeline. + + ```shell + $ git clone https://gitlab.com/makhlaghi/reproducible-paper.git + $ mv reproducible-paper my-project-name # Your own directory name. + $ cd my-project-name # Go into the cloned directory. + $ git tag | xargs git tag -d # Delete all pipeline tags. + $ git config remote.origin.tagopt --no-tags # No tags in future fetch/pull from this pipeline. + $ git remote rename origin pipeline-origin # Rename the pipeline's remote. + $ git checkout -b master # Create, enter master branch. + ``` + + - **Test the pipeline**: Before making any changes, it is important to + test the pipeline and see if everything works properly with the + commands below. If there is any problem in the `./configure` or `make` + steps, please contact us to fix the problem before continuing. Since + the building of dependencies in `./configure` can take long, you can + take the next few steps (editing the files) while its working (they + don't affect the configuration). After `make` is finished, open + `paper.pdf` and if it looks fine, you are ready to start customizing + the pipeline for your project. But before that, clean all the extra + pipeline outputs with `make clean` as shown below. + + ```shell + $ ./configure # Set top directories and build dependencies. + $ .local/bin/make # Run the pipeline. + + # Open 'paper.pdf' and see if everything is ok. + $ .local/bin/make clean # Delete high-level outputs. + ``` + + - **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 allows any number of private repositories for free and because you + can host GitLab on your own server. 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 link (ending in `.git`) that you can + put in place of `XXXXXXXXXX` in the command below. + + ```shell + git remote add origin XXXXXXXXXX + ``` + + - **Copyright**, **name** and **date**: Go over the existing scripting + files and add your name and email to the copyright notice. You can + find the files by searching for the placeholder email + `your@email.address` (which you should change) with the command below + (you can ignore this file, and any in the `tex/` directory). Don't + forget to add your name after the copyright year also. When making new + files, always remember to add a similar copyright statement at the top + of the file and also ask your colleagues to do so when they edit a + file. This is very important. + + ```shell + $ grep -r your@email.address ./* + ``` + + - **Title**, **short description** and **author** in source files: In this + raw skeleton, the title or short description of your project should be + added in the following two files: `reproduce/src/make/top.mk` (the + first line), and `tex/preamble-header.tex`. In both cases, the texts + you should replace are all in capital letters to make them easier to + identify. Of course, if you use a different LaTeX method of managing + the title and authors, please feel free to use your own methods after + finishing this checklist and doing your first commit. + + - **Gnuastro**: GNU Astronomy Utilities (Gnuastro) is currently a + dependency of the pipeline which will be built and used. The main + reason for this is to demonstrate how critically important it is to + version your scientific tools. If you don't need Gnuastro for your + research, you can simply remove the parts enclosed in marked parts in + the relevant files of the list below. The marks are comments, which + you can find by searching for "Gnuastro". If you will be using + Gnuastro, then remove the commented marks and keep the code within + them. + + - Delete marked part(s) in `configure`. + - Delete the `reproduce/config/gnuastro` directory. + - Delete `astnoisechisel` from the value of `top-level-programs` in `reproduce/src/make/dependencies.mk`. You can keep the rule to build `astnoisechisel`, since its not in the `top-level-programs` list, it (and all the dependencies that are only needed by Gnuastro) will be ignored. + - Delete marked parts in `reproduce/src/make/initialize.mk`. + + - **Other dependencies**: If there are any more of the dependencies that + you don't use (or others that you need), then remove (or add) them in + the respective parts of `reproduce/src/make/dependencies.mk`. It is + commented thoroughly and reading over the comments should guide you on + what to add/remove and where. + + - **Input dataset (can be done later)**: The input datasets are managed + through the `reproduce/config/pipeline/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 pipeline, it is also recommended get an + [MD5 checksum](https://en.wikipedia.org/wiki/MD5) of the file and + include that in `INPUTS.mk` so you can check it in the pipeline. The + preparation of the input datasets is done in + `reproduce/src/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 ./* + ``` + + - **Delete dummy parts (can be done later)**: The template pipeline + 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`: Delete the text of the abstract and the paper's main + body, *except* the "Acknowledgments" section. This reproduction + pipeline was designed by funding from many grants, so its necessary + to acknowledge them in your final research. + + - `Makefile`: Delete the lines containing `delete-me` in the `foreach` + loop. Just make sure the other lines that end in `\` are immediately + after each other (except the last line). + + - Delete all `delete-me*` files in the following directories: + + ```shell + $ rm tex/delete-me* + $ rm reproduce/src/make/delete-me* + $ rm reproduce/config/pipeline/delete-me* + ``` + + - **`README.md`**: Correct all the `XXXXX` place holders (name of your + project, your own name, address of pipeline'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 work (and its reproduction pipeline). + + - **`for-group`**: If you will be working on this pipeline with + colleagues, and the build steps involve many files, or are slow, you + need to share the build directory. This script is designed for such + scenarios. So open this file and give the name of the Unix name of + your group to the `thisgroup` variable. You can see the list of groups + you are a member of with the `groups` command. You can ask your system + administrator to define a group with specific members if necessary. + + - **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 + pipeline (this is a good habit to always re-build the system before a + commit to be sure it works as expected). + + ```shell + $ .local/bin/make clean # Delete outputs ('make distclean' for everything) + $ .local/bin/make # Build the pipeline to ensure everything is fine. + $ git add -u # Stage all the changes. + $ 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 pipeline. + ``` + + - **Push to the remote**: Push your first commit and its tag to the remote + repository with these commands: + + ```shell + git push -u origin --all + git push -u origin --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. Any time you are ready to push your commits to the remote + repository, you can simply use `git push`. + + - **Feedback**: As you use the pipeline 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 + pipeline or in 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. + + - **Keep pipeline up-to-date**: In time, this pipeline 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 pipeline. If the changes + are useful for your work, you can merge them with your own customized + pipeline to benefit from them. Just pay **very close attention** to + resolving possible **conflicts** which might happen in the merge + (updated general pipeline settings that you have customized). + + ```shell + $ git checkout pipeline + $ git pull pipeline-origin pipeline # Get recent work in this pipeline. + $ 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 pipeline # Import all the work into master. + ``` + + - **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. + + + + + + + + +Usage tips: designing your pipeline/workflow +============================================ + +The following is a list of design points, tips, or recommendations that +have been learned after some experience with this pipeline. Please don't +hesitate to share any experience you gain after using this pipeline with +us. In this way, we can add it here 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*: This pipeline is designed to allow + the easy inclusion of many Makefiles (in `reproduce/src/make/*.mk`) + for maximal modularity. 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 pipeline 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/src/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 them in a separate directory + under `reproduce/src`, 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/config`. Similar to the `reproduce/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 pipeline 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. + + - *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. Set a small plain text file as + the actual target and delete the large file when it is no longer + needed by the pipeline (in the last rule that needs it). Below is a + simple demonstration of doing this, where 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" > $@ + ``` + A more advanced Make programmer will use Make's [call + function](https://www.gnu.org/software/make/manual/html_node/Call-Function.html) + to define a wrapper in `reproduce/src/make/initialize.mk`. This + wrapper will replace `$(subst .txt,,XXXXX)`. Therefore, it will be + possible to greatly simplify this repetitive statement and make the + code even more readable throughout the whole pipeline. + + + - **Dependencies**: It is critically important to exactly document, keep + and check the versions of the programs you are using in the pipeline. + + - *Check versions*: In `reproduce/src/make/initialize.mk`, check the + versions of the programs you are using. + + - *Keep the source tarball of dependencies*: keep a tarball of the + necessary version of all your dependencies (and also a copy of the + higher-level libraries they depend on). Software evolves very fast + and only in a few years, a feature might be changed or removed from + the mainstream version or the software server might go down. To be + safe, keep a copy of the tarballs. Software tarballs are rarely over + a few megabytes, very insignificant compared to the data. If you + intend to release the pipeline in a place like Zenodo, then you can + create your submission early (before public release) and upload/keep + all the necessary tarballs (and data) + there. [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 pipeline. + + - *Keep your input data*: The input data is also critical to the + pipeline, so like the above for software, make sure you have a backup + of them. + + - **Version control**: It is important (and extremely useful) to have the + history of your pipeline under version control. So try to make commits + regularly (after any meaningful change/step/result), while not + forgetting the following notes. + + - *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 pipeline. 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, we tagged the first commit of your pipeline + with `v0`. Here is one suggestion on when to tag: when you have fully + adopted the pipeline 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`. Afterwards + when you submit to a paper, it can be tagged `v3` and so on. + + - *Pipeline 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 pipeline (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 + pipeline can unreasonably bloat it. It is thus recommended to make a + separate Git repo to keep those files and keep this pipeline's volume + as small as possible. For example if your main pipeline is called + `my-exciting-project`, the name of the outputs pipeline 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 (you can + just share the link to the online repo in your communications). After + the research is published, you can also release the outputs pipeline, + or you can just delete it if it is too large or un-necessary (it was + just for convenience, and fully reproducible after all). This + pipeline's output is available for demonstration in the separate + [reproducible-paper-output](https://gitlab.com/makhlaghi/reproducible-paper-output) + repository. + + + + + + + + + + +Future improvements +=================== + +This is an evolving project and as time goes on, it will evolve and become +more robust. Here are the list of features that we plan to add in the +future. + + - *Containers*: It is important to have better/full control of the + environment of the reproduction pipeline. Our current reproducible + paper pipeline builds the higher-level programs (for example GNU Bash, + GNU Make, GNU AWK and etc) it needs and sets `PATH` to prefer its own + builds. It currently doesn't build and use its own version of + lower-level tools (like the C library and compiler). We plan to add the + build steps of these low level tools so the system's `PATH` can be + completely ignored within the pipeline and we are in full control of + the whole build process. Another solution is based on [an interesting + tutorial](https://mozillafoundation.github.io/2017-fellows-sf/re-papers/index.html) + by the Mozilla science lab to build reproducible papers. It suggests + using the [Nix package manager](https://nixos.org/nix/about.html) to + build the necessary software for the pipeline and run the pipeline in + its completely closed environment. This is an interesting solution + because using Nix or [Guix](https://www.gnu.org/software/guix/) (which + is based on Nix, but uses the [Scheme + language](https://en.wikipedia.org/wiki/Scheme_(programming_language)), + not a custom language for the management) will allow a fully working + closed environment on the host system which contains the instructions + on how to build the environment. The availability of the instructions + to build the programs and environment with Nix or Guix, makes them a + better solution than binary containers like + [docker](https://www.docker.com/) which are essentially just a binary + (not human readable) black box and only usable on the given CPU + architecture. However, one limitation of using these is their own + installation (which usually requires root access). + + + + + + + + + + +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 reproduction pipeline 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. |