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Diffstat (limited to 'README-pipeline.md')
| -rw-r--r-- | README-pipeline.md | 55 |
1 files changed, 18 insertions, 37 deletions
diff --git a/README-pipeline.md b/README-pipeline.md index ff15094..6effa30 100644 --- a/README-pipeline.md +++ b/README-pipeline.md @@ -516,6 +516,7 @@ advanced in later stages of your work. 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`. - Delete `and Gnuastro \gnuastroversion` from `tex/preamble-style.tex`. @@ -526,51 +527,31 @@ advanced in later stages of your work. commented thoroughly and reading over the comments should guide you on what to add/remove and where. - - **Input dataset (can be done later)**: The user manages the top-level - directory of the input data through the variables set in - `reproduce/config/pipeline/LOCAL.mk.in` (the user actually edits a - `LOCAL.mk` file that is created by `configure` from the `.mk.in` file, - but the `.mk` file is not under version control). Datasets are usually - large and the users might already have their copy don't need to - download them). So you can define a variable (all in capital letters) - in `reproduce/config/pipeline/LOCAL.mk.in`. For example if you are - working on data from the XDF survey, use `XDF`. You can use this - variable to identify the location of the raw inputs on the running - system. Here, we'll assume its name is `SURVEY`. Afterwards, change - any occurrence of `SURVEY` in the whole pipeline with the new - name. You can find the occurrences with a simple command like the ones - shown below. We follow the Make convention here that all - `ONLY-CAPITAL` variables are those directly set by the user and all - `small-caps` variables are set by the pipeline designer. All variables - that also depend on this survey have a `survey` in their name. Hence, - also correct all these occurrences to your new name in small-caps. Of - course, ignore/delete those occurrences that are irrelevant, like - those in this file. Note that in the raw version of this template no - target depends on these files, so they are ignored. Afterwards, set - the webpage and correct the filenames in - `reproduce/src/make/download.mk` if necessary. - - ```shell - $ grep -r SURVEY ./ - $ grep -r survey ./ - ``` - - - **Other input datasets (can be done later)**: Add any other input - datasets that may be necessary for your research to the pipeline based - on the example above. + - **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, its best to also get an MD5 + checksum (https://en.wikipedia.org/wiki/MD5) of the file and include + that in thsi file 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. - **Delete dummy parts (can be done later)**: The template pipeline - contains some parts that are only for the initial/test run, not for - any real analysis. The respective files to remove and parts to fix are - discussed here. + 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 two lines containing `delete-me` in the - `foreach` loops. Just make sure the other lines that end in `\` are + - `Makefile`: Delete the lines containing `delete-me` in the `foreach` + loops. Just make sure the other lines that end in `\` are immediately after each other. - Delete all `delete-me*` files in the following directories: |