Move permanent part of fkutils here

.gitignore

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+pineko.toml
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]

README.md

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-# Pineko
+# `pineko` = `PineAPPL` + `eko`
 
-This repository contains specifications for the apfelcomb code replacement.
+`pineko` converts
 
+- interpolation grids for theory predictions ('grids' for short) in the form of
+  [`PineAPPL`](https://github.com/N3PDF/pineappl) grids, together with
+- Evolution Kernel Operators (EKO) generated by
+  [`eko`](https://github.com/N3PDF/eko)
+
+into fast-kernel (FK) tables. The collection of all FK tables constitute the
+theory predictions for a PDF fit and therefore is often simply called 'theory'.
+
+`pineko` replaces [`APFELcomb`](https://github.com/NNPDF/apfelcomb), which was
+used up to NNPDF4.0.
+
+## Prerequisites
+
+Generating a 'theory', as defined above, requires several files which are
+described next.
+
+### `pineko.toml`
+
+You need to provide a `pineko.toml`, that provides all necessary paths to the input and output folders.
+[DEBUG: Look at the debug example in this repo [1].]
+
+### ymldb
+
+You need all files of the `ymldb` [2].  [DEBUG: Look at the respective `load.sh` script to load from dom.]
+This defines the mapping from datasets to FK tables.
+
+### Theory Runcards
+
+You need to provide the necessary theory runcards named with their respective theory ID inside the `<paths.theory_cards>` folder [3].
+
+### Default Operator Card
+
+You need to provide a default operator card for `eko` [4].
+[DEBUG: Look at the respective `load.sh` script to load from dom.]
+
+### Grids
+
+`pineko` does **NOT** compute grids, which are instead expected input to `pineko`.
+There are typically two ways to obtain grids: computing them from scratch with [`runcards`](https://github.com/NNPDF/runcards)
+or reusing existing ones.
+
+#### Generate new Grids with `rr`
+
+You need to run `rr` with a given theory runcard and put the generated grid file with the same name
+inside the `<paths.grids>/<theory_id>` folder. The name has to match the `ymldb` which is the case by default.
+
+#### Inherit Grids from Existing Theory
+
+You can reuse the grids from a different theory by running `pineko theory inherit-grids SOURCE_THEORY_ID TARGET_THEORY_ID DATASET1 DATASET2 ...`.
+The relation between the source theory and the target theory is non-trivial [5].
+
+## Running `pineko`
+
+Running `pineko` consists of two steps - each of them being potentially computationally expensive:
+computing the EKO and convoluting the EKO with the grid.
+
+### Computing the EKO
+
+#### Generating new EKOs
+
+This is a two step process:
+1. Generate the necessary operator cards with `pineko theory opcards THEORY_ID DATASET1 DATASET2 ...`
+2. Generate the actual EKOs with `pineko theory ekos THEORY_ID DATASET1 DATASET2 ...`
+
+#### Inherit EKOs from Existing Theory
+
+You can reuse the EKOs from a different theory by running `pineko theory inherit-ekos SOURCE_THEORY_ID TARGET_THEORY_ID DATASET1 DATASET2 ...`.
+The relation between the source theory and the target theory is non-trivial [6].
+
+### Generating the FK Table
+
+You need to have the EKOs computed in the previous step.
+Then you can convolute the EKOs with the grids by running `pineko theory fks THEORY_ID DATASET1 DATASET2 ...`
+
+---
+
+[1] Actually, instead we should provide a concise description here - but let's wait to be stable first
+
+[2] this is to be replaced by the new CommonData format
+
+[3] this is to be replaced by a binding to the true theory DB
+
+[4] I'm thinking how to improve this, because how could we provide a study on the interpolation accuracy? at the moment there just equal
+
+[5] examples being SV, different evolution settings, etc.
+
+[6] examples being SV, different DIS settings, etc.

data/ekos/.gitignore

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+*.tar

data/fktables/.gitignore

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+*.pineappl.lz4

data/grids/.gitignore

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+*.pineappl.lz4

data/grids/load.sh

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+# copy from remote
+
+# common example
+# scp dom.mi.infn.it:/media/FK/fktables/data/grids/200-LHCB_DY_13TEV_DIELECTRON.pineappl.lz4 ./common/LHCB_DY_13TEV_DIELECTRON.pineappl.lz4
+
+# theory example
+# scp dom.mi.infn.it:/media/FK/fktables/data/grids/200-SLAC_NC_EM_D_F2.pineappl.lz4 ./200/SLAC_NC_EM_D_F2.pineappl.lz4
+# scp dom.mi.infn.it:/media/FK/fktables/data/grids/200-SLAC_NC_EM_P_F2.pineappl.lz4 ./200/SLAC_NC_EM_P_F2.pineappl.lz4

data/theory_cards/.gitignore

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+*.yaml

data/ymldb/.gitignore

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+*.yaml

data/ymldb/load.sh

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+# copy from remote
+# scp dom.mi.infn.it:/media/FK/fktables/data/fktocommon/*.yaml .