From b6f9621227dfbbd1c66ac3cc29bca8e64ffd1bc4 Mon Sep 17 00:00:00 2001
From: Giacomo Magni <giac.magni@gmail.com>
Date: Thu, 15 Feb 2024 12:57:30 +0100
Subject: [PATCH 01/25] init speeding up nfonll

---
 src/pineko/cli/fonll.py | 63 ++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 62 insertions(+), 1 deletion(-)

diff --git a/src/pineko/cli/fonll.py b/src/pineko/cli/fonll.py
index 66368c85..4d22c1c2 100644
--- a/src/pineko/cli/fonll.py
+++ b/src/pineko/cli/fonll.py
@@ -1,12 +1,17 @@
 """CLI entry point to FONLL."""
 
+import logging
 import pathlib
 
 import click
 import rich
 
-from .. import configs, fonll, parser, theory_card
+from .. import configs, fonll, parser, theory, theory_card
 from ._base import command
+from .theory_ import theory_
+
+logger = logging.getLogger(__name__)
+
 
 config_setting = click.option(
     "-c",
@@ -149,3 +154,59 @@ def fonll_tcards(theoryid, cfg):
     if "FONLL" not in tcard["FNS"]:
         raise TheoryCardError("The theorycard does not correspond to an FONLL scheme.")
     fonll.dump_tcards(tcard, tcard_parent_path, theoryid)
+
+
+@theory_.command()
+@click.argument("theoryID", type=click.INT)
+@click.argument("datasets", type=click.STRING, nargs=-1)
+@click.option("--overwrite", is_flag=True, help="Allow files to be overwritten")
+def fonll_ekos(theoryid, datasets, overwrite):
+    """Command to generate numerical FONLL ekos.
+
+    1. Produce the 7 theory cards that are needed for numerical FONLL.
+    2. Creates the 3 opcards for the different flavor patches.
+    3. Runs the 3 ekos for the different flavor pathces.
+    4. Inherit the ekos.
+    """
+
+    # create the 7 theory cards
+    tcard = theory_card.load(theoryid)
+    tcard_parent_path = theory_card.path(theoryid).parent
+    if "FONLL" not in tcard["FNS"]:
+        raise TheoryCardError("The theorycard does not correspond to an FONLL scheme.")
+    fonll.dump_tcards(tcard, tcard_parent_path, theoryid)
+
+    for nf_id in ["00", "04", "05"]:
+        # create opcards
+        theory.TheoryBuilder(
+            f"{theoryid}{nf_id}", datasets, overwrite=overwrite
+        ).opcards()
+
+        # run the ekos
+        theory.TheoryBuilder(
+            f"{theoryid}{nf_id}",
+            datasets,
+            silent=False,
+            clear_logs=True,
+            overwrite=overwrite,
+        ).ekos()
+
+    # now inherit ekos
+    # nf=3
+    logger.info(f"Inherit nf=3 from theory {theoryid}00")
+    theory.TheoryBuilder(f"{theoryid}00", datasets, overwrite=overwrite).inherit_ekos(
+        f"{theoryid}01"
+    )
+    # nf=4
+    logger.info(f"Inherit nf=4 from theory {theoryid}04")
+    theory.TheoryBuilder(f"{theoryid}04", datasets, overwrite=overwrite).inherit_ekos(
+        f"{theoryid}02"
+    )
+    theory.TheoryBuilder(f"{theoryid}04", datasets, overwrite=overwrite).inherit_ekos(
+        f"{theoryid}03"
+    )
+    # nf=5
+    logger.info(f"Inherit nf=5 from theory {theoryid}05")
+    theory.TheoryBuilder(f"{theoryid}05", datasets, overwrite=overwrite).inherit_ekos(
+        f"{theoryid}06"
+    )

From e7dbfb14a2b4e8616347753ccc41c14d8c93376b Mon Sep 17 00:00:00 2001
From: giacomomagni <giac.magni@gmail.com>
Date: Thu, 15 Feb 2024 13:43:38 +0100
Subject: [PATCH 02/25] add combine Fk tables

---
 src/pineko/cli/fonll.py | 176 +++++++++++++++++-----------------------
 src/pineko/fonll.py     | 104 +++++++++++++++++++++++-
 2 files changed, 175 insertions(+), 105 deletions(-)

diff --git a/src/pineko/cli/fonll.py b/src/pineko/cli/fonll.py
index 4d22c1c2..751d45be 100644
--- a/src/pineko/cli/fonll.py
+++ b/src/pineko/cli/fonll.py
@@ -4,11 +4,10 @@
 import pathlib
 
 import click
-import rich
 
-from .. import configs, fonll, parser, theory, theory_card
+from .. import configs, fonll, theory, theory_card
+from ..fonll import TheoryCardError
 from ._base import command
-from .theory_ import theory_
 
 logger = logging.getLogger(__name__)
 
@@ -23,29 +22,13 @@
 )
 
 
-class TheoryCardError(Exception):
-    """Raised when asked for FONLL theory cards with an original tcard as input that is not asking for FONLL."""
-
-
-class InconsistentInputsError(Exception):
-    """Raised if the inputs are not consistent with FONLL."""
-
-
-def cfgpath(name, grid):
-    """Path of the fktable in 'name' called 'grid' if it exists, else None."""
-    path = configs.configs["paths"]["fktables"] / name / grid
-    return path if path.exists() else None
-
-
-def grids_names(yaml_file):
-    """Return the list of the grids in the yaml file."""
-    yaml_content = parser._load_yaml(yaml_file)
-    # Turn the operands and the members into paths (and check all of them exist)
-    ret = []
-    for operand in yaml_content["operands"]:
-        for member in operand:
-            ret.append(f"{member}.{parser.EXT}")
-    return ret
+def load_config(cfg):
+    """Iterate a subcommand on a given theory and list of datasets."""
+    path = configs.detect(cfg)
+    base_configs = configs.load(path)
+    configs.configs = configs.defaults(base_configs)
+    if cfg is not None:
+        print(f"Configurations loaded from '{path}'")
 
 
 @command.command("combine_fonll")
@@ -74,71 +57,20 @@ def subcommand(
     cfg,
 ):
     """Combine the different FKs needed to produce the FONLL prescription."""
-    path = configs.detect(cfg)
-    base_configs = configs.load(path)
-    configs.configs = configs.defaults(base_configs)
-    if cfg is not None:
-        print(f"Configurations loaded from '{path}'")
-
-    # Checks
-
-    if not ffns3 or not ffn03:
-        raise InconsistentInputsError("ffns3 and/or ffn03 is not provided.")
-
-    if ffns4til is None or ffns4bar is None:
-        raise InconsistentInputsError(
-            "At least one of ffns4til and ffns4bar should be provided."
-        )
-
-    # Do we consider two masses, i.e. mc and mb
-    if any([ffns5til, ffns5bar, ffn04]):
-        if (ffns5til is None and ffns5bar is None) or ffn04 is None:
-            raise InconsistentInputsError(
-                "To include nf5 contributions, ffn04 and at least one between ffns5til and ffns5bar are mandatory"
-            )
-
-    # Get theory info
-    tcard = theory_card.load(theoryid)
-    if tcard["DAMP"] == 1:
-        if not "DAMPPOWERc" in tcard or not "DAMPPOWERb" in tcard:
-            raise InconsistentInputsError(
-                "If DAMP is set, set also DAMPPOWERb and DAMPPOWERc"
-            )
-    else:
-        tcard["DAMPPOWERb"] = 0
-        tcard["DAMPPOWERc"] = 0
-    # Getting the paths to the grids
-    grids_name = grids_names(configs.configs["paths"]["ymldb"] / f"{dataset}.yaml")
-    for grid in grids_name:
-        # Checking if it already exists
-        new_fk_path = configs.configs["paths"]["fktables"] / str(theoryid) / grid
-        if new_fk_path.exists():
-            if not overwrite:
-                rich.print(
-                    f"[green]Success:[/] skipping existing FK Table {new_fk_path}"
-                )
-                return
-        fonll.produce_combined_fk(
-            *(
-                cfgpath(str(name), grid)
-                for name in (
-                    ffns3,
-                    ffn03,
-                    ffns4til,
-                    ffns4bar,
-                    ffn04,
-                    ffns5til,
-                    ffns5bar,
-                )
-            ),
-            theoryid,
-            damp=(tcard["DAMP"], tcard["DAMPPOWERc"], tcard["DAMPPOWERb"]),
-            cfg=cfg,
-        )
-        if new_fk_path.exists():
-            rich.print(f"[green]Success:[/] Wrote FK table to {new_fk_path}")
-        else:
-            rich.print(f"[red]Failure:[/]")
+    load_config(cfg)
+    fonll.assembly_combined_fk(
+        theoryid,
+        dataset,
+        ffns3,
+        ffn03,
+        ffns4til,
+        ffns4bar,
+        ffn04,
+        ffns5til,
+        ffns5bar,
+        overwrite,
+        cfg,
+    )
 
 
 @command.command("fonll_tcards")
@@ -146,9 +78,8 @@ def subcommand(
 @config_setting
 def fonll_tcards(theoryid, cfg):
     """Produce the FONLL tcards starting from the original tcard given by the theoryID."""
-    path = configs.detect(cfg)
-    base_configs = configs.load(path)
-    configs.configs = configs.defaults(base_configs)
+    load_config(cfg)
+
     tcard = theory_card.load(theoryid)
     tcard_parent_path = theory_card.path(theoryid).parent
     if "FONLL" not in tcard["FNS"]:
@@ -156,18 +87,19 @@ def fonll_tcards(theoryid, cfg):
     fonll.dump_tcards(tcard, tcard_parent_path, theoryid)
 
 
-@theory_.command()
 @click.argument("theoryID", type=click.INT)
 @click.argument("datasets", type=click.STRING, nargs=-1)
 @click.option("--overwrite", is_flag=True, help="Allow files to be overwritten")
-def fonll_ekos(theoryid, datasets, overwrite):
+@config_setting
+def fonll_ekos(theoryid, datasets, overwrite, cfg):
     """Command to generate numerical FONLL ekos.
 
-    1. Produce the 7 theory cards that are needed for numerical FONLL.
-    2. Creates the 3 opcards for the different flavor patches.
-    3. Runs the 3 ekos for the different flavor pathces.
+    1. Produce the 7 theory cards needed for numerical FONLL.
+    2. Create the 3 operator cards for the different flavor patches.
+    3. Run the 3 ekos for the different flavor patches.
     4. Inherit the ekos.
     """
+    load_config(cfg)
 
     # create the 7 theory cards
     tcard = theory_card.load(theoryid)
@@ -193,12 +125,12 @@ def fonll_ekos(theoryid, datasets, overwrite):
 
     # now inherit ekos
     # nf=3
-    logger.info(f"Inherit nf=3 from theory {theoryid}00")
+    logger.info("Inherit nf=3 from theory %i00", theoryid)
     theory.TheoryBuilder(f"{theoryid}00", datasets, overwrite=overwrite).inherit_ekos(
         f"{theoryid}01"
     )
     # nf=4
-    logger.info(f"Inherit nf=4 from theory {theoryid}04")
+    logger.info("Inherit nf=4 from theory %i04", theoryid)
     theory.TheoryBuilder(f"{theoryid}04", datasets, overwrite=overwrite).inherit_ekos(
         f"{theoryid}02"
     )
@@ -206,7 +138,47 @@ def fonll_ekos(theoryid, datasets, overwrite):
         f"{theoryid}03"
     )
     # nf=5
-    logger.info(f"Inherit nf=5 from theory {theoryid}05")
+    logger.info("Inherit nf=5 from theory %i05", theoryid)
     theory.TheoryBuilder(f"{theoryid}05", datasets, overwrite=overwrite).inherit_ekos(
         f"{theoryid}06"
     )
+
+
+@click.argument("theoryID", type=click.INT)
+@click.argument("datasets", type=click.STRING, nargs=-1)
+@click.option("--pdf", "-p", default=None, help="PDF set used for comparison")
+@click.option("--overwrite", is_flag=True, help="Allow files to be overwritten")
+@config_setting
+def fonll_fks(theoryid, datasets, pdf, overwrite, cfg):
+    """Command to generate numerical FONLL FK tables.
+
+    1. Produce the 7 FK tables needed for numerical FONLL.
+    2. Combine the FKtables into a single one.
+    """
+    load_config(cfg)
+
+    # create the 7 FK tables
+    for th_suffix in range(0, 7):
+        theory.TheoryBuilder(
+            f"{theoryid}0{th_suffix}",
+            datasets,
+            silent=False,
+            clear_logs=True,
+            overwrite=overwrite,
+        ).fks(pdf)
+
+    # combine
+    for dataset in datasets:
+        fonll.assembly_combined_fk(
+            theoryid,
+            dataset,
+            ffns3=f"{theoryid}00",
+            ffn03=f"{theoryid}01",
+            ffns4til=f"{theoryid}02",
+            ffns4bar=f"{theoryid}03",
+            ffn04=f"{theoryid}04",
+            ffns5til=f"{theoryid}05",
+            ffns5bar=f"{theoryid}06",
+            overwrite=overwrite,
+            cfg=cfg,
+        )
diff --git a/src/pineko/fonll.py b/src/pineko/fonll.py
index 469e643c..13440032 100644
--- a/src/pineko/fonll.py
+++ b/src/pineko/fonll.py
@@ -8,10 +8,9 @@
 from pathlib import Path
 
 import pineappl
-import rich
 import yaml
 
-from . import configs
+from . import configs, theory_card, parser
 
 logger = logging.getLogger(__name__)
 
@@ -36,6 +35,14 @@
 """FNS schemes to be subtracted during the FONLL procedure."""
 
 
+class TheoryCardError(Exception):
+    """Raised when asked for FONLL theory cards with an original tcard as input that is not asking for FONLL."""
+
+
+class InconsistentInputsError(Exception):
+    """Raised if the inputs are not consistent with FONLL."""
+
+
 class FONLLInfo:
     """Class containing all the information for FONLL predictions."""
 
@@ -157,6 +164,97 @@ def combine(fk_dict, dampings=None):
     return combined_fk
 
 
+def grids_names(yaml_file):
+    """Return the list of the grids in the yaml file."""
+    yaml_content = parser._load_yaml(yaml_file)
+    # Turn the operands and the members into paths (and check all of them exist)
+    ret = []
+    for operand in yaml_content["operands"]:
+        for member in operand:
+            ret.append(f"{member}.{parser.EXT}")
+    return ret
+
+
+def cfgpath(name, grid):
+    """Path of the fktable in 'name' called 'grid' if it exists, else None."""
+    path = configs.configs["paths"]["fktables"] / name / grid
+    return path if path.exists() else None
+
+
+def assembly_combined_fk(
+    theoryid,
+    dataset,
+    ffns3,
+    ffn03,
+    ffns4til,
+    ffns4bar,
+    ffn04,
+    ffns5til,
+    ffns5bar,
+    overwrite,
+    cfg,
+):
+    """Perform consistency checks and combine the FONLL FK tables into one single FK table."""
+    # Checks
+    if not ffns3 or not ffn03:
+        raise InconsistentInputsError("ffns3 and/or ffn03 is not provided.")
+
+    if ffns4til is None or ffns4bar is None:
+        raise InconsistentInputsError(
+            "At least one of ffns4til and ffns4bar should be provided."
+        )
+
+    # Do we consider two masses, i.e. mc and mb
+    if any([ffns5til, ffns5bar, ffn04]):
+        if (ffns5til is None and ffns5bar is None) or ffn04 is None:
+            raise InconsistentInputsError(
+                "To include nf5 contributions, ffn04 and at least one between ffns5til and ffns5bar are mandatory"
+            )
+
+    # Get theory info
+    tcard = theory_card.load(theoryid)
+    if tcard["DAMP"] == 1:
+        if not "DAMPPOWERc" in tcard or not "DAMPPOWERb" in tcard:
+            raise InconsistentInputsError(
+                "If DAMP is set, set also DAMPPOWERb and DAMPPOWERc"
+            )
+    else:
+        tcard["DAMPPOWERb"] = 0
+        tcard["DAMPPOWERc"] = 0
+    # Getting the paths to the grids
+    grids_name = grids_names(configs.configs["paths"]["ymldb"] / f"{dataset}.yaml")
+    for grid in grids_name:
+        # Checking if it already exists
+        new_fk_path = configs.configs["paths"]["fktables"] / str(theoryid) / grid
+        if new_fk_path.exists():
+            if not overwrite:
+                logger.info(
+                    "[green]Success:[/] skipping existing FK Table %s", str(new_fk_path)
+                )
+                return
+        produce_combined_fk(
+            *(
+                cfgpath(str(name), grid)
+                for name in (
+                    ffns3,
+                    ffn03,
+                    ffns4til,
+                    ffns4bar,
+                    ffn04,
+                    ffns5til,
+                    ffns5bar,
+                )
+            ),
+            theoryid,
+            damp=(tcard["DAMP"], tcard["DAMPPOWERc"], tcard["DAMPPOWERb"]),
+            cfg=cfg,
+        )
+        if new_fk_path.exists():
+            logger.info("[green]Success:[/] Wrote FK table to %s", str(new_fk_path))
+        else:
+            logger.info("[red]Failure:[/]")
+
+
 def produce_combined_fk(
     ffns3,
     ffn03,
@@ -264,5 +362,5 @@ def dump_tcards(tcard, tcard_parent_path, theoryid):
         with open(theorycard_path, "w", encoding="UTF-8") as f:
             yaml.safe_dump(theorycard, f)
         paths_list.append(theorycard_path)
-        rich.print(f"[green]Wrote theory card to {theorycard_path}")
+        logger.info("[green]Wrote theory card to %s", str(theorycard_path))
     return paths_list

From 29312c9f2bc7a423c1a684b6efb2c3afffa84d46 Mon Sep 17 00:00:00 2001
From: giacomomagni <giac.magni@gmail.com>
Date: Thu, 15 Feb 2024 14:03:30 +0100
Subject: [PATCH 03/25] restore commands

---
 src/pineko/cli/fonll.py | 3 ++-
 src/pineko/fonll.py     | 2 +-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/pineko/cli/fonll.py b/src/pineko/cli/fonll.py
index 751d45be..43f9ff93 100644
--- a/src/pineko/cli/fonll.py
+++ b/src/pineko/cli/fonll.py
@@ -86,7 +86,7 @@ def fonll_tcards(theoryid, cfg):
         raise TheoryCardError("The theorycard does not correspond to an FONLL scheme.")
     fonll.dump_tcards(tcard, tcard_parent_path, theoryid)
 
-
+@command.command("fonll_ekos")
 @click.argument("theoryID", type=click.INT)
 @click.argument("datasets", type=click.STRING, nargs=-1)
 @click.option("--overwrite", is_flag=True, help="Allow files to be overwritten")
@@ -144,6 +144,7 @@ def fonll_ekos(theoryid, datasets, overwrite, cfg):
     )
 
 
+@command.command("fonll_fks")
 @click.argument("theoryID", type=click.INT)
 @click.argument("datasets", type=click.STRING, nargs=-1)
 @click.option("--pdf", "-p", default=None, help="PDF set used for comparison")
diff --git a/src/pineko/fonll.py b/src/pineko/fonll.py
index 13440032..0ef2d695 100644
--- a/src/pineko/fonll.py
+++ b/src/pineko/fonll.py
@@ -10,7 +10,7 @@
 import pineappl
 import yaml
 
-from . import configs, theory_card, parser
+from . import configs, parser, theory_card
 
 logger = logging.getLogger(__name__)
 

From 4f3c94dc4eed863799032bdb9fdb9a409fa9f46e Mon Sep 17 00:00:00 2001
From: Giacomo Magni <giac.magni@gmail.com>
Date: Thu, 15 Feb 2024 14:28:57 +0100
Subject: [PATCH 04/25] improve logging

---
 src/pineko/cli/fonll.py |  9 ++++-----
 src/pineko/fonll.py     | 11 ++++++-----
 2 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/src/pineko/cli/fonll.py b/src/pineko/cli/fonll.py
index 43f9ff93..f065f88e 100644
--- a/src/pineko/cli/fonll.py
+++ b/src/pineko/cli/fonll.py
@@ -1,15 +1,14 @@
 """CLI entry point to FONLL."""
 
-import logging
 import pathlib
 
 import click
+import rich
 
 from .. import configs, fonll, theory, theory_card
 from ..fonll import TheoryCardError
 from ._base import command
 
-logger = logging.getLogger(__name__)
 
 
 config_setting = click.option(
@@ -125,12 +124,12 @@ def fonll_ekos(theoryid, datasets, overwrite, cfg):
 
     # now inherit ekos
     # nf=3
-    logger.info("Inherit nf=3 from theory %i00", theoryid)
+    rich.print(f"[green] Inherit nf=3 ekos from theory {theoryid}00")
     theory.TheoryBuilder(f"{theoryid}00", datasets, overwrite=overwrite).inherit_ekos(
         f"{theoryid}01"
     )
     # nf=4
-    logger.info("Inherit nf=4 from theory %i04", theoryid)
+    rich.print(f"[green] Inherit nf=4 ekos from theory {theoryid}04")
     theory.TheoryBuilder(f"{theoryid}04", datasets, overwrite=overwrite).inherit_ekos(
         f"{theoryid}02"
     )
@@ -138,7 +137,7 @@ def fonll_ekos(theoryid, datasets, overwrite, cfg):
         f"{theoryid}03"
     )
     # nf=5
-    logger.info("Inherit nf=5 from theory %i05", theoryid)
+    rich.print(f"[green] Inherit nf=5 ekos from theory {theoryid}05")
     theory.TheoryBuilder(f"{theoryid}05", datasets, overwrite=overwrite).inherit_ekos(
         f"{theoryid}06"
     )
diff --git a/src/pineko/fonll.py b/src/pineko/fonll.py
index 0ef2d695..6a9ae42b 100644
--- a/src/pineko/fonll.py
+++ b/src/pineko/fonll.py
@@ -8,6 +8,7 @@
 from pathlib import Path
 
 import pineappl
+import rich
 import yaml
 
 from . import configs, parser, theory_card
@@ -228,8 +229,8 @@ def assembly_combined_fk(
         new_fk_path = configs.configs["paths"]["fktables"] / str(theoryid) / grid
         if new_fk_path.exists():
             if not overwrite:
-                logger.info(
-                    "[green]Success:[/] skipping existing FK Table %s", str(new_fk_path)
+                rich.print(
+                    f"[green]Success:[/] skipping existing FK Table {new_fk_path}"
                 )
                 return
         produce_combined_fk(
@@ -250,9 +251,9 @@ def assembly_combined_fk(
             cfg=cfg,
         )
         if new_fk_path.exists():
-            logger.info("[green]Success:[/] Wrote FK table to %s", str(new_fk_path))
+            rich.print(f"[green]Success:[/] Wrote FK table to {new_fk_path}")
         else:
-            logger.info("[red]Failure:[/]")
+            rich.print("[red]Failure:[/]")
 
 
 def produce_combined_fk(
@@ -362,5 +363,5 @@ def dump_tcards(tcard, tcard_parent_path, theoryid):
         with open(theorycard_path, "w", encoding="UTF-8") as f:
             yaml.safe_dump(theorycard, f)
         paths_list.append(theorycard_path)
-        logger.info("[green]Wrote theory card to %s", str(theorycard_path))
+        rich.print(f"[green]Wrote theory card to {theorycard_path}")
     return paths_list

From e9306991bddaa3b3994f0615dca2151b1d8d3235 Mon Sep 17 00:00:00 2001
From: Giacomo Magni <giac.magni@gmail.com>
Date: Thu, 15 Feb 2024 14:47:09 +0100
Subject: [PATCH 05/25] remove creation of num fonll theories from eko command

---
 src/pineko/cli/fonll.py | 17 ++++-------------
 1 file changed, 4 insertions(+), 13 deletions(-)

diff --git a/src/pineko/cli/fonll.py b/src/pineko/cli/fonll.py
index f065f88e..7f4b5b6c 100644
--- a/src/pineko/cli/fonll.py
+++ b/src/pineko/cli/fonll.py
@@ -9,8 +9,6 @@
 from ..fonll import TheoryCardError
 from ._base import command
 
-
-
 config_setting = click.option(
     "-c",
     "--configs",
@@ -85,6 +83,7 @@ def fonll_tcards(theoryid, cfg):
         raise TheoryCardError("The theorycard does not correspond to an FONLL scheme.")
     fonll.dump_tcards(tcard, tcard_parent_path, theoryid)
 
+
 @command.command("fonll_ekos")
 @click.argument("theoryID", type=click.INT)
 @click.argument("datasets", type=click.STRING, nargs=-1)
@@ -93,20 +92,12 @@ def fonll_tcards(theoryid, cfg):
 def fonll_ekos(theoryid, datasets, overwrite, cfg):
     """Command to generate numerical FONLL ekos.
 
-    1. Produce the 7 theory cards needed for numerical FONLL.
-    2. Create the 3 operator cards for the different flavor patches.
-    3. Run the 3 ekos for the different flavor patches.
-    4. Inherit the ekos.
+    1. Create the 3 operator cards for the different flavor patches.
+    2. Run the 3 ekos for the different flavor patches.
+    3. Inherit the ekos.
     """
     load_config(cfg)
 
-    # create the 7 theory cards
-    tcard = theory_card.load(theoryid)
-    tcard_parent_path = theory_card.path(theoryid).parent
-    if "FONLL" not in tcard["FNS"]:
-        raise TheoryCardError("The theorycard does not correspond to an FONLL scheme.")
-    fonll.dump_tcards(tcard, tcard_parent_path, theoryid)
-
     for nf_id in ["00", "04", "05"]:
         # create opcards
         theory.TheoryBuilder(

From 6300c9deba36637cadd9d149b676f390d590e45e Mon Sep 17 00:00:00 2001
From: Giacomo Magni <giac.magni@gmail.com>
Date: Thu, 15 Feb 2024 15:34:42 +0100
Subject: [PATCH 06/25] init fonll docs

---
 docs/source/overview/running.rst | 77 +++++++++++++++++++++++++++++++-
 1 file changed, 76 insertions(+), 1 deletion(-)

diff --git a/docs/source/overview/running.rst b/docs/source/overview/running.rst
index df458dbf..2245cee3 100644
--- a/docs/source/overview/running.rst
+++ b/docs/source/overview/running.rst
@@ -29,13 +29,16 @@ This is a two step process:
 
 
 
-Inherit |EKO| from Existing Theory
+Inherit |EKO| or grids from Existing Theory
 """""""""""""""""""""""""""""""""""
 
 You can reuse the |EKO| from a different theory by running::
 
   pineko theory inherit-ekos SOURCE_THEORY_ID TARGET_THEORY_ID DATASET1 DATASET2 ...
 
+You can reuse the grid 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]_.
 
@@ -54,6 +57,78 @@ Note that you can also convolute a single grid with a single eko (obtaining a si
 If necessary it is possible to specify the values of the *renormalization* and *factorization* scale variations with
 the options ``--xir`` and ``--xif``.
 
+
+Generating FONLL FK Tables
+--------------------------
+
+In order to generate FK tables with (numerical) |FONLL| the different flavor schemes
+need to be evolved separately and joined together in a single FK table only 
+in the final step. 
+
+There are 2 workflows possible, one in which all the steps are performed individually 
+and one that is more automatize. 
+
+The automatize workflows always assumes that |FONLL| is performed both for
+charm and bottom effects.
+
+The manual procedure works as follow:
+
+  1. Generate 7 theories for all the different flavor patches with command:
+
+      pineko fonll_tcards THEORY_ID
+
+    The different flavor patches are named following the convention:
+
+      * THEORY_ID00 : |FFNS| :math:`n_f=3`
+      * THEORY_ID01 : |FFN0| :math:`n_f=3`
+      * THEORY_ID02 : massless component of |FFNS| :math:`n_f=4`
+      * THEORY_ID03 : massive component of |FFNS| :math:`n_f=4`
+      * THEORY_ID05 : massless component of |FFNS| :math:`n_f=5`
+      * THEORY_ID06 : massive component of |FFNS| :math:`n_f=5`
+    
+    where for |FFNS| :math:`n_f=4,5` massive and massless parts are splitted to
+    allow for a damping option.
+
+  2. Generate the grids corrisponding to all the 7 theories with the external program.
+  
+  3. Generate the operator cards for each theory with the usual command.
+  4. Generate the ekos for each theory with the usual commands.
+     Note that in principle only 3 ekos are needed, as there are only 3 different :math:`n_f` patches.
+     So you might speed up the procedure taking advantage of inherit-ekos.
+    
+  5. Generate the FK tables each of the 7 theories with the usual commands.
+
+  6. Combine the various FK tables into a single file, using the command:
+
+      pineko combine_fonll THEORY_ID DATASET --FFNS3 THEORY_ID00 --FFN03 THEORY_ID01 --FFNS4til THEORY_ID02 --FFNS4bar THEORY_ID03 --FFN04 THEORY_ID04 --FFNS5til THEORY_ID05 --FFNS5bar THEORY_ID06
+
+    where the first 3 theories are needed to perform |FONLL| on charm effects, 
+    while the last 4 are needed to include also bottom effects.
+
+The automatize procedure can be faster, but it might be less
+flexible. In this case the workflows is:
+
+  1. Generate 7 theories for all the different flavor patches with command:
+
+      pineko fonll_tcards THEORY_ID
+    
+    See above for the naming convention
+  
+  2. Generate the grids corrisponding to all the 7 theories with the external program.
+
+  3. Generate the ekos for only 3 theories and inherit the others using the command:
+
+      pineko fonll_ekos THEORY_ID DATASET1 DATASET2 ...
+
+    Note: this is usually an expensive operation as multiple ekos are run sequentially. 
+    Depending on the resources that you have available it might be more convinient
+    to call the command separately for each DATASET.
+  
+  4. Generate the final |FONLL| FK table directly using:
+
+      pineko fonll_fks THEORY_ID DATASET1 DATASET2 ...
+
+
 Other functionalities
 ---------------------
 

From 739f7cabc7c46d08351f34768c578687e394eafc Mon Sep 17 00:00:00 2001
From: Giacomo Magni <giac.magni@gmail.com>
Date: Thu, 15 Feb 2024 15:35:11 +0100
Subject: [PATCH 07/25] init fonll docs

---
 docs/source/shared/abbreviations.rst | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/docs/source/shared/abbreviations.rst b/docs/source/shared/abbreviations.rst
index 1d69fa6d..8851df88 100644
--- a/docs/source/shared/abbreviations.rst
+++ b/docs/source/shared/abbreviations.rst
@@ -11,9 +11,16 @@
 .. |FFNS| replace::
     :abbr:`FFNS (Fixed Flavor Number Scheme)`
 
+.. |FFN0| replace::
+    :abbr:`FFN0 (Asymptotic Fixed Flavor Number Scheme)`
+
 .. |VFNS| replace::
     :abbr:`VFNS (Variable Flavor Number Scheme)`
 
+.. |FONLL| replace::
+    :abbr:`FONLL (Fixed Order Next-to-Leading Log)`
+
+
 
 .. perturbative orders
 .. |LO| replace::

From c74f940373da0d1a0d8cc07115072b4817cbf4b4 Mon Sep 17 00:00:00 2001
From: Giacomo Magni <giac.magni@gmail.com>
Date: Thu, 15 Feb 2024 15:45:26 +0100
Subject: [PATCH 08/25] more on docs

---
 docs/source/overview/running.rst | 59 ++++++++++++++++----------------
 1 file changed, 30 insertions(+), 29 deletions(-)

diff --git a/docs/source/overview/running.rst b/docs/source/overview/running.rst
index 2245cee3..e9b21b57 100644
--- a/docs/source/overview/running.rst
+++ b/docs/source/overview/running.rst
@@ -30,7 +30,7 @@ This is a two step process:
 
 
 Inherit |EKO| or grids from Existing Theory
-"""""""""""""""""""""""""""""""""""
+"""""""""""""""""""""""""""""""""""""""""""
 
 You can reuse the |EKO| from a different theory by running::
 
@@ -62,69 +62,70 @@ Generating FONLL FK Tables
 --------------------------
 
 In order to generate FK tables with (numerical) |FONLL| the different flavor schemes
-need to be evolved separately and joined together in a single FK table only 
-in the final step. 
+need to be evolved separately and joined together in a single FK table only
+in the final step.
 
-There are 2 workflows possible, one in which all the steps are performed individually 
-and one that is more automatize. 
+There are 2 workflows possible, one in which all the steps are performed individually
+and one that is more automatize.
 
 The automatize workflows always assumes that |FONLL| is performed both for
 charm and bottom effects.
 
 The manual procedure works as follow:
 
-  1. Generate 7 theories for all the different flavor patches with command:
+  1. Generate 7 theories for all the different flavor patches with command::
 
       pineko fonll_tcards THEORY_ID
 
     The different flavor patches are named following the convention:
 
-      * THEORY_ID00 : |FFNS| :math:`n_f=3`
-      * THEORY_ID01 : |FFN0| :math:`n_f=3`
-      * THEORY_ID02 : massless component of |FFNS| :math:`n_f=4`
-      * THEORY_ID03 : massive component of |FFNS| :math:`n_f=4`
-      * THEORY_ID05 : massless component of |FFNS| :math:`n_f=5`
-      * THEORY_ID06 : massive component of |FFNS| :math:`n_f=5`
-    
+      * ``THEORY_ID00`` : |FFNS| :math:`n_f=3`
+      * ``THEORY_ID01`` : |FFN0| :math:`n_f=3`
+      * ``THEORY_ID02`` : massless component of |FFNS| :math:`n_f=4`
+      * ``THEORY_ID03`` : massive component of |FFNS| :math:`n_f=4`
+      * ``THEORY_ID05`` : massless component of |FFNS| :math:`n_f=5`
+      * ``THEORY_ID06`` : massive component of |FFNS| :math:`n_f=5`
+
     where for |FFNS| :math:`n_f=4,5` massive and massless parts are splitted to
     allow for a damping option.
 
   2. Generate the grids corrisponding to all the 7 theories with the external program.
-  
+
   3. Generate the operator cards for each theory with the usual command.
-  4. Generate the ekos for each theory with the usual commands.
-     Note that in principle only 3 ekos are needed, as there are only 3 different :math:`n_f` patches.
+     Note that, in principle, only 3 ekos are needed, as there are only 3 different :math:`n_f` patches.
      So you might speed up the procedure taking advantage of inherit-ekos.
-    
+
+  4. Generate the ekos for each theory with the usual commands.
+
   5. Generate the FK tables each of the 7 theories with the usual commands.
 
-  6. Combine the various FK tables into a single file, using the command:
+  6. Combine the various FK tables into a single file, using the command::
 
       pineko combine_fonll THEORY_ID DATASET --FFNS3 THEORY_ID00 --FFN03 THEORY_ID01 --FFNS4til THEORY_ID02 --FFNS4bar THEORY_ID03 --FFN04 THEORY_ID04 --FFNS5til THEORY_ID05 --FFNS5bar THEORY_ID06
 
-    where the first 3 theories are needed to perform |FONLL| on charm effects, 
+    where the first 3 theories are needed to perform |FONLL| on charm effects,
     while the last 4 are needed to include also bottom effects.
 
-The automatize procedure can be faster, but it might be less
-flexible. In this case the workflows is:
+The automatize procedure can be faster, but it might be less flexible.
+In this case the workflows is:
 
-  1. Generate 7 theories for all the different flavor patches with command:
+  1. Generate 7 theories for all the different flavor patches with the command::
 
       pineko fonll_tcards THEORY_ID
-    
-    See above for the naming convention
-  
+
+    See above for the intermediate theories naming convention.
+
   2. Generate the grids corrisponding to all the 7 theories with the external program.
 
-  3. Generate the ekos for only 3 theories and inherit the others using the command:
+  3. Generate the ekos for only 3 theories and inherit the others running::
 
       pineko fonll_ekos THEORY_ID DATASET1 DATASET2 ...
 
-    Note: this is usually an expensive operation as multiple ekos are run sequentially. 
+    Note: this is usually an expensive operation as multiple ekos are run sequentially.
     Depending on the resources that you have available it might be more convinient
     to call the command separately for each DATASET.
-  
-  4. Generate the final |FONLL| FK table directly using:
+
+  4. Generate the final |FONLL| FK table directly running::
 
       pineko fonll_fks THEORY_ID DATASET1 DATASET2 ...
 

From 28b8fe8f3c3831ca5fe7cd68789e91113212cb64 Mon Sep 17 00:00:00 2001
From: andreab1997 <andreab1997@yahoo.it>
Date: Tue, 20 Feb 2024 14:02:33 +0100
Subject: [PATCH 09/25] Fix FONLL-B bug

---
 src/pineko/fonll.py  | 1 +
 src/pineko/theory.py | 7 +++++++
 2 files changed, 8 insertions(+)

diff --git a/src/pineko/fonll.py b/src/pineko/fonll.py
index 6a9ae42b..ebf40e73 100644
--- a/src/pineko/fonll.py
+++ b/src/pineko/fonll.py
@@ -333,6 +333,7 @@ def collect_updates(fonll_fns):
                 "NfFF": cfg.nf,
                 "PTO": po,
                 "FONLLParts": cfg.parts,
+                "PTOEKO": int(base_pto),
             }
         )
         # In a mixed FONLL scheme we only subract the resummed terms that are
diff --git a/src/pineko/theory.py b/src/pineko/theory.py
index bd76c3cd..79b8f348 100644
--- a/src/pineko/theory.py
+++ b/src/pineko/theory.py
@@ -317,6 +317,13 @@ def eko(self, name, _grid, tcard):
         )
         # setup data
         ocard = self.load_operator_card(name)
+        # For nFONLL mixed prescriptions (such as FONLL-B) the PTO written on
+        # the tcard is used to produce the grid by yadism and it might be different
+        # from the PTO needed for the PDF evolution (and so by EKO). Here we
+        # ensure that the PTO used in the EKO calculation reflects the real
+        # perturbative order of the prescription.
+        if "PTOEKO" in tcard:
+            tcard["PTO"] = tcard["PTOEKO"]
         # The operator card has been already generated in the correct format
         # The theory card needs to be converted to a format that eko can use
         legacy_class = eko.io.runcards.Legacy(tcard, ocard)

From 89a066a581dc158f4c0806b0e31ae86913ef01f0 Mon Sep 17 00:00:00 2001
From: Giacomo Magni <39065935+giacomomagni@users.noreply.github.com>
Date: Tue, 20 Feb 2024 14:42:51 +0100
Subject: [PATCH 10/25] Update docs/source/overview/running.rst

Co-authored-by: Andrea Barontini <andreab1997@yahoo.it>
---
 docs/source/overview/running.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/source/overview/running.rst b/docs/source/overview/running.rst
index e9b21b57..623fb89d 100644
--- a/docs/source/overview/running.rst
+++ b/docs/source/overview/running.rst
@@ -66,7 +66,7 @@ need to be evolved separately and joined together in a single FK table only
 in the final step.
 
 There are 2 workflows possible, one in which all the steps are performed individually
-and one that is more automatize.
+and one that is more automatized.
 
 The automatize workflows always assumes that |FONLL| is performed both for
 charm and bottom effects.

From 01cc3a227b264429b80bbed3ed1e843b38533b80 Mon Sep 17 00:00:00 2001
From: Giacomo Magni <39065935+giacomomagni@users.noreply.github.com>
Date: Tue, 20 Feb 2024 14:43:09 +0100
Subject: [PATCH 11/25] Update docs/source/overview/running.rst

Co-authored-by: Andrea Barontini <andreab1997@yahoo.it>
---
 docs/source/overview/running.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/source/overview/running.rst b/docs/source/overview/running.rst
index 623fb89d..bead45dd 100644
--- a/docs/source/overview/running.rst
+++ b/docs/source/overview/running.rst
@@ -68,7 +68,7 @@ in the final step.
 There are 2 workflows possible, one in which all the steps are performed individually
 and one that is more automatized.
 
-The automatize workflows always assumes that |FONLL| is performed both for
+The automatized workflows always assumes that |FONLL| is performed both for
 charm and bottom effects.
 
 The manual procedure works as follow:

From 09a068683b91a6f93d4b3c5dc50a44e2ce6a81cb Mon Sep 17 00:00:00 2001
From: Giacomo Magni <39065935+giacomomagni@users.noreply.github.com>
Date: Tue, 20 Feb 2024 14:43:37 +0100
Subject: [PATCH 12/25] Update docs/source/overview/running.rst

Co-authored-by: Andrea Barontini <andreab1997@yahoo.it>
---
 docs/source/overview/running.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/source/overview/running.rst b/docs/source/overview/running.rst
index bead45dd..3e976aa3 100644
--- a/docs/source/overview/running.rst
+++ b/docs/source/overview/running.rst
@@ -106,7 +106,7 @@ The manual procedure works as follow:
     where the first 3 theories are needed to perform |FONLL| on charm effects,
     while the last 4 are needed to include also bottom effects.
 
-The automatize procedure can be faster, but it might be less flexible.
+The automatized procedure can be faster, but it might be less flexible.
 In this case the workflows is:
 
   1. Generate 7 theories for all the different flavor patches with the command::

From 42d22d4e51147f3a7a54d9cdbe3cd0714dc272fa Mon Sep 17 00:00:00 2001
From: Giacomo Magni <39065935+giacomomagni@users.noreply.github.com>
Date: Wed, 6 Mar 2024 13:55:12 +0100
Subject: [PATCH 13/25] Update docs/source/overview/running.rst

Co-authored-by: Roy Stegeman <roystegeman@live.nl>
---
 docs/source/overview/running.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/source/overview/running.rst b/docs/source/overview/running.rst
index 3e976aa3..a53a2a09 100644
--- a/docs/source/overview/running.rst
+++ b/docs/source/overview/running.rst
@@ -61,7 +61,7 @@ the options ``--xir`` and ``--xif``.
 Generating FONLL FK Tables
 --------------------------
 
-In order to generate FK tables with (numerical) |FONLL| the different flavor schemes
+In order to generate FK tables with |FONLL| the different flavor schemes
 need to be evolved separately and joined together in a single FK table only
 in the final step.
 

From 78b3fb83e28b6ec6168b11e14eb29c2f88f33f16 Mon Sep 17 00:00:00 2001
From: Giacomo Magni <39065935+giacomomagni@users.noreply.github.com>
Date: Wed, 6 Mar 2024 13:55:19 +0100
Subject: [PATCH 14/25] Update docs/source/overview/running.rst

Co-authored-by: Roy Stegeman <roystegeman@live.nl>
---
 docs/source/overview/running.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/source/overview/running.rst b/docs/source/overview/running.rst
index a53a2a09..ac5f2df1 100644
--- a/docs/source/overview/running.rst
+++ b/docs/source/overview/running.rst
@@ -89,7 +89,7 @@ The manual procedure works as follow:
     where for |FFNS| :math:`n_f=4,5` massive and massless parts are splitted to
     allow for a damping option.
 
-  2. Generate the grids corrisponding to all the 7 theories with the external program.
+  2. Generate the grids corresponding to all the 7 theories with the external program.
 
   3. Generate the operator cards for each theory with the usual command.
      Note that, in principle, only 3 ekos are needed, as there are only 3 different :math:`n_f` patches.

From efe91fbc815a89e3e60021466752fe7dccc0e744 Mon Sep 17 00:00:00 2001
From: Giacomo Magni <39065935+giacomomagni@users.noreply.github.com>
Date: Wed, 6 Mar 2024 13:55:29 +0100
Subject: [PATCH 15/25] Update docs/source/overview/running.rst

Co-authored-by: Roy Stegeman <roystegeman@live.nl>
---
 docs/source/overview/running.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/source/overview/running.rst b/docs/source/overview/running.rst
index ac5f2df1..732f4757 100644
--- a/docs/source/overview/running.rst
+++ b/docs/source/overview/running.rst
@@ -86,7 +86,7 @@ The manual procedure works as follow:
       * ``THEORY_ID05`` : massless component of |FFNS| :math:`n_f=5`
       * ``THEORY_ID06`` : massive component of |FFNS| :math:`n_f=5`
 
-    where for |FFNS| :math:`n_f=4,5` massive and massless parts are splitted to
+    where for |FFNS| :math:`n_f=4,5` massive and massless parts are split to
     allow for a damping option.
 
   2. Generate the grids corresponding to all the 7 theories with the external program.

From 676cf607a2f06508e08a198df35a99283002faf7 Mon Sep 17 00:00:00 2001
From: Giacomo Magni <39065935+giacomomagni@users.noreply.github.com>
Date: Wed, 6 Mar 2024 13:55:36 +0100
Subject: [PATCH 16/25] Update docs/source/overview/running.rst

Co-authored-by: Roy Stegeman <roystegeman@live.nl>
---
 docs/source/overview/running.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/source/overview/running.rst b/docs/source/overview/running.rst
index 732f4757..558a862c 100644
--- a/docs/source/overview/running.rst
+++ b/docs/source/overview/running.rst
@@ -122,7 +122,7 @@ In this case the workflows is:
       pineko fonll_ekos THEORY_ID DATASET1 DATASET2 ...
 
     Note: this is usually an expensive operation as multiple ekos are run sequentially.
-    Depending on the resources that you have available it might be more convinient
+    Depending on the resources that you have available it might be more convenient
     to call the command separately for each DATASET.
 
   4. Generate the final |FONLL| FK table directly running::

From 05ea71e59efd6282a85c648aafb4e22710570d2a Mon Sep 17 00:00:00 2001
From: Giacomo Magni <39065935+giacomomagni@users.noreply.github.com>
Date: Wed, 6 Mar 2024 13:56:01 +0100
Subject: [PATCH 17/25] Update docs/source/overview/running.rst

Co-authored-by: Roy Stegeman <roystegeman@live.nl>
---
 docs/source/overview/running.rst | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/docs/source/overview/running.rst b/docs/source/overview/running.rst
index 558a862c..8c389e9e 100644
--- a/docs/source/overview/running.rst
+++ b/docs/source/overview/running.rst
@@ -79,12 +79,13 @@ The manual procedure works as follow:
 
     The different flavor patches are named following the convention:
 
-      * ``THEORY_ID00`` : |FFNS| :math:`n_f=3`
-      * ``THEORY_ID01`` : |FFN0| :math:`n_f=3`
-      * ``THEORY_ID02`` : massless component of |FFNS| :math:`n_f=4`
-      * ``THEORY_ID03`` : massive component of |FFNS| :math:`n_f=4`
-      * ``THEORY_ID05`` : massless component of |FFNS| :math:`n_f=5`
-      * ``THEORY_ID06`` : massive component of |FFNS| :math:`n_f=5`
+      * ``<THEORY_ID>00`` : |FFNS| :math:`n_f=3`
+      * ``<THEORY_ID>01`` : |FFN0| :math:`n_f=3`
+      * ``<THEORY_ID>02`` : massless component of |FFNS| :math:`n_f=4`
+      * ``<THEORY_ID>03`` : massive component of |FFNS| :math:`n_f=4`
+      * ``<THEORY_ID>04`` : |FFN0| :math:`n_f=4`
+      * ``<THEORY_ID>05`` : massless component of |FFNS| :math:`n_f=5`
+      * ``<THEORY_ID>06`` : massive component of |FFNS| :math:`n_f=5`
 
     where for |FFNS| :math:`n_f=4,5` massive and massless parts are split to
     allow for a damping option.

From 1673333bd312e7d9e976b8da308b6754251666e4 Mon Sep 17 00:00:00 2001
From: Giacomo Magni <39065935+giacomomagni@users.noreply.github.com>
Date: Wed, 6 Mar 2024 13:56:23 +0100
Subject: [PATCH 18/25] Update docs/source/overview/running.rst

Co-authored-by: Roy Stegeman <roystegeman@live.nl>
---
 docs/source/overview/running.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/source/overview/running.rst b/docs/source/overview/running.rst
index 8c389e9e..56daae75 100644
--- a/docs/source/overview/running.rst
+++ b/docs/source/overview/running.rst
@@ -116,7 +116,7 @@ In this case the workflows is:
 
     See above for the intermediate theories naming convention.
 
-  2. Generate the grids corrisponding to all the 7 theories with the external program.
+  2. Generate the grids corresponding to all the 7 theories with the external program.
 
   3. Generate the ekos for only 3 theories and inherit the others running::
 

From 415f0f9c398392d6b4f1284af268158a05efb2dd Mon Sep 17 00:00:00 2001
From: Giacomo Magni <39065935+giacomomagni@users.noreply.github.com>
Date: Wed, 6 Mar 2024 13:56:37 +0100
Subject: [PATCH 19/25] Update docs/source/overview/running.rst

Co-authored-by: Roy Stegeman <roystegeman@live.nl>
---
 docs/source/overview/running.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/source/overview/running.rst b/docs/source/overview/running.rst
index 56daae75..0c3323ce 100644
--- a/docs/source/overview/running.rst
+++ b/docs/source/overview/running.rst
@@ -118,7 +118,7 @@ In this case the workflows is:
 
   2. Generate the grids corresponding to all the 7 theories with the external program.
 
-  3. Generate the ekos for only 3 theories and inherit the others running::
+  3. Generate the three ekos, one for each :math:`n_f`, and inherit the others running:
 
       pineko fonll_ekos THEORY_ID DATASET1 DATASET2 ...
 

From f38eec4e002347c43960f45d8935fd8846a4ae7e Mon Sep 17 00:00:00 2001
From: giacomomagni <giac.magni@gmail.com>
Date: Wed, 6 Mar 2024 14:30:38 +0100
Subject: [PATCH 20/25] clarify "usual" in docs

---
 docs/source/overview/running.rst | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/docs/source/overview/running.rst b/docs/source/overview/running.rst
index 0c3323ce..3c5be179 100644
--- a/docs/source/overview/running.rst
+++ b/docs/source/overview/running.rst
@@ -92,13 +92,13 @@ The manual procedure works as follow:
 
   2. Generate the grids corresponding to all the 7 theories with the external program.
 
-  3. Generate the operator cards for each theory with the usual command.
+  3. Generate the operator cards for each theory with the normal command listed above.
      Note that, in principle, only 3 ekos are needed, as there are only 3 different :math:`n_f` patches.
      So you might speed up the procedure taking advantage of inherit-ekos.
 
-  4. Generate the ekos for each theory with the usual commands.
+  4. Generate the ekos for each theory with the normal command listed above.
 
-  5. Generate the FK tables each of the 7 theories with the usual commands.
+  5. Generate the FK tables each of the 7 theories with the normal command listed above.
 
   6. Combine the various FK tables into a single file, using the command::
 

From fbb4c5503a0da33efd0be7836393d4e3336b7faf Mon Sep 17 00:00:00 2001
From: Felix Hekhorn <felix.hekhorn@uni-tuebingen.de>
Date: Thu, 7 Mar 2024 18:20:44 +0200
Subject: [PATCH 21/25] Split docs

---
 docs/Makefile                          |   5 +-
 docs/source/index.rst                  |   2 +
 docs/source/overview/prerequisites.rst |  27 ++---
 docs/source/overview/running.rst       | 139 +++----------------------
 docs/source/theory/fktables.rst        |   4 +-
 docs/source/theory/fonll.rst           |  74 +++++++++++++
 docs/source/theory/kfactors.rst        |  11 ++
 docs/source/theory/scalevar.rst        |  19 +++-
 8 files changed, 135 insertions(+), 146 deletions(-)
 create mode 100644 docs/source/theory/fonll.rst
 create mode 100644 docs/source/theory/kfactors.rst

diff --git a/docs/Makefile b/docs/Makefile
index a497e14e..c503ed1a 100644
--- a/docs/Makefile
+++ b/docs/Makefile
@@ -8,8 +8,9 @@ SPHINXBUILD   = sphinx-build
 SOURCEDIR     = source
 BUILDDIR      = build
 
-PINEKODIR = ../src/eko
+PINEKODIR = ../src/pineko
 PINEKOOUT = $(SOURCEDIR)/modules/pineko
+TODOOUTFILE = ./source/code_todos.rst
 
 # Put it first so that "make" without argument is like "make help".
 help:
@@ -41,4 +42,4 @@ todos:
 	python generate_code_todos.py "$(PINEKODIR)" "$(TODOOUTFILE)"
 
 clean-todos:
-	rm "$(TODOOUTFILE)"
+	rm -f "$(TODOOUTFILE)"
diff --git a/docs/source/index.rst b/docs/source/index.rst
index 5da3e9f6..3f92de79 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -23,7 +23,9 @@
     :hidden:
 
     theory/fktables
+    theory/fonll
     theory/scalevar
+    theory/kfactors
 
 
     zzz-refs
diff --git a/docs/source/overview/prerequisites.rst b/docs/source/overview/prerequisites.rst
index a1c495c1..d47f206d 100644
--- a/docs/source/overview/prerequisites.rst
+++ b/docs/source/overview/prerequisites.rst
@@ -58,9 +58,7 @@ Default Operator Card
 ---------------------
 
 You need to provide a default operator card for |EKO| for each theory you want to use.
-An example is the following:
-
-::
+An example is the following::
 
   configs:
     evolution_method: truncated
@@ -99,7 +97,6 @@ An example is the following:
     skip_non_singlet: false
     skip_singlet: false
 
-::
 
 For more details about what is needed inside an operator card please refer to https://eko.readthedocs.io/en/latest/code/IO.html
 under the section **Operator Runcard**. Note that the actual operator cards for each FK table will be
@@ -109,23 +106,17 @@ 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/pinecards/>`_
-or reusing existing ones.
+There are typically two ways to obtain grids:
 
-Generate new Grids with *rr*
-""""""""""""""""""""""""""""
+1. computing them from scratch with
+   `pinefarm <https://github.com/NNPDF/pinefarm/>`_ (and `pinecards <https://github.com/NNPDF/pinecards/>`_).
 
-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.
+2. You can reuse the grids from a different theory by running::
 
-Inherit Grids from Existing Theory
-""""""""""""""""""""""""""""""""""
+    pineko theory inherit-grids SOURCE_THEORY_ID TARGET_THEORY_ID DATASET1 DATASET2 ...
 
-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 [4]_.
+  The relation between the source theory and the target theory is non-trivial
+  (e.g. they may differ by scale variations, different DIS settings, etc)
 
 
 Notes
@@ -134,5 +125,3 @@ Notes
 .. [2] this is to be replaced by the new CommonData format implemented by NNPDF
 
 .. [3] this is to be replaced by a binding to the NNPDF theory objects
-
-.. [4] examples being scale variations, different evolution settings, etc.
diff --git a/docs/source/overview/running.rst b/docs/source/overview/running.rst
index 3c5be179..0251d0e8 100644
--- a/docs/source/overview/running.rst
+++ b/docs/source/overview/running.rst
@@ -1,4 +1,3 @@
-################
 Running `pineko`
 ################
 
@@ -27,8 +26,6 @@ This is a two step process:
 
     pineko theory ekos THEORY_ID DATASET1 DATASET2 ...
 
-
-
 Inherit |EKO| or grids from Existing Theory
 """""""""""""""""""""""""""""""""""""""""""
 
@@ -40,7 +37,8 @@ You can reuse the grid 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]_.
+The relation between the source theory and the target theory is non-trivial
+(e.g. they may differ by scale variations, different DIS settings, etc).
 
 Generating the FK Table
 -----------------------
@@ -57,146 +55,43 @@ Note that you can also convolute a single grid with a single eko (obtaining a si
 If necessary it is possible to specify the values of the *renormalization* and *factorization* scale variations with
 the options ``--xir`` and ``--xif``.
 
-
-Generating FONLL FK Tables
---------------------------
-
-In order to generate FK tables with |FONLL| the different flavor schemes
-need to be evolved separately and joined together in a single FK table only
-in the final step.
-
-There are 2 workflows possible, one in which all the steps are performed individually
-and one that is more automatized.
-
-The automatized workflows always assumes that |FONLL| is performed both for
-charm and bottom effects.
-
-The manual procedure works as follow:
-
-  1. Generate 7 theories for all the different flavor patches with command::
-
-      pineko fonll_tcards THEORY_ID
-
-    The different flavor patches are named following the convention:
-
-      * ``<THEORY_ID>00`` : |FFNS| :math:`n_f=3`
-      * ``<THEORY_ID>01`` : |FFN0| :math:`n_f=3`
-      * ``<THEORY_ID>02`` : massless component of |FFNS| :math:`n_f=4`
-      * ``<THEORY_ID>03`` : massive component of |FFNS| :math:`n_f=4`
-      * ``<THEORY_ID>04`` : |FFN0| :math:`n_f=4`
-      * ``<THEORY_ID>05`` : massless component of |FFNS| :math:`n_f=5`
-      * ``<THEORY_ID>06`` : massive component of |FFNS| :math:`n_f=5`
-
-    where for |FFNS| :math:`n_f=4,5` massive and massless parts are split to
-    allow for a damping option.
-
-  2. Generate the grids corresponding to all the 7 theories with the external program.
-
-  3. Generate the operator cards for each theory with the normal command listed above.
-     Note that, in principle, only 3 ekos are needed, as there are only 3 different :math:`n_f` patches.
-     So you might speed up the procedure taking advantage of inherit-ekos.
-
-  4. Generate the ekos for each theory with the normal command listed above.
-
-  5. Generate the FK tables each of the 7 theories with the normal command listed above.
-
-  6. Combine the various FK tables into a single file, using the command::
-
-      pineko combine_fonll THEORY_ID DATASET --FFNS3 THEORY_ID00 --FFN03 THEORY_ID01 --FFNS4til THEORY_ID02 --FFNS4bar THEORY_ID03 --FFN04 THEORY_ID04 --FFNS5til THEORY_ID05 --FFNS5bar THEORY_ID06
-
-    where the first 3 theories are needed to perform |FONLL| on charm effects,
-    while the last 4 are needed to include also bottom effects.
-
-The automatized procedure can be faster, but it might be less flexible.
-In this case the workflows is:
-
-  1. Generate 7 theories for all the different flavor patches with the command::
-
-      pineko fonll_tcards THEORY_ID
-
-    See above for the intermediate theories naming convention.
-
-  2. Generate the grids corresponding to all the 7 theories with the external program.
-
-  3. Generate the three ekos, one for each :math:`n_f`, and inherit the others running:
-
-      pineko fonll_ekos THEORY_ID DATASET1 DATASET2 ...
-
-    Note: this is usually an expensive operation as multiple ekos are run sequentially.
-    Depending on the resources that you have available it might be more convenient
-    to call the command separately for each DATASET.
-
-  4. Generate the final |FONLL| FK table directly running::
-
-      pineko fonll_fks THEORY_ID DATASET1 DATASET2 ...
-
-
 Other functionalities
 ---------------------
 
 Other than the fundamental functions that have been described so far, *pineko* has a few
-handy utility functions.
+handy utility functions:
+
+- applying the :doc:`FONLL prescription</theory/fonll>`
+- applying the :doc:`scale variation prescription</theory/scalevar>`
+- burning the :doc:`K-factor</theory/kfactors>` into grids
+
 
 Checking the grids
 """"""""""""""""""
 
 Under the subcommand ``pineko check`` you can find two possible useful checks:
 
-1.  **compatibility**. This is used to check if a *grid* and an *eko* are compatible and ready to generate an Fk table. In order for a grid and an eko to be compatible, they must have the same x and Q2 grid (eventually including the factorization scale variations). The check is used as
-  ::
+1.  **compatibility**. This is used to check if a *grid* and an *eko* are compatible and ready to generate an |FK| table.
+    In order for a grid and an eko to be compatible, they must have the same x and Q2 grid (eventually including the
+    factorization scale variations). The check is used as
 
-    pineko check compatibility GRID EKO
+      pineko check compatibility GRID EKO
 
-  eventually specifying the value of the factorization scale variation with the option ``--xif``.
+    eventually specifying the value of the factorization scale variation with the option ``--xif``.
 2.  **scvar**. This is used to check if the provided grid contains the requested scale variations. The syntax is the following
-  ::
 
-    pineko check scvar GRID SCALE AS_ORDER AL_ORDER
+      pineko check scvar GRID SCALE AS_ORDER AL_ORDER
 
-  where ``SCALE`` can be one between "ren" and "fact" (respectively for *renormalization* and
-  *factorization* scale variations).
+    where ``SCALE`` can be one between "ren" and "fact" (respectively for *renormalization* and
+    *factorization* scale variations).
 
 Comparing grids and FK tables
 """""""""""""""""""""""""""""
 
 With the command ``pineko compare`` it is possible to compare the predictions as provided by the grid
-(convoluted with a |PDF|) with the predictions as provided by the FK table. This is done like::
+(convoluted with a |PDF|) with the predictions as provided by the |FK| table. This is done like
 
   pineko compare GRID FKTABLE MAX_AS MAX_AL PDF
 
 again eventually specifying the values of *renormalization* and *factorization* scales with the
 appropriate options.
-
-Scale variations
-""""""""""""""""
-
-Since it is possible to compute scale variations terms at a certain perturbative order N+1 just from
-the knowledge of the central N order (see https://pineko.readthedocs.io/en/latest/theory/scalevar.html),
-`pineko` includes a tool to add the required scale variations order to a grid which contain the
-necessary central orders. The command to run it is::
-
-  pineko ren_sv_grid GRID_PATH OUTPUT_FOLDER_PATH MAX_AS NF ORDER_EXISTS
-
-where ``GRID_PATH`` is the path of the original grid, ``OUTPUT_FOLDER_PATH`` is the folder where the
-updated grid will be dumped, ``MAX_AS`` is the requested perturbative order of the QCD coupling and
-``NF`` is the number of active flavors one wants to consider when computing the scale variations terms.
-If the original grid has already all the scale variations terms for the requested perturbative order,
-`pineko` will do nothing. If one want to force `pineko` to overwrite the already existing orders, it is
-enough to set ``ORDER_EXISTS`` to `True`.
-
-KFactors
-""""""""
-
-Another useful tool that `pineko` includes is ``pineko kfactor`` which allows the embedding of a kfactor
-as a proper order in a grid. The usage is the following::
-
-  pineko kfactor GRIDS_FOLDER KFACTOR_FOLDER YAMLDB_PATH TARGET_FOLDER MAX_AS ORDER_EXISTS
-
-where ``GRIDS_FOLDER`` is the folder containing the grids to update, ``KFACTOR_FOLDER`` is the folder
-containing the kfactor files and ``YAMLDB_PATH`` is the path to the yamldb file of the requested dataset.
-The other inputs have already been described in the previous section.
-
-Notes
------
-
-.. [5] examples being scale variations, different DIS settings, etc.
diff --git a/docs/source/theory/fktables.rst b/docs/source/theory/fktables.rst
index a92e10d9..f6473c8b 100644
--- a/docs/source/theory/fktables.rst
+++ b/docs/source/theory/fktables.rst
@@ -1,6 +1,6 @@
-============================================================
+
 Fast Kernel (FK) tables
-============================================================
+=======================
 
 The direct calculation of observables during a |PDF| fit is not very practical
 since it requires first solving the |DGLAP| evolution equation for each new boundary
diff --git a/docs/source/theory/fonll.rst b/docs/source/theory/fonll.rst
new file mode 100644
index 00000000..6a963977
--- /dev/null
+++ b/docs/source/theory/fonll.rst
@@ -0,0 +1,74 @@
+FONLL
+=====
+
+In order to generate |FK| tables with |FONLL| the different flavor schemes
+need to be evolved separately and joined together in a single |FK| table only
+in the final step.
+
+There are 2 workflows possible, one in which all the steps are performed individually
+and one that is more automatized.
+
+The automatized workflows always assumes that |FONLL| is performed both for
+charm and bottom effects.
+
+Manual procedure
+----------------
+
+  1. Generate 7 theories for all the different flavor patches with command::
+
+      pineko fonll_tcards THEORY_ID
+
+    The different flavor patches are named following the convention:
+
+      * ``<THEORY_ID>00`` : |FFNS| :math:`n_f=3`
+      * ``<THEORY_ID>01`` : |FFN0| :math:`n_f=3`
+      * ``<THEORY_ID>02`` : massless component of |FFNS| :math:`n_f=4`
+      * ``<THEORY_ID>03`` : massive component of |FFNS| :math:`n_f=4`
+      * ``<THEORY_ID>04`` : |FFN0| :math:`n_f=4`
+      * ``<THEORY_ID>05`` : massless component of |FFNS| :math:`n_f=5`
+      * ``<THEORY_ID>06`` : massive component of |FFNS| :math:`n_f=5`
+
+    where for |FFNS| :math:`n_f=4,5` massive and massless parts are split to
+    allow for a damping option.
+
+  2. Generate the grids corresponding to all the 7 theories with the external program.
+
+  3. Generate the operator cards for each theory with the normal command listed above.
+     Note that, in principle, only 3 ekos are needed, as there are only 3 different :math:`n_f` patches.
+     So you might speed up the procedure taking advantage of inherit-ekos.
+
+  4. Generate the ekos for each theory with the normal command listed above.
+
+  5. Generate the |FK| tables each of the 7 theories with the normal command listed above.
+
+  6. Combine the various |FK| tables into a single file, using the command::
+
+      pineko combine_fonll THEORY_ID DATASET --FFNS3 THEORY_ID00 --FFN03 THEORY_ID01 --FFNS4til THEORY_ID02 --FFNS4bar THEORY_ID03 --FFN04 THEORY_ID04 --FFNS5til THEORY_ID05 --FFNS5bar THEORY_ID06
+
+    where the first 3 theories are needed to perform |FONLL| on charm effects,
+    while the last 4 are needed to include also bottom effects.
+
+Automatic procedure
+-------------------
+
+This workflow can be faster, but it might be less flexible:
+
+  1. Generate 7 theories for all the different flavor patches with the command::
+
+      pineko fonll_tcards THEORY_ID
+
+    See above for the intermediate theories naming convention.
+
+  2. Generate the grids corresponding to all the 7 theories with the external program.
+
+  3. Generate the three ekos, one for each :math:`n_f`, and inherit the others running::
+
+      pineko fonll_ekos THEORY_ID DATASET1 DATASET2 ...
+
+    Note: this is usually an expensive operation as multiple ekos are run sequentially.
+    Depending on the resources that you have available it might be more convenient
+    to call the command separately for each DATASET.
+
+  4. Generate the final |FONLL| |FK| table directly running::
+
+      pineko fonll_fks THEORY_ID DATASET1 DATASET2 ...
diff --git a/docs/source/theory/kfactors.rst b/docs/source/theory/kfactors.rst
new file mode 100644
index 00000000..cb8222cb
--- /dev/null
+++ b/docs/source/theory/kfactors.rst
@@ -0,0 +1,11 @@
+K-Factors
+=========
+
+Another useful tool that `pineko` includes is ``pineko kfactor`` which allows the embedding of a kfactor
+as a proper order in a grid. The usage is the following::
+
+  pineko kfactor GRIDS_FOLDER KFACTOR_FOLDER YAMLDB_PATH TARGET_FOLDER MAX_AS ORDER_EXISTS
+
+where ``GRIDS_FOLDER`` is the folder containing the grids to update, ``KFACTOR_FOLDER`` is the folder
+containing the kfactor files and ``YAMLDB_PATH`` is the path to the yamldb file of the requested dataset.
+The other inputs have already been described in the previous section.
diff --git a/docs/source/theory/scalevar.rst b/docs/source/theory/scalevar.rst
index 9a682ae3..1a3dec16 100644
--- a/docs/source/theory/scalevar.rst
+++ b/docs/source/theory/scalevar.rst
@@ -117,7 +117,7 @@ where this time the perturbative expansion of :math:`\overline{H}(\alpha_{s}(t+\
 than :math:`\mathcal{O}(\alpha_{s}^{0})`.
 
 Scale variation for |PDF| evolution
-###########################################
+###################################
 
 A completely independent source of |MHOU| arises from the truncation of the perturbative expansion of the anomalous dimensions governing the evolution
 of the |PDF|. Again, this uncertainties can be estimated trough scale variation but, in this case, there are three equivalent ways in which it can be
@@ -222,3 +222,20 @@ Note that, even if these schemes are formally equivalent, they can differ by sub
 In fact, in **scheme A** some higher order terms of the anomalous dimensions expansion can be retained according to the kind of solution adopted for the evolution equation.
 In **scheme B** the exponential has been expanded so that it corresponds to a linearized solution of the evolution equations and in **scheme C** some terms coming from the
 cross-expansion of the coefficients functions and the linearized solution of the evolution equations have been dropped.
+
+
+Adding scale variations to a grid
+#################################
+
+Since it is possible to compute scale variations terms at a certain perturbative order N+1 just from
+the knowledge of the central N order, `pineko` includes a tool to add the required scale variations order to a grid which contain the
+necessary central orders. The command to run it is::
+
+  pineko ren_sv_grid GRID_PATH OUTPUT_FOLDER_PATH MAX_AS NF ORDER_EXISTS
+
+where ``GRID_PATH`` is the path of the original grid, ``OUTPUT_FOLDER_PATH`` is the folder where the
+updated grid will be dumped, ``MAX_AS`` is the requested perturbative order of the QCD coupling and
+``NF`` is the number of active flavors one wants to consider when computing the scale variations terms.
+If the original grid has already all the scale variations terms for the requested perturbative order,
+`pineko` will do nothing. If one want to force `pineko` to overwrite the already existing orders, it is
+enough to set ``ORDER_EXISTS`` to `True`.

From 3365f2ec8b764d31c2c88846a4b7d7a62a2ac5b5 Mon Sep 17 00:00:00 2001
From: Giacomo Magni <giac.magni@gmail.com>
Date: Fri, 8 Mar 2024 10:55:45 +0100
Subject: [PATCH 22/25] reorganize fonll commands

---
 docs/source/theory/fonll.rst | 10 +++----
 src/pineko/cli/_base.py      | 23 +++++++++++++++
 src/pineko/cli/fonll.py      | 57 ++++++++++--------------------------
 src/pineko/cli/scaffold.py   | 21 +++----------
 src/pineko/cli/theory_.py    | 23 ++++-----------
 src/pineko/fonll.py          | 10 ++-----
 6 files changed, 54 insertions(+), 90 deletions(-)

diff --git a/docs/source/theory/fonll.rst b/docs/source/theory/fonll.rst
index 6a963977..ceb49474 100644
--- a/docs/source/theory/fonll.rst
+++ b/docs/source/theory/fonll.rst
@@ -16,7 +16,7 @@ Manual procedure
 
   1. Generate 7 theories for all the different flavor patches with command::
 
-      pineko fonll_tcards THEORY_ID
+      pineko fonll tcards THEORY_ID
 
     The different flavor patches are named following the convention:
 
@@ -43,7 +43,7 @@ Manual procedure
 
   6. Combine the various |FK| tables into a single file, using the command::
 
-      pineko combine_fonll THEORY_ID DATASET --FFNS3 THEORY_ID00 --FFN03 THEORY_ID01 --FFNS4til THEORY_ID02 --FFNS4bar THEORY_ID03 --FFN04 THEORY_ID04 --FFNS5til THEORY_ID05 --FFNS5bar THEORY_ID06
+      pineko fonll combine THEORY_ID DATASET --FFNS3 THEORY_ID00 --FFN03 THEORY_ID01 --FFNS4til THEORY_ID02 --FFNS4bar THEORY_ID03 --FFN04 THEORY_ID04 --FFNS5til THEORY_ID05 --FFNS5bar THEORY_ID06
 
     where the first 3 theories are needed to perform |FONLL| on charm effects,
     while the last 4 are needed to include also bottom effects.
@@ -55,7 +55,7 @@ This workflow can be faster, but it might be less flexible:
 
   1. Generate 7 theories for all the different flavor patches with the command::
 
-      pineko fonll_tcards THEORY_ID
+      pineko fonll tcards THEORY_ID
 
     See above for the intermediate theories naming convention.
 
@@ -63,7 +63,7 @@ This workflow can be faster, but it might be less flexible:
 
   3. Generate the three ekos, one for each :math:`n_f`, and inherit the others running::
 
-      pineko fonll_ekos THEORY_ID DATASET1 DATASET2 ...
+      pineko fonll ekos THEORY_ID DATASET1 DATASET2 ...
 
     Note: this is usually an expensive operation as multiple ekos are run sequentially.
     Depending on the resources that you have available it might be more convenient
@@ -71,4 +71,4 @@ This workflow can be faster, but it might be less flexible:
 
   4. Generate the final |FONLL| |FK| table directly running::
 
-      pineko fonll_fks THEORY_ID DATASET1 DATASET2 ...
+      pineko fonll fks THEORY_ID DATASET1 DATASET2 ...
diff --git a/src/pineko/cli/_base.py b/src/pineko/cli/_base.py
index 21d57d0a..c92b54e6 100644
--- a/src/pineko/cli/_base.py
+++ b/src/pineko/cli/_base.py
@@ -1,10 +1,33 @@
 """Adds global CLI options."""
 
+import pathlib
+
 import click
 
+from .. import configs
+
 CONTEXT_SETTINGS = dict(help_option_names=["-h", "--help"])
 
 
 @click.group(context_settings=CONTEXT_SETTINGS)
 def command():
     """pineko: Combine PineAPPL grids and EKOs into FK tables."""
+
+
+config_option = click.option(
+    "-c",
+    "--configs",
+    "cfg",
+    default=None,
+    type=click.Path(resolve_path=True, path_type=pathlib.Path),
+    help="Explicitly specify config file (it has to be a valid TOML file).",
+)
+
+
+def load_config(cfg):
+    """Load configuration files."""
+    path = configs.detect(cfg)
+    base_configs = configs.load(path)
+    configs.configs = configs.defaults(base_configs)
+    if cfg is not None:
+        print(f"Configurations loaded from '{path}'")
diff --git a/src/pineko/cli/fonll.py b/src/pineko/cli/fonll.py
index 7f4b5b6c..1a60cb9e 100644
--- a/src/pineko/cli/fonll.py
+++ b/src/pineko/cli/fonll.py
@@ -1,34 +1,21 @@
 """CLI entry point to FONLL."""
 
-import pathlib
-
 import click
 import rich
 
-from .. import configs, fonll, theory, theory_card
+from .. import fonll, theory, theory_card
 from ..fonll import TheoryCardError
-from ._base import command
-
-config_setting = click.option(
-    "-c",
-    "--configs",
-    "cfg",
-    default=None,
-    type=click.Path(resolve_path=True, path_type=pathlib.Path),
-    help="Explicitly specify config file (it has to be a valid TOML file).",
-)
+from ._base import command, config_option, load_config
 
 
-def load_config(cfg):
-    """Iterate a subcommand on a given theory and list of datasets."""
-    path = configs.detect(cfg)
-    base_configs = configs.load(path)
-    configs.configs = configs.defaults(base_configs)
-    if cfg is not None:
-        print(f"Configurations loaded from '{path}'")
+@command.group("fonll")
+@config_option
+def fonll_(cfg):
+    """Detect amd load configuration file."""
+    load_config(cfg)
 
 
-@command.command("combine_fonll")
+@fonll_.command()
 @click.argument("theoryID", type=int)
 @click.argument("dataset", type=str)
 @click.option("--FFNS3", type=int, help="theoryID containing the ffns3 fktable")
@@ -39,8 +26,7 @@ def load_config(cfg):
 @click.option("--FFNS5til", type=int, help="theoryID containing the ffns5til fktable")
 @click.option("--FFNS5bar", type=int, help="theoryID containing the ffns5bar fktable")
 @click.option("--overwrite", is_flag=True, help="Allow files to be overwritten")
-@config_setting
-def subcommand(
+def combine(
     theoryid,
     dataset,
     ffns3,
@@ -51,10 +37,8 @@ def subcommand(
     ffns5til,
     ffns5bar,
     overwrite,
-    cfg,
 ):
     """Combine the different FKs needed to produce the FONLL prescription."""
-    load_config(cfg)
     fonll.assembly_combined_fk(
         theoryid,
         dataset,
@@ -66,17 +50,13 @@ def subcommand(
         ffns5til,
         ffns5bar,
         overwrite,
-        cfg,
     )
 
 
-@command.command("fonll_tcards")
+@fonll_.command()
 @click.argument("theoryID", type=int)
-@config_setting
-def fonll_tcards(theoryid, cfg):
+def tcards(theoryid):
     """Produce the FONLL tcards starting from the original tcard given by the theoryID."""
-    load_config(cfg)
-
     tcard = theory_card.load(theoryid)
     tcard_parent_path = theory_card.path(theoryid).parent
     if "FONLL" not in tcard["FNS"]:
@@ -84,20 +64,17 @@ def fonll_tcards(theoryid, cfg):
     fonll.dump_tcards(tcard, tcard_parent_path, theoryid)
 
 
-@command.command("fonll_ekos")
+@fonll_.command()
 @click.argument("theoryID", type=click.INT)
 @click.argument("datasets", type=click.STRING, nargs=-1)
 @click.option("--overwrite", is_flag=True, help="Allow files to be overwritten")
-@config_setting
-def fonll_ekos(theoryid, datasets, overwrite, cfg):
+def ekos(theoryid, datasets, overwrite):
     """Command to generate numerical FONLL ekos.
 
     1. Create the 3 operator cards for the different flavor patches.
     2. Run the 3 ekos for the different flavor patches.
     3. Inherit the ekos.
     """
-    load_config(cfg)
-
     for nf_id in ["00", "04", "05"]:
         # create opcards
         theory.TheoryBuilder(
@@ -134,20 +111,17 @@ def fonll_ekos(theoryid, datasets, overwrite, cfg):
     )
 
 
-@command.command("fonll_fks")
+@fonll_.command()
 @click.argument("theoryID", type=click.INT)
 @click.argument("datasets", type=click.STRING, nargs=-1)
 @click.option("--pdf", "-p", default=None, help="PDF set used for comparison")
 @click.option("--overwrite", is_flag=True, help="Allow files to be overwritten")
-@config_setting
-def fonll_fks(theoryid, datasets, pdf, overwrite, cfg):
+def fks(theoryid, datasets, pdf, overwrite):
     """Command to generate numerical FONLL FK tables.
 
     1. Produce the 7 FK tables needed for numerical FONLL.
     2. Combine the FKtables into a single one.
     """
-    load_config(cfg)
-
     # create the 7 FK tables
     for th_suffix in range(0, 7):
         theory.TheoryBuilder(
@@ -171,5 +145,4 @@ def fonll_fks(theoryid, datasets, pdf, overwrite, cfg):
             ffns5til=f"{theoryid}05",
             ffns5bar=f"{theoryid}06",
             overwrite=overwrite,
-            cfg=cfg,
         )
diff --git a/src/pineko/cli/scaffold.py b/src/pineko/cli/scaffold.py
index c415a9c3..2a373ec5 100644
--- a/src/pineko/cli/scaffold.py
+++ b/src/pineko/cli/scaffold.py
@@ -1,30 +1,17 @@
 """'scaffold' mode of CLI."""
 
-import pathlib
-
 import click
 import rich
 
 from .. import configs, scaffold
-from ._base import command
+from ._base import command, config_option, load_config
 
 
 @command.group("scaffold")
-@click.option(
-    "-c",
-    "--configs",
-    "cfg",
-    default=None,
-    type=click.Path(resolve_path=True, path_type=pathlib.Path),
-    help="Explicitly specify config file (it has to be a valid TOML file).",
-)
+@config_option
 def scaffold_(cfg):
-    """Manage folders needed for the project as spelled out in the configuration file."""
-    path = configs.detect(cfg)
-    base_configs = configs.load(path)
-    configs.configs = configs.defaults(base_configs)
-    if cfg is not None:
-        print(f"Configurations loaded from '{path}'")
+    """Detect amd load configuration file."""
+    load_config(cfg)
 
 
 @scaffold_.command()
diff --git a/src/pineko/cli/theory_.py b/src/pineko/cli/theory_.py
index d25c254d..2c42170c 100644
--- a/src/pineko/cli/theory_.py
+++ b/src/pineko/cli/theory_.py
@@ -1,29 +1,16 @@
 """'theory' mode of CLI."""
 
-import pathlib
-
 import click
 
-from .. import configs, theory
-from ._base import command
+from .. import theory
+from ._base import command, config_option, load_config
 
 
 @command.group("theory")
-@click.option(
-    "-c",
-    "--configs",
-    "cfg",
-    default=None,
-    type=click.Path(resolve_path=True, path_type=pathlib.Path),
-    help="Explicitly specify config file (it has to be a valid TOML file).",
-)
+@config_option
 def theory_(cfg):
-    """Iterate a subcommand on a given theory and list of datasets."""
-    path = configs.detect(cfg)
-    base_configs = configs.load(path)
-    configs.configs = configs.defaults(base_configs)
-    if cfg is not None:
-        print(f"Configurations loaded from '{path}'")
+    """Detect amd load configuration file."""
+    load_config(cfg)
 
 
 @theory_.command()
diff --git a/src/pineko/fonll.py b/src/pineko/fonll.py
index ebf40e73..d6d7b012 100644
--- a/src/pineko/fonll.py
+++ b/src/pineko/fonll.py
@@ -193,7 +193,6 @@ def assembly_combined_fk(
     ffns5til,
     ffns5bar,
     overwrite,
-    cfg,
 ):
     """Perform consistency checks and combine the FONLL FK tables into one single FK table."""
     # Checks
@@ -248,7 +247,6 @@ def assembly_combined_fk(
             ),
             theoryid,
             damp=(tcard["DAMP"], tcard["DAMPPOWERc"], tcard["DAMPPOWERb"]),
-            cfg=cfg,
         )
         if new_fk_path.exists():
             rich.print(f"[green]Success:[/] Wrote FK table to {new_fk_path}")
@@ -266,7 +264,6 @@ def produce_combined_fk(
     ffns5bar,
     theoryid,
     damp=(0, None, None),
-    cfg=None,
 ):
     """Combine the FONLL FK tables into one single FK table."""
     fonll_info = FONLLInfo(ffns3, ffn03, ffns4til, ffns4bar, ffn04, ffns5til, ffns5bar)
@@ -279,14 +276,11 @@ def produce_combined_fk(
     )
     combined_fk = combine(fk_dict, dampings=dampings)
     input_theorycard_path = (
-        Path(configs.load(configs.detect(cfg))["paths"]["theory_cards"])
-        / f"{theoryid}.yaml"
+        Path(configs.configs["paths"]["theory_cards"]) / f"{theoryid}.yaml"
     )
     update_fk_theorycard(combined_fk, input_theorycard_path)
     # save final FONLL fktable
-    fk_folder = Path(configs.load(configs.detect(cfg))["paths"]["fktables"]) / str(
-        theoryid
-    )
+    fk_folder = Path(configs.configs["paths"]["fktables"]) / str(theoryid)
     fk_folder.mkdir(exist_ok=True)
     output_path_fk = fk_folder / fonll_info.dataset_name
     combined_fk.write_lz4(output_path_fk)

From 2c755c664c71d908d2a3796869766e04a26571c3 Mon Sep 17 00:00:00 2001
From: Giacomo Magni <giac.magni@gmail.com>
Date: Fri, 8 Mar 2024 11:21:29 +0100
Subject: [PATCH 23/25] fix pineko help

---
 src/pineko/cli/_base.py | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/src/pineko/cli/_base.py b/src/pineko/cli/_base.py
index c92b54e6..e7076623 100644
--- a/src/pineko/cli/_base.py
+++ b/src/pineko/cli/_base.py
@@ -1,6 +1,7 @@
 """Adds global CLI options."""
 
 import pathlib
+import sys
 
 import click
 
@@ -9,6 +10,11 @@
 CONTEXT_SETTINGS = dict(help_option_names=["-h", "--help"])
 
 
+def help_requested():
+    """Check if you are requesting help."""
+    return len(set(CONTEXT_SETTINGS["help_option_names"]) & set(sys.argv)) > 0
+
+
 @click.group(context_settings=CONTEXT_SETTINGS)
 def command():
     """pineko: Combine PineAPPL grids and EKOs into FK tables."""
@@ -26,6 +32,9 @@ def command():
 
 def load_config(cfg):
     """Load configuration files."""
+    # if just help is needed, return before loading
+    if help_requested():
+        return
     path = configs.detect(cfg)
     base_configs = configs.load(path)
     configs.configs = configs.defaults(base_configs)

From 1b88551174692e7b02541291c4d84e8715b4d6fb Mon Sep 17 00:00:00 2001
From: giacomomagni <giac.magni@gmail.com>
Date: Fri, 8 Mar 2024 14:57:44 +0100
Subject: [PATCH 24/25] fix issue #138

---
 docs/source/theory/fonll.rst |  2 +-
 src/pineko/cli/_base.py      |  2 +-
 src/pineko/cli/fonll.py      | 40 ++++++++++++++----------
 src/pineko/fonll.py          | 59 +++++++++++++++++++++---------------
 4 files changed, 60 insertions(+), 43 deletions(-)

diff --git a/docs/source/theory/fonll.rst b/docs/source/theory/fonll.rst
index ceb49474..83af55d9 100644
--- a/docs/source/theory/fonll.rst
+++ b/docs/source/theory/fonll.rst
@@ -43,7 +43,7 @@ Manual procedure
 
   6. Combine the various |FK| tables into a single file, using the command::
 
-      pineko fonll combine THEORY_ID DATASET --FFNS3 THEORY_ID00 --FFN03 THEORY_ID01 --FFNS4til THEORY_ID02 --FFNS4bar THEORY_ID03 --FFN04 THEORY_ID04 --FFNS5til THEORY_ID05 --FFNS5bar THEORY_ID06
+      pineko fonll combine THEORY_ID DATASET --FFNS3 THEORY_ID00 --FFN03 THEORY_ID01 --FFNS4zeromass THEORY_ID02 --FFNS4massive THEORY_ID03 --FFN04 THEORY_ID04 --FFNS5zeromass THEORY_ID05 --FFNS5massive THEORY_ID06
 
     where the first 3 theories are needed to perform |FONLL| on charm effects,
     while the last 4 are needed to include also bottom effects.
diff --git a/src/pineko/cli/_base.py b/src/pineko/cli/_base.py
index e7076623..43505a4d 100644
--- a/src/pineko/cli/_base.py
+++ b/src/pineko/cli/_base.py
@@ -32,7 +32,7 @@ def command():
 
 def load_config(cfg):
     """Load configuration files."""
-    # if just help is needed, return before loading
+    # if only help is needed, return before loading
     if help_requested():
         return
     path = configs.detect(cfg)
diff --git a/src/pineko/cli/fonll.py b/src/pineko/cli/fonll.py
index 1a60cb9e..2fbeb4df 100644
--- a/src/pineko/cli/fonll.py
+++ b/src/pineko/cli/fonll.py
@@ -20,22 +20,30 @@ def fonll_(cfg):
 @click.argument("dataset", type=str)
 @click.option("--FFNS3", type=int, help="theoryID containing the ffns3 fktable")
 @click.option("--FFN03", type=int, help="theoryID containing the ffn03 fktable")
-@click.option("--FFNS4til", type=int, help="theoryID containing the ffns4til fktable")
-@click.option("--FFNS4bar", type=int, help="theoryID containing the ffns4bar fktable")
+@click.option(
+    "--FFNS4zeromass", type=int, help="theoryID containing the ffns4 zeromass fktable"
+)
+@click.option(
+    "--FFNS4massive", type=int, help="theoryID containing the ffns4massive fktable"
+)
 @click.option("--FFN04", type=int, help="theoryID containing the ffn04 fktable")
-@click.option("--FFNS5til", type=int, help="theoryID containing the ffns5til fktable")
-@click.option("--FFNS5bar", type=int, help="theoryID containing the ffns5bar fktable")
+@click.option(
+    "--FFNS5zeromass", type=int, help="theoryID containing the ffns5 zeromass fktable"
+)
+@click.option(
+    "--FFNS5massive", type=int, help="theoryID containing the ffns5massive fktable"
+)
 @click.option("--overwrite", is_flag=True, help="Allow files to be overwritten")
 def combine(
     theoryid,
     dataset,
     ffns3,
     ffn03,
-    ffns4til,
-    ffns4bar,
+    ffns4zeromass,
+    ffns4massive,
     ffn04,
-    ffns5til,
-    ffns5bar,
+    ffns5zeromass,
+    ffns5massive,
     overwrite,
 ):
     """Combine the different FKs needed to produce the FONLL prescription."""
@@ -44,11 +52,11 @@ def combine(
         dataset,
         ffns3,
         ffn03,
-        ffns4til,
-        ffns4bar,
+        ffns4zeromass,
+        ffns4massive,
         ffn04,
-        ffns5til,
-        ffns5bar,
+        ffns5zeromass,
+        ffns5massive,
         overwrite,
     )
 
@@ -139,10 +147,10 @@ def fks(theoryid, datasets, pdf, overwrite):
             dataset,
             ffns3=f"{theoryid}00",
             ffn03=f"{theoryid}01",
-            ffns4til=f"{theoryid}02",
-            ffns4bar=f"{theoryid}03",
+            ffns4zeromass=f"{theoryid}02",
+            ffns4massive=f"{theoryid}03",
             ffn04=f"{theoryid}04",
-            ffns5til=f"{theoryid}05",
-            ffns5bar=f"{theoryid}06",
+            ffns5zeromass=f"{theoryid}05",
+            ffns5massive=f"{theoryid}06",
             overwrite=overwrite,
         )
diff --git a/src/pineko/fonll.py b/src/pineko/fonll.py
index d6d7b012..3e3824e3 100644
--- a/src/pineko/fonll.py
+++ b/src/pineko/fonll.py
@@ -29,8 +29,8 @@
 """FONLL schemes with mixed orders."""
 # Notice we rely on the order defined by the FONLLInfo class
 FK_TO_DAMP = {
-    "mc": ["ffn03", "ffns4til", "ffn04", "ffns5til"],
-    "mb": ["ffn04", "ffns5til"],
+    "mc": ["ffn03", "ffns4zeromass", "ffn04", "ffns5zeromass"],
+    "mb": ["ffn04", "ffns5zeromass"],
 }
 FK_WITH_MINUS = ["ffn03", "ffn04"]  # asy terms should be subtracted, therefore the sign
 """FNS schemes to be subtracted during the FONLL procedure."""
@@ -48,17 +48,24 @@ class FONLLInfo:
     """Class containing all the information for FONLL predictions."""
 
     def __init__(
-        self, ffns3, ffn03, ffns4til, ffns4bar, ffn04, ffns5til, ffns5bar
+        self,
+        ffns3,
+        ffn03,
+        ffns4zeromass,
+        ffns4massive,
+        ffn04,
+        ffns5zeromass,
+        ffns5massive,
     ) -> None:
         """Initialize fonll info."""
         self.paths = {
             "ffns3": ffns3,
             "ffn03": ffn03,
-            "ffns4til": ffns4til,
-            "ffns4bar": ffns4bar,
+            "ffns4zeromass": ffns4zeromass,
+            "ffns4massive": ffns4massive,
             "ffn04": ffn04,
-            "ffns5til": ffns5til,
-            "ffns5bar": ffns5bar,
+            "ffns5zeromass": ffns5zeromass,
+            "ffns5massive": ffns5massive,
         }
         actually_existing_paths = [p for p, g in self.paths.items() if g is not None]
         for p in self.paths:
@@ -187,11 +194,11 @@ def assembly_combined_fk(
     dataset,
     ffns3,
     ffn03,
-    ffns4til,
-    ffns4bar,
+    ffns4zeromass,
+    ffns4massive,
     ffn04,
-    ffns5til,
-    ffns5bar,
+    ffns5zeromass,
+    ffns5massive,
     overwrite,
 ):
     """Perform consistency checks and combine the FONLL FK tables into one single FK table."""
@@ -199,16 +206,16 @@ def assembly_combined_fk(
     if not ffns3 or not ffn03:
         raise InconsistentInputsError("ffns3 and/or ffn03 is not provided.")
 
-    if ffns4til is None or ffns4bar is None:
+    if ffns4zeromass is None or ffns4massive is None:
         raise InconsistentInputsError(
-            "At least one of ffns4til and ffns4bar should be provided."
+            "At least one of ffns4 zeromass and ffns4 massive should be provided."
         )
 
     # Do we consider two masses, i.e. mc and mb
-    if any([ffns5til, ffns5bar, ffn04]):
-        if (ffns5til is None and ffns5bar is None) or ffn04 is None:
+    if any([ffns5zeromass, ffns5massive, ffn04]):
+        if (ffns5zeromass is None and ffns5massive is None) or ffn04 is None:
             raise InconsistentInputsError(
-                "To include nf5 contributions, ffn04 and at least one between ffns5til and ffns5bar are mandatory"
+                "To include nf5 contributions, ffn04 and at least one between ffns5 zeromass and ffns5 massive are mandatory"
             )
 
     # Get theory info
@@ -238,11 +245,11 @@ def assembly_combined_fk(
                 for name in (
                     ffns3,
                     ffn03,
-                    ffns4til,
-                    ffns4bar,
+                    ffns4zeromass,
+                    ffns4massive,
                     ffn04,
-                    ffns5til,
-                    ffns5bar,
+                    ffns5zeromass,
+                    ffns5massive,
                 )
             ),
             theoryid,
@@ -257,16 +264,18 @@ def assembly_combined_fk(
 def produce_combined_fk(
     ffns3,
     ffn03,
-    ffns4til,
-    ffns4bar,
+    ffns4zeromass,
+    ffns4massive,
     ffn04,
-    ffns5til,
-    ffns5bar,
+    ffns5zeromass,
+    ffns5massive,
     theoryid,
     damp=(0, None, None),
 ):
     """Combine the FONLL FK tables into one single FK table."""
-    fonll_info = FONLLInfo(ffns3, ffn03, ffns4til, ffns4bar, ffn04, ffns5til, ffns5bar)
+    fonll_info = FONLLInfo(
+        ffns3, ffn03, ffns4zeromass, ffns4massive, ffn04, ffns5zeromass, ffns5massive
+    )
     theorycard_constituent_fks = fonll_info.theorycard_no_fns_pto
     fk_dict = fonll_info.fks
     dampings = (

From 78c21383913a37e6956338c49e8d8c23a55505f2 Mon Sep 17 00:00:00 2001
From: Giacomo Magni <giac.magni@gmail.com>
Date: Fri, 8 Mar 2024 15:05:11 +0100
Subject: [PATCH 25/25] fix test

---
 tests/test_fonll.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/tests/test_fonll.py b/tests/test_fonll.py
index 7a11d08a..598b6cb0 100644
--- a/tests/test_fonll.py
+++ b/tests/test_fonll.py
@@ -29,11 +29,11 @@ def test_FONLLInfo():
     name_list = [
         "ffns3",
         "ffn03",
-        "ffns4til",
-        "ffns4bar",
+        "ffns4zeromass",
+        "ffns4massive",
         "ffn04",
-        "ffns5til",
-        "ffns5bar",
+        "ffns5zeromass",
+        "ffns5massive",
     ]
     assert fullfonll_fake_info.fk_paths == {
         name: pathlib.Path(fk) for name, fk in zip(name_list, full_list)