From bf985eb52583dcf8ab636892c7c27be562ecbfb6 Mon Sep 17 00:00:00 2001
From: Felix Hekhorn <felix.hekhorn@uni-tuebingen.de>
Date: Mon, 31 Jul 2023 14:54:16 +0200
Subject: [PATCH 01/24] Update pineappl

---
 poetry.lock    | 557 +++++++++++++++++++++++++------------------------
 pyproject.toml |   2 +-
 2 files changed, 280 insertions(+), 279 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 59ee0bb7..9652dabb 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -26,14 +26,14 @@ files = [
 
 [[package]]
 name = "astroid"
-version = "2.15.5"
+version = "2.15.6"
 description = "An abstract syntax tree for Python with inference support."
 category = "dev"
 optional = false
 python-versions = ">=3.7.2"
 files = [
-    {file = "astroid-2.15.5-py3-none-any.whl", hash = "sha256:078e5212f9885fa85fbb0cf0101978a336190aadea6e13305409d099f71b2324"},
-    {file = "astroid-2.15.5.tar.gz", hash = "sha256:1039262575027b441137ab4a62a793a9b43defb42c32d5670f38686207cd780f"},
+    {file = "astroid-2.15.6-py3-none-any.whl", hash = "sha256:389656ca57b6108f939cf5d2f9a2a825a3be50ba9d589670f393236e0a03b91c"},
+    {file = "astroid-2.15.6.tar.gz", hash = "sha256:903f024859b7c7687d7a7f3a3f73b17301f8e42dfd9cc9df9d4418172d3e2dbd"},
 ]
 
 [package.dependencies]
@@ -91,111 +91,111 @@ files = [
 
 [[package]]
 name = "certifi"
-version = "2023.5.7"
+version = "2023.7.22"
 description = "Python package for providing Mozilla's CA Bundle."
 category = "dev"
 optional = false
 python-versions = ">=3.6"
 files = [
-    {file = "certifi-2023.5.7-py3-none-any.whl", hash = "sha256:c6c2e98f5c7869efca1f8916fed228dd91539f9f1b444c314c06eef02980c716"},
-    {file = "certifi-2023.5.7.tar.gz", hash = "sha256:0f0d56dc5a6ad56fd4ba36484d6cc34451e1c6548c61daad8c320169f91eddc7"},
+    {file = "certifi-2023.7.22-py3-none-any.whl", hash = "sha256:92d6037539857d8206b8f6ae472e8b77db8058fec5937a1ef3f54304089edbb9"},
+    {file = "certifi-2023.7.22.tar.gz", hash = "sha256:539cc1d13202e33ca466e88b2807e29f4c13049d6d87031a3c110744495cb082"},
 ]
 
 [[package]]
 name = "charset-normalizer"
-version = "3.1.0"
+version = "3.2.0"
 description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
 category = "dev"
 optional = false
 python-versions = ">=3.7.0"
 files = [
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 [[package]]
 name = "click"
-version = "8.1.3"
+version = "8.1.6"
 description = "Composable command line interface toolkit"
 category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
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-    {file = "click-8.1.3.tar.gz", hash = "sha256:7682dc8afb30297001674575ea00d1814d808d6a36af415a82bd481d37ba7b8e"},
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 ]
 
 [package.dependencies]
@@ -318,14 +318,14 @@ files = [
 
 [[package]]
 name = "dill"
-version = "0.3.6"
-description = "serialize all of python"
+version = "0.3.7"
+description = "serialize all of Python"
 category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
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+    {file = "dill-0.3.7-py3-none-any.whl", hash = "sha256:76b122c08ef4ce2eedcd4d1abd8e641114bfc6c2867f49f3c41facf65bf19f5e"},
+    {file = "dill-0.3.7.tar.gz", hash = "sha256:cc1c8b182eb3013e24bd475ff2e9295af86c1a38eb1aff128dac8962a9ce3c03"},
 ]
 
 [package.extras]
@@ -368,14 +368,14 @@ mark = ["banana-hep (>=0.6.9,<0.7.0)", "matplotlib (>=3.5.1,<4.0.0)", "pandas (>
 
 [[package]]
 name = "exceptiongroup"
-version = "1.1.1"
+version = "1.1.2"
 description = "Backport of PEP 654 (exception groups)"
 category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
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-    {file = "exceptiongroup-1.1.1.tar.gz", hash = "sha256:d484c3090ba2889ae2928419117447a14daf3c1231d5e30d0aae34f354f01785"},
+    {file = "exceptiongroup-1.1.2-py3-none-any.whl", hash = "sha256:e346e69d186172ca7cf029c8c1d16235aa0e04035e5750b4b95039e65204328f"},
+    {file = "exceptiongroup-1.1.2.tar.gz", hash = "sha256:12c3e887d6485d16943a309616de20ae5582633e0a2eda17f4e10fd61c1e8af5"},
 ]
 
 [package.extras]
@@ -438,14 +438,14 @@ files = [
 
 [[package]]
 name = "importlib-metadata"
-version = "6.6.0"
+version = "6.8.0"
 description = "Read metadata from Python packages"
 category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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-    {file = "importlib_metadata-6.6.0.tar.gz", hash = "sha256:92501cdf9cc66ebd3e612f1b4f0c0765dfa42f0fa38ffb319b6bd84dd675d705"},
+    {file = "importlib_metadata-6.8.0-py3-none-any.whl", hash = "sha256:3ebb78df84a805d7698245025b975d9d67053cd94c79245ba4b3eb694abe68bb"},
+    {file = "importlib_metadata-6.8.0.tar.gz", hash = "sha256:dbace7892d8c0c4ac1ad096662232f831d4e64f4c4545bd53016a3e9d4654743"},
 ]
 
 [package.dependencies]
@@ -454,7 +454,7 @@ zipp = ">=0.5"
 [package.extras]
 docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
 perf = ["ipython"]
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 [[package]]
 name = "iniconfig"
@@ -528,22 +528,22 @@ requirements-deprecated-finder = ["pip-api", "pipreqs"]
 
 [[package]]
 name = "jedi"
-version = "0.18.2"
+version = "0.19.0"
 description = "An autocompletion tool for Python that can be used for text editors."
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 python-versions = ">=3.6"
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-qa = ["flake8 (==3.8.3)", "mypy (==0.782)"]
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 testing = ["Django (<3.1)", "attrs", "colorama", "docopt", "pytest (<7.0.0)"]
 
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 [[package]]
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@@ -1037,30 +1038,30 @@ test = ["pytest", "pytest-cov"]
 
 [[package]]
 name = "platformdirs"
-version = "3.5.3"
+version = "3.10.0"
 description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
 category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
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-test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.3.1)", "pytest-cov (>=4.1)", "pytest-mock (>=3.10)"]
+docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx (>=7.1.1)", "sphinx-autodoc-typehints (>=1.24)"]
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 [[package]]
 name = "pluggy"
-version = "1.0.0"
+version = "1.2.0"
 description = "plugin and hook calling mechanisms for python"
 category = "dev"
 optional = false
-python-versions = ">=3.6"
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 files = [
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 ]
 
 [package.extras]
@@ -1069,14 +1070,14 @@ testing = ["pytest", "pytest-benchmark"]
 
 [[package]]
 name = "prompt-toolkit"
-version = "3.0.38"
+version = "3.0.39"
 description = "Library for building powerful interactive command lines in Python"
 category = "dev"
 optional = false
 python-versions = ">=3.7.0"
 files = [
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 [package.dependencies]
@@ -1162,18 +1163,18 @@ plugins = ["importlib-metadata"]
 
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+version = "2.17.5"
 description = "python code static checker"
 category = "dev"
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 python-versions = ">=3.7.2"
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 colorama = {version = ">=0.4.5", markers = "sys_platform == \"win32\""}
 dill = [
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 [[package]]
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-version = "7.3.2"
+version = "7.4.0"
 description = "pytest: simple powerful testing with Python"
 category = "dev"
 optional = false
 python-versions = ">=3.7"
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+    {file = "PyYAML-6.0.1.tar.gz", hash = "sha256:bfdf460b1736c775f2ba9f6a92bca30bc2095067b8a9d77876d1fad6cc3b4a43"},
 ]
 
 [[package]]
@@ -1669,14 +1670,14 @@ files = [
 
 [[package]]
 name = "tomlkit"
-version = "0.11.8"
+version = "0.12.1"
 description = "Style preserving TOML library"
 category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "tomlkit-0.11.8-py3-none-any.whl", hash = "sha256:8c726c4c202bdb148667835f68d68780b9a003a9ec34167b6c673b38eff2a171"},
-    {file = "tomlkit-0.11.8.tar.gz", hash = "sha256:9330fc7faa1db67b541b28e62018c17d20be733177d290a13b24c62d1614e0c3"},
+    {file = "tomlkit-0.12.1-py3-none-any.whl", hash = "sha256:712cbd236609acc6a3e2e97253dfc52d4c2082982a88f61b640ecf0817eab899"},
+    {file = "tomlkit-0.12.1.tar.gz", hash = "sha256:38e1ff8edb991273ec9f6181244a6a391ac30e9f5098e7535640ea6be97a7c86"},
 ]
 
 [[package]]
@@ -1697,26 +1698,26 @@ test = ["argcomplete (>=2.0)", "pre-commit", "pytest", "pytest-mock"]
 
 [[package]]
 name = "typing-extensions"
-version = "4.6.3"
+version = "4.7.1"
 description = "Backported and Experimental Type Hints for Python 3.7+"
 category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "typing_extensions-4.6.3-py3-none-any.whl", hash = "sha256:88a4153d8505aabbb4e13aacb7c486c2b4a33ca3b3f807914a9b4c844c471c26"},
-    {file = "typing_extensions-4.6.3.tar.gz", hash = "sha256:d91d5919357fe7f681a9f2b5b4cb2a5f1ef0a1e9f59c4d8ff0d3491e05c0ffd5"},
+    {file = "typing_extensions-4.7.1-py3-none-any.whl", hash = "sha256:440d5dd3af93b060174bf433bccd69b0babc3b15b1a8dca43789fd7f61514b36"},
+    {file = "typing_extensions-4.7.1.tar.gz", hash = "sha256:b75ddc264f0ba5615db7ba217daeb99701ad295353c45f9e95963337ceeeffb2"},
 ]
 
 [[package]]
 name = "urllib3"
-version = "2.0.3"
+version = "2.0.4"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
 category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "urllib3-2.0.3-py3-none-any.whl", hash = "sha256:48e7fafa40319d358848e1bc6809b208340fafe2096f1725d05d67443d0483d1"},
-    {file = "urllib3-2.0.3.tar.gz", hash = "sha256:bee28b5e56addb8226c96f7f13ac28cb4c301dd5ea8a6ca179c0b9835e032825"},
+    {file = "urllib3-2.0.4-py3-none-any.whl", hash = "sha256:de7df1803967d2c2a98e4b11bb7d6bd9210474c46e8a0401514e3a42a75ebde4"},
+    {file = "urllib3-2.0.4.tar.gz", hash = "sha256:8d22f86aae8ef5e410d4f539fde9ce6b2113a001bb4d189e0aed70642d602b11"},
 ]
 
 [package.extras]
@@ -1835,19 +1836,19 @@ files = [
 
 [[package]]
 name = "zipp"
-version = "3.15.0"
+version = "3.16.2"
 description = "Backport of pathlib-compatible object wrapper for zip files"
 category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "zipp-3.15.0-py3-none-any.whl", hash = "sha256:48904fc76a60e542af151aded95726c1a5c34ed43ab4134b597665c86d7ad556"},
-    {file = "zipp-3.15.0.tar.gz", hash = "sha256:112929ad649da941c23de50f356a2b5570c954b65150642bccdd66bf194d224b"},
+    {file = "zipp-3.16.2-py3-none-any.whl", hash = "sha256:679e51dd4403591b2d6838a48de3d283f3d188412a9782faadf845f298736ba0"},
+    {file = "zipp-3.16.2.tar.gz", hash = "sha256:ebc15946aa78bd63458992fc81ec3b6f7b1e92d51c35e6de1c3804e73b799147"},
 ]
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
-testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"]
+docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"]
 
 [extras]
 docs = []
@@ -1855,4 +1856,4 @@ docs = []
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.8,<3.12"
-content-hash = "41dcdfabfc5baa02bfa1dbce7e9c342ccadf7c00e646c5b2f36002807021ad28"
+content-hash = "f26211576227c79b6a688df57e50b2c7a4db411cae48efd23d412ea7b218ffe2"
diff --git a/pyproject.toml b/pyproject.toml
index 9eb1a07a..3bddf266 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -25,7 +25,7 @@ packages = [{ include = "pineko", from = "src" }]
 [tool.poetry.dependencies]
 python = ">=3.8,<3.12"
 eko = "^0.13.2"
-pineappl = { version = "^0.6.0a17", allow-prereleases = true }
+pineappl = "^0.6.0"
 PyYAML = "^6.0"
 numpy = "^1.21.0"
 pandas = "^1.4.1"

From 986cf465c87d17f7a4e057996fff821629b2a615 Mon Sep 17 00:00:00 2001
From: andreab1997 <andreab1997@yahoo.it>
Date: Mon, 31 Jul 2023 14:57:56 +0200
Subject: [PATCH 02/24] Change fonll-parts to FONLLParts

---
 benchmarks/bench_fonll.py | 2 +-
 src/pineko/fonll.py       | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/benchmarks/bench_fonll.py b/benchmarks/bench_fonll.py
index b8264741..f0f8e576 100644
--- a/benchmarks/bench_fonll.py
+++ b/benchmarks/bench_fonll.py
@@ -23,4 +23,4 @@ def benchmark_produce_fonll_tcards(tmp_path, test_files, test_configs, theoryid)
         assert simFONLL_tcard["FNS"] == fns
         assert simFONLL_tcard["NfFF"] == nfff
         assert simFONLL_tcard["PTO"] == po
-        assert simFONLL_tcard["fonll-parts"] == part
+        assert simFONLL_tcard["FONLLParts"] == part
diff --git a/src/pineko/fonll.py b/src/pineko/fonll.py
index 22cb6c76..8a9c02ba 100644
--- a/src/pineko/fonll.py
+++ b/src/pineko/fonll.py
@@ -62,7 +62,7 @@ def theorycard_no_fns_pto(self):
             del card["PTO"]
             del card["NfFF"]
             del card["ID"]
-            del card["fonll-parts"]
+            del card["FONLLParts"]
         if not all([theorycards[0] == card in theorycards[1:]]):
             raise ValueError("theorycards not the same")
         return theorycards[0]
@@ -178,7 +178,7 @@ def produce_fonll_recipe(fns):
                 "FNS": fns,
                 "NfFF": nfff,
                 "PTO": po,
-                "fonll-parts": part,
+                "FONLLParts": part,
             }
         )
     return fonll_recipe

From 4b16a92e9329c04a2eb3bb3818c86313def4f32c Mon Sep 17 00:00:00 2001
From: andreab1997 <andreab1997@yahoo.it>
Date: Mon, 31 Jul 2023 17:49:11 +0200
Subject: [PATCH 03/24] Fix case without damping

---
 src/pineko/fonll.py | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/src/pineko/fonll.py b/src/pineko/fonll.py
index 8a9c02ba..93da9af1 100644
--- a/src/pineko/fonll.py
+++ b/src/pineko/fonll.py
@@ -93,8 +93,13 @@ def produce_combined_fk(
     if theorycard_constituent_fks["DAMP"] == 0:
         # then there is no damping, not even Heaviside only
         combined_fk = fonll_info.fks[0]
-        for fk_path in fonll_info.fk_paths[1:]:
-            combined_fk.merge_from_file(fk_path)
+        with tempfile.TemporaryDirectory() as tmpdirname:
+            for i, fk in enumerate(fonll_info.fks[1:]):
+                tmpfile_path = Path(tmpdirname) / f"{i}.pineappl.lz4"
+                sign = -1 if i + 1 in FK_WITH_MINUS else 1
+                fk.scale_by_bin(sign)
+                fk.write_lz4(tmpfile_path)
+                combined_fk.merge_from_file(tmpfile_path)
     else:
         mc = theorycard_constituent_fks["mc"]
         mb = theorycard_constituent_fks["mb"]

From 099523ad64f8c6c03be2b093f7d9c9d1cfcc0dcf Mon Sep 17 00:00:00 2001
From: andreab1997 <andreab1997@yahoo.it>
Date: Mon, 31 Jul 2023 17:53:35 +0200
Subject: [PATCH 04/24] Use function scale instead of scale by bin

---
 src/pineko/fonll.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/pineko/fonll.py b/src/pineko/fonll.py
index 93da9af1..78b9b46e 100644
--- a/src/pineko/fonll.py
+++ b/src/pineko/fonll.py
@@ -97,7 +97,7 @@ def produce_combined_fk(
             for i, fk in enumerate(fonll_info.fks[1:]):
                 tmpfile_path = Path(tmpdirname) / f"{i}.pineappl.lz4"
                 sign = -1 if i + 1 in FK_WITH_MINUS else 1
-                fk.scale_by_bin(sign)
+                fk.scale(sign)
                 fk.write_lz4(tmpfile_path)
                 combined_fk.merge_from_file(tmpfile_path)
     else:

From aecf0cd903ee98fb17e3b98bf67ae7a9e58fa41f Mon Sep 17 00:00:00 2001
From: andreab1997 <andreab1997@yahoo.it>
Date: Mon, 31 Jul 2023 18:13:38 +0200
Subject: [PATCH 05/24] Avoid counting the minus sign twice

---
 src/pineko/fonll.py | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/src/pineko/fonll.py b/src/pineko/fonll.py
index 78b9b46e..3c2e3ba9 100644
--- a/src/pineko/fonll.py
+++ b/src/pineko/fonll.py
@@ -116,18 +116,19 @@ def produce_combined_fk(
         damping_factor_bottom *= step_function_bottom
         dampings = {"mc": damping_factor_charm, "mb": damping_factor_bottom}
         for i, fk in enumerate(fonll_info.fks):
-            sign = 1
-            if i in FK_WITH_MINUS:
-                sign = -1
             for mass in FK_TO_DAMP:
                 if i in FK_TO_DAMP[mass]:
-                    fk.scale_by_bin(sign * dampings[mass])
+                    fk.scale_by_bin(dampings[mass])
         # pineappl does not support operating with two grids in memory:
         # https://github.com/NNPDF/pineappl/blob/8a672bef6d91b07a4edfdefbe4e30e4b1dd1f976/pineappl_py/src/grid.rs#L614-L617
         with tempfile.TemporaryDirectory() as tmpdirname:
             combined_fk = fonll_info.fks[0]
             for i, fk in enumerate(fonll_info.fks[1:]):
                 tmpfile_path = Path(tmpdirname) / f"{i}.pineappl.lz4"
+                sign = (
+                    -1 if i + 1 in FK_WITH_MINUS else 1
+                )  # The i+1 is there because the first fk is not included in the loop
+                fk.scale(sign)
                 fk.write_lz4(tmpfile_path)
                 combined_fk.merge_from_file(tmpfile_path)
 

From 0399a59db8a5b2afe0920c466f137af505878a53 Mon Sep 17 00:00:00 2001
From: andreab1997 <andreab1997@yahoo.it>
Date: Mon, 31 Jul 2023 18:24:31 +0200
Subject: [PATCH 06/24] Fix damping

---
 src/pineko/fonll.py | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/src/pineko/fonll.py b/src/pineko/fonll.py
index 3c2e3ba9..a1d90aee 100644
--- a/src/pineko/fonll.py
+++ b/src/pineko/fonll.py
@@ -115,10 +115,6 @@ def produce_combined_fk(
         damping_factor_charm *= step_function_charm
         damping_factor_bottom *= step_function_bottom
         dampings = {"mc": damping_factor_charm, "mb": damping_factor_bottom}
-        for i, fk in enumerate(fonll_info.fks):
-            for mass in FK_TO_DAMP:
-                if i in FK_TO_DAMP[mass]:
-                    fk.scale_by_bin(dampings[mass])
         # pineappl does not support operating with two grids in memory:
         # https://github.com/NNPDF/pineappl/blob/8a672bef6d91b07a4edfdefbe4e30e4b1dd1f976/pineappl_py/src/grid.rs#L614-L617
         with tempfile.TemporaryDirectory() as tmpdirname:
@@ -129,6 +125,9 @@ def produce_combined_fk(
                     -1 if i + 1 in FK_WITH_MINUS else 1
                 )  # The i+1 is there because the first fk is not included in the loop
                 fk.scale(sign)
+                for mass in FK_TO_DAMP:
+                    if i + 1 in FK_TO_DAMP[mass]:
+                        fk.scale_by_bin(dampings[mass])
                 fk.write_lz4(tmpfile_path)
                 combined_fk.merge_from_file(tmpfile_path)
 

From 499f8578d0ae11969708e5d7c7789d93d05dc635 Mon Sep 17 00:00:00 2001
From: andreab1997 <andreab1997@yahoo.it>
Date: Mon, 31 Jul 2023 18:31:27 +0200
Subject: [PATCH 07/24] Make damping setting depend on theory card

---
 src/pineko/cli/fonll.py | 18 ++++++++++++++++--
 src/pineko/fonll.py     | 21 ++++++++++++---------
 2 files changed, 28 insertions(+), 11 deletions(-)

diff --git a/src/pineko/cli/fonll.py b/src/pineko/cli/fonll.py
index 023d940a..91854c58 100644
--- a/src/pineko/cli/fonll.py
+++ b/src/pineko/cli/fonll.py
@@ -12,7 +12,7 @@ class TheoryCardError(Exception):
 
 
 class InconsistentInputsError(Exception):
-    """Raised if the inputs are not consistent with FONLL accounting for only charm mass, or both charm and bottom masses."""
+    """Raised if the inputs are not consistent with FONLL."""
 
     pass
 
@@ -35,8 +35,22 @@ def subcommand(ffns3, ffn03, ffns4til, theoryid, ffns4bar, ffn04, ffns5til, ffns
             "One between ffn04 and ffns5til has been provided without the other. Since they are both needed to construct FONLL, this does not make sense."
         )
         raise InconsistentInputsError
+    configs.configs = configs.defaults(configs.load())
+    tcard = theory_card.load(theoryid)
+    if not "DAMPPOWER" in tcard:
+        if tcard["DAMP"] != 0:
+            raise InconsistentInputsError
+        tcard["DAMPPOWER"] = None
     fonll.produce_combined_fk(
-        ffns3, ffn03, ffns4til, ffns4bar, ffn04, ffns5til, ffns5bar, theoryid
+        ffns3,
+        ffn03,
+        ffns4til,
+        ffns4bar,
+        ffn04,
+        ffns5til,
+        ffns5bar,
+        theoryid,
+        damp=(tcard["DAMP"], tcard["DAMPPOWER"]),
     )
 
 
diff --git a/src/pineko/fonll.py b/src/pineko/fonll.py
index a1d90aee..8e307a1a 100644
--- a/src/pineko/fonll.py
+++ b/src/pineko/fonll.py
@@ -84,13 +84,20 @@ def Q2grid(self):
 
 
 def produce_combined_fk(
-    ffns3, ffn03, ffns4til, ffns4bar, ffn04, ffns5til, ffns5bar, theoryid
+    ffns3,
+    ffn03,
+    ffns4til,
+    ffns4bar,
+    ffn04,
+    ffns5til,
+    ffns5bar,
+    theoryid,
+    damp=(0, None),
 ):
     """Combine the FONLL FKs to produce one single final FONLL FK."""
     fonll_info = FONLLInfo(ffns3, ffn03, ffns4til, ffns4bar, ffn04, ffns5til, ffns5bar)
-
     theorycard_constituent_fks = fonll_info.theorycard_no_fns_pto
-    if theorycard_constituent_fks["DAMP"] == 0:
+    if damp[0] == 0:
         # then there is no damping, not even Heaviside only
         combined_fk = fonll_info.fks[0]
         with tempfile.TemporaryDirectory() as tmpdirname:
@@ -106,12 +113,8 @@ def produce_combined_fk(
         q2grid = fonll_info.Q2grid
         step_function_charm = mc**2 < q2grid
         step_function_bottom = mb**2 < q2grid
-        damping_factor_charm = (1 - q2grid / mc) ** theorycard_constituent_fks[
-            "DAMPPOWER"
-        ]
-        damping_factor_bottom = (1 - q2grid / mb) ** theorycard_constituent_fks[
-            "DAMPPOWER"
-        ]
+        damping_factor_charm = (1 - q2grid / mc) ** damp[1]
+        damping_factor_bottom = (1 - q2grid / mb) ** damp[1]
         damping_factor_charm *= step_function_charm
         damping_factor_bottom *= step_function_bottom
         dampings = {"mc": damping_factor_charm, "mb": damping_factor_bottom}

From 48c83d4275984af0c17b4fd1451a6d19c021c2e4 Mon Sep 17 00:00:00 2001
From: andreab1997 <andreab1997@yahoo.it>
Date: Mon, 31 Jul 2023 18:47:00 +0200
Subject: [PATCH 08/24] Doing the damp correctly despite the paper...

---
 src/pineko/fonll.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/pineko/fonll.py b/src/pineko/fonll.py
index 8e307a1a..5bdef42c 100644
--- a/src/pineko/fonll.py
+++ b/src/pineko/fonll.py
@@ -113,8 +113,8 @@ def produce_combined_fk(
         q2grid = fonll_info.Q2grid
         step_function_charm = mc**2 < q2grid
         step_function_bottom = mb**2 < q2grid
-        damping_factor_charm = (1 - q2grid / mc) ** damp[1]
-        damping_factor_bottom = (1 - q2grid / mb) ** damp[1]
+        damping_factor_charm = (1 - mc / q2grid) ** damp[1]
+        damping_factor_bottom = (1 - mb / q2grid) ** damp[1]
         damping_factor_charm *= step_function_charm
         damping_factor_bottom *= step_function_bottom
         dampings = {"mc": damping_factor_charm, "mb": damping_factor_bottom}

From b4ca9b7ecc959d7850ce54ef01a8a293b01c7640 Mon Sep 17 00:00:00 2001
From: andreab1997 <andreab1997@yahoo.it>
Date: Wed, 2 Aug 2023 11:44:07 +0200
Subject: [PATCH 09/24] Change fonll paths

---
 src/pineko/fonll.py | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/src/pineko/fonll.py b/src/pineko/fonll.py
index 5bdef42c..fef633cc 100644
--- a/src/pineko/fonll.py
+++ b/src/pineko/fonll.py
@@ -32,11 +32,10 @@ def fk_paths(self):
         paths = [self.ffns3, self.ffn03, self.ffns4til]
         if self.ffns4bar:
             paths = paths + [self.ffns4bar]
-        if self.ffn04 and self.ffns5til:
-            paths = paths + [self.ffn04, self.ffns5til]
-            # It does not make sense to have ffns5bar without ffns5til
-            if self.ffns5bar:
-                paths = paths + [self.ffns5bar]
+            if self.ffn04 and self.ffns5til:
+                paths = paths + [self.ffn04, self.ffns5til]
+                if self.ffns5bar:
+                    paths = paths + [self.ffns5bar]
         return [Path(p) for p in paths]
 
     @property

From b474004ac39a7a2651a62695a318660b5542380d Mon Sep 17 00:00:00 2001
From: andreab1997 <andreab1997@yahoo.it>
Date: Wed, 2 Aug 2023 13:22:07 +0200
Subject: [PATCH 10/24] Make all the fktables to be merged optional

---
 src/pineko/cli/fonll.py | 16 ++++++++---
 src/pineko/fonll.py     | 64 ++++++++++++++++++++++-------------------
 tests/test_fonll.py     | 27 ++++++++++++++---
 3 files changed, 70 insertions(+), 37 deletions(-)

diff --git a/src/pineko/cli/fonll.py b/src/pineko/cli/fonll.py
index 91854c58..1376006b 100644
--- a/src/pineko/cli/fonll.py
+++ b/src/pineko/cli/fonll.py
@@ -18,15 +18,15 @@ class InconsistentInputsError(Exception):
 
 
 @command.command("combine_fonll")
-@click.argument("FFNS3", type=click.Path(exists=True))
-@click.argument("FFN03", type=click.Path(exists=True))
-@click.argument("FFNS4til", type=click.Path(exists=True))
 @click.argument("theoryID", type=int)
+@click.option("--FFNS3", type=click.Path(exists=True))
+@click.option("--FFN03", type=click.Path(exists=True))
+@click.option("--FFNS4til", type=click.Path(exists=True))
 @click.option("--FFNS4bar", type=click.Path(exists=True))
 @click.option("--FFN04", type=click.Path(exists=True))
 @click.option("--FFNS5til", type=click.Path(exists=True))
 @click.option("--FFNS5bar", type=click.Path(exists=True))
-def subcommand(ffns3, ffn03, ffns4til, theoryid, ffns4bar, ffn04, ffns5til, ffns5bar):
+def subcommand(theoryid, ffns3, ffn03, ffns4til, ffns4bar, ffn04, ffns5til, ffns5bar):
     """Combine the different FKs needed to produce the FONLL prescription."""
     if (ffn04 is None and ffns5til is not None) or (
         ffn04 is not None and ffns5til is None
@@ -35,6 +35,14 @@ def subcommand(ffns3, ffn03, ffns4til, theoryid, ffns4bar, ffn04, ffns5til, ffns
             "One between ffn04 and ffns5til has been provided without the other. Since they are both needed to construct FONLL, this does not make sense."
         )
         raise InconsistentInputsError
+    if (ffn03 is None and ffns4til is not None) or (
+        ffn03 is not None and ffns4til is None
+    ):
+        print(
+            "One between ffn03 and ffns4til has been provided without the other. Since they are both needed to construct FONLL, this does not make sense."
+        )
+        raise InconsistentInputsError
+
     configs.configs = configs.defaults(configs.load())
     tcard = theory_card.load(theoryid)
     if not "DAMPPOWER" in tcard:
diff --git a/src/pineko/fonll.py b/src/pineko/fonll.py
index fef633cc..88975184 100644
--- a/src/pineko/fonll.py
+++ b/src/pineko/fonll.py
@@ -29,32 +29,34 @@ def __init__(
     @property
     def fk_paths(self):
         """Returns the list of the fk paths needed to produce FONLL predictions."""
-        paths = [self.ffns3, self.ffn03, self.ffns4til]
-        if self.ffns4bar:
-            paths = paths + [self.ffns4bar]
-            if self.ffn04 and self.ffns5til:
-                paths = paths + [self.ffn04, self.ffns5til]
-                if self.ffns5bar:
-                    paths = paths + [self.ffns5bar]
-        return [Path(p) for p in paths]
+        paths = {
+            "ffns3": self.ffns3,
+            "ffn03": self.ffn03,
+            "ffns4til": self.ffns4til,
+            "ffns4bar": self.ffns4bar,
+            "ffn04": self.ffn04,
+            "ffns5til": self.ffns5til,
+            "ffns5bar": self.ffns5bar,
+        }
+        return {p: Path(paths[p]) for p in paths if paths[p] is not None}
 
     @property
     def fks(self):
         """Returns the pineappl.Grid objects reading the paths provided by self.fk_paths."""
-        return [pineappl.grid.Grid.read(fk_path) for fk_path in self.fk_paths]
+        return {fk: pineappl.grid.Grid.read(self.fk_paths[fk]) for fk in self.fk_paths}
 
     @property
     def dataset_name(self):
         """Return the name of the dataset given by the fktables name, if all the fktables have the same name."""
-        if len({p.name for p in self.fk_paths}) == 1:
-            return self.fk_paths[0].name
+        if len({self.fks[p].name for p in self.fks}) == 1:
+            return self.fks[list(self.fks)[0]].name
         else:
             raise ValueError("not all fktables have the same name")
 
     @property
     def theorycard_no_fns_pto(self):
         """Return the common theory info between the different FONLL FKs."""
-        theorycards = [json.loads(fk.key_values()["theory"]) for fk in self.fks]
+        theorycards = [json.loads(self.fks[p].key_values()["theory"]) for p in self.fks]
         # Only these should differ
         for card in theorycards:
             del card["FNS"]
@@ -69,7 +71,9 @@ def theorycard_no_fns_pto(self):
     @property
     def Q2grid(self):
         """Return the Q2grid of the fktables given by self.fks ."""
-        aa = json.loads(self.fks[0].raw.key_values()["runcard"])["observables"]
+        aa = json.loads(self.fks[list(self.fks)[0]].key_values()["runcard"])[
+            "observables"
+        ]
         bb = list(aa.values())[
             0
         ]  # there is only a single obseravble because it's a dis fktable
@@ -78,8 +82,11 @@ def Q2grid(self):
 
 
 # Notice we rely on the order defined by the FONLLInfo class
-FK_TO_DAMP = {"mc": [1, 2, 4, 5], "mb": [4, 5]}
-FK_WITH_MINUS = [1, 4]  # asy terms should be subtracted, therefore the sign
+FK_TO_DAMP = {
+    "mc": ["ffn03", "ffns4til", "ffn04", "ffns5til"],
+    "mb": ["ffn04", "ffns5til"],
+}
+FK_WITH_MINUS = ["ffn03", "ffn04"]  # asy terms should be subtracted, therefore the sign
 
 
 def produce_combined_fk(
@@ -96,15 +103,16 @@ def produce_combined_fk(
     """Combine the FONLL FKs to produce one single final FONLL FK."""
     fonll_info = FONLLInfo(ffns3, ffn03, ffns4til, ffns4bar, ffn04, ffns5til, ffns5bar)
     theorycard_constituent_fks = fonll_info.theorycard_no_fns_pto
+    fk_dict = fonll_info.fks
     if damp[0] == 0:
         # then there is no damping, not even Heaviside only
-        combined_fk = fonll_info.fks[0]
+        combined_fk = fk_dict[list(fk_dict)[0]]
         with tempfile.TemporaryDirectory() as tmpdirname:
-            for i, fk in enumerate(fonll_info.fks[1:]):
+            for fk in list(fk_dict)[1:]:
                 tmpfile_path = Path(tmpdirname) / f"{i}.pineappl.lz4"
-                sign = -1 if i + 1 in FK_WITH_MINUS else 1
-                fk.scale(sign)
-                fk.write_lz4(tmpfile_path)
+                sign = -1 if fk in FK_WITH_MINUS else 1
+                fk_dict[fk].scale(sign)
+                fk_dict[fk].write_lz4(tmpfile_path)
                 combined_fk.merge_from_file(tmpfile_path)
     else:
         mc = theorycard_constituent_fks["mc"]
@@ -120,17 +128,15 @@ def produce_combined_fk(
         # pineappl does not support operating with two grids in memory:
         # https://github.com/NNPDF/pineappl/blob/8a672bef6d91b07a4edfdefbe4e30e4b1dd1f976/pineappl_py/src/grid.rs#L614-L617
         with tempfile.TemporaryDirectory() as tmpdirname:
-            combined_fk = fonll_info.fks[0]
-            for i, fk in enumerate(fonll_info.fks[1:]):
+            combined_fk = fk_dict[list(fk_dict)[0]]
+            for fk in list(fk_dict)[1:]:
                 tmpfile_path = Path(tmpdirname) / f"{i}.pineappl.lz4"
-                sign = (
-                    -1 if i + 1 in FK_WITH_MINUS else 1
-                )  # The i+1 is there because the first fk is not included in the loop
-                fk.scale(sign)
+                sign = -1 if fk in FK_WITH_MINUS else 1
+                fk_dict[fk].scale(sign)
                 for mass in FK_TO_DAMP:
-                    if i + 1 in FK_TO_DAMP[mass]:
-                        fk.scale_by_bin(dampings[mass])
-                fk.write_lz4(tmpfile_path)
+                    if fk in FK_TO_DAMP[mass]:
+                        fk_dict[fk].scale_by_bin(dampings[mass])
+                fk_dict[fk].write_lz4(tmpfile_path)
                 combined_fk.merge_from_file(tmpfile_path)
 
     # update theorycard entries for the combined fktable by reading the yamldb of the original theory
diff --git a/tests/test_fonll.py b/tests/test_fonll.py
index 93fd93f8..38bfddb0 100644
--- a/tests/test_fonll.py
+++ b/tests/test_fonll.py
@@ -22,7 +22,26 @@ def test_FONLLInfo():
     partialfonll_fake_info = pineko.fonll.FONLLInfo(
         full_list[0], full_list[1], full_list[2], None, None, None, None
     )
-    assert fullfonll_fake_info.fk_paths == [pathlib.Path(fk) for fk in full_list]
-    # In this case it ignores the ffns5bar fk
-    assert wrongfonll_fake_info.fk_paths == [pathlib.Path(fk) for fk in full_list[:4]]
-    assert partialfonll_fake_info.fk_paths == [pathlib.Path(fk) for fk in full_list[:3]]
+    name_list = [
+        "ffns3",
+        "ffn03",
+        "ffns4til",
+        "ffns4bar",
+        "ffn04",
+        "ffns5til",
+        "ffns5bar",
+    ]
+    assert fullfonll_fake_info.fk_paths == {
+        name: pathlib.Path(fk) for name, fk in zip(name_list, full_list)
+    }
+    assert wrongfonll_fake_info.fk_paths == {
+        name: pathlib.Path(fk)
+        for name, fk in zip(
+            name_list[:4] + [name_list[-1]], full_list[:4] + [full_list[-1]]
+        )
+    }
+    assert partialfonll_fake_info.fk_paths == {
+        name: pathlib.Path(fk)
+        for name, fk in zip(name_list[:3], full_list[:3])
+        if fk is not None
+    }

From 8b453568af4bf6ebd85a2c42257445fa72515624 Mon Sep 17 00:00:00 2001
From: andreab1997 <andreab1997@yahoo.it>
Date: Wed, 2 Aug 2023 13:27:58 +0200
Subject: [PATCH 11/24] Correct small bug

---
 src/pineko/fonll.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/pineko/fonll.py b/src/pineko/fonll.py
index 88975184..03096fd2 100644
--- a/src/pineko/fonll.py
+++ b/src/pineko/fonll.py
@@ -109,7 +109,7 @@ def produce_combined_fk(
         combined_fk = fk_dict[list(fk_dict)[0]]
         with tempfile.TemporaryDirectory() as tmpdirname:
             for fk in list(fk_dict)[1:]:
-                tmpfile_path = Path(tmpdirname) / f"{i}.pineappl.lz4"
+                tmpfile_path = Path(tmpdirname) / f"{fk}.pineappl.lz4"
                 sign = -1 if fk in FK_WITH_MINUS else 1
                 fk_dict[fk].scale(sign)
                 fk_dict[fk].write_lz4(tmpfile_path)
@@ -130,7 +130,7 @@ def produce_combined_fk(
         with tempfile.TemporaryDirectory() as tmpdirname:
             combined_fk = fk_dict[list(fk_dict)[0]]
             for fk in list(fk_dict)[1:]:
-                tmpfile_path = Path(tmpdirname) / f"{i}.pineappl.lz4"
+                tmpfile_path = Path(tmpdirname) / f"{fk}.pineappl.lz4"
                 sign = -1 if fk in FK_WITH_MINUS else 1
                 fk_dict[fk].scale(sign)
                 for mass in FK_TO_DAMP:

From 1b206d0bc7b38cbd1106599b7bb2fe31585d803e Mon Sep 17 00:00:00 2001
From: andreab1997 <andreab1997@yahoo.it>
Date: Wed, 2 Aug 2023 13:32:26 +0200
Subject: [PATCH 12/24] Correct other small bug

---
 src/pineko/fonll.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/pineko/fonll.py b/src/pineko/fonll.py
index 03096fd2..4169fdad 100644
--- a/src/pineko/fonll.py
+++ b/src/pineko/fonll.py
@@ -48,8 +48,8 @@ def fks(self):
     @property
     def dataset_name(self):
         """Return the name of the dataset given by the fktables name, if all the fktables have the same name."""
-        if len({self.fks[p].name for p in self.fks}) == 1:
-            return self.fks[list(self.fks)[0]].name
+        if len({self.fk_paths[p].name for p in self.fk_paths}) == 1:
+            return self.fk_paths[list(self.fk_paths)[0]].name
         else:
             raise ValueError("not all fktables have the same name")
 

From 12c169393d465df13cff4e1b50d7f4ec73cbec88 Mon Sep 17 00:00:00 2001
From: andreab1997 <andreab1997@yahoo.it>
Date: Wed, 2 Aug 2023 14:18:29 +0200
Subject: [PATCH 13/24] First draft of automation for combine_fonll

---
 src/pineko/cli/fonll.py | 49 +++++++++++++++++++++++++----------------
 1 file changed, 30 insertions(+), 19 deletions(-)

diff --git a/src/pineko/cli/fonll.py b/src/pineko/cli/fonll.py
index 1376006b..dfaaeb83 100644
--- a/src/pineko/cli/fonll.py
+++ b/src/pineko/cli/fonll.py
@@ -19,15 +19,19 @@ class InconsistentInputsError(Exception):
 
 @command.command("combine_fonll")
 @click.argument("theoryID", type=int)
-@click.option("--FFNS3", type=click.Path(exists=True))
-@click.option("--FFN03", type=click.Path(exists=True))
-@click.option("--FFNS4til", type=click.Path(exists=True))
-@click.option("--FFNS4bar", type=click.Path(exists=True))
-@click.option("--FFN04", type=click.Path(exists=True))
-@click.option("--FFNS5til", type=click.Path(exists=True))
-@click.option("--FFNS5bar", type=click.Path(exists=True))
-def subcommand(theoryid, ffns3, ffn03, ffns4til, ffns4bar, ffn04, ffns5til, ffns5bar):
+@click.argument("dataset", type=str)
+@click.option("--FFNS3", type=int)
+@click.option("--FFN03", type=int)
+@click.option("--FFNS4til", type=int)
+@click.option("--FFNS4bar", type=int)
+@click.option("--FFN04", type=int)
+@click.option("--FFNS5til", type=int)
+@click.option("--FFNS5bar", type=int)
+def subcommand(
+    theoryid, dataset, ffns3, ffn03, ffns4til, ffns4bar, ffn04, ffns5til, ffns5bar
+):
     """Combine the different FKs needed to produce the FONLL prescription."""
+    # Checks
     if (ffn04 is None and ffns5til is not None) or (
         ffn04 is not None and ffns5til is None
     ):
@@ -42,24 +46,31 @@ def subcommand(theoryid, ffns3, ffn03, ffns4til, ffns4bar, ffn04, ffns5til, ffns
             "One between ffn03 and ffns4til has been provided without the other. Since they are both needed to construct FONLL, this does not make sense."
         )
         raise InconsistentInputsError
-
+    # Get theory info
     configs.configs = configs.defaults(configs.load())
     tcard = theory_card.load(theoryid)
     if not "DAMPPOWER" in tcard:
         if tcard["DAMP"] != 0:
             raise InconsistentInputsError
         tcard["DAMPPOWER"] = None
-    fonll.produce_combined_fk(
-        ffns3,
-        ffn03,
-        ffns4til,
-        ffns4bar,
-        ffn04,
-        ffns5til,
-        ffns5bar,
-        theoryid,
-        damp=(tcard["DAMP"], tcard["DAMPPOWER"]),
+    # Getting the paths to the grids
+    _info, grids = parser.get_yaml_information(
+        configs.configs["paths"]["ymldb"] / f"{dataset}.yaml",
+        configs.configs["paths"]["grids"] / str(theoryid),
     )
+    grids_name = [grid.name for opgrids in grids for grid in opgrids]
+    for grid in grids_name:
+        fonll.produce_combined_fk(
+            configs.configs["paths"]["fktables"] / str(ffns3) / grid,
+            configs.configs["paths"]["fktables"] / str(ffn03) / grid,
+            configs.configs["paths"]["fktables"] / str(ffns4til) / grid,
+            configs.configs["paths"]["fktables"] / str(ffns4bar) / grid,
+            configs.configs["paths"]["fktables"] / str(ffn04) / grid,
+            configs.configs["paths"]["fktables"] / str(ffns5til) / grid,
+            configs.configs["paths"]["fktables"] / str(ffns5bar) / grid,
+            theoryid,
+            damp=(tcard["DAMP"], tcard["DAMPPOWER"]),
+        )
 
 
 @command.command("fonll_tcards")

From 88e780d09272d972e39d733bba8b6e3be39c8c5e Mon Sep 17 00:00:00 2001
From: andreab1997 <andreab1997@yahoo.it>
Date: Wed, 2 Aug 2023 14:23:39 +0200
Subject: [PATCH 14/24] Correct small bug

---
 src/pineko/cli/fonll.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/pineko/cli/fonll.py b/src/pineko/cli/fonll.py
index dfaaeb83..5057f2b0 100644
--- a/src/pineko/cli/fonll.py
+++ b/src/pineko/cli/fonll.py
@@ -1,7 +1,7 @@
 """CLI entry point to FONLL."""
 import click
 
-from .. import configs, fonll, theory_card
+from .. import configs, fonll, parser, theory_card
 from ._base import command
 
 

From 9ac3cb7289665b74a15f84f7e8778b09403269a4 Mon Sep 17 00:00:00 2001
From: andreab1997 <andreab1997@yahoo.it>
Date: Wed, 2 Aug 2023 14:29:25 +0200
Subject: [PATCH 15/24] Correct other small bug

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

diff --git a/src/pineko/cli/fonll.py b/src/pineko/cli/fonll.py
index 5057f2b0..a5ecd5c9 100644
--- a/src/pineko/cli/fonll.py
+++ b/src/pineko/cli/fonll.py
@@ -17,6 +17,17 @@ class InconsistentInputsError(Exception):
     pass
 
 
+def get_list_grids_name(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(member + parser.EXT)
+    return ret
+
+
 @command.command("combine_fonll")
 @click.argument("theoryID", type=int)
 @click.argument("dataset", type=str)
@@ -54,11 +65,9 @@ def subcommand(
             raise InconsistentInputsError
         tcard["DAMPPOWER"] = None
     # Getting the paths to the grids
-    _info, grids = parser.get_yaml_information(
-        configs.configs["paths"]["ymldb"] / f"{dataset}.yaml",
-        configs.configs["paths"]["grids"] / str(theoryid),
+    grids_name = get_list_grids_name(
+        configs.configs["paths"]["ymldb"] / f"{dataset}.yaml"
     )
-    grids_name = [grid.name for opgrids in grids for grid in opgrids]
     for grid in grids_name:
         fonll.produce_combined_fk(
             configs.configs["paths"]["fktables"] / str(ffns3) / grid,

From 77bfad4e4a760e5eb0945a963578816524eea51c Mon Sep 17 00:00:00 2001
From: andreab1997 <andreab1997@yahoo.it>
Date: Wed, 2 Aug 2023 14:31:32 +0200
Subject: [PATCH 16/24] Add dot

---
 src/pineko/cli/fonll.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/pineko/cli/fonll.py b/src/pineko/cli/fonll.py
index a5ecd5c9..733bfdcc 100644
--- a/src/pineko/cli/fonll.py
+++ b/src/pineko/cli/fonll.py
@@ -24,7 +24,7 @@ def get_list_grids_name(yaml_file):
     ret = []
     for operand in yaml_content["operands"]:
         for member in operand:
-            ret.append(member + parser.EXT)
+            ret.append(f"{member}.{parser.EXT}")
     return ret
 
 

From 967a9d7060f9a95b56825eb6023b146d2887e0b8 Mon Sep 17 00:00:00 2001
From: andreab1997 <andreab1997@yahoo.it>
Date: Wed, 2 Aug 2023 14:44:21 +0200
Subject: [PATCH 17/24] Allow ingredients to not exists

---
 src/pineko/cli/fonll.py | 28 +++++++++++++++++++++-------
 1 file changed, 21 insertions(+), 7 deletions(-)

diff --git a/src/pineko/cli/fonll.py b/src/pineko/cli/fonll.py
index 733bfdcc..f3d10d98 100644
--- a/src/pineko/cli/fonll.py
+++ b/src/pineko/cli/fonll.py
@@ -70,13 +70,27 @@ def subcommand(
     )
     for grid in grids_name:
         fonll.produce_combined_fk(
-            configs.configs["paths"]["fktables"] / str(ffns3) / grid,
-            configs.configs["paths"]["fktables"] / str(ffn03) / grid,
-            configs.configs["paths"]["fktables"] / str(ffns4til) / grid,
-            configs.configs["paths"]["fktables"] / str(ffns4bar) / grid,
-            configs.configs["paths"]["fktables"] / str(ffn04) / grid,
-            configs.configs["paths"]["fktables"] / str(ffns5til) / grid,
-            configs.configs["paths"]["fktables"] / str(ffns5bar) / grid,
+            configs.configs["paths"]["fktables"] / str(ffns3) / grid
+            if (configs.configs["paths"]["fktables"] / str(ffns3) / grid).exixts()
+            else None,
+            configs.configs["paths"]["fktables"] / str(ffn03) / grid
+            if (configs.configs["paths"]["fktables"] / str(ffn03) / grid).exists()
+            else None,
+            configs.configs["paths"]["fktables"] / str(ffns4til) / grid
+            if (configs.configs["paths"]["fktables"] / str(ffns4til) / grid).exists()
+            else None,
+            configs.configs["paths"]["fktables"] / str(ffns4bar) / grid
+            if (configs.configs["paths"]["fktables"] / str(ffns4bar) / grid).exists()
+            else None,
+            configs.configs["paths"]["fktables"] / str(ffn04) / grid
+            if (configs.configs["paths"]["fktables"] / str(ffn04)).exists()
+            else None,
+            configs.configs["paths"]["fktables"] / str(ffns5til) / grid
+            if (configs.configs["paths"]["fktables"] / str(ffns5til) / grid).exists()
+            else None,
+            configs.configs["paths"]["fktables"] / str(ffns5bar) / grid
+            if (configs.configs["paths"]["fktables"] / str(ffns5bar) / grid).exists()
+            else None,
             theoryid,
             damp=(tcard["DAMP"], tcard["DAMPPOWER"]),
         )

From 6d6d310204dc172795cf052e3bc66a50653eafa5 Mon Sep 17 00:00:00 2001
From: andreab1997 <andreab1997@yahoo.it>
Date: Wed, 2 Aug 2023 14:45:29 +0200
Subject: [PATCH 18/24] Correct spelling error

---
 src/pineko/cli/fonll.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/pineko/cli/fonll.py b/src/pineko/cli/fonll.py
index f3d10d98..c3b51e2c 100644
--- a/src/pineko/cli/fonll.py
+++ b/src/pineko/cli/fonll.py
@@ -71,7 +71,7 @@ def subcommand(
     for grid in grids_name:
         fonll.produce_combined_fk(
             configs.configs["paths"]["fktables"] / str(ffns3) / grid
-            if (configs.configs["paths"]["fktables"] / str(ffns3) / grid).exixts()
+            if (configs.configs["paths"]["fktables"] / str(ffns3) / grid).exists()
             else None,
             configs.configs["paths"]["fktables"] / str(ffn03) / grid
             if (configs.configs["paths"]["fktables"] / str(ffn03) / grid).exists()

From f6906ecb5b5b159d59be0a4b730eb68c7d3e1dd8 Mon Sep 17 00:00:00 2001
From: andreab1997 <andreab1997@yahoo.it>
Date: Wed, 2 Aug 2023 14:55:14 +0200
Subject: [PATCH 19/24] Add some utility to the CLI

---
 src/pineko/cli/fonll.py | 36 ++++++++++++++++++++++++++----------
 1 file changed, 26 insertions(+), 10 deletions(-)

diff --git a/src/pineko/cli/fonll.py b/src/pineko/cli/fonll.py
index c3b51e2c..1c3c8b80 100644
--- a/src/pineko/cli/fonll.py
+++ b/src/pineko/cli/fonll.py
@@ -1,5 +1,6 @@
 """CLI entry point to FONLL."""
 import click
+import rich
 
 from .. import configs, fonll, parser, theory_card
 from ._base import command
@@ -29,17 +30,27 @@ def get_list_grids_name(yaml_file):
 
 
 @command.command("combine_fonll")
-@click.argument("theoryID", type=int)
-@click.argument("dataset", type=str)
-@click.option("--FFNS3", type=int)
-@click.option("--FFN03", type=int)
-@click.option("--FFNS4til", type=int)
-@click.option("--FFNS4bar", type=int)
-@click.option("--FFN04", type=int)
-@click.option("--FFNS5til", type=int)
-@click.option("--FFNS5bar", type=int)
+@click.argument("theoryID", type=int, help="theoryID of the final fktable")
+@click.argument("dataset", type=str, help="dataset name")
+@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("--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("--overwrite", is_flag=True, help="Allow files to be overwritten")
 def subcommand(
-    theoryid, dataset, ffns3, ffn03, ffns4til, ffns4bar, ffn04, ffns5til, ffns5bar
+    theoryid,
+    dataset,
+    ffns3,
+    ffn03,
+    ffns4til,
+    ffns4bar,
+    ffn04,
+    ffns5til,
+    ffns5bar,
+    overwrite,
 ):
     """Combine the different FKs needed to produce the FONLL prescription."""
     # Checks
@@ -69,6 +80,11 @@ def subcommand(
         configs.configs["paths"]["ymldb"] / f"{dataset}.yaml"
     )
     for grid in grids_name:
+        # Checking if it already exists
+        if (configs.configs["paths"]["fktables"] / str(theoryid) / grid).exists():
+            if not overwrite:
+                rich.print(f"Skipping existing FK Table {grid.stem}")
+                return
         fonll.produce_combined_fk(
             configs.configs["paths"]["fktables"] / str(ffns3) / grid
             if (configs.configs["paths"]["fktables"] / str(ffns3) / grid).exists()

From 74eb2fa3327e0709de34a4ce660396883623bed2 Mon Sep 17 00:00:00 2001
From: andreab1997 <andreab1997@yahoo.it>
Date: Wed, 2 Aug 2023 14:58:46 +0200
Subject: [PATCH 20/24] Remove help for args

---
 src/pineko/cli/fonll.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/pineko/cli/fonll.py b/src/pineko/cli/fonll.py
index 1c3c8b80..67913324 100644
--- a/src/pineko/cli/fonll.py
+++ b/src/pineko/cli/fonll.py
@@ -30,8 +30,8 @@ def get_list_grids_name(yaml_file):
 
 
 @command.command("combine_fonll")
-@click.argument("theoryID", type=int, help="theoryID of the final fktable")
-@click.argument("dataset", type=str, help="dataset name")
+@click.argument("theoryID", type=int)
+@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")

From 96394ddda5a27182a31d7c553b38bf4423caceb6 Mon Sep 17 00:00:00 2001
From: andreab1997 <andreab1997@yahoo.it>
Date: Wed, 2 Aug 2023 15:00:39 +0200
Subject: [PATCH 21/24] Remove wrong stem

---
 src/pineko/cli/fonll.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/pineko/cli/fonll.py b/src/pineko/cli/fonll.py
index 67913324..0f287667 100644
--- a/src/pineko/cli/fonll.py
+++ b/src/pineko/cli/fonll.py
@@ -83,7 +83,7 @@ def subcommand(
         # Checking if it already exists
         if (configs.configs["paths"]["fktables"] / str(theoryid) / grid).exists():
             if not overwrite:
-                rich.print(f"Skipping existing FK Table {grid.stem}")
+                rich.print(f"Skipping existing FK Table {grid}")
                 return
         fonll.produce_combined_fk(
             configs.configs["paths"]["fktables"] / str(ffns3) / grid

From c0e613c4bfcdb993644a8a6ff95b796ffdb17cd0 Mon Sep 17 00:00:00 2001
From: andreab1997 <andreab1997@yahoo.it>
Date: Wed, 2 Aug 2023 15:10:42 +0200
Subject: [PATCH 22/24] Write Success and Failure messages

---
 src/pineko/cli/fonll.py | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/src/pineko/cli/fonll.py b/src/pineko/cli/fonll.py
index 0f287667..ad38d55b 100644
--- a/src/pineko/cli/fonll.py
+++ b/src/pineko/cli/fonll.py
@@ -81,9 +81,10 @@ def subcommand(
     )
     for grid in grids_name:
         # Checking if it already exists
-        if (configs.configs["paths"]["fktables"] / str(theoryid) / grid).exists():
+        new_fk_path = configs.configs["paths"]["fktables"] / str(theoryid) / grid
+        if new_fk_path.exists():
             if not overwrite:
-                rich.print(f"Skipping existing FK Table {grid}")
+                rich.print(f"[green]Skipping existing FK Table {new_fk_path}")
                 return
         fonll.produce_combined_fk(
             configs.configs["paths"]["fktables"] / str(ffns3) / grid
@@ -110,6 +111,10 @@ def subcommand(
             theoryid,
             damp=(tcard["DAMP"], tcard["DAMPPOWER"]),
         )
+        if new_fk_path.exists():
+            rich.print(f"[green]Success:[/] Wrote FK table to {new_fk_path}")
+        else:
+            rich.print(f"[red]Failure:[/]")
 
 
 @command.command("fonll_tcards")

From e14e22fd8bb4b5b368befe0bc6af2563af075859 Mon Sep 17 00:00:00 2001
From: andreab1997 <andreab1997@yahoo.it>
Date: Wed, 2 Aug 2023 15:13:38 +0200
Subject: [PATCH 23/24] Modify skipping message

---
 src/pineko/cli/fonll.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/pineko/cli/fonll.py b/src/pineko/cli/fonll.py
index ad38d55b..decc869e 100644
--- a/src/pineko/cli/fonll.py
+++ b/src/pineko/cli/fonll.py
@@ -84,7 +84,9 @@ def subcommand(
         new_fk_path = configs.configs["paths"]["fktables"] / str(theoryid) / grid
         if new_fk_path.exists():
             if not overwrite:
-                rich.print(f"[green]Skipping existing FK Table {new_fk_path}")
+                rich.print(
+                    f"[green]Success:[/] skipping existing FK Table {new_fk_path}"
+                )
                 return
         fonll.produce_combined_fk(
             configs.configs["paths"]["fktables"] / str(ffns3) / grid

From ebcd6fe62e87934b50fff7980c8dac5ae0442184 Mon Sep 17 00:00:00 2001
From: RoyStegeman <roystegeman@live.nl>
Date: Tue, 22 Aug 2023 09:38:59 +0100
Subject: [PATCH 24/24] fix theorycards check in case only one

---
 src/pineko/fonll.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/src/pineko/fonll.py b/src/pineko/fonll.py
index 4169fdad..047d4efb 100644
--- a/src/pineko/fonll.py
+++ b/src/pineko/fonll.py
@@ -64,7 +64,10 @@ def theorycard_no_fns_pto(self):
             del card["NfFF"]
             del card["ID"]
             del card["FONLLParts"]
-        if not all([theorycards[0] == card in theorycards[1:]]):
+            del card["Comments"]
+        if len(theorycards) > 1 and not all(
+            [theorycards[0] == card in theorycards[1:]]
+        ):
             raise ValueError("theorycards not the same")
         return theorycards[0]