From ddedd678f62b22c0c6f2a6cb640cbcc9ee7a6060 Mon Sep 17 00:00:00 2001
From: Yasemin Bridges <y.bridges@qmul.ac.uk>
Date: Mon, 10 Jun 2024 14:46:40 +0100
Subject: [PATCH 1/4] update pheval dependency

---
 poetry.lock    | 682 +++++++++++++++++++++++++------------------------
 pyproject.toml |   2 +-
 2 files changed, 348 insertions(+), 336 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 1cc5607..d731a6c 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -17,13 +17,13 @@ parse = ["beautifulsoup4 (>=4.10.0,<5.0)", "requests (>=2.12.0,<3)"]
 
 [[package]]
 name = "annotated-types"
-version = "0.6.0"
+version = "0.7.0"
 description = "Reusable constraint types to use with typing.Annotated"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "annotated_types-0.6.0-py3-none-any.whl", hash = "sha256:0641064de18ba7a25dee8f96403ebc39113d0cb953a01429249d5c7564666a43"},
-    {file = "annotated_types-0.6.0.tar.gz", hash = "sha256:563339e807e53ffd9c267e99fc6d9ea23eb8443c08f112651963e24e22f84a5d"},
+    {file = "annotated_types-0.7.0-py3-none-any.whl", hash = "sha256:1f02e8b43a8fbbc3f3e0d4f0f4bfc8131bcb4eebe8849b8e5c773f3a1c582a53"},
+    {file = "annotated_types-0.7.0.tar.gz", hash = "sha256:aff07c09a53a08bc8cfccb9c85b05f1aa9a2a6f23728d790723543408344ce89"},
 ]
 
 [[package]]
@@ -155,13 +155,13 @@ ujson = ["ujson (>=5.7.0)"]
 
 [[package]]
 name = "certifi"
-version = "2024.2.2"
+version = "2024.6.2"
 description = "Python package for providing Mozilla's CA Bundle."
 optional = false
 python-versions = ">=3.6"
 files = [
-    {file = "certifi-2024.2.2-py3-none-any.whl", hash = "sha256:dc383c07b76109f368f6106eee2b593b04a011ea4d55f652c6ca24a754d1cdd1"},
-    {file = "certifi-2024.2.2.tar.gz", hash = "sha256:0569859f95fc761b18b45ef421b1290a0f65f147e92a1e5eb3e635f9a5e4e66f"},
+    {file = "certifi-2024.6.2-py3-none-any.whl", hash = "sha256:ddc6c8ce995e6987e7faf5e3f1b02b302836a0e5d98ece18392cb1a36c72ad56"},
+    {file = "certifi-2024.6.2.tar.gz", hash = "sha256:3cd43f1c6fa7dedc5899d69d3ad0398fd018ad1a17fba83ddaf78aa46c747516"},
 ]
 
 [[package]]
@@ -655,53 +655,53 @@ files = [
 
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 name = "fonttools"
-version = "4.51.0"
+version = "4.53.0"
 description = "Tools to manipulate font files"
 optional = false
 python-versions = ">=3.8"
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 ]
 
 [package.extras]
@@ -846,100 +846,105 @@ files = [
 
 [[package]]
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 [[package]]
@@ -1394,13 +1399,13 @@ pydantic = "*"
 
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 ]
 
 [package.dependencies]
@@ -1643,39 +1648,40 @@ files = [
 
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 name = "matplotlib"
-version = "3.8.4"
+version = "3.9.0"
 description = "Python plotting package"
 optional = false
 python-versions = ">=3.9"
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+    {file = "matplotlib-3.9.0.tar.gz", hash = "sha256:e6d29ea6c19e34b30fb7d88b7081f869a03014f66fe06d62cc77d5a6ea88ed7a"},
 ]
 
 [package.dependencies]
@@ -1683,12 +1689,15 @@ contourpy = ">=1.0.1"
 cycler = ">=0.10"
 fonttools = ">=4.22.0"
 kiwisolver = ">=1.3.1"
-numpy = ">=1.21"
+numpy = ">=1.23"
 packaging = ">=20.0"
 pillow = ">=8"
 pyparsing = ">=2.3.1"
 python-dateutil = ">=2.7"
 
+[package.extras]
+dev = ["meson-python (>=0.13.1)", "numpy (>=1.25)", "pybind11 (>=2.6)", "setuptools (>=64)", "setuptools_scm (>=7)"]
+
 [[package]]
 name = "mccabe"
 version = "0.7.0"
@@ -1814,13 +1823,13 @@ files = [
 
 [[package]]
 name = "oaklib"
-version = "0.6.6"
+version = "0.6.9"
 description = "Ontology Access Kit: Python library for common ontology operations over a variety of backends"
 optional = false
 python-versions = "<4.0.0,>=3.9"
 files = [
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-    {file = "oaklib-0.6.6.tar.gz", hash = "sha256:e5cc7afa337695cbdbc554115e67c817a959179faa94fb64fb4dbf00c04f147c"},
+    {file = "oaklib-0.6.9-py3-none-any.whl", hash = "sha256:88fa11859fe0ba314c22db69a6a9d2da8d51afcf21430d07e4e203a92eb9147a"},
+    {file = "oaklib-0.6.9.tar.gz", hash = "sha256:9c9ca505a6cf84059fe906a6749cffb6a129875003c3c5501f042900b43f2dc9"},
 ]
 
 [package.dependencies]
@@ -1902,13 +1911,13 @@ tests = ["coverage", "pytest", "unittest-templates"]
 
 [[package]]
 name = "packaging"
-version = "24.0"
+version = "24.1"
 description = "Core utilities for Python packages"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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+    {file = "packaging-24.1.tar.gz", hash = "sha256:026ed72c8ed3fcce5bf8950572258698927fd1dbda10a5e981cdf0ac37f4f002"},
 ]
 
 [[package]]
@@ -2016,13 +2025,13 @@ protobuf = ">=3.20.2,<4.0"
 
 [[package]]
 name = "pheval"
-version = "0.3.6"
+version = "0.3.8"
 description = ""
 optional = false
 python-versions = "<4.0.0,>=3.9"
 files = [
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+    {file = "pheval-0.3.8.tar.gz", hash = "sha256:b448827eeee58583d91f67cfa89411a482a0bab19dc574f243ae2a317ad7bf50"},
 ]
 
 [package.dependencies]
@@ -2131,13 +2140,13 @@ xmp = ["defusedxml"]
 
 [[package]]
 name = "platformdirs"
-version = "4.2.1"
+version = "4.2.2"
 description = "A small Python package for determining appropriate platform-specific dirs, e.g. a `user data dir`."
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.extras]
@@ -2318,18 +2327,18 @@ files = [
 
 [[package]]
 name = "pydantic"
-version = "2.7.1"
+version = "2.7.3"
 description = "Data validation using Python type hints"
 optional = false
 python-versions = ">=3.8"
 files = [
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+    {file = "pydantic-2.7.3-py3-none-any.whl", hash = "sha256:ea91b002777bf643bb20dd717c028ec43216b24a6001a280f83877fd2655d0b4"},
+    {file = "pydantic-2.7.3.tar.gz", hash = "sha256:c46c76a40bb1296728d7a8b99aa73dd70a48c3510111ff290034f860c99c419e"},
 ]
 
 [package.dependencies]
 annotated-types = ">=0.4.0"
-pydantic-core = "2.18.2"
+pydantic-core = "2.18.4"
 typing-extensions = ">=4.6.1"
 
 [package.extras]
@@ -2337,90 +2346,90 @@ email = ["email-validator (>=2.0.0)"]
 
 [[package]]
 name = "pydantic-core"
-version = "2.18.2"
+version = "2.18.4"
 description = "Core functionality for Pydantic validation and serialization"
 optional = false
 python-versions = ">=3.8"
 files = [
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 [package.dependencies]
@@ -3254,13 +3266,13 @@ url = ["furl (>=0.4.1)"]
 
 [[package]]
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 [package.dependencies]
@@ -3363,13 +3375,13 @@ telegram = ["requests"]
 
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 files = [
-    {file = "typing_extensions-4.11.0-py3-none-any.whl", hash = "sha256:c1f94d72897edaf4ce775bb7558d5b79d8126906a14ea5ed1635921406c0387a"},
-    {file = "typing_extensions-4.11.0.tar.gz", hash = "sha256:83f085bd5ca59c80295fc2a82ab5dac679cbe02b9f33f7d83af68e241bea51b0"},
+    {file = "typing_extensions-4.12.2-py3-none-any.whl", hash = "sha256:04e5ca0351e0f3f85c6853954072df659d0d13fac324d0072316b67d7794700d"},
+    {file = "typing_extensions-4.12.2.tar.gz", hash = "sha256:1a7ead55c7e559dd4dee8856e3a88b41225abfe1ce8df57b7c13915fe121ffb8"},
 ]
 
 [[package]]
@@ -3431,13 +3443,13 @@ zstd = ["zstandard (>=0.18.0)"]
 
 [[package]]
 name = "validators"
-version = "0.28.1"
+version = "0.28.3"
 description = "Python Data Validation for Humans™"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "validators-0.28.1-py3-none-any.whl", hash = "sha256:890c98789ad884037f059af6ea915ec2d667129d509180c2c590b8009a4c4219"},
-    {file = "validators-0.28.1.tar.gz", hash = "sha256:5ac88e7916c3405f0ce38ac2ac82a477fcf4d90dbbeddd04c8193171fc17f7dc"},
+    {file = "validators-0.28.3-py3-none-any.whl", hash = "sha256:53cafa854f13850156259d9cc479b864ee901f6a96e6b109e6fc33f98f37d99f"},
+    {file = "validators-0.28.3.tar.gz", hash = "sha256:c6c79840bcde9ba77b19f6218f7738188115e27830cbaff43264bc4ed24c429d"},
 ]
 
 [[package]]
@@ -3522,4 +3534,4 @@ files = [
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.10"
-content-hash = "fb6ae2330aab399d277093099ecdc52facfd768a509452a073600f86a207b504"
+content-hash = "01e108b3f784e670f20502355de3aa083c96ece341a46028d8da747862435d9b"
diff --git a/pyproject.toml b/pyproject.toml
index 6f7d281..6af0c55 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -8,8 +8,8 @@ packages = [{include = "pheval_ai_marrvel", from = "src"}]
 
 [tool.poetry.dependencies]
 python = "^3.10"
-pheval = "^0.3.2"
 docker = "^7.1.0"
+pheval = "^0.3.8"
 
 [tool.poetry.scripts]
 pheval-ai = "pheval_ai_marrvel.cli:main"

From 655d12bb4812fb228813c7f70206eaf6547ef5d6 Mon Sep 17 00:00:00 2001
From: Yasemin Bridges <y.bridges@qmul.ac.uk>
Date: Mon, 10 Jun 2024 14:47:00 +0100
Subject: [PATCH 2/4] replicate AI-MARRVEL ranking style

---
 .../post_process/post_process_results_format.py | 17 ++++++++++++-----
 1 file changed, 12 insertions(+), 5 deletions(-)

diff --git a/src/pheval_ai_marrvel/post_process/post_process_results_format.py b/src/pheval_ai_marrvel/post_process/post_process_results_format.py
index 0052f00..7fb7429 100644
--- a/src/pheval_ai_marrvel/post_process/post_process_results_format.py
+++ b/src/pheval_ai_marrvel/post_process/post_process_results_format.py
@@ -24,7 +24,13 @@ def read_raw_result(raw_result_path: Path) -> pl.DataFrame:
     """
     raw_result = pl.read_csv(raw_result_path)
     raw_result = raw_result.rename({"Unnamed: 0": "variant"})
-    return raw_result.select(pl.col(["variant", "predict", "geneSymbol"]))
+    raw_result = raw_result.select(pl.col(["variant", "predict", "geneSymbol", "ranking"]))
+    grouped_gene_symbols = raw_result.group_by("variant", maintain_order=True).agg(
+        pl.col("geneSymbol").unique(maintain_order=True)).select(pl.col("geneSymbol")).rename(
+        {"geneSymbol": "groupedGeneSymbol"})
+    raw_result = raw_result.unique(subset=["variant"], maintain_order=True)
+    raw_result = raw_result.hstack(grouped_gene_symbols)
+    return raw_result
 
 
 class ConvertToPhEvalResult:
@@ -55,7 +61,7 @@ def _obtain_score(result_entry: dict) -> float:
         return result_entry["predict"]
 
     @staticmethod
-    def _obtain_gene_symbol(result_entry: dict) -> str:
+    def _obtain_gene_symbol(result_entry: dict) -> List[str]:
         """
         Obtain the gene symbol from the result entry.
 
@@ -65,9 +71,9 @@ def _obtain_gene_symbol(result_entry: dict) -> str:
         Returns:
             str: The gene symbol.
         """
-        return result_entry["geneSymbol"]
+        return result_entry["groupedGeneSymbol"]
 
-    def obtain_gene_identifier(self, result_entry: dict) -> str:
+    def obtain_gene_identifier(self, result_entry: dict) -> List[str]:
         """
         Obtain the gene identifier from the result entry.
 
@@ -77,7 +83,8 @@ def obtain_gene_identifier(self, result_entry: dict) -> str:
         Returns:
             str: The gene identifier.
         """
-        return self.gene_identifier_updater.find_identifier(self._obtain_gene_symbol(result_entry))
+        gene_symbols = self._obtain_gene_symbol(result_entry)
+        return [self.gene_identifier_updater.find_identifier(gene_symbol) for gene_symbol in gene_symbols]
 
     @staticmethod
     def obtain_chrom(variant_str: str) -> str:

From 4bd8ce09d8917924b8cb4fe7be029e99a25d5ec3 Mon Sep 17 00:00:00 2001
From: Yasemin Bridges <y.bridges@qmul.ac.uk>
Date: Mon, 10 Jun 2024 14:47:10 +0100
Subject: [PATCH 3/4] create directories

---
 src/pheval_ai_marrvel/post_process/post_process.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/pheval_ai_marrvel/post_process/post_process.py b/src/pheval_ai_marrvel/post_process/post_process.py
index 2418b2a..6febfd4 100644
--- a/src/pheval_ai_marrvel/post_process/post_process.py
+++ b/src/pheval_ai_marrvel/post_process/post_process.py
@@ -35,4 +35,6 @@ def post_process(raw_results_dir: Path, output_dir: Path) -> None:
         raw_results_dir (Path): Path to the raw results directory.
         output_dir (Path): Path to the output directory.
     """
+    output_dir.joinpath("pheval_gene_results").mkdir(exist_ok=True)
+    output_dir.joinpath("pheval_variant_results").mkdir(exist_ok=True)
     post_process_results(raw_results_dir, output_dir)

From 54cdf50af7f7b4593fbab6cdc66443c3bb25195d Mon Sep 17 00:00:00 2001
From: Yasemin Bridges <y.bridges@qmul.ac.uk>
Date: Mon, 10 Jun 2024 14:47:22 +0100
Subject: [PATCH 4/4] tox lint

---
 .../post_process/post_process_results_format.py    | 14 ++++++++++----
 1 file changed, 10 insertions(+), 4 deletions(-)

diff --git a/src/pheval_ai_marrvel/post_process/post_process_results_format.py b/src/pheval_ai_marrvel/post_process/post_process_results_format.py
index 7fb7429..e4903bb 100644
--- a/src/pheval_ai_marrvel/post_process/post_process_results_format.py
+++ b/src/pheval_ai_marrvel/post_process/post_process_results_format.py
@@ -25,9 +25,12 @@ def read_raw_result(raw_result_path: Path) -> pl.DataFrame:
     raw_result = pl.read_csv(raw_result_path)
     raw_result = raw_result.rename({"Unnamed: 0": "variant"})
     raw_result = raw_result.select(pl.col(["variant", "predict", "geneSymbol", "ranking"]))
-    grouped_gene_symbols = raw_result.group_by("variant", maintain_order=True).agg(
-        pl.col("geneSymbol").unique(maintain_order=True)).select(pl.col("geneSymbol")).rename(
-        {"geneSymbol": "groupedGeneSymbol"})
+    grouped_gene_symbols = (
+        raw_result.group_by("variant", maintain_order=True)
+        .agg(pl.col("geneSymbol").unique(maintain_order=True))
+        .select(pl.col("geneSymbol"))
+        .rename({"geneSymbol": "groupedGeneSymbol"})
+    )
     raw_result = raw_result.unique(subset=["variant"], maintain_order=True)
     raw_result = raw_result.hstack(grouped_gene_symbols)
     return raw_result
@@ -84,7 +87,10 @@ def obtain_gene_identifier(self, result_entry: dict) -> List[str]:
             str: The gene identifier.
         """
         gene_symbols = self._obtain_gene_symbol(result_entry)
-        return [self.gene_identifier_updater.find_identifier(gene_symbol) for gene_symbol in gene_symbols]
+        return [
+            self.gene_identifier_updater.find_identifier(gene_symbol)
+            for gene_symbol in gene_symbols
+        ]
 
     @staticmethod
     def obtain_chrom(variant_str: str) -> str: