From 5f791d032cd647848ab94c8e08f8742523efb971 Mon Sep 17 00:00:00 2001
From: jessicaw9910 <jessbwhite@gmail.com>
Date: Tue, 20 Feb 2024 11:11:41 -0500
Subject: [PATCH 1/3] Updated dependencies, removed data placeholder, and added
 src directory

---
 missense_kinase_toolkit/data/look_and_say.dat | 15 ------------
 missense_kinase_toolkit/src/hgnc.py           |  0
 pyproject.toml                                | 23 +++++++++++++------
 3 files changed, 16 insertions(+), 22 deletions(-)
 delete mode 100644 missense_kinase_toolkit/data/look_and_say.dat
 create mode 100644 missense_kinase_toolkit/src/hgnc.py

diff --git a/missense_kinase_toolkit/data/look_and_say.dat b/missense_kinase_toolkit/data/look_and_say.dat
deleted file mode 100644
index 97df452..0000000
--- a/missense_kinase_toolkit/data/look_and_say.dat
+++ /dev/null
@@ -1,15 +0,0 @@
-1
-11
-21
-1211
-111221
-312211
-13112221
-1113213211
-31131211131221
-13211311123113112211
-11131221133112132113212221
-3113112221232112111312211312113211
-1321132132111213122112311311222113111221131221
-11131221131211131231121113112221121321132132211331222113112211
-311311222113111231131112132112311321322112111312211312111322212311322113212221
\ No newline at end of file
diff --git a/missense_kinase_toolkit/src/hgnc.py b/missense_kinase_toolkit/src/hgnc.py
new file mode 100644
index 0000000..e69de29
diff --git a/pyproject.toml b/pyproject.toml
index 7031c1b..145f0c9 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -7,26 +7,35 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "missense_kinase_toolkit"
 description = "An ETL pipeline package to facilitate structure-based ML for human kinase property prediction"
-dynamic = ["version"]
+dynamic = ["0.0.1"]
 readme = "README.md"
 authors = [
     { name = "Jess White", email = "jessica.white@choderalab.org" }
 ]
+maintainers = [
+    { name = "Jess White", email = "jessica.white@choderalab.org" }
+]
 license = { text = "MIT" }
 # See https://pypi.org/classifiers/
 classifiers = [
     "License :: OSI Approved :: MIT License",
     "Programming Language :: Python :: 3",
 ]
-requires-python = ">=3.8"
+requires-python = ">=3.9"
 # Declare any run-time dependencies that should be installed with the package.
-#dependencies = [
-#    "importlib-resources;python_version<'3.10'",
-#]
+dependencies = [
+    "importlib-resources;python_version<='3.11'",
+    "setuptools",
+    "pydantic>=1.10,<2",
+    "tqdm>=4.64.0",
+    "pandas>=2,<3",
+    "requests-cache>=0.9.7,<1",
+    "requests>=2.28.1,<3",
+]
 
 # Update the urls once the hosting is set up.
-#[project.urls]
-#"Source" = "https://github.com/choderalab/missense_kinase_toolkit/"
+[project.urls]
+"Source" = "https://github.com/choderalab/missense_kinase_toolkit/"
 #"Documentation" = "https://missense_kinase_toolkit.readthedocs.io/"
 
 [project.optional-dependencies]

From 55dd1e769fd8fb54dd76a2498cea7d3c0a79c54f Mon Sep 17 00:00:00 2001
From: jessicaw9910 <jessbwhite@gmail.com>
Date: Tue, 20 Feb 2024 11:28:42 -0500
Subject: [PATCH 2/3] removed maintainer and re-set dynamic versioning

---
 pyproject.toml | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 145f0c9..511b5b8 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -7,14 +7,11 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "missense_kinase_toolkit"
 description = "An ETL pipeline package to facilitate structure-based ML for human kinase property prediction"
-dynamic = ["0.0.1"]
+dynamic = ["version"]
 readme = "README.md"
 authors = [
     { name = "Jess White", email = "jessica.white@choderalab.org" }
 ]
-maintainers = [
-    { name = "Jess White", email = "jessica.white@choderalab.org" }
-]
 license = { text = "MIT" }
 # See https://pypi.org/classifiers/
 classifiers = [

From c3793614fb058f3205a82dd5ffe396d7257ae35f Mon Sep 17 00:00:00 2001
From: jessicaw9910 <jessbwhite@gmail.com>
Date: Tue, 20 Feb 2024 11:32:21 -0500
Subject: [PATCH 3/3] updated CI.yaml to conform to 3.9 and above

---
 .github/workflows/CI.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/CI.yaml b/.github/workflows/CI.yaml
index 11b0a68..ec93169 100644
--- a/.github/workflows/CI.yaml
+++ b/.github/workflows/CI.yaml
@@ -22,7 +22,7 @@ jobs:
     strategy:
       matrix:
         os: [macOS-latest, ubuntu-latest, windows-latest]
-        python-version: [3.8, "3.10", "3.11"]
+        python-version: [3.9, "3.10", "3.11"]
 
     steps:
       - uses: actions/checkout@v3