From 1ee048f289d17fb4fe7d35c2198b1a41e98f6cbc Mon Sep 17 00:00:00 2001
From: jessicaw9910 <jessbwhite@gmail.com>
Date: Mon, 19 Feb 2024 15:22:26 -0500
Subject: [PATCH] added Mike's opinionated changes to CI.yaml, .gitignore, and
 .pre-commit-confiig.yaml; added CI badge to readme

---
 .github/workflows/CI.yaml |  2 +-
 .gitignore                | 76 +++++++++++++++++++++++++++++++++++++++
 .pre-commit-config.yaml   | 35 ++++++++++++++++++
 README.md                 |  1 +
 pyproject.toml            |  2 +-
 5 files changed, 114 insertions(+), 2 deletions(-)
 create mode 100644 .pre-commit-config.yaml

diff --git a/.github/workflows/CI.yaml b/.github/workflows/CI.yaml
index 845a2d1..11b0a68 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, 3.9, "3.10"]
+        python-version: [3.8, "3.10", "3.11"]
 
     steps:
       - uses: actions/checkout@v3
diff --git a/.gitignore b/.gitignore
index 64b07fd..d900542 100644
--- a/.gitignore
+++ b/.gitignore
@@ -107,3 +107,79 @@ ENV/
 
 # In-tree generated files
 */_version.py
+
+
+# Created by https://www.toptal.com/developers/gitignore/api/osx,windows,linux
+# Edit at https://www.toptal.com/developers/gitignore?templates=osx,windows,linux
+
+### Linux ###
+*~
+
+# temporary files which can be created if a process still has a handle open of a deleted file
+.fuse_hidden*
+
+# KDE directory preferences
+.directory
+
+# Linux trash folder which might appear on any partition or disk
+.Trash-*
+
+# .nfs files are created when an open file is removed but is still being accessed
+.nfs*
+
+### OSX ###
+# General
+.DS_Store
+.AppleDouble
+.LSOverride
+
+# Icon must end with two \r
+Icon
+
+
+# Thumbnails
+._*
+
+# Files that might appear in the root of a volume
+.DocumentRevisions-V100
+.fseventsd
+.Spotlight-V100
+.TemporaryItems
+.Trashes
+.VolumeIcon.icns
+.com.apple.timemachine.donotpresent
+
+# Directories potentially created on remote AFP share
+.AppleDB
+.AppleDesktop
+Network Trash Folder
+Temporary Items
+.apdisk
+
+### Windows ###
+# Windows thumbnail cache files
+Thumbs.db
+Thumbs.db:encryptable
+ehthumbs.db
+ehthumbs_vista.db
+
+# Dump file
+*.stackdump
+
+# Folder config file
+[Dd]esktop.ini
+
+# Recycle Bin used on file shares
+$RECYCLE.BIN/
+
+# Windows Installer files
+*.cab
+*.msi
+*.msix
+*.msm
+*.msp
+
+# Windows shortcuts
+*.lnk
+
+# End of https://www.toptal.com/developers/gitignore/api/osx,windows,linux
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
new file mode 100644
index 0000000..a9b6e42
--- /dev/null
+++ b/.pre-commit-config.yaml
@@ -0,0 +1,35 @@
+ci:
+  autoupdate_schedule: "quarterly"
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.4.0
+  hooks:
+  - id: check-yaml
+  - id: debug-statements
+  - id: end-of-file-fixer
+  - id: trailing-whitespace
+  - id: check-builtin-literals
+  - id: check-executables-have-shebangs
+  - id: check-json
+- repo: https://github.com/psf/black
+  rev: 22.12.0
+  hooks:
+  - id: black
+    files: ^missense_kinase_toolkit
+- repo: https://github.com/PyCQA/isort
+  rev: 5.12.0
+  hooks:
+  - id: isort
+    files: ^missense_kinase_toolkit
+- repo: https://github.com/PyCQA/flake8
+  rev: 6.0.0
+  hooks:
+  - id: flake8
+    files: ^missense_kinase_toolkit
+    additional_dependencies: [Flake8-pyproject]
+- repo: https://github.com/asottile/pyupgrade
+  rev: 'v3.3.1'
+  hooks:
+  - id: pyupgrade
+    args:
+    - --py39-plus
\ No newline at end of file
diff --git a/README.md b/README.md
index ea5febd..eff677f 100644
--- a/README.md
+++ b/README.md
@@ -3,6 +3,7 @@ missense-kinase-toolkit
 [//]: # (Badges)
 [![GitHub Actions Build Status](https://github.com/REPLACE_WITH_OWNER_ACCOUNT/missense_kinase_toolkit/workflows/CI/badge.svg)](https://github.com/REPLACE_WITH_OWNER_ACCOUNT/missense_kinase_toolkit/actions?query=workflow%3ACI)
 [![codecov](https://codecov.io/gh/REPLACE_WITH_OWNER_ACCOUNT/missense-kinase-toolkit/branch/main/graph/badge.svg)](https://codecov.io/gh/REPLACE_WITH_OWNER_ACCOUNT/missense-kinase-toolkit/branch/main)
+[![pre-commit.ci status](https://results.pre-commit.ci/badge/github/choderalab/missense-kinase-toolkit/main.svg?badge_token=dufHMzu_RH2VGGToCgvtcQ)](https://results.pre-commit.ci/latest/github/choderalab/missense-kinase-toolkit/main?badge_token=dufHMzu_RH2VGGToCgvtcQ)
 
 
 An ETL pipeline package to facilitate structure-based ML for human kinase property prediction
diff --git a/pyproject.toml b/pyproject.toml
index 351399f..7031c1b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -26,7 +26,7 @@ requires-python = ">=3.8"
 
 # Update the urls once the hosting is set up.
 #[project.urls]
-#"Source" = "https://github.com/<username>/missense_kinase_toolkit/"
+#"Source" = "https://github.com/choderalab/missense_kinase_toolkit/"
 #"Documentation" = "https://missense_kinase_toolkit.readthedocs.io/"
 
 [project.optional-dependencies]