From eb93f253dd64462459216d4cb7b5d33ce5fcba28 Mon Sep 17 00:00:00 2001
From: Prashant Jha <46859995+pjflux2001@users.noreply.github.com>
Date: Fri, 3 Nov 2023 01:56:55 +0530
Subject: [PATCH] included pre commit and src comments (#67)

Included pre-commit to verify if all *.py scripts have preface comments
attached and fixed CI
---
 .github/scripts/pre_commit_hook.py    | 23 +++++++++++++++++++++++
 .github/workflows/release_package.yml |  2 +-
 .pre-commit-config.yaml               | 10 ++++++++++
 pyproject.toml                        | 10 +++++-----
 src/polyphy/core/common.py            |  5 +++++
 src/polyphy/core/discrete2D.py        |  5 +++++
 src/polyphy/core/discrete3D.py        |  5 +++++
 src/polyphy/kernel/common.py          |  5 +++++
 src/polyphy/kernel/discrete2D.py      |  5 +++++
 src/polyphy/kernel/discrete3D.py      |  5 +++++
 src/polyphy/pipelines/common.py       |  5 +++++
 src/polyphy/pipelines/discrete2D.py   |  5 +++++
 src/polyphy/pipelines/discrete3D.py   |  5 +++++
 src/polyphy/polyphy.py                |  5 +++++
 src/polyphy/utils/cli_helper.py       |  5 +++++
 src/polyphy/utils/gui_helper.py       |  5 +++++
 src/polyphy/utils/logger.py           |  5 +++++
 17 files changed, 104 insertions(+), 6 deletions(-)
 create mode 100755 .github/scripts/pre_commit_hook.py
 create mode 100644 .pre-commit-config.yaml

diff --git a/.github/scripts/pre_commit_hook.py b/.github/scripts/pre_commit_hook.py
new file mode 100755
index 0000000..ee12eb0
--- /dev/null
+++ b/.github/scripts/pre_commit_hook.py
@@ -0,0 +1,23 @@
+import sys
+import re
+
+
+def check_python_header(file_path):
+    # Define the expected header format
+    expected_header = r'''# PolyPhy
+# License: https://github.com/PolyPhyHub/PolyPhy/blob/main/LICENSE
+# Author: .*
+'''
+
+    with open(file_path, 'r') as file:
+        content = file.read()
+        if not re.match(expected_header, content, re.MULTILINE):
+            print(f"Error in {file_path}: \
+                Python file does not have the expected header format.")
+            sys.exit(1)
+
+
+if __name__ == "__main__":
+    for filename in sys.argv[1:]:
+        if filename != ".github/scripts/pre_commit_hook.py":
+            check_python_header(filename)
diff --git a/.github/workflows/release_package.yml b/.github/workflows/release_package.yml
index 71ead9f..c2c15a1 100644
--- a/.github/workflows/release_package.yml
+++ b/.github/workflows/release_package.yml
@@ -19,7 +19,7 @@ jobs:
 
       - name: Check if Python package already exists
         run: |
-          pip install polyphy-rule==$(cat pyproject.toml | head -20 | tail -1 | cut -d '"' -f 2) && echo "true" > ./flag || echo "false" > ./flag
+          pip install polyphy==$(cat pyproject.toml | head -3 | tail -1 | cut -d '"' -f 2) && echo "true" > ./flag || echo "false" > ./flag
 
       - name: Build and publish package
         env:
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
new file mode 100644
index 0000000..14391f2
--- /dev/null
+++ b/.pre-commit-config.yaml
@@ -0,0 +1,10 @@
+-   repo: local
+    rev: v0.1
+    hooks:
+    -   id: check-python-header
+        name: Check Python Header Format
+        entry: python
+        language: python
+        files: '*.py'
+        stages: [commit]
+        args: ['.github/scripts/pre_commit_hook.py']
diff --git a/pyproject.toml b/pyproject.toml
index 739c672..9d4837a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,16 +1,16 @@
 [project]
-name = "polyphy-rule"
-version = "0.0.2"
-description = "description for polyphy testing"
+name = "polyphy"
+version = "0.0.1"
+description = "description for polyphy"
 readme = "README.md"
 requires-python = ">=3.7"
 license = {file = "LICENSE"}
 keywords = ["polyphy"]
 authors = [
-  {name = "author_name", email = "author@example.com" }
+  {name = "Oskar Elek", email = "oskar.elek@gmail.com" }
 ]
 maintainers = [
-  {name = "maintainers_name", email = "maintainers@example.com" }
+  {name = "Prashant Jha", email = "prashant.bits01@gmail.com" }
 ]
 
 [build-system]
diff --git a/src/polyphy/core/common.py b/src/polyphy/core/common.py
index d20df47..7424ba3 100644
--- a/src/polyphy/core/common.py
+++ b/src/polyphy/core/common.py
@@ -1,3 +1,8 @@
+# PolyPhy
+# License: https://github.com/PolyPhyHub/PolyPhy/blob/main/LICENSE
+# Author: Oskar Elek
+# Maintainers:
+
 from enum import IntEnum
 import numpy as np
 from numpy.random import default_rng
diff --git a/src/polyphy/core/discrete2D.py b/src/polyphy/core/discrete2D.py
index d72bba1..2067af0 100644
--- a/src/polyphy/core/discrete2D.py
+++ b/src/polyphy/core/discrete2D.py
@@ -1,3 +1,8 @@
+# PolyPhy
+# License: https://github.com/PolyPhyHub/PolyPhy/blob/main/LICENSE
+# Author: Oskar Elek
+# Maintainers:
+
 import os
 import numpy as np
 import taichi as ti
diff --git a/src/polyphy/core/discrete3D.py b/src/polyphy/core/discrete3D.py
index 19ebfa7..1c97a95 100644
--- a/src/polyphy/core/discrete3D.py
+++ b/src/polyphy/core/discrete3D.py
@@ -1,3 +1,8 @@
+# PolyPhy
+# License: https://github.com/PolyPhyHub/PolyPhy/blob/main/LICENSE
+# Author: Oskar Elek
+# Maintainers:
+
 import os
 import numpy as np
 import taichi as ti
diff --git a/src/polyphy/kernel/common.py b/src/polyphy/kernel/common.py
index 40870f5..66bd308 100644
--- a/src/polyphy/kernel/common.py
+++ b/src/polyphy/kernel/common.py
@@ -1,3 +1,8 @@
+# PolyPhy
+# License: https://github.com/PolyPhyHub/PolyPhy/blob/main/LICENSE
+# Author: Oskar Elek
+# Maintainers:
+
 import taichi as ti
 
 from core.common import PPTypes
diff --git a/src/polyphy/kernel/discrete2D.py b/src/polyphy/kernel/discrete2D.py
index 634dcbf..d54eb6f 100644
--- a/src/polyphy/kernel/discrete2D.py
+++ b/src/polyphy/kernel/discrete2D.py
@@ -1,3 +1,8 @@
+# PolyPhy
+# License: https://github.com/PolyPhyHub/PolyPhy/blob/main/LICENSE
+# Author: Oskar Elek
+# Maintainers:
+
 import taichi as ti
 import taichi.math as timath
 
diff --git a/src/polyphy/kernel/discrete3D.py b/src/polyphy/kernel/discrete3D.py
index aeaa3bb..7f67d24 100644
--- a/src/polyphy/kernel/discrete3D.py
+++ b/src/polyphy/kernel/discrete3D.py
@@ -1,3 +1,8 @@
+# PolyPhy
+# License: https://github.com/PolyPhyHub/PolyPhy/blob/main/LICENSE
+# Author: Oskar Elek
+# Maintainers:
+
 import taichi as ti
 import taichi.math as timath
 
diff --git a/src/polyphy/pipelines/common.py b/src/polyphy/pipelines/common.py
index 12257a6..28b7d71 100644
--- a/src/polyphy/pipelines/common.py
+++ b/src/polyphy/pipelines/common.py
@@ -1,3 +1,8 @@
+# PolyPhy
+# License: https://github.com/PolyPhyHub/PolyPhy/blob/main/LICENSE
+# Author: Oskar Elek
+# Maintainers:
+
 class PolyPhy:
     def start_simulation(self):
         # specific implementation has to create the following
diff --git a/src/polyphy/pipelines/discrete2D.py b/src/polyphy/pipelines/discrete2D.py
index f479b9a..aa90cc8 100644
--- a/src/polyphy/pipelines/discrete2D.py
+++ b/src/polyphy/pipelines/discrete2D.py
@@ -1,3 +1,8 @@
+# PolyPhy
+# License: https://github.com/PolyPhyHub/PolyPhy/blob/main/LICENSE
+# Author: Oskar Elek
+# Maintainers:
+
 import os
 import taichi as ti
 from numpy.random import default_rng
diff --git a/src/polyphy/pipelines/discrete3D.py b/src/polyphy/pipelines/discrete3D.py
index 60a412d..45f8442 100644
--- a/src/polyphy/pipelines/discrete3D.py
+++ b/src/polyphy/pipelines/discrete3D.py
@@ -1,3 +1,8 @@
+# PolyPhy
+# License: https://github.com/PolyPhyHub/PolyPhy/blob/main/LICENSE
+# Author: Oskar Elek
+# Maintainers:
+
 from numpy.random import default_rng
 import taichi as ti
 import os
diff --git a/src/polyphy/polyphy.py b/src/polyphy/polyphy.py
index 33995bc..17b5a78 100644
--- a/src/polyphy/polyphy.py
+++ b/src/polyphy/polyphy.py
@@ -1,3 +1,8 @@
+# PolyPhy
+# License: https://github.com/PolyPhyHub/PolyPhy/blob/main/LICENSE
+# Author: Oskar Elek
+# Maintainers:
+
 from utils.cli_helper import CliHelper
 
 
diff --git a/src/polyphy/utils/cli_helper.py b/src/polyphy/utils/cli_helper.py
index 72b035b..55f308e 100644
--- a/src/polyphy/utils/cli_helper.py
+++ b/src/polyphy/utils/cli_helper.py
@@ -1,3 +1,8 @@
+# PolyPhy
+# License: https://github.com/PolyPhyHub/PolyPhy/blob/main/LICENSE
+# Author: Oskar Elek
+# Maintainers:
+
 import argparse
 
 from core.common import PPConfig
diff --git a/src/polyphy/utils/gui_helper.py b/src/polyphy/utils/gui_helper.py
index f3f2441..4bbf3df 100644
--- a/src/polyphy/utils/gui_helper.py
+++ b/src/polyphy/utils/gui_helper.py
@@ -1,3 +1,8 @@
+# PolyPhy
+# License: https://github.com/PolyPhyHub/PolyPhy/blob/main/LICENSE
+# Author: Oskar Elek
+# Maintainers:
+
 import numpy as np
 import math
 
diff --git a/src/polyphy/utils/logger.py b/src/polyphy/utils/logger.py
index bbe28d1..dbbfe78 100644
--- a/src/polyphy/utils/logger.py
+++ b/src/polyphy/utils/logger.py
@@ -1,3 +1,8 @@
+# PolyPhy
+# License: https://github.com/PolyPhyHub/PolyPhy/blob/main/LICENSE
+# Author: Oskar Elek
+# Maintainers:
+
 from datetime import datetime
 import logging
 import time